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Commit 2735ab45 authored by Zepei Xu's avatar Zepei Xu
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complete mol2 parser, and its unit tests

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src/reader/mol2/parser.ts
+ 86
− 81
View file @ 2735ab45
// 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
import Tokenizer from '../common/text/tokenizer'
import FixedColumn from '../common/text/column/fixed'
import { ColumnType, UndefinedColumn } from '../common/column'
import * as Schema from './schema'
import Result from '../result'
import Computation from '../../utils/computation' ////////// not using this
/*////////////////////////// NOTES //////////////////////////////
Not using async, wait, promises, computation, chunker.
Formatting is not clear, different exmaples mol2 files has different field sizes, so making
columns using col() is not possible. Need to implement checks for optional columns, but not clear
about the names of each entry in a row in the example files.
Don't know when to use str and when to use pooledStr
Unlike gro file, mol2 file don't save 'hasSomthing' properties in the header-like Molecule
///////////////////////////////////////////////////////////////*/
import Computation from '../../utils/computation'
interface State {
tokenizer: Tokenizer,
molecule: Schema.Molecule,
///////////// not including Computation.chunker /////////////
chunker: Computation.Chunker
}
......@@ -44,11 +37,11 @@ function createEmptyMolecule(): Schema.Molecule {
function State(tokenizer: Tokenizer): State { //////////// not having ctx: Computation.Context as a parameter //////////////
function State(tokenizer: Tokenizer, ctx: Computation.Context): State {
return {
tokenizer,
molecule: createEmptyMolecule(),
//////////// not having chunker: Computation.chunker(ctx, 100000) ///////////
chunker: Computation.chunker(ctx, 100000)
};
}
......@@ -58,18 +51,18 @@ function State(tokenizer: Tokenizer): State { //////////// not having ctx: Compu
function handleMolecule(state: State) {
const { tokenizer, molecule } = state;
Tokenizer.markLine(tokenizer); // skip the line '@<TRIPOS>MOLECULE'
Tokenizer.markLine(tokenizer);
let name = Tokenizer.getTokenString(tokenizer);
molecule.mol_name = name;
Tokenizer.markLine(tokenizer);
const values = Tokenizer.getTokenString(tokenizer).trim().split(/\s+/g);
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]);
molecule.num_atoms = parseInt(values[0]) ? parseInt(values[1]) : 0;
molecule.num_bonds = parseInt(values[1]) ? parseInt(values[1]) : 0;
molecule.num_subst = parseInt(values[2]) ? parseInt(values[1]) : 0;
molecule.num_feat = parseInt(values[3]) ? parseInt(values[1]) : 0;
molecule.num_sets = parseInt(values[4]) ? parseInt(values[1]) : 0;
Tokenizer.markLine(tokenizer);
molecule.mol_type = Tokenizer.getTokenString(tokenizer);
......@@ -77,56 +70,71 @@ function handleMolecule(state: State) {
Tokenizer.markLine(tokenizer);
molecule.charge_type = Tokenizer.getTokenString(tokenizer);
// skip the empty line
Tokenizer.markLine(tokenizer)
Tokenizer.markLine(tokenizer);
if(Tokenizer.getTokenString(tokenizer) == ''){return}
else{molecule.status_bits = Tokenizer.getTokenString(tokenizer)}
Tokenizer.markLine(tokenizer);
if(Tokenizer.getTokenString(tokenizer) == ''){return}
else{molecule.mol_comment = Tokenizer.getTokenString(tokenizer)}
}
function handleAtoms(state: State): Schema.Atoms {
async function handleAtoms(state: State): Promise<Schema.Atoms> {
const { tokenizer, molecule } = state;
