← Files Molecular Structure ViewerARCHIVED FILE
dist/scientific-viewer-platform/structure-backend.mjs
298 KB · Oct 4, 2026 · 12:18 UTC
// node_modules/.pnpm/@openai+scientific-viewer-platform@file+..+scientific-viewer-platform/node_modules/@openai/scientific-viewer-platform/src/structure/scientific-structure-backend-entrypoint.mjs
import process from "node:process";
// node_modules/.pnpm/@openai+scientific-viewer-platform@file+..+scientific-viewer-platform/node_modules/@openai/scientific-viewer-platform/src/structure/scientific-structure-backend-runtime.mjs
import { Buffer as Buffer2 } from "node:buffer";
import { createHash as createHash2, randomUUID } from "node:crypto";
// node_modules/.pnpm/@openai+scientific-viewer-platform@file+..+scientific-viewer-platform/node_modules/@openai/scientific-viewer-platform/src/structure/scientific-structure-compressed-byte-source.mjs
import { Readable } from "node:stream";
import { createGunzip } from "node:zlib";
var MAX_COMPRESSED_CHUNK_BYTES = 64 * 1024;
var MAX_INFLATED_CHUNK_BYTES = 64 * 1024;
var MAX_EXPANSION_RATIO = 256n;
var MAX_LOGICAL_BYTES = 1024n * 1024n * 1024n * 1024n;
function createScientificStructureCompressedByteSource(options) {
if (options.sizeBytes <= 0n || options.sourceRevision.length === 0 || options.preview.byteLength === 0 || options.preview.byteLength > MAX_COMPRESSED_CHUNK_BYTES || BigInt(options.preview.byteLength) > options.sizeBytes) {
compressedFailure(
"RESOURCE_EXHAUSTED",
"The compressed Structure source exceeds its authenticated range budget"
);
}
let physicalOffset = 0n;
let compressedBytes = 0n;
let expandedBytes = 0n;
let logicalOffset = 0n;
let buffered = new Uint8Array(0);
let bufferedOffset = 0;
let exhausted2 = false;
let closed = false;
let activeRead = false;
let activeSignal;
let permanentError;
const compressed = Readable.from(readCompressedChunks(), {
highWaterMark: MAX_COMPRESSED_CHUNK_BYTES,
objectMode: false
});
const gunzip = createGunzip({ chunkSize: MAX_INFLATED_CHUNK_BYTES });
compressed.once("error", (error) => gunzip.destroy(error));
const iterator = compressed.pipe(gunzip)[Symbol.asyncIterator]();
async function* readCompressedChunks() {
physicalOffset = BigInt(options.preview.byteLength);
compressedBytes = physicalOffset;
yield options.preview;
while (physicalOffset < options.sizeBytes) {
if (activeSignal == null) {
compressedFailure(
"PERMISSION_DENIED",
"Compressed Structure ranges require an active approved request"
);
}
activeSignal.throwIfAborted();
const remaining = options.sizeBytes - physicalOffset;
const length = remaining < BigInt(MAX_COMPRESSED_CHUNK_BYTES) ? Number(remaining) : MAX_COMPRESSED_CHUNK_BYTES;
const result = await options.readCompressedRange({
offset: physicalOffset,
length,
signal: activeSignal
});
activeSignal.throwIfAborted();
if (result.bytes.byteLength !== length || result.eof !== (physicalOffset + BigInt(length) === options.sizeBytes)) {
compressedFailure(
"SOURCE_CHANGED",
"The compressed Structure source revision or physical range changed"
);
}
physicalOffset += BigInt(length);
compressedBytes += BigInt(length);
yield result.bytes;
}
}
async function fillBuffer() {
if (bufferedOffset < buffered.byteLength) {
return true;
}
if (exhausted2) {
return false;
}
let next;
try {
next = await iterator.next();
} catch (error) {
if (typeof error === "object" && error != null && "code" in error && [
"CANCELLED",
"CHECKSUM_MISMATCH",
"CONFLICT",
"PERMISSION_DENIED",
"RESOURCE_EXHAUSTED",
"SOURCE_CHANGED"
].includes(String(error.code))) {
throw error;
}
compressedFailure(
"CHECKSUM_MISMATCH",
"The compressed Structure gzip/BGZF stream is corrupt or incomplete"
);
}
if (next.done) {
exhausted2 = true;
buffered = new Uint8Array(0);
bufferedOffset = 0;
return false;
}
if (next.value.byteLength > MAX_INFLATED_CHUNK_BYTES) {
compressedFailure(
"RESOURCE_EXHAUSTED",
"The compressed Structure output exceeded its bounded chunk size"
);
}
expandedBytes += BigInt(next.value.byteLength);
if (expandedBytes > MAX_LOGICAL_BYTES || expandedBytes > compressedBytes * MAX_EXPANSION_RATIO) {
compressedFailure(
"RESOURCE_EXHAUSTED",
"The compressed Structure source exceeded its bounded inflation policy"
);
}
buffered = next.value;
bufferedOffset = 0;
return true;
}
function close() {
if (closed) {
return;
}
closed = true;
compressed.destroy();
gunzip.destroy();
}
return {
sizeBytes: MAX_LOGICAL_BYTES,
sourceRevision: options.sourceRevision,
close,
async readRange({ offset, length, signal }) {
signal.throwIfAborted();
const previousError = permanentError;
if (previousError instanceof Error) {
throw Object.assign(
new Error(previousError.message, { cause: previousError }),
previousError
);
}
if (closed) {
compressedFailure(
"PERMISSION_DENIED",
"The compressed Structure source has already been closed"
);
}
if (typeof offset !== "bigint" || offset !== logicalOffset || !Number.isSafeInteger(length) || length <= 0 || length > MAX_INFLATED_CHUNK_BYTES || offset + BigInt(length) > MAX_LOGICAL_BYTES) {
compressedFailure(
"RESOURCE_EXHAUSTED",
"Compressed Structure geometry supports only bounded forward reads"
);
}
if (activeRead) {
compressedFailure(
"CONFLICT",
"Compressed Structure geometry cannot be read concurrently"
);
}
activeRead = true;
activeSignal = signal;
const abort = () => {
const reason = signal.reason instanceof Error ? signal.reason : new Error("The approved compressed Structure read was cancelled");
compressed.destroy(reason);
gunzip.destroy(reason);
};
signal.addEventListener("abort", abort, { once: true });
try {
const result = new Uint8Array(length);
let written = 0;
while (written < length) {
signal.throwIfAborted();
if (!await fillBuffer()) {
break;
}
const count = Math.min(
length - written,
buffered.byteLength - bufferedOffset
);
result.set(
buffered.subarray(bufferedOffset, bufferedOffset + count),
written
);
bufferedOffset += count;
logicalOffset += BigInt(count);
written += count;
}
return {
bytes: written === result.byteLength ? result : result.slice(0, written),
eof: exhausted2 && bufferedOffset === buffered.byteLength
};
} catch (error) {
permanentError = error instanceof Error ? error : Object.assign(
new Error("The compressed Structure source failed"),
{
code: "CHECKSUM_MISMATCH"
}
);
close();
throw permanentError;
} finally {
activeRead = false;
signal.removeEventListener("abort", abort);
}
}
};
}
function compressedFailure(code, message) {
throw Object.assign(new Error(message), {
code,
name: "ScientificStructureCompressedSourceError"
});
}
// node_modules/.pnpm/@openai+scientific-viewer-platform@file+..+scientific-viewer-platform/node_modules/@openai/scientific-viewer-platform/src/structure/scientific-structure-native-project.mjs
var MAX_PROJECT_BYTES = 180 * 1024;
var MAX_PROJECT_RANGE_BYTES = 64 * 1024;
var MAX_DEPENDENCIES = 128;
var RESOURCE_URI = /^viewer-(?:file|data|live-data):\/\/structure-viewer\//u;
function record(value) {
return typeof value === "object" && value != null && !Array.isArray(value);
}
function safeRelativePath(value) {
return typeof value === "string" && value.length > 0 && value.length <= 1024 && !value.startsWith("/") && !value.includes("\\") && !value.includes("\0") && !/^[a-z][a-z0-9+.-]*:/iu.test(value) && value.split("/").every((part) => part !== "" && part !== "." && part !== "..");
}
function repair(code, dependencyId, label, message) {
return {
structuredContent: {
available: true,
restorable: false,
repairPlan: [{ code, dependencyId, label, message }]
}
};
}
async function resolveScientificStructureNativeProject(input) {
if (input.projectGrant.sourceIdentity.sizeBytes < 1n || input.projectGrant.sourceIdentity.sizeBytes > BigInt(MAX_PROJECT_BYTES)) {
return repair(
"oversize",
"project",
typeof input.command.relativePath === "string" ? input.command.relativePath : "project",
"The approved project manifest exceeds its bounded native window."
);
}
const bytes = new Uint8Array(
Number(input.projectGrant.sourceIdentity.sizeBytes)
);
for (let offset = 0; offset < bytes.byteLength; offset += MAX_PROJECT_RANGE_BYTES) {
input.signal.throwIfAborted();
const length = Math.min(MAX_PROJECT_RANGE_BYTES, bytes.byteLength - offset);
const chunk = await input.readSource({
grant: input.projectGrant,
logicalSessionId: input.logicalSessionId,
offset: BigInt(offset),
length,
signal: input.signal
});
if (chunk.bytes.byteLength !== length) {
return repair(
"changed",
"project",
"project",
"The approved project source changed while loading."
);
}
bytes.set(chunk.bytes, offset);
}
let manifest;
try {
manifest = JSON.parse(
new TextDecoder("utf-8", { fatal: true }).decode(bytes)
);
} catch {
return repair(
"unsupported",
"project",
"project",
"The approved project manifest is malformed."
);
}
if (!record(manifest) || manifest.kind !== "openai.structure-viewer.project" || manifest.version !== 1 || !record(manifest.primary) || !safeRelativePath(manifest.primary.relativePath) || !Array.isArray(manifest.dependencies) || manifest.dependencies.length > MAX_DEPENDENCIES) {
return repair(
"unsupported",
"project",
"project",
"The approved project manifest has an invalid dependency graph."
);
}
const primary = await input.describeSource({
format: input.primaryFormat,
grant: input.primaryGrant,
relativePath: manifest.primary.relativePath
});
if (primary == null || primary.byteLength !== manifest.primary.byteLength || primary.format !== manifest.primary.format || primary.sha256 !== manifest.primary.sha256 || !input.sameIntegrity(
primary.sourceIntegrity,
manifest.primary.sourceIntegrity
)) {
return repair(
"changed",
"primary",
manifest.primary.relativePath,
"The approved primary source no longer matches the saved project."
);
}
if (!Array.isArray(input.command.projectResources)) {
return repair(
"missing",
"project",
"project",
"The host has not restored this project's approved companions."
);
}
const authorizedResources = input.command.projectResources;
const manifestDependencies = manifest.dependencies;
const seen = /* @__PURE__ */ new Set();
const dependencies = [];
for (const dependency of manifestDependencies) {
input.signal.throwIfAborted();
if (!record(dependency) || typeof dependency.id !== "string" || seen.has(dependency.id) || !safeRelativePath(dependency.relativePath) || typeof dependency.format !== "string" || ![
"structure",
"trajectory-coordinates",
"trajectory-topology",
"volume"
].includes(String(dependency.kind))) {
return repair(
"escape",
"project",
"project",
"The project contains an invalid or escaping dependency."
);
}
seen.add(dependency.id);
const resource = authorizedResources.find(
(candidate) => record(candidate) && candidate.id === dependency.id
);
if (!record(resource) || typeof resource.name !== "string" || resource.name !== dependency.relativePath.split("/").at(-1) || typeof resource.resourceUri !== "string" || !RESOURCE_URI.test(resource.resourceUri)) {
return repair(
"missing",
dependency.id,
dependency.relativePath,
"A saved project companion is no longer authorized."
);
}
const grant = input.validateGrant(resource.grant);
const actual = await input.describeSource({
format: dependency.format,
grant,
relativePath: dependency.relativePath
});
if (actual == null || actual.byteLength !== dependency.byteLength || actual.format !== dependency.format || actual.sha256 !== dependency.sha256 || !input.sameIntegrity(actual.sourceIntegrity, dependency.sourceIntegrity)) {
return repair(
"changed",
dependency.id,
dependency.relativePath,
"An approved project companion no longer matches the saved manifest."
);
}
dependencies.push({
id: dependency.id,
name: resource.name,
resourceUri: resource.resourceUri,
sourceRevision: grant.sourceRevision,
sourceSizeBytesDecimal: grant.sourceIdentity.sizeBytes.toString(),
format: dependency.format
});
}
return {
structuredContent: {
available: true,
restorable: true,
manifest,
dependencies
}
};
}
// node_modules/.pnpm/@openai+scientific-viewer-platform@file+..+scientific-viewer-platform/node_modules/@openai/scientific-viewer-platform/src/structure/scientific-structure-native-text-parser.mjs
import { Buffer } from "node:buffer";
var MAX_RESIDENT_ATOMS = 16 * 1024;
var MAX_STRUCTURE_LINE_BYTES = 1024 * 1024;
var MAX_MMCIF_HEADERS = 256;
var MAX_MMCIF_METADATA_RECORDS = 4096;
var MAX_MMCIF_METADATA_VALUE_LENGTH = 512;
function appendStructureBytes(state, bytes, offset, eof) {
if (bytes.byteLength > MAX_STRUCTURE_LINE_BYTES) {
fail("RESOURCE_EXHAUSTED", "The molecular read exceeds its line budget");
}
const pendingByteLength = state.pendingByteLength ?? Buffer.byteLength(state.pending, "utf8");
let text;
try {
text = state.decoder.decode(bytes, { stream: !eof });
} catch {
fail(
"MALFORMED_STRUCTURE",
"The authorized molecular bytes are not valid UTF-8"
);
}
const combined = state.pending + text;
if (Buffer.byteLength(combined, "utf8") > MAX_STRUCTURE_LINE_BYTES) {
fail("RESOURCE_EXHAUSTED", "A molecular record exceeds its line budget");
}
const segments = combined.split(/\r?\n/u);
state.pending = eof ? "" : segments.pop() ?? "";
if (eof && state.pending.length > 0) {
segments.push(state.pending);
state.pending = "";
}
const firstRecordStart = offset - BigInt(pendingByteLength);
let lineByteOffset = firstRecordStart;
let byteOffset = 0;
for (const line of segments) {
if (Buffer.byteLength(line, "utf8") > MAX_STRUCTURE_LINE_BYTES) {
fail("RESOURCE_EXHAUSTED", "A molecular record exceeds its line budget");
}
const newlineOffset = bytes.indexOf(10, byteOffset);
byteOffset = newlineOffset < 0 ? bytes.byteLength : newlineOffset + 1;
const recordEnd = offset + BigInt(byteOffset);
if (state.recordEndOffsets != null || state.format === "mmcif") {
state.currentRecordStart = lineByteOffset;
state.currentRecordEnd = recordEnd;
}
switch (state.format) {
case "pdb":
case "pdbqt":
parsePdbLine(state, line);
break;
case "mmcif":
parseMmcifLine(state, line);
break;
case "pqr":
parsePqrLine(state, line);
break;
case "mol":
case "sdf":
parseMolLine(state, line);
break;
case "mol2":
parseMol2Line(state, line);
break;
case "gro":
parseGroLine(state, line);
break;
case "xyz":
parseXyzLine(state, line);
break;
}
lineByteOffset = recordEnd;
}
if (eof) assertCompleteMmcifRecords(state);
state.scanOffset = offset + BigInt(bytes.byteLength);
state.pendingByteLength = eof ? 0 : Number(state.scanOffset - lineByteOffset);
state.complete = eof && !state.evicted;
if (state.mmcifTrustedRange && state.mmcifFraming != null && firstRecordStart <= state.mmcifFraming.scannedThrough && lineByteOffset > state.mmcifFraming.scannedThrough) {
state.mmcifFraming.scannedThrough = lineByteOffset;
}
applyMmcifResidueMetadata(state);
}
function parsePdbLine(state, line) {
if (line.startsWith("MODEL")) {
const model = Number.parseInt(line.slice(10).trim(), 10);
if (Number.isSafeInteger(model) && model > 0) {
state.model = model;
}
return;
}
if (!line.startsWith("ATOM ") && !line.startsWith("HETATM")) {
return;
}
const serial = line.slice(6, 11).trim();
const atomName = line.slice(12, 16).trim();
const residueName = line.slice(17, 20).trim();
const chainId = line.slice(21, 22).trim();
const residueNumber = Number.parseInt(line.slice(22, 26).trim(), 10);
const x = Number.parseFloat(line.slice(30, 38).trim());
const y = Number.parseFloat(line.slice(38, 46).trim());
const z = Number.parseFloat(line.slice(46, 54).trim());
if (!serial || !atomName || !residueName || !Number.isSafeInteger(residueNumber) || !Number.isFinite(x) || !Number.isFinite(y) || !Number.isFinite(z)) {
fail(
"MALFORMED_STRUCTURE",
"An authorized PDB atom has invalid fixed-column coordinates"
);
}
const atomId = `${state.model}:${serial}`;
const insertionCode = line.slice(26, 27).trim();
const altLoc = line.slice(16, 17).trim();
const element = line.slice(76, 78).trim();
const occupancy = Number.parseFloat(line.slice(54, 60));
const bFactor = Number.parseFloat(line.slice(60, 66));
setBoundedStructureAtom(state, atomId, {
atomId,
atomName,
authAtomName: atomName,
authChainId: chainId,
authResidueName: residueName,
authSequenceId: residueNumber,
...element ? { element } : {},
...Number.isFinite(occupancy) ? { occupancy } : {},
...Number.isFinite(bFactor) ? { bFactor } : {},
residueName,
chainId,
residueNumber,
model: state.model,
recordType: line.startsWith("HETATM") ? "HETATM" : "ATOM",
...insertionCode ? { insertionCode } : {},
...altLoc ? { altLoc } : {},
x,
y,
z
});
}
function parseMmcifLine(state, line) {
if (state.mmcifTrustedRange === false && state.mmcifFraming != null && state.currentRecordStart != null && state.currentRecordStart < state.mmcifFraming.scannedThrough && !state.mmcifFraming.atomRanges.some(
({ start, end }) => state.currentRecordStart >= start && state.currentRecordStart < end
)) {
return;
}
if (state.mmcifMultiline) {
if (line.startsWith(";")) state.mmcifMultiline = false;
return;
}
if (line.startsWith(";")) {
state.mmcifMultiline = true;
if (state.mmcifPendingScalar != null) {
state.mmcifPendingScalar = void 0;
} else {
consumeMmcifMetadataTokens(state, ["?"]);
}
return;
}
const trimmed = line.trim();
if (!trimmed || trimmed.startsWith("#")) return;
const control = /^(loop_|stop_)(?:\s+#.*)?$/iu.exec(trimmed)?.[1].toLowerCase();
const isDataBlock = /^data_/iu.test(trimmed);
if (trimmed.startsWith("_") || control != null || isDataBlock) {
assertCompleteMmcifRecords(state);
}
if (control != null || isDataBlock) {
state.headers = [];
state.mmcifAtomHeadersInferred = false;
state.mmcifCurrentAtomRange = void 0;
state.mmcifLoop = control === "loop_";
state.mmcifRowColumn = 0;
state.mmcifRowValues = /* @__PURE__ */ new Map();
state.mmcifPendingScalar = void 0;
if (isDataBlock) {
state.mmcifBlockStart = state.currentRecordStart ?? 0n;
state.mmcifScalarValues = void 0;
}
return;
}
const positionedTokens = tokenizeMmcifLine(line);
const tokens = positionedTokens.map(({ value }) => value);
if (trimmed.startsWith("_")) {
const header = tokens[0]?.toLowerCase();
if (header == null) return;
const sameCategory = state.headers.length === 0 || header.split(".")[0] === state.headers[0]?.split(".")[0];
if (state.mmcifLoop && tokens.length === 1 && sameCategory) {
if (state.mmcifAtomHeadersInferred && state.headers.includes(header)) {
return;
}
if (state.headers.length >= MAX_MMCIF_HEADERS) {
fail("RESOURCE_EXHAUSTED", "The mmCIF header budget is exceeded");
}
if (state.headers.includes(header)) {
fail("MALFORMED_STRUCTURE", "The mmCIF loop repeats a column");
}
state.headers.push(header);
if (header.startsWith("_atom_site.")) {
state.mmcifAtomHeaders = [...state.headers];
}
} else {
state.headers = [];
state.mmcifLoop = false;
state.mmcifCurrentAtomRange = void 0;
if (tokens[1] == null) state.mmcifPendingScalar = header;
else retainMmcifScalarMetadata(state, header, tokens[1]);
}
return;
}
if (state.mmcifPendingScalar != null) {
if (tokens[0] != null) {
retainMmcifScalarMetadata(state, state.mmcifPendingScalar, tokens[0]);
}
state.mmcifPendingScalar = void 0;
return;
}
if (!state.headers[0]?.startsWith("_atom_site.")) {
consumeMmcifMetadataTokens(state, tokens);
return;
}
const groupColumn = state.headers.indexOf("_atom_site.group_pdb");
if (state.mmcifAtomHeadersInferred && state.mmcifTrustedRange === false && (state.mmcifAtomRow?.length ?? 0) === 0 && groupColumn >= 0 && tokens[groupColumn] !== "ATOM" && tokens[groupColumn] !== "HETATM") {
return;
}
if ((state.mmcifAtomRow?.length ?? 0) > 0 && state.mmcifAtomRowLineStart !== state.currentRecordStart) {
state.mmcifComplexPackets = true;
}
for (const [index, token] of positionedTokens.entries()) {
state.mmcifAtomRow ??= [];
if (state.mmcifAtomRow.length === 0) {
state.mmcifAtomRowStart = (state.currentRecordStart ?? 0n) + BigInt(index === 0 ? 0 : token.start);
state.mmcifAtomRowLineStart = state.currentRecordStart;
}
const start = state.mmcifAtomRowStart ?? 0n;
if ((state.currentRecordStart ?? 0n) + BigInt(token.end) - start > BigInt(MAX_STRUCTURE_LINE_BYTES)) {
fail(
"RESOURCE_EXHAUSTED",
"An mmCIF atom packet exceeds its byte budget"
);
}
state.mmcifAtomRow.push(token.value);
if (state.mmcifAtomRow.length === state.headers.length) {
const nextToken = positionedTokens[index + 1];
const end = nextToken == null ? state.currentRecordEnd : (state.currentRecordStart ?? 0n) + BigInt(nextToken.start);
const lineAligned = state.mmcifAtomRowLineStart === state.currentRecordStart && index + 1 === state.headers.length && nextToken == null;
if (!lineAligned) state.mmcifComplexPackets = true;
if (!state.mmcifComplexPackets || state.mmcifTrustedRange !== false) {
parseMmcifAtomRow(state, state.mmcifAtomRow, end);
retainMmcifAtomRange(state, start, end, lineAligned);
}
state.mmcifAtomRow = void 0;
state.mmcifAtomRowStart = void 0;
state.mmcifAtomRowLineStart = void 0;
}
}
if ((state.mmcifAtomRow?.length ?? 0) > 0) state.mmcifComplexPackets = true;
}
function parseMmcifAtomRow(state, tokens, recordEnd) {
const values = /* @__PURE__ */ new Map();
for (const [index, header] of state.headers.entries()) {
values.set(header, tokens[index]);
}
function get(key) {
const value = values.get(`_atom_site.${key}`);
return value === "." || value === "?" ? void 0 : value;
}
const serial = get("id");
const x = Number(get("cartn_x"));
const y = Number(get("cartn_y"));
const z = Number(get("cartn_z"));
const model = Number(get("pdbx_pdb_model_num") ?? 1);
const residueNumber = Number(
get("auth_seq_id") ?? get("label_seq_id") ?? Number.NaN
);
const labelSequenceId = get("label_seq_id") == null ? void 0 : Number(get("label_seq_id"));
const authSequenceId = get("auth_seq_id") == null ? void 0 : Number(get("auth_seq_id"));
const occupancy = get("occupancy") == null ? void 0 : Number(get("occupancy"));
const bFactor = get("b_iso_or_equiv") == null ? void 0 : Number(get("b_iso_or_equiv"));
if (!serial || !Number.isSafeInteger(model) || !Number.isSafeInteger(residueNumber) || labelSequenceId != null && !Number.isSafeInteger(labelSequenceId) || authSequenceId != null && !Number.isSafeInteger(authSequenceId) || occupancy != null && !Number.isFinite(occupancy) || bFactor != null && !Number.isFinite(bFactor) || !Number.isFinite(x) || !Number.isFinite(y) || !Number.isFinite(z)) {
fail(
"MALFORMED_STRUCTURE",
"An authorized mmCIF atom has invalid coordinates"
);
}
const atomId = `${model}:${serial}`;
const insertionCode = get("pdbx_pdb_ins_code");
const altLoc = get("label_alt_id");
retainMmcifEntityMembership(
state,
get("label_asym_id"),
get("label_entity_id"),
"observed"
);
setBoundedStructureAtom(
state,
atomId,
{
atomId,
atomName: get("auth_atom_id") ?? get("label_atom_id") ?? serial,
authAtomName: get("auth_atom_id"),
authChainId: get("auth_asym_id"),
authResidueName: get("auth_comp_id"),
authSequenceId,
...occupancy == null ? {} : { occupancy },
...bFactor == null ? {} : { bFactor },
chainId: get("auth_asym_id") ?? get("label_asym_id") ?? "",
labelAtomName: get("label_atom_id"),
labelChainId: get("label_asym_id"),
labelResidueName: get("label_comp_id"),
labelSequenceId,
entityId: get("label_entity_id"),
element: get("type_symbol"),
residueName: get("auth_comp_id") ?? get("label_comp_id") ?? "UNK",
residueNumber,
model,
recordType: get("group_pdb") === "HETATM" ? "HETATM" : "ATOM",
...insertionCode ? { insertionCode } : {},
...altLoc ? { altLoc } : {},
x,
y,
z
},
recordEnd
);
}
function tokenizeMmcifLine(line) {
const tokens = [];
let cursor = 0;
let byteCursor = 0;
let previousCursor = 0;
while (cursor < line.length) {
while (cursor < line.length && /\s/u.test(line[cursor])) cursor += 1;
if (cursor === line.length || line[cursor] === "#") break;
byteCursor += Buffer.byteLength(line.slice(previousCursor, cursor), "utf8");
const tokenStart = byteCursor;
const tokenCursor = cursor;
let value;
const quote = line[cursor];
if (quote === "'" || quote === '"') {
const start = ++cursor;
while (cursor < line.length && (line[cursor] !== quote || cursor + 1 < line.length && !/\s/u.test(line[cursor + 1]))) {
cursor += 1;
}
if (cursor === line.length) {
fail("MALFORMED_STRUCTURE", "A quoted mmCIF token is incomplete");
}
value = line.slice(start, cursor);
cursor += 1;
} else {
const start = cursor;
while (cursor < line.length && !/\s/u.test(line[cursor])) cursor += 1;
value = line.slice(start, cursor);
}
byteCursor += Buffer.byteLength(line.slice(tokenCursor, cursor), "utf8");
previousCursor = cursor;
tokens.push({ value, start: tokenStart, end: byteCursor });
}
return tokens;
}
var MMCIF_RESIDUE_METADATA_FIELDS = /* @__PURE__ */ new Set([
"_chem_comp.id",
"_chem_comp.type",
"_entity.id",
"_entity.type",
"_entity_poly.entity_id",
"_entity_poly.type",
"_struct_asym.id",
"_struct_asym.entity_id"
]);
function isMmcifEntityMappingField(header) {
return header === "_struct_asym.id" || header === "_struct_asym.entity_id";
}
function assertCompleteMmcifRecords(state) {
if ((state.mmcifAtomRow?.length ?? 0) > 0 && !(state.mmcifComplexPackets && state.mmcifTrustedRange === false)) {
fail(
"MALFORMED_STRUCTURE",
"An authorized mmCIF atom-site row is incomplete"
);
}
if (state.mmcifTrustedRange === false) return;
if (isMmcifEntityMappingField(state.mmcifPendingScalar)) {
fail(
"MALFORMED_STRUCTURE",
"A native mmCIF entity mapping value is missing"
);
}
if ((state.mmcifRowColumn ?? 0) > 0 && state.headers.some(isMmcifEntityMappingField)) {
fail(
"MALFORMED_STRUCTURE",
"A native mmCIF entity mapping row is incomplete"
);
}
}
function assertMmcifEntityIdentifier(value) {
if (value.trim().length === 0) {
fail("MALFORMED_STRUCTURE", "A native mmCIF entity identifier is empty");
}
if (value.length > MAX_MMCIF_METADATA_VALUE_LENGTH) {
fail(
"RESOURCE_EXHAUSTED",
"A native mmCIF entity identifier exceeds its value budget"
);
}
}
function consumeMmcifMetadataTokens(state, tokens) {
if (!state.headers.some((header) => MMCIF_RESIDUE_METADATA_FIELDS.has(header))) {
return;
}
let column = state.mmcifRowColumn ?? 0;
let values = state.mmcifRowValues ?? /* @__PURE__ */ new Map();
for (const token of tokens) {
const header = state.headers[column];
if (state.mmcifTrustedRange !== false && isMmcifEntityMappingField(header)) {
assertMmcifEntityIdentifier(token);
}
if (header != null && MMCIF_RESIDUE_METADATA_FIELDS.has(header) && token !== "." && token !== "?" && token.trim().length > 0 && token.length <= MAX_MMCIF_METADATA_VALUE_LENGTH) {
values.set(header, token);
}
column += 1;
if (column === state.headers.length) {
retainMmcifResidueMetadata(state, values);
column = 0;
values = /* @__PURE__ */ new Map();
}
}
state.mmcifRowColumn = column;
state.mmcifRowValues = values;
}
function retainMmcifScalarMetadata(state, header, value) {
if (state.mmcifTrustedRange === false) return;
if (isMmcifEntityMappingField(header)) assertMmcifEntityIdentifier(value);
if (!MMCIF_RESIDUE_METADATA_FIELDS.has(header) || value === "." || value === "?" || value.trim().length === 0 || value.length > MAX_MMCIF_METADATA_VALUE_LENGTH) {
return;
}
state.mmcifScalarValues ??= /* @__PURE__ */ new Map();
setMmcifMetadataValue(state.mmcifScalarValues, header, value);
retainMmcifResidueMetadata(state, state.mmcifScalarValues);
}
function setMmcifMetadataValue(values, key, value, id = key) {
const existing = values.get(key);
if (existing != null && existing !== value) {
fail(
"MALFORMED_STRUCTURE",
`Conflicting mmCIF residue metadata declarations for ${id}`
);
}
values.set(key, value);
}
function mmcifMetadataKey(blockStart, id) {
return `${blockStart}:${id}`;
}
function retainMmcifEntityMembership(state, labelChainId, entityId, provenance) {
const metadata = state.mmcifMetadata;
if (metadata == null || state.mmcifTrustedRange === false || labelChainId == null || entityId == null) {
return;
}
assertMmcifEntityIdentifier(labelChainId);
assertMmcifEntityIdentifier(entityId);
const memberships = metadata.entityMemberships;
const key = mmcifMetadataKey(state.mmcifBlockStart, labelChainId);
const existing = memberships.get(key);
if (existing == null && memberships.size >= MAX_MMCIF_METADATA_RECORDS) {
fail(
"RESOURCE_EXHAUSTED",
"The native mmCIF entity membership budget is exceeded"
);
}
const membership = existing ?? {};
if (provenance === "declared" && membership.declaredEntityId != null && membership.declaredEntityId !== entityId) {
fail(
"MALFORMED_STRUCTURE",
`Conflicting mmCIF residue metadata declarations for ${labelChainId}`
);
}
if (membership.declaredEntityId != null && membership.declaredEntityId !== entityId || provenance === "declared" && (membership.observedConflict || membership.observedEntityId != null && membership.observedEntityId !== entityId)) {
fail(
"AMBIGUOUS_IDENTITY",
`Conflicting mmCIF entity identities for label chain ${labelChainId}`
);
}
if (provenance === "declared") {
membership.declaredEntityId = entityId;
} else if (membership.observedEntityId == null) {
membership.observedEntityId = entityId;
} else if (membership.observedEntityId !== entityId) {
membership.observedConflict = true;
}
memberships.set(key, membership);
}
function retainMmcifResidueMetadata(state, values) {
const metadata = state.mmcifMetadata;
if (metadata == null || state.mmcifTrustedRange === false) return;
const retain = (target, id, value) => {
if (id == null || value == null) return;
const key = mmcifMetadataKey(state.mmcifBlockStart, id);
if (target.has(key) || target.size < MAX_MMCIF_METADATA_RECORDS) {
setMmcifMetadataValue(target, key, value, id);
}
};
retain(
metadata.entityTypes,
values.get("_entity.id"),
values.get("_entity.type")
);
const polymerEntityId = values.get("_entity_poly.entity_id");
if (polymerEntityId != null && metadata.polymerEntities.size < MAX_MMCIF_METADATA_RECORDS) {
metadata.polymerEntities.add(
mmcifMetadataKey(state.mmcifBlockStart, polymerEntityId)
);
}
retain(
metadata.polymerTypes,
polymerEntityId,
values.get("_entity_poly.type")
);
retain(
metadata.chemicalComponentTypes,
values.get("_chem_comp.id"),
values.get("_chem_comp.type")
);
retainMmcifEntityMembership(
state,
values.get("_struct_asym.id"),
values.get("_struct_asym.entity_id"),
"declared"
);
}
function applyMmcifResidueMetadata(state) {
const metadata = state.mmcifMetadata;
if (state.format !== "mmcif" || metadata == null || state.mmcifTrustedRange === false) {
return;
}
for (const [id, atom] of state.atoms) {
const blockStart = state.mmcifAtomBlocks.get(id);
if (blockStart == null) continue;
const declaredEntityId = atom.labelChainId == null ? void 0 : metadata.entityMemberships.get(
mmcifMetadataKey(blockStart, atom.labelChainId)
)?.declaredEntityId;
if (atom.entityId != null && declaredEntityId != null && atom.entityId !== declaredEntityId) {
fail(
"AMBIGUOUS_IDENTITY",
`Conflicting mmCIF entity identities for label chain ${atom.labelChainId}`
);
}
const entityId = atom.entityId ?? declaredEntityId;
const entityKey = entityId == null ? void 0 : mmcifMetadataKey(blockStart, entityId);
const entityType = entityKey == null ? void 0 : metadata.entityTypes.get(entityKey) ?? (metadata.polymerEntities.has(entityKey) ? "polymer" : void 0);
const polymerType = entityKey == null ? void 0 : metadata.polymerTypes.get(entityKey);
const chemicalComponentType = metadata.chemicalComponentTypes.get(
mmcifMetadataKey(blockStart, atom.labelResidueName ?? atom.residueName)
);
state.atoms.set(id, {
...atom,
...entityId == null ? {} : { entityId },
...entityType == null ? {} : { entityType },
...polymerType == null ? {} : { polymerType },
...chemicalComponentType == null ? {} : { chemicalComponentType },
classificationMetadata: entityType != null || polymerType != null ? "declared" : "unavailable"
});
}
}
function retainMmcifAtomRange(state, start, end, lineAligned) {
const framing = state.mmcifFraming;
if (!state.mmcifTrustedRange || framing == null || start == null || end == null) {
return;
}
state.mmcifCurrentAtomRange ??= framing.atomRanges.find(
(range) => start >= range.start && start < range.end
);
if (state.mmcifCurrentAtomRange == null) {
state.mmcifCurrentAtomRange = {
start,
end,
lineAligned,
headers: [...state.headers],
blockStart: state.mmcifBlockStart
};
if (framing.atomRanges.length < MAX_MMCIF_METADATA_RECORDS) {
framing.atomRanges.push(state.mmcifCurrentAtomRange);
}
} else if (end > state.mmcifCurrentAtomRange.end) {
state.mmcifCurrentAtomRange.end = end;
}
if (!lineAligned) state.mmcifCurrentAtomRange.lineAligned = false;
}
function nativeClassificationMetadata(atoms) {
const declared = atoms.filter(
(atom) => atom.classificationMetadata === "declared"
).length;
return declared === 0 ? "unavailable" : declared === atoms.length ? "declared" : "partial";
}
function parsePqrLine(state, line) {
const fields = line.trim().split(/\s+/u);
if (fields[0] === "MODEL") {
const model = Number(fields[1]);
if (Number.isSafeInteger(model) && model > 0) {
state.model = model;
}
return;
}
if (fields[0] !== "ATOM" && fields[0] !== "HETATM") {
return;
}
if (fields.length < 10) {
fail("MALFORMED_STRUCTURE", "An authorized PQR atom row is incomplete");
}
const hasChain = fields.length >= 11;
const residue = /^(-?\d+)([A-Za-z]?)$/u.exec(fields[hasChain ? 5 : 4]);
const coordinate = hasChain ? 6 : 5;
if (residue == null) {
fail("MALFORMED_STRUCTURE", "An authorized PQR residue is invalid");
}
appendParsedStructureAtom(state, {
