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Commit b64faed5 authored by Alexander Rose's avatar Alexander Rose
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fixed mol2 parser

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src/mol-io/reader/_spec/mol2.spec.ts
+ 178
− 166
View file @ b64faed5
......@@ -62,126 +62,126 @@ GASTEIGER
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 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
......@@ -251,6 +251,10 @@ describe('mol2 reader', () => {
throw new Error(parsed.message);
}
const mol2File = parsed.result;
// number of structures
expect(mol2File.structures.length).toBe(1);
const data = mol2File.structures[0];
const { molecule, atoms, bonds } = data;
......@@ -292,52 +296,56 @@ describe('mol2 reader', () => {
expect(bonds.status_bits.value(0)).toBe('');
});
// it('multiblocks', async () => {
// const parsed = await Mol2(Mol2StringMultiBlocks)();
// if (parsed.isError) {
// 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);
// 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("");
// // 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");
// // 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) {
throw new Error(parsed.message);
}
const mol2File = parsed.result;
// number of structures
expect(mol2File.structures.length).toBe(2);
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);
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("");
// 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");
// 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('minimal', async () => {
const parsed = await Mol2(Mol2StringMinimal)();
......@@ -345,6 +353,10 @@ describe('mol2 reader', () => {
throw new Error(parsed.message);
}
const mol2File = parsed.result;
// number of structures
expect(mol2File.structures.length).toBe(1);
const data = mol2File.structures[0];
const { molecule, atoms, bonds } = data;
......
src/mol-io/reader/mol2/parser.ts
+ 16
− 10
View file @ b64faed5
......@@ -53,17 +53,21 @@ const reWhitespace = /\s+/g;
function handleMolecule(state: State) {
const { tokenizer, molecule } = state;
while(getTokenString(tokenizer) !== '@<TRIPOS>MOLECULE'){
markLine(tokenizer);
}
markLine(tokenizer);
molecule.mol_name = getTokenString(tokenizer);
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[2]) : 0;
molecule.num_feat = parseInt(values[3]) ? parseInt(values[3]) : 0;
molecule.num_sets = parseInt(values[4]) ? parseInt(values[4]) : 0;
molecule.num_atoms = parseInt(values[0]);
molecule.num_bonds = parseInt(values[1]);
molecule.num_subst = parseInt(values[2]);
molecule.num_feat = parseInt(values[3]);
molecule.num_sets = parseInt(values[4]);
markLine(tokenizer);
molecule.mol_type = getTokenString(tokenizer);
......@@ -252,20 +256,20 @@ async function handleBonds(state: State): Promise<Schema.Bonds> {
hasStatus_bit = true;
}
// required columns
const bond_idTokens = TokenBuilder.create(tokenizer, molecule.num_bonds * 2);
const origin_bond_idTokens = TokenBuilder.create(tokenizer, molecule.num_bonds * 2);
const target_bond_idTokens = TokenBuilder.create(tokenizer, molecule.num_bonds * 2);
const bondTypeTokens = TokenBuilder.create(tokenizer, molecule.num_bonds * 2);
// optional
const status_bitTokens = TokenBuilder.create(tokenizer, molecule.num_bonds * 2);
const bond_idTokenColumn = TokenColumn(bond_idTokens);
const origin_bond_idTokenColumn = TokenColumn(origin_bond_idTokens);
const target_bond_idTokenColumn = TokenColumn(target_bond_idTokens);
const bondTypeTokenColumn = TokenColumn(bondTypeTokens);
// optional
const status_bitTokenColumn = TokenColumn(status_bitTokens);
// optional columns
const status_bitTokens = TokenBuilder.create(tokenizer, molecule.num_bonds * 2);
const status_bitTokenColumn = TokenColumn(status_bitTokens);
const undefStr = Column.Undefined(molecule.num_bonds, Column.Schema.str);
let numberOfColumn = 4;
......@@ -312,6 +316,8 @@ async function handleBonds(state: State): Promise<Schema.Bonds> {
origin_atom_id: origin_bond_idTokenColumn(Column.Schema.int),
target_atom_id: target_bond_idTokenColumn(Column.Schema.int),
bond_type: bondTypeTokenColumn(Column.Schema.str),
// optional columns
status_bits: hasStatus_bit ? status_bitTokenColumn(Column.Schema.str) : undefStr,
};
......
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