////////// not using readLinesAsync /////////
const lines = Tokenizer.readLines(tokenizer, molecule.num_atoms);
// default all false
const hasSubst_id = false;
const hasSubst_name = false;
const hasCharge = false;
const hasStatus_bit = false;
/*
const pO = 20;
const pW = state.header.precision.position + 5;
const vO = pO + 3 * pW;
const vW = state.header.precision.velocity + 4;
*/
let hasSubst_id = false;
let hasSubst_name = false;
let hasCharge = false;
let hasStatus_bit = false;
// skip empty lines and '@<TRIPOS>ATOM'
while(Tokenizer.getTokenString(tokenizer) != '@<TRIPOS>ATOM'){
Tokenizer.markLine(tokenizer);
}
const lines = await Tokenizer.readLinesAsync(tokenizer, molecule.num_atoms, state.chunker);
const firstLine = tokenizer.data.substring(lines.indices[0], lines.indices[1]);
const firstLineArray = firstLine.trim().split(/\s+/g)
const length = firstLineArray.length;
if(length == 9){
hasSubst_id = true;
hasSubst_name = true;
hasCharge = true;
}else if(length == 10){
hasSubst_id = true;
hasSubst_name = true;
hasCharge = true;
hasStatus_bit = true;
}
const col = FixedColumn(lines);
const undefInt = UndefinedColumn(molecule.num_atoms, ColumnType.int);
const undefFloat = UndefinedColumn(molecule.num_atoms, ColumnType.float);
//const undefPooledStr = UndefinedColumn(molecule.num_atoms, ColumnType.pooledStr);
// created below column to pass unit tests
const undefStr = UndefinedColumn(molecule.num_atoms, ColumnType.str);
const undefPooledStr = UndefinedColumn(molecule.num_atoms, ColumnType.pooledStr);
/////// wanted to have const undef = UndefinedColumn(molecule.num_atoms) like col, but failed
/////// some unclear about the formatting, like the field sizes
const ret = {
count: molecule.num_atoms,
atom_id: col(0, 7, ColumnType.int),
atom_name: col(7, 9, ColumnType.str), ////// don't know use str or pooledStr
atom_name: col(7, 9, ColumnType.pooledStr),
x: col(16, 10, ColumnType.float),
y: col(26, 10, ColumnType.float),
z: col(36, 10, ColumnType.float),
atom_type: col(46, 0, ColumnType.str), ////// don't know use str or pooledStr //////// don't know which is the atom_type
atom_type: col(46, 6, ColumnType.pooledStr),
// optional properties
subst_id: hasSubst_id ? col(0, 0, ColumnType.int) : undefInt,
subst_name: hasSubst_name ? col(0, 0, ColumnType.str) : undefStr,///////// don't know use str or pooledStr
charge: hasCharge ? col(0, 0, ColumnType.float) : undefFloat, //////// don't know use int or float
status_bit: hasStatus_bit ? col(0, 0, ColumnType.pooledStr) : undefPooledStr, ////////// don't know use str or pooledStr
subst_id: hasSubst_id ? col(52, 6, ColumnType.int) : undefInt,
subst_name: hasSubst_name ? col(58, 8, ColumnType.pooledStr) : undefStr,
charge: hasCharge ? col(66, 10, ColumnType.float) : undefFloat,
// undefPooledStr cannot pass unit tests because it create a column of zeros but not empty strings
//status_bit: hasStatus_bit ? col(76, 100, ColumnType.pooledStr) : undefPooledStr,
// use undefStr instead to pass unit tests
status_bit: hasStatus_bit ? col(76, 100, ColumnType.pooledStr) : undefStr,
};
return ret;
......@@ -135,39 +143,35 @@ function handleAtoms(state: State): Schema.Atoms {
function handleBonds(state: State): Schema.Bonds {
async function handleBonds(state: State): Promise<Schema.Bonds> {
const { tokenizer, molecule } = state;
let hasStatus_bit = false;
////////// not using readLinesAsync /////////
const lines = Tokenizer.readLines(tokenizer, molecule.num_bonds);
// default all false
const hasStatus_bit = false;
/*
const pO = 20;
const pW = state.header.precision.position + 5;