serial: fields[1],
atomName: fields[2],
chainId: hasChain ? fields[4] : "A",
residueName: fields[3],
residueNumber: Number(residue[1]),
recordType: fields[0],
...residue[2] ? { insertionCode: residue[2] } : {},
x: Number(fields[coordinate]),
y: Number(fields[coordinate + 1]),
z: Number(fields[coordinate + 2])
});
}
function parseMolLine(state, line) {
if (state.format === "sdf" && line.trim() === "$$$$") {
state.model += 1;
state.formatLine = 0;
state.blockAtomCount = void 0;
state.blockAtomIndex = 0;
state.formatSection = void 0;
return;
}
const lineNumber = state.formatLine ?? 0;
state.formatLine = lineNumber + 1;
if (lineNumber === 3) {
if (/V3000/u.test(line)) {
state.formatSection = "v3000";
return;
}
const count2 = Number(line.slice(0, 3).trim());
if (!Number.isSafeInteger(count2) || count2 <= 0) {
fail("MALFORMED_STRUCTURE", "An authorized MOL atom count is invalid");
}
state.blockAtomCount = count2;
state.blockAtomIndex = 0;
return;
}
if (state.formatSection === "v3000" || state.formatSection === "v3000-atoms") {
if (/^M\s+V30\s+BEGIN ATOM\s*$/u.test(line)) {
state.formatSection = "v3000-atoms";
return;
}
if (/^M\s+V30\s+END ATOM\s*$/u.test(line)) {
state.formatSection = "v3000";
return;
}
if (state.formatSection !== "v3000-atoms") {
return;
}
const fields = line.replace(/^M\s+V30\s+/u, "").trim().split(/\s+/u);
if (fields.length < 5) {
fail("MALFORMED_STRUCTURE", "An authorized MOL V3000 atom is incomplete");
}
appendParsedStructureAtom(state, {
serial: fields[0],
atomName: `${fields[1]}${fields[0]}`,
x: Number(fields[2]),
y: Number(fields[3]),
z: Number(fields[4])
});
return;
}
const count = state.blockAtomCount;
const index = state.blockAtomIndex ?? 0;
if (count == null || index >= count || lineNumber < 4) {
return;
}
const element = line.slice(31, 34).trim();
if (!element) {
fail("MALFORMED_STRUCTURE", "An authorized MOL atom element is missing");
}
const serial = String(index + 1);
appendParsedStructureAtom(state, {
serial,
atomName: `${element}${serial}`,
x: Number(line.slice(0, 10).trim()),
y: Number(line.slice(10, 20).trim()),
z: Number(line.slice(20, 30).trim())
});
state.blockAtomIndex = index + 1;
}
function parseMol2Line(state, line) {
if (line.startsWith("@<TRIPOS>MOLECULE")) {
if (state.formatLine != null) {
state.model += 1;
}
state.formatLine = 0;
state.formatSection = void 0;
return;
}
if (line.startsWith("@<TRIPOS>ATOM")) {
state.formatSection = "atoms";
return;
}
if (line.startsWith("@<TRIPOS>")) {
state.formatSection = void 0;
return;
}
if (state.formatSection !== "atoms" || !line.trim()) {
return;
}
const fields = line.trim().split(/\s+/u);
if (fields.length < 6) {
fail("MALFORMED_STRUCTURE", "An authorized MOL2 atom row is incomplete");
}
appendParsedStructureAtom(state, {
serial: fields[0],
atomName: fields[1],
residueName: fields[7] ?? "LIG",
residueNumber: fields[6] == null ? 1 : Number(fields[6]),
x: Number(fields[2]),
y: Number(fields[3]),
z: Number(fields[4])
});
}
function parseGroLine(state, line) {
const lineNumber = state.formatLine ?? 0;
state.formatLine = lineNumber + 1;
if (lineNumber === 0) {
return;
}
if (lineNumber === 1) {
const count2 = Number(line.trim());
if (!Number.isSafeInteger(count2) || count2 <= 0) {
fail("MALFORMED_STRUCTURE", "An authorized GRO atom count is invalid");
}
state.blockAtomCount = count2;
state.blockAtomIndex = 0;
return;
}
const count = state.blockAtomCount ?? 0;
const index = state.blockAtomIndex ?? 0;
if (index >= count) {
state.model += 1;
state.formatLine = 0;
state.blockAtomCount = void 0;
state.blockAtomIndex = 0;
return;
}
if (line.length < 44) {
fail("MALFORMED_STRUCTURE", "An authorized GRO atom row is incomplete");
}
appendParsedStructureAtom(state, {
serial: line.slice(15, 20).trim(),
atomName: line.slice(10, 15).trim(),
residueName: line.slice(5, 10).trim(),
residueNumber: Number(line.slice(0, 5).trim()),
recordType: "ATOM",
x: 10 * Number(line.slice(20, 28).trim()),
y: 10 * Number(line.slice(28, 36).trim()),
z: 10 * Number(line.slice(36, 44).trim())
});
state.blockAtomIndex = index + 1;
}
function parseXyzLine(state, line) {
const lineNumber = state.formatLine ?? 0;
if (lineNumber === 0 && !line.trim()) {
return;
}
state.formatLine = lineNumber + 1;
if (lineNumber === 0) {
const count = Number(line.trim());
if (!Number.isSafeInteger(count) || count <= 0) {
fail("MALFORMED_STRUCTURE", "An authorized XYZ atom count is invalid");
}
state.blockAtomCount = count;
state.blockAtomIndex = 0;
return;
}
if (lineNumber === 1) {
return;
}
const fields = line.trim().split(/\s+/u);
if (fields.length < 4) {
fail("MALFORMED_STRUCTURE", "An authorized XYZ atom row is incomplete");
}
const index = state.blockAtomIndex ?? 0;
const serial = String(index + 1);
appendParsedStructureAtom(state, {
serial,
atomName: `${fields[0]}${serial}`,
residueName: "MOL",
x: Number(fields[1]),
y: Number(fields[2]),
z: Number(fields[3])
});
state.blockAtomIndex = index + 1;
if (state.blockAtomIndex === state.blockAtomCount) {
state.model += 1;
state.formatLine = 0;
state.blockAtomCount = void 0;
state.blockAtomIndex = 0;
}
}
function appendParsedStructureAtom(state, atom) {
if (!atom.serial || !atom.atomName || !Number.isSafeInteger(atom.residueNumber ?? 1) || !Number.isFinite(atom.x) || !Number.isFinite(atom.y) || !Number.isFinite(atom.z)) {
fail("MALFORMED_STRUCTURE", "An authorized structure atom is invalid");
}
const atomId = `${state.model}:${atom.serial}`;
setBoundedStructureAtom(state, atomId, {
atomId,
atomName: atom.atomName,
chainId: atom.chainId ?? "A",
residueName: atom.residueName ?? "LIG",
residueNumber: atom.residueNumber ?? 1,
model: state.model,
recordType: atom.recordType ?? "HETATM",
...atom.insertionCode ? { insertionCode: atom.insertionCode } : {},
x: atom.x,
y: atom.y,
z: atom.z
});
}
function setBoundedStructureAtom(state, atomId, atom, recordEnd = state.currentRecordEnd) {
if (state.atoms.has(atomId)) {
fail("AMBIGUOUS_IDENTITY", "The molecular source repeats an atom identity");
}
if (!state.atoms.has(atomId) && state.atoms.size >= MAX_RESIDENT_ATOMS) {
let evicted = false;
for (const retainedAtomId of state.atoms.keys()) {
if (!state.selectedAtomIds?.has(retainedAtomId)) {
state.atoms.delete(retainedAtomId);
state.mmcifAtomBlocks.delete(retainedAtomId);
state.recordEndOffsets?.delete(retainedAtomId);
state.evicted = true;
evicted = true;
break;
}
}
if (!evicted) {
fail(
"RESOURCE_EXHAUSTED",
"The selected molecular atoms exceed their resident index budget"
);
}
}
state.atoms.set(atomId, {
...atom,
sourceFormat: state.format,
classificationMetadata: atom.classificationMetadata ?? "unavailable"
});
if (state.format === "mmcif" && state.mmcifTrustedRange !== false) {
state.mmcifAtomBlocks.set(atomId, state.mmcifBlockStart);
}
if (state.recordEndOffsets != null && recordEnd != null) {
state.recordEndOffsets.set(atomId, recordEnd);
}
}
function fail(code, message) {
const error = Object.assign(new Error(message), {
name: "ScientificStructureRuntimeError",
code
});
throw error;
}
// node_modules/.pnpm/@openai+scientific-viewer-platform@file+..+scientific-viewer-platform/node_modules/@openai/scientific-viewer-platform/src/structure/scientific-structure-native-trajectory-bundle.mjs
import { createHash } from "node:crypto";
var _SCIENTIFIC_STRUCTURE_LIMITS = Object.freeze({
maxAtoms: 1e6,
maxComparisons: 5e6,
maxContacts: 5e4,
maxRmsdAtoms: 2e4,
maxSelectionAtoms: 1e5,
maxSourceBytes: 128 * 1024 * 1024
});
var ScientificStructureError = class extends Error {
constructor(code, message) {
super(message);
this.code = code;
this.name = "ScientificStructureError";
}
code;
};
var SCIENTIFIC_STRUCTURE_TRAJECTORY_LIMITS = Object.freeze({
maxAlignmentAtoms: 1e5,
maxFrames: 2e4,
maxTopologyAtoms: 1e6
});
function validateScientificStructureTrajectoryTopology(topology) {
if (!/^sha256:[\da-f]{64}$/iu.test(topology.sourceDigest)) {
throw trajectoryError("Trajectory sourceDigest must be a SHA-256 digest");
}
assertText(topology.sourceRevision, "sourceRevision");
if (topology.atomIds.length === 0) {
throw trajectoryError("Trajectory topology must contain at least one atom");
}
if (topology.atomIds.length > SCIENTIFIC_STRUCTURE_TRAJECTORY_LIMITS.maxTopologyAtoms) {
throw resourceError("Trajectory topology atom limit exceeded");
}
const identities = /* @__PURE__ */ new Set();
for (const atomId of topology.atomIds) {
assertText(atomId, "topology atom ID");
if (identities.has(atomId)) {
throw trajectoryError(`Duplicate topology atom identity: ${atomId}`);
}
identities.add(atomId);
}
return {
atomCount: topology.atomIds.length,
complete: true,
sourceDigest: topology.sourceDigest,
sourceRevision: topology.sourceRevision
};
}
function validateScientificStructureTrajectoryFrame({
frame,
topology
}) {
const validated = validateScientificStructureTrajectoryTopology(topology);
if (frame.topologyDigest !== topology.sourceDigest) {
throw trajectoryError("Trajectory frame topology digest does not match");
}
if (!Number.isSafeInteger(frame.index) || frame.index < 0) {
throw trajectoryError(
"Trajectory frame index must be a nonnegative integer"
);
}
if (frame.timePicoseconds != null && !Number.isFinite(frame.timePicoseconds)) {
throw trajectoryError("Trajectory frame time must be finite");
}
if (frame.coordinates.length !== validated.atomCount * 3) {
throw trajectoryError(
"Trajectory frame coordinate count does not match topology"
);
}
if (Array.from(frame.coordinates).some((value) => !Number.isFinite(value))) {
throw trajectoryError("Trajectory frame contains non-finite coordinates");
}
if (frame.boxAngstrom?.some((length) => !Number.isFinite(length) || length <= 0)) {
throw trajectoryError(
"Trajectory periodic box lengths must be positive and finite"
);
}
return {
atomCount: validated.atomCount,
complete: true,
frameIndex: frame.index,
timePicoseconds: frame.timePicoseconds ?? null,
topologyDigest: frame.topologyDigest
};
}
function assertText(value, field) {
if (value.trim().length === 0 || value.length > 256) {
throw trajectoryError(`${field} is invalid or exceeds its limit`);
}
}
function trajectoryError(message) {
return new ScientificStructureError("INVALID_REQUEST", message);
}
function resourceError(message) {
return new ScientificStructureError("RESOURCE_EXHAUSTED", message);
}
var ScientificStructureBinaryIoError = class extends Error {
constructor(code, message) {
super(message);
this.code = code;
this.name = "ScientificStructureBinaryIoError";
}
code;
};
var SCIENTIFIC_STRUCTURE_BINARY_IO_LIMITS = Object.freeze({
maxAtoms: 1e6,
maxBcifExpandedBytes: 512 * 1024 * 1024,
maxBcifScanBytes: 16n * 1024n * 1024n * 1024n,
maxDecodedFrameBytes: 128 * 1024 * 1024,
maxFrameBytes: 4n * 1024n * 1024n * 1024n,
maxFrames: 1e6,
maxMetadataBytes: 16 * 1024 * 1024,
maxRangeBytes: 1024 * 1024,
maxSdfRecordBytes: 128 * 1024 * 1024,
maxSdfRecords: 1e6
});
var ARCHIVE_SIGNATURES = [
{ bytes: [31, 139], label: "gzip" },
{ bytes: [66, 90, 104], label: "bzip2" },
{ bytes: [80, 75, 3, 4], label: "ZIP" },
{ bytes: [80, 75, 5, 6], label: "ZIP" },
{ bytes: [80, 75, 7, 8], label: "ZIP" },
{ bytes: [253, 55, 122, 88, 90, 0], label: "XZ" },
{ bytes: [40, 181, 47, 253], label: "Zstandard" },
{ bytes: [55, 122, 188, 175, 39, 28], label: "7-Zip" },
{ bytes: [82, 97, 114, 33, 26, 7], label: "RAR" }
];
async function indexScientificStructureBinaryTrajectory(input) {
const budget = getBudget(input.budget);
assertSource(input.source);
await revalidateSource(input.source, input.signal);
assertNotCancelled(input.signal);
await assertNotArchive(input.source, input.signal, budget);
const topology = validateScientificStructureTrajectoryTopology(
input.topology
);
if (topology.atomCount > budget.maxAtoms) {
throw exhausted("Trajectory topology exceeds maxAtoms");
}
const format = input.format === "nc" || input.format === "nctraj" ? "netcdf" : input.format;
let indexed;
if (format === "xtc") {
indexed = await indexXtc(
input.source,
topology.atomCount,
input.signal,
budget
);
} else if (format === "dcd") {
indexed = await indexDcd(
input.source,
topology.atomCount,
input.signal,
budget
);
} else if (format === "trr") {
indexed = await indexTrr(
input.source,
topology.atomCount,
input.signal,
budget
);
} else {
indexed = await indexNetcdf(
input.source,
topology.atomCount,
input.signal,
budget
);
}
await revalidateSource(input.source, input.signal);
return {
...indexed,
atomCount: topology.atomCount,
format,
sourceDigest: input.source.sourceDigest,
sourceRevision: input.source.sourceRevision,
sourceSizeBytes: input.source.sizeBytes,
topologyDigest: topology.sourceDigest,
topologyRevision: topology.sourceRevision
};
}
var ScientificStructureBinaryFrameReader = class {
constructor(input) {
this.input = input;
this.budget = getBudget(input.budget);
assertSource(input.source);
const topology = validateScientificStructureTrajectoryTopology(
input.topology
);
if (input.index.sourceDigest !== input.source.sourceDigest || input.index.sourceRevision !== input.source.sourceRevision || input.index.sourceSizeBytes !== input.source.sizeBytes) {
throw sourceChanged(
"Trajectory frame index belongs to another source revision"
);
}
if (input.index.topologyDigest !== topology.sourceDigest || input.index.topologyRevision !== topology.sourceRevision || input.index.atomCount !== topology.atomCount) {
throw topologyMismatch(
"Trajectory frame index does not match the selected topology"
);
}
}
input;
budget;
async readFrames(input) {
const stride = input.stride ?? 1;
if (!Number.isSafeInteger(stride) || stride < 1) {
throw malformed("Trajectory frame stride must be a positive integer");
}
if (!Number.isSafeInteger(input.start) || !Number.isSafeInteger(input.endExclusive) || input.start < 0 || input.endExclusive < input.start || input.endExclusive > this.input.index.frameCount) {
throw malformed("Requested trajectory frame window is invalid");
}
const sampledFrameCount = Math.ceil(
(input.endExclusive - input.start) / stride
);
if (sampledFrameCount > this.budget.maxFrames) {
throw exhausted("Requested trajectory frame window exceeds maxFrames");
}
await revalidateSource(this.input.source, input.signal);
const frames = [];
for (let frameIndex = input.start; frameIndex < input.endExclusive; frameIndex += stride) {
assertNotCancelled(input.signal);
const descriptor = this.input.index.frames[frameIndex];
if (descriptor == null || descriptor.frameIndex !== frameIndex) {
throw malformed("Trajectory frame index is incomplete or out of order");
}
const frame = this.input.decoder == null ? await decodeScientificStructureBinaryFrame({
budget: this.budget,
descriptor,
signal: input.signal,
source: this.input.source,
topology: this.input.topology
}) : await this.input.decoder.decodeFrame({
descriptor,
format: this.input.index.format,
signal: input.signal,
source: this.input.source,
topology: this.input.topology
});
validateDecodedFrame(frame, descriptor, this.input.topology);
frames.push(frame);
}
await revalidateSource(this.input.source, input.signal);
return {
complete: true,
frames,
indexComplete: this.input.index.complete,
sampledFrameCount,
sourceFrameCount: this.input.index.frameCount,
stride
};
}
};
async function decodeScientificStructureBinaryFrame(input) {
const budget = getBudget(input.budget);
const descriptor = input.descriptor;
if (!descriptor.coordinatesComplete) {
throw malformed("Trajectory frame does not contain coordinates");
}
if (descriptor.coordinateEncoding === "xtc-compressed") {
throw new ScientificStructureBinaryIoError(
"UNSUPPORTED",
"Compressed XTC coordinates require an injected governed decoder"
);
}
const coordinateBytes = descriptor.coordinateRanges.reduce(
(total, range) => total + range.length,
0
);
if (coordinateBytes > budget.maxDecodedFrameBytes) {
throw exhausted("Decoded trajectory frame exceeds maxDecodedFrameBytes");
}
const parts = await Promise.all(
descriptor.coordinateRanges.map(
(range) => readExactChunked(
input.source,
range.offset,
range.length,
input.signal,
budget
)
)
);
const coordinates = decodeCoordinates(descriptor, parts);
const lengths = descriptor.cell?.lengthsAngstrom;
const frame = {
...lengths == null ? {} : { boxAngstrom: lengths },
coordinates,
index: descriptor.frameIndex,
...descriptor.timePicoseconds == null ? {} : { timePicoseconds: descriptor.timePicoseconds },
topologyDigest: input.topology.sourceDigest
};
validateDecodedFrame(frame, descriptor, input.topology);
return frame;
}
async function indexXtc(source, topologyAtoms, signal, budget) {
const frames = [];
let offset = 0n;
while (offset < source.sizeBytes) {
if (frames.length === budget.maxFrames) {
return partialIndex(frames, offset);
}
const header = await readExact(source, offset, 56, signal, budget);
const view = dataView(header);
if (view.getInt32(0, false) !== 1995) {
throw malformed("XTC frame has an invalid magic number");
}
const atomCount = view.getInt32(4, false);
assertFrameAtomCount(atomCount, topologyAtoms, budget, "XTC");
if (view.getInt32(52, false) !== atomCount) {
throw malformed("XTC coordinate count does not match its atom count");
}
const step = view.getInt32(8, false);
const timePicoseconds = view.getFloat32(12, false);
if (!Number.isFinite(timePicoseconds)) {
throw malformed("XTC frame time is not finite");
}
const vectors = readCellVectors(view, 16, 4, false, 10);
let byteLength;
let coordinateEncoding;
let coordinateRange;
if (atomCount <= 9) {
const coordinateBytes = safeNumberProduct(
[atomCount, 12],
"XTC coordinate payload"
);
byteLength = 56n + BigInt(coordinateBytes);
coordinateEncoding = "float32-be-interleaved-nanometre";
coordinateRange = { length: coordinateBytes, offset: offset + 56n };
} else {
const compressedHeader = await readExact(
source,
offset,
92,
signal,
budget
);
const compressedView = dataView(compressedHeader);
const smallIndex = compressedView.getInt32(84, false);
const compressedBytes = compressedView.getInt32(88, false);
if (smallIndex < 9 || smallIndex > 72 || compressedBytes < 1) {
throw malformed("XTC compressed frame has invalid packing metadata");
}
const padded = safeNumberProduct(
[Math.ceil(compressedBytes / 4), 4],
"XTC compressed coordinate payload"
);
byteLength = 92n + BigInt(padded);
coordinateEncoding = "xtc-compressed";
coordinateRange = { length: padded, offset: offset + 92n };
}
assertFrameSpan(source, offset, byteLength, budget, "XTC frame");
frames.push({
atomCount,
byteLength,
byteOffset: offset,
cell: cellFromVectors(vectors),
coordinateEncoding,
coordinateRanges: [coordinateRange],
coordinatesComplete: true,
frameIndex: frames.length,
step,
timePicoseconds
});
offset += byteLength;
}
return completeIndex(frames, offset);
}
async function indexDcd(source, topologyAtoms, signal, budget) {
const header = await readExact(source, 0n, 104, signal, budget);
const view = dataView(header);
let littleEndian = null;
if (view.getInt32(0, true) === 84) {
littleEndian = true;
} else if (view.getInt32(0, false) === 84) {
littleEndian = false;
}
if (littleEndian == null || !bytesEqualAt(header, 4, [67, 79, 82, 68])) {
throw malformed("DCD CORD header is invalid");
}
const declaredFrameCount = view.getInt32(8, littleEndian);
const startStep = view.getInt32(12, littleEndian);
const saveInterval = view.getInt32(16, littleEndian);
const hasCell = view.getInt32(48, littleEndian) !== 0;
const hasFourthDimension = view.getInt32(52, littleEndian) === 1;
if (declaredFrameCount < 0 || view.getInt32(88, littleEndian) !== 84) {
throw malformed("DCD frame header is invalid");
}
const titleBytes = view.getInt32(92, littleEndian);
const titleLineCount = view.getInt32(96, littleEndian);
if (titleBytes < 4 || (titleBytes - 4) % 80 !== 0 || titleLineCount < 0) {
throw malformed("DCD title block is invalid");
}
const countedTitleBytes = safeNumberSum(
[4, safeNumberProduct([titleLineCount, 80], "DCD title records")],
"DCD title records"
);
if (titleBytes > budget.maxMetadataBytes || countedTitleBytes > budget.maxMetadataBytes) {
throw exhausted("DCD title block exceeds maxMetadataBytes");
}
let atomCount;
let firstFrameOffset;
let mismatchedAtomCount;
let candidateWithinSource = false;
for (const payloadBytes of /* @__PURE__ */ new Set([countedTitleBytes, titleBytes])) {
const titleEnd = 96n + BigInt(payloadBytes);
if (titleEnd + 16n > source.sizeBytes) {
continue;
}
candidateWithinSource = true;
const titleAndAtomBlock = dataView(
await readExact(source, titleEnd, 16, signal, budget)
);
if (titleAndAtomBlock.getInt32(0, littleEndian) !== titleBytes || titleAndAtomBlock.getInt32(4, littleEndian) !== 4 || titleAndAtomBlock.getInt32(12, littleEndian) !== 4) {
continue;
}
const candidateAtomCount = titleAndAtomBlock.getInt32(8, littleEndian);
if (candidateAtomCount !== topologyAtoms) {
mismatchedAtomCount ??= candidateAtomCount;
continue;
}
if (firstFrameOffset != null) {
throw malformed("DCD title block has ambiguous authorized atom records");
}
atomCount = candidateAtomCount;
firstFrameOffset = titleEnd + 16n;
}
if (atomCount == null || firstFrameOffset == null) {
if (mismatchedAtomCount != null) {
assertFrameAtomCount(mismatchedAtomCount, topologyAtoms, budget, "DCD");
}
if (!candidateWithinSource) {
throw truncated("DCD title or atom-count block exceeds retained source bytes");
}
throw malformed("DCD title or atom-count block is invalid");
}
assertFrameAtomCount(atomCount, topologyAtoms, budget, "DCD");
const axisBytes = safeNumberProduct([atomCount, 4], "DCD coordinate block");
const minimumFrameBytes = BigInt(
safeNumberProduct([axisBytes + 8, 3], "DCD coordinate frame") + (hasCell ? 56 : 0) + (hasFourthDimension ? 8 : 0)
);
if (minimumFrameBytes > budget.maxFrameBytes) {
throw exhausted("DCD coordinate frame exceeds maxFrameBytes");
}
let offset = firstFrameOffset;
const availableFrameBytes = source.sizeBytes - offset;
if (availableFrameBytes === 0n && declaredFrameCount > 0) {
throw truncated("DCD contains no retained declared coordinate frames");
}
if (!hasFourthDimension && availableFrameBytes % minimumFrameBytes !== 0n) {
throw truncated("DCD source contains an incomplete coordinate frame");
}
const frames = [];
while (offset < source.sizeBytes) {
if (frames.length === budget.maxFrames) {
return partialIndex(frames, offset);
}
if (source.sizeBytes - offset < minimumFrameBytes) {
throw truncated("DCD source contains an incomplete coordinate frame");
}
const frameIndex = frames.length;
const start = offset;
let cell;
if (hasCell) {
const cellBytes = dataView(
await readExact(source, offset, 56, signal, budget)
);
if (cellBytes.getInt32(0, littleEndian) !== 48 || cellBytes.getInt32(52, littleEndian) !== 48) {
throw malformed("DCD unit-cell block is invalid");
}
const a = cellBytes.getFloat64(4, littleEndian);
const gamma = cellBytes.getFloat64(12, littleEndian);
const b = cellBytes.getFloat64(20, littleEndian);
const beta = cellBytes.getFloat64(28, littleEndian);
const alpha = cellBytes.getFloat64(36, littleEndian);
const c = cellBytes.getFloat64(44, littleEndian);
assertFinite([a, b, c, alpha, beta, gamma], "DCD unit cell");
if (a <= 0 || b <= 0 || c <= 0) {
throw malformed("DCD periodic-cell lengths must be positive");
}
cell = {
anglesOrCosines: [alpha, beta, gamma],
lengthsAngstrom: [a, b, c]
};
offset += 56n;
}
const ranges = [];
for (const axis of ["x", "y", "z"]) {
const markers = await readMarkers(
source,
offset,
axisBytes,
littleEndian,
signal,
budget
);
if (markers[0] !== axisBytes || markers[1] !== axisBytes) {
throw malformed("DCD coordinate block is invalid");
}
ranges.push({ axis, length: axisBytes, offset: offset + 4n });
offset += BigInt(axisBytes + 8);
}
if (hasFourthDimension) {
const lead = dataView(
await readExact(source, offset, 4, signal, budget)
).getInt32(0, littleEndian);
if (lead < 0) {
throw malformed("DCD fourth-dimension block is invalid");
}
const markers = await readMarkers(
source,
offset,
lead,
littleEndian,
signal,
budget
);
if (markers[0] !== lead || markers[1] !== lead) {
throw malformed("DCD fourth-dimension block is invalid");
}
offset += BigInt(lead + 8);
}
const byteLength = offset - start;
assertFrameSpan(source, start, byteLength, budget, "DCD frame");
frames.push({
atomCount,
byteLength,
byteOffset: start,
...cell == null ? {} : { cell },
coordinateEncoding: littleEndian ? "float32-le-planar-angstrom" : "float32-be-planar-angstrom",
coordinateRanges: ranges,
coordinatesComplete: true,
frameIndex,
step: startStep + frameIndex * saveInterval
});
}
return completeIndex(frames, offset);
}
async function indexTrr(source, topologyAtoms, signal, budget) {
const frames = [];
let offset = 0n;
while (offset < source.sizeBytes) {
if (frames.length === budget.maxFrames) {
return partialIndex(frames, offset);
}
const prefix = dataView(
await readExact(source, offset, 12, signal, budget)
);
if (prefix.getInt32(0, false) !== 1993) {
throw malformed("TRR frame has an invalid magic number");
}
const versionBytes = prefix.getInt32(8, false);
if (versionBytes < 1 || versionBytes > 256) {
throw malformed("TRR frame has an invalid version header");
}
const sizesOffset = offset + 12n + BigInt(versionBytes);
const header = dataView(
await readExact(source, sizesOffset, 52, signal, budget)
);
const sizes = Array.from(
{ length: 10 },
(_value, index) => header.getInt32(index * 4, false)
);
if (sizes.some((size) => size < 0)) {
throw malformed("TRR frame has a negative section size");
}
const [
irBytes,
energyBytes,
boxBytes,
virialBytes,
pressureBytes,
topologyBytes,
symmetryBytes,
coordinateBytes,
velocityBytes,
forceBytes
] = sizes;
if (irBytes !== 0 || energyBytes !== 0 || topologyBytes !== 0 || symmetryBytes !== 0) {
throw malformed("TRR contains unsupported non-coordinate sections");
}
const atomCount = header.getInt32(40, false);
assertFrameAtomCount(atomCount, topologyAtoms, budget, "TRR");
const step = header.getInt32(44, false);
const floatBytes = boxBytes / 9;
if (floatBytes !== 4 && floatBytes !== 8) {
throw malformed("TRR frame has invalid precision metadata");
}
const vectorBytes = safeNumberProduct(
[atomCount, 3, floatBytes],
"TRR vector section"
);
for (const [label, bytes] of [
["coordinates", coordinateBytes],
["velocities", velocityBytes],
["forces", forceBytes]
]) {
if (bytes !== 0 && bytes !== vectorBytes) {
throw malformed(`TRR ${label} size does not match its atom count`);
}
}
const payloadOffset = sizesOffset + 52n;
const metadataBytes = 2 * floatBytes + boxBytes;
const metadata = dataView(
await readExact(source, payloadOffset, metadataBytes, signal, budget)
);
const timePicoseconds = floatBytes === 4 ? metadata.getFloat32(0, false) : metadata.getFloat64(0, false);
if (!Number.isFinite(timePicoseconds)) {
throw malformed("TRR frame time is not finite");
}
const vectors = readCellVectors(
metadata,
2 * floatBytes,
floatBytes,
false,
10
);
const coordinateOffset = payloadOffset + BigInt(2 * floatBytes + boxBytes + virialBytes + pressureBytes);
const payloadBytes = safeNumberSum(
[
2 * floatBytes,
boxBytes,
virialBytes,
pressureBytes,
coordinateBytes,
velocityBytes,
forceBytes
],
"TRR frame payload"
);
const byteLength = payloadOffset + BigInt(payloadBytes) - offset;
assertFrameSpan(source, offset, byteLength, budget, "TRR frame");
frames.push({
atomCount,
byteLength,
byteOffset: offset,
cell: cellFromVectors(vectors),
coordinateEncoding: floatBytes === 4 ? "float32-be-interleaved-nanometre" : "float64-be-interleaved-nanometre",
coordinateRanges: coordinateBytes === 0 ? [] : [{ length: coordinateBytes, offset: coordinateOffset }],
coordinatesComplete: coordinateBytes !== 0,
frameIndex: frames.length,
step,
timePicoseconds
});
offset += byteLength;
}
return completeIndex(frames, offset);
}
async function indexNetcdf(source, topologyAtoms, signal, budget) {
const cursor = new NetcdfHeaderCursor(source, signal, budget);
const signature = await cursor.bytes(4, "NetCDF header");
if (!bytesEqualAt(signature, 0, [67, 68, 70])) {
throw malformed("NetCDF CDF signature is missing");
}
const version = signature[3];
if (version !== 1 && version !== 2) {
throw malformed("NetCDF file version is unsupported");
}
const recordCount = await cursor.uint32("NetCDF record count");
if (recordCount === 4294967295) {
throw malformed("NetCDF streaming record counts are not supported");
}
const dimensions = await readNetcdfDimensions(cursor, budget);
const recordDimension = dimensions.findIndex(({ size }) => size === 0);
await readNetcdfAttributes(cursor, budget, "NetCDF global attributes");
const variables = await readNetcdfVariables(
cursor,
dimensions,
recordDimension,
version,
budget
);
const coordinates = variables.find(
(variable) => variable.name.toLowerCase() === "coordinates"
);
if (coordinates == null || !coordinates.record) {
throw malformed(
"NetCDF trajectory is missing a record coordinates variable"
);
}
if (coordinates.type !== 5 && coordinates.type !== 6) {
throw malformed("NetCDF coordinates must use float32 or float64 values");
}
const atomDimension = coordinates.dimensions.map((id) => dimensions[id]).find((dimension) => /^(?:atom|atoms)$/iu.test(dimension?.name ?? ""));
if (atomDimension != null && atomDimension.size !== topologyAtoms) {
throw topologyMismatch(
"NetCDF atom dimension does not match the selected topology"
);
}
const scalarBytes = netcdfTypeBytes(coordinates.type);
const minimumCoordinateBytes = safeNumberProduct(
[topologyAtoms, 3, scalarBytes],
"NetCDF coordinate frame"
);
if (coordinates.size < minimumCoordinateBytes) {
throw truncated("NetCDF coordinates variable is smaller than the topology");
}
const recordVariables = variables.filter(({ record: record2 }) => record2);
const recordStep = safeNumberSum(
recordVariables.map(({ size }) => size),
"NetCDF record step"
);
for (const variable of variables) {
const end = variable.offset + BigInt(variable.size) + (variable.record && recordCount > 0 ? BigInt(recordCount - 1) * BigInt(recordStep) : 0n);
if (end > source.sizeBytes) {
throw truncated(
"NetCDF variable points outside the retained source bytes"
);
}
}
const time = variables.find(
(variable) => variable.record && variable.name.toLowerCase() === "time"
);
const lengths = variables.find(
(variable) => variable.record && /^(?:cell_lengths|cell_length)$/iu.test(variable.name)
);
const angles = variables.find(
(variable) => variable.record && /^(?:cell_angles|cell_angle)$/iu.test(variable.name)
);
const frames = [];
const indexedFrameCount = Math.min(recordCount, budget.maxFrames);
for (let frameIndex = 0; frameIndex < indexedFrameCount; frameIndex += 1) {
const displacement = BigInt(frameIndex) * BigInt(recordStep);
const timePicoseconds = time == null ? void 0 : (await readNetcdfValues(
source,
time,
displacement,
1,
signal,
budget
))[0];
const cellLengths = lengths == null ? void 0 : await readNetcdfValues(
source,
lengths,
displacement,
3,
signal,
budget
);
const cellAngles = angles == null ? void 0 : await readNetcdfValues(
source,
angles,
displacement,
3,
signal,
budget
);
if (timePicoseconds != null && !Number.isFinite(timePicoseconds)) {
throw malformed("NetCDF trajectory time is not finite");
}
if (cellLengths != null) {
assertFinite(cellLengths, "NetCDF cell lengths");
if (cellLengths.some((value) => value <= 0)) {
throw malformed("NetCDF periodic-cell lengths must be positive");
}
}
if (cellAngles != null) {
assertFinite(cellAngles, "NetCDF cell angles");
}
const coordinateOffset = coordinates.offset + displacement;
const byteLength = BigInt(coordinates.size);
assertFrameSpan(
source,
coordinateOffset,
byteLength,
budget,
"NetCDF coordinate frame"
);
frames.push({
atomCount: topologyAtoms,
byteLength,
byteOffset: coordinateOffset,
...cellLengths == null ? {} : {
cell: {
...cellAngles == null ? {} : {
anglesOrCosines: [
cellAngles[0],
cellAngles[1],
cellAngles[2]
]
},
lengthsAngstrom: [cellLengths[0], cellLengths[1], cellLengths[2]]
}
},
coordinateEncoding: coordinates.type === 5 ? "float32-be-interleaved-angstrom" : "float64-be-interleaved-angstrom",
coordinateRanges: [
{ length: minimumCoordinateBytes, offset: coordinateOffset }
],
coordinatesComplete: true,
frameIndex,
...timePicoseconds == null ? {} : { timePicoseconds }
});
}
const indexedThroughOffset = indexedFrameCount === 0 ? coordinates.offset : coordinates.offset + BigInt(indexedFrameCount - 1) * BigInt(recordStep) + BigInt(coordinates.size);
return recordCount > budget.maxFrames ? partialIndex(frames, indexedThroughOffset) : completeIndex(frames, indexedThroughOffset);
}
var NetcdfHeaderCursor = class {
constructor(source, signal, budget) {
this.source = source;
this.signal = signal;
this.budget = budget;
}
source;
signal;
budget;
offset = 0n;
async bytes(length, label) {
if (!Number.isSafeInteger(length) || length < 0) {
throw malformed(`${label} length is invalid`);
}
this.assertHeaderBudget(BigInt(length), label);
const bytes = await readExact(
this.source,
this.offset,
length,
this.signal,
this.budget
);
this.offset += BigInt(length);
return bytes;
}
async uint32(label) {
return dataView(await this.bytes(4, label)).getUint32(0, false);
}
async name(label) {
const length = await this.uint32(`${label} length`);
if (length > this.budget.maxMetadataBytes) {
