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Commit 923404c2 authored by Alexander Rose's avatar Alexander Rose
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wip, fixing mol2 parser (multi model still broken)

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src/mol-io/reader/_spec/mol2.spec.ts
+ 131
− 122
View file @ 923404c2
import Mol2 from '../mol2/parser' import Mol2 from '../mol2/parser'
// const Mol2String = `@<TRIPOS>MOLECULE const Mol2String = `@<TRIPOS>MOLECULE
// 5816 5816
// 26 26 0 0 0 26 26 0 0 0
// SMALL SMALL
// GASTEIGER 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 3 2 10 1
// 4 2 25 1 4 2 25 1
// 5 3 12 1 5 3 12 1
// 6 3 26 1 6 3 26 1
// 7 4 7 1 7 4 7 1
// 8 4 13 1 8 4 13 1
// 9 4 19 1 9 4 19 1
// 10 5 6 1 10 5 6 1
// 11 5 7 1 11 5 7 1
// 12 5 14 1 12 5 14 1
// 13 6 8 ar 13 6 8 ar
// 14 6 9 ar 14 6 9 ar
// 15 7 15 1 15 7 15 1
// 16 7 16 1 16 7 16 1
// 17 8 10 ar 17 8 10 ar
// 18 8 17 1 18 8 17 1
// 19 9 11 ar 19 9 11 ar
// 20 9 18 1 20 9 18 1
// 21 10 12 ar 21 10 12 ar
// 22 11 12 ar 22 11 12 ar
// 23 11 20 1 23 11 20 1
// 24 13 22 1 24 13 22 1
// 25 13 23 1 25 13 23 1
// 26 13 24 1` 26 13 24 1`
// const Mol2StringMultiBlocks = `@<TRIPOS>MOLECULE // const Mol2StringMultiBlocks = `@<TRIPOS>MOLECULE
// 5816 // 5816
...@@ -245,60 +245,63 @@ GASTEIGER ...@@ -245,60 +245,63 @@ GASTEIGER
26 13 24 1` 26 13 24 1`
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) { if (parsed.isError) {
// console.log(parsed) throw new Error(parsed.message);
// 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') // molecule fields
// expect(molecule.num_atoms).toBe(26) expect(molecule.mol_name).toBe('5816')
// expect(molecule.num_bonds).toBe(26); expect(molecule.num_atoms).toBe(26)
// expect(molecule.num_subst).toBe(0); expect(molecule.num_bonds).toBe(26);
// expect(molecule.num_feat).toBe(0); expect(molecule.num_subst).toBe(0);
// expect(molecule.num_sets).toBe(0); expect(molecule.num_feat).toBe(0);
// expect(molecule.mol_type).toBe("SMALL") expect(molecule.num_sets).toBe(0);
// expect(molecule.charge_type).toBe("GASTEIGER"); expect(molecule.mol_type).toBe("SMALL")
// expect(molecule.status_bits).toBe(""); expect(molecule.charge_type).toBe("GASTEIGER");
// expect(molecule.mol_comment).toBe(""); expect(molecule.status_bits).toBe("");
expect(molecule.mol_comment).toBe("");
// expect(atoms.count).toBe(26); // required atom fields
// expect(atoms.atom_id.value(0)).toBe(1); expect(atoms.count).toBe(26);
// expect(atoms.atom_name.value(0)).toBe('O'); expect(atoms.atom_id.value(0)).toBe(1);
// expect(atoms.x.value(0)).toBeCloseTo(1.7394, 0.001); expect(atoms.atom_name.value(0)).toBe('O');
// expect(atoms.y.value(0)).toBeCloseTo(-2.1169, 0.0001); expect(atoms.x.value(0)).toBeCloseTo(1.7394, 0.001);
// expect(atoms.z.value(0)).toBeCloseTo(-1.0893, 0.0001); expect(atoms.y.value(0)).toBeCloseTo(-2.1169, 0.0001);
// expect(atoms.atom_type.value(0)).toBe("O.3"); expect(atoms.z.value(0)).toBeCloseTo(-1.0893, 0.0001);
// ///// optionals expect(atoms.atom_type.value(0)).toBe("O.3");
// 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); // optional atom fields
// expect(bonds.bond_id.value(0)).toBe(1); expect(atoms.subst_id.value(0)).toBe(1);
// expect(bonds.origin_atom_id.value(0)).toBe(1); expect(atoms.subst_name.value(0)).toBe('LIG1');
// expect(bonds.target_atom_id.value(0)).toBe(5); expect(atoms.charge.value(0)).toBeCloseTo(-0.3859);
// expect(bonds.bond_type.value(0)).toBe('1'); expect(atoms.status_bit.value(0)).toBe('');
// /////// optional
// expect(bonds.status_bits.value(0)).toBe('');
// }); // required bond fields
