complete mol2 parser, and its unit tests

src/reader/mol2/parser.ts

@@ -1,27 +1,20 @@
+//               NOTES                
+//When want to created undefined string column, must use 
+// undefStr = UndefinedColumn(molecule.num_atoms, ColumnType.str)
+// but not 
+// const undefPooledStr = UndefinedColumn(molecule.num_atoms, ColumnType.pooledStr);
+// because latter actuall return a column of zeros
 import Tokenizer from '../common/text/tokenizer'
 import FixedColumn from '../common/text/column/fixed'
 import { ColumnType, UndefinedColumn } from '../common/column'
 import * as Schema from './schema'
 import Result from '../result'
-import Computation from '../../utils/computation' ////////// not using this
-
-
-/*////////////////////////// NOTES //////////////////////////////
-    Not using async, wait, promises, computation, chunker.
-    Formatting is not clear, different exmaples mol2 files has different field sizes, so making
-columns using col() is not possible. Need to implement checks for optional columns, but not clear 
-about the names of each entry in a row in the example files.
-    Don't know when to use str and when to use pooledStr
-    Unlike gro file, mol2 file don't save 'hasSomthing' properties in the header-like Molecule 
-///////////////////////////////////////////////////////////////*/
-
-
-
+import Computation from '../../utils/computation' 
 
 interface State {
     tokenizer: Tokenizer,
     molecule: Schema.Molecule,
-    ///////////// not including Computation.chunker /////////////
+    chunker: Computation.Chunker
 }
 
 
@@ -44,11 +37,11 @@ function createEmptyMolecule(): Schema.Molecule {
 
 
 
-function State(tokenizer: Tokenizer): State { //////////// not having ctx: Computation.Context as a parameter //////////////
+function State(tokenizer: Tokenizer, ctx: Computation.Context): State { 
     return {
         tokenizer,
         molecule: createEmptyMolecule(),
-        //////////// not having chunker: Computation.chunker(ctx, 100000) ///////////
+        chunker: Computation.chunker(ctx, 100000)
     };
 }
 
@@ -58,18 +51,18 @@ function State(tokenizer: Tokenizer): State { //////////// not having ctx: Compu
 
 function handleMolecule(state: State) {
     const { tokenizer, molecule } = state;
-    
+    Tokenizer.markLine(tokenizer); // skip the line '@<TRIPOS>MOLECULE'
     Tokenizer.markLine(tokenizer);
     let name = Tokenizer.getTokenString(tokenizer);
     molecule.mol_name = name;
 
     Tokenizer.markLine(tokenizer);
     const values = Tokenizer.getTokenString(tokenizer).trim().split(/\s+/g);
-    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]);
+    molecule.num_atoms = parseInt(values[0]) ? parseInt(values[1]) : 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;
 
     Tokenizer.markLine(tokenizer);
     molecule.mol_type = Tokenizer.getTokenString(tokenizer);
@@ -77,56 +70,71 @@ function handleMolecule(state: State) {
     Tokenizer.markLine(tokenizer);
     molecule.charge_type = Tokenizer.getTokenString(tokenizer);
 
-    // skip the empty line
-    Tokenizer.markLine(tokenizer)
+    Tokenizer.markLine(tokenizer);
+    if(Tokenizer.getTokenString(tokenizer) == ''){return}
+    else{molecule.status_bits = Tokenizer.getTokenString(tokenizer)}
 
+
+    Tokenizer.markLine(tokenizer);
+    if(Tokenizer.getTokenString(tokenizer) == ''){return}
+    else{molecule.mol_comment = Tokenizer.getTokenString(tokenizer)}
 }
 
 
 
 
 
