molstar
Version:
A comprehensive macromolecular library.
278 lines • 14.9 kB
JavaScript
/**
* Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { __awaiter, __generator } from "tslib";
import { Task, chunkedSubtask } from '../../../mol-task';
import { Tokenizer, TokenBuilder } from '../common/text/tokenizer';
import { ReaderResult as Result } from '../result';
import { TokenColumnProvider as TokenColumn } from '../common/text/column/token';
import { Column } from '../../../mol-data/db';
var readLine = Tokenizer.readLine, skipWhitespace = Tokenizer.skipWhitespace, eatValue = Tokenizer.eatValue, eatLine = Tokenizer.eatLine, markStart = Tokenizer.markStart;
var reWhitespace = /\s+/;
var reTitle = /(^\*|REMARK)*/;
function State(tokenizer, runtimeCtx) {
return {
tokenizer: tokenizer,
runtimeCtx: runtimeCtx,
};
}
function handleAtoms(state, count) {
return __awaiter(this, void 0, void 0, function () {
var tokenizer, atomId, segmentName, residueId, residueName, atomName, atomType, charge, mass, position, line, isLammpsFull, n, length, linesAlreadyRead;
return __generator(this, function (_a) {
switch (_a.label) {
case 0:
tokenizer = state.tokenizer;
atomId = TokenBuilder.create(tokenizer.data, count * 2);
segmentName = TokenBuilder.create(tokenizer.data, count * 2);
residueId = TokenBuilder.create(tokenizer.data, count * 2);
residueName = TokenBuilder.create(tokenizer.data, count * 2);
atomName = TokenBuilder.create(tokenizer.data, count * 2);
atomType = TokenBuilder.create(tokenizer.data, count * 2);
charge = TokenBuilder.create(tokenizer.data, count * 2);
mass = TokenBuilder.create(tokenizer.data, count * 2);
position = tokenizer.position;
line = readLine(tokenizer).trim();
tokenizer.position = position;
isLammpsFull = line.split(reWhitespace).length === 7;
n = isLammpsFull ? 6 : 8;
length = tokenizer.length;
linesAlreadyRead = 0;
return [4 /*yield*/, chunkedSubtask(state.runtimeCtx, 100000, void 0, function (chunkSize) {
var linesToRead = Math.min(count - linesAlreadyRead, chunkSize);
for (var i = 0; i < linesToRead; ++i) {
for (var j = 0; j < n; ++j) {
skipWhitespace(tokenizer);
markStart(tokenizer);
eatValue(tokenizer);
if (isLammpsFull) {
switch (j) {
case 0:
TokenBuilder.addUnchecked(atomId, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
case 1:
TokenBuilder.addUnchecked(residueId, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
case 2:
TokenBuilder.addUnchecked(atomName, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
case 3:
TokenBuilder.addUnchecked(atomType, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
case 4:
TokenBuilder.addUnchecked(charge, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
case 5:
TokenBuilder.addUnchecked(mass, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
}
}
else {
switch (j) {
case 0:
TokenBuilder.addUnchecked(atomId, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
case 1:
TokenBuilder.addUnchecked(segmentName, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
case 2:
TokenBuilder.addUnchecked(residueId, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
case 3:
TokenBuilder.addUnchecked(residueName, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
case 4:
TokenBuilder.addUnchecked(atomName, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
case 5:
TokenBuilder.addUnchecked(atomType, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
case 6:
TokenBuilder.addUnchecked(charge, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
case 7:
TokenBuilder.addUnchecked(mass, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
}
}
}
// ignore any extra columns
eatLine(tokenizer);
markStart(tokenizer);
}
linesAlreadyRead += linesToRead;
return linesToRead;
}, function (ctx) { return ctx.update({ message: 'Parsing...', current: tokenizer.position, max: length }); })];
case 1:
_a.sent();
return [2 /*return*/, {
count: count,
atomId: TokenColumn(atomId)(Column.Schema.int),
segmentName: isLammpsFull
? TokenColumn(residueId)(Column.Schema.str)
: TokenColumn(segmentName)(Column.Schema.str),
residueId: TokenColumn(residueId)(Column.Schema.int),
residueName: isLammpsFull
? TokenColumn(residueId)(Column.Schema.str)