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 bond fields
expect(bonds.status_bits.value(0)).toBe('');
});
// it('multiblocks', async () => { // it('multiblocks', async () => {
// const parsed = await Mol2(Mol2StringMultiBlocks)(); // const parsed = await Mol2(Mol2StringMultiBlocks)();
// if (parsed.isError) { // if (parsed.isError) {
// console.log(parsed) // throw new Error(parsed.message);
// return;
// } // }
// const mol2File = parsed.result; // const mol2File = parsed.result;
// const data = mol2File.structures[1]; // const data = mol2File.structures[1];
// const { molecule, atoms, bonds } = data; // const { molecule, atoms, bonds } = data;
// // molecule fields
// 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);
...@@ -310,6 +313,7 @@ describe('mol2 reader', () => { ...@@ -310,6 +313,7 @@ describe('mol2 reader', () => {
// expect(molecule.status_bits).toBe(""); // expect(molecule.status_bits).toBe("");
// expect(molecule.mol_comment).toBe(""); // expect(molecule.mol_comment).toBe("");
// // required atom fields
// expect(atoms.count).toBe(26); // 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');
...@@ -317,32 +321,34 @@ describe('mol2 reader', () => { ...@@ -317,32 +321,34 @@ describe('mol2 reader', () => {
// 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("O.3"); // expect(atoms.atom_type.value(0)).toBe("O.3");
// ///// optionals
// // optional atom fields
// expect(atoms.subst_id.value(0)).toBe(1); // expect(atoms.subst_id.value(0)).toBe(1);
// expect(atoms.subst_name.value(0)).toBe('LIG1'); // expect(atoms.subst_name.value(0)).toBe('LIG1');
// expect(atoms.charge.value(0)).toBeCloseTo(-0.3859); // expect(atoms.charge.value(0)).toBeCloseTo(-0.3859);
// expect(atoms.status_bit.value(0)).toBe(''); // expect(atoms.status_bit.value(0)).toBe('');
// // required bond fields
// expect(bonds.count).toBe(26); // 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);
// expect(bonds.bond_type.value(0)).toBe('1'); // expect(bonds.bond_type.value(0)).toBe('1');
// /////// optional
// expect(bonds.status_bits.value(0)).toBe('');
// // optional bond fields
// expect(bonds.status_bits.value(0)).toBe('');
// }); // });
it('minimal', async () => { it('minimal', async () => {
const parsed = await Mol2(Mol2StringMinimal)(); const parsed = await Mol2(Mol2StringMinimal)();
if (parsed.isError) { if (parsed.isError) {
console.log(parsed) throw new Error(parsed.message);
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;
// molecule fields
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);
...@@ -354,26 +360,29 @@ describe('mol2 reader', () => { ...@@ -354,26 +360,29 @@ describe('mol2 reader', () => {
expect(molecule.status_bits).toBe(""); expect(molecule.status_bits).toBe("");
expect(molecule.mol_comment).toBe(""); expect(molecule.mol_comment).toBe("");
// required atom fields
expect(atoms.count).toBe(26); 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("O.3"); 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);
// expect(atoms.status_bit.value(0)).toBe('');
// optional atom fields
expect(atoms.subst_id.value(0)).toBe(0);
expect(atoms.subst_name.value(0)).toBe('');
expect(atoms.charge.value(0)).toBeCloseTo(0);
expect(atoms.status_bit.value(0)).toBe('');
// required bond fields
expect(bonds.count).toBe(26); 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);
// expect(bonds.bond_type.value(0)).toBe('1'); expect(bonds.bond_type.value(0)).toBe('1');
// /////// optional
// expect(bonds.status_bits.value(0)).toBe('');
// optional bond fields
expect(bonds.status_bits.value(0)).toBe('');
}); });
}); });
