fixed mol2 parser

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;
 

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,
     };