throw exhausted(`${label} exceeds maxMetadataBytes`);
}
const padded = safeNumberProduct(
[Math.ceil(length / 4), 4],
`${label} padded length`
);
const bytes = await this.bytes(padded, label);
try {
return new TextDecoder("utf-8", { fatal: true }).decode(
bytes.subarray(0, length)
);
} catch {
throw malformed(`${label} is not valid UTF-8`);
}
}
skip(length, label) {
if (!Number.isSafeInteger(length) || length < 0) {
throw malformed(`${label} length is invalid`);
}
this.assertHeaderBudget(BigInt(length), label);
if (this.offset + BigInt(length) > this.source.sizeBytes) {
throw truncated(`${label} is truncated`);
}
this.offset += BigInt(length);
}
assertHeaderBudget(length, label) {
if (this.offset + length > BigInt(this.budget.maxMetadataBytes)) {
throw exhausted(`${label} exceeds maxMetadataBytes`);
}
}
};
async function readNetcdfDimensions(cursor, budget) {
const count = await readNetcdfListCount(cursor, 10, "NetCDF dimensions");
assertMetadataCount(count, 24, budget, "NetCDF dimensions");
const dimensions = [];
for (let index = 0; index < count; index += 1) {
dimensions.push({
name: await cursor.name("NetCDF dimension name"),
size: await cursor.uint32("NetCDF dimension size")
});
}
return dimensions;
}
async function readNetcdfAttributes(cursor, budget, label) {
const count = await readNetcdfListCount(cursor, 12, label);
assertMetadataCount(count, 32, budget, label);
for (let index = 0; index < count; index += 1) {
await cursor.name(`${label} name`);
const type = await cursor.uint32(`${label} type`);
const values = await cursor.uint32(`${label} element count`);
const bytes = safeNumberProduct(
[values, netcdfTypeBytes(type)],
`${label} payload`
);
cursor.skip(
safeNumberProduct([Math.ceil(bytes / 4), 4], `${label} padded payload`),
`${label} payload`
);
}
}
async function readNetcdfVariables(cursor, dimensions, recordDimension, version, budget) {
const count = await readNetcdfListCount(cursor, 11, "NetCDF variables");
assertMetadataCount(count, 48, budget, "NetCDF variables");
const variables = [];
for (let index = 0; index < count; index += 1) {
const name = await cursor.name("NetCDF variable name");
const dimensionCount = await cursor.uint32(
"NetCDF variable dimensionality"
);
assertMetadataCount(
dimensionCount,
8,
budget,
"NetCDF variable dimensions"
);
const ids = [];
for (let dimension = 0; dimension < dimensionCount; dimension += 1) {
const id = await cursor.uint32("NetCDF variable dimension ID");
if (id >= dimensions.length) {
throw malformed("NetCDF variable references an unknown dimension");
}
ids.push(id);
}
await readNetcdfAttributes(cursor, budget, "NetCDF variable attributes");
const type = await cursor.uint32("NetCDF variable type");
netcdfTypeBytes(type);
const size = await cursor.uint32("NetCDF variable size");
const high = await cursor.uint32("NetCDF variable offset");
const offset = version === 2 ? BigInt(high) * 4294967296n + BigInt(await cursor.uint32("NetCDF variable offset")) : BigInt(high);
variables.push({
dimensions: ids,
name,
offset,
record: ids[0] === recordDimension,
size,
type
});
}
return variables;
}
async function readNetcdfListCount(cursor, expectedTag, label) {
const tag = await cursor.uint32(`${label} tag`);
const count = await cursor.uint32(`${label} count`);
if (tag === 0 && count !== 0 || tag !== 0 && tag !== expectedTag) {
throw malformed(`${label} are malformed`);
}
return count;
}
async function readNetcdfValues(source, variable, displacement, count, signal, budget) {
if (variable.type !== 5 && variable.type !== 6) {
throw malformed(
`NetCDF ${variable.name} must use float32 or float64 values`
);
}
const scalarBytes = netcdfTypeBytes(variable.type);
const bytes = safeNumberProduct(
[count, scalarBytes],
"NetCDF metadata values"
);
if (bytes > variable.size) {
throw truncated(`NetCDF ${variable.name} frame is truncated`);
}
const view = dataView(
await readExact(
source,
variable.offset + displacement,
bytes,
signal,
budget
)
);
return Array.from(
{ length: count },
(_value, index) => scalarBytes === 4 ? view.getFloat32(index * scalarBytes, false) : view.getFloat64(index * scalarBytes, false)
);
}
function netcdfTypeBytes(type) {
if (!Number.isSafeInteger(type) || type < 1 || type > 6) {
throw malformed("NetCDF variable type is invalid");
}
if (type <= 2) {
return 1;
}
if (type === 3) {
return 2;
}
return type <= 5 ? 4 : 8;
}
function decodeCoordinates(descriptor, parts) {
const encoding = descriptor.coordinateEncoding;
const planar = encoding.includes("planar");
const littleEndian = encoding.includes("-le-");
const float64 = encoding.startsWith("float64");
const scalarBytes = float64 ? 8 : 4;
const scale = encoding.endsWith("nanometre") ? 10 : 1;
const output = float64 ? new Float64Array(descriptor.atomCount * 3) : new Float32Array(descriptor.atomCount * 3);
if (planar) {
if (parts.length !== 3) {
throw malformed(
"Planar trajectory frame must contain three coordinate ranges"
);
}
for (const [axisIndex, part] of parts.entries()) {
if (part.byteLength !== descriptor.atomCount * scalarBytes) {
throw truncated("Planar trajectory coordinate range is truncated");
}
const view = dataView(part);
for (let atom = 0; atom < descriptor.atomCount; atom += 1) {
output[atom * 3 + axisIndex] = (float64 ? view.getFloat64(atom * scalarBytes, littleEndian) : view.getFloat32(atom * scalarBytes, littleEndian)) * scale;
}
}
} else {
if (parts.length !== 1) {
throw malformed(
"Interleaved trajectory frame must contain one coordinate range"
);
}
const part = parts[0];
if (part.byteLength !== descriptor.atomCount * 3 * scalarBytes) {
throw truncated("Interleaved trajectory coordinate range is truncated");
}
const view = dataView(part);
for (let coordinate = 0; coordinate < output.length; coordinate += 1) {
output[coordinate] = (float64 ? view.getFloat64(coordinate * scalarBytes, littleEndian) : view.getFloat32(coordinate * scalarBytes, littleEndian)) * scale;
}
}
if (Array.from(output).some((value) => !Number.isFinite(value))) {
throw malformed("Trajectory frame contains non-finite coordinates");
}
return output;
}
function validateDecodedFrame(frame, descriptor, topology) {
if (frame.index !== descriptor.frameIndex) {
throw malformed("Trajectory decoder returned a different frame index");
}
if (descriptor.atomCount !== topology.atomIds.length) {
throw topologyMismatch(
"Trajectory frame atom count does not match topology"
);
}
if (descriptor.timePicoseconds != null && frame.timePicoseconds !== descriptor.timePicoseconds) {
throw sourceChanged(
"Trajectory decoder returned inconsistent frame-time metadata"
);
}
const lengths = descriptor.cell?.lengthsAngstrom;
if (lengths != null && (frame.boxAngstrom == null || lengths.some(
(length, axis) => Math.abs(length - (frame.boxAngstrom?.[axis] ?? Number.NaN)) > 1e-5
))) {
throw sourceChanged(
"Trajectory decoder returned inconsistent periodic-cell metadata"
);
}
try {
validateScientificStructureTrajectoryFrame({ frame, topology });
} catch (error) {
const message = error instanceof Error ? error.message : "Trajectory frame is invalid";
if (/topology/iu.test(message)) {
throw topologyMismatch(message);
}
throw malformed(message);
}
}
function readCellVectors(view, offset, scalarBytes, littleEndian, scale) {
const values = Array.from(
{ length: 9 },
(_value, index) => scalarBytes === 4 ? view.getFloat32(offset + index * scalarBytes, littleEndian) * scale : view.getFloat64(offset + index * scalarBytes, littleEndian) * scale
);
assertFinite(values, "Trajectory periodic-cell vectors");
return [
values[0],
values[1],
values[2],
values[3],
values[4],
values[5],
values[6],
values[7],
values[8]
];
}
function cellFromVectors(vectors) {
const lengths = [
Math.hypot(vectors[0], vectors[1], vectors[2]),
Math.hypot(vectors[3], vectors[4], vectors[5]),
Math.hypot(vectors[6], vectors[7], vectors[8])
];
if (lengths.some((length) => length <= 0 || !Number.isFinite(length))) {
throw malformed(
"Trajectory periodic-cell vectors must have positive lengths"
);
}
return { lengthsAngstrom: lengths, vectorsAngstrom: vectors };
}
async function readMarkers(source, offset, payloadBytes, littleEndian, signal, budget) {
if (!Number.isSafeInteger(payloadBytes) || payloadBytes < 0) {
throw malformed("Trajectory block size is invalid");
}
const [lead, trailer] = await Promise.all([
readExact(source, offset, 4, signal, budget),
readExact(source, offset + BigInt(payloadBytes) + 4n, 4, signal, budget)
]);
return [
dataView(lead).getInt32(0, littleEndian),
dataView(trailer).getInt32(0, littleEndian)
];
}
async function assertNotArchive(source, signal, budget) {
if (source.sizeBytes === 0n) {
throw truncated("Scientific structure source is empty");
}
const prefix = await readExactChunked(
source,
0n,
Number(minBigInt(source.sizeBytes, 8n)),
signal,
budget
);
const archive = ARCHIVE_SIGNATURES.find(
({ bytes }) => bytesEqualAt(prefix, 0, bytes)
);
if (archive != null) {
throw new ScientificStructureBinaryIoError(
"ARCHIVE_REFUSED",
`Scientific structure input contains ${archive.label}-compressed or archived data; extract it before opening`
);
}
}
async function readExact(source, offset, length, signal, budget) {
assertNotCancelled(signal);
if (typeof offset !== "bigint" || offset < 0n || !Number.isSafeInteger(length) || length < 0) {
throw malformed("Scientific binary range is invalid");
}
if (length > budget.maxRangeBytes) {
throw exhausted("Scientific binary range exceeds maxRangeBytes");
}
if (offset + BigInt(length) > source.sizeBytes) {
throw truncated("Scientific binary range exceeds retained source bytes");
}
const bytes = await source.readRange({ length, offset, signal });
assertNotCancelled(signal);
if (!(bytes instanceof Uint8Array) || bytes.byteLength !== length) {
throw sourceChanged("Scientific binary range returned incomplete bytes");
}
return bytes;
}
async function readExactChunked(source, offset, length, signal, budget) {
const result = new Uint8Array(length);
let written = 0;
while (written < length) {
const bytes = await readExact(
source,
offset + BigInt(written),
Math.min(length - written, budget.maxRangeBytes),
signal,
budget
);
result.set(bytes, written);
written += bytes.byteLength;
}
return result;
}
async function revalidateSource(source, signal) {
assertNotCancelled(signal);
if (source.revalidate == null) {
return;
}
const current = await source.revalidate({ signal });
assertNotCancelled(signal);
if (current.sizeBytes !== source.sizeBytes || current.sourceDigest !== source.sourceDigest || current.sourceRevision !== source.sourceRevision) {
throw sourceChanged(
"Scientific structure source changed during ranged access"
);
}
}
function assertSource(source) {
if (typeof source.sizeBytes !== "bigint" || source.sizeBytes < 0n || !/^sha256:[\da-f]{64}$/iu.test(source.sourceDigest) || typeof source.sourceRevision !== "string" || source.sourceRevision.length === 0 || source.sourceRevision.length > 512 || hasControlCharacter(source.sourceRevision)) {
throw malformed("Scientific structure source identity is invalid");
}
}
function assertFrameAtomCount(atomCount, topologyAtoms, budget, format) {
if (!Number.isSafeInteger(atomCount) || atomCount < 1) {
throw malformed(`${format} frame atom count is invalid`);
}
if (atomCount > budget.maxAtoms) {
throw exhausted(`${format} frame exceeds maxAtoms`);
}
if (atomCount !== topologyAtoms) {
throw topologyMismatch(
`${format} frame atom count does not match topology`
);
}
if (BigInt(atomCount) * 12n > BigInt(budget.maxDecodedFrameBytes)) {
throw exhausted(
`${format} decoded coordinate memory exceeds maxDecodedFrameBytes`
);
}
}
function assertFrameSpan(source, offset, length, budget, label) {
if (length < 1n || length > budget.maxFrameBytes) {
throw exhausted(`${label} exceeds maxFrameBytes`);
}
if (offset < 0n || offset + length > source.sizeBytes) {
throw truncated(`${label} is truncated`);
}
}
function completeIndex(frames, indexedThroughOffset) {
return {
complete: true,
frameCount: frames.length,
frames,
indexedThroughOffset
};
}
function partialIndex(frames, indexedThroughOffset) {
return {
complete: false,
completenessReason: "FRAME_BUDGET",
frameCount: frames.length,
frames,
indexedThroughOffset
};
}
function getBudget(input = {}) {
const budget = { ...SCIENTIFIC_STRUCTURE_BINARY_IO_LIMITS, ...input };
for (const [name, value] of Object.entries(budget)) {
if (typeof value === "bigint") {
if (value < 1n) {
throw exhausted(`${name} must be positive`);
}
} else if (!Number.isSafeInteger(value) || value < 1) {
throw exhausted(`${name} must be a positive integer`);
}
}
return budget;
}
function safeNumberProduct(values, label) {
let product = 1;
for (const value of values) {
if (!Number.isSafeInteger(value) || value < 0 || value > 0 && product > Number.MAX_SAFE_INTEGER / value) {
throw malformed(`${label} declared size is not safe`);
}
product *= value;
}
return product;
}
function safeNumberSum(values, label) {
let sum = 0;
for (const value of values) {
if (!Number.isSafeInteger(value) || value < 0 || sum > Number.MAX_SAFE_INTEGER - value) {
throw malformed(`${label} declared size is not safe`);
}
sum += value;
}
return sum;
}
function assertMetadataCount(count, bytesPerEntry, budget, label) {
if (safeNumberProduct([count, bytesPerEntry], `${label} memory`) > budget.maxMetadataBytes) {
throw exhausted(`${label} exceeds maxMetadataBytes`);
}
}
function assertFinite(values, label) {
if (values.some((value) => !Number.isFinite(value))) {
throw malformed(`${label} must contain finite values`);
}
}
function assertNotCancelled(signal) {
if (!signal?.aborted) {
return;
}
throw new ScientificStructureBinaryIoError(
"CANCELLED",
"Scientific structure binary operation was cancelled"
);
}
function hasControlCharacter(value) {
for (let index = 0; index < value.length; index += 1) {
const code = value.charCodeAt(index);
if (code < 32 || code === 127) {
return true;
}
}
return false;
}
function bytesEqualAt(data, offset, expected) {
return offset >= 0 && data.byteLength - offset >= expected.length && expected.every((value, index) => data[offset + index] === value);
}
function dataView(bytes) {
return new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);
}
function minBigInt(left, right) {
return left < right ? left : right;
}
function exhausted(message) {
return new ScientificStructureBinaryIoError("RESOURCE_EXHAUSTED", message);
}
function malformed(message) {
return new ScientificStructureBinaryIoError("MALFORMED_BINARY", message);
}
function sourceChanged(message) {
return new ScientificStructureBinaryIoError("SOURCE_CHANGED", message);
}
function topologyMismatch(message) {
return new ScientificStructureBinaryIoError("TOPOLOGY_MISMATCH", message);
}
function truncated(message) {
return new ScientificStructureBinaryIoError("TRUNCATED", message);
}
var XTC_MAGIC_INTS = new Uint32Array([
0,
0,
0,
0,
0,
0,
0,
0,
0,
8,
10,
12,
16,
20,
25,
32,
40,
50,
64,
80,
101,
128,
161,
203,
256,
322,
406,
512,
645,
812,
1024,
1290,
1625,
2048,
2580,
3250,
4096,
5060,
6501,
8192,
10321,
13003,
16384,
20642,
26007,
32768,
41285,
52015,
65536,
82570,
104031,
131072,
165140,
208063,
262144,
330280,
416127,
524287,
660561,
832255,
1048576,
1321122,
1664510,
2097152,
2642245,
3329021,
4194304,
5284491,
6658042,
8388607,
10568983,
13316085,
16777216
]);
var MAX_RANGE_BYTES = 64 * 1024;
var MAX_COMPRESSED_FRAME_BYTES = 32 * 1024 * 1024;
var MAX_FRAME_ATOMS = 1e6;
var MAX_TEXT_LINE_BYTES = 1024 * 1024;
var MAX_TEXT_FRAMES = 65536;
var NativeTrajectoryCodecError = class extends Error {
constructor(code, message) {
super(message);
this.code = code;
this.name = "NativeTrajectoryCodecError";
}
code;
};
function createScientificStructureNativeTrajectorySource(input) {
const identity = input.grant.sourceIdentity;
const identityDigest = createHash("sha256").update("openai.scientific.source-identity-fingerprint.v1\0").update(input.logicalSessionId).update("\0").update(identity.fileId).update("\0").update(input.grant.sourceRevision).update("\0").update(identity.sizeBytes.toString()).digest("hex");
return {
sourceDigest: `sha256:${identityDigest}`,
sourceRevision: input.grant.sourceRevision,
sizeBytes: identity.sizeBytes,
readRange: async ({ offset, length, signal }) => {
input.signal.throwIfAborted();
const authoritySignal = signal ?? input.signal;
authoritySignal.throwIfAborted();
if (offset < 0n || !Number.isSafeInteger(length) || length < 0 || length > MAX_RANGE_BYTES || offset + BigInt(length) > identity.sizeBytes) {
throw new NativeTrajectoryCodecError(
"RESOURCE_EXHAUSTED",
"The authenticated trajectory range exceeds its bounded source"
);
}
const result = await input.readSource({
grant: input.grant,
logicalSessionId: input.logicalSessionId,
offset,
length,
signal: authoritySignal
});
input.signal.throwIfAborted();
authoritySignal.throwIfAborted();
if (result.bytes.byteLength !== length) {
invalid("The approved trajectory range is truncated");
}
return result.bytes;
}
};
}
function invalid(message) {
throw new NativeTrajectoryCodecError("MALFORMED_TRAJECTORY", message);
}
async function readExactBounded(source, offset, length, signal) {
if (offset < 0n || !Number.isSafeInteger(length) || length < 0 || length > MAX_COMPRESSED_FRAME_BYTES || offset + BigInt(length) > source.sizeBytes) {
throw new NativeTrajectoryCodecError(
"RESOURCE_EXHAUSTED",
"The trajectory range exceeds its authenticated source or frame budget"
);
}
const bytes = new Uint8Array(length);
for (let cursor = 0; cursor < length; cursor += MAX_RANGE_BYTES) {
signal?.throwIfAborted();
const requestLength = Math.min(MAX_RANGE_BYTES, length - cursor);
const chunk = await source.readRange({
length: requestLength,
offset: offset + BigInt(cursor),
signal
});
signal?.throwIfAborted();
if (chunk.byteLength !== requestLength) {
invalid("The authenticated trajectory frame is truncated");
}
bytes.set(chunk, cursor);
}
return bytes;
}
var XtcBitReader = class {
constructor(bytes) {
this.bytes = bytes;
}
bytes;
position = 0;
read(count) {
if (!Number.isSafeInteger(count) || count < 0 || count > 32) {
invalid("An XTC packed coordinate uses an invalid bit width");
}
if (this.position + count > this.bytes.byteLength * 8) {
invalid("The XTC compressed coordinate bitstream is truncated");
}
let value = 0;
for (let index = 0; index < count; index += 1) {
const bit = this.position + index;
const source = this.bytes[Math.floor(bit / 8)];
const bitValue = Math.floor(source / 2 ** (7 - bit % 8)) % 2;
value = value * 2 + bitValue;
}
this.position += count;
return value;
}
};
function xtcIntegerBits(size) {
if (!Number.isSafeInteger(size) || size < 1 || size > 4294967296) {
invalid("An XTC packed coordinate has an invalid integer span");
}
let bits = 0;
let capacity = 1;
while (size >= capacity && bits < 32) {
bits += 1;
capacity *= 2;
}
return bits;
}
function xtcCombinedBits(sizes) {
const bytes = new Uint8Array(32);
bytes[0] = 1;
let count = 1;
for (const size of sizes) {
let carry = 0;
for (let index = 0; index < count; index += 1) {
const product = bytes[index] * size + carry;
bytes[index] = product % 256;
carry = Math.floor(product / 256);
}
while (carry !== 0) {
if (count === bytes.byteLength) {
invalid("An XTC coordinate packing span is too large");
}
bytes[count] = carry % 256;
count += 1;
carry = Math.floor(carry / 256);
}
}
let highestBits = 0;
let threshold = 1;
while (bytes[count - 1] >= threshold) {
highestBits += 1;
threshold *= 2;
}
return highestBits + (count - 1) * 8;
}
function decodeXtcIntegers(reader, bitCount, sizes) {
if (bitCount > 256) {
invalid("The XTC mixed-radix packing exceeds its byte budget");
}
const bytes = new Uint8Array(32);
let remaining = bitCount;
let count = 0;
while (remaining > 8) {
bytes[count] = reader.read(8);
count += 1;
remaining -= 8;
}
if (remaining > 0) {
bytes[count] = reader.read(remaining);
count += 1;
}
const values = [0, 0, 0];
for (let dimension = 2; dimension > 0; dimension -= 1) {
const divisor = sizes[dimension];
if (!Number.isSafeInteger(divisor) || divisor < 1) {
invalid("An XTC mixed-radix divisor is invalid");
}
let remainder = 0;
for (let index = count - 1; index >= 0; index -= 1) {
const value = remainder * 256 + bytes[index];
bytes[index] = Math.floor(value / divisor);
remainder = value % divisor;
}
values[dimension] = remainder;
}
values[0] = bytes[0] + bytes[1] * 256 + bytes[2] * 65536 + bytes[3] * 16777216;
return values;
}
async function decodeScientificStructureCompressedXtcFrame({
descriptor,
signal,
source,
topology
}) {
if (descriptor.coordinateEncoding !== "xtc-compressed" || descriptor.atomCount <= 9 || descriptor.atomCount > MAX_FRAME_ATOMS || descriptor.atomCount !== topology.atomIds.length || descriptor.coordinateRanges.length !== 1) {
invalid("The selected XTC descriptor does not authorize compressed atoms");
}
const header = await readExactBounded(
source,
descriptor.byteOffset,
92,
signal
);
const view = new DataView(
header.buffer,
header.byteOffset,
header.byteLength
);
const count = view.getInt32(52, false);
const precision = view.getFloat32(56, false);
const minimum = [
view.getInt32(60, false),
view.getInt32(64, false),
view.getInt32(68, false)
];
const sizes = [
view.getInt32(72, false) - minimum[0] + 1,
view.getInt32(76, false) - minimum[1] + 1,
view.getInt32(80, false) - minimum[2] + 1
];
let smallIndex = view.getInt32(84, false);
const compressedBytes = view.getInt32(88, false);
const range = descriptor.coordinateRanges[0];
if (count !== descriptor.atomCount || !Number.isFinite(precision) || precision <= 0 || sizes.some((size) => !Number.isSafeInteger(size) || size < 1) || smallIndex < 9 || smallIndex >= XTC_MAGIC_INTS.length || compressedBytes < 1 || compressedBytes > MAX_COMPRESSED_FRAME_BYTES || compressedBytes > range.length || range.offset !== descriptor.byteOffset + 92n) {
invalid("The compressed XTC coordinate metadata is inconsistent");
}
const payload = await readExactBounded(
source,
range.offset,
compressedBytes,
signal
);
const reader = new XtcBitReader(payload);
const separate = sizes.some((size) => size > 16777215);
const bits = [
xtcIntegerBits(sizes[0]),
xtcIntegerBits(sizes[1]),
xtcIntegerBits(sizes[2])
];
const combined = separate ? 0 : xtcCombinedBits(sizes);
const coordinates = new Float32Array(count * 3);
const previous = [0, 0, 0];
let output = 0;
let processed = 0;
let run = 0;
let smaller = Math.floor(XTC_MAGIC_INTS[Math.max(9, smallIndex - 1)] / 2);
let smallNumber = Math.floor(XTC_MAGIC_INTS[smallIndex] / 2);
const append = (values) => {
if (output >= count) {
invalid("The XTC coordinate run exceeds the approved topology");
}
for (let axis = 0; axis < 3; axis += 1) {
const coordinate = values[axis] * 10 / precision;
if (!Number.isFinite(coordinate)) {
invalid("An XTC coordinate is not finite");
}
coordinates[output * 3 + axis] = coordinate;
}
output += 1;
};
while (processed < count) {
if (processed % 1024 === 0) {
signal?.throwIfAborted();
}
let current = separate ? [reader.read(bits[0]), reader.read(bits[1]), reader.read(bits[2])] : decodeXtcIntegers(reader, combined, sizes);
processed += 1;
for (let axis = 0; axis < 3; axis += 1) {
current[axis] += minimum[axis];
previous[axis] = current[axis];
}
let adjustment = 0;
if (reader.read(1) === 1) {
run = reader.read(5);
adjustment = run % 3;
run -= adjustment;
adjustment -= 1;
}
if (run > 0) {
for (let component = 0; component < run; component += 3) {
if (processed >= count) {
invalid("The compressed XTC run exceeds its declared atom count");
}
const magic = XTC_MAGIC_INTS[smallIndex];
current = decodeXtcIntegers(reader, smallIndex, [magic, magic, magic]);
processed += 1;
for (let axis = 0; axis < 3; axis += 1) {
current[axis] += previous[axis] - smallNumber;
}
if (component === 0) {
const swapped = [...current];
current = [...previous];
previous[0] = swapped[0];
previous[1] = swapped[1];
previous[2] = swapped[2];
append(previous);
} else {
previous[0] = current[0];
previous[1] = current[1];
previous[2] = current[2];
}
append(current);
}
} else {
append(current);
}
smallIndex += adjustment;
if (smallIndex < 9 || smallIndex >= XTC_MAGIC_INTS.length) {
invalid("The XTC compressed coordinate scale is outside its safe range");
}
if (adjustment < 0) {
smallNumber = smaller;
smaller = smallIndex > 9 ? Math.floor(XTC_MAGIC_INTS[smallIndex - 1] / 2) : 0;
} else if (adjustment > 0) {
smaller = smallNumber;
smallNumber = Math.floor(XTC_MAGIC_INTS[smallIndex] / 2);
}
}
if (output !== count) {
invalid("The XTC decoded coordinate count does not match its topology");
}
const lengths = descriptor.cell?.lengthsAngstrom;
return {
...lengths == null ? {} : { boxAngstrom: lengths },
coordinates,
index: descriptor.frameIndex,
...descriptor.timePicoseconds == null ? {} : { timePicoseconds: descriptor.timePicoseconds },
topologyDigest: topology.sourceDigest
};
}
async function* readLammpsLines(input) {
const decoder = new TextDecoder("utf-8", { fatal: true });
let pending = new Uint8Array();
let cursor = input.offset;
let lineOffset = input.offset;
while (cursor < input.end) {
input.signal?.throwIfAborted();
const length = Number(
input.end - cursor > BigInt(MAX_RANGE_BYTES) ? BigInt(MAX_RANGE_BYTES) : input.end - cursor
);
const chunk = await input.source.readRange({
length,
offset: cursor,
signal: input.signal
});
input.signal?.throwIfAborted();
if (chunk.byteLength !== length) {
invalid("The LAMMPS trajectory is truncated");
}
const bytes = new Uint8Array(pending.byteLength + chunk.byteLength);
bytes.set(pending);
bytes.set(chunk, pending.byteLength);
let start = 0;
for (let index = 0; index < bytes.byteLength; index += 1) {
if (bytes[index] !== 10) {
continue;
}
const line = bytes.subarray(start, index);
if (line.byteLength > MAX_TEXT_LINE_BYTES) {
invalid("A LAMMPS trajectory record exceeds its bounded line budget");
}
let text;
try {
text = decoder.decode(
line[line.byteLength - 1] === 13 ? line.subarray(0, -1) : line
);
} catch {
invalid("A LAMMPS trajectory record is not valid UTF-8");
}
const end = lineOffset + BigInt(index - start + 1);
yield { end, offset: lineOffset, text };
lineOffset = end;
start = index + 1;
}
pending = bytes.subarray(start);
if (pending.byteLength > MAX_TEXT_LINE_BYTES) {
invalid("A LAMMPS trajectory record exceeds its bounded line budget");
}
cursor += BigInt(chunk.byteLength);
}
if (pending.byteLength > 0) {
let text;
try {
text = decoder.decode(pending);
} catch {
invalid("A LAMMPS trajectory record is not valid UTF-8");
}
yield { end: input.end, offset: lineOffset, text };
}
}
async function requireLammpsLine(iterator, expected) {
const result = await iterator.next();
if (result.done || expected != null && result.value.text !== expected) {
invalid(
expected == null ? "A LAMMPS trajectory frame ends before its required records" : `A LAMMPS trajectory frame is missing ${expected}`
);
}
return result.value;
}
function parseLammpsPositive(text, field) {
const value = Number(text.trim());
if (!Number.isSafeInteger(value) || value < 1 || value > MAX_FRAME_ATOMS) {
invalid(`The LAMMPS ${field} is outside its safe atom budget`);
}
return value;
}
async function indexScientificStructureLammpsTrajectory(input) {
if (input.topology.atomIds.length < 1 || input.topology.atomIds.length > MAX_FRAME_ATOMS) {
throw new NativeTrajectoryCodecError(
"TOPOLOGY_MISMATCH",
"The approved LAMMPS topology is outside its safe atom budget"
);
}
const iterator = readLammpsLines({
end: input.source.sizeBytes,
offset: 0n,
signal: input.signal,
source: input.source
});
const frames = [];
let next = await iterator.next();
while (!next.done) {
input.signal?.throwIfAborted();
if (frames.length === MAX_TEXT_FRAMES) {
return {
atomCount: input.topology.atomIds.length,
complete: false,
format: "lammpstrj",
frameCount: frames.length,
frames,
indexedThroughOffset: next.value.offset,
sourceDigest: input.source.sourceDigest,
sourceRevision: input.source.sourceRevision,
sourceSizeBytes: input.source.sizeBytes,
topologyDigest: input.topology.sourceDigest,
topologyRevision: input.topology.sourceRevision
};
}
const start = next.value;
if (start.text !== "ITEM: TIMESTEP") {
invalid("A LAMMPS trajectory frame must begin with ITEM: TIMESTEP");
}
const stepLine = await requireLammpsLine(iterator);
const step = Number(stepLine.text.trim());
if (!Number.isSafeInteger(step)) {
invalid("A LAMMPS trajectory timestep is invalid");
}
await requireLammpsLine(iterator, "ITEM: NUMBER OF ATOMS");
const countLine = await requireLammpsLine(iterator);
const atomCount = parseLammpsPositive(countLine.text, "atom count");
if (atomCount !== input.topology.atomIds.length) {
throw new NativeTrajectoryCodecError(
"TOPOLOGY_MISMATCH",
"The LAMMPS frame atom count differs from its approved topology"
);
}
const boundsHeader = await requireLammpsLine(iterator);
if (!/^ITEM: BOX BOUNDS(?:\s|$)/u.test(boundsHeader.text)) {
invalid("A LAMMPS frame does not declare orthogonal box bounds");
}
if (/\b(?:xy|xz|yz|abc)\b/u.test(boundsHeader.text)) {
invalid(
"Tilted LAMMPS cells require an explicitly bounded triclinic decoder"
);
}
const bounds = [];
for (let axis = 0; axis < 3; axis += 1) {
const line = await requireLammpsLine(iterator);
const values = line.text.trim().split(/\s+/u).map(Number);
if (values.length < 2 || !Number.isFinite(values[0]) || !Number.isFinite(values[1]) || values[1] <= values[0]) {
invalid("A LAMMPS periodic box bound is not finite or ordered");
}
bounds.push([values[0], values[1]]);
}
const [xBounds, yBounds, zBounds] = bounds;
if (xBounds == null || yBounds == null || zBounds == null) {
invalid("A LAMMPS periodic box does not declare all three axes");
}
const atomHeader = await requireLammpsLine(iterator);
if (!atomHeader.text.startsWith("ITEM: ATOMS ")) {
invalid("A LAMMPS frame does not declare atom coordinate columns");
}
const columns = atomHeader.text.slice("ITEM: ATOMS ".length).trim().split(/\s+/u);
if (!columns.includes("id")) {
invalid("A LAMMPS trajectory must bind every coordinate to an atom id");
}
const coordinateModes = [
["x", "y", "z"],
["xu", "yu", "zu"],
["xs", "ys", "zs"],
["xsu", "ysu", "zsu"]
];
if (!coordinateModes.some(
(mode) => mode.every((column) => columns.includes(column))
)) {
invalid("A LAMMPS frame has no complete supported coordinate triplet");
}
let end = atomHeader.end;
for (let atom = 0; atom < atomCount; atom += 1) {
const line = await requireLammpsLine(iterator);
if (line.text.startsWith("ITEM: ")) {
invalid("The LAMMPS atom rows end before the declared atom count");
}
end = line.end;
}
frames.push({
atomCount,
atomLineOffset: atomHeader.end,
bounds: [xBounds, yBounds, zBounds],
byteLength: end - start.offset,
byteOffset: start.offset,
columns,
frameIndex: frames.length,
step
});
next = await iterator.next();
}
if (frames.length === 0) {
invalid("The LAMMPS trajectory contains no complete frames");
}
return {
atomCount: input.topology.atomIds.length,
complete: true,
format: "lammpstrj",
frameCount: frames.length,
frames,
indexedThroughOffset: input.source.sizeBytes,
sourceDigest: input.source.sourceDigest,
sourceRevision: input.source.sourceRevision,
sourceSizeBytes: input.source.sizeBytes,
topologyDigest: input.topology.sourceDigest,
topologyRevision: input.topology.sourceRevision
};
}
async function readScientificStructureLammpsFrame(input) {
const descriptor = input.index.frames[input.frameIndex];
if (descriptor == null || input.index.sourceDigest !== input.source.sourceDigest || input.index.sourceRevision !== input.source.sourceRevision || input.index.sourceSizeBytes !== input.source.sizeBytes || input.index.topologyDigest !== input.topology.sourceDigest || input.index.topologyRevision !== input.topology.sourceRevision || input.index.atomCount !== input.topology.atomIds.length) {
throw new NativeTrajectoryCodecError(
"SOURCE_CHANGED",
"The requested LAMMPS frame is not bound to its current source and topology"
);
}
if (!Number.isSafeInteger(input.atomOffset) || !Number.isSafeInteger(input.atomCount) || input.atomOffset < 0 || input.atomCount < 1 || input.atomOffset + input.atomCount > descriptor.atomCount) {
throw new NativeTrajectoryCodecError(
"INVALID_REQUEST",
"The requested LAMMPS atom window is invalid"
);
}
const idIndex = descriptor.columns.indexOf("id");
const axes = [
["x", "y", "z"],
["xu", "yu", "zu"],
["xs", "ys", "zs"],
["xsu", "ysu", "zsu"]
].find((mode) => mode.every((column) => descriptor.columns.includes(column)));
if (axes == null) {
invalid("The approved LAMMPS coordinate column set is invalid");
}
const scaled = axes[0] === "xs" || axes[0] === "xsu";
const coordinateColumns = axes.map(
(axis) => descriptor.columns.indexOf(axis)
);
const bytes = new Uint8Array(input.atomCount * 12);
const view = new DataView(bytes.buffer);
const selected = /* @__PURE__ */ new Set();
let seen = 0;
for await (const line of readLammpsLines({
end: descriptor.byteOffset + descriptor.byteLength,
offset: descriptor.atomLineOffset,
signal: input.signal,
source: input.source
})) {
const fields = line.text.trim().split(/\s+/u);
const identity = parseLammpsPositive(
fields[idIndex] ?? "",
"atom identity"
);
if (identity > descriptor.atomCount || selected.has(identity)) {
invalid(