src/mol-io/reader/mol2/parser.ts
+ 58
− 45
View file @ 923404c2
/**
* Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Zepei Xu <xuzepei19950617@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
// NOTES // NOTES
//When want to created undefined string column, must use //When want to created undefined string column, must use
// undefStr = UndefinedColumn(molecule.num_atoms, ColumnType.str) // undefStr = UndefinedColumn(molecule.num_atoms, ColumnType.str)
...@@ -11,6 +18,8 @@ import * as Schema from './schema' ...@@ -11,6 +18,8 @@ import * as Schema from './schema'
import Result from '../result' import Result from '../result'
import Computation from 'mol-util/computation' import Computation from 'mol-util/computation'
const { skipWhitespace, eatValue, markLine, getTokenString, readLine } = Tokenizer;
interface State { interface State {
tokenizer: Tokenizer, tokenizer: Tokenizer,
molecule: Schema.Molecule, molecule: Schema.Molecule,
...@@ -40,36 +49,37 @@ function State(tokenizer: Tokenizer, ctx: Computation.Context): State { ...@@ -40,36 +49,37 @@ function State(tokenizer: Tokenizer, ctx: Computation.Context): State {
}; };
} }
const reWhitespace = /\s+/g;
function handleMolecule(state: State) { function handleMolecule(state: State) {
const { tokenizer, molecule } = state; const { tokenizer, molecule } = state;
Tokenizer.markLine(tokenizer); markLine(tokenizer);
Tokenizer.markLine(tokenizer); markLine(tokenizer);
molecule.mol_name = Tokenizer.getTokenString(tokenizer); molecule.mol_name = getTokenString(tokenizer);
Tokenizer.markLine(tokenizer); markLine(tokenizer);
const values = Tokenizer.getTokenString(tokenizer).trim().split(/\s+/g); const values = getTokenString(tokenizer).trim().split(reWhitespace);
molecule.num_atoms = parseInt(values[0]) ? parseInt(values[1]) : 0; molecule.num_atoms = parseInt(values[0]) ? parseInt(values[0]) : 0;
molecule.num_bonds = parseInt(values[1]) ? 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_subst = parseInt(values[2]) ? parseInt(values[2]) : 0;
molecule.num_feat = parseInt(values[3]) ? parseInt(values[1]) : 0; molecule.num_feat = parseInt(values[3]) ? parseInt(values[3]) : 0;
molecule.num_sets = parseInt(values[4]) ? parseInt(values[1]) : 0; molecule.num_sets = parseInt(values[4]) ? parseInt(values[4]) : 0;
Tokenizer.markLine(tokenizer); markLine(tokenizer);
molecule.mol_type = Tokenizer.getTokenString(tokenizer); molecule.mol_type = getTokenString(tokenizer);
Tokenizer.markLine(tokenizer); markLine(tokenizer);
molecule.charge_type = Tokenizer.getTokenString(tokenizer); molecule.charge_type = getTokenString(tokenizer);
Tokenizer.markLine(tokenizer); markLine(tokenizer);
if (Tokenizer.getTokenString(tokenizer) == '') return if (getTokenString(tokenizer) === '') return
molecule.status_bits = Tokenizer.getTokenString(tokenizer) molecule.status_bits = getTokenString(tokenizer)
Tokenizer.markLine(tokenizer); markLine(tokenizer);
if (Tokenizer.getTokenString(tokenizer) == '') return if (getTokenString(tokenizer) === '') return
molecule.mol_comment = Tokenizer.getTokenString(tokenizer) molecule.mol_comment = getTokenString(tokenizer)
} }
function isStatus_bit(aString: String): Boolean{ function isStatus_bit(aString: String): Boolean{
if(aString.includes('DSPMOD') || aString.includes('TYPECOL') || aString.includes('CAP') if(aString.includes('DSPMOD') || aString.includes('TYPECOL') || aString.includes('CAP')
|| aString.includes('BACKBONE') || aString.includes('DICT') || aString.includes('ESSENTIAL') || aString.includes('BACKBONE') || aString.includes('DICT') || aString.includes('ESSENTIAL')