-function handleAtoms(state: State): Schema.Atoms {
+async function handleAtoms(state: State): Promise<Schema.Atoms> {
     const { tokenizer, molecule } = state;
-
-    ////////// not using readLinesAsync /////////
-    const lines =  Tokenizer.readLines(tokenizer, molecule.num_atoms);
-
-    // default all false
-    const hasSubst_id = false;
-    const hasSubst_name = false;
-    const hasCharge = false;
-    const hasStatus_bit = false;
-
-    /*
-    const pO = 20;
-    const pW = state.header.precision.position + 5;
-    const vO = pO + 3 * pW;
-    const vW = state.header.precision.velocity + 4;
-    */
+    let hasSubst_id = false;
+    let hasSubst_name = false;
+    let hasCharge = false;
+    let hasStatus_bit = false;
+
+    // skip empty lines and '@<TRIPOS>ATOM'
+    while(Tokenizer.getTokenString(tokenizer) != '@<TRIPOS>ATOM'){
+        Tokenizer.markLine(tokenizer);
+    }
+    const lines =  await Tokenizer.readLinesAsync(tokenizer, molecule.num_atoms, state.chunker);
+    const firstLine = tokenizer.data.substring(lines.indices[0], lines.indices[1]);
+    const firstLineArray = firstLine.trim().split(/\s+/g)
+    const length = firstLineArray.length;
+    if(length == 9){
+        hasSubst_id = true;
+        hasSubst_name = true;
+        hasCharge = true;
+    }else if(length == 10){
+        hasSubst_id = true;
+        hasSubst_name = true;
+        hasCharge = true;
+        hasStatus_bit = true;
+    }    
 
     const col = FixedColumn(lines);
     const undefInt = UndefinedColumn(molecule.num_atoms, ColumnType.int);
     const undefFloat = UndefinedColumn(molecule.num_atoms, ColumnType.float);
+    //const undefPooledStr = UndefinedColumn(molecule.num_atoms, ColumnType.pooledStr);
+    // created below column to pass unit tests
     const undefStr = UndefinedColumn(molecule.num_atoms, ColumnType.str);
-    const undefPooledStr = UndefinedColumn(molecule.num_atoms, ColumnType.pooledStr);
-
-    /////// wanted to have const undef = UndefinedColumn(molecule.num_atoms) like col, but failed
 
-    /////// some unclear about the formatting, like the field sizes
     const ret = {
         count: molecule.num_atoms,
         atom_id: col(0, 7, ColumnType.int),
-        atom_name: col(7, 9, ColumnType.str), ////// don't know use str or pooledStr
+        atom_name: col(7, 9, ColumnType.pooledStr), 
         x: col(16, 10, ColumnType.float),
         y: col(26, 10, ColumnType.float),
         z: col(36, 10, ColumnType.float),
-        atom_type: col(46, 0, ColumnType.str), ////// don't know use str or pooledStr //////// don't know which is the atom_type
+        atom_type: col(46, 6, ColumnType.pooledStr),
         // optional properties
-        subst_id: hasSubst_id ? col(0, 0, ColumnType.int) : undefInt, 
-        subst_name: hasSubst_name ? col(0, 0, ColumnType.str) : undefStr,///////// don't know use str or pooledStr
-        charge: hasCharge ? col(0, 0, ColumnType.float) : undefFloat, //////// don't know use int or float
-        status_bit: hasStatus_bit ? col(0, 0, ColumnType.pooledStr) : undefPooledStr, ////////// don't know use str or pooledStr
+        subst_id: hasSubst_id ? col(52, 6, ColumnType.int) : undefInt, 
+        subst_name: hasSubst_name ? col(58, 8, ColumnType.pooledStr) : undefStr,
+        charge: hasCharge ? col(66, 10, ColumnType.float) : undefFloat, 
+        // undefPooledStr cannot pass unit tests because it create a column of zeros but not empty strings
+        //status_bit: hasStatus_bit ? col(76, 100, ColumnType.pooledStr) : undefPooledStr, 
+
+        // use undefStr instead to pass unit tests
+        status_bit: hasStatus_bit ? col(76, 100, ColumnType.pooledStr) : undefStr, 
+
     };
 
     return ret;
@@ -135,39 +143,35 @@ function handleAtoms(state: State): Schema.Atoms {
 
 
 
-function handleBonds(state: State): Schema.Bonds {
+async function handleBonds(state: State): Promise<Schema.Bonds> {
     const { tokenizer, molecule } = state;
+    let hasStatus_bit = false;
 
