molstar
Version:
A comprehensive macromolecular library.
271 lines (270 loc) • 12 kB
JavaScript
"use strict";
/**
* Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Zepei Xu <xuzepei19950617@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author Eric E <etongfu@@outlook.com>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.parseMol2 = parseMol2;
// NOTES
// When want to created undefined string column, must use
// undefStr = UndefinedColumn(molecule.num_atoms, ColumnType.str)
// but not
// const undefPooledStr = UndefinedColumn(molecule.num_atoms, ColumnType.pooledStr);
// because latter actuall return a column of zeros
const db_1 = require("../../../mol-data/db");
const tokenizer_1 = require("../common/text/tokenizer");
const token_1 = require("../common/text/column/token");
const result_1 = require("../result");
const mol_task_1 = require("../../../mol-task");
const { skipWhitespace, eatValue, markLine, getTokenString, skipStrictWhitespace } = tokenizer_1.Tokenizer;
function createEmptyMolecule() {
return {
mol_name: '',
num_atoms: 0,
num_bonds: 0,
num_subst: 0,
num_feat: 0,
num_sets: 0,
mol_type: '',
charge_type: '',
status_bits: '',
mol_comment: ''
};
}
function State(tokenizer, runtimeCtx) {
return {
tokenizer,
molecule: createEmptyMolecule(),
runtimeCtx
};
}
const reWhitespace = /\s+/g;
function handleMolecule(state) {
const { tokenizer, molecule } = state;
while (getTokenString(tokenizer) !== '@<TRIPOS>MOLECULE' && tokenizer.position < tokenizer.data.length) {
markLine(tokenizer);
}
markLine(tokenizer);
molecule.mol_name = getTokenString(tokenizer);
markLine(tokenizer);
const values = getTokenString(tokenizer).trim().split(reWhitespace);
molecule.num_atoms = parseInt(values[0]);
molecule.num_bonds = parseInt(values[1]);
molecule.num_subst = parseInt(values[2]);
molecule.num_feat = parseInt(values[3]);
molecule.num_sets = parseInt(values[4]);
markLine(tokenizer);
const mol_type = getTokenString(tokenizer);
if (mol_type.startsWith('@<TRIPOS>'))
return;
molecule.mol_type = mol_type;
markLine(tokenizer);
const charge_type = getTokenString(tokenizer);
if (charge_type.startsWith('@<TRIPOS>'))
return;
molecule.charge_type = charge_type;
markLine(tokenizer);
const status_bits = getTokenString(tokenizer);
if (status_bits.startsWith('@<TRIPOS>'))
return;
molecule.status_bits = status_bits;
markLine(tokenizer);
const mol_comment = getTokenString(tokenizer);
if (mol_comment.startsWith('@<TRIPOS>'))
return;
molecule.mol_comment = mol_comment;
}
/**
* Just read the columns and get the max count of columns for the **atoms** and **bonds**
* @param linesToRead The total lines
* @param tokenIndexColums
* @param tokenizer
* @description
* !!!This function has side effects!!!
* 1. Called inside of the `chunkedSubtask`
* 2. It will change the parameters of the `tokenIndexColums` , `tokenizer` and `linesToRead`
* @returns The max count of columns
*/
function _readColumnsAndGetMaxCount(linesToRead, tokenIndexColums, tokenizer) {
let maxColumnCount = 0;
for (let i = 0; i < linesToRead; i++) {
let tokenIndex = 0;
skipWhitespace(tokenizer);
while (true) {
skipStrictWhitespace(tokenizer);
tokenizer.tokenStart = tokenizer.position;
eatValue(tokenizer);
if (tokenizer.tokenStart === tokenizer.tokenEnd)
break;
const col = tokenIndexColums[tokenIndex++];
if (!col)
continue;
tokenizer_1.TokenBuilder.addUnchecked(col, tokenizer.tokenStart, tokenizer.tokenEnd);
}
if (tokenIndex > maxColumnCount)
maxColumnCount = tokenIndex;
for (let cI = tokenIndex; cI < tokenIndexColums.length; cI++) {