const vO = pO + 3 * pW;
const vW = state.header.precision.velocity + 4;
*/
while(Tokenizer.getTokenString(tokenizer) != '@<TRIPOS>BOND'){
Tokenizer.markLine(tokenizer);
}
const lines = await Tokenizer.readLinesAsync(tokenizer, molecule.num_bonds, state.chunker);
const firstLine = tokenizer.data.substring(lines.indices[0], lines.indices[1]);
const length = firstLine.split(' ').length;
if(length == 4){
hasStatus_bit = true;
}
const col = FixedColumn(lines);
const undefInt = UndefinedColumn(molecule.num_bonds, ColumnType.int);
const undefFloat = UndefinedColumn(molecule.num_bonds, ColumnType.float);
const undefStr = UndefinedColumn(molecule.num_bonds, ColumnType.str);
const undefPooledStr = UndefinedColumn(molecule.num_bonds, ColumnType.pooledStr);
/////// wanted to have const undef = UndefinedColumn(molecule.num_atoms) like col, but failed
//const undefPooledStr = UndefinedColumn(molecule.num_bonds, ColumnType.pooledStr);
// created below column to pass unit tests
const undefStr = UndefinedColumn(molecule.num_atoms, ColumnType.str);
/////// some unclear about the formatting, like the field sizes
const ret = {
count: molecule.num_bonds,
bond_id: col(0, 6, ColumnType.int),
origin_atom_id: col(6, 6, ColumnType.int),
target_atom_id: col(12, 6, ColumnType.int),
bond_type: col(18, 5, ColumnType.str), ///////// don't know use str or pooledStr
bond_type: col(18, 5, ColumnType.pooledStr),
// optional properties
status_bits: hasStatus_bit ? col(0, 0, ColumnType.str) : undefStr, ///////// don't know use str or pooledStr
// undefPooledStr cannot pass unit tests because it create a column of zeros but not empty strings
//status_bits: hasStatus_bit ? col(23, 50, ColumnType.pooledStr) : undefPooledStr,
status_bits: hasStatus_bit ? col(23, 50, ColumnType.pooledStr) : undefStr,
};
return ret;
......@@ -176,16 +180,16 @@ function handleBonds(state: State): Schema.Bonds {
//////// not using async here
function parseInternal(data: string): Result<Schema.File> { /////// not having ctx as a parameter, and not returning Promise
async function parseInternal(data: string, ctx: Computation.Context): Promise<Result<Schema.File>> {
const tokenizer = Tokenizer(data);
ctx.update({ message: 'Parsing...', current: 0, max: data.length });
const structures: Schema.Structure[] = [];
while (tokenizer.position < data.length) {
const state = State(tokenizer);//////////different
const state = State(tokenizer, ctx);
handleMolecule(state);
const atoms = handleAtoms(state);
const bonds = handleBonds(state);
const atoms = await handleAtoms(state);
const bonds = await handleBonds(state);
structures.push({ molecule: state.molecule, atoms, bonds });
}
......@@ -197,9 +201,10 @@ function parseInternal(data: string): Result<Schema.File> { /////// not having c
///////// diffrent than gro parser
export function parse(data: string) {
return parseInternal(data);
return Computation.create<Result<Schema.File>>(async ctx => {
return await parseInternal(data, ctx);
});
}
export default parse;
\ No newline at end of file
src/reader/mol2/schema.d.ts
+ 0
− 1
View file @ 2735ab45
......@@ -25,7 +25,6 @@ export interface Molecule {
charge_type: string
status_bits: string
mol_comment: string
///////////// precisions are not saved for later use, and there is not 'hasSomthing' properties
}
export interface Atoms {
......
src/reader/spec/gro.spec.ts
+ 0
− 1
View file @ 2735ab45
......@@ -32,7 +32,6 @@ describe('gro reader', () => {
console.log(parsed)
return;
}
const groFile = parsed.result;
const data = groFile.structures[0];
......
