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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 ...@@ -62,126 +62,126 @@ GASTEIGER
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
// 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
// @<TRIPOS>MOLECULE @<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 Mol2StringMinimal = `@<TRIPOS>MOLECULE const Mol2StringMinimal = `@<TRIPOS>MOLECULE
5816 5816
...@@ -251,6 +251,10 @@ describe('mol2 reader', () => { ...@@ -251,6 +251,10 @@ describe('mol2 reader', () => {
throw new Error(parsed.message); throw new Error(parsed.message);
} }
const mol2File = parsed.result; const mol2File = parsed.result;
// number of structures
expect(mol2File.structures.length).toBe(1);
const data = mol2File.structures[0]; const data = mol2File.structures[0];
const { molecule, atoms, bonds } = data; const { molecule, atoms, bonds } = data;
...@@ -292,52 +296,56 @@ describe('mol2 reader', () => { ...@@ -292,52 +296,56 @@ describe('mol2 reader', () => {
expect(bonds.status_bits.value(0)).toBe(''); 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) {
// throw new Error(parsed.message); throw new Error(parsed.message);
// } }
// const mol2File = parsed.result; const mol2File = parsed.result;
// const data = mol2File.structures[1];
// const { molecule, atoms, bonds } = data; // number of structures
expect(mol2File.structures.length).toBe(2);
// // molecule fields
// expect(molecule.mol_name).toBe('5816') const data = mol2File.structures[1];
// expect(molecule.num_atoms).toBe(26) const { molecule, atoms, bonds } = data;
// expect(molecule.num_bonds).toBe(26);
// expect(molecule.num_subst).toBe(0); // molecule fields
// expect(molecule.num_feat).toBe(0); expect(molecule.mol_name).toBe('5816')
// expect(molecule.num_sets).toBe(0); expect(molecule.num_atoms).toBe(26)
// expect(molecule.mol_type).toBe("SMALL") expect(molecule.num_bonds).toBe(26);
// expect(molecule.charge_type).toBe("GASTEIGER"); expect(molecule.num_subst).toBe(0);
// expect(molecule.status_bits).toBe(""); expect(molecule.num_feat).toBe(0);
// expect(molecule.mol_comment).toBe(""); expect(molecule.num_sets).toBe(0);
expect(molecule.mol_type).toBe("SMALL")
// // required atom fields expect(molecule.charge_type).toBe("GASTEIGER");
// expect(atoms.count).toBe(26); expect(molecule.status_bits).toBe("");
// expect(atoms.atom_id.value(0)).toBe(1); expect(molecule.mol_comment).toBe("");
// expect(atoms.atom_name.value(0)).toBe('O');
// expect(atoms.x.value(0)).toBeCloseTo(1.7394, 0.001); // required atom fields
// expect(atoms.y.value(0)).toBeCloseTo(-2.1169, 0.0001); expect(atoms.count).toBe(26);
// expect(atoms.z.value(0)).toBeCloseTo(-1.0893, 0.0001); expect(atoms.atom_id.value(0)).toBe(1);
// expect(atoms.atom_type.value(0)).toBe("O.3"); expect(atoms.atom_name.value(0)).toBe('O');
expect(atoms.x.value(0)).toBeCloseTo(1.7394, 0.001);
// // optional atom fields expect(atoms.y.value(0)).toBeCloseTo(-2.1169, 0.0001);
// expect(atoms.subst_id.value(0)).toBe(1); expect(atoms.z.value(0)).toBeCloseTo(-1.0893, 0.0001);
// expect(atoms.subst_name.value(0)).toBe('LIG1'); expect(atoms.atom_type.value(0)).toBe("O.3");
// expect(atoms.charge.value(0)).toBeCloseTo(-0.3859);
// expect(atoms.status_bit.value(0)).toBe(''); // optional atom fields
expect(atoms.subst_id.value(0)).toBe(1);
// // required bond fields expect(atoms.subst_name.value(0)).toBe('LIG1');
// expect(bonds.count).toBe(26); expect(atoms.charge.value(0)).toBeCloseTo(-0.3859);
// expect(bonds.bond_id.value(0)).toBe(1); expect(atoms.status_bit.value(0)).toBe('');
// expect(bonds.origin_atom_id.value(0)).toBe(1);
// expect(bonds.target_atom_id.value(0)).toBe(5); // required bond fields
// expect(bonds.bond_type.value(0)).toBe('1'); expect(bonds.count).toBe(26);
expect(bonds.bond_id.value(0)).toBe(1);
// // optional bond fields expect(bonds.origin_atom_id.value(0)).toBe(1);
