diff --git a/src/mol-io/reader/_spec/mol2.spec.ts b/src/mol-io/reader/_spec/mol2.spec.ts
index b960eb4165951523b68d2965f52451f814a57db3..bb792004a96763a6ab87674d7aa823050ba8be55 100644
--- a/src/mol-io/reader/_spec/mol2.spec.ts
+++ b/src/mol-io/reader/_spec/mol2.spec.ts
@@ -1,66 +1,66 @@
import Mol2 from '../mol2/parser'
-// const Mol2String = `@<TRIPOS>MOLECULE
-// 5816
-// 26 26 0 0 0
-// SMALL
-// GASTEIGER
+const Mol2String = `@<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>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 Mol2StringMultiBlocks = `@<TRIPOS>MOLECULE
// 5816
@@ -245,60 +245,63 @@ GASTEIGER
26 13 24 1`
describe('mol2 reader', () => {
- // it('basic', async () => {
- // 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;
+ it('basic', async () => {
+ const parsed = await Mol2(Mol2String)();
+ if (parsed.isError) {
+ throw new Error(parsed.message);
+ }
+ 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("");
+ // molecule fields
+ 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('');
+ // required atom fields
+ 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");
- // 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('');
+ // optional atom fields
+ 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('');
- // });
+ // 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 () => {
// const parsed = await Mol2(Mol2StringMultiBlocks)();
// if (parsed.isError) {
- // console.log(parsed)
- // return;
+ // throw new Error(parsed.message);
// }
// const mol2File = parsed.result;
// const data = mol2File.structures[1];
// const { molecule, atoms, bonds } = data;
+ // // molecule fields
// expect(molecule.mol_name).toBe('5816')
// expect(molecule.num_atoms).toBe(26)
// expect(molecule.num_bonds).toBe(26);
@@ -310,6 +313,7 @@ describe('mol2 reader', () => {
// expect(molecule.status_bits).toBe("");
// expect(molecule.mol_comment).toBe("");
+ // // required atom fields
// expect(atoms.count).toBe(26);
// expect(atoms.atom_id.value(0)).toBe(1);
// expect(atoms.atom_name.value(0)).toBe('O');
@@ -317,32 +321,34 @@ describe('mol2 reader', () => {
// 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
+
+ // // optional atom fields
// 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('');
+ // // 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
- // expect(bonds.status_bits.value(0)).toBe('');
+ // // optional bond fields
+ // expect(bonds.status_bits.value(0)).toBe('');
// });
it('minimal', async () => {
const parsed = await Mol2(Mol2StringMinimal)();
if (parsed.isError) {
- console.log(parsed)
- return;
+ throw new Error(parsed.message);
}
const mol2File = parsed.result;
const data = mol2File.structures[0];
const { molecule, atoms, bonds } = data;
+ // molecule fields
expect(molecule.mol_name).toBe('5816')
expect(molecule.num_atoms).toBe(26)
expect(molecule.num_bonds).toBe(26);
@@ -354,26 +360,29 @@ describe('mol2 reader', () => {
expect(molecule.status_bits).toBe("");
expect(molecule.mol_comment).toBe("");
+ // required atom fields
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(0);
- // expect(atoms.subst_name.value(0)).toBe('');
- // expect(atoms.charge.value(0)).toBeCloseTo(0);
- // expect(atoms.status_bit.value(0)).toBe('');
+ 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");
+
+ // 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.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('');
+ 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('');
});
});
diff --git a/src/mol-io/reader/mol2/parser.ts b/src/mol-io/reader/mol2/parser.ts
index 83b33488b7326315d401e3cb53b8ba86242465c0..5613570b979740aa13252591a7e60b3af4117714 100644
--- a/src/mol-io/reader/mol2/parser.ts
+++ b/src/mol-io/reader/mol2/parser.ts