src/reader/spec/mol2.spec.ts
+ 326
− 14
View file @ 2735ab45
import Mol2 from '../mol2/parser'
const Mol2String = `@<TRIPOS>MOLECULE
......@@ -11,51 +10,364 @@ GASTEIGER
@<TRIPOS>ATOM
1 O 1.7394 -2.1169 -1.0894 O.3 1 LIG1 -0.3859
2 O -2.2941 1.0781 -1.7979 O.3 1 LIG1 -0.5033
3 O -3.6584 0.5842 0.5722 O.3 1 LIG1 -0.5033
4 N 2.6359 1.0243 0.7030 N.3 1 LIG1 -0.3162
5 C 1.6787 -1.1447 -0.0373 C.3 1 LIG1 0.0927
6 C 0.2684 -0.6866 0.1208 C.ar 1 LIG1 -0.0143
7 C 2.6376 0.0193 -0.3576 C.3 1 LIG1 0.0258
8 C -0.3658 -0.0099 -0.9212 C.ar 1 LIG1 -0.0109
9 C -0.4164 -0.9343 1.3105 C.ar 1 LIG1 -0.0524
10 C -1.6849 0.4191 -0.7732 C.ar 1 LIG1 0.1586
11 C -1.7353 -0.5053 1.4585 C.ar 1 LIG1 -0.0162
12 C -2.3696 0.1713 0.4166 C.ar 1 LIG1 0.1582
13 C 3.5645 2.1013 0.3950 C.3 1 LIG1 -0.0157
14 H 2.0210 -1.6511 0.8741 H 1 LIG1 0.0656
15 H 2.3808 0.4742 -1.3225 H 1 LIG1 0.0453
16 H 3.6478 -0.3931 -0.4831 H 1 LIG1 0.0453
17 H 0.1501 0.1801 -1.8589 H 1 LIG1 0.0659
18 H 0.0640 -1.4598 2.1315 H 1 LIG1 0.0622
19 H 2.9013 0.5888 1.5858 H 1 LIG1 0.1217
20 H -2.2571 -0.7050 2.3907 H 1 LIG1 0.0655
21 H 2.6646 -2.4067 -1.1652 H 1 LIG1 0.2103
22 H 3.2862 2.6124 -0.5325 H 1 LIG1 0.0388
23 H 4.5925 1.7346 0.3078 H 1 LIG1 0.0388
24 H 3.5401 2.8441 1.1985 H 1 LIG1 0.0388
25 H -3.2008 1.2997 -1.5231 H 1 LIG1 0.2923
26 H -3.9690 0.3259 1.4570 H 1 LIG1 0.2923
@<TRIPOS>BOND
1 1 5 1
2 1 21 1`
2 1 21 1
3 2 10 1
4 2 25 1
5 3 12 1
6 3 26 1
7 4 7 1
8 4 13 1
9 4 19 1
10 5 6 1
11 5 7 1
12 5 14 1
13 6 8 ar
14 6 9 ar
15 7 15 1
16 7 16 1
17 8 10 ar
18 8 17 1
19 9 11 ar
20 9 18 1
21 10 12 ar
22 11 12 ar
23 11 20 1
24 13 22 1
25 13 23 1
26 13 24 1`
const Mol2StringMultiBlocks = `@<TRIPOS>MOLECULE
5816
26 26 0 0 0
SMALL
GASTEIGER
@<TRIPOS>ATOM
1 O 1.7394 -2.1169 -1.0894 O.3 1 LIG1 -0.3859
2 O -2.2941 1.0781 -1.7979 O.3 1 LIG1 -0.5033
3 O -3.6584 0.5842 0.5722 O.3 1 LIG1 -0.5033
4 N 2.6359 1.0243 0.7030 N.3 1 LIG1 -0.3162
5 C 1.6787 -1.1447 -0.0373 C.3 1 LIG1 0.0927
6 C 0.2684 -0.6866 0.1208 C.ar 1 LIG1 -0.0143
7 C 2.6376 0.0193 -0.3576 C.3 1 LIG1 0.0258
8 C -0.3658 -0.0099 -0.9212 C.ar 1 LIG1 -0.0109
9 C -0.4164 -0.9343 1.3105 C.ar 1 LIG1 -0.0524
10 C -1.6849 0.4191 -0.7732 C.ar 1 LIG1 0.1586
11 C -1.7353 -0.5053 1.4585 C.ar 1 LIG1 -0.0162
12 C -2.3696 0.1713 0.4166 C.ar 1 LIG1 0.1582
13 C 3.5645 2.1013 0.3950 C.3 1 LIG1 -0.0157
14 H 2.0210 -1.6511 0.8741 H 1 LIG1 0.0656
15 H 2.3808 0.4742 -1.3225 H 1 LIG1 0.0453
16 H 3.6478 -0.3931 -0.4831 H 1 LIG1 0.0453
17 H 0.1501 0.1801 -1.8589 H 1 LIG1 0.0659
18 H 0.0640 -1.4598 2.1315 H 1 LIG1 0.0622
19 H 2.9013 0.5888 1.5858 H 1 LIG1 0.1217
20 H -2.2571 -0.7050 2.3907 H 1 LIG1 0.0655
