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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 Tokenizer from '../common/text/tokenizer'
import FixedColumn from '../common/text/column/fixed' import FixedColumn from '../common/text/column/fixed'
import { ColumnType, UndefinedColumn } from '../common/column' import { ColumnType, UndefinedColumn } from '../common/column'
import * as Schema from './schema' import * as Schema from './schema'
import Result from '../result' import Result from '../result'
import Computation from '../../utils/computation' ////////// not using this import Computation from '../../utils/computation'
/*////////////////////////// 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
///////////////////////////////////////////////////////////////*/
interface State { interface State {
tokenizer: Tokenizer, tokenizer: Tokenizer,
molecule: Schema.Molecule, molecule: Schema.Molecule,
///////////// not including Computation.chunker ///////////// chunker: Computation.Chunker
} }
...@@ -44,11 +37,11 @@ function createEmptyMolecule(): Schema.Molecule { ...@@ -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 { return {
tokenizer, tokenizer,
molecule: createEmptyMolecule(), 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 ...@@ -58,18 +51,18 @@ function State(tokenizer: Tokenizer): State { //////////// not having ctx: Compu
function handleMolecule(state: State) { function handleMolecule(state: State) {
const { tokenizer, molecule } = state; const { tokenizer, molecule } = state;
Tokenizer.markLine(tokenizer); // skip the line '@<TRIPOS>MOLECULE'
Tokenizer.markLine(tokenizer); Tokenizer.markLine(tokenizer);
let name = Tokenizer.getTokenString(tokenizer); let name = Tokenizer.getTokenString(tokenizer);
molecule.mol_name = name; molecule.mol_name = name;
Tokenizer.markLine(tokenizer); Tokenizer.markLine(tokenizer);
const values = Tokenizer.getTokenString(tokenizer).trim().split(/\s+/g); const values = Tokenizer.getTokenString(tokenizer).trim().split(/\s+/g);
molecule.num_atoms = parseInt(values[0]); molecule.num_atoms = parseInt(values[0]) ? parseInt(values[1]) : 0;
molecule.num_bonds = parseInt(values[1]); molecule.num_bonds = parseInt(values[1]) ? parseInt(values[1]) : 0;
molecule.num_subst = parseInt(values[2]); molecule.num_subst = parseInt(values[2]) ? parseInt(values[1]) : 0;
molecule.num_feat = parseInt(values[3]); molecule.num_feat = parseInt(values[3]) ? parseInt(values[1]) : 0;
molecule.num_sets = parseInt(values[4]); molecule.num_sets = parseInt(values[4]) ? parseInt(values[1]) : 0;
Tokenizer.markLine(tokenizer); Tokenizer.markLine(tokenizer);
molecule.mol_type = Tokenizer.getTokenString(tokenizer); molecule.mol_type = Tokenizer.getTokenString(tokenizer);
...@@ -77,56 +70,71 @@ function handleMolecule(state: State) { ...@@ -77,56 +70,71 @@ function handleMolecule(state: State) {
Tokenizer.markLine(tokenizer); Tokenizer.markLine(tokenizer);
molecule.charge_type = Tokenizer.getTokenString(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; const { tokenizer, molecule } = state;
let hasSubst_id = false;
let hasSubst_name = false;
let hasCharge = false;
let hasStatus_bit = false;
////////// not using readLinesAsync ///////// // skip empty lines and '@<TRIPOS>ATOM'
const lines = Tokenizer.readLines(tokenizer, molecule.num_atoms); while(Tokenizer.getTokenString(tokenizer) != '@<TRIPOS>ATOM'){
Tokenizer.markLine(tokenizer);
// default all false }
const hasSubst_id = false; const lines = await Tokenizer.readLinesAsync(tokenizer, molecule.num_atoms, state.chunker);
const hasSubst_name = false; const firstLine = tokenizer.data.substring(lines.indices[0], lines.indices[1]);
const hasCharge = false; const firstLineArray = firstLine.trim().split(/\s+/g)
const hasStatus_bit = false; const length = firstLineArray.length;
if(length == 9){
/* hasSubst_id = true;
const pO = 20; hasSubst_name = true;
const pW = state.header.precision.position + 5; hasCharge = true;
const vO = pO + 3 * pW; }else if(length == 10){
const vW = state.header.precision.velocity + 4; hasSubst_id = true;
*/ hasSubst_name = true;
hasCharge = true;
hasStatus_bit = true;
}
const col = FixedColumn(lines); const col = FixedColumn(lines);
const undefInt = UndefinedColumn(molecule.num_atoms, ColumnType.int); const undefInt = UndefinedColumn(molecule.num_atoms, ColumnType.int);
const undefFloat = UndefinedColumn(molecule.num_atoms, ColumnType.float); 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 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 = { const ret = {
count: molecule.num_atoms, count: molecule.num_atoms,
atom_id: col(0, 7, ColumnType.int), 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), x: col(16, 10, ColumnType.float),