-    ////////// not using readLinesAsync /////////
-    const lines =  Tokenizer.readLines(tokenizer, molecule.num_bonds);
-
-    // default all false
-    const hasStatus_bit = false;
-
-    /*
-    const pO = 20;
-    const pW = state.header.precision.position + 5;
-    const vO = pO + 3 * pW;
-    const vW = state.header.precision.velocity + 4;
-    */
+    while(Tokenizer.getTokenString(tokenizer) != '@<TRIPOS>BOND'){
+        Tokenizer.markLine(tokenizer);
+    }
+    const lines =  await Tokenizer.readLinesAsync(tokenizer, molecule.num_bonds, state.chunker);
+    const firstLine = tokenizer.data.substring(lines.indices[0], lines.indices[1]);
+    const length = firstLine.split(' ').length;
+    if(length == 4){
+        hasStatus_bit = true;
+    }
 
     const col = FixedColumn(lines);
-    const undefInt = UndefinedColumn(molecule.num_bonds, ColumnType.int);
-    const undefFloat = UndefinedColumn(molecule.num_bonds, ColumnType.float);
-    const undefStr = UndefinedColumn(molecule.num_bonds, ColumnType.str);
-    const undefPooledStr = UndefinedColumn(molecule.num_bonds, ColumnType.pooledStr);
-
-    /////// wanted to have const undef = UndefinedColumn(molecule.num_atoms) like col, but failed
+    //const undefPooledStr = UndefinedColumn(molecule.num_bonds, ColumnType.pooledStr);
+    // created below column to pass unit tests
+    const undefStr = UndefinedColumn(molecule.num_atoms, ColumnType.str);
 
-    /////// some unclear about the formatting, like the field sizes
     const ret = {
         count: molecule.num_bonds,
         bond_id: col(0, 6, ColumnType.int),
         origin_atom_id: col(6, 6, ColumnType.int), 
         target_atom_id: col(12, 6, ColumnType.int),
-        bond_type: col(18, 5, ColumnType.str), ///////// don't know use str or pooledStr
+        bond_type: col(18, 5, ColumnType.pooledStr), 
         // optional properties
-        status_bits: hasStatus_bit ? col(0, 0, ColumnType.str) : undefStr, ///////// don't know use str or pooledStr
+        // undefPooledStr cannot pass unit tests because it create a column of zeros but not empty strings
+        //status_bits: hasStatus_bit ? col(23, 50, ColumnType.pooledStr) : undefPooledStr, 
+        status_bits: hasStatus_bit ? col(23, 50, ColumnType.pooledStr) : undefStr, 
     };
 
     return ret;
@@ -176,16 +180,16 @@ function handleBonds(state: State): Schema.Bonds {
 
 
 
-//////// not using async here
-function parseInternal(data: string): Result<Schema.File> { /////// not having ctx as a parameter, and not returning Promise
+async function parseInternal(data: string, ctx: Computation.Context): Promise<Result<Schema.File>> {
     const tokenizer = Tokenizer(data);
 
+    ctx.update({ message: 'Parsing...', current: 0, max: data.length });
     const structures: Schema.Structure[] = [];
     while (tokenizer.position < data.length) {
-        const state = State(tokenizer);//////////different
+        const state = State(tokenizer, ctx);
         handleMolecule(state);
-        const atoms = handleAtoms(state);
-        const bonds = handleBonds(state);
+        const atoms = await handleAtoms(state);
+        const bonds = await handleBonds(state);
         structures.push({ molecule: state.molecule, atoms, bonds });
     }
 
@@ -197,9 +201,10 @@ function parseInternal(data: string): Result<Schema.File> { /////// not having c
 
 
 