21 H 2.6646 -2.4067 -1.1652 H 1 LIG1 0.2103
22 H 3.2862 2.6124 -0.5325 H 1 LIG1 0.0388
23 H 4.5925 1.7346 0.3078 H 1 LIG1 0.0388
24 H 3.5401 2.8441 1.1985 H 1 LIG1 0.0388
25 H -3.2008 1.2997 -1.5231 H 1 LIG1 0.2923
26 H -3.9690 0.3259 1.4570 H 1 LIG1 0.2923
@<TRIPOS>BOND
1 1 5 1
2 1 21 1
3 2 10 1
4 2 25 1
5 3 12 1
6 3 26 1
7 4 7 1
8 4 13 1
9 4 19 1
10 5 6 1
11 5 7 1
12 5 14 1
13 6 8 ar
14 6 9 ar
15 7 15 1
16 7 16 1
17 8 10 ar
18 8 17 1
19 9 11 ar
20 9 18 1
21 10 12 ar
22 11 12 ar
23 11 20 1
24 13 22 1
25 13 23 1
26 13 24 1
@<TRIPOS>MOLECULE
5816
26 26 0 0 0
SMALL
GASTEIGER
@<TRIPOS>ATOM
1 O 1.7394 -2.1169 -1.0894 O.3 1 LIG1 -0.3859
2 O -2.2941 1.0781 -1.7979 O.3 1 LIG1 -0.5033
3 O -3.6584 0.5842 0.5722 O.3 1 LIG1 -0.5033
4 N 2.6359 1.0243 0.7030 N.3 1 LIG1 -0.3162
5 C 1.6787 -1.1447 -0.0373 C.3 1 LIG1 0.0927
6 C 0.2684 -0.6866 0.1208 C.ar 1 LIG1 -0.0143
7 C 2.6376 0.0193 -0.3576 C.3 1 LIG1 0.0258
8 C -0.3658 -0.0099 -0.9212 C.ar 1 LIG1 -0.0109
9 C -0.4164 -0.9343 1.3105 C.ar 1 LIG1 -0.0524
10 C -1.6849 0.4191 -0.7732 C.ar 1 LIG1 0.1586
11 C -1.7353 -0.5053 1.4585 C.ar 1 LIG1 -0.0162
12 C -2.3696 0.1713 0.4166 C.ar 1 LIG1 0.1582
13 C 3.5645 2.1013 0.3950 C.3 1 LIG1 -0.0157
14 H 2.0210 -1.6511 0.8741 H 1 LIG1 0.0656
15 H 2.3808 0.4742 -1.3225 H 1 LIG1 0.0453
16 H 3.6478 -0.3931 -0.4831 H 1 LIG1 0.0453
17 H 0.1501 0.1801 -1.8589 H 1 LIG1 0.0659
18 H 0.0640 -1.4598 2.1315 H 1 LIG1 0.0622
19 H 2.9013 0.5888 1.5858 H 1 LIG1 0.1217
20 H -2.2571 -0.7050 2.3907 H 1 LIG1 0.0655
21 H 2.6646 -2.4067 -1.1652 H 1 LIG1 0.2103
22 H 3.2862 2.6124 -0.5325 H 1 LIG1 0.0388
23 H 4.5925 1.7346 0.3078 H 1 LIG1 0.0388
24 H 3.5401 2.8441 1.1985 H 1 LIG1 0.0388
25 H -3.2008 1.2997 -1.5231 H 1 LIG1 0.2923
26 H -3.9690 0.3259 1.4570 H 1 LIG1 0.2923
@<TRIPOS>BOND
1 1 5 1
2 1 21 1
3 2 10 1
4 2 25 1
5 3 12 1
6 3 26 1
7 4 7 1
8 4 13 1
9 4 19 1
10 5 6 1
11 5 7 1
12 5 14 1
13 6 8 ar
14 6 9 ar
15 7 15 1
16 7 16 1
17 8 10 ar
18 8 17 1
19 9 11 ar
20 9 18 1
21 10 12 ar
22 11 12 ar
23 11 20 1
24 13 22 1
25 13 23 1
26 13 24 1`
const Mol2StringMinimal = `@<TRIPOS>MOLECULE
5816
26 26 0 0 0
SMALL
GASTEIGER
@<TRIPOS>ATOM
1 O 1.7394 -2.1169 -1.0894 O.3
2 O -2.2941 1.0781 -1.7979 O.3
3 O -3.6584 0.5842 0.5722 O.3
4 N 2.6359 1.0243 0.7030 N.3
5 C 1.6787 -1.1447 -0.0373 C.3
6 C 0.2684 -0.6866 0.1208 C.ar
7 C 2.6376 0.0193 -0.3576 C.3
8 C -0.3658 -0.0099 -0.9212 C.ar
9 C -0.4164 -0.9343 1.3105 C.ar
10 C -1.6849 0.4191 -0.7732 C.ar
11 C -1.7353 -0.5053 1.4585 C.ar
12 C -2.3696 0.1713 0.4166 C.ar
13 C 3.5645 2.1013 0.3950 C.3
14 H 2.0210 -1.6511 0.8741 H
15 H 2.3808 0.4742 -1.3225 H
16 H 3.6478 -0.3931 -0.4831 H
17 H 0.1501 0.1801 -1.8589 H