...@@ -79,7 +89,6 @@ function isStatus_bit(aString: String): Boolean{ ...@@ -79,7 +89,6 @@ function isStatus_bit(aString: String): Boolean{
return false; return false;
} }
async function handleAtoms(state: State): Promise<Schema.Atoms> { async function handleAtoms(state: State): Promise<Schema.Atoms> {
const { tokenizer, molecule } = state; const { tokenizer, molecule } = state;
let hasSubst_id = false; let hasSubst_id = false;
...@@ -88,17 +97,17 @@ async function handleAtoms(state: State): Promise<Schema.Atoms> { ...@@ -88,17 +97,17 @@ async function handleAtoms(state: State): Promise<Schema.Atoms> {
let hasStatus_bit = false; let hasStatus_bit = false;
// skip empty lines and '@<TRIPOS>ATOM' // skip empty lines and '@<TRIPOS>ATOM'
while(Tokenizer.getTokenString(tokenizer) != '@<TRIPOS>ATOM'){ while(getTokenString(tokenizer) != '@<TRIPOS>ATOM'){
Tokenizer.markLine(tokenizer); markLine(tokenizer);
} }
const initialTokenizerPosition = tokenizer.position; const initialTokenizerPosition = tokenizer.position;
const initialTokenizerLineNumber = tokenizer.lineNumber; const initialTokenizerLineNumber = tokenizer.lineNumber;
const firstLine = Tokenizer.readLine(tokenizer); const firstLine = readLine(tokenizer);
const firstLineArray = firstLine.trim().split(/\s+/g) const firstLineArray = firstLine.trim().split(/\s+/g)
const firstLineLength = firstLineArray.length; const firstLineLength = firstLineArray.length;
// optionals are in order "integer string float string". // optional columns are in order "integer string float string".
// Use this to find out which column is missing or empty // Use this to find out which column is missing or empty
for(let i = 6; i < firstLineLength; i++){ for(let i = 6; i < firstLineLength; i++){
if(!isNaN(Number(firstLineArray[i]))){ if(!isNaN(Number(firstLineArray[i]))){
...@@ -116,17 +125,13 @@ async function handleAtoms(state: State): Promise<Schema.Atoms> { ...@@ -116,17 +125,13 @@ async function handleAtoms(state: State): Promise<Schema.Atoms> {
} }
} }
// required columns
const atom_idTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2); const atom_idTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2);
const atom_nameTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2);; const atom_nameTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2);;
const xTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2); const xTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2);
const yTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2); const yTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2);
const zTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2); const zTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2);
const atom_typeTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2); const atom_typeTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2);
// optionals
const subst_idTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2);
const subst_nameTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2);
const chargeTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2);
const status_bitTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2);
const atom_idTokenColumn = TokenColumn(atom_idTokens); const atom_idTokenColumn = TokenColumn(atom_idTokens);
const atom_nameTokenColumn = TokenColumn(atom_nameTokens); const atom_nameTokenColumn = TokenColumn(atom_nameTokens);
...@@ -134,7 +139,13 @@ async function handleAtoms(state: State): Promise<Schema.Atoms> { ...@@ -134,7 +139,13 @@ async function handleAtoms(state: State): Promise<Schema.Atoms> {