: TokenColumn(residueName)(Column.Schema.str),
atomName: TokenColumn(atomName)(Column.Schema.str),
atomType: TokenColumn(atomType)(Column.Schema.str),
charge: TokenColumn(charge)(Column.Schema.float),
mass: TokenColumn(mass)(Column.Schema.float)
}];
}
});
});
}
function handleBonds(state, count) {
return __awaiter(this, void 0, void 0, function () {
var tokenizer, atomIdA, atomIdB, length, bondsAlreadyRead;
return __generator(this, function (_a) {
switch (_a.label) {
case 0:
tokenizer = state.tokenizer;
atomIdA = TokenBuilder.create(tokenizer.data, count * 2);
atomIdB = TokenBuilder.create(tokenizer.data, count * 2);
length = tokenizer.length;
bondsAlreadyRead = 0;
return [4 /*yield*/, chunkedSubtask(state.runtimeCtx, 10, void 0, function (chunkSize) {
var bondsToRead = Math.min(count - bondsAlreadyRead, chunkSize);
for (var i = 0; i < bondsToRead; ++i) {
for (var j = 0; j < 2; ++j) {
skipWhitespace(tokenizer);
markStart(tokenizer);
eatValue(tokenizer);
switch (j) {
case 0:
TokenBuilder.addUnchecked(atomIdA, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
case 1:
TokenBuilder.addUnchecked(atomIdB, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
}
}
}
bondsAlreadyRead += bondsToRead;
return bondsToRead;
}, function (ctx) { return ctx.update({ message: 'Parsing...', current: tokenizer.position, max: length }); })];
case 1:
_a.sent();
return [2 /*return*/, {
count: count,
atomIdA: TokenColumn(atomIdA)(Column.Schema.int),
atomIdB: TokenColumn(atomIdB)(Column.Schema.int),
}];
}
});
});
}
function parseTitle(state, count) {
var title = [];
for (var i = 0; i < count; ++i) {
var line = readLine(state.tokenizer);
title.push(line.replace(reTitle, '').trim());
}
return title;
}
function parseInternal(data, ctx) {
return __awaiter(this, void 0, void 0, function () {
var tokenizer, state, title, atoms, bonds, id, line, numTitle, numAtoms, numBonds, result;
return __generator(this, function (_a) {
switch (_a.label) {
case 0:
tokenizer = Tokenizer(data);
state = State(tokenizer, ctx);
title = undefined;
atoms = undefined;
bonds = undefined;
id = readLine(state.tokenizer).trim();
_a.label = 1;
case 1:
if (!(tokenizer.tokenEnd < tokenizer.length)) return [3 /*break*/, 8];
line = readLine(state.tokenizer).trim();
if (!line.includes('!NTITLE')) return [3 /*break*/, 2];
numTitle = parseInt(line.split(reWhitespace)[0]);
title = parseTitle(state, numTitle);
return [3 /*break*/, 7];
case 2:
if (!line.includes('!NATOM')) return [3 /*break*/, 4];
numAtoms = parseInt(line.split(reWhitespace)[0]);
return [4 /*yield*/, handleAtoms(state, numAtoms)];
case 3:
atoms = _a.sent();
return [3 /*break*/, 7];
case 4:
if (!line.includes('!NBOND')) return [3 /*break*/, 6];
numBonds = parseInt(line.split(reWhitespace)[0]);
return [4 /*yield*/, handleBonds(state, numBonds)];
case 5:
bonds = _a.sent();
return [3 /*break*/, 8]; // TODO: don't break when the below are implemented
case 6:
if (line.includes('!NTHETA')) {
// TODO
}
else if (line.includes('!NPHI')) {
// TODO
}
else if (line.includes('!NIMPHI')) {
// TODO
}
else if (line.includes('!NDON')) {
// TODO
}
else if (line.includes('!NACC')) {
// TODO
}
else if (line.includes('!NNB')) {
// TODO
}
else if (line.includes('!NGRP NST2')) {
// TODO
}
else if (line.includes('!MOLNT')) {
// TODO
}
else if (line.includes('!NUMLP NUMLPH')) {
// TODO
}
else if (line.includes('!NCRTERM')) {
// TODO
}
_a.label = 7;
case 7: return [3 /*break*/, 1];
case 8:
if (title === undefined) {
title = [];
}
if (atoms === undefined) {
return [2 /*return*/, Result.error('no atoms data')];
}
if (bonds === undefined) {
return [2 /*return*/, Result.error('no bonds data')];
}
result = {
id: id,
title: title,
atoms: atoms,
bonds: bonds
};
return [2 /*return*/, Result.success(result)];
}
});
});
}
export function parsePsf(data) {
var _this = this;
return Task.create('Parse PSF', function (ctx) { return __awaiter(_this, void 0, void 0, function () {
return __generator(this, function (_a) {
switch (_a.label) {
case 0: return [4 /*yield*/, parseInternal(data, ctx)];
case 1: return [2 /*return*/, _a.sent()];
}
});
}); });
}
//# sourceMappingURL=parser.js.map