"A LAMMPS coordinate identity is duplicated or outside its topology"
);
}
selected.add(identity);
const target = identity - 1 - input.atomOffset;
if (target >= 0 && target < input.atomCount) {
for (let axis = 0; axis < 3; axis += 1) {
const raw = Number(fields[coordinateColumns[axis]]);
const bounds = descriptor.bounds[axis];
const coordinate = scaled ? bounds[0] + raw * (bounds[1] - bounds[0]) : raw;
if (!Number.isFinite(coordinate)) {
invalid("A LAMMPS trajectory contains a non-finite coordinate");
}
view.setFloat32((target * 3 + axis) * 4, coordinate, true);
}
}
seen += 1;
}
if (seen !== descriptor.atomCount || selected.size !== descriptor.atomCount) {
invalid("A LAMMPS trajectory frame does not cover its complete topology");
}
return {
atomCount: input.atomCount,
atomOffset: input.atomOffset,
complete: input.atomOffset === 0 && input.atomCount === descriptor.atomCount,
coordinates: bytes,
frameIndex: descriptor.frameIndex,
frameOffsetDecimal: descriptor.byteOffset.toString(),
step: descriptor.step,
topologyAtomCount: descriptor.atomCount
};
}
async function readScientificStructureNativeTrajectoryWindow(input) {
const { command, index } = input;
const first = command.frameIndex ?? command.start ?? 0;
const defaultEndExclusive = typeof first === "number" ? first + 1 : Number.NaN;
const endExclusive = input.multiple ? command.endExclusive ?? defaultEndExclusive : defaultEndExclusive;
const stride = command.stride ?? 1;
const atomOffset = command.atomOffset ?? 0;
if (typeof first !== "number" || !Number.isSafeInteger(first) || first < 0 || first >= index.frameCount || typeof endExclusive !== "number" || !Number.isSafeInteger(endExclusive) || endExclusive <= first || endExclusive > index.frameCount || typeof stride !== "number" || !Number.isSafeInteger(stride) || stride < 1 || Math.ceil((endExclusive - first) / stride) > 64 || typeof atomOffset !== "number" || !Number.isSafeInteger(atomOffset) || atomOffset < 0 || atomOffset >= index.atomCount) {
throw new NativeTrajectoryCodecError(
"RESOURCE_EXHAUSTED",
"The requested native trajectory frame or atom window is unsafe"
);
}
const atomCount = command.atomCount ?? Math.min(index.atomCount - atomOffset, 512);
if (typeof atomCount !== "number" || !Number.isSafeInteger(atomCount) || atomCount < 1 || atomCount > 512 || atomOffset + atomCount > index.atomCount) {
throw new NativeTrajectoryCodecError(
"RESOURCE_EXHAUSTED",
"The requested native trajectory atom window is unsafe"
);
}
const frames = [];
if (index.format === "lammpstrj") {
const appendLammpsFrame = async (position) => {
if (position >= endExclusive) {
return;
}
input.signal.throwIfAborted();
frames.push(
await readScientificStructureLammpsFrame({
index,
frameIndex: position,
atomOffset,
atomCount,
source: input.source,
topology: input.topology,
signal: input.signal
})
);
await appendLammpsFrame(position + stride);
};
await appendLammpsFrame(first);
} else {
const decoder = input.format === "xtc" && index.atomCount > 9 ? { decodeFrame: decodeScientificStructureCompressedXtcFrame } : void 0;
const reader = new ScientificStructureBinaryFrameReader({
...decoder == null ? {} : { decoder },
index,
source: input.source,
topology: input.topology,
budget: {
maxAtoms: MAX_FRAME_ATOMS,
maxDecodedFrameBytes: MAX_COMPRESSED_FRAME_BYTES,
maxFrames: 64,
maxRangeBytes: MAX_RANGE_BYTES
}
});
const result = await reader.readFrames({
start: first,
endExclusive,
stride,
signal: input.signal
});
for (const decoded of result.frames) {
const descriptor = index.frames[decoded.index];
if (descriptor == null) {
invalid("A native trajectory frame has no approved descriptor");
}
const coordinates = new Uint8Array(atomCount * 12);
const view = new DataView(coordinates.buffer);
for (let atom = 0; atom < atomCount; atom += 1) {
for (let axis = 0; axis < 3; axis += 1) {
view.setFloat32(
(atom * 3 + axis) * 4,
decoded.coordinates[(atomOffset + atom) * 3 + axis],
true
);
}
}
frames.push({
frameIndex: decoded.index,
frameOffsetDecimal: descriptor.byteOffset.toString(),
atomOffset,
atomCount,
topologyAtomCount: index.atomCount,
coordinates,
complete: atomOffset === 0 && atomCount === index.atomCount,
...descriptor.step == null ? {} : { step: descriptor.step }
});
}
}
return input.multiple ? {
complete: true,
frames,
indexComplete: index.complete,
sampledFrameCount: frames.length,
sourceFrameCount: index.frameCount,
stride
} : frames[0];
}
async function countScientificStructureNativeTopologyAtoms(input) {
const format = input.format === "cif" ? "mmcif" : input.format;
if (!["pdb", "mmcif", "gro", "xyz", "psf", "prmtop", "top"].includes(format)) {
throw new NativeTrajectoryCodecError(
"INVALID_REQUEST",
"The approved trajectory topology has an unsupported format"
);
}
const requestedModel = input.model ?? 1;
if (!Number.isSafeInteger(requestedModel) || requestedModel < 1) {
throw new NativeTrajectoryCodecError(
"INVALID_REQUEST",
"The approved trajectory topology model is invalid"
);
}
const iterator = readLammpsLines({
end: input.source.sizeBytes,
offset: 0n,
signal: input.signal,
source: input.source
});
let count = 0;
let currentModel = 1;
let lineNumber = 0;
let declared;
let section = "";
const atomHeaders = [];
for await (const line of iterator) {
input.signal?.throwIfAborted();
const text = line.text.trim();
if (format === "pdb") {
if (/^MODEL\b/u.test(text)) {
currentModel = Number(text.slice("MODEL".length).trim());
if (!Number.isSafeInteger(currentModel) || currentModel < 1) {
invalid("An approved PDB topology model identity is invalid");
}
} else if (/^ENDMDL\b/u.test(text) && count > 0) {
break;
} else if (currentModel === requestedModel && (line.text.startsWith("ATOM ") || line.text.startsWith("HETATM"))) {
count += 1;
}
} else if (format === "gro" || format === "xyz") {
if (format === "gro" && lineNumber === 1 || format === "xyz" && lineNumber === 0) {
declared = parseLammpsPositive(text, `${format} topology atom count`);
} else if (declared != null && (format === "gro" && lineNumber >= 2 || format === "xyz" && lineNumber >= 2)) {
if (!text) {
invalid(`An approved ${format} topology atom record is empty`);
}
count += 1;
if (count === declared) {
break;
}
}
lineNumber += 1;
} else if (format === "psf") {
if (declared == null) {
const match = /^(\d+)\s+!NATOM\b/u.exec(text);
if (match != null) {
declared = parseLammpsPositive(match[1], "PSF topology atom count");
}
} else if (text) {
const fields = text.split(/\s+/u);
if (fields.length < 6 || Number(fields[0]) !== count + 1) {
invalid(
"An approved PSF topology atom identity or record is invalid"
);
}
count += 1;
if (count === declared) {
break;
}
}
} else if (format === "prmtop") {
if (text.startsWith("%FLAG ")) {
if (section === "ATOM_NAME" && count > 0) {
break;
}
section = text.slice("%FLAG ".length).trim();
} else if (!text.startsWith("%FORMAT") && text) {
if (section === "POINTERS" && declared == null) {
declared = parseLammpsPositive(
text.split(/\s+/u)[0],
"PRMTOP topology atom count"
);
} else if (section === "ATOM_NAME" && declared != null) {
const width = 4;
for (let offset = 0; offset < line.text.length; offset += width) {
if (line.text.slice(offset, offset + width).trim()) {
count += 1;
}
}
if (count >= declared) {
break;
}
}
}
} else if (format === "top") {
if (text.startsWith("#include")) {
invalid(
"A GROMACS topology include requires its own approved companion grant"
);
}
const match = /^\[\s*([^\]]+)\s*\]/u.exec(text);
if (match != null) {
if (section === "atoms" && count > 0) {
break;
}
section = match[1].trim().toLowerCase();
} else if (section === "atoms" && text && !text.startsWith(";")) {
const fields = text.split(/\s+/u);
if (fields.length < 5 || Number(fields[0]) !== count + 1) {
invalid("A GROMACS topology atom record is incomplete or unordered");
}
count += 1;
}
} else if (format === "mmcif") {
if (text === "loop_" || /^data_/iu.test(text) || text.startsWith("#")) {
if (count > 0) {
break;
}
atomHeaders.length = 0;
} else if (text.startsWith("_atom_site.")) {
if (atomHeaders.length >= 256) {
invalid("An mmCIF topology exceeds its atom-site header budget");
}
atomHeaders.push(text.toLowerCase());
} else if (text.startsWith("_")) {
if (count > 0) {
break;
}
atomHeaders.length = 0;
} else if (text && atomHeaders.length > 0) {
const fields = text.match(/(?:"[^"]*"|'[^']*'|\S+)/gu) ?? [];
if (fields.length < atomHeaders.length) {
invalid("An approved mmCIF topology atom row is incomplete");
}
const modelIndex = atomHeaders.indexOf("_atom_site.pdbx_pdb_model_num");
const model = modelIndex < 0 ? 1 : Number(fields[modelIndex]);
if (model === requestedModel) {
count += 1;
} else if (count > 0) {
break;
}
}
}
if (count > MAX_FRAME_ATOMS) {
throw new NativeTrajectoryCodecError(
"RESOURCE_EXHAUSTED",
"The approved trajectory topology exceeds one million atoms"
);
}
}
if (count < 1 || declared != null && count !== declared) {
throw new NativeTrajectoryCodecError(
"TOPOLOGY_MISMATCH",
"The approved topology atom section is missing, truncated, or inconsistent"
);
}
return count;
}
async function readScientificStructureNativeTopologyPage(input) {
const format = input.format === "cif" ? "mmcif" : input.format;
if (!["pdb", "mmcif", "gro", "xyz", "psf", "prmtop", "top"].includes(format)) {
throw new NativeTrajectoryCodecError(
"INVALID_REQUEST",
"Unsupported topology page format"
);
}
const offset = input.offset ?? 0n;
const firstAtom = input.atomOffset ?? 0;
const limit = input.limit ?? 512;
if (offset < 0n || offset >= input.source.sizeBytes || !Number.isSafeInteger(firstAtom) || firstAtom < 0 || firstAtom >= MAX_FRAME_ATOMS || !Number.isSafeInteger(limit) || limit < 1 || limit > 512) {
throw new NativeTrajectoryCodecError(
"RESOURCE_EXHAUSTED",
"The topology atom page is unbounded"
);
}
const atoms = [];
let section = "";
if (firstAtom > 0) {
section = format === "prmtop" ? "ATOM_NAME" : "atoms";
}
let lineNumber = firstAtom > 0 ? 2 : 0;
let declared;
let model = 1;
const headers = [];
let lastEnd = offset;
for await (const line of readLammpsLines({
end: input.source.sizeBytes,
offset,
signal: input.signal,
source: input.source
})) {
lastEnd = line.end;
const text = line.text.trim();
let candidates = [];
if (format === "pdb") {
if (/^MODEL\b/u.test(text)) {
model = Number(text.slice("MODEL".length).trim());
}
if (line.text.startsWith("ATOM ") || line.text.startsWith("HETATM")) {
candidates = [
{
atomName: line.text.slice(12, 16).trim(),
chainId: line.text.slice(21, 22).trim(),
residueName: line.text.slice(17, 20).trim(),
residueNumber: Number(line.text.slice(22, 26).trim()),
x: Number(line.text.slice(30, 38).trim()),
y: Number(line.text.slice(38, 46).trim()),
z: Number(line.text.slice(46, 54).trim())
}
];
}
} else if (format === "psf") {
if (section !== "atoms") {
const match = /^(\d+)\s+!NATOM\b/u.exec(text);
if (match != null) {
declared = parseLammpsPositive(match[1], "PSF topology atom count");
section = "atoms";
}
} else if (text) {
const fields = text.split(/\s+/u);
if (fields.length < 6) {
invalid("An approved PSF topology atom record is incomplete");
}
candidates = [
{
atomName: fields[4],
chainId: fields[1],
residueName: fields[3],
residueNumber: Number(fields[2])
}
];
}
} else if (format === "prmtop") {
if (text.startsWith("%FLAG ")) {
section = text.slice("%FLAG ".length).trim();
} else if (section === "ATOM_NAME" && !text.startsWith("%FORMAT")) {
for (let position = 0; position < line.text.length; position += 4) {
const atomName = line.text.slice(position, position + 4).trim();
if (atomName) {
candidates.push({ atomName });
}
}
}
} else if (format === "top") {
const match = /^\[\s*([^\]]+)\s*\]/u.exec(text);
if (match != null) {
section = match[1].trim().toLowerCase();
} else if (section === "atoms" && text && !text.startsWith(";")) {
const fields = text.split(/\s+/u);
if (fields.length < 5) {
invalid("An approved GROMACS topology atom record is incomplete");
}
candidates = [
{
atomName: fields[4],
residueName: fields[3],
residueNumber: Number(fields[2])
}
];
}
} else if (format === "gro") {
if (lineNumber === 1) {
declared = parseLammpsPositive(text, "GRO topology atom count");
} else if (lineNumber >= 2 && (declared == null || firstAtom + atoms.length < declared)) {
candidates = [
{
atomName: line.text.slice(10, 15).trim(),
residueName: line.text.slice(5, 10).trim(),
residueNumber: Number(line.text.slice(0, 5).trim()),
x: Number(line.text.slice(20, 28).trim()) * 10,
y: Number(line.text.slice(28, 36).trim()) * 10,
z: Number(line.text.slice(36, 44).trim()) * 10
}
];
}
lineNumber += 1;
} else if (format === "xyz") {
if (lineNumber === 0) {
declared = parseLammpsPositive(text, "XYZ topology atom count");
} else if (lineNumber >= 2 && (declared == null || firstAtom + atoms.length < declared)) {
const fields = text.split(/\s+/u);
candidates = [
{
atomName: fields[0],
x: Number(fields[1]),
y: Number(fields[2]),
z: Number(fields[3])
}
];
}
lineNumber += 1;
} else if (format === "mmcif") {
if (text.startsWith("_atom_site.")) {
headers.push(text.toLowerCase());
} else if (text && headers.length > 0 && !text.startsWith("#")) {
const fields = text.match(/(?:"[^"]*"|'[^']*'|\S+)/gu) ?? [];
const get = (name) => {
const index = headers.indexOf(`_atom_site.${name}`);
return index < 0 ? void 0 : fields[index];
};
candidates = [
{
atomName: get("auth_atom_id") ?? get("label_atom_id") ?? get("id") ?? "",
chainId: get("auth_asym_id") ?? get("label_asym_id"),
residueName: get("auth_comp_id") ?? get("label_comp_id"),
residueNumber: Number(
get("auth_seq_id") ?? get("label_seq_id") ?? "1"
),
x: Number(get("cartn_x")),
y: Number(get("cartn_y")),
z: Number(get("cartn_z"))
}
];
model = Number(get("pdbx_pdb_model_num") ?? "1");
}
}
for (const candidate of candidates) {
if (!candidate.atomName || !Number.isSafeInteger(model) || candidate.residueNumber != null && !Number.isSafeInteger(candidate.residueNumber) || [candidate.x, candidate.y, candidate.z].some(
(coordinate) => coordinate != null && !Number.isFinite(coordinate)
)) {
invalid("An approved topology atom record is malformed");
}
const identity = firstAtom + atoms.length + 1;
atoms.push({ ...candidate, atomId: `${model}:${identity}`, model });
if (atoms.length === limit || declared != null && identity === declared) {
return {
atomOffset: firstAtom,
atoms,
complete: declared != null ? identity === declared : lastEnd === input.source.sizeBytes,
...declared != null && identity === declared ? {} : { nextAtomOffset: identity, nextOffset: lastEnd },
offset
};
}
}
}
return { atomOffset: firstAtom, atoms, complete: true, offset };
}
// node_modules/.pnpm/@openai+scientific-viewer-platform@file+..+scientific-viewer-platform/node_modules/@openai/scientific-viewer-platform/src/structure/scientific-structure-native-volume.mjs
var MAX_RANGE_BYTES2 = 256 * 1024;
var MAX_HEADER_BYTES = 4 * 1024 * 1024;
var MAX_HEADER_LINE_BYTES = 256 * 1024;
var MAX_REGION_VALUES = MAX_RANGE_BYTES2 / Float32Array.BYTES_PER_ELEMENT;
var MAX_REGION_READS = 4096;
var MAX_TEXT_SCAN_BYTES = 64n * 1024n * 1024n;
var HEADER_CHUNK_BYTES = 16 * 1024;
var NUMBER_TOKEN = /^[+-]?(?:\d+(?:\.\d*)?|\.\d+)(?:[de][+-]?\d+)?$/iu;
var DECIMAL = /^(0|[1-9]\d*)$/u;
var BOHR_TO_ANGSTROM = 0.529177210859;
var BRIX_NUMBER = "[+-]?(?:\\d+(?:\\.\\d*)?|\\.\\d+)(?:[de][+-]?\\d+)?";
var BRIX_HEADER = new RegExp(
`^\\s*:-\\)\\s+origin\\s+([+-]?\\d+)\\s+([+-]?\\d+)\\s+([+-]?\\d+)\\s+extent\\s+([+-]?\\d+)\\s+([+-]?\\d+)\\s+([+-]?\\d+)\\s+grid\\s+([+-]?\\d+)\\s+([+-]?\\d+)\\s+([+-]?\\d+)\\s+cell\\s+(${BRIX_NUMBER})\\s+(${BRIX_NUMBER})\\s+(${BRIX_NUMBER})\\s+(${BRIX_NUMBER})\\s+(${BRIX_NUMBER})\\s+(${BRIX_NUMBER})\\s+prod\\s+(${BRIX_NUMBER})\\s+plus\\s+([+-]?\\d+)`,
"iu"
);
async function indexScientificStructureNativeVolume(input) {
const { grant, logicalSessionId, signal } = input;
assertGrant(grant, logicalSessionId);
signal.throwIfAborted();
const format = normalizeFormat(input.format);
const sizeBytes = grant.sourceIdentity.sizeBytes;
let parsed;
if (format === "ccp4") {
parsed = parseMrcHeader(await readExact2(input, 0n, 1024));
} else if (format === "dsn6") {
parsed = parseDsn6Header(await readExact2(input, 0n, 512));
} else if (format === "cube" || format === "dx") {
parsed = await indexTextVolume(input, format);
} else {
parsed = await indexDensityServer(input);
}
const dataOffset = BigInt(parsed.dataOffsetDecimal);
const payloadBytesDecimal = "payloadBytesDecimal" in parsed ? parsed.payloadBytesDecimal : void 0;
if (dataOffset > sizeBytes || payloadBytesDecimal != null && dataOffset + BigInt(payloadBytesDecimal) > sizeBytes) {
fail2("TRUNCATED", "Scientific density-map payload is truncated");
}
return Object.freeze({
...parsed,
format,
viewerSessionId: logicalSessionId,
sourceGrantId: grant.grantId,
sourceHandleId: grant.sourceHandleId,
sourceRevision: grant.sourceRevision,
sourceSizeBytesDecimal: sizeBytes.toString(),
unit: "density",
maxTileBytes: MAX_RANGE_BYTES2
});
}
async function readScientificStructureNativeVolumeTile(input) {
const { grant, index, logicalSessionId, signal } = input;
assertGrant(grant, logicalSessionId);
signal.throwIfAborted();
if (index.viewerSessionId !== logicalSessionId || index.sourceGrantId !== grant.grantId || index.sourceHandleId !== grant.sourceHandleId || index.sourceRevision !== grant.sourceRevision || index.sourceSizeBytesDecimal !== grant.sourceIdentity.sizeBytes.toString()) {
fail2("SOURCE_CHANGED", "The indexed density map is no longer authorized");
}
if (input.region != null) {
return readVolumeRegion(input);
}
const offsetText = input.offsetDecimal ?? "0";
if (typeof offsetText !== "string" || !DECIMAL.test(offsetText)) {
fail2("INVALID_REQUEST", "The density-map tile offset is invalid");
}
const offset = BigInt(offsetText);
const requestedLength = input.length ?? MAX_RANGE_BYTES2;
if (!Number.isSafeInteger(requestedLength) || requestedLength < 1 || requestedLength > MAX_RANGE_BYTES2 || offset > grant.sourceIdentity.sizeBytes) {
fail2("RESOURCE_EXHAUSTED", "The density-map tile exceeds its byte budget");
}
const remaining = grant.sourceIdentity.sizeBytes - offset;
const length = Number(
remaining < BigInt(requestedLength) ? remaining : BigInt(requestedLength)
);
const bytes = length === 0 ? new Uint8Array() : await readExact2(input, offset, length);
return {
viewerSessionId: logicalSessionId,
sourceRevision: grant.sourceRevision,
format: index.format,
offsetDecimal: offset.toString(),
bytes,
eof: offset + BigInt(bytes.byteLength) === grant.sourceIdentity.sizeBytes
};
}
function parseMrcHeader(bytes) {
if (bytes[208] !== 77 || bytes[209] !== 65 || bytes[210] !== 80 || bytes[211] !== 32) {
fail2("MALFORMED_SOURCE", "CCP4/MRC header is missing the MAP signature");
}
let little = null;
if (bytes[212] === 68 && bytes[213] === 65) {
little = true;
} else if (bytes[212] === 17 && bytes[213] === 17) {
little = false;
}
if (little == null) {
fail2("MALFORMED_SOURCE", "CCP4/MRC machine stamp is not supported");
}
const view = new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);
const mode = view.getInt32(12, little);
const modeSizes = /* @__PURE__ */ new Map([
[0, 1],
[1, 2],
[2, 4],
[6, 2],
[12, 2]
]);
const bytesPerValue = modeSizes.get(mode);
if (bytesPerValue == null) {
fail2("UNSUPPORTED", `Unsupported CCP4/MRC voxel mode ${mode}`);
}
const storageDimensions = [0, 4, 8].map(
(offset) => view.getInt32(offset, little)
);
const starts = [16, 20, 24].map((offset) => view.getInt32(offset, little));
const gridSampling = [28, 32, 36].map(
(offset) => view.getInt32(offset, little)
);
const cellDimensions = [40, 44, 48].map(
(offset) => view.getFloat32(offset, little)
);
const cellAngles = [52, 56, 60].map(
(offset) => view.getFloat32(offset, little)
);
const axisOrder = [64, 68, 72].map(
(offset) => view.getInt32(offset, little) - 1
);
if (storageDimensions.some((value) => value < 1) || gridSampling.some((value) => value < 1) || axisOrder.some((axis) => axis < 0 || axis > 2) || new Set(axisOrder).size !== 3) {
fail2("MALFORMED_SOURCE", "CCP4/MRC grid dimensions or axes are invalid");
}
validateCell(cellDimensions, cellAngles);
const symmetryBytes = view.getInt32(92, little);
if (symmetryBytes < 0) {
fail2("MALFORMED_SOURCE", "CCP4/MRC symmetry header is invalid");
}
const dimensions = [0, 0, 0];
const logicalStarts = [0, 0, 0];
for (let axis = 0; axis < 3; axis += 1) {
dimensions[axisOrder[axis]] = storageDimensions[axis];
logicalStarts[axisOrder[axis]] = starts[axis];
}
const basis = cellBasis(cellDimensions, cellAngles, gridSampling);
const explicitOrigin = [196, 200, 204].map(
(offset) => view.getFloat32(offset, little)
);
if (explicitOrigin.some((value) => !Number.isFinite(value))) {
fail2("MALFORMED_SOURCE", "CCP4/MRC Cartesian origin is invalid");
}
const origin = explicitOrigin.some((value) => value !== 0) ? explicitOrigin : transformBasis(basis, logicalStarts);
const voxelTypes = /* @__PURE__ */ new Map([
[0, "int8"],
[1, "int16"],
[2, "float32"],
[6, "uint16"],
[12, "float16"]
]);
const voxelType = voxelTypes.get(mode);
if (voxelType == null) {
fail2("UNSUPPORTED", `Unsupported CCP4/MRC voxel mode ${mode}`);
}
return {
dimensions,
storageDimensions,
axisOrder,
starts,
gridSampling,
cellDimensionsAngstrom: cellDimensions,
cellAnglesDegrees: cellAngles,
gridToCartesian: affine(basis, origin),
dataOffsetDecimal: (1024n + BigInt(symmetryBytes)).toString(),
payloadBytesDecimal: storageDimensions.reduce((total, value) => total * BigInt(value), BigInt(bytesPerValue)).toString(),
bytesPerValue,
mode,
voxelType,
endianness: little ? "little" : "big",
dataLayout: "linear"
};
}
function parseDsn6Header(bytes) {
const isBrix = bytes[0] === 58 && bytes[1] === 45 && bytes[2] === 41;
let starts;
let dimensions;
let gridSampling;
let cellDimensions;
let cellAngles;
let divisor;
let summand;
let little;
if (isBrix) {
const fields = BRIX_HEADER.exec(
new TextDecoder("ascii").decode(bytes)
)?.slice(1);
if (fields == null) {
fail2("MALFORMED_SOURCE", "BRIX density-map header is malformed");
}
const value = (index) => Number(fields[index].replace(/[dD]/gu, "E"));
starts = [value(0), value(1), value(2)];
dimensions = [value(3), value(4), value(5)];
gridSampling = [value(6), value(7), value(8)];
cellDimensions = [value(9), value(10), value(11)];
cellAngles = [value(12), value(13), value(14)];
divisor = value(15);
summand = value(16);
little = true;
} else {
const view = new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);
little = view.getInt16(36, true) === 100;
if (view.getInt16(36, little) !== 100) {
fail2("MALFORMED_SOURCE", "DSN6 endian marker is invalid");
}
const word = (index) => view.getInt16(index * 2, little);
const scale = word(17);
if (scale < 1) {
fail2("MALFORMED_SOURCE", "DSN6 cell scale is invalid");
}
starts = [word(0), word(1), word(2)];
dimensions = [word(3), word(4), word(5)];
gridSampling = [word(6), word(7), word(8)];
cellDimensions = [word(9) / scale, word(10) / scale, word(11) / scale];
cellAngles = [word(12) / scale, word(13) / scale, word(14) / scale];
divisor = word(15) / 100;
summand = word(16);
}
if (dimensions.some((value) => !Number.isSafeInteger(value) || value < 1) || gridSampling.some((value) => !Number.isSafeInteger(value) || value < 1) || starts.some((value) => !Number.isSafeInteger(value)) || !Number.isFinite(divisor) || divisor <= 0 || !Number.isSafeInteger(summand)) {
fail2("MALFORMED_SOURCE", "DSN6/BRIX density-map grid is invalid");
}
validateCell(cellDimensions, cellAngles);
const basis = cellBasis(cellDimensions, cellAngles, gridSampling);
return {
dimensions,
storageDimensions: [...dimensions],
axisOrder: [0, 1, 2],
starts,
gridSampling,
cellDimensionsAngstrom: cellDimensions,
cellAnglesDegrees: cellAngles,
gridToCartesian: affine(basis, transformBasis(basis, starts)),
dataOffsetDecimal: "512",
payloadBytesDecimal: dimensions.map((value) => BigInt(Math.ceil(value / 8))).reduce((total, value) => total * value, 512n).toString(),
bytesPerValue: 1,
voxelType: "uint8",
endianness: little ? "little" : "big",
divisor,
summand,
dataLayout: "brick",
sourceEncoding: isBrix ? "brix" : "dsn6"
};
}
async function indexTextVolume(input, format) {
const lines = sourceLines(input, 0n, MAX_HEADER_BYTES);
const next = async (label) => {
const line = await lines.next();
if (line.done) {
fail2("TRUNCATED", `${format.toUpperCase()} ${label} is truncated`);
}
return line.value;
};
let dimensions;
let origin;
let deltas;
let dataOffset;
let scale = 1;
if (format === "cube") {
await next("first comment");
await next("second comment");
const declaration = await next("atom and origin declaration");
const fields = splitNumeric(declaration.value);
if (fields.length < 4 || fields.length > 5 || !/^[+-]?\d+$/u.test(fields[0])) {
fail2("MALFORMED_SOURCE", "CUBE atom and origin declaration is invalid");
}
const rawAtoms = Number(fields[0]);
if (!Number.isSafeInteger(rawAtoms) || Math.abs(rawAtoms) > 1e6) {
fail2("RESOURCE_EXHAUSTED", "CUBE atom declarations exceed their budget");
}
if (fields[4] != null && fields[4] !== "1") {
fail2("UNSUPPORTED", "Multiple CUBE density datasets are unsupported");
}
origin = numericVector(fields.slice(1, 4));
dimensions = [];
deltas = [];
let negativeAxes = 0;
for await (const row of orderedSourceLines(next, 3, "axis")) {
const axisFields = splitNumeric(row.value);
const count = Number(axisFields[0]);
if (axisFields.length !== 4 || !Number.isSafeInteger(count) || count === 0) {
fail2("MALFORMED_SOURCE", "CUBE axis declaration is invalid");
}
negativeAxes += count < 0 ? 1 : 0;
dimensions.push(Math.abs(count));
deltas.push(numericVector(axisFields.slice(1)));
dataOffset = row.end;
}
if (negativeAxes !== 0 && negativeAxes !== 3) {
fail2("MALFORMED_SOURCE", "CUBE axes mix incompatible coordinate units");
}
scale = negativeAxes === 3 ? 1 : BOHR_TO_ANGSTROM;
for await (const row of orderedSourceLines(
next,
Math.abs(rawAtoms),
"atom"
)) {
const atomFields = splitNumeric(row.value);
if (atomFields.length !== 5 || !/^[+-]?\d+$/u.test(atomFields[0])) {
fail2("MALFORMED_SOURCE", "CUBE atom declaration is invalid");
}
for (const field of atomFields.slice(1)) {
numeric(field);
}
dataOffset = row.end;
}
if (rawAtoms < 0) {
const orbitals = await next("orbital declaration");
const orbitalFields = splitNumeric(orbitals.value);
if (orbitalFields.length !== 2 || orbitalFields[0] !== "1") {
fail2("UNSUPPORTED", "Multiple CUBE orbitals are unsupported");
}
dataOffset = orbitals.end;
}
} else {
let connections;
deltas = [];
let hasScalarArray = false;
for await (const row of lines) {
const line = row.value.replace(/#.*/u, "").trim();
if (line.length === 0) {
continue;
}
if (/^object\s+\S+\s+class\s+gridpositions\b/iu.test(line)) {
dimensions = parseDxCounts(line);
} else if (/^object\s+\S+\s+class\s+gridconnections\b/iu.test(line)) {
connections = parseDxCounts(line);
} else if (/^origin\b/iu.test(line)) {
origin = numericVector(line.split(/\s+/u).slice(1));
} else if (/^delta\b/iu.test(line)) {
deltas.push(numericVector(line.split(/\s+/u).slice(1)));
} else if (/^object\s+\S+\s+class\s+array\b/iu.test(line)) {
const type = /\btype\s+(byte|double|float|int|short)\b/iu.exec(line);
const rank = /\brank\s+0\b/iu.exec(line);
const items = /\bitems\s+(\d+)\b/iu.exec(line)?.[1];
if (type == null || rank == null || items == null || !/\bdata\s+follows\s*$/iu.test(line) || dimensions == null || connections == null || origin == null || deltas.length !== 3 || connections.some((value, axis) => value !== dimensions[axis]) || BigInt(items) !== dimensions.reduce((total, value) => total * BigInt(value), 1n)) {
fail2("MALFORMED_SOURCE", "OpenDX scalar grid declaration is invalid");
}
dataOffset = row.end;
hasScalarArray = true;
break;
} else {
fail2(
"MALFORMED_SOURCE",
"OpenDX contains an unsupported header declaration"
);
}
if (deltas.length > 3) {
fail2("MALFORMED_SOURCE", "OpenDX has too many coordinate axes");
}
}
if (!hasScalarArray) {
fail2("TRUNCATED", "DX scalar-array declaration is truncated");
}
}
const scaledDeltas = deltas.map(
(vector) => vector.map((value) => value * scale)
);
const scaledOrigin = origin.map((value) => value * scale);
return {
dimensions,
storageDimensions: [dimensions[2], dimensions[1], dimensions[0]],
axisOrder: [2, 1, 0],
gridToCartesian: [
scaledDeltas[0][0],
scaledDeltas[1][0],
scaledDeltas[2][0],
scaledOrigin[0],
scaledDeltas[0][1],
scaledDeltas[1][1],
scaledDeltas[2][1],
scaledOrigin[1],
scaledDeltas[0][2],
scaledDeltas[1][2],
scaledDeltas[2][2],
scaledOrigin[2],
0,
0,
0,
1
],
dataOffsetDecimal: dataOffset.toString(),
bytesPerValue: 0,
voxelType: "text-float",
endianness: "little",
dataLayout: "text"
};
}
async function indexDensityServer(input) {
const expectsBinary = input.format.toLowerCase().replace(/^\./u, "") === "bcif";
const maximum = Number(
input.grant.sourceIdentity.sizeBytes < BigInt(MAX_HEADER_BYTES) ? input.grant.sourceIdentity.sizeBytes : BigInt(MAX_HEADER_BYTES)
);
let previous = "";
let info = false;
let data = false;
let binary = false;
for await (const { offset, bytes } of sourceChunks(input, 0n, maximum)) {
if (offset === 0n) {
binary = bytes[0] >= 128 && bytes[0] <= 143;
if (expectsBinary && !binary) {
fail2(
"MALFORMED_SOURCE",
"The BinaryCIF density-map root is not a MessagePack map"
);
}
}
const text = previous + new TextDecoder("latin1").decode(bytes);
info = info || text.includes("_volume_data_3d_info");
data = data || /_volume_data_3d(?!_info)/u.test(text);
previous = text.slice(-128);
if (info && data) {
return {
dataOffsetDecimal: "0",
bytesPerValue: 0,
voxelType: binary ? "binary-cif" : "density-cif",
endianness: "little",
dataLayout: "density-server"
};
}
}
fail2(
"UNSUPPORTED",
"The CIF companion is not an authenticated DensityServer density map"
);
}
async function readVolumeRegion(input) {
const { index, region } = input;
if (index.dimensions == null || index.dataLayout === "density-server") {
fail2(
"UNSUPPORTED",
"DensityServer CIF requires bounded encoded source tiles"
);
}
if (!Array.isArray(region.start) || !Array.isArray(region.size) || region.start.length !== 3 || region.size.length !== 3 || region.start.some((value) => !Number.isSafeInteger(value) || value < 0) || region.size.some((value) => !Number.isSafeInteger(value) || value < 1) || region.start.some(
(value, axis) => value + region.size[axis] > index.dimensions[axis]
)) {
fail2("INVALID_REQUEST", "The density-map region is outside its voxel grid");
}
const count = region.size.reduce((total, value) => total * value, 1);
if (!Number.isSafeInteger(count) || count > MAX_REGION_VALUES) {
fail2(
"RESOURCE_EXHAUSTED",
"The density-map region exceeds its voxel budget"
);
}
const values = new Float32Array(count);
const counters = { reads: 0, bytes: 0n };
if (index.dataLayout === "linear") {
await readMrcRegion(input, values, counters);
} else if (index.dataLayout === "brick") {
await readDsn6Region(input, values, counters);
} else {
await readTextRegion(input, values, counters);
}
const bytes = new Uint8Array(
values.buffer,
values.byteOffset,
values.byteLength
);
return {
viewerSessionId: input.logicalSessionId,
sourceRevision: input.grant.sourceRevision,
format: index.format,
offsetDecimal: index.dataOffsetDecimal,
bytes,
eof: false,
region: { start: [...region.start], size: [...region.size] },
voxelType: "float32",
values: Array.from(values),
rangeReads: counters.reads,
sourceBytesReadDecimal: counters.bytes.toString()
};
}
async function readMrcRegion(input, output, counters) {
const { index, region } = input;
const storageStart = index.axisOrder.map((axis) => region.start[axis]);
const storageSize = index.axisOrder.map((axis) => region.size[axis]);
const maxValues = Math.floor(MAX_RANGE_BYTES2 / index.bytesPerValue);
for await (const {
bytes,
storageX,
storageY,
storageZ,
valueCount
} of mrcRegionRows(input, storageStart, storageSize, maxValues, counters)) {
const view = new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);
for (let valueIndex = 0; valueIndex < valueCount; valueIndex += 1) {
const value = decodeMrc(
view,
valueIndex * index.bytesPerValue,
index.mode,
index.endianness === "little"
);
if (!Number.isFinite(value)) {
fail2("MALFORMED_SOURCE", "The density-map voxel is not finite");
}
const logical = [0, 0, 0];
logical[index.axisOrder[0]] = storageX + valueIndex;
logical[index.axisOrder[1]] = storageY;
logical[index.axisOrder[2]] = storageZ;
output[logical[0] + region.size[0] * (logical[1] + region.size[1] * logical[2])] = value;
}
}
}
async function* mrcRegionRows(input, storageStart, storageSize, maxValues, counters) {
const { index } = input;
for (let storageZ = 0; storageZ < storageSize[2]; storageZ += 1) {
for (let storageY = 0; storageY < storageSize[1]; storageY += 1) {
for (let storageX = 0; storageX < storageSize[0]; storageX += maxValues) {
const valueCount = Math.min(maxValues, storageSize[0] - storageX);
const flat = BigInt(storageStart[0] + storageX) + BigInt(index.storageDimensions[0]) * (BigInt(storageStart[1] + storageY) + BigInt(index.storageDimensions[1]) * BigInt(storageStart[2] + storageZ));
const result = countedRead(
input,
BigInt(index.dataOffsetDecimal) + flat * BigInt(index.bytesPerValue),