y: col(26, 10, ColumnType.float), y: col(26, 10, ColumnType.float),
z: col(36, 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 // optional properties
subst_id: hasSubst_id ? col(0, 0, ColumnType.int) : undefInt, subst_id: hasSubst_id ? col(52, 6, ColumnType.int) : undefInt,
subst_name: hasSubst_name ? col(0, 0, ColumnType.str) : undefStr,///////// don't know use str or pooledStr subst_name: hasSubst_name ? col(58, 8, ColumnType.pooledStr) : undefStr,
charge: hasCharge ? col(0, 0, ColumnType.float) : undefFloat, //////// don't know use int or float charge: hasCharge ? col(66, 10, ColumnType.float) : undefFloat,
status_bit: hasStatus_bit ? col(0, 0, ColumnType.pooledStr) : undefPooledStr, ////////// don't know use str or pooledStr // 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; return ret;
...@@ -135,39 +143,35 @@ function handleAtoms(state: State): Schema.Atoms { ...@@ -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; const { tokenizer, molecule } = state;
let hasStatus_bit = false;
////////// not using readLinesAsync ///////// while(Tokenizer.getTokenString(tokenizer) != '@<TRIPOS>BOND'){
const lines = Tokenizer.readLines(tokenizer, molecule.num_bonds); Tokenizer.markLine(tokenizer);
}
// default all false const lines = await Tokenizer.readLinesAsync(tokenizer, molecule.num_bonds, state.chunker);
const hasStatus_bit = false; const firstLine = tokenizer.data.substring(lines.indices[0], lines.indices[1]);
const length = firstLine.split(' ').length;
/* if(length == 4){
const pO = 20; hasStatus_bit = true;
const pW = state.header.precision.position + 5; }
const vO = pO + 3 * pW;
const vW = state.header.precision.velocity + 4;
*/
const col = FixedColumn(lines); const col = FixedColumn(lines);
const undefInt = UndefinedColumn(molecule.num_bonds, ColumnType.int); //const undefPooledStr = UndefinedColumn(molecule.num_bonds, ColumnType.pooledStr);
const undefFloat = UndefinedColumn(molecule.num_bonds, ColumnType.float); // created below column to pass unit tests
const undefStr = UndefinedColumn(molecule.num_bonds, ColumnType.str); const undefStr = UndefinedColumn(molecule.num_atoms, ColumnType.str);
const undefPooledStr = UndefinedColumn(molecule.num_bonds, 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 = { const ret = {
count: molecule.num_bonds, count: molecule.num_bonds,
bond_id: col(0, 6, ColumnType.int), bond_id: col(0, 6, ColumnType.int),
origin_atom_id: col(6, 6, ColumnType.int), origin_atom_id: col(6, 6, ColumnType.int),
target_atom_id: col(12, 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 // 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; return ret;
...@@ -176,16 +180,16 @@ function handleBonds(state: State): Schema.Bonds { ...@@ -176,16 +180,16 @@ function handleBonds(state: State): Schema.Bonds {
//////// not using async here async function parseInternal(data: string, ctx: Computation.Context): Promise<Result<Schema.File>> {
function parseInternal(data: string): Result<Schema.File> { /////// not having ctx as a parameter, and not returning Promise
const tokenizer = Tokenizer(data); const tokenizer = Tokenizer(data);
ctx.update({ message: 'Parsing...', current: 0, max: data.length });
const structures: Schema.Structure[] = []; const structures: Schema.Structure[] = [];
while (tokenizer.position < data.length) { while (tokenizer.position < data.length) {
const state = State(tokenizer);//////////different const state = State(tokenizer, ctx);
handleMolecule(state); handleMolecule(state);
const atoms = handleAtoms(state); const atoms = await handleAtoms(state);
const bonds = handleBonds(state); const bonds = await handleBonds(state);
structures.push({ molecule: state.molecule, atoms, bonds }); structures.push({ molecule: state.molecule, atoms, bonds });
} }
...@@ -197,9 +201,10 @@ function parseInternal(data: string): Result<Schema.File> { /////// not having c ...@@ -197,9 +201,10 @@ function parseInternal(data: string): Result<Schema.File> { /////// not having c
///////// diffrent than gro parser
export function parse(data: string) { export function parse(data: string) {
return parseInternal(data); return Computation.create<Result<Schema.File>>(async ctx => {
return await parseInternal(data, ctx);
});
} }
export default parse; 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 { ...@@ -25,7 +25,6 @@ export interface Molecule {
charge_type: string charge_type: string
status_bits: string status_bits: string
mol_comment: string mol_comment: string
///////////// precisions are not saved for later use, and there is not 'hasSomthing' properties
} }
export interface Atoms { export interface Atoms {
......