const yTokenColumn = TokenColumn(yTokens); const yTokenColumn = TokenColumn(yTokens);
const zTokenColumn = TokenColumn(zTokens); const zTokenColumn = TokenColumn(zTokens);
const atom_typeColumn = TokenColumn(atom_typeTokens); const atom_typeColumn = TokenColumn(atom_typeTokens);
// optionals
// optional columns
const subst_idTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2);
const subst_nameTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2);
const chargeTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2);
const status_bitTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2);
const subst_idTokenColumn = TokenColumn(subst_idTokens); const subst_idTokenColumn = TokenColumn(subst_idTokens);
const subst_nameTokenColumn = TokenColumn(subst_nameTokens); const subst_nameTokenColumn = TokenColumn(subst_nameTokens);
const chargeTokenColumn = TokenColumn(chargeTokens); const chargeTokenColumn = TokenColumn(chargeTokens);
...@@ -144,7 +155,7 @@ async function handleAtoms(state: State): Promise<Schema.Atoms> { ...@@ -144,7 +155,7 @@ async function handleAtoms(state: State): Promise<Schema.Atoms> {
const undefInt = Column.Undefined(molecule.num_atoms, Column.Schema.int); const undefInt = Column.Undefined(molecule.num_atoms, Column.Schema.int);
const undefStr = Column.Undefined(molecule.num_atoms, Column.Schema.str); const undefStr = Column.Undefined(molecule.num_atoms, Column.Schema.str);
let numOfColumn = 5; let numOfColumn = 6;
if(hasSubst_id){numOfColumn++} if(hasSubst_id){numOfColumn++}
if(hasSubst_name){numOfColumn++} if(hasSubst_name){numOfColumn++}
if(hasCharge){numOfColumn++} if(hasCharge){numOfColumn++}
...@@ -163,8 +174,9 @@ async function handleAtoms(state: State): Promise<Schema.Atoms> { ...@@ -163,8 +174,9 @@ async function handleAtoms(state: State): Promise<Schema.Atoms> {
let chargeWritten = false; let chargeWritten = false;
let status_bitWritten = false; let status_bitWritten = false;
for(let j = 0; j < numOfColumn; j++){ for(let j = 0; j < numOfColumn; j++){
Tokenizer.skipWhitespace(tokenizer); skipWhitespace(tokenizer);
Tokenizer.eatValue(tokenizer); tokenizer.tokenStart = tokenizer.position;
eatValue(tokenizer);
switch(j){ switch(j){
case 0: case 0:
TokenBuilder.addUnchecked(atom_idTokens, tokenizer.tokenStart, tokenizer.tokenEnd); TokenBuilder.addUnchecked(atom_idTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
...@@ -185,16 +197,16 @@ async function handleAtoms(state: State): Promise<Schema.Atoms> { ...@@ -185,16 +197,16 @@ async function handleAtoms(state: State): Promise<Schema.Atoms> {
TokenBuilder.addUnchecked(atom_typeTokens, tokenizer.tokenStart, tokenizer.tokenEnd); TokenBuilder.addUnchecked(atom_typeTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
break; break;
default: default:
if(hasSubst_id == true && subst_idWritten == false){ if(hasSubst_id === true && subst_idWritten === false){
TokenBuilder.addUnchecked(subst_idTokens, tokenizer.tokenStart, tokenizer.tokenEnd); TokenBuilder.addUnchecked(subst_idTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
subst_idWritten = true; subst_idWritten = true;
}else if(hasSubst_name == true && subst_nameWritten == false){ }else if(hasSubst_name === true && subst_nameWritten === false){
TokenBuilder.addUnchecked(subst_nameTokens, tokenizer.tokenStart, tokenizer.tokenEnd); TokenBuilder.addUnchecked(subst_nameTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
subst_nameWritten = true; subst_nameWritten = true;
}else if(hasCharge == true && chargeWritten == false){ }else if(hasCharge === true && chargeWritten === false){