valueCount * index.bytesPerValue,
counters
);
yield result.then((bytes) => ({
bytes,
storageX,
storageY,
storageZ,
valueCount
}));
}
}
}
}
async function readDsn6Region(input, output, counters) {
const { index, region } = input;
const blocks = index.dimensions.map((value) => Math.ceil(value / 8));
const first = region.start.map((value) => Math.floor(value / 8));
const last = region.start.map(
(value, axis) => Math.floor((value + region.size[axis] - 1) / 8)
);
for await (const { bytes, blockX, blockY, blockZ } of dsn6RegionBricks(
input,
blocks,
first,
last,
counters
)) {
for (let z = 0; z < 8; z += 1) {
for (let y = 0; y < 8; y += 1) {
for (let x = 0; x < 8; x += 1) {
const coordinate = [blockX * 8 + x, blockY * 8 + y, blockZ * 8 + z];
if (coordinate.some(
(value2, axis) => value2 < region.start[axis] || value2 >= region.start[axis] + region.size[axis]
)) {
continue;
}
const brickOffset = x + 8 * (y + 8 * z);
const encoded = index.endianness === "little" ? brickOffset : brickOffset + (brickOffset % 2 === 0 ? 1 : -1);
const value = (bytes[encoded] - index.summand) / index.divisor;
output[coordinate[0] - region.start[0] + region.size[0] * (coordinate[1] - region.start[1] + region.size[1] * (coordinate[2] - region.start[2]))] = value;
}
}
}
}
}
async function* dsn6RegionBricks(input, blocks, first, last, counters) {
for (let blockZ = first[2]; blockZ <= last[2]; blockZ += 1) {
for (let blockY = first[1]; blockY <= last[1]; blockY += 1) {
for (let blockX = first[0]; blockX <= last[0]; blockX += 1) {
const flat = BigInt(blockX) + BigInt(blocks[0]) * (BigInt(blockY) + BigInt(blocks[1]) * BigInt(blockZ));
const result = countedRead(
input,
BigInt(input.index.dataOffsetDecimal) + flat * 512n,
512,
counters
);
yield result.then((bytes) => ({ bytes, blockX, blockY, blockZ }));
}
}
}
}
async function readTextRegion(input, output, counters) {
const { index, region } = input;
const wanted = /* @__PURE__ */ new Map();
for (let x = 0; x < region.size[0]; x += 1) {
for (let y = 0; y < region.size[1]; y += 1) {
for (let z = 0; z < region.size[2]; z += 1) {
const absoluteX = BigInt(region.start[0] + x);
const absoluteY = BigInt(region.start[1] + y);
const absoluteZ = BigInt(region.start[2] + z);
const sourcePosition = absoluteZ + BigInt(index.dimensions[2]) * (absoluteY + BigInt(index.dimensions[1]) * absoluteX);
wanted.set(
sourcePosition,
x + region.size[0] * (y + region.size[1] * z)
);
}
}
}
const maxPosition = Array.from(wanted.keys()).reduce(
(max, value) => value > max ? value : max,
0n
);
let seen = 0n;
for await (const line of sourceLines(
input,
BigInt(index.dataOffsetDecimal),
Number(MAX_TEXT_SCAN_BYTES),
counters
)) {
const content = line.value.replace(/#.*/u, "").trim();
if (content.length === 0) {
continue;
}
for (const token of content.split(/\s+/u)) {
if (!NUMBER_TOKEN.test(token)) {
if (index.format === "dx" && /^(?:attribute|component|object)$/iu.test(token)) {
fail2(
"TRUNCATED",
"OpenDX voxel payload ended before the requested region"
);
}
fail2("MALFORMED_SOURCE", "The text density-map voxel is invalid");
}
const target = wanted.get(seen);
if (target != null) {
output[target] = numeric(token);
}
if (seen === maxPosition) {
return;
}
seen += 1n;
}
}
fail2(
"RESOURCE_EXHAUSTED",
"The requested text density region exceeds its incremental scan budget"
);
}
async function* sourceLines(input, offset, budget, counters) {
const decoder = new TextDecoder("utf-8", { fatal: true });
let carry = new Uint8Array();
let carryOffset = offset;
let endOffset = offset;
for await (const { offset: chunkOffset, bytes: chunk } of sourceChunks(
input,
offset,
budget,
counters
)) {
endOffset = chunkOffset + BigInt(chunk.byteLength);
const joined = new Uint8Array(carry.byteLength + chunk.byteLength);
joined.set(carry);
joined.set(chunk, carry.byteLength);
let lineStart = 0;
for (let index = 0; index < joined.byteLength; index += 1) {
if (joined[index] !== 10) {
continue;
}
const line = joined.subarray(lineStart, index);
if (line.byteLength > MAX_HEADER_LINE_BYTES) {
fail2("RESOURCE_EXHAUSTED", "A text density-map line exceeds its limit");
}
let value;
try {
value = decoder.decode(line).replace(/\r$/u, "");
} catch {
fail2("MALFORMED_SOURCE", "The density-map source is not valid UTF-8");
}
if (value.includes("\0")) {
fail2("MALFORMED_SOURCE", "The text density map contains a NUL byte");
}
yield { value, end: carryOffset + BigInt(index + 1) };
lineStart = index + 1;
}
carry = joined.subarray(lineStart);
carryOffset += BigInt(lineStart);
if (carry.byteLength > MAX_HEADER_LINE_BYTES) {
fail2("RESOURCE_EXHAUSTED", "A text density-map line exceeds its limit");
}
}
if (endOffset - offset >= BigInt(budget) && endOffset < input.grant.sourceIdentity.sizeBytes) {
fail2(
"RESOURCE_EXHAUSTED",
"The text density-map header or scan exceeds its budget"
);
}
if (carry.byteLength > 0) {
try {
yield {
value: decoder.decode(carry).replace(/\r$/u, ""),
end: endOffset
};
} catch {
fail2("MALFORMED_SOURCE", "The density-map source is not valid UTF-8");
}
}
}
async function* sourceChunks(input, start, budget, counters) {
let offset = start;
while (offset < input.grant.sourceIdentity.sizeBytes) {
const available = BigInt(budget) - (offset - start);
if (available < 1n) {
return;
}
const remaining = input.grant.sourceIdentity.sizeBytes - offset;
let readable = remaining < available ? remaining : available;
if (readable > BigInt(HEADER_CHUNK_BYTES)) {
readable = BigInt(HEADER_CHUNK_BYTES);
}
const length = Number(readable);
const currentOffset = offset;
const result = counters == null ? readExact2(input, currentOffset, length) : countedRead(input, currentOffset, length, counters);
yield result.then((bytes) => ({ offset: currentOffset, bytes }));
offset += BigInt(length);
}
}
async function* orderedSourceLines(next, count, label) {
for (let index = 0; index < count; index += 1) {
yield next(`${label} ${index + 1}`);
}
}
async function countedRead(input, offset, length, counters) {
counters.reads += 1;
counters.bytes += BigInt(length);
if (counters.reads > MAX_REGION_READS) {
fail2(
"RESOURCE_EXHAUSTED",
"The density-map tile exceeds its range-read budget"
);
}
return readExact2(input, offset, length);
}
async function readExact2(input, offset, length) {
input.signal.throwIfAborted();
if (offset < 0n || !Number.isSafeInteger(length) || length < 1 || length > MAX_RANGE_BYTES2 || offset + BigInt(length) > input.grant.sourceIdentity.sizeBytes) {
fail2(
"TRUNCATED",
"The authenticated density-map range is outside its source"
);
}
const result = await input.readSource({
grant: input.grant,
logicalSessionId: input.logicalSessionId,
offset,
length,
signal: input.signal
});
input.signal.throwIfAborted();
if (!(result.bytes instanceof Uint8Array) || result.bytes.byteLength !== length) {
fail2(
"SOURCE_CHANGED",
"The authenticated density map returned a short range"
);
}
return result.bytes;
}
function assertGrant(grant, logicalSessionId) {
if (grant?.family !== "structure" || grant.logicalSessionId !== logicalSessionId || typeof grant.grantId !== "string" || grant.grantId.length === 0 || typeof grant.sourceHandleId !== "string" || grant.sourceHandleId.length === 0 || typeof grant.sourceRevision !== "string" || grant.sourceRevision.length === 0 || grant.sourceIdentity == null || grant.sourceIdentity.etag !== grant.sourceRevision || typeof grant.sourceIdentity.sizeBytes !== "bigint" || grant.sourceIdentity.sizeBytes < 1n || !Array.isArray(grant.operations) || !grant.operations.includes("range-read")) {
fail2(
"PERMISSION_DENIED",
"The density-map companion grant is not authorized"
);
}
if ((grant.sourceAccessPattern ?? grant.sourceIdentity.accessPattern) === "forward-only") {
fail2(
"UNSUPPORTED",
"Density-map companions require authenticated random access"
);
}
}
function normalizeFormat(format) {
if (typeof format !== "string") {
fail2("UNSUPPORTED", "The density-map format is not supported");
}
const normalized = format.toLowerCase().replace(/^\./u, "");
if (["ccp4", "map", "mrc"].includes(normalized)) {
return "ccp4";
}
if (["dsn6", "brix"].includes(normalized)) {
return "dsn6";
}
if (["cube", "cub"].includes(normalized)) {
return "cube";
}
if (normalized === "dx") {
return "dx";
}
if (["bcif", "cif", "dscif"].includes(normalized)) {
return "dscif";
}
fail2("UNSUPPORTED", `The density-map format ${format} is not supported`);
}
function decodeMrc(view, offset, mode, little) {
if (mode === 0) {
return view.getInt8(offset);
}
if (mode === 1) {
return view.getInt16(offset, little);
}
if (mode === 2) {
return view.getFloat32(offset, little);
}
if (mode === 6) {
return view.getUint16(offset, little);
}
const bits = view.getUint16(offset, little);
const sign = bits >= 32768 ? -1 : 1;
const magnitude = bits % 32768;
const exponent = Math.floor(magnitude / 1024);
const fraction = magnitude % 1024;
if (exponent === 0) {
return sign * 2 ** -14 * (fraction / 1024);
}
if (exponent === 31) {
return fraction === 0 ? sign * Number.POSITIVE_INFINITY : Number.NaN;
}
return sign * 2 ** (exponent - 15) * (1 + fraction / 1024);
}
function splitNumeric(value) {
return value.trim().split(/\s+/u);
}
function numeric(value) {
if (typeof value !== "string" || !NUMBER_TOKEN.test(value)) {
fail2("MALFORMED_SOURCE", "The density-map numeric value is invalid");
}
const parsed = Number(value.replace(/[dD]/gu, "E"));
if (!Number.isFinite(parsed)) {
fail2("MALFORMED_SOURCE", "The density-map numeric value is not finite");
}
return parsed;
}
function numericVector(fields) {
if (fields.length !== 3) {
fail2("MALFORMED_SOURCE", "The density-map coordinate vector is invalid");
}
return fields.map(numeric);
}
function parseDxCounts(line) {
const match = /\bcounts\s+([1-9]\d*)\s+([1-9]\d*)\s+([1-9]\d*)\s*$/iu.exec(
line
);
if (match == null) {
fail2("MALFORMED_SOURCE", "OpenDX grid counts are invalid");
}
const counts = match.slice(1).map(Number);
if (counts.some((value) => !Number.isSafeInteger(value))) {
fail2("RESOURCE_EXHAUSTED", "OpenDX grid counts exceed their safe range");
}
return counts;
}
function validateCell(dimensions, angles) {
if (dimensions.some((value) => !Number.isFinite(value) || value <= 0) || angles.some(
(value) => !Number.isFinite(value) || value <= 0 || value >= 180
)) {
fail2("MALFORMED_SOURCE", "The density-map unit cell is invalid");
}
}
function cellBasis(dimensions, angles, sampling) {
const [a, b, c] = dimensions;
const [alpha, beta, gamma] = angles.map((value) => value * Math.PI / 180);
const sinGamma = Math.sin(gamma);
if (Math.abs(sinGamma) < 1e-12) {
fail2("MALFORMED_SOURCE", "The density-map unit cell is degenerate");
}
const cosBeta = Math.cos(beta);
const cy = (Math.cos(alpha) - cosBeta * Math.cos(gamma)) / sinGamma;
const cz = 1 - cosBeta ** 2 - cy ** 2;
if (cz <= 1e-12) {
fail2("MALFORMED_SOURCE", "The density-map unit cell is degenerate");
}
return [
a / sampling[0],
b * Math.cos(gamma) / sampling[1],
c * cosBeta / sampling[2],
0,
b * sinGamma / sampling[1],
c * cy / sampling[2],
0,
0,
c * Math.sqrt(cz) / sampling[2]
].map((value) => Math.abs(value) < 1e-12 ? 0 : value);
}
function transformBasis(basis, point) {
return [
basis[0] * point[0] + basis[1] * point[1] + basis[2] * point[2],
basis[3] * point[0] + basis[4] * point[1] + basis[5] * point[2],
basis[6] * point[0] + basis[7] * point[1] + basis[8] * point[2]
];
}
function affine(basis, origin) {
return [
basis[0],
basis[1],
basis[2],
origin[0],
basis[3],
basis[4],
basis[5],
origin[1],
basis[6],
basis[7],
basis[8],
origin[2],
0,
0,
0,
1
];
}
function fail2(code, message) {
throw Object.assign(new Error(message), {
code,
name: "ScientificStructureNativeVolumeError"
});
}
// node_modules/.pnpm/@openai+scientific-viewer-platform@file+..+scientific-viewer-platform/node_modules/@openai/scientific-viewer-platform/src/structure/scientific-structure-workspace-integrity.mjs
var WORKSPACE_IDENTITY_DECIMAL = /^(?:0|[1-9][0-9]{0,19})$/u;
function isSafeProjectRelativePath(value) {
return typeof value === "string" && value.length > 0 && value.length <= 1024 && value.trim() === value && !value.startsWith("/") && !/^[a-z]:/iu.test(value) && !/^[a-z][a-z0-9+.-]*:/iu.test(value) && !value.includes("\\") && !value.includes("\0") && value.split("/").every((part) => part !== "" && part !== "." && part !== "..");
}
function verifiedStructureWorkspaceIntegrity(sourceIdentity) {
const integrity = sourceIdentity.sourceIntegrity;
if (!isRecord(integrity) || integrity.kind !== "workspace-file-identity-v1" || !isRecord(integrity.identity)) {
return void 0;
}
const identity = integrity.identity;
if (identity.links !== "1" || ![
"changedAtNanoseconds",
"device",
"inode",
"modifiedAtNanoseconds",
"size"
].every(
(field) => typeof identity[field] === "string" && WORKSPACE_IDENTITY_DECIMAL.test(identity[field])
) || BigInt(identity.size) !== sourceIdentity.sizeBytes) {
return void 0;
}
return {
kind: "workspace-file-identity-v1",
identity: {
changedAtNanoseconds: identity.changedAtNanoseconds,
device: identity.device,
inode: identity.inode,
links: "1",
modifiedAtNanoseconds: identity.modifiedAtNanoseconds,
size: identity.size
}
};
}
function sameVerifiedStructureWorkspaceIntegrity(current, expected) {
if (current == null || expected == null) {
return current === expected;
}
if (!isRecord(current) || !isRecord(expected) || current.kind !== "workspace-file-identity-v1" || expected.kind !== "workspace-file-identity-v1" || !isRecord(current.identity) || !isRecord(expected.identity) || current.identity.links !== "1" || expected.identity.links !== "1") {
return false;
}
const currentIdentity = current.identity;
const expectedIdentity = expected.identity;
return [
"changedAtNanoseconds",
"device",
"inode",
"modifiedAtNanoseconds",
"size"
].every((field) => {
const currentValue = currentIdentity[field];
return typeof currentValue === "string" && WORKSPACE_IDENTITY_DECIMAL.test(currentValue) && currentValue === expectedIdentity[field];
});
}
function isRecord(value) {
return typeof value === "object" && value != null && !Array.isArray(value);
}
// node_modules/.pnpm/@openai+scientific-viewer-platform@file+..+scientific-viewer-platform/node_modules/@openai/scientific-viewer-platform/src/structure/scientific-structure-backend-runtime.mjs
var PREVIEW_BYTES = 64 * 1024;
var MAX_SOURCE_RANGE_BYTES = 256 * 1024;
var MAX_QUERY_SCAN_BYTES = 512 * 1024;
var MAX_RESULT_ATOMS = 512;
var MAX_MMCIF_PAGE_BOUNDARIES = 4096;
var MAX_TRAJECTORIES = 16;
var MAX_VALIDATED_TRAJECTORY_FRAMES = 64;
var MAX_TOPOLOGY_RANGE_BYTES = 64 * 1024;
var MAX_TOPOLOGY_SCAN_BYTES = 128 * 1024 * 1024;
var MAX_SESSIONS = 128;
var MAX_ARTIFACT_TRANSACTIONS = 128;
var MAX_ARTIFACT_CHUNK_BYTES = 256 * 1024;
var MAX_PROJECT_HASH_BYTES = 8 * 1024 * 1024;
var MAX_PROJECT_MANIFEST_BYTES = 180 * 1024;
var MAX_PROJECT_DEPENDENCIES = 128;
var MAX_PENDING_COMMANDS = 128;
var MAX_COMMAND_WAITERS = 16;
var MAX_COMMAND_WAIT_MS = 30 * 1e3;
var DECIMAL2 = /^(0|[1-9][0-9]*)$/u;
var UUID = /^[0-9a-f]{8}-[0-9a-f]{4}-[1-5][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}$/iu;
var ARTIFACT_MEMBER_NAME = /^[A-Za-z0-9][A-Za-z0-9_.-]*(?:\/[A-Za-z0-9][A-Za-z0-9_.-]*)*$/u;
var ARTIFACT_MEMBER_ROLES = /* @__PURE__ */ new Set([
"data",
"index",
"topology",
"annotation",
"image",
"label-mask",
"probability-map",
"measurement-table",
"spatial-matrix",
"registration",
"class-dictionary",
"project",
"reference-manifest",
"provenance"
]);
var VIEWER_COMMAND_ACTIONS = /* @__PURE__ */ new Set([
"add_structure",
"align_structures",
"analyze",
"apply_scene",
"delete_scene",
"derive_object",
"export",
"focus_ligand",
"focus_residue",
"get_state",
"list_scenes",
"load_scene",
"load_structure",
"load_trajectory",
"load_volume",
"measure",
"measure_residue_distance",
"query",
"redo",
"remove_structure",
"render_image",
"render_movie",
"reset_view",
"select_chain",
"select_residue_range",
"select_residues",
"set_color",
"set_display_mode",
"set_object_visibility",
"set_representation",
"set_selection",
"set_trajectory_state",
"set_view_options",
"show_ligand_contacts",
"transform_object",
"undo",
"validate_render"
]);
var PRIVATE_VIEWER_COMMAND_FIELDS = /* @__PURE__ */ new Set([
"backendGeneration",
"backendInstanceId",
"channelId",
"destinationGrant",
"destinationGrantId",
"family",
"logicalSessionId",
"resourceUri",
"sourceGrant",
"sourceGrantId",
"sourceHandleId",
"sourceIdentity",
"sourceRevision",
"trajectorySourceGrant",
"trajectorySourceGrantId",
"trajectoryRelativePath",
"trajectoryResources",
"topologySourceGrant",
"topologyRelativePath",
"structureSourceGrant",
"structureSourceGrants",
"structureRelativePath",
"structureResources",
"volumeSourceGrant",
"volumeSourceGrants",
"volumeRelativePath",
"volumeResources",
"projectSourceGrant",
"projectResources"
]);
async function executeScientificStructureTool({
operation,
payload,
sessions,
identity,
readSource,
writeArtifact,
artifactTransactions,
now,
signal
}) {
signal.throwIfAborted();
if (!isRecord2(payload) || !isOpaqueIdentity(payload.logicalSessionId)) {
fail3(
"INVALID_REQUEST",
"Structure operations require an owned logical session"
);
}
const logicalSessionId = payload.logicalSessionId;
const command = isRecord2(payload.payload) ? payload.payload : payload;
const sourceGrant = validateSourceGrant({
grant: command.sourceGrant,
identity,
logicalSessionId,
now: now()
});
if (operation === "open" || operation === "open_from_chat") {
return openStructure({
sessions,
logicalSessionId,
grant: sourceGrant,
command,
readSource,
signal,
exposeInitialGeometry: operation === "open"
});
}
const state = sessions.get(logicalSessionId);
if (state == null || !isRecord2(state.molecular)) {
fail3(
"NOT_FOUND",
"The Structure source has not been opened in this process"
);
}
if (state.molecular.sourceGrantId !== sourceGrant.grantId || state.molecular.sourceRevision !== sourceGrant.sourceRevision) {
fail3("SOURCE_CHANGED", "The Structure session source or revision is stale");
}
const readMolecularSource = state.molecular.compressedSource == null ? readSource : async ({ grant, offset, length, signal: signal2 }) => {
if (grant.grantId !== state.molecular.sourceGrantId || grant.sourceRevision !== state.molecular.sourceRevision) {
fail3(
"SOURCE_CHANGED",
"The compressed Structure source or revision is no longer owned"
);
}
const source = state.molecular.compressedSource;
if (source == null || source.sourceRevision !== grant.sourceRevision) {
fail3(
"SOURCE_CHANGED",
"The compressed Structure decoder is no longer revision-bound"
);
}
return source.readRange({ offset, length, signal: signal2 });
};
switch (operation) {
case "wait_for_command":
return waitForStructureCommand({
logicalSessionId,
state,
command,
signal
});
case "get_command_control": {
const result = await getStructureCommandControl({ state, command, signal });
if (sessions.get(logicalSessionId) !== state) {
fail3("SOURCE_CHANGED", "The Structure session source or revision is stale");
}
validateSourceGrant({
grant: sourceGrant,
identity,
logicalSessionId,
now: now()
});
return result;
}
case "complete_command":
return completeStructureCommand({ state, command });
case "get_project_context":
return getStructureProjectContext({
logicalSessionId,
state,
grant: sourceGrant,
command,
readSource,
signal
});
case "project/resolve": {
const projectGrant = validateSourceGrant({
grant: command.projectSourceGrant,
identity,
logicalSessionId,
now: now()
});
return resolveScientificStructureNativeProject({
command,
logicalSessionId,
primaryGrant: sourceGrant,
primaryFormat: state.molecular.format,
projectGrant,
readSource,
signal,
describeSource: ({ grant, format, relativePath }) => verifiedStructureProjectSource({
logicalSessionId,
state,
grant,
format,
relativePath,
readSource,
signal
}),
sameIntegrity: sameVerifiedStructureWorkspaceIntegrity,
validateGrant: (grant) => validateSourceGrant({
grant,
identity,
logicalSessionId,
now: now()
})
});
}
case "resolve_live_project_checkpoint":
return resolveStructureLiveProjectCheckpoint({
logicalSessionId,
state,
grant: sourceGrant,
command,
readSource,
signal,
identity,
now
});
case "export/begin":
case "export/append":
case "export/commit":
case "export/abort":
case "export/resume":
return executeStructureArtifactOperation({
operation,
logicalSessionId,
state,
sourceGrant,
command,
identity,
writeArtifact,
artifactTransactions,
now,
signal
});
case "get_state":
case "list_structures":
return structureState(logicalSessionId, state);
case "list_scenes":
return {
structuredContent: {
viewerSessionId: logicalSessionId,
viewerCommandRevision: state.revision,
scenes: [...state.molecular.scenes.keys()]
}
};
case "query":
case "read_atoms":
case "focus_residue":
case "focus_ligand":
if (command.offsetDecimal != null && (state.molecular.compressedSource != null || (sourceGrant.sourceAccessPattern ?? sourceGrant.sourceIdentity.accessPattern) === "forward-only")) {
fail3(
"UNSUPPORTED",
"A forward-only molecular source cannot run positioned atom queries"
);
}
return queryStructure({
logicalSessionId,
state,
grant: sourceGrant,
command,
readSource: readMolecularSource,
signal
});
case "read_atoms_page":
if (state.molecular.compressedSource != null || (sourceGrant.sourceAccessPattern ?? sourceGrant.sourceIdentity.accessPattern) === "forward-only") {
fail3(
"UNSUPPORTED",
"A forward-only molecular source cannot provide random-access atom pages"
);
}
return readStructureAtomPage({
logicalSessionId,
state,
grant: sourceGrant,
command,
readSource: readMolecularSource,
signal
});
case "index_trajectory":
if (state.molecular.compressedSource != null || (sourceGrant.sourceAccessPattern ?? sourceGrant.sourceIdentity.accessPattern) === "forward-only") {
fail3(
"UNSUPPORTED",
"A forward-only molecular topology cannot index random-access trajectories"
);
}
return indexStructureTrajectory({
logicalSessionId,
state,
grant: sourceGrant,
command,
readSource,
signal,
identity,
now
});
case "read_trajectory_frame":
case "read_trajectory_frames":
return readStructureTrajectory({
logicalSessionId,
state,
grant: sourceGrant,
command,
readSource,
signal,
identity,
now,
multiple: operation === "read_trajectory_frames"
});
case "read_topology_atoms_page":
return readStructureTopologyPage({
logicalSessionId,
state,
grant: sourceGrant,
command,
readSource,
signal,
identity,
now
});
case "index_volume":
return indexStructureVolume({
logicalSessionId,
state,
grant: sourceGrant,
command,
readSource,
signal,
identity,
now
});
case "read_volume_tile":
case "read_companion_range":
return readStructureVolume({
logicalSessionId,
state,
grant: sourceGrant,
command,
readSource,
signal,
identity,
now
});
case "load_data":
case "read_range":
case "read_geometry":
case "geometry_tile":
return readStructureGeometry({
logicalSessionId,
state,
grant: sourceGrant,
command,
readSource: readMolecularSource,
signal
});
case "measure":
return measureStructure({
logicalSessionId,
state,
grant: sourceGrant,
command,
readSource: readMolecularSource,
signal
});
case "analyze":
case "ligand_contacts":
case "show_ligand_contacts":
return analyzeStructureContacts({
logicalSessionId,
state,
grant: sourceGrant,
command,
readSource,
signal
});
case "control_viewer":
case "set_selection":
case "apply_scene":
case "set_object_visibility":
case "set_trajectory_state":
case "transform_object":
case "save_scene":
case "load_scene":
case "undo":
case "redo":
return mutateStructure({
logicalSessionId,
operation,
state,
grant: sourceGrant,
command,
readSource: readMolecularSource,
signal,
identity,
now
});
default:
fail3("UNSUPPORTED", "The requested Structure operation is not available");
}
}
function enqueueStructureViewerCommand({ state, command, createdAt, deadlineAt }) {
if (typeof command.action !== "string" || !VIEWER_COMMAND_ACTIONS.has(command.action)) {
fail3(
"UNSUPPORTED",
"The requested Structure viewer command is unavailable"
);
}
if (state.molecular.commands.size >= MAX_PENDING_COMMANDS) {
for (const [commandId2, queued] of state.molecular.commands) {
if (queued.completion != null) {
state.molecular.commands.delete(commandId2);
}
if (state.molecular.commands.size < MAX_PENDING_COMMANDS) {
break;
}
}
}
if (state.molecular.commands.size >= MAX_PENDING_COMMANDS) {
fail3(
"RESOURCE_EXHAUSTED",
"The Structure viewer command queue is exhausted"
);
}
const commandId = randomUUID();
const deliveredCommand = {
...Object.fromEntries(
Object.entries(command).filter(
([field]) => !PRIVATE_VIEWER_COMMAND_FIELDS.has(field)
)
),
commandId,
revision: state.revision,
createdAt,
deadlineAt
};
let serialized;
try {
serialized = JSON.stringify(deliveredCommand);
} catch {
fail3(
"INVALID_REQUEST",
"The Structure viewer command cannot be serialized"
);
}
if (Buffer2.byteLength(serialized, "utf8") > MAX_SOURCE_RANGE_BYTES) {
fail3(
"RESOURCE_EXHAUSTED",
"The Structure viewer command exceeds its bounded budget"
);
}
state.molecular.commands.set(commandId, {
command: deliveredCommand,
completionWaiters: /* @__PURE__ */ new Set(),
cancelRequested: false
});
for (const wake of state.molecular.commandWaiters) {
wake();
}
return commandId;
}
async function waitForStructureCommand({ state, command, signal }) {
if (typeof command.afterRevision !== "number" || !Number.isSafeInteger(command.afterRevision) || command.afterRevision < 0) {
fail3("INVALID_REQUEST", "The Structure command revision is invalid");
}
const timeoutMs = readPositive(
command.timeoutMs,
MAX_COMMAND_WAIT_MS,
"Structure command wait"
);
const next = () => {
const now = Date.now();
for (const [commandId, queued] of state.molecular.commands) {
if (typeof queued.command.deadlineAt === "number" && queued.command.deadlineAt <= now && queued.completion == null) {
state.molecular.commands.delete(commandId);
continue;
}
if (queued.completion == null && typeof queued.command.revision === "number" && queued.command.revision > command.afterRevision) {
return queued.command;
}
}
return null;
};
const immediate = next();
if (immediate != null) {
return { structuredContent: { command: immediate } };
}
if (state.molecular.commandWaiters.size >= MAX_COMMAND_WAITERS) {
fail3(
"RESOURCE_EXHAUSTED",
"The Structure command wait budget is exhausted"
);
}
signal.throwIfAborted();
await new Promise((resolve, reject) => {
const finish = () => {
clearTimeout(timer);
signal.removeEventListener("abort", abort);
state.molecular.commandWaiters.delete(finish);
resolve(void 0);
};
const abort = () => {
clearTimeout(timer);
signal.removeEventListener("abort", abort);
state.molecular.commandWaiters.delete(finish);
reject(
signal.reason instanceof Error ? signal.reason : new Error("The Structure command wait was aborted")
);
};
const timer = setTimeout(finish, timeoutMs);
state.molecular.commandWaiters.add(finish);
signal.addEventListener("abort", abort, { once: true });
if (signal.aborted) {
abort();
}
});
signal.throwIfAborted();
return { structuredContent: { command: next() } };
}
async function getStructureCommandControl({ state, command, signal }) {
if (typeof command.commandId !== "string" || !UUID.test(command.commandId)) {
fail3("INVALID_REQUEST", "The Structure command identity is invalid");
}
const queued = state.molecular.commands.get(command.commandId);
if (queued == null) {
fail3("NOT_FOUND", "The Structure process does not own that viewer command");
}
const waitMs = command.waitMs ?? 0;
if (typeof waitMs !== "number" || !Number.isSafeInteger(waitMs) || waitMs < 0 || waitMs > MAX_COMMAND_WAIT_MS) {
fail3("INVALID_REQUEST", "The Structure command result wait is invalid");
}
const deadlineAt = queued.command.deadlineAt;
const timeoutMs = Math.min(
waitMs,
typeof deadlineAt === "number" ? Math.max(0, deadlineAt - Date.now()) : 0
);
if (timeoutMs > 0 && queued.completion == null && !queued.cancelRequested) {
if (state.molecular.commandWaiters.size >= MAX_COMMAND_WAITERS) {
fail3("RESOURCE_EXHAUSTED", "The Structure command wait budget is exhausted");
}
signal.throwIfAborted();
await new Promise((resolve, reject) => {
const cleanup = () => {
clearTimeout(timer);
signal.removeEventListener("abort", abort);
state.molecular.commandWaiters.delete(wake);
queued.completionWaiters.delete(wake);
};
const finish = () => {
cleanup();
resolve(void 0);
};
const wake = () => {
if (queued.completion != null || queued.cancelRequested) {
finish();
}
};
const abort = () => {
cleanup();
reject(
signal.reason instanceof Error ? signal.reason : new Error("The Structure command result wait was aborted")
);
};
const timer = setTimeout(finish, timeoutMs);
state.molecular.commandWaiters.add(wake);
queued.completionWaiters.add(wake);
signal.addEventListener("abort", abort, { once: true });
if (signal.aborted) {
abort();
}
});
signal.throwIfAborted();
}
return {
structuredContent: {
cancelRequested: queued.cancelRequested,
...queued.completion == null ? { completed: false } : { completed: true, result: queued.completion }
}
};
}
function completeStructureCommand({ state, command }) {
if (typeof command.commandId !== "string" || !UUID.test(command.commandId) || typeof command.applied !== "boolean" || typeof command.message !== "string" || command.message.length === 0 || command.message.length > 4096 || command.state != null && !isRecord2(command.state)) {
fail3("INVALID_REQUEST", "The Structure command completion is invalid");
}
const queued = state.molecular.commands.get(command.commandId);
if (queued == null) {
fail3("NOT_FOUND", "The Structure process does not own that viewer command");
}
const result = {
applied: command.applied,
message: command.message,
...command.state == null ? {} : { state: command.state }
};
let serialized;
try {
serialized = JSON.stringify(result);
} catch {
fail3(
"INVALID_REQUEST",
"The Structure command completion cannot be serialized"
);
}
if (Buffer2.byteLength(serialized, "utf8") > MAX_SOURCE_RANGE_BYTES) {
fail3(
"RESOURCE_EXHAUSTED",
"The Structure command completion exceeds its budget"
);
}
if (queued.completion != null) {
if (JSON.stringify(queued.completion) !== serialized) {
fail3(
"CONFLICT",
"The Structure command already has a different terminal result"
);
}
return {
structuredContent: {
completed: true,
replayed: true,
result: queued.completion
}
};
}
queued.completion = result;
for (const wake of queued.completionWaiters) {
wake();
}
return { structuredContent: { completed: true, replayed: false, result } };
}
async function hashVerifiedStructureProjectRange({
digest,
grant,
logicalSessionId,
offset,
readSource,
signal
}) {
if (offset >= grant.sourceIdentity.sizeBytes) {
return;
}
signal.throwIfAborted();
const remaining = grant.sourceIdentity.sizeBytes - offset;
const length = Number(
remaining < BigInt(MAX_SOURCE_RANGE_BYTES) ? remaining : BigInt(MAX_SOURCE_RANGE_BYTES)
);
const chunk = await readSource({
grant,
logicalSessionId,
offset,
length,
signal
});
if (chunk.bytes.byteLength === 0 || chunk.bytes.byteLength > length || chunk.eof && offset + BigInt(chunk.bytes.byteLength) !== grant.sourceIdentity.sizeBytes) {
fail3(
"SOURCE_CHANGED",
"The Structure source changed during project verification"
);
}
digest.update(chunk.bytes);
await hashVerifiedStructureProjectRange({
digest,
grant,
logicalSessionId,
offset: offset + BigInt(chunk.bytes.byteLength),
readSource,
signal
});
}
async function verifiedStructureProjectSource({
logicalSessionId,
state,
grant,
format,
relativePath,
readSource,
signal
}) {
if (!isSafeProjectRelativePath(relativePath) || grant.sourceIdentity.sizeBytes > BigInt(Number.MAX_SAFE_INTEGER) || (grant.sourceSizePolicy ?? grant.sourceIdentity.sizePolicy) === "bounded-unknown") {
return null;
}
const descriptor = {
byteLength: Number(grant.sourceIdentity.sizeBytes),
format,
relativePath
};
const sourceIntegrity = verifiedStructureWorkspaceIntegrity(
grant.sourceIdentity
);
if (sourceIntegrity != null) {
return { ...descriptor, sourceIntegrity };
}
if (grant.sourceIdentity.sizeBytes > BigInt(MAX_PROJECT_HASH_BYTES) || (grant.sourceAccessPattern ?? grant.sourceIdentity.accessPattern) === "forward-only") {
return null;
}
let sha256 = state.molecular.projectDigests.get(grant.grantId);
if (sha256 == null) {
const digest = createHash2("sha256");
await hashVerifiedStructureProjectRange({
digest,
grant,
logicalSessionId,
offset: 0n,
readSource,
signal
});
sha256 = digest.digest("hex");
state.molecular.projectDigests.set(grant.grantId, sha256);
}
return { ...descriptor, sha256 };
}
async function getStructureProjectContext({
logicalSessionId,
state,
grant,
command,
readSource,
signal
}) {
signal.throwIfAborted();
if (!isSafeProjectRelativePath(command.primaryRelativePath) || !isStringArray(command.objectIds) || !isStringArray(command.volumeIds) || command.objectIds.length > MAX_PROJECT_DEPENDENCIES || command.volumeIds.length > MAX_PROJECT_DEPENDENCIES || command.commandId != null && (typeof command.commandId !== "string" || !UUID.test(command.commandId))) {
fail3("INVALID_REQUEST", "The Structure project context request is invalid");
}
const unavailable = {
structuredContent: {
available: false,
message: "The host has not exposed the verified file identity or companion authority required to checkpoint this Structure source."