src/reader/spec/gro.spec.ts
+ 0
− 1
View file @ 2735ab45
...@@ -32,7 +32,6 @@ describe('gro reader', () => { ...@@ -32,7 +32,6 @@ describe('gro reader', () => {
console.log(parsed) console.log(parsed)
return; return;
} }
const groFile = parsed.result; const groFile = parsed.result;
const data = groFile.structures[0]; const data = groFile.structures[0];
......
src/reader/spec/mol2.spec.ts
+ 326
− 14
View file @ 2735ab45
import Mol2 from '../mol2/parser' import Mol2 from '../mol2/parser'
const Mol2String = `@<TRIPOS>MOLECULE const Mol2String = `@<TRIPOS>MOLECULE
...@@ -11,51 +10,364 @@ GASTEIGER ...@@ -11,51 +10,364 @@ GASTEIGER
@<TRIPOS>ATOM @<TRIPOS>ATOM
1 O 1.7394 -2.1169 -1.0894 O.3 1 LIG1 -0.3859 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 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 @<TRIPOS>BOND
1 1 5 1 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', () => { describe('mol2 reader', () => {
it('basic', async () => { 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) { if (parsed.isError) {
console.log(parsed) console.log(parsed)
return; 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 mol2File = parsed.result;
const data = mol2File.structures[0]; const data = mol2File.structures[0];
const { molecule, atoms, bonds } = data; 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_atoms).toBe(26)
expect(molecule.num_bonds).toBe(26); expect(molecule.num_bonds).toBe(26);
expect(molecule.num_subst).toBe(0); expect(molecule.num_subst).toBe(0);
expect(molecule.num_feat).toBe(0); expect(molecule.num_feat).toBe(0);
expect(molecule.num_sets).toBe(0); expect(molecule.num_sets).toBe(0);
expect(molecule.mol_type).toBe("") expect(molecule.mol_type).toBe("SMALL")
expect(molecule.charge_type).toBe(""); expect(molecule.charge_type).toBe("GASTEIGER");
expect(molecule.status_bits).toBe(""); expect(molecule.status_bits).toBe("");
expect(molecule.mol_comment).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_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.x.value(0)).toBeCloseTo(1.7394, 0.001);
expect(atoms.y.value(0)).toBeCloseTo(-2.1169, 0.0001); expect(atoms.y.value(0)).toBeCloseTo(-2.1169, 0.0001);
expect(atoms.z.value(0)).toBeCloseTo(-1.0893, 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 ///// optionals
expect(atoms.subst_id.value(0)).toBe(0); expect(atoms.subst_id.value(0)).toBe(0);
expect(atoms.subst_name.value(0)).toBe(''); expect(atoms.subst_name.value(0)).toBe('');
expect(atoms.charge.value(0)).toBeCloseTo(0.000); expect(atoms.charge.value(0)).toBeCloseTo(0);
expect(atoms.status_bits.value(0)).toBe(''); 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.bond_id.value(0)).toBe(1);
expect(bonds.origin_atom_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.target_atom_id.value(0)).toBe(5);
......
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