diff --git a/src/mol-io/reader/_spec/mol2.spec.ts b/src/mol-io/reader/_spec/mol2.spec.ts
index bb792004a96763a6ab87674d7aa823050ba8be55..c329f61a4e5c66a28588d8424eb4327dbafb25ff 100644
--- a/src/mol-io/reader/_spec/mol2.spec.ts
+++ b/src/mol-io/reader/_spec/mol2.spec.ts
@@ -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;
diff --git a/src/mol-io/reader/mol2/parser.ts b/src/mol-io/reader/mol2/parser.ts
index 5613570b979740aa13252591a7e60b3af4117714..f807f4ff7b78d1c3f7a051fbba88a0a69c6216de 100644
--- a/src/mol-io/reader/mol2/parser.ts
+++ b/src/mol-io/reader/mol2/parser.ts
@@ -53,17 +53,21 @@ const reWhitespace = /\s+/g;
function handleMolecule(state: State) {
const { tokenizer, molecule } = state;
- markLine(tokenizer);
+
+ 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,
};