}
};
const primary = await verifiedStructureProjectSource({
logicalSessionId,
state,
grant,
format: state.molecular.format,
relativePath: command.primaryRelativePath,
readSource,
signal
});
if (primary == null) {
return unavailable;
}
const objectIds = new Set(command.objectIds);
const projects = [...state.molecular.trajectoryProjects.values()].filter(
(project) => objectIds.has(project.objectId)
);
const secondaryStructures = [...state.molecular.structureProjects.entries()].filter(([objectId]) => objectIds.has(objectId)).map(([objectId, source]) => ({ kind: "structure", objectId, source }));
if (objectIds.size > projects.length + secondaryStructures.length + 1) {
return unavailable;
}
const volumeIds = new Set(command.volumeIds);
const volumeSources = [...state.molecular.volumes.values()].flatMap(
(volume) => {
const objectId = volume.objectId;
return typeof objectId === "string" && volumeIds.has(objectId) ? [
{
kind: "volume",
objectId,
source: {
format: volume.index.format,
grant: volume.grant,
relativePath: volume.relativePath ?? "",
resourceUri: volume.resourceUri
}
}
] : [];
}
);
if (volumeSources.length !== volumeIds.size) {
return unavailable;
}
const projectSources = [
...secondaryStructures,
...volumeSources,
...projects.flatMap((project) => [
{
kind: "trajectory-topology",
objectId: project.objectId,
source: project.topology
},
{
kind: "trajectory-coordinates",
objectId: project.objectId,
source: project.coordinates
}
])
];
const initialDependencies = Promise.resolve([]);
const dependencies = await projectSources.reduce(
async (pending, { kind, objectId, source }) => {
const previous = await pending;
if (previous == null) {
return null;
}
signal.throwIfAborted();
if (!isRecord2(source)) {
fail3("INVALID_REQUEST", "The Structure trajectory source is invalid");
}
const descriptor = await verifiedStructureProjectSource({
logicalSessionId,
state,
grant: source.grant,
format: source.format,
relativePath: source.relativePath,
readSource,
signal
});
return descriptor == null ? null : [
...previous,
{ ...descriptor, id: `${objectId}:${kind}`, kind, objectId }
];
},
initialDependencies
);
if (dependencies == null) {
return unavailable;
}
return {
structuredContent: { available: true, dependencies, primary }
};
}
async function resolveStructureLiveProjectCheckpoint(input) {
const checkpoint = input.command.checkpoint;
if (!isRecord2(checkpoint) || checkpoint.kind !== "openai.structure-viewer.live-project-checkpoint" || checkpoint.version !== 1 || typeof checkpoint.sessionId !== "string" || !UUID.test(checkpoint.sessionId) || typeof checkpoint.presentationToken !== "string" || !UUID.test(checkpoint.presentationToken) || typeof checkpoint.commandRevision !== "number" || !Number.isSafeInteger(checkpoint.commandRevision) || checkpoint.commandRevision < 0 || !isRecord2(checkpoint.manifest) || checkpoint.manifest.kind !== "openai.structure-viewer.project" || checkpoint.manifest.version !== 1 || !isRecord2(checkpoint.manifest.primary) || !isSafeProjectRelativePath(checkpoint.manifest.primary.relativePath) || !Array.isArray(checkpoint.manifest.dependencies) || checkpoint.manifest.dependencies.length > MAX_PROJECT_DEPENDENCIES) {
fail3("INVALID_REQUEST", "The Structure live project checkpoint is invalid");
}
let serialized;
try {
serialized = JSON.stringify(checkpoint.manifest);
} catch {
fail3(
"INVALID_REQUEST",
"The Structure project checkpoint cannot be serialized"
);
}
if (Buffer2.byteLength(serialized, "utf8") > MAX_PROJECT_MANIFEST_BYTES) {
fail3(
"RESOURCE_EXHAUSTED",
"The Structure project checkpoint exceeds its bounded manifest"
);
}
const checkpointDependencies = checkpoint.manifest.dependencies;
const dependencyIds = /* @__PURE__ */ new Set();
const trajectoryObjectIds = /* @__PURE__ */ new Set();
const volumeObjectIds = /* @__PURE__ */ new Set();
const structureObjectIds = /* @__PURE__ */ new Set();
let volumeRestorations = Promise.resolve();
for (const dependency of checkpointDependencies) {
if (!isRecord2(dependency) || !isOpaqueIdentity(dependency.id) || !isOpaqueIdentity(dependency.objectId) || !isSafeProjectRelativePath(dependency.relativePath) || dependencyIds.has(dependency.id)) {
fail3(
"INVALID_REQUEST",
"The Structure project dependency is invalid or duplicated"
);
}
dependencyIds.add(dependency.id);
if (dependency.kind !== "trajectory-topology" && dependency.kind !== "trajectory-coordinates" && dependency.kind !== "volume" && dependency.kind !== "structure") {
return {
structuredContent: {
available: true,
restorable: false,
repairPlan: [
{
code: "unsupported",
dependencyId: dependency.id,
label: dependency.relativePath,
message: "The host has not granted access to this Structure project companion."
}
]
}
};
}
if (dependency.kind === "volume") {
volumeObjectIds.add(dependency.objectId);
} else if (dependency.kind === "structure") {
structureObjectIds.add(dependency.objectId);
} else {
trajectoryObjectIds.add(dependency.objectId);
}
}
for (const dependency of checkpointDependencies) {
if (!isRecord2(dependency) || dependency.kind !== "volume" && dependency.kind !== "structure") {
continue;
}
const authorized = dependency.kind === "volume" ? input.command.volumeResources : input.command.structureResources;
const resource = Array.isArray(authorized) ? authorized.find(
(candidate) => isRecord2(candidate) && candidate.id === dependency.id
) : void 0;
if (!isRecord2(resource) || !isStructureProjectResourceUri(resource.resourceUri) || typeof dependency.relativePath !== "string" || resource.name !== dependency.relativePath.split("/").at(-1) || typeof dependency.format !== "string") {
return {
structuredContent: {
available: true,
restorable: false,
repairPlan: [
{
code: "missing",
dependencyId: dependency.id,
label: dependency.relativePath,
message: "The host has not restored this approved Structure companion."
}
]
}
};
}
const sealedGrants = dependency.kind === "volume" ? input.command.volumeSourceGrants : input.command.structureSourceGrants;
const sealed = Array.isArray(sealedGrants) ? sealedGrants.find(
(candidate) => isRecord2(candidate) && candidate.resourceUri === resource.resourceUri
) : void 0;
const fallbackGrant = dependency.kind === "volume" ? input.command.volumeSourceGrant : input.command.structureSourceGrant;
const grant = validateSourceGrant({
grant: isRecord2(sealed) && sealed.grant != null ? sealed.grant : fallbackGrant,
identity: input.identity,
logicalSessionId: input.logicalSessionId,
now: input.now()
});
if (dependency.kind === "volume") {
volumeRestorations = volumeRestorations.then(
() => indexStructureVolume({
...input,
command: {
resourceUri: resource.resourceUri,
relativePath: dependency.relativePath,
format: dependency.format,
volumeSourceGrant: grant
}
})
).then(() => {
const restored = input.state.molecular.volumes.get(
resource.resourceUri
);
if (restored != null && typeof dependency.objectId === "string") {
restored.objectId = dependency.objectId;
}
});
} else if (typeof dependency.objectId === "string") {
input.state.molecular.structureProjects.set(dependency.objectId, {
format: dependency.format,
grant,
relativePath: dependency.relativePath,
resourceUri: resource.resourceUri
});
}
}
await volumeRestorations;
for (const objectId of trajectoryObjectIds) {
if (input.state.molecular.trajectoryProjects.has(objectId)) {
continue;
}
const topology = checkpointDependencies.find(
(dependency) => isRecord2(dependency) && dependency.objectId === objectId && dependency.kind === "trajectory-topology"
);
const coordinates = checkpointDependencies.find(
(dependency) => isRecord2(dependency) && dependency.objectId === objectId && dependency.kind === "trajectory-coordinates"
);
const authorizedResources = input.command.trajectoryResources;
if (!isRecord2(topology) || !isRecord2(coordinates) || !Array.isArray(authorizedResources)) {
return {
structuredContent: {
available: true,
restorable: false,
repairPlan: [
{
code: "missing",
dependencyId: `${objectId}:trajectory-coordinates`,
label: isRecord2(coordinates) && typeof coordinates.relativePath === "string" ? coordinates.relativePath : objectId,
message: "The host has not restored both authorized molecular trajectory sources."
}
]
}
};
}
const topologyResource = authorizedResources.find(
(resource) => isRecord2(resource) && resource.id === topology.id
);
const coordinateResource = authorizedResources.find(
(resource) => isRecord2(resource) && resource.id === coordinates.id
);
if (!isRecord2(topologyResource) || !isRecord2(coordinateResource) || !isStructureProjectResourceUri(topologyResource.resourceUri) || !isStructureProjectResourceUri(coordinateResource.resourceUri) || typeof topologyResource.name !== "string" || typeof coordinateResource.name !== "string" || typeof topology.relativePath !== "string" || typeof coordinates.relativePath !== "string" || topologyResource.name !== topology.relativePath.split("/").at(-1) || coordinateResource.name !== coordinates.relativePath.split("/").at(-1) || typeof topology.format !== "string" || typeof coordinates.format !== "string") {
fail3(
"PERMISSION_DENIED",
"The restored trajectory resource is not host-authorized"
);
}
rememberStructureTrajectoryProject({
...input,
operation: "control_viewer",
command: {
action: "load_trajectory",
alignment: "none",
objectId,
coordinates: {
encoding: "binary",
name: coordinateResource.name,
resourceUri: coordinateResource.resourceUri
},
coordinatesFormat: coordinates.format,
topology: {
encoding: "text",
name: topologyResource.name,
resourceUri: topologyResource.resourceUri
},
topologyFormat: topology.format,
trajectorySourceGrant: input.command.trajectorySourceGrant,
trajectoryRelativePath: coordinates.relativePath,
topologyRelativePath: topology.relativePath,
...input.command.topologySourceGrant == null ? {} : { topologySourceGrant: input.command.topologySourceGrant }
}
});
}
const context = await getStructureProjectContext({
...input,
command: {
objectIds: [...trajectoryObjectIds, ...structureObjectIds],
volumeIds: [...volumeObjectIds],
primaryRelativePath: checkpoint.manifest.primary.relativePath
}
});
if (context.structuredContent.available !== true) {
return context;
}
const currentPrimary = context.structuredContent.primary;
const expectedPrimary = checkpoint.manifest.primary;
if (!isRecord2(currentPrimary) || currentPrimary.byteLength !== expectedPrimary.byteLength || currentPrimary.format !== expectedPrimary.format || currentPrimary.relativePath !== expectedPrimary.relativePath || currentPrimary.sha256 !== expectedPrimary.sha256 || !sameVerifiedStructureWorkspaceIntegrity(
currentPrimary.sourceIntegrity,
expectedPrimary.sourceIntegrity
)) {
return {
structuredContent: {
available: true,
restorable: false,
repairPlan: [
{
code: "changed",
dependencyId: "primary",
label: expectedPrimary.relativePath,
message: "The approved Structure source no longer matches the checkpointed project."
}
]
}
};
}
if (!Array.isArray(context.structuredContent.dependencies)) {
fail3(
"INVALID_REQUEST",
"The verified Structure project dependency graph is invalid"
);
}
const currentDependencies = new Map(
context.structuredContent.dependencies.filter(isRecord2).map((dependency) => [dependency.id, dependency])
);
if (currentDependencies.size !== checkpointDependencies.length) {
return {
structuredContent: {
available: true,
restorable: false,
repairPlan: [
{
code: "missing",
dependencyId: "trajectory",
label: "Molecular trajectory",
message: "The approved trajectory dependency graph is incomplete."
}
]
}
};
}
const resources = [];
for (const dependency of checkpointDependencies) {
if (!isRecord2(dependency)) {
fail3("INVALID_REQUEST", "The Structure project dependency is invalid");
}
const current = currentDependencies.get(dependency.id);
const objectId = typeof dependency.objectId === "string" ? dependency.objectId : void 0;
const project = objectId == null ? void 0 : input.state.molecular.trajectoryProjects.get(objectId);
const volume = [...input.state.molecular.volumes.values()].find(
(candidate) => candidate.objectId === objectId
);
let source;
if (dependency.kind === "trajectory-topology") {
source = project?.topology;
} else if (dependency.kind === "trajectory-coordinates") {
source = project?.coordinates;
} else if (dependency.kind === "structure" && objectId != null) {
source = input.state.molecular.structureProjects.get(objectId);
} else if (volume != null) {
source = {
format: volume.index.format,
grant: volume.grant,
relativePath: volume.relativePath ?? "",
resourceUri: volume.resourceUri
};
}
if (!isRecord2(current) || source == null || current.byteLength !== dependency.byteLength || current.format !== dependency.format || current.id !== dependency.id || current.kind !== dependency.kind || current.objectId !== dependency.objectId || current.relativePath !== dependency.relativePath || current.sha256 !== dependency.sha256 || !sameVerifiedStructureWorkspaceIntegrity(
current.sourceIntegrity,
dependency.sourceIntegrity
)) {
return {
structuredContent: {
available: true,
restorable: false,
repairPlan: [
{
code: "changed",
dependencyId: dependency.id,
label: dependency.relativePath,
message: "The approved trajectory source no longer matches the checkpointed project."
}
]
}
};
}
resources.push({
id: dependency.id,
name: source.relativePath.split("/").at(-1) ?? source.relativePath,
resourceUri: source.resourceUri,
format: source.format,
sourceRevision: source.grant.sourceRevision,
sourceSizeBytesDecimal: source.grant.sourceIdentity.sizeBytes.toString()
});
}
return {
structuredContent: {
available: true,
restorable: true,
manifest: checkpoint.manifest,
dependencies: resources
}
};
}
async function executeStructureArtifactOperation({
operation,
logicalSessionId,
state,
sourceGrant,
command,
identity,
writeArtifact,
artifactTransactions,
now,
signal
}) {
signal.throwIfAborted();
const suppliedGrant = validateStructureDestinationGrant({
grant: command.destinationGrant,
sourceGrant,
identity,
logicalSessionId,
now: now()
});
if (operation === "export/begin") {
if (!isOpaqueIdentity(command.idempotencyKey)) {
fail3(
"INVALID_REQUEST",
"The Structure artifact idempotency key is invalid"
);
}
if (artifactTransactions.size >= MAX_ARTIFACT_TRANSACTIONS) {
for (const [transactionId, transaction2] of artifactTransactions) {
if (transaction2.state === "published") {
artifactTransactions.delete(transactionId);
break;
}
}
}
if (artifactTransactions.size >= MAX_ARTIFACT_TRANSACTIONS) {
fail3(
"RESOURCE_EXHAUSTED",
"The Structure artifact transaction budget is exhausted"
);
}
const result2 = await writeArtifact({
logicalSessionId,
operation: "begin",
payload: {
destinationGrantId: suppliedGrant.destinationGrantId,
idempotencyKey: command.idempotencyKey
},
signal
});
validateStructureArtifactHostResult(result2);
const existing = artifactTransactions.get(result2.transactionId);
if (existing == null) {
artifactTransactions.set(result2.transactionId, {
grant: suppliedGrant,
logicalSessionId,
sourceRevision: sourceGrant.sourceRevision,
artifactKind: suppliedGrant.artifactKind,
collisionPolicy: suppliedGrant.collisionPolicy,
publicationId: result2.publicationId,
members: /* @__PURE__ */ new Map(),
state: result2.state
});
} else {
assertStructureArtifactBinding({
transaction: existing,
grant: suppliedGrant,
logicalSessionId,
sourceRevision: sourceGrant.sourceRevision
});
}
return {
structuredContent: {
...result2,
viewerSessionId: logicalSessionId,
sourceRevision: sourceGrant.sourceRevision
}
};
}
if (!isOpaqueIdentity(command.transactionId)) {
fail3(
"INVALID_REQUEST",
"The Structure artifact transaction identity is invalid"
);
}
const transaction = artifactTransactions.get(command.transactionId);
if (transaction == null) {
fail3(
"NOT_FOUND",
"The Structure artifact transaction is not owned by this session"
);
}
assertStructureArtifactBinding({
transaction,
grant: suppliedGrant,
logicalSessionId,
sourceRevision: sourceGrant.sourceRevision
});
const originalGrant = transaction.grant;
if (!isRecord2(originalGrant)) {
fail3(
"PERMISSION_DENIED",
"The original Structure destination grant is unavailable"
);
}
if (operation === "export/append") {
if (!(command.bytes instanceof Uint8Array) || command.bytes.byteLength === 0 || command.bytes.byteLength > MAX_ARTIFACT_CHUNK_BYTES) {
fail3(
"RESOURCE_EXHAUSTED",
"The Structure artifact chunk exceeds its host budget"
);
}
if (typeof command.memberName !== "string" || command.memberName.length > 1024 || !ARTIFACT_MEMBER_NAME.test(command.memberName) || command.memberName.split("/").some((component) => component === "." || component === "..") || typeof command.role !== "string" || !ARTIFACT_MEMBER_ROLES.has(command.role) || typeof command.offsetDecimal !== "string" || !DECIMAL2.test(command.offsetDecimal) || !isOpaqueIdentity(command.requestId)) {
fail3(
"INVALID_REQUEST",
"The Structure artifact member or chunk identity is invalid"
);
}
if (command.expectedChunkDigest != null && (typeof command.expectedChunkDigest !== "string" || !/^sha256:[a-f0-9]{64}$/u.test(command.expectedChunkDigest))) {
fail3(
"INVALID_REQUEST",
"The Structure artifact chunk checksum is invalid"
);
}
const result2 = await writeArtifact({
logicalSessionId,
operation: "append",
payload: {
destinationGrantId: originalGrant.destinationGrantId,
transactionId: command.transactionId,
memberName: command.memberName,
role: command.role,
offsetDecimal: command.offsetDecimal,
bytes: command.bytes,
requestId: command.requestId,
...command.expectedChunkDigest == null ? {} : { expectedChunkDigest: command.expectedChunkDigest }
},
signal
});
validateStructureArtifactHostResult(result2, command.transactionId);
if (transaction.members instanceof Map) {
transaction.members.set(command.memberName, command.role);
}
transaction.state = result2.state;
return {
structuredContent: {
...result2,
viewerSessionId: logicalSessionId,
sourceRevision: sourceGrant.sourceRevision
}
};
}
if (operation === "export/abort") {
const result2 = await writeArtifact({
logicalSessionId,
operation: "abort",
payload: {
destinationGrantId: originalGrant.destinationGrantId,
transactionId: command.transactionId
},
signal
});
if (result2.transactionId !== command.transactionId || result2.aborted !== true) {
fail3(
"PERMISSION_DENIED",
"The host did not abort the approved Structure transaction"
);
}
artifactTransactions.delete(command.transactionId);
return {
structuredContent: {
transactionId: command.transactionId,
aborted: true,
viewerSessionId: logicalSessionId,
sourceRevision: sourceGrant.sourceRevision
}
};
}
if (operation === "export/resume") {
const result2 = await writeArtifact({
logicalSessionId,
operation: "resume",
payload: {
destinationGrantId: originalGrant.destinationGrantId,
transactionId: command.transactionId
},
signal
});
validateStructureArtifactHostResult(result2, command.transactionId);
transaction.state = result2.state;
return {
structuredContent: {
...result2,
viewerSessionId: logicalSessionId,
sourceRevision: sourceGrant.sourceRevision
}
};
}
const result = await writeArtifact({
logicalSessionId,
operation: "commit",
payload: {
destinationGrantId: originalGrant.destinationGrantId,
transactionId: command.transactionId,
sources: [
{
safeSourceId: sourceGrant.sourceIdentity.fileId,
sourceRevision: sourceGrant.sourceRevision,
identityStrength: "verified-file-identity",
sizeBytesDecimal: sourceGrant.sourceIdentity.sizeBytes.toString(),
format: state.molecular.format,
parser: { name: "codex-scientific-structure-viewer", version: "1" },
companions: []
}
],
exactness: "exact",
evidenceClass: "computed",
software: [{ name: "codex-scientific-structure-viewer", version: "1" }],
coordinateConventions: ["cartesian-angstrom", "source-atom-identity"],
publication: transaction.members instanceof Map && transaction.members.size > 1 ? "manifest-pointer" : "single-file"
},
signal
});
validateStructureArtifactHostResult(result, command.transactionId);
if (result.state !== "published" || !isRecord2(result.manifest) || result.manifest.family !== "structure" || result.manifest.publicationId !== result.publicationId || result.manifest.artifactKind !== transaction.artifactKind || !Array.isArray(result.manifest.sources) || result.manifest.sources.length === 0 || result.manifest.sources.some(
(source) => !isRecord2(source) || source.sourceRevision !== sourceGrant.sourceRevision
)) {
fail3(
"CHECKSUM_MISMATCH",
"The Structure artifact manifest does not match its authorized source"
);
}
transaction.state = "published";
return {
structuredContent: {
...result,
viewerSessionId: logicalSessionId,
sourceRevision: sourceGrant.sourceRevision
}
};
}
function validateStructureDestinationGrant({
grant,
sourceGrant,
identity,
logicalSessionId,
now
}) {
if (!isRecord2(grant) || grant.family !== "structure" || grant.logicalSessionId !== logicalSessionId || grant.backendInstanceId !== identity.backendInstanceId || grant.backendGeneration !== identity.backendGeneration || grant.revocationEpoch !== identity.revocationEpoch || grant.sourceRevision !== sourceGrant.sourceRevision || !isOpaqueIdentity(grant.grantId) || !isOpaqueIdentity(grant.destinationGrantId) || !isOpaqueIdentity(grant.destinationIdentity) || typeof grant.artifactKind !== "string" || grant.artifactKind.length === 0 || grant.artifactKind.length > 128 || !isStringArray(grant.approvedArtifactKinds) || !grant.approvedArtifactKinds.includes(grant.artifactKind) || !isStringArray(grant.operations) || !grant.operations.includes("stage-derived-artifact") || !grant.operations.includes("commit-artifact-set") || !grant.operations.includes("abort-write") || grant.collisionPolicy !== "fail" && grant.collisionPolicy !== "next-version" || !Number.isSafeInteger(grant.issuedAtMs) || !Number.isSafeInteger(grant.expiresAtMs) || grant.issuedAtMs > now || grant.expiresAtMs <= now) {
fail3(
"PERMISSION_DENIED",
"The Structure artifact destination grant is not authorized"
);
}
for (const field of [
"accountId",
"organizationId",
"hostId",
"workspaceId"
]) {
if (typeof sourceGrant[field] === "string" && grant[field] !== sourceGrant[field]) {
fail3(
"PERMISSION_DENIED",
"The Structure artifact destination belongs to another scope"
);
}
}
return grant;
}
function assertStructureArtifactBinding({
transaction,
grant,
logicalSessionId,
sourceRevision
}) {
const originalGrant = transaction.grant;
if (!isRecord2(originalGrant) || originalGrant.grantId !== grant.grantId || originalGrant.destinationGrantId !== grant.destinationGrantId || originalGrant.destinationIdentity !== grant.destinationIdentity || transaction.logicalSessionId !== logicalSessionId || transaction.sourceRevision !== sourceRevision || transaction.artifactKind !== grant.artifactKind || transaction.collisionPolicy !== grant.collisionPolicy) {
fail3(
"PERMISSION_DENIED",
"The Structure artifact transaction belongs to another destination"
);
}
}
function validateStructureArtifactHostResult(result, transactionId) {
if (!isRecord2(result) || !isOpaqueIdentity(result.transactionId) || !isOpaqueIdentity(result.publicationId) || typeof result.state !== "string" || !["reserved", "staging", "validating", "publishing", "published"].includes(
result.state
) || typeof result.bytesWrittenDecimal !== "string" || !DECIMAL2.test(result.bytesWrittenDecimal) || transactionId != null && result.transactionId !== transactionId) {
fail3(
"PERMISSION_DENIED",
"The host returned an invalid Structure artifact transaction"
);
}
}
async function openStructure({
sessions,
logicalSessionId,
grant,
command,
readSource,
signal,
exposeInitialGeometry
}) {
if (sessions.size >= MAX_SESSIONS && !sessions.has(logicalSessionId)) {
fail3("RESOURCE_EXHAUSTED", "The Structure session budget is exhausted");
}
const physicalSizeBytes = grant.sourceIdentity.sizeBytes;
if (physicalSizeBytes <= 0n) {
fail3("MALFORMED_STRUCTURE", "The authorized Structure source is empty");
}
const previewLength = Number(
physicalSizeBytes < BigInt(PREVIEW_BYTES) ? physicalSizeBytes : BigInt(PREVIEW_BYTES)
);
const physicalPreview = await readSource({
grant,
logicalSessionId,
offset: 0n,
length: previewLength,
signal
});
signal.throwIfAborted();
const compressed = physicalPreview.bytes.byteLength >= 2 && physicalPreview.bytes[0] === 31 && physicalPreview.bytes[1] === 139 ? createScientificStructureCompressedByteSource({
sizeBytes: physicalSizeBytes,
sourceRevision: grant.sourceRevision,
preview: physicalPreview.bytes,
readCompressedRange: ({ offset, length, signal: signal2 }) => readSource({
grant,
logicalSessionId,
offset,
length,
signal: signal2
})
}) : void 0;
const preview = compressed == null ? physicalPreview : await compressed.readRange({
offset: 0n,
length: PREVIEW_BYTES,
signal
});
signal.throwIfAborted();
const sizeBytes = compressed?.sizeBytes ?? physicalSizeBytes;
const sourceAccessPattern = compressed == null ? grant.sourceAccessPattern ?? grant.sourceIdentity.accessPattern ?? "random-access" : "forward-only";
const sourceSizePolicy = compressed == null ? grant.sourceSizePolicy ?? grant.sourceIdentity.sizePolicy ?? "exact" : "bounded-unknown";
const format = detectStructureFormat(preview.bytes, command.formatHint);
const previous = sessions.get(logicalSessionId);
previous?.molecular?.compressedSource?.close();
const state = {
revision: previous?.revision ?? 0,
checkpoint: previous?.checkpoint,
molecular: {
sourceGrantId: grant.grantId,
sourceRevision: grant.sourceRevision,
sizeBytes,
...compressed == null ? {} : { compressedSource: compressed },
format,
atoms: /* @__PURE__ */ new Map(),
decoder: new TextDecoder("utf-8", { fatal: true }),
evicted: false,
model: 1,
headers: [],
mmcifBlockStart: 0n,
mmcifAtomBlocks: /* @__PURE__ */ new Map(),
mmcifMetadata: {
chemicalComponentTypes: /* @__PURE__ */ new Map(),
entityTypes: /* @__PURE__ */ new Map(),
polymerTypes: /* @__PURE__ */ new Map(),
polymerEntities: /* @__PURE__ */ new Set(),
entityMemberships: /* @__PURE__ */ new Map()
},
mmcifFraming: { atomRanges: [], scannedThrough: 0n },
mmcifTrustedRange: true,
pending: "",
scanOffset: 0n,
complete: false,
selectedAtomIds: /* @__PURE__ */ new Set(),
scene: { representation: "cartoon", visibility: true },
scenes: /* @__PURE__ */ new Map(),
history: [],
topologyAtomCounts: /* @__PURE__ */ new Map(),
trajectories: /* @__PURE__ */ new Map(),
extendedTrajectories: /* @__PURE__ */ new Map(),
trajectoryProjects: previous?.molecular?.sourceRevision === grant.sourceRevision ? previous.molecular.trajectoryProjects : /* @__PURE__ */ new Map(),
structureProjects: previous?.molecular?.sourceRevision === grant.sourceRevision ? previous.molecular.structureProjects : /* @__PURE__ */ new Map(),
volumes: previous?.molecular?.sourceRevision === grant.sourceRevision ? previous.molecular.volumes : /* @__PURE__ */ new Map(),
commands: previous?.molecular?.sourceRevision === grant.sourceRevision ? previous.molecular.commands : /* @__PURE__ */ new Map(),
commandWaiters: /* @__PURE__ */ new Set(),
projectDigests: previous?.molecular?.sourceRevision === grant.sourceRevision ? previous.molecular.projectDigests : /* @__PURE__ */ new Map()
}
};
appendStructureBytes(state.molecular, preview.bytes, 0n, preview.eof);
if (state.molecular.atoms.size === 0 && !hasStructureHeader(preview.bytes, format)) {
fail3(
"MALFORMED_STRUCTURE",
"The approved source contains no valid molecular header"
);
}
sessions.set(logicalSessionId, state);
return {
structuredContent: {
viewerReady: true,
viewerSessionId: logicalSessionId,
viewerCommandRevision: state.revision,
format,
sourceRevision: grant.sourceRevision,
...sourceSizePolicy === "exact" ? { sourceSizeBytesDecimal: sizeBytes.toString() } : { sourceSizeUpperBoundBytesDecimal: sizeBytes.toString() },
sourceAccessPattern,
sourceSizePolicy,
effectiveCapabilities: { sourceAccessPattern, sourceSizePolicy },
...exposeInitialGeometry || sourceAccessPattern === "forward-only" ? {
initialGeometry: {
bytes: preview.bytes,
eof: preview.eof,
offsetDecimal: "0",
sourceRevision: grant.sourceRevision
}
} : {},
indexedAtomCount: state.molecular.atoms.size,
complete: state.molecular.complete,
models: uniqueModels(state.molecular.atoms),
maxRangeBytes: MAX_SOURCE_RANGE_BYTES,
maxPageAtoms: MAX_RESULT_ATOMS,
...state.molecular.complete ? {} : { nextOffsetDecimal: state.molecular.scanOffset.toString() }
}
};
}
async function readStructureAtomPage({
logicalSessionId,
state,
grant,
command,
readSource,
signal
}) {
let offset = state.molecular.scanOffset;
if (command.offsetDecimal == null && state.molecular.format === "mmcif") {
offset = state.molecular.mmcifAtomRowStart ?? offset - BigInt(state.molecular.pendingByteLength ?? 0);
retainMmcifPageBoundary(state.molecular, offset);
}
if (command.offsetDecimal != null) {
offset = command.offsetDecimal === state.molecular.sizeBytes.toString() ? state.molecular.sizeBytes : parseOffset(command.offsetDecimal, state.molecular.sizeBytes);
}
if (offset === state.molecular.sizeBytes) {
return {
structuredContent: {
viewerSessionId: logicalSessionId,
viewerCommandRevision: state.revision,
sourceRevision: state.molecular.sourceRevision,
sourceSizeBytesDecimal: state.molecular.sizeBytes.toString(),
format: state.molecular.format,
offsetDecimal: offset.toString(),
atoms: [],
classificationMetadata: "unavailable",
complete: true
}
};
}
const limit = readPositive(
command.limit ?? MAX_RESULT_ATOMS,
MAX_RESULT_ATOMS,
"atom page limit"
);
const requested = readPositive(
command.length ?? PREVIEW_BYTES,
MAX_SOURCE_RANGE_BYTES,
"atom page range"
);
const remaining = state.molecular.sizeBytes - offset;
const length = Number(
remaining < BigInt(requested) ? remaining : BigInt(requested)
);
let chunk = await readSource({
grant,
logicalSessionId,
offset,
length,
signal
});
signal.throwIfAborted();
if (chunk.bytes.byteLength === 0 && !chunk.eof) {
fail3(
"MALFORMED_STRUCTURE",
"The authorized source returned an empty non-terminal molecular page"
);
}
const packetBoundary = state.molecular.format === "mmcif" ? state.molecular.mmcifFraming?.pageBoundaries?.get(offset) : void 0;
const unprovenPacketOffset = state.molecular.format === "mmcif" && packetBoundary == null && state.molecular.mmcifFraming?.atomRanges.some(
({ start, end, lineAligned }) => lineAligned === false && offset > start && offset <= end
);
if (unprovenPacketOffset)
return atomPageCursorRequired(logicalSessionId, state, offset);
let leadingPartialLine = false;
if (offset > 0n) {
const preceding = await readSource({
grant,
logicalSessionId,
offset: offset - 1n,
length: 1,
signal
});
signal.throwIfAborted();
if (preceding.bytes.byteLength !== 1) {
fail3(
"SOURCE_CHANGED",
"The molecular page boundary is no longer current"
);
}
leadingPartialLine = packetBoundary == null && preceding.bytes[0] !== 10 && preceding.bytes[0] !== 13;
}
let bytes = chunk.bytes;
let finalNewline = bytes.lastIndexOf(10);
while (!chunk.eof && finalNewline < 0) {
if (bytes.byteLength >= MAX_STRUCTURE_LINE_BYTES) {
fail3("RESOURCE_EXHAUSTED", "The molecular page exceeds its line budget");
}
const nextOffset2 = offset + BigInt(bytes.byteLength);
const nextRemaining = state.molecular.sizeBytes - nextOffset2;
if (nextRemaining <= 0n) {
fail3("SOURCE_CHANGED", "The molecular page ended before a line boundary");
}
const nextLength = Number(
nextRemaining < BigInt(requested) ? nextRemaining : BigInt(requested)
);
chunk = await readSource({
grant,
logicalSessionId,
offset: nextOffset2,
length: nextLength,
signal
});
signal.throwIfAborted();
if (chunk.bytes.byteLength === 0 && !chunk.eof) {
fail3("MALFORMED_STRUCTURE", "The molecular page continuation is empty");
}
if (bytes.byteLength + chunk.bytes.byteLength > MAX_STRUCTURE_LINE_BYTES) {
fail3("RESOURCE_EXHAUSTED", "The molecular page exceeds its line budget");
}
const combined = new Uint8Array(bytes.byteLength + chunk.bytes.byteLength);
combined.set(bytes);
combined.set(chunk.bytes, bytes.byteLength);
bytes = combined;
finalNewline = bytes.lastIndexOf(10);
}
let consumedBytes = chunk.eof ? bytes.byteLength : finalNewline + 1;
if (consumedBytes <= 0) {
fail3("MALFORMED_STRUCTURE", "The molecular page has no complete records");
}
const firstNewline = bytes.indexOf(10);
let firstRecord = 0;
if (leadingPartialLine) {
firstRecord = firstNewline < 0 ? consumedBytes : firstNewline + 1;
}
const pageBytes = bytes.subarray(firstRecord, consumedBytes);
const region = createRegionState(
state.molecular,
command.model,
offset + BigInt(firstRecord)
);
if (pageBytes.byteLength > 0) {
appendStructureBytes(
region,
pageBytes,
offset + BigInt(firstRecord),
chunk.eof
);
}
let pageReadBytes = bytes.byteLength;
while (region.mmcifAtomRowStart != null && region.mmcifAtomRowStart <= offset && (!region.mmcifComplexPackets || region.mmcifTrustedRange) && region.atoms.size === 0 && !chunk.eof) {
const nextOffset2 = region.scanOffset;
const nextRemaining = state.molecular.sizeBytes - nextOffset2;
const budget = Math.min(
MAX_STRUCTURE_LINE_BYTES - pageReadBytes,
requested - Number(nextOffset2 - offset)
);
if (budget <= 0) {
fail3(
"RESOURCE_EXHAUSTED",
"The molecular page exceeds its packet budget"
);
}
const nextLength = Math.min(requested, budget, Number(nextRemaining));
if (nextLength <= 0) {
fail3(
"SOURCE_CHANGED",
"The molecular page ended before its packet boundary"
);
}
chunk = await readSource({
grant,
logicalSessionId,
offset: nextOffset2,
length: nextLength,
signal
});
signal.throwIfAborted();
if (chunk.bytes.byteLength === 0 && !chunk.eof) {
fail3("MALFORMED_STRUCTURE", "The molecular page continuation is empty");
}
pageReadBytes += chunk.bytes.byteLength;
appendStructureBytes(region, chunk.bytes, nextOffset2, chunk.eof);
consumedBytes = Number(region.scanOffset - offset) - (region.pendingByteLength ?? 0);
}
if (region.evicted) {
fail3(
"RESOURCE_EXHAUSTED",
"The molecular page exceeds its resident atom budget"
);
}
if (region.mmcifComplexPackets && !region.mmcifTrustedRange) {
return atomPageCursorRequired(logicalSessionId, state, offset);
}
const packetLimit = offset + BigInt(requested);
const complexPackets = region.format === "mmcif" && (region.mmcifComplexPackets || region.mmcifFraming?.atomRanges.some(
({ start, end, lineAligned }) => lineAligned === false && start < region.scanOffset && end > offset
));
const allMatches = matchAtoms(region.atoms, command);
const matches = complexPackets ? allMatches.filter(
(atom) => (region.recordEndOffsets?.get(atom.atomId) ?? packetLimit + 1n) <= packetLimit
) : allMatches;
applyMmcifResidueMetadata(state.molecular);