TokenBuilder.addUnchecked(chargeTokens, tokenizer.tokenStart, tokenizer.tokenEnd); TokenBuilder.addUnchecked(chargeTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
chargeWritten = true; chargeWritten = true;
}else if(hasStatus_bit == true && status_bitWritten == false){ }else if(hasStatus_bit === true && status_bitWritten === false){
TokenBuilder.addUnchecked(status_bitTokens, tokenizer.tokenStart, tokenizer.tokenEnd); TokenBuilder.addUnchecked(status_bitTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
status_bitWritten = true; status_bitWritten = true;
} }
...@@ -213,12 +225,12 @@ async function handleAtoms(state: State): Promise<Schema.Atoms> { ...@@ -213,12 +225,12 @@ async function handleAtoms(state: State): Promise<Schema.Atoms> {
y: yTokenColumn(Column.Schema.float), y: yTokenColumn(Column.Schema.float),
z: zTokenColumn(Column.Schema.float), z: zTokenColumn(Column.Schema.float),
atom_type: atom_typeColumn(Column.Schema.str), atom_type: atom_typeColumn(Column.Schema.str),
// optional properties
// optional columns
subst_id: hasSubst_id ? subst_idTokenColumn(Column.Schema.int) : undefInt, subst_id: hasSubst_id ? subst_idTokenColumn(Column.Schema.int) : undefInt,
subst_name: hasSubst_name ? subst_nameTokenColumn(Column.Schema.str) : undefStr, subst_name: hasSubst_name ? subst_nameTokenColumn(Column.Schema.str) : undefStr,
charge: hasCharge ? chargeTokenColumn(Column.Schema.float) : undefFloat, charge: hasCharge ? chargeTokenColumn(Column.Schema.float) : undefFloat,
status_bit: hasStatus_bit ? status_bitTokenColumn(Column.Schema.str) : undefStr, status_bit: hasStatus_bit ? status_bitTokenColumn(Column.Schema.str) : undefStr,
}; };
return ret; return ret;
} }
...@@ -227,13 +239,13 @@ async function handleBonds(state: State): Promise<Schema.Bonds> { ...@@ -227,13 +239,13 @@ async function handleBonds(state: State): Promise<Schema.Bonds> {
const { tokenizer, molecule } = state; const { tokenizer, molecule } = state;
let hasStatus_bit = false; let hasStatus_bit = false;
while(Tokenizer.getTokenString(tokenizer) != '@<TRIPOS>BOND'){ while(getTokenString(tokenizer) !== '@<TRIPOS>BOND'){
Tokenizer.markLine(tokenizer); markLine(tokenizer);
} }
const initialTokenizerPosition = tokenizer.position; const initialTokenizerPosition = tokenizer.position;
const initialTokenizerLineNumber = tokenizer.lineNumber; const initialTokenizerLineNumber = tokenizer.lineNumber;
const firstLine = Tokenizer.readLine(tokenizer); const firstLine = readLine(tokenizer);
const firstLineArray = firstLine.trim().split(/\s+/g) const firstLineArray = firstLine.trim().split(/\s+/g)
const firstLineLength = firstLineArray.length; const firstLineLength = firstLineArray.length;
if(firstLineLength === 5){ if(firstLineLength === 5){
...@@ -268,8 +280,9 @@ async function handleBonds(state: State): Promise<Schema.Bonds> { ...@@ -268,8 +280,9 @@ async function handleBonds(state: State): Promise<Schema.Bonds> {
const linesToRead = Math.min(molecule.num_bonds - linesAlreadyRead, chunkSize); const linesToRead = Math.min(molecule.num_bonds - linesAlreadyRead, chunkSize);
for(let i = 0; i < linesToRead; i++){ for(let i = 0; i < linesToRead; i++){
for(let j = 0; j < numberOfColumn; j++){ for(let j = 0; j < numberOfColumn; j++){
Tokenizer.skipWhitespace(tokenizer); skipWhitespace(tokenizer);
Tokenizer.eatValue(tokenizer); tokenizer.tokenStart = tokenizer.position;
eatValue(tokenizer);
switch(j){ switch(j){
case 0: case 0:
TokenBuilder.addUnchecked(bond_idTokens, tokenizer.tokenStart, tokenizer.tokenEnd); TokenBuilder.addUnchecked(bond_idTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
......
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