tokenizer_1.TokenBuilder.addUnchecked(tokenIndexColums[cI], 0, 0);
}
}
return maxColumnCount + 1;
}
async function handleAtoms(state) {
const { tokenizer, molecule } = state;
// skip empty lines and '@<TRIPOS>ATOM'
while (getTokenString(tokenizer) !== '@<TRIPOS>ATOM' && tokenizer.position < tokenizer.data.length) {
markLine(tokenizer);
}
const initialTokenizerPosition = tokenizer.position;
const initialTokenizerLineNumber = tokenizer.lineNumber;
// columns
const atom_idTokens = tokenizer_1.TokenBuilder.create(tokenizer.data, molecule.num_atoms * 2);
const atom_nameTokens = tokenizer_1.TokenBuilder.create(tokenizer.data, molecule.num_atoms * 2);
const xTokens = tokenizer_1.TokenBuilder.create(tokenizer.data, molecule.num_atoms * 2);
const yTokens = tokenizer_1.TokenBuilder.create(tokenizer.data, molecule.num_atoms * 2);
const zTokens = tokenizer_1.TokenBuilder.create(tokenizer.data, molecule.num_atoms * 2);
const atom_typeTokens = tokenizer_1.TokenBuilder.create(tokenizer.data, molecule.num_atoms * 2);
const subst_idTokens = tokenizer_1.TokenBuilder.create(tokenizer.data, molecule.num_atoms * 2);
const subst_nameTokens = tokenizer_1.TokenBuilder.create(tokenizer.data, molecule.num_atoms * 2);
const chargeTokens = tokenizer_1.TokenBuilder.create(tokenizer.data, molecule.num_atoms * 2);
const status_bitTokens = tokenizer_1.TokenBuilder.create(tokenizer.data, molecule.num_atoms * 2);
const undefFloat = db_1.Column.Undefined(molecule.num_atoms, db_1.Column.Schema.float);
const undefInt = db_1.Column.Undefined(molecule.num_atoms, db_1.Column.Schema.int);
const undefStr = db_1.Column.Undefined(molecule.num_atoms, db_1.Column.Schema.str);
tokenizer.position = initialTokenizerPosition;
tokenizer.lineNumber = initialTokenizerLineNumber;
let maxColumnCount = 0;
const tokenIndexToColumn = [
atom_idTokens,
atom_nameTokens,
xTokens,
yTokens,
zTokens,
atom_typeTokens,
subst_idTokens,
subst_nameTokens,
chargeTokens,
status_bitTokens
];
const { length } = tokenizer;
let linesAlreadyRead = 0;
await (0, mol_task_1.chunkedSubtask)(state.runtimeCtx, 100000, void 0, chunkSize => {
const linesToRead = Math.min(molecule.num_atoms - linesAlreadyRead, chunkSize);
maxColumnCount = _readColumnsAndGetMaxCount(linesToRead, tokenIndexToColumn, tokenizer);
linesAlreadyRead += linesToRead;
return linesToRead;
}, ctx => ctx.update({ message: 'Parsing...', current: tokenizer.position, max: length }));
const ret = {
count: molecule.num_atoms,
atom_id: (0, token_1.TokenColumnProvider)(atom_idTokens)(db_1.Column.Schema.int),
atom_name: (0, token_1.TokenColumnProvider)(atom_nameTokens)(db_1.Column.Schema.str),
x: (0, token_1.TokenColumnProvider)(xTokens)(db_1.Column.Schema.float),
y: (0, token_1.TokenColumnProvider)(yTokens)(db_1.Column.Schema.float),
z: (0, token_1.TokenColumnProvider)(zTokens)(db_1.Column.Schema.float),
atom_type: maxColumnCount > 5 ? (0, token_1.TokenColumnProvider)(atom_typeTokens)(db_1.Column.Schema.str) : undefStr,
subst_id: maxColumnCount > 6 ? (0, token_1.TokenColumnProvider)(subst_idTokens)(db_1.Column.Schema.int) : undefInt,
subst_name: maxColumnCount > 7 ? (0, token_1.TokenColumnProvider)(subst_nameTokens)(db_1.Column.Schema.str) : undefStr,
charge: maxColumnCount > 8 ? (0, token_1.TokenColumnProvider)(chargeTokens)(db_1.Column.Schema.float) : undefFloat,
status_bit: maxColumnCount > 9 ? (0, token_1.TokenColumnProvider)(status_bitTokens)(db_1.Column.Schema.str) : undefStr,
};
return ret;
}
async function handleBonds(state) {
const { tokenizer, molecule } = state;