const atoms = matches.slice(0, limit);
let nextOffset = region.mmcifAtomRowStart ?? offset + BigInt(consumedBytes);
let complete = chunk.eof;
if (complexPackets && nextOffset > packetLimit) {
let lastPacketEnd;
for (const end of region.recordEndOffsets?.values() ?? []) {
if (end > offset && end <= packetLimit && (lastPacketEnd == null || end > lastPacketEnd))
lastPacketEnd = end;
}
if (lastPacketEnd == null) {
fail3(
"RESOURCE_EXHAUSTED",
"An mmCIF packet exceeds the requested atom-page range"
);
}
nextOffset = lastPacketEnd;
complete = false;
}
if (matches.length >= limit) {
const lastAtom = atoms[atoms.length - 1];
const recordEnd = lastAtom == null ? void 0 : region.recordEndOffsets?.get(lastAtom.atomId);
if (recordEnd == null || recordEnd <= offset || recordEnd > nextOffset) {
fail3(
"MALFORMED_STRUCTURE",
"The molecular page has no safe continuation after its last atom"
);
}
complete = complete && recordEnd === nextOffset;
nextOffset = recordEnd;
}
if (!complete) retainMmcifPageBoundary(region, nextOffset);
return {
structuredContent: {
viewerSessionId: logicalSessionId,
viewerCommandRevision: state.revision,
sourceRevision: state.molecular.sourceRevision,
sourceSizeBytesDecimal: state.molecular.sizeBytes.toString(),
format: state.molecular.format,
offsetDecimal: offset.toString(),
atoms,
classificationMetadata: nativeClassificationMetadata(atoms),
complete,
...complete ? {} : { nextOffsetDecimal: nextOffset.toString() }
}
};
}
async function indexStructureTrajectory({
logicalSessionId,
state,
grant,
command,
readSource,
signal,
identity,
now
}) {
const trajectoryGrant = validateSourceGrant({
grant: command.trajectorySourceGrant,
identity,
logicalSessionId,
now: now()
});
const topologyGrant = command.topologySourceGrant == null ? grant : validateSourceGrant({
grant: command.topologySourceGrant,
identity,
logicalSessionId,
now: now()
});
const selectedModel = readPositive(
command.model ?? 1,
Number.MAX_SAFE_INTEGER,
"trajectory topology model"
);
const actualTopologyAtomCount = topologyGrant.grantId === grant.grantId && state.molecular.format === "pdb" ? await readStructureTopologyAtomCount({
grant,
logicalSessionId,
model: selectedModel,
readSource,
signal,
state
}) : await countScientificStructureNativeTopologyAtoms({
format: typeof command.topologyFormat === "string" ? command.topologyFormat : state.molecular.format,
model: selectedModel,
signal,
source: createScientificStructureNativeTrajectorySource({
grant: topologyGrant,
logicalSessionId,
readSource,
signal
})
});
const topologyAtomCount = command.topologyAtomCount == null ? actualTopologyAtomCount : readPositive(
command.topologyAtomCount,
1e6,
"trajectory topology atom count"
);
if (topologyAtomCount !== actualTopologyAtomCount) {
fail3(
"TOPOLOGY_MISMATCH",
"The trajectory atom count does not match the approved molecular model"
);
}
if (command.format !== "dcd") {
return indexExtendedStructureTrajectory({
logicalSessionId,
state,
trajectoryGrant,
topologyGrant,
topologyAtomCount,
command,
readSource,
signal
});
}
const index = await indexScientificStructureBackendTrajectory({
format: command.format,
grant: trajectoryGrant,
logicalSessionId,
readSource,
signal,
topologyAtomCount
});
if (!state.molecular.trajectories.has(trajectoryGrant.grantId) && state.molecular.trajectories.size >= MAX_TRAJECTORIES) {
fail3("RESOURCE_EXHAUSTED", "The Structure trajectory budget is exhausted");
}
state.molecular.trajectories.set(trajectoryGrant.grantId, index);
return {
structuredContent: {
viewerSessionId: logicalSessionId,
viewerCommandRevision: state.revision,
format: index.format,
sourceRevision: index.sourceRevision,
sourceSizeBytesDecimal: index.sourceSizeBytes.toString(),
frameCount: index.frameCount,
atomCount: index.atomCount,
complete: index.complete,
indexedThroughOffsetDecimal: index.indexedThroughOffset.toString()
}
};
}
async function readStructureTrajectory({
logicalSessionId,
state,
command,
readSource,
signal,
identity,
multiple,
now
}) {
const trajectoryGrant = validateSourceGrant({
grant: command.trajectorySourceGrant,
identity,
logicalSessionId,
now: now()
});
const index = state.molecular.trajectories.get(trajectoryGrant.grantId);
const extended = state.molecular.extendedTrajectories.get(
trajectoryGrant.grantId
);
if (extended != null) {
if (extended.index.sourceRevision !== trajectoryGrant.sourceRevision || extended.index.sourceSizeBytes !== trajectoryGrant.sourceIdentity.sizeBytes) {
fail3(
"SOURCE_CHANGED",
"The trajectory has not been indexed for its current source revision"
);
}
const result2 = await readScientificStructureNativeTrajectoryWindow({
command,
...extended,
multiple,
signal
});
return {
structuredContent: {
viewerSessionId: logicalSessionId,
viewerCommandRevision: state.revision,
sourceRevision: extended.index.sourceRevision,
sourceSizeBytesDecimal: extended.index.sourceSizeBytes.toString(),
format: extended.format,
...result2
}
};
}
if (index == null || index.sourceRevision !== trajectoryGrant.sourceRevision || index.sourceSizeBytes !== trajectoryGrant.sourceIdentity.sizeBytes) {
fail3(
"SOURCE_CHANGED",
"The trajectory has not been indexed for its current source revision"
);
}
const result = await readScientificStructureBackendTrajectoryFrames({
command,
grant: trajectoryGrant,
index,
logicalSessionId,
multiple,
readSource,
signal
});
return {
structuredContent: {
viewerSessionId: logicalSessionId,
viewerCommandRevision: state.revision,
sourceRevision: index.sourceRevision,
sourceSizeBytesDecimal: index.sourceSizeBytes.toString(),
format: index.format,
...result
}
};
}
async function readStructureTopologyPage(input) {
if (!isStructureProjectResourceUri(input.command.resourceUri) || typeof input.command.format !== "string") {
fail3("PERMISSION_DENIED", "The approved trajectory topology is invalid");
}
const topologyGrant = validateSourceGrant({
grant: input.command.topologySourceGrant,
identity: input.identity,
logicalSessionId: input.logicalSessionId,
now: input.now()
});
const offset = input.command.offsetDecimal ?? "0";
if (typeof offset !== "string" || !DECIMAL2.test(offset)) {
fail3("INVALID_REQUEST", "The approved topology page offset is invalid");
}
const result = await readScientificStructureNativeTopologyPage({
format: input.command.format,
offset: BigInt(offset),
...typeof input.command.atomOffset === "number" ? { atomOffset: input.command.atomOffset } : {},
...typeof input.command.limit === "number" ? { limit: input.command.limit } : {},
source: createScientificStructureNativeTrajectorySource({
grant: topologyGrant,
logicalSessionId: input.logicalSessionId,
readSource: input.readSource,
signal: input.signal
}),
signal: input.signal
});
const { nextOffset, offset: pageOffset, ...page } = result;
return {
structuredContent: {
viewerSessionId: input.logicalSessionId,
viewerCommandRevision: input.state.revision,
sourceRevision: topologyGrant.sourceRevision,
sourceSizeBytesDecimal: topologyGrant.sourceIdentity.sizeBytes.toString(),
format: input.command.format,
offsetDecimal: pageOffset.toString(),
...page,
...nextOffset == null ? {} : { nextOffsetDecimal: nextOffset.toString() }
}
};
}
async function indexExtendedStructureTrajectory(input) {
const requested = input.command.format === "nc" || input.command.format === "netcdf" ? "nctraj" : input.command.format;
if (requested !== "xtc" && requested !== "trr" && requested !== "nctraj" && requested !== "lammpstrj") {
fail3("UNSUPPORTED", "The approved trajectory format has no native codec");
}
if (!input.state.molecular.extendedTrajectories.has(
input.trajectoryGrant.grantId
) && input.state.molecular.extendedTrajectories.size + input.state.molecular.trajectories.size >= MAX_TRAJECTORIES) {
fail3("RESOURCE_EXHAUSTED", "The Structure trajectory budget is exhausted");
}
const source = createScientificStructureNativeTrajectorySource({
grant: input.trajectoryGrant,
logicalSessionId: input.logicalSessionId,
readSource: input.readSource,
signal: input.signal
});
const topologySource = createScientificStructureNativeTrajectorySource({
grant: input.topologyGrant,
logicalSessionId: input.logicalSessionId,
readSource: input.readSource,
signal: input.signal
});
const topology = {
atomIds: Array.from(
{ length: input.topologyAtomCount },
(_value, index2) => `${input.topologyGrant.sourceHandleId}:${index2 + 1}`
),
sourceDigest: topologySource.sourceDigest,
sourceRevision: input.topologyGrant.sourceRevision
};
const index = requested === "lammpstrj" ? await indexScientificStructureLammpsTrajectory({
source,
topology,
signal: input.signal
}) : await indexScientificStructureBinaryTrajectory({
budget: {
maxAtoms: 1e6,
maxDecodedFrameBytes: 32 * 1024 * 1024,
maxFrameBytes: 32n * 1024n * 1024n,
maxFrames: 65536,
maxRangeBytes: MAX_TOPOLOGY_RANGE_BYTES
},
format: requested,
source,
topology,
signal: input.signal
});
const extended = { format: requested, index, source, topology };
input.state.molecular.extendedTrajectories.set(
input.trajectoryGrant.grantId,
extended
);
return {
structuredContent: {
viewerSessionId: input.logicalSessionId,
viewerCommandRevision: input.state.revision,
format: requested,
sourceRevision: index.sourceRevision,
sourceSizeBytesDecimal: index.sourceSizeBytes.toString(),
frameCount: index.frameCount,
atomCount: index.atomCount,
complete: index.complete,
indexedThroughOffsetDecimal: index.indexedThroughOffset.toString()
}
};
}
async function indexStructureVolume(input) {
const volumeGrant = validateSourceGrant({
grant: input.command.volumeSourceGrant,
identity: input.identity,
logicalSessionId: input.logicalSessionId,
now: input.now()
});
if (!isStructureProjectResourceUri(input.command.resourceUri) || typeof input.command.format !== "string" || input.command.relativePath != null && !isSafeProjectRelativePath(input.command.relativePath) || volumeGrant.sourceIdentity.fileId === input.grant.sourceIdentity.fileId) {
fail3("PERMISSION_DENIED", "The molecular volume has no approved companion");
}
if (!input.state.molecular.volumes.has(input.command.resourceUri) && input.state.molecular.volumes.size >= MAX_PROJECT_DEPENDENCIES) {
fail3(
"RESOURCE_EXHAUSTED",
"The molecular volume companion budget is exhausted"
);
}
const index = await indexScientificStructureNativeVolume({
grant: volumeGrant,
logicalSessionId: input.logicalSessionId,
format: input.command.format,
readSource: input.readSource,
signal: input.signal
});
const previous = input.state.molecular.volumes.get(input.command.resourceUri);
if (previous != null && (previous.grant.grantId !== volumeGrant.grantId || previous.grant.sourceHandleId !== volumeGrant.sourceHandleId || previous.grant.sourceRevision !== volumeGrant.sourceRevision)) {
fail3("SOURCE_CHANGED", "The approved molecular volume source was replaced");
}
const relativePath = typeof input.command.relativePath === "string" ? input.command.relativePath : previous?.relativePath;
input.state.molecular.volumes.set(input.command.resourceUri, {
grant: volumeGrant,
index,
...previous?.objectId == null ? {} : { objectId: previous.objectId },
...relativePath == null ? {} : { relativePath },
resourceUri: input.command.resourceUri
});
const { sourceGrantId, sourceHandleId, ...metadata } = index;
void sourceGrantId;
void sourceHandleId;
return {
structuredContent: {
viewerCommandRevision: input.state.revision,
...metadata
}
};
}
async function readStructureVolume(input) {
if (!isStructureProjectResourceUri(input.command.resourceUri)) {
fail3("PERMISSION_DENIED", "The molecular volume has no approved resource");
}
const volume = input.state.molecular.volumes.get(input.command.resourceUri);
const volumeGrant = validateSourceGrant({
grant: input.command.volumeSourceGrant,
identity: input.identity,
logicalSessionId: input.logicalSessionId,
now: input.now()
});
if (volume == null || volume.grant.grantId !== volumeGrant.grantId || volume.grant.sourceHandleId !== volumeGrant.sourceHandleId || volume.grant.sourceRevision !== volumeGrant.sourceRevision) {
fail3("SOURCE_CHANGED", "The approved molecular volume source has changed");
}
const region = input.command.region;
if (region != null && (!isRecord2(region) || !isStructureVolumeAxis(region.start) || !isStructureVolumeAxis(region.size))) {
fail3("INVALID_REQUEST", "The molecular volume region is invalid");
}
const result = await readScientificStructureNativeVolumeTile({
grant: volumeGrant,
logicalSessionId: input.logicalSessionId,
index: volume.index,
...typeof input.command.offsetDecimal === "string" ? { offsetDecimal: input.command.offsetDecimal } : {},
...typeof input.command.length === "number" ? { length: input.command.length } : {},
...region == null ? {} : { region },
readSource: input.readSource,
signal: input.signal
});
return {
structuredContent: {
viewerCommandRevision: input.state.revision,
...result
}
};
}
function isStructureVolumeAxis(axis) {
return Array.isArray(axis) && axis.length === 3 && axis.every(Number.isSafeInteger);
}
async function readStructureTopologyAtomCount(input) {
const cached = input.state.molecular.topologyAtomCounts.get(input.model);
if (cached != null) {
return cached;
}
if (input.state.molecular.format !== "pdb") {
fail3(
"UNSUPPORTED",
"Trajectory indexing requires an independently verified PDB topology"
);
}
const accessPattern = input.grant.sourceAccessPattern ?? input.grant.sourceIdentity.accessPattern ?? "random-access";
if (input.state.molecular.compressedSource != null || accessPattern !== "random-access") {
fail3(
"UNSUPPORTED",
"A trajectory topology requires an authorized random-access source"
);
}
const topology = createRegionState(input.state.molecular, input.model);
const resumeIndexedModel = !input.state.molecular.evicted && input.state.molecular.model === input.model && [...input.state.molecular.atoms.values()].every(
(atom) => atom.model === input.model
);
let offset = resumeIndexedModel ? input.state.molecular.scanOffset : 0n;
let currentModel = resumeIndexedModel ? input.state.molecular.model : 1;
let atomCount = resumeIndexedModel ? input.state.molecular.atoms.size : 0;
let foundModel = resumeIndexedModel && atomCount > 0;
let complete = resumeIndexedModel && input.state.molecular.complete;
if (resumeIndexedModel) {
topology.pending = input.state.molecular.pending;
}
while (!complete && offset < input.state.molecular.sizeBytes) {
input.signal.throwIfAborted();
if (offset >= BigInt(MAX_TOPOLOGY_SCAN_BYTES)) {
fail3(
"RESOURCE_EXHAUSTED",
"The approved molecular topology exceeds its bounded model scan"
);
}
const remaining = input.state.molecular.sizeBytes - offset;
const budget = BigInt(MAX_TOPOLOGY_SCAN_BYTES) - offset;
const length = Number(
[BigInt(MAX_TOPOLOGY_RANGE_BYTES), remaining, budget].reduce(
(smallest, value) => value < smallest ? value : smallest
)
);
const chunk = await readStructureTrajectoryRange(input, offset, length);
input.signal.throwIfAborted();
let decoded;
try {
decoded = topology.decoder.decode(chunk, {
stream: offset + BigInt(chunk.byteLength) < input.state.molecular.sizeBytes
});
} catch {
fail3("MALFORMED_STRUCTURE", "The approved topology is not valid UTF-8");
}
const combined = topology.pending + decoded;
if (Buffer2.byteLength(combined, "utf8") > MAX_STRUCTURE_LINE_BYTES) {
fail3("RESOURCE_EXHAUSTED", "An approved topology record is too large");
}
const lines = combined.split(/\r?\n/u);
const eof = offset + BigInt(chunk.byteLength) === input.state.molecular.sizeBytes;
topology.pending = eof ? "" : lines.pop() ?? "";
for (const line of lines) {
if (line.startsWith("MODEL")) {
const nextModel = Number.parseInt(line.slice(10).trim(), 10);
if (!Number.isSafeInteger(nextModel) || nextModel <= 0) {
fail3("MALFORMED_STRUCTURE", "A molecular model identity is invalid");
}
if (foundModel && currentModel === input.model && atomCount > 0) {
complete = true;
break;
}
currentModel = nextModel;
topology.model = nextModel;
if (nextModel === input.model) {
foundModel = true;
}
continue;
}
if (line.startsWith("ENDMDL")) {
if (currentModel === input.model && foundModel) {
complete = true;
break;
}
continue;
}
if (currentModel === input.model && (line.startsWith("ATOM ") || line.startsWith("HETATM"))) {
foundModel = true;
parsePdbLine(topology, line);
atomCount += 1;
if (atomCount > 1e6) {
fail3(
"RESOURCE_EXHAUSTED",
"The approved topology has too many atoms"
);
}
}
}
offset += BigInt(chunk.byteLength);
if (eof) {
complete = true;
}
}
if (!complete || !foundModel || atomCount === 0) {
fail3("TOPOLOGY_MISMATCH", "The approved molecular model was not found");
}
if (input.state.molecular.topologyAtomCounts.size >= MAX_TRAJECTORIES) {
fail3("RESOURCE_EXHAUSTED", "The molecular topology cache is exhausted");
}
input.state.molecular.topologyAtomCounts.set(input.model, atomCount);
return atomCount;
}
async function indexScientificStructureBackendTrajectory(input) {
if (input.format !== "dcd") {
fail3(
"UNSUPPORTED",
"Only validated, range-indexed DCD trajectories are enabled in the Structure backend"
);
}
const sourceSizeBytes = input.grant.sourceIdentity.sizeBytes;
const header = await readStructureTrajectoryRange(input, 0n, 116);
const view = structureTrajectoryDataView(header);
let littleEndian = null;
if (view.getInt32(0, true) === 84) {
littleEndian = true;
} else if (view.getInt32(0, false) === 84) {
littleEndian = false;
}
if (littleEndian == null || header[4] !== 67 || header[5] !== 79 || header[6] !== 82 || header[7] !== 68 || view.getInt32(88, littleEndian) !== 84) {
fail3("MALFORMED_TRAJECTORY", "The DCD coordinate header is invalid");
}
const advertisedFrameCount = view.getInt32(8, littleEndian);
const titleBytes = view.getInt32(92, littleEndian);
const titleLineCount = view.getInt32(96, littleEndian);
if (advertisedFrameCount < 0 || titleBytes < 4 || titleBytes > MAX_SOURCE_RANGE_BYTES || (titleBytes - 4) % 80 !== 0 || titleLineCount < 0 || titleLineCount > Math.floor((MAX_SOURCE_RANGE_BYTES - 4) / 80)) {
fail3("MALFORMED_TRAJECTORY", "The DCD frame or title block is invalid");
}
if (view.getInt32(52, littleEndian) !== 0) {
fail3(
"UNSUPPORTED",
"A DCD fourth coordinate requires a separately bounded trajectory decoder"
);
}
const countedTitleBytes = 4 + titleLineCount * 80;
const titlePayloadCandidates = [countedTitleBytes];
if (countedTitleBytes !== titleBytes) {
titlePayloadCandidates.push(titleBytes);
}
let atomBlockOffset;
let matchingTitleRecord = false;
let matchingAtomRecord = false;
for (const titlePayloadBytes of titlePayloadCandidates) {
const titleEnd = 96n + BigInt(titlePayloadBytes);
if (titleEnd + 16n > sourceSizeBytes) {
continue;
}
const titleAndAtomBlock = titleEnd + 16n <= BigInt(header.byteLength) ? header.subarray(Number(titleEnd), Number(titleEnd) + 16) : await readStructureTrajectoryRange(input, titleEnd, 16);
const records = structureTrajectoryDataView(titleAndAtomBlock);
if (records.getInt32(0, littleEndian) !== titleBytes) {
continue;
}
matchingTitleRecord = true;
if (records.getInt32(4, littleEndian) !== 4 || records.getInt32(12, littleEndian) !== 4) {
continue;
}
matchingAtomRecord = true;
if (records.getInt32(8, littleEndian) === input.topologyAtomCount) {
if (atomBlockOffset != null) {
fail3(
"MALFORMED_TRAJECTORY",
"The DCD title record has ambiguous authorized atom-count boundaries"
);
}
atomBlockOffset = titleEnd + 4n;
}
}
if (atomBlockOffset == null) {
if (matchingAtomRecord) {
fail3(
"TOPOLOGY_MISMATCH",
"The DCD atom-count record does not match its authorized topology"
);
}
fail3(
"MALFORMED_TRAJECTORY",
matchingTitleRecord ? "The DCD atom-count record marker is invalid" : "The DCD title record marker is invalid"
);
}
const hasCell = view.getInt32(48, littleEndian) !== 0;
const axisBytes = input.topologyAtomCount * 4;
const firstFrameOffset = atomBlockOffset + 12n;
const frameBytes = BigInt((axisBytes + 8) * 3 + (hasCell ? 56 : 0));
const retainedFrameBytes = sourceSizeBytes - firstFrameOffset;
if (retainedFrameBytes < 0n || retainedFrameBytes % frameBytes !== 0n || retainedFrameBytes === 0n && advertisedFrameCount > 0) {
fail3(
"MALFORMED_TRAJECTORY",
"The retained DCD frames do not match the authorized source length"
);
}
const physicalFrameCount = retainedFrameBytes / frameBytes;
if (physicalFrameCount > 0x7fffffffn) {
fail3(
"RESOURCE_EXHAUSTED",
"The retained DCD frame count exceeds its bounded range"
);
}
const frameCount = Number(physicalFrameCount);
const index = {
format: "dcd",
atomCount: input.topologyAtomCount,
complete: true,
firstFrameOffset,
frameBytes,
frameCount,
hasCell,
indexedThroughOffset: sourceSizeBytes,
littleEndian,
saveInterval: view.getInt32(16, littleEndian),
sourceRevision: input.grant.sourceRevision,
sourceSizeBytes,
startStep: view.getInt32(12, littleEndian),
validatedFrames: /* @__PURE__ */ new Map()
};
if (frameCount > 0) {
await validateStructureDcdFrame(input, index, 0);
if (frameCount > 1) {
await validateStructureDcdFrame(input, index, frameCount - 1);
}
}
return index;
}
async function readScientificStructureBackendTrajectoryFrames(input) {
const first = input.command.frameIndex ?? input.command.start ?? 0;
if (typeof first !== "number" || !Number.isSafeInteger(first) || first < 0 || first >= input.index.frameCount) {
fail3("INVALID_REQUEST", "The requested trajectory frame is out of range");
}
const endExclusive = input.multiple ? input.command.endExclusive ?? first + 1 : first + 1;
const stride = input.command.stride ?? 1;
if (typeof endExclusive !== "number" || !Number.isSafeInteger(endExclusive) || endExclusive <= first || endExclusive > input.index.frameCount || typeof stride !== "number" || !Number.isSafeInteger(stride) || stride <= 0 || Math.ceil((endExclusive - first) / stride) > 64) {
fail3("RESOURCE_EXHAUSTED", "The requested trajectory window is unbounded");
}
const atomOffset = input.command.atomOffset ?? 0;
if (typeof atomOffset !== "number" || !Number.isSafeInteger(atomOffset) || atomOffset < 0 || atomOffset >= input.index.atomCount) {
fail3("INVALID_REQUEST", "The requested trajectory atom is out of range");
}
const atomCount = readPositive(
input.command.atomCount ?? Math.min(input.index.atomCount - atomOffset, MAX_RESULT_ATOMS),
MAX_RESULT_ATOMS,
"trajectory frame atom count"
);
if (atomCount > input.index.atomCount - atomOffset) {
fail3(
"RESOURCE_EXHAUSTED",
"The requested trajectory atom range is invalid"
);
}
const frames = [];
for (let frameIndex = first; frameIndex < endExclusive; frameIndex += stride) {
input.signal.throwIfAborted();
const { axisOffsets, frameOffset } = await validateStructureDcdFrame(
input,
input.index,
frameIndex
);
const parts = await Promise.all(
axisOffsets.map(
(offset) => readStructureTrajectoryRange(
input,
offset + BigInt(atomOffset * 4),
atomCount * 4
)
)
);
input.signal.throwIfAborted();
const coordinates = new Uint8Array(atomCount * 3 * 4);
const coordinateView = structureTrajectoryDataView(coordinates);
for (let atom = 0; atom < atomCount; atom += 1) {
for (let axis = 0; axis < 3; axis += 1) {
const value = structureTrajectoryDataView(parts[axis]).getFloat32(
atom * 4,
input.index.littleEndian
);
if (!Number.isFinite(value)) {
fail3(
"MALFORMED_TRAJECTORY",
"The DCD frame contains a non-finite coordinate"
);
}
coordinateView.setFloat32((atom * 3 + axis) * 4, value, true);
}
}
const step = input.index.startStep + frameIndex * input.index.saveInterval;
if (!Number.isSafeInteger(step)) {
fail3("MALFORMED_TRAJECTORY", "The DCD trajectory step is not safe");
}
frames.push({
frameIndex,
frameOffsetDecimal: frameOffset.toString(),
atomOffset,
atomCount,
topologyAtomCount: input.index.atomCount,
coordinates,
complete: atomOffset === 0 && atomCount === input.index.atomCount,
step
});
}
if (!input.multiple) {
return frames[0];
}
return {
complete: true,
frames,
indexComplete: input.index.complete,
sampledFrameCount: frames.length,
sourceFrameCount: input.index.frameCount,
stride
};
}
async function validateStructureDcdFrame(input, index, frameIndex) {
const validated = index.validatedFrames.get(frameIndex);
if (validated != null) {
return validated;
}
const frameOffset = index.firstFrameOffset + BigInt(frameIndex) * index.frameBytes;
let cursor = frameOffset;
if (index.hasCell) {
const cell = structureTrajectoryDataView(
await readStructureTrajectoryRange(input, cursor, 56)
);
if (cell.getInt32(0, index.littleEndian) !== 48 || cell.getInt32(52, index.littleEndian) !== 48) {
fail3("MALFORMED_TRAJECTORY", "The DCD unit-cell markers are invalid");
}
for (const position of [4, 12, 20, 28, 36, 44]) {
if (!Number.isFinite(cell.getFloat64(position, index.littleEndian))) {
fail3("MALFORMED_TRAJECTORY", "The DCD unit cell is not finite");
}
}
cursor += 56n;
}
const axisBytes = index.atomCount * 4;
const axisOffsets = [];
const markers = await Promise.all([
readStructureTrajectoryRange(input, cursor, 4),
...Array.from(
{ length: 3 },
(_value, axis) => readStructureTrajectoryRange(
input,
cursor + BigInt(axis * (axisBytes + 8) + axisBytes + 4),
axis === 2 ? 4 : 8
)
)
]);
if (structureTrajectoryDataView(markers[0]).getInt32(0, index.littleEndian) !== axisBytes) {
fail3(
"MALFORMED_TRAJECTORY",
"The DCD coordinate record markers are invalid"
);
}
for (let axis = 0; axis < 3; axis += 1) {
const marker = structureTrajectoryDataView(markers[axis + 1]);
if (marker.getInt32(0, index.littleEndian) !== axisBytes || axis < 2 && marker.getInt32(4, index.littleEndian) !== axisBytes) {
fail3(
"MALFORMED_TRAJECTORY",
"The DCD coordinate record markers are invalid"
);
}
axisOffsets.push(cursor + 4n);
cursor += BigInt(axisBytes + 8);
}
if (cursor !== frameOffset + index.frameBytes) {
fail3("MALFORMED_TRAJECTORY", "The DCD frame length is inconsistent");
}
const result = { axisOffsets, frameOffset };
if (index.validatedFrames.size >= MAX_VALIDATED_TRAJECTORY_FRAMES) {
const oldestFrame = index.validatedFrames.keys().next().value;
if (oldestFrame != null) {
index.validatedFrames.delete(oldestFrame);
}
}
index.validatedFrames.set(frameIndex, result);
return result;
}
async function readStructureTrajectoryRange(input, offset, length) {
input.signal.throwIfAborted();
const sizeBytes = input.grant.sourceIdentity.sizeBytes;
if (typeof offset !== "bigint" || offset < 0n || !Number.isSafeInteger(length) || length <= 0 || length > MAX_SOURCE_RANGE_BYTES || offset > sizeBytes || BigInt(length) > sizeBytes - offset) {
fail3(
"RESOURCE_EXHAUSTED",
"The requested trajectory range exceeds its authorized source"
);
}
const result = await input.readSource({
grant: input.grant,
logicalSessionId: input.logicalSessionId,
offset,
length,
signal: input.signal
});
input.signal.throwIfAborted();
if (result.bytes.byteLength !== length) {
fail3("SOURCE_CHANGED", "The authorized trajectory range is incomplete");
}
return result.bytes;
}
function structureTrajectoryDataView(bytes) {
return new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);
}
async function queryStructure({
logicalSessionId,
state,
grant,
command,
readSource,
signal
}) {
const limit = readPositive(
command.limit ?? 64,
MAX_RESULT_ATOMS,
"atom limit"
);
if (command.offsetDecimal != null) {
const offset = parseOffset(
command.offsetDecimal,
state.molecular.sizeBytes
);
const remaining = state.molecular.sizeBytes - offset;
const length = Math.min(
readPositive(
command.length ?? PREVIEW_BYTES,
PREVIEW_BYTES,
"atom range"
),
Number(
remaining < BigInt(PREVIEW_BYTES) ? remaining : BigInt(PREVIEW_BYTES)
)
);
if (length <= 0) {
fail3("INVALID_REQUEST", "The requested molecular range is empty");
}
const result = await readSource({
grant,
logicalSessionId,
offset,
length,
signal
});
const direct = createRegionState(
state.molecular,
command.model,
offset === 0n ? offset : void 0
);
appendStructureBytes(direct, result.bytes, offset, result.eof);
const matched2 = matchAtoms(direct.atoms, command).slice(0, limit);
return atomResult(logicalSessionId, state, matched2, result.eof, offset);
}
await scanForStructureAtoms({
logicalSessionId,
state,
grant,
command,
readSource,
signal
});
const matched = matchAtoms(state.molecular.atoms, command).slice(0, limit);
return atomResult(
logicalSessionId,
state,
matched,
state.molecular.complete,
void 0
);
}
async function scanForStructureAtoms(args, scanned = 0) {
const { logicalSessionId, state, grant, command, readSource, signal } = args;
if (state.molecular.complete || matchAtoms(state.molecular.atoms, command).length > 0 || scanned >= MAX_QUERY_SCAN_BYTES) {
return;
}
signal.throwIfAborted();
const remaining = state.molecular.sizeBytes - state.molecular.scanOffset;
if (remaining <= 0n) {
state.molecular.complete = !state.molecular.evicted;
return;
}
const length = Number(
remaining < BigInt(PREVIEW_BYTES) ? remaining : BigInt(PREVIEW_BYTES)
);
const chunk = await readSource({
grant,
logicalSessionId,
offset: state.molecular.scanOffset,
length,
signal
});
if (chunk.bytes.byteLength === 0 && !chunk.eof) {
fail3(
"MALFORMED_STRUCTURE",
"The authorized source returned an empty non-terminal molecular range"
);
}
appendStructureBytes(
state.molecular,
chunk.bytes,
state.molecular.scanOffset,
chunk.eof
);
return scanForStructureAtoms(args, scanned + chunk.bytes.byteLength);
}
async function readStructureGeometry({
logicalSessionId,
state,
grant,
command,
readSource,
signal
}) {
const offset = parseOffset(
command.offsetDecimal ?? "0",
state.molecular.sizeBytes
);
const remaining = state.molecular.sizeBytes - offset;
const requested = readPositive(
command.length ?? PREVIEW_BYTES,
PREVIEW_BYTES,
"geometry range"
);
const length = Math.min(
requested,
Number(
remaining < BigInt(PREVIEW_BYTES) ? remaining : BigInt(PREVIEW_BYTES)
)
);
if (length === 0) {
fail3("INVALID_REQUEST", "The requested Structure geometry range is empty");
}
const chunk = await readSource({
grant,
logicalSessionId,
offset,
length,
signal
});
if ((state.molecular.compressedSource != null || (grant.sourceAccessPattern ?? grant.sourceIdentity.accessPattern) === "forward-only") && offset === state.molecular.scanOffset) {
appendStructureBytes(state.molecular, chunk.bytes, offset, chunk.eof);
}
return {
structuredContent: {
viewerSessionId: logicalSessionId,
viewerCommandRevision: state.revision,
format: state.molecular.format,
sourceRevision: state.molecular.sourceRevision,
offsetDecimal: offset.toString(),
bytes: chunk.bytes,
eof: chunk.eof
}
};
}
async function measureStructure(args) {
const { logicalSessionId, state, command } = args;
const atomIds = command.atomIds;
if (!isStringArray(atomIds) || atomIds.length !== 2) {
fail3(
"INVALID_REQUEST",
"A molecular distance requires exactly two atom identities"
);
}
await ensureStructureAtom(args, atomIds[0]);
await ensureStructureAtom(args, atomIds[1]);
const first = state.molecular.atoms.get(atomIds[0]);
const second = state.molecular.atoms.get(atomIds[1]);
if (first == null || second == null) {
fail3(
"INCOMPLETE_INDEX",
"The requested measurement atoms are not yet indexed"
);
}
const distance = Math.hypot(
first.x - second.x,
first.y - second.y,
first.z - second.z
);
return {
structuredContent: {
viewerSessionId: logicalSessionId,
viewerCommandRevision: state.revision,
atomIds: [first.atomId, second.atomId],
value: distance,
unit: "angstrom",
complete: true
}
};
}
async function ensureStructureAtom(args, atomId) {
if (!args.state.molecular.atoms.has(atomId)) {
await queryStructure({
...args,
command: { atomIds: [atomId], limit: 1 }
});
}
}
async function analyzeStructureContacts(args) {
const { logicalSessionId, state, command, signal } = args;
signal.throwIfAborted();
const cutoff = command.cutoffAngstrom ?? command.cutoff ?? 4;
if (typeof cutoff !== "number" || !Number.isFinite(cutoff) || cutoff <= 0 || cutoff > 100) {
fail3(
"INVALID_REQUEST",
"A molecular contact cutoff must be between 0 and 100 angstrom"
);
}
if (!state.molecular.complete) {
fail3(
"INCOMPLETE_INDEX",
"A complete source-backed molecular index is required for authoritative contacts"
);
}
const requestedIds = command.ligandAtomIds ?? command.atomIds;
if (requestedIds != null && (!isStringArray(requestedIds) || requestedIds.length === 0 || requestedIds.length > MAX_RESULT_ATOMS)) {
fail3(
"INVALID_REQUEST",
"Ligand contacts require bounded source-backed atom identities"
);
}
const explicit = requestedIds == null ? void 0 : new Set(requestedIds);
const atoms = [...state.molecular.atoms.values()];
if (atoms.length > MAX_RESULT_ATOMS) {
fail3(
"RESOURCE_EXHAUSTED",
"The complete molecular contact request exceeds its atom budget"
);
}
const ligands = atoms.filter(
(atom) => explicit == null ? atom.recordType === "HETATM" : explicit.has(atom.atomId)
);
if (ligands.length === 0 || explicit != null && ligands.length !== explicit.size) {
fail3(
"NOT_FOUND",
"The requested contact atoms are not present in the approved source"
);
}
const ligandIds = new Set(ligands.map((atom) => atom.atomId));
const contacts = [];
for (const ligand of ligands) {
signal.throwIfAborted();
for (const atom of atoms) {
if (ligandIds.has(atom.atomId) || atom.model !== ligand.model) {
continue;
}
const distance = Math.hypot(
ligand.x - atom.x,
ligand.y - atom.y,
ligand.z - atom.z
);
if (distance <= cutoff) {
contacts.push({
ligandAtomId: ligand.atomId,
atomId: atom.atomId,
chainId: atom.chainId,
residueName: atom.residueName,
residueNumber: atom.residueNumber,
...atom.insertionCode == null ? {} : { insertionCode: atom.insertionCode },
distance,
unit: "angstrom"
});
if (contacts.length > MAX_RESULT_ATOMS) {
fail3(
"RESOURCE_EXHAUSTED",
"The molecular contact result exceeds its bounded budget"
);
}
}
}
}
return {
structuredContent: {
viewerSessionId: logicalSessionId,
viewerCommandRevision: state.revision,
sourceRevision: state.molecular.sourceRevision,
cutoffAngstrom: cutoff,
contacts,
complete: true
}
};
}
function isStructureProjectResourceUri(value) {
return typeof value === "string" && value.length <= 4096 && /^viewer-(?:file|data|live-data):\/\/structure-viewer\//u.test(value) && !value.includes("\\") && !value.includes("\0");
}
function rememberStructureTrajectoryProject(args) {
const { logicalSessionId, state, command, grant, identity, now } = args;
if (!isOpaqueIdentity(command.objectId) || command.objectId.length > 100 || !isRecord2(command.coordinates) || !isRecord2(command.topology) || !["dcd", "xtc", "trr", "nctraj", "lammpstrj"].includes(
String(command.coordinatesFormat)
) || !["pdb", "mmcif", "gro", "xyz", "psf", "prmtop", "top"].includes(
String(command.topologyFormat)