-///////// diffrent than gro parser
 export function parse(data: string) {
-    return parseInternal(data);
+    return Computation.create<Result<Schema.File>>(async ctx => {
+        return await parseInternal(data, ctx);
+    });
 }
 
 export default parse;

src/reader/mol2/schema.d.ts

@@ -25,7 +25,6 @@ export interface Molecule {
     charge_type: string
     status_bits: string
     mol_comment: string
-    ///////////// precisions are not saved for later use, and there is not 'hasSomthing' properties 
 }
 
 export interface Atoms {

src/reader/spec/gro.spec.ts

@@ -32,7 +32,6 @@ describe('gro reader', () => {
             console.log(parsed)
             return;
         }
-
         const groFile = parsed.result;
         const data = groFile.structures[0];
 

src/reader/spec/mol2.spec.ts

@@ -1,5 +1,4 @@
 
-
 import Mol2 from '../mol2/parser'
 
 const Mol2String = `@<TRIPOS>MOLECULE
@@ -11,51 +10,364 @@ 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`
+     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
+ 26 26 0 0 0
+SMALL
+GASTEIGER
+
+@<TRIPOS>ATOM
+      1 O           1.7394   -2.1169   -1.0894 O.3 
+      2 O          -2.2941    1.0781   -1.7979 O.3 
+      3 O          -3.6584    0.5842    0.5722 O.3 
+      4 N           2.6359    1.0243    0.7030 N.3
+      5 C           1.6787   -1.1447   -0.0373 C.3
+      6 C           0.2684   -0.6866    0.1208 C.ar 
+      7 C           2.6376    0.0193   -0.3576 C.3  
+      8 C          -0.3658   -0.0099   -0.9212 C.ar  
+      9 C          -0.4164   -0.9343    1.3105 C.ar 
+     10 C          -1.6849    0.4191   -0.7732 C.ar 
+     11 C          -1.7353   -0.5053    1.4585 C.ar  
+     12 C          -2.3696    0.1713    0.4166 C.ar   
+     13 C           3.5645    2.1013    0.3950 C.3     
+     14 H           2.0210   -1.6511    0.8741 H       
+     15 H           2.3808    0.4742   -1.3225 H       
+     16 H           3.6478   -0.3931   -0.4831 H      
+     17 H           0.1501    0.1801   -1.8589 H   
+     18 H           0.0640   -1.4598    2.1315 H   
+     19 H           2.9013    0.5888    1.5858 H       
+     20 H          -2.2571   -0.7050    2.3907 H       
+     21 H           2.6646   -2.4067   -1.1652 H       
+     22 H           3.2862    2.6124   -0.5325 H      
+     23 H           4.5925    1.7346    0.3078 H      
+     24 H           3.5401    2.8441    1.1985 H      
+     25 H          -3.2008    1.2997   -1.5231 H   
+     26 H          -3.9690    0.3259    1.4570 H   
+@<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`
 
-////////// nothing works until add async and await and promise to parser.mol2 file.
 describe('mol2 reader', () => {
     it('basic', async () => {
-        const parsed = await Mol2(Mol2String)();
+        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;
+
+        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('');
+
+        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('');
+
+    });
+
+    it('multiblocks', async () => {
+        const parsed =  await Mol2(Mol2StringMultiBlocks)();
         if (parsed.isError) {
             console.log(parsed)
             return;
         }
+        const mol2File = parsed.result;
+        const data = mol2File.structures[1];
+        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("");
+
+        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('');
+
+        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('');
+
+    });
+
+    it('minimal', async () => {
+        const parsed =  await Mol2(Mol2StringMinimal)();
+        if (parsed.isError) {
+            console.log(parsed)
+            return;
+        }
         const mol2File = parsed.result;
         const data = mol2File.structures[0];
-
         const { molecule, atoms, bonds } = data;
 
-        expect(molecule.mol_name).toBe(5816)
+        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("")
-        expect(molecule.charge_type).toBe("");
+        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(2);
+        expect(atoms.count).toBe(26);
         expect(atoms.atom_id.value(0)).toBe(1);
-        expect(atoms.atom_name.value(0)).toBe('o');
+        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('');
+        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(0.000);
-        expect(atoms.status_bits.value(0)).toBe('');
+        expect(atoms.charge.value(0)).toBeCloseTo(0);
+        expect(atoms.status_bit.value(0)).toBe('');
 
-        expect(bonds.count).toBe(2);
+        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);