@@ -1,3 +1,10 @@
+/**
+ * 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
//When want to created undefined string column, must use
// undefStr = UndefinedColumn(molecule.num_atoms, ColumnType.str)
@@ -11,6 +18,8 @@ import * as Schema from './schema'
import Result from '../result'
import Computation from 'mol-util/computation'
+const { skipWhitespace, eatValue, markLine, getTokenString, readLine } = Tokenizer;
+
interface State {
tokenizer: Tokenizer,
molecule: Schema.Molecule,
@@ -40,36 +49,37 @@ function State(tokenizer: Tokenizer, ctx: Computation.Context): State {
};
}
+const reWhitespace = /\s+/g;
+
function handleMolecule(state: State) {
const { tokenizer, molecule } = state;
- Tokenizer.markLine(tokenizer);
- Tokenizer.markLine(tokenizer);
- molecule.mol_name = Tokenizer.getTokenString(tokenizer);
+ markLine(tokenizer);
+ markLine(tokenizer);
+ molecule.mol_name = getTokenString(tokenizer);
- Tokenizer.markLine(tokenizer);
- const values = Tokenizer.getTokenString(tokenizer).trim().split(/\s+/g);
- molecule.num_atoms = parseInt(values[0]) ? parseInt(values[1]) : 0;
+ markLine(tokenizer);
+ const values = getTokenString(tokenizer).trim().split(reWhitespace);
+ molecule.num_atoms = parseInt(values[0]) ? parseInt(values[0]) : 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;
+ molecule.num_subst = parseInt(values[2]) ? parseInt(values[2]) : 0;
+ molecule.num_feat = parseInt(values[3]) ? parseInt(values[3]) : 0;
+ molecule.num_sets = parseInt(values[4]) ? parseInt(values[4]) : 0;
- Tokenizer.markLine(tokenizer);
- molecule.mol_type = Tokenizer.getTokenString(tokenizer);
+ markLine(tokenizer);
+ molecule.mol_type = getTokenString(tokenizer);
- Tokenizer.markLine(tokenizer);
- molecule.charge_type = Tokenizer.getTokenString(tokenizer);
+ markLine(tokenizer);
+ molecule.charge_type = getTokenString(tokenizer);
- Tokenizer.markLine(tokenizer);
- if (Tokenizer.getTokenString(tokenizer) == '') return
- molecule.status_bits = Tokenizer.getTokenString(tokenizer)
+ markLine(tokenizer);
+ if (getTokenString(tokenizer) === '') return
+ molecule.status_bits = getTokenString(tokenizer)
- Tokenizer.markLine(tokenizer);
- if (Tokenizer.getTokenString(tokenizer) == '') return
- molecule.mol_comment = Tokenizer.getTokenString(tokenizer)
+ markLine(tokenizer);
+ if (getTokenString(tokenizer) === '') return
+ molecule.mol_comment = getTokenString(tokenizer)
}
-
function isStatus_bit(aString: String): Boolean{
if(aString.includes('DSPMOD') || aString.includes('TYPECOL') || aString.includes('CAP')
|| aString.includes('BACKBONE') || aString.includes('DICT') || aString.includes('ESSENTIAL')
@@ -79,7 +89,6 @@ function isStatus_bit(aString: String): Boolean{
return false;
}
-
async function handleAtoms(state: State): Promise<Schema.Atoms> {
const { tokenizer, molecule } = state;
let hasSubst_id = false;
@@ -88,17 +97,17 @@ async function handleAtoms(state: State): Promise<Schema.Atoms> {
let hasStatus_bit = false;
// skip empty lines and '@<TRIPOS>ATOM'
- while(Tokenizer.getTokenString(tokenizer) != '@<TRIPOS>ATOM'){
- Tokenizer.markLine(tokenizer);
+ while(getTokenString(tokenizer) != '@<TRIPOS>ATOM'){
+ markLine(tokenizer);
}
const initialTokenizerPosition = tokenizer.position;
const initialTokenizerLineNumber = tokenizer.lineNumber;
- const firstLine = Tokenizer.readLine(tokenizer);
+ const firstLine = readLine(tokenizer);
const firstLineArray = firstLine.trim().split(/\s+/g)
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
for(let i = 6; i < firstLineLength; i++){
if(!isNaN(Number(firstLineArray[i]))){
@@ -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_nameTokens = 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 zTokens = 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_nameTokenColumn = TokenColumn(atom_nameTokens);