18 H 0.0640 -1.4598 2.1315 H
19 H 2.9013 0.5888 1.5858 H
20 H -2.2571 -0.7050 2.3907 H
21 H 2.6646 -2.4067 -1.1652 H
22 H 3.2862 2.6124 -0.5325 H
23 H 4.5925 1.7346 0.3078 H
24 H 3.5401 2.8441 1.1985 H
25 H -3.2008 1.2997 -1.5231 H
26 H -3.9690 0.3259 1.4570 H
@<TRIPOS>BOND
1 1 5 1
2 1 21 1
3 2 10 1
4 2 25 1
5 3 12 1
6 3 26 1
7 4 7 1
8 4 13 1
9 4 19 1
10 5 6 1
11 5 7 1
12 5 14 1
13 6 8 ar
14 6 9 ar
15 7 15 1
16 7 16 1
17 8 10 ar
18 8 17 1
19 9 11 ar
20 9 18 1
21 10 12 ar
22 11 12 ar
23 11 20 1
24 13 22 1
25 13 23 1
26 13 24 1`
////////// nothing works until add async and await and promise to parser.mol2 file.
describe('mol2 reader', () => {
it('basic', async () => {
const parsed = await Mol2(Mol2String)();
const parsed = await Mol2(Mol2String)();
if (parsed.isError) {
console.log(parsed)
return;
}
const mol2File = parsed.result;
const data = mol2File.structures[0];
const { molecule, atoms, bonds } = data;
expect(molecule.mol_name).toBe('5816')
expect(molecule.num_atoms).toBe(26)
expect(molecule.num_bonds).toBe(26);
expect(molecule.num_subst).toBe(0);
expect(molecule.num_feat).toBe(0);
expect(molecule.num_sets).toBe(0);
expect(molecule.mol_type).toBe("SMALL")
expect(molecule.charge_type).toBe("GASTEIGER");
expect(molecule.status_bits).toBe("");
expect(molecule.mol_comment).toBe("");
expect(atoms.count).toBe(26);
expect(atoms.atom_id.value(0)).toBe(1);
expect(atoms.atom_name.value(0)).toBe('O');
expect(atoms.x.value(0)).toBeCloseTo(1.7394, 0.001);
expect(atoms.y.value(0)).toBeCloseTo(-2.1169, 0.0001);
expect(atoms.z.value(0)).toBeCloseTo(-1.0893, 0.0001);
expect(atoms.atom_type.value(0)).toBe("O.3");
///// optionals
expect(atoms.subst_id.value(0)).toBe(1);
expect(atoms.subst_name.value(0)).toBe('LIG1');
expect(atoms.charge.value(0)).toBeCloseTo(-0.3859);
expect(atoms.status_bit.value(0)).toBe('');
expect(bonds.count).toBe(26);
expect(bonds.bond_id.value(0)).toBe(1);
expect(bonds.origin_atom_id.value(0)).toBe(1);
expect(bonds.target_atom_id.value(0)).toBe(5);
expect(bonds.bond_type.value(0)).toBe('1');
/////// optional
expect(bonds.status_bits.value(0)).toBe('');
});
it('multiblocks', async () => {
const parsed = await Mol2(Mol2StringMultiBlocks)();
if (parsed.isError) {
console.log(parsed)
return;
}
const mol2File = parsed.result;
const data = mol2File.structures[1];
const { molecule, atoms, bonds } = data;
expect(molecule.mol_name).toBe('5816')
expect(molecule.num_atoms).toBe(26)
expect(molecule.num_bonds).toBe(26);
expect(molecule.num_subst).toBe(0);
expect(molecule.num_feat).toBe(0);
expect(molecule.num_sets).toBe(0);
expect(molecule.mol_type).toBe("SMALL")