) || !["none", "backbone", "selection"].includes(String(command.alignment)) || !isSafeProjectRelativePath(command.coordinates.name) || !isSafeProjectRelativePath(command.topology.name) || command.trajectoryRelativePath != null && (!isSafeProjectRelativePath(command.trajectoryRelativePath) || command.trajectoryRelativePath.split("/").at(-1) !== command.coordinates.name) || command.topologyRelativePath != null && (!isSafeProjectRelativePath(command.topologyRelativePath) || command.topologyRelativePath.split("/").at(-1) !== command.topology.name) || !isStructureProjectResourceUri(command.coordinates.resourceUri) || !isStructureProjectResourceUri(command.topology.resourceUri)) {
fail3(
"INVALID_REQUEST",
"The Structure trajectory companion request is invalid"
);
}
const trajectoryGrant = validateSourceGrant({
grant: command.trajectorySourceGrant,
identity,
logicalSessionId,
now: now()
});
const topologyGrant = command.topologySourceGrant == null ? grant : validateSourceGrant({
grant: command.topologySourceGrant,
identity,
logicalSessionId,
now: now()
});
if (topologyGrant.grantId === grant.grantId && command.topologyFormat !== state.molecular.format) {
fail3("TOPOLOGY_MISMATCH", "The primary topology format is inconsistent");
}
if (trajectoryGrant.sourceIdentity.fileId === grant.sourceIdentity.fileId || trajectoryGrant.sourceIdentity.sizeBytes <= 0n) {
fail3(
"PERMISSION_DENIED",
"The Structure trajectory has no distinct approved source"
);
}
const existing = state.molecular.trajectoryProjects.get(command.objectId);
if (existing != null && (existing.coordinates.grant.sourceRevision !== trajectoryGrant.sourceRevision || existing.coordinates.resourceUri !== command.coordinates.resourceUri || existing.topology.resourceUri !== command.topology.resourceUri)) {
fail3(
"CONFLICT",
"The Structure trajectory object has a different approved source"
);
}
if (existing == null && state.molecular.trajectoryProjects.size >= MAX_TRAJECTORIES) {
fail3(
"RESOURCE_EXHAUSTED",
"The Structure trajectory companion budget is exhausted"
);
}
state.molecular.trajectoryProjects.set(command.objectId, {
objectId: command.objectId,
coordinates: {
format: command.coordinatesFormat,
grant: trajectoryGrant,
relativePath: typeof command.trajectoryRelativePath === "string" ? command.trajectoryRelativePath : command.coordinates.name,
resourceUri: command.coordinates.resourceUri
},
topology: {
format: command.topologyFormat,
grant: topologyGrant,
relativePath: typeof command.topologyRelativePath === "string" ? command.topologyRelativePath : command.topology.name,
resourceUri: command.topology.resourceUri
}
});
}
async function mutateStructure(args) {
const { logicalSessionId, operation, state, command, signal } = args;
signal.throwIfAborted();
const action = operation === "control_viewer" && typeof command.action === "string" ? command.action : operation;
const queueForViewer = operation === "control_viewer" && VIEWER_COMMAND_ACTIONS.has(action);
const createdAt = Date.now();
let deadlineAt = createdAt + 12e4;
if (queueForViewer && command.nativeDeadlineAt !== void 0) {
if (typeof command.nativeDeadlineAt !== "number" || !Number.isFinite(command.nativeDeadlineAt)) {
fail3("INVALID_REQUEST", "The Structure viewer command deadline is invalid");
}
if (command.nativeDeadlineAt <= createdAt) {
fail3("DEADLINE_EXCEEDED", "The Structure viewer command has expired");
}
deadlineAt = Math.min(deadlineAt, command.nativeDeadlineAt);
}
if (queueForViewer && state.molecular.commands.size >= MAX_PENDING_COMMANDS && ![...state.molecular.commands.values()].some(
(queued) => queued.completion != null
)) {
fail3(
"RESOURCE_EXHAUSTED",
"The Structure viewer command queue is exhausted"
);
}
if (action === "show_ligand_contacts" || action === "ligand_contacts" || action === "contacts") {
return analyzeStructureContacts(args);
}
let viewerOnly = false;
switch (action) {
case "set_selection":
case "select_chain":
case "select_residue_range":
case "select_residues":
case "focus_residue":
case "focus_ligand": {
const queried = await queryStructure({ ...args, command });
const atoms = queried.structuredContent.atoms;
if (atoms.length === 0) {
fail3(
"INCOMPLETE_INDEX",
"The requested selection has no indexed molecular atoms"
);
}
state.molecular.history.push({
selectedAtomIds: [...state.molecular.selectedAtomIds],
scene: { ...state.molecular.scene }
});
state.molecular.selectedAtomIds = new Set(
atoms.map((atom) => atom.atomId)
);
break;
}
case "set_representation": {
if (typeof command.representation !== "string" || !["cartoon", "surface", "sphere", "ballStick", "stick"].includes(
command.representation
)) {
fail3(
"INVALID_REQUEST",
"The requested molecular representation is unsupported"
);
}
state.molecular.history.push({
selectedAtomIds: [...state.molecular.selectedAtomIds],
scene: { ...state.molecular.scene }
});
state.molecular.scene.representation = command.representation;
break;
}
case "set_object_visibility":
if (typeof command.visible !== "boolean") {
fail3(
"INVALID_REQUEST",
"Structure object visibility requires a boolean"
);
}
state.molecular.scene.visibility = command.visible;
break;
case "save_scene":
if (!isOpaqueIdentity(command.name)) {
fail3(
"INVALID_REQUEST",
"A named Structure scene requires a safe identity"
);
}
state.molecular.scenes.set(command.name, {
selectedAtomIds: [...state.molecular.selectedAtomIds],
scene: { ...state.molecular.scene }
});
break;
case "load_scene": {
if (!isOpaqueIdentity(command.name)) {
fail3(
"INVALID_REQUEST",
"A named Structure scene requires a safe identity"
);
}
const scene = state.molecular.scenes.get(command.name);
if (scene == null) {
fail3("NOT_FOUND", "The requested Structure scene has not been saved");
}
state.molecular.selectedAtomIds = new Set(scene.selectedAtomIds);
state.molecular.scene = { ...scene.scene };
break;
}
case "undo": {
const previous = state.molecular.history.pop();
if (previous == null) {
fail3(
"NOT_FOUND",
"No acknowledged Structure scene operation can be undone"
);
}
state.molecular.selectedAtomIds = new Set(previous.selectedAtomIds);
state.molecular.scene = previous.scene;
break;
}
case "add_structure":
case "align_structures":
case "analyze":
case "apply_scene":
case "delete_scene":
case "derive_object":
case "export":
case "get_state":
case "list_scenes":
case "measure":
case "measure_residue_distance":
case "query":
case "redo":
case "remove_structure":
case "render_image":
case "render_movie":
case "reset_view":
case "set_color":
case "set_display_mode":
case "set_view_options":
case "transform_object":
case "validate_render":
if (!queueForViewer) {
fail3(
"UNSUPPORTED",
"The requested Structure operation requires the attached viewer"
);
}
viewerOnly = true;
break;
case "load_structure": {
if (!queueForViewer || !isOpaqueIdentity(command.objectId) || !isRecord2(command.file) || !isSafeProjectRelativePath(command.file.name) || command.structureRelativePath != null && !isSafeProjectRelativePath(command.structureRelativePath) || !isStructureProjectResourceUri(command.file.resourceUri)) {
fail3("INVALID_REQUEST", "The approved companion structure is invalid");
}
const structureGrant = validateSourceGrant({
grant: command.structureSourceGrant,
identity: args.identity,
logicalSessionId,
now: args.now()
});
if (structureGrant.sourceIdentity.fileId === args.grant.sourceIdentity.fileId) {
fail3("PERMISSION_DENIED", "The companion structure must be distinct");
}
state.molecular.structureProjects.set(command.objectId, {
format: typeof command.format === "string" ? command.format : "pdb",
grant: structureGrant,
relativePath: typeof command.structureRelativePath === "string" && isSafeProjectRelativePath(command.structureRelativePath) ? command.structureRelativePath : command.file.name,
resourceUri: command.file.resourceUri
});
viewerOnly = true;
break;
}
case "load_volume": {
if (!queueForViewer || !isRecord2(command.file) || !isRecord2(command.volume) || !isOpaqueIdentity(command.volume.id) || !isSafeProjectRelativePath(command.file.name) || command.volumeRelativePath != null && !isSafeProjectRelativePath(command.volumeRelativePath) || !isStructureProjectResourceUri(command.file.resourceUri) || typeof command.volume.format !== "string") {
fail3(
"INVALID_REQUEST",
"The approved molecular density volume is invalid"
);
}
await indexStructureVolume({
...args,
command: {
resourceUri: command.file.resourceUri,
relativePath: typeof command.volumeRelativePath === "string" && isSafeProjectRelativePath(command.volumeRelativePath) ? command.volumeRelativePath : command.file.name,
format: command.volume.format,
volumeSourceGrant: command.volumeSourceGrant
}
});
const volume = state.molecular.volumes.get(command.file.resourceUri);
if (volume == null) {
fail3("NOT_FOUND", "The approved molecular volume was not indexed");
}
volume.objectId = command.volume.id;
viewerOnly = true;
break;
}
case "load_trajectory":
if (!queueForViewer) {
fail3(
"UNSUPPORTED",
"A molecular trajectory requires an attached viewer"
);
}
rememberStructureTrajectoryProject(args);
viewerOnly = true;
break;
case "set_trajectory_state":
if (!queueForViewer || !isRecord2(command.state) || !isOpaqueIdentity(command.state.objectId) || !state.molecular.trajectoryProjects.has(command.state.objectId)) {
fail3("NOT_FOUND", "The approved molecular trajectory is not attached");
}
viewerOnly = true;
break;
default:
fail3(
"UNSUPPORTED",
"The requested Structure control has no molecular implementation"
);
}
signal.throwIfAborted();
state.revision += 1;
const viewerCommandId = queueForViewer ? enqueueStructureViewerCommand({ state, command, createdAt, deadlineAt }) : void 0;
return {
structuredContent: {
...viewerOnly ? { queued: true } : { applied: true },
viewerSessionId: logicalSessionId,
viewerCommandRevision: state.revision,
selection: [...state.molecular.selectedAtomIds],
scene: { ...state.molecular.scene },
...viewerCommandId == null ? {} : { viewerCommandId }
}
};
}
function structureState(logicalSessionId, state) {
return {
structuredContent: {
viewerSessionId: logicalSessionId,
viewerCommandRevision: state.revision,
state: {
format: state.molecular.format,
sourceRevision: state.molecular.sourceRevision,
indexedAtomCount: state.molecular.atoms.size,
indexComplete: state.molecular.complete,
selectedAtomIds: [...state.molecular.selectedAtomIds],
models: uniqueModels(state.molecular.atoms),
scene: { ...state.molecular.scene }
}
}
};
}
function validateSourceGrant({ grant, identity, logicalSessionId, now }) {
if (!isCurrentSourceGrant(grant, identity, logicalSessionId, now)) {
fail3(
"PERMISSION_DENIED",
"The Structure source capability is not current or authorized"
);
}
return grant;
}
function isCurrentSourceGrant(grant, identity, logicalSessionId, now) {
return isRecord2(grant) && grant.family === "structure" && grant.logicalSessionId === logicalSessionId && grant.backendInstanceId === identity.backendInstanceId && grant.backendGeneration === identity.backendGeneration && grant.revocationEpoch === identity.revocationEpoch && isOpaqueIdentity(grant.grantId) && isOpaqueIdentity(grant.sourceHandleId) && typeof grant.sourceRevision === "string" && isRecord2(grant.sourceIdentity) && isOpaqueIdentity(grant.sourceIdentity.fileId) && grant.sourceIdentity.etag === grant.sourceRevision && typeof grant.sourceIdentity.sizeBytes === "bigint" && isStringArray(grant.operations) && grant.operations.includes("range-read") && typeof grant.issuedAtMs === "number" && Number.isSafeInteger(grant.issuedAtMs) && typeof grant.expiresAtMs === "number" && Number.isSafeInteger(grant.expiresAtMs) && grant.issuedAtMs <= now && grant.expiresAtMs > now;
}
function detectStructureFormat(bytes, hint) {
let text;
try {
text = new TextDecoder("utf-8", { fatal: true }).decode(bytes);
} catch {
fail3(
"MALFORMED_STRUCTURE",
"The approved molecular header is not valid UTF-8"
);
}
if (hint === "pdb" || hint === "pdbqt" || hint === "pqr" || hint === "mol" || hint === "sdf" || hint === "mol2" || hint === "gro" || hint === "xyz") {
return hint;
}
if (hint === "mmcif" || hint === "cif" || /^data_/mu.test(text) || /_atom_site\./u.test(text)) {
return "mmcif";
}
if (/^(?:HEADER|TITLE|REMARK|MODEL\s|ATOM\s|HETATM)/mu.test(text)) {
return "pdb";
}
fail3(
"UNSUPPORTED",
"The authorized source is not a supported molecular structure"
);
}
function hasStructureHeader(bytes, format) {
const text = new TextDecoder("utf-8", { fatal: true }).decode(bytes);
switch (format) {
case "pdb":
case "pdbqt":
case "pqr":
return /^(?:HEADER|TITLE|REMARK|MODEL\s|ATOM\s|HETATM)/mu.test(text);
case "mmcif":
return /^data_/mu.test(text) || /_atom_site\./u.test(text);
case "mol":
case "sdf":
return /^.{0,80}V(?:2000|3000)/mu.test(text);
case "mol2":
return /^@<TRIPOS>(?:MOLECULE|ATOM)/mu.test(text);
case "gro":
return /^[^\n]*\n\s*\d+/u.test(text);
case "xyz":
return /^\s*\d+/u.test(text);
}
}
function atomPageCursorRequired(logicalSessionId, state, offset) {
return {
structuredContent: {
viewerSessionId: logicalSessionId,
viewerCommandRevision: state.revision,
sourceRevision: state.molecular.sourceRevision,
sourceSizeBytesDecimal: state.molecular.sizeBytes.toString(),
format: state.molecular.format,
offsetDecimal: offset.toString(),
atomPageStatus: "cursor-required"
}
};
}
function retainMmcifPageBoundary(state, offset) {
const framing = state.mmcifFraming;
if (state.format !== "mmcif" || !state.mmcifTrustedRange || framing == null)
return;
framing.pageBoundaries ??= /* @__PURE__ */ new Map();
if (!framing.pageBoundaries.has(offset) && framing.pageBoundaries.size >= MAX_MMCIF_PAGE_BOUNDARIES) {
const oldest = framing.pageBoundaries.keys().next().value;
if (oldest != null) framing.pageBoundaries.delete(oldest);
}
const range = framing.atomRanges.find(
({ start, end }) => offset >= start && offset <= end
);
framing.pageBoundaries.set(offset, {
headers: [...range?.headers ?? state.headers],
blockStart: range?.blockStart ?? state.mmcifBlockStart
});
}
function createRegionState(state, model, framedOffset) {
if (model != null && (typeof model !== "number" || !Number.isSafeInteger(model) || model <= 0)) {
fail3(
"INVALID_REQUEST",
"A selected molecular model must be a positive integer"
);
}
const packetBoundary = framedOffset == null ? void 0 : state.mmcifFraming?.pageBoundaries?.get(framedOffset);
const knownAtomRange = framedOffset == null ? void 0 : state.mmcifFraming?.atomRanges.find(
({ start, end }) => framedOffset >= start && framedOffset <= end
);
if (knownAtomRange?.lineAligned === false && framedOffset !== knownAtomRange.start && packetBoundary == null) {
fail3(
"INVALID_REQUEST",
"Use a returned atom-page cursor to resume a wrapped mmCIF packet range"
);
}
return {
format: state.format,
atoms: /* @__PURE__ */ new Map(),
decoder: new TextDecoder("utf-8", { fatal: true }),
evicted: false,
headers: [
...packetBoundary?.headers ?? knownAtomRange?.headers ?? state.mmcifAtomHeaders ?? state.headers
],
mmcifAtomHeaders: state.mmcifAtomHeaders,
mmcifAtomHeadersInferred: state.format === "mmcif",
mmcifBlockStart: framedOffset === 0n ? 0n : packetBoundary?.blockStart ?? knownAtomRange?.blockStart ?? 0n,
mmcifAtomBlocks: /* @__PURE__ */ new Map(),
mmcifMetadata: state.mmcifMetadata,
mmcifFraming: state.mmcifFraming,
mmcifTrustedRange: framedOffset === 0n || packetBoundary != null || knownAtomRange != null,
mmcifCurrentAtomRange: knownAtomRange,
mmcifLoop: state.format === "mmcif",
model: model ?? state.model,
pending: "",
complete: false,
scanOffset: 0n,
recordEndOffsets: /* @__PURE__ */ new Map()
};
}
function matchAtoms(atoms, command) {
const atomIds = isStringArray(command.atomIds) ? new Set(command.atomIds) : null;
const residueStart = readOptionalResidue(
command.residueStart,
"residue start"
);
const residueEnd = readOptionalResidue(command.residueEnd, "residue end");
return [...atoms.values()].filter(
(atom) => (atomIds == null || atomIds.has(atom.atomId)) && (command.chainId == null || command.chainId === atom.chainId) && (command.model == null || command.model === atom.model) && (command.residueNumber == null || command.residueNumber === atom.residueNumber) && (residueStart == null || atom.residueNumber >= residueStart) && (residueEnd == null || atom.residueNumber <= residueEnd) && (command.insertionCode == null || command.insertionCode === atom.insertionCode)
);
}
function readOptionalResidue(value, name) {
if (value == null) {
return void 0;
}
if (typeof value !== "number" || !Number.isSafeInteger(value)) {
fail3("INVALID_REQUEST", `The ${name} must be a safe integer`);
}
return value;
}
function atomResult(logicalSessionId, state, atoms, complete, offset) {
return {
structuredContent: {
viewerSessionId: logicalSessionId,
viewerCommandRevision: state.revision,
sourceRevision: state.molecular.sourceRevision,
atoms,
complete,
...offset == null ? {} : { offsetDecimal: offset.toString() }
}
};
}
function uniqueModels(atoms) {
return [...new Set([...atoms.values()].map((atom) => atom.model))].sort(
(left, right) => left - right
);
}
function parseOffset(value, sizeBytes) {
if (typeof value !== "string" || !DECIMAL2.test(value)) {
fail3("INVALID_REQUEST", "A Structure offset must be an unsigned decimal");
}
const offset = BigInt(value);
if (offset >= sizeBytes) {
fail3(
"RESOURCE_EXHAUSTED",
"The requested Structure range is outside the source"
);
}
return offset;
}
function readPositive(value, maximum, name) {
if (typeof value !== "number" || !Number.isSafeInteger(value) || value <= 0 || value > maximum) {
fail3("RESOURCE_EXHAUSTED", `The ${name} exceeds its bounded source policy`);
}
return value;
}
function isOpaqueIdentity(value) {
return typeof value === "string" && value.length <= 256 && /^[A-Za-z0-9][A-Za-z0-9._:-]*$/u.test(value);
}
function isRecord2(value) {
return typeof value === "object" && value != null && !Array.isArray(value);
}
function isStringArray(value) {
return Array.isArray(value) && value.every((entry) => typeof entry === "string");
}
function fail3(code, message) {
const error = Object.assign(new Error(message), {
name: "ScientificStructureRuntimeError",
code
});
throw error;
}
// node_modules/.pnpm/@openai+scientific-viewer-platform@file+..+scientific-viewer-platform/node_modules/@openai/scientific-viewer-platform/src/structure/scientific-structure-backend-entrypoint.mjs
var MAX_CHECKPOINT_BYTES = 256 * 1024;
var MAX_SESSIONS2 = 128;
var MAX_REQUEST_ID_LENGTH = 128;
var MAX_ARTIFACT_CHUNK_BYTES2 = 256 * 1024;
var MAX_ARTIFACT_REQUESTS = 16;
function startScientificStructureBackend({
environment = process.env,
channel = process,
now = Date.now
} = {}) {
const identity = readStructureIdentity(environment);
if (typeof channel.send !== "function" || typeof channel.on !== "function") {
throw new Error(
"The Structure backend requires a private host IPC channel"
);
}
const sessions = /* @__PURE__ */ new Map();
const activeRequests = /* @__PURE__ */ new Map();
const pendingSourceReads = /* @__PURE__ */ new Map();
const pendingArtifactWrites = /* @__PURE__ */ new Map();
const artifactTransactions = /* @__PURE__ */ new Map();
let nextSourceReadId = 0;
let nextArtifactRequestId = 0;
let disposed = false;
const send = (message) => {
if (!disposed && channel.connected !== false) {
channel.send(message);
}
};
const reply = (request, result, error) => {
send({
type: "scientific-viewer/response",
requestId: request.requestId,
backendInstanceId: identity.backendInstanceId,
backendGeneration: identity.backendGeneration,
instanceNonce: identity.instanceNonce,
...error == null ? { result } : { error: `${error.code}: ${error.message}` }
});
};
const readSource = ({ grant, logicalSessionId, offset, length, signal }) => {
signal?.throwIfAborted();
if (typeof offset !== "bigint" || offset < 0n || !Number.isSafeInteger(length) || length <= 0 || length > 256 * 1024) {
throw new StructureBackendError(
"RESOURCE_EXHAUSTED",
"The Structure source read exceeds its positioned request budget"
);
}
const requestId = `structure-range-${++nextSourceReadId}`;
return new Promise((resolve, reject) => {
const abort = () => {
pendingSourceReads.delete(requestId);
reject(
new StructureBackendError(
"CANCELLED",
"The Structure source read was cancelled"
)
);
};
pendingSourceReads.set(requestId, {
resolve,
reject,
signal,
abort,
logicalSessionId,
sourceRevision: grant.sourceRevision,
offsetDecimal: offset.toString(),
length
});
signal?.addEventListener("abort", abort, { once: true });
send({
type: "scientific-viewer/source-read",
requestId,
family: "structure",
logicalSessionId,
backendInstanceId: identity.backendInstanceId,
backendGeneration: identity.backendGeneration,
revocationEpoch: identity.revocationEpoch,
instanceNonce: identity.instanceNonce,
sourceGrantId: grant.grantId,
sourceRevision: grant.sourceRevision,
offsetDecimal: offset.toString(),
length
});
});
};
const settleSourceRead = (message) => {
const pending = pendingSourceReads.get(message.requestId);
if (pending == null || message.family !== "structure" || message.logicalSessionId !== pending.logicalSessionId || message.backendInstanceId !== identity.backendInstanceId || message.backendGeneration !== identity.backendGeneration || message.instanceNonce !== identity.instanceNonce || message.revocationEpoch !== identity.revocationEpoch) {
return;
}
pendingSourceReads.delete(message.requestId);
pending.signal?.removeEventListener("abort", pending.abort);
if (message.type === "scientific-viewer/source-read-error") {
pending.reject(
new StructureBackendError(
typeof message.code === "string" ? message.code : "PERMISSION_DENIED",
"The host refused the authorized Structure source range"
)
);
return;
}
if (message.sourceRevision !== pending.sourceRevision || message.offsetDecimal !== pending.offsetDecimal || !(message.bytes instanceof Uint8Array) || message.bytes.byteLength > pending.length || typeof message.eof !== "boolean" || message.bytes.byteLength < pending.length && !message.eof) {
pending.reject(
new StructureBackendError(
"SOURCE_CHANGED",
"The host returned an invalid or stale Structure source range"
)
);
return;
}
pending.resolve({ bytes: message.bytes, eof: message.eof });
};
const writeArtifact = ({ logicalSessionId, operation, payload, signal }) => {
signal?.throwIfAborted();
if (!isOpaqueIdentity2(logicalSessionId, 512) || !["begin", "append", "commit", "abort", "resume"].includes(operation) || !isRecord3(payload) || !isOpaqueIdentity2(payload.destinationGrantId, 512)) {
throw new StructureBackendError(
"PERMISSION_DENIED",
"The Structure artifact request is not host-authorized"
);
}
if (operation === "append" && (!(payload.bytes instanceof Uint8Array) || payload.bytes.byteLength === 0 || payload.bytes.byteLength > MAX_ARTIFACT_CHUNK_BYTES2)) {
throw new StructureBackendError(
"RESOURCE_EXHAUSTED",
"The Structure artifact chunk exceeds its host IPC budget"
);
}
if (pendingArtifactWrites.size >= MAX_ARTIFACT_REQUESTS) {
throw new StructureBackendError(
"RESOURCE_EXHAUSTED",
"The Structure artifact request budget is exhausted"
);
}
const requestId = `structure-artifact-${++nextArtifactRequestId}`;
return new Promise((resolve, reject) => {
const abort = () => {
pendingArtifactWrites.delete(requestId);
reject(
new StructureBackendError(
"CANCELLED",
"The Structure artifact write was cancelled"
)
);
};
pendingArtifactWrites.set(requestId, {
abort,
logicalSessionId,
reject,
resolve,
signal
});
signal?.addEventListener("abort", abort, { once: true });
send({
type: "scientific-viewer/artifact-request",
requestId,
family: "structure",
logicalSessionId,
backendInstanceId: identity.backendInstanceId,
backendGeneration: identity.backendGeneration,
revocationEpoch: identity.revocationEpoch,
instanceNonce: identity.instanceNonce,
operation,
payload
});
});
};
const settleArtifactWrite = (message) => {
const pending = pendingArtifactWrites.get(message.requestId);
if (pending == null || message.family !== "structure" || message.logicalSessionId !== pending.logicalSessionId || message.backendInstanceId !== identity.backendInstanceId || message.backendGeneration !== identity.backendGeneration || message.revocationEpoch !== identity.revocationEpoch || message.instanceNonce !== identity.instanceNonce) {
return;
}
pendingArtifactWrites.delete(message.requestId);
pending.signal?.removeEventListener("abort", pending.abort);
if (message.type === "scientific-viewer/artifact-error") {
const code = typeof message.error === "string" && /^[A-Z][A-Z_]{0,63}$/u.test(message.error) ? message.error : "PERMISSION_DENIED";
pending.reject(
new StructureBackendError(
code,
"The host refused the authorized Structure artifact write"
)
);
return;
}
if (!isRecord3(message.result)) {
pending.reject(
new StructureBackendError(
"INVALID_REQUEST",
"The host returned an invalid Structure artifact transaction"
)
);
return;
}
pending.resolve(message.result);
};
const heartbeat = () => send({
type: "scientific-viewer/heartbeat",
backendInstanceId: identity.backendInstanceId,
backendGeneration: identity.backendGeneration,
instanceNonce: identity.instanceNonce,
processId: process.pid,
sentAtMs: now(),
activeSessions: sessions.size,
activeStreams: activeRequests.size,
bufferedBytes: 0
});
const handleRequest = async (request) => {
if (!validRequestIdentity(request, identity)) {
return;
}
if (!isOpaqueIdentity2(request.requestId, MAX_REQUEST_ID_LENGTH)) {
return;
}
if (activeRequests.has(request.requestId)) {
reply(request, void 0, {
code: "CONFLICT",
message: "A Structure request with that identity is already active"
});
return;
}
const controller = new AbortController();
activeRequests.set(request.requestId, controller);
try {
const result = await dispatchStructureRequest({
request,
sessions,
identity,
readSource,
writeArtifact,
artifactTransactions,
now,
signal: controller.signal
});
controller.signal.throwIfAborted();
reply(request, result);
} catch (error) {
reply(request, void 0, {
code: error instanceof Error && "code" in error && typeof error.code === "string" ? error.code : "INVALID_REQUEST",
message: error instanceof Error ? error.message : "The Structure request failed"
});
} finally {
activeRequests.delete(request.requestId);
}
};
const onMessage = (message) => {
if (disposed || !isRecord3(message)) {
return;
}
switch (message.type) {
case "scientific-viewer/heartbeat-request":
if (validRequestIdentity(message, identity, true)) {
heartbeat();
}
return;
case "scientific-viewer/request":
void handleRequest(message);
return;
case "scientific-viewer/source-read-result":
case "scientific-viewer/source-read-error":
settleSourceRead(message);
return;
case "scientific-viewer/artifact-result":
case "scientific-viewer/artifact-error":
settleArtifactWrite(message);
return;
case "scientific-viewer/cancel":
if (validRequestIdentity(message, identity)) {
activeRequests.get(message.requestId)?.abort();
}
return;
case "scientific-viewer/shutdown":
if (validRequestIdentity(message, identity)) {
dispose();
}
return;
default:
return;
}
};
const dispose = () => {
if (disposed) {
return;
}
disposed = true;
channel.removeListener("message", onMessage);
for (const controller of activeRequests.values()) {
controller.abort();
}
activeRequests.clear();
for (const pending of pendingSourceReads.values()) {
pending.signal?.removeEventListener("abort", pending.abort);
pending.reject(
new StructureBackendError(
"CANCELLED",
"The Structure backend source channel was closed"
)
);
}
pendingSourceReads.clear();
for (const pending of pendingArtifactWrites.values()) {
pending.signal?.removeEventListener("abort", pending.abort);
pending.reject(
new StructureBackendError(
"CANCELLED",
"The Structure backend artifact channel was closed"
)
);
}
pendingArtifactWrites.clear();
artifactTransactions.clear();
sessions.clear();
};
channel.on("message", onMessage);
send({
type: "scientific-viewer/hello",
protocolVersion: 1,
family: "structure",
backendInstanceId: identity.backendInstanceId,
backendGeneration: identity.backendGeneration,
revocationEpoch: identity.revocationEpoch,
instanceNonce: identity.instanceNonce,
processId: process.pid,
startedAtMs: now()
});
return { dispose };
}
var StructureBackendError = class extends Error {
/** @type {string} */
code;
/**
* @param {string} code
* @param {string} message
*/
constructor(code, message) {
super(message);
this.name = "StructureBackendError";
this.code = code;
}
};
async function dispatchStructureRequest({
request,
sessions,
identity,
readSource,
writeArtifact,
artifactTransactions,
now,
signal
}) {
signal.throwIfAborted();
const payload = request.payload;
if (typeof request.operation === "string" && request.operation.startsWith("ui/scientific/structure/")) {
return executeScientificStructureTool({
operation: request.operation.slice("ui/scientific/structure/".length),
payload,
sessions,
identity,
readSource,
writeArtifact,
artifactTransactions,
now,
signal
});
}
switch (request.operation) {
case "session/restore": {
if (!isRecord3(payload) || !isOpaqueIdentity2(payload.logicalSessionId, 256)) {
throw new StructureBackendError(
"INVALID_REQUEST",
"Structure restore requires an opaque logical session identity"
);
}
const state = isRecord3(payload.payload) ? payload.payload : payload;
const checkpoint = state.checkpoint;
const revision = state.lastAcknowledgedRevision ?? state.revision ?? 0;
if (!Number.isSafeInteger(revision) || revision < 0) {
throw new StructureBackendError(
"INVALID_REQUEST",
"The Structure checkpoint revision is invalid"
);
}
const checkpointBytes = checkpointSize(checkpoint);
if (checkpointBytes > MAX_CHECKPOINT_BYTES) {
throw new StructureBackendError(
"RESOURCE_EXHAUSTED",
"The Structure checkpoint exceeds the 256 KiB recovery limit"
);
}
const previous = sessions.get(payload.logicalSessionId);
if (previous != null && revision < previous.revision) {
throw new StructureBackendError(
"CONFLICT",
"The Structure checkpoint revision is older than acknowledged state"
);
}
if (previous == null && sessions.size >= MAX_SESSIONS2) {
throw new StructureBackendError(
"RESOURCE_EXHAUSTED",
"The Structure backend session budget is exhausted"
);
}
signal.throwIfAborted();
sessions.set(payload.logicalSessionId, {
revision,
checkpoint: checkpoint instanceof Uint8Array ? checkpoint.slice() : checkpoint
});
return {
logicalSessionId: payload.logicalSessionId,
revision,
restored: true
};
}
case "session/get": {
if (!isRecord3(payload) || !isOpaqueIdentity2(payload.logicalSessionId, 256)) {
throw new StructureBackendError(
"INVALID_REQUEST",
"Structure session lookup requires an opaque logical identity"
);
}
const state = sessions.get(payload.logicalSessionId);
if (state == null) {
throw new StructureBackendError(
"NOT_FOUND",
"The Structure backend does not own that logical session"
);
}
return {
logicalSessionId: payload.logicalSessionId,
revision: state.revision
};
}
case "session/release": {
if (!isRecord3(payload) || !isOpaqueIdentity2(payload.logicalSessionId, 256)) {
throw new StructureBackendError(
"INVALID_REQUEST",
"Structure session release requires an opaque logical identity"
);
}
return {
logicalSessionId: payload.logicalSessionId,
released: sessions.delete(payload.logicalSessionId)
};
}
case "backend/health":
return {
family: "structure",
activeSessions: sessions.size,
maxCheckpointBytes: MAX_CHECKPOINT_BYTES
};
default:
throw new StructureBackendError(
"UNSUPPORTED",
"The requested operation is not enabled in the Structure backend"
);
}
}
function readStructureIdentity(environment) {
if (environment.SCIENTIFIC_VIEWER_FAMILY !== "structure") {
throw new Error("The Structure backend cannot serve another viewer family");
}
const backendInstanceId = environment.SCIENTIFIC_VIEWER_BACKEND_INSTANCE;
const instanceNonce = environment.SCIENTIFIC_VIEWER_INSTANCE_NONCE;
if (!isOpaqueIdentity2(backendInstanceId, 256) || !isOpaqueIdentity2(instanceNonce, 256)) {
throw new Error("The Structure backend process identity is unavailable");
}
return {
backendInstanceId,
instanceNonce,
backendGeneration: readCounter(
environment.SCIENTIFIC_VIEWER_BACKEND_GENERATION,
"generation"
),
revocationEpoch: readCounter(
environment.SCIENTIFIC_VIEWER_REVOCATION_EPOCH,
"revocation epoch"
)
};
}
function validRequestIdentity(message, identity, allowUnidentified = false) {
if (allowUnidentified && message.backendInstanceId == null) {
return true;
}
return message.backendInstanceId === identity.backendInstanceId && message.backendGeneration === identity.backendGeneration && message.instanceNonce === identity.instanceNonce && (message.family == null || message.family === "structure");
}
function checkpointSize(value) {
if (value == null) {
return 0;
}
if (value instanceof Uint8Array) {
return value.byteLength;
}
if (typeof value === "string") {
return new TextEncoder().encode(value).byteLength;
}
try {
const serialized = JSON.stringify(value);
if (serialized == null) {
throw new Error("Invalid checkpoint");
}
return new TextEncoder().encode(serialized).byteLength;
} catch {
throw new StructureBackendError(
"INVALID_REQUEST",
"The Structure checkpoint cannot be safely serialized"
);
}
}
function readCounter(value, label) {
if (typeof value !== "string" || !/^(0|[1-9][0-9]*)$/u.test(value)) {
throw new Error(`The Structure backend ${label} is invalid`);
}
const counter = Number(value);
if (!Number.isSafeInteger(counter)) {
throw new Error(`The Structure backend ${label} exceeds the safe range`);
}
return counter;
}
function isOpaqueIdentity2(value, maxLength) {
return typeof value === "string" && value.length <= maxLength && /^[A-Za-z0-9][A-Za-z0-9._:-]*$/u.test(value);
}
function isRecord3(value) {
return typeof value === "object" && value != null && !Array.isArray(value);
}
if (process.env.SCIENTIFIC_VIEWER_FAMILY === "structure" && typeof process.send === "function") {
startScientificStructureBackend();
}
export {
startScientificStructureBackend
};
/*! Bundled license information:
@openai/scientific-viewer-platform/src/structure/scientific-structure-native-trajectory-bundle.mjs:
(*!
* Portions of the GROMACS XTC xdr3dfcoord decoder are derived from the Mol*
* project, Copyright (c) 2020 Mol* contributors, under the MIT License:
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to
* deal in the Software without restriction, including without limitation the
* rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
* sell copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
* IN THE SOFTWARE.
*)
*/
SHA-256: d615a4b9f9f8877f8fe71a14759cb5b007d67c3e740c849e413e35c4d888ae92