@@ -134,7 +139,13 @@ async function handleAtoms(state: State): Promise<Schema.Atoms> {
const yTokenColumn = TokenColumn(yTokens);
const zTokenColumn = TokenColumn(zTokens);
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_nameTokenColumn = TokenColumn(subst_nameTokens);
const chargeTokenColumn = TokenColumn(chargeTokens);
@@ -144,7 +155,7 @@ async function handleAtoms(state: State): Promise<Schema.Atoms> {
const undefInt = Column.Undefined(molecule.num_atoms, Column.Schema.int);
const undefStr = Column.Undefined(molecule.num_atoms, Column.Schema.str);
- let numOfColumn = 5;
+ let numOfColumn = 6;
if(hasSubst_id){numOfColumn++}
if(hasSubst_name){numOfColumn++}
if(hasCharge){numOfColumn++}
@@ -163,8 +174,9 @@ async function handleAtoms(state: State): Promise<Schema.Atoms> {
let chargeWritten = false;
let status_bitWritten = false;
for(let j = 0; j < numOfColumn; j++){
- Tokenizer.skipWhitespace(tokenizer);
- Tokenizer.eatValue(tokenizer);
+ skipWhitespace(tokenizer);
+ tokenizer.tokenStart = tokenizer.position;
+ eatValue(tokenizer);
switch(j){
case 0:
TokenBuilder.addUnchecked(atom_idTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
@@ -185,16 +197,16 @@ async function handleAtoms(state: State): Promise<Schema.Atoms> {
TokenBuilder.addUnchecked(atom_typeTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
default:
- if(hasSubst_id == true && subst_idWritten == false){
+ if(hasSubst_id === true && subst_idWritten === false){
TokenBuilder.addUnchecked(subst_idTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
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);
subst_nameWritten = true;
- }else if(hasCharge == true && chargeWritten == false){
+ }else if(hasCharge === true && chargeWritten === false){
TokenBuilder.addUnchecked(chargeTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
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);
status_bitWritten = true;
}
@@ -213,12 +225,12 @@ async function handleAtoms(state: State): Promise<Schema.Atoms> {
y: yTokenColumn(Column.Schema.float),
z: zTokenColumn(Column.Schema.float),
atom_type: atom_typeColumn(Column.Schema.str),
- // optional properties
+
+ // optional columns
subst_id: hasSubst_id ? subst_idTokenColumn(Column.Schema.int) : undefInt,
subst_name: hasSubst_name ? subst_nameTokenColumn(Column.Schema.str) : undefStr,
charge: hasCharge ? chargeTokenColumn(Column.Schema.float) : undefFloat,
status_bit: hasStatus_bit ? status_bitTokenColumn(Column.Schema.str) : undefStr,
-
};
return ret;
}
@@ -227,13 +239,13 @@ async function handleBonds(state: State): Promise<Schema.Bonds> {
const { tokenizer, molecule } = state;
let hasStatus_bit = false;
- while(Tokenizer.getTokenString(tokenizer) != '@<TRIPOS>BOND'){
- Tokenizer.markLine(tokenizer);
+ while(getTokenString(tokenizer) !== '@<TRIPOS>BOND'){
+ markLine(tokenizer);
}
const initialTokenizerPosition = tokenizer.position;
const initialTokenizerLineNumber = tokenizer.lineNumber;
- const firstLine = Tokenizer.readLine(tokenizer);
+ const firstLine = readLine(tokenizer);
const firstLineArray = firstLine.trim().split(/\s+/g)
const firstLineLength = firstLineArray.length;
if(firstLineLength === 5){
@@ -268,8 +280,9 @@ async function handleBonds(state: State): Promise<Schema.Bonds> {
const linesToRead = Math.min(molecule.num_bonds - linesAlreadyRead, chunkSize);
for(let i = 0; i < linesToRead; i++){
for(let j = 0; j < numberOfColumn; j++){
- Tokenizer.skipWhitespace(tokenizer);
- Tokenizer.eatValue(tokenizer);
+ skipWhitespace(tokenizer);
+ tokenizer.tokenStart = tokenizer.position;
+ eatValue(tokenizer);
switch(j){
case 0:
TokenBuilder.addUnchecked(bond_idTokens, tokenizer.tokenStart, tokenizer.tokenEnd);