expect(molecule.charge_type).toBe("GASTEIGER");
expect(molecule.status_bits).toBe("");
expect(molecule.mol_comment).toBe("");
expect(atoms.count).toBe(26);
expect(atoms.atom_id.value(0)).toBe(1);
expect(atoms.atom_name.value(0)).toBe('O');
expect(atoms.x.value(0)).toBeCloseTo(1.7394, 0.001);
expect(atoms.y.value(0)).toBeCloseTo(-2.1169, 0.0001);
expect(atoms.z.value(0)).toBeCloseTo(-1.0893, 0.0001);
expect(atoms.atom_type.value(0)).toBe("O.3");
///// optionals
expect(atoms.subst_id.value(0)).toBe(1);
expect(atoms.subst_name.value(0)).toBe('LIG1');
expect(atoms.charge.value(0)).toBeCloseTo(-0.3859);
expect(atoms.status_bit.value(0)).toBe('');
expect(bonds.count).toBe(26);
expect(bonds.bond_id.value(0)).toBe(1);
expect(bonds.origin_atom_id.value(0)).toBe(1);
expect(bonds.target_atom_id.value(0)).toBe(5);
expect(bonds.bond_type.value(0)).toBe('1');
/////// optional
expect(bonds.status_bits.value(0)).toBe('');
});
it('minimal', async () => {
const parsed = await Mol2(Mol2StringMinimal)();
if (parsed.isError) {
console.log(parsed)
return;
}
const mol2File = parsed.result;
const data = mol2File.structures[0];
const { molecule, atoms, bonds } = data;
expect(molecule.mol_name).toBe(5816)
expect(molecule.mol_name).toBe('5816')
expect(molecule.num_atoms).toBe(26)
expect(molecule.num_bonds).toBe(26);
expect(molecule.num_subst).toBe(0);
expect(molecule.num_feat).toBe(0);
expect(molecule.num_sets).toBe(0);
expect(molecule.mol_type).toBe("")
expect(molecule.charge_type).toBe("");
expect(molecule.mol_type).toBe("SMALL")
expect(molecule.charge_type).toBe("GASTEIGER");
expect(molecule.status_bits).toBe("");
expect(molecule.mol_comment).toBe("");
expect(atoms.count).toBe(2);
expect(atoms.count).toBe(26);
expect(atoms.atom_id.value(0)).toBe(1);
expect(atoms.atom_name.value(0)).toBe('o');
expect(atoms.atom_name.value(0)).toBe('O');
expect(atoms.x.value(0)).toBeCloseTo(1.7394, 0.001);
expect(atoms.y.value(0)).toBeCloseTo(-2.1169, 0.0001);
expect(atoms.z.value(0)).toBeCloseTo(-1.0893, 0.0001);
expect(atoms.atom_type.value(0)).toBe('');
expect(atoms.atom_type.value(0)).toBe("O.3");
///// optionals
expect(atoms.subst_id.value(0)).toBe(0);
expect(atoms.subst_name.value(0)).toBe('');
expect(atoms.charge.value(0)).toBeCloseTo(0.000);
expect(atoms.status_bits.value(0)).toBe('');
expect(atoms.charge.value(0)).toBeCloseTo(0);
expect(atoms.status_bit.value(0)).toBe('');
expect(bonds.count).toBe(2);
expect(bonds.count).toBe(26);
expect(bonds.bond_id.value(0)).toBe(1);
expect(bonds.origin_atom_id.value(0)).toBe(1);
expect(bonds.target_atom_id.value(0)).toBe(5);
......
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