// expect(bonds.status_bits.value(0)).toBe(''); 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 () => { it('minimal', async () => {
const parsed = await Mol2(Mol2StringMinimal)(); const parsed = await Mol2(Mol2StringMinimal)();
...@@ -345,6 +353,10 @@ describe('mol2 reader', () => { ...@@ -345,6 +353,10 @@ describe('mol2 reader', () => {
throw new Error(parsed.message); throw new Error(parsed.message);
} }
const mol2File = parsed.result; const mol2File = parsed.result;
// number of structures
expect(mol2File.structures.length).toBe(1);
const data = mol2File.structures[0]; const data = mol2File.structures[0];
const { molecule, atoms, bonds } = data; 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; ...@@ -53,17 +53,21 @@ const reWhitespace = /\s+/g;
function handleMolecule(state: State) { function handleMolecule(state: State) {
const { tokenizer, molecule } = state; const { tokenizer, molecule } = state;
markLine(tokenizer);
while(getTokenString(tokenizer) !== '@<TRIPOS>MOLECULE'){
markLine(tokenizer);
}
markLine(tokenizer); markLine(tokenizer);
molecule.mol_name = getTokenString(tokenizer); molecule.mol_name = getTokenString(tokenizer);
markLine(tokenizer); markLine(tokenizer);
const values = getTokenString(tokenizer).trim().split(reWhitespace); const values = getTokenString(tokenizer).trim().split(reWhitespace);
molecule.num_atoms = parseInt(values[0]) ? parseInt(values[0]) : 0; molecule.num_atoms = parseInt(values[0]);
molecule.num_bonds = parseInt(values[1]) ? parseInt(values[1]) : 0; molecule.num_bonds = parseInt(values[1]);
molecule.num_subst = parseInt(values[2]) ? parseInt(values[2]) : 0; molecule.num_subst = parseInt(values[2]);
molecule.num_feat = parseInt(values[3]) ? parseInt(values[3]) : 0; molecule.num_feat = parseInt(values[3]);
molecule.num_sets = parseInt(values[4]) ? parseInt(values[4]) : 0; molecule.num_sets = parseInt(values[4]);
markLine(tokenizer); markLine(tokenizer);
molecule.mol_type = getTokenString(tokenizer); molecule.mol_type = getTokenString(tokenizer);
...@@ -252,20 +256,20 @@ async function handleBonds(state: State): Promise<Schema.Bonds> { ...@@ -252,20 +256,20 @@ async function handleBonds(state: State): Promise<Schema.Bonds> {
hasStatus_bit = true; hasStatus_bit = true;
} }
// required columns
const bond_idTokens = TokenBuilder.create(tokenizer, molecule.num_bonds * 2); const bond_idTokens = TokenBuilder.create(tokenizer, molecule.num_bonds * 2);
const origin_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 target_bond_idTokens = TokenBuilder.create(tokenizer, molecule.num_bonds * 2);
const bondTypeTokens = 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 bond_idTokenColumn = TokenColumn(bond_idTokens);
const origin_bond_idTokenColumn = TokenColumn(origin_bond_idTokens); const origin_bond_idTokenColumn = TokenColumn(origin_bond_idTokens);
const target_bond_idTokenColumn = TokenColumn(target_bond_idTokens); const target_bond_idTokenColumn = TokenColumn(target_bond_idTokens);
const bondTypeTokenColumn = TokenColumn(bondTypeTokens); 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); const undefStr = Column.Undefined(molecule.num_bonds, Column.Schema.str);
let numberOfColumn = 4; let numberOfColumn = 4;
...@@ -312,6 +316,8 @@ async function handleBonds(state: State): Promise<Schema.Bonds> { ...@@ -312,6 +316,8 @@ async function handleBonds(state: State): Promise<Schema.Bonds> {
origin_atom_id: origin_bond_idTokenColumn(Column.Schema.int), origin_atom_id: origin_bond_idTokenColumn(Column.Schema.int),
target_atom_id: target_bond_idTokenColumn(Column.Schema.int), target_atom_id: target_bond_idTokenColumn(Column.Schema.int),
bond_type: bondTypeTokenColumn(Column.Schema.str), bond_type: bondTypeTokenColumn(Column.Schema.str),
// optional columns
status_bits: hasStatus_bit ? status_bitTokenColumn(Column.Schema.str) : undefStr, status_bits: hasStatus_bit ? status_bitTokenColumn(Column.Schema.str) : undefStr,
}; };
......
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