while (getTokenString(tokenizer) !== '@<TRIPOS>BOND' && tokenizer.position < tokenizer.data.length) {
markLine(tokenizer);
}
const initialTokenizerPosition = tokenizer.position;
const initialTokenizerLineNumber = tokenizer.lineNumber;
// columns
const bond_idTokens = tokenizer_1.TokenBuilder.create(tokenizer.data, molecule.num_bonds * 2);
const origin_bond_idTokens = tokenizer_1.TokenBuilder.create(tokenizer.data, molecule.num_bonds * 2);
const target_bond_idTokens = tokenizer_1.TokenBuilder.create(tokenizer.data, molecule.num_bonds * 2);
const bondTypeTokens = tokenizer_1.TokenBuilder.create(tokenizer.data, molecule.num_bonds * 2);
const status_bitTokens = tokenizer_1.TokenBuilder.create(tokenizer.data, molecule.num_bonds * 2);
tokenizer.position = initialTokenizerPosition;
tokenizer.lineNumber = initialTokenizerLineNumber;
let maxColumnCount = 0;
const tokenIndexToColumn = [
bond_idTokens,
origin_bond_idTokens,
target_bond_idTokens,
bondTypeTokens,
status_bitTokens
];
const { length } = tokenizer;
let linesAlreadyRead = 0;
await (0, mol_task_1.chunkedSubtask)(state.runtimeCtx, 100000, void 0, chunkSize => {
const linesToRead = Math.min(molecule.num_bonds - linesAlreadyRead, chunkSize);
maxColumnCount = _readColumnsAndGetMaxCount(linesToRead, tokenIndexToColumn, tokenizer);
linesAlreadyRead += linesToRead;
return linesToRead;
}, ctx => ctx.update({ message: 'Parsing...', current: tokenizer.position, max: length }));
const ret = {
count: molecule.num_bonds,
bond_id: (0, token_1.TokenColumnProvider)(bond_idTokens)(db_1.Column.Schema.int),
origin_atom_id: (0, token_1.TokenColumnProvider)(origin_bond_idTokens)(db_1.Column.Schema.int),
target_atom_id: (0, token_1.TokenColumnProvider)(target_bond_idTokens)(db_1.Column.Schema.int),
bond_type: (0, token_1.TokenColumnProvider)(bondTypeTokens)(db_1.Column.Schema.str),
status_bits: maxColumnCount > 4
? (0, token_1.TokenColumnProvider)(status_bitTokens)(db_1.Column.Schema.str)
: db_1.Column.Undefined(molecule.num_bonds, db_1.Column.Schema.str),
};
return ret;
}
function handleCrysin(state) {
const { tokenizer } = state;
while (tokenizer.position < tokenizer.data.length) {
const l = getTokenString(tokenizer);
if (l === '@<TRIPOS>MOLECULE') {
return;
}
else if (l === '@<TRIPOS>CRYSIN') {
break;
}
else {
markLine(tokenizer);
}
}
if (tokenizer.position >= tokenizer.data.length)
return;
markLine(tokenizer);
const values = getTokenString(tokenizer).trim().split(reWhitespace);
return {
a: parseFloat(values[0]),
b: parseFloat(values[1]),
c: parseFloat(values[2]),
alpha: parseFloat(values[3]),
beta: parseFloat(values[4]),
gamma: parseFloat(values[5]),
spaceGroup: parseInt(values[6], 10),
setting: parseInt(values[7], 10),
};
}
async function parseInternal(ctx, data, name) {
const tokenizer = (0, tokenizer_1.Tokenizer)(data);
ctx.update({ message: 'Parsing...', current: 0, max: data.length });
const structures = [];
while (tokenizer.position < data.length) {
const state = State(tokenizer, ctx);
handleMolecule(state);
const atoms = await handleAtoms(state);
const bonds = await handleBonds(state);
const crysin = handleCrysin(state);
structures.push({ molecule: state.molecule, atoms, bonds, crysin });
skipWhitespace(tokenizer);
while (getTokenString(tokenizer) !== '@<TRIPOS>MOLECULE' && tokenizer.position < tokenizer.data.length) {
markLine(tokenizer);
}
}
const result = { name, structures };
return result_1.ReaderResult.success(result);
}
function parseMol2(data, name) {
return mol_task_1.Task.create('Parse MOL2', async (ctx) => {
return await parseInternal(ctx, data, name);
});
}