Used TokenColumns. Read first line to determine which column is missing. Read each value at a time and add start and end indices to corresponding tokens. There is an error about async wait of handleAtoms and handlebonds Funcitons because they don't have async functions inside them and maybe they don't return Promises anymore. Used to use readLinesAsync which is a async function. But now use skipWhitespace and eatValue, which don't have async versions.

src/mol-io/reader/mol2/parser.ts

@@ -5,8 +5,8 @@
 // const undefPooledStr = UndefinedColumn(molecule.num_atoms, ColumnType.pooledStr);
 // because latter actuall return a column of zeros
 import { Column } from 'mol-data/db'
-import Tokenizer from '../common/text/tokenizer'
-import FixedColumn from '../common/text/column/fixed'
+import { TokenBuilder, Tokenizer } from '../common/text/tokenizer'
+import TokenColumn from '../common/text/column/token'
 import * as Schema from './schema'
 import Result from '../result'
 import Computation from 'mol-util/computation' 
@@ -81,7 +81,14 @@ function handleMolecule(state: State) {
 }
 
 
-
+function isStatus_bit(aString: String): Boolean{
+    if(aString.includes('DSPMOD') || aString.includes('TYPECOL') || aString.includes('CAP')
+       || aString.includes('BACKBONE') || aString.includes('DICT') || aString.includes('ESSENTIAL')
+       || aString.includes('WATER') || aString.includes('DIRECT')){
+        return true;
+    }
+    return false;
+}
 
 
 async function handleAtoms(state: State): Promise<Schema.Atoms> {
@@ -95,44 +102,123 @@ async function handleAtoms(state: State): Promise<Schema.Atoms> {
     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 initialTokenizerPosition = tokenizer.position;
+    const initialTOkenizerLineNumber = tokenizer.lineNumber;
+    const firstLine = Tokenizer.readLine(tokenizer);
     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 firstLineLength = firstLineArray.length;
+    
+
+    // optionals are in order "integer string float string". Use this to find out which column is missing or empty
+    for(let i = 6; i < firstLineLength; i++){
+        if(!isNaN(Number(firstLineArray[i]))){
+            if(firstLineArray[i].indexOf('.') == -1){
+                hasSubst_id = true;
+            }else{
+                hasCharge = true;
+            }
+        }else if(isNaN(Number(firstLineArray[i]))){
+            if(!isStatus_bit(firstLineArray[i])){
+                hasSubst_name = true;
+            }else{
+                hasStatus_bit = true;
+            }
+    }
 
-    const col = FixedColumn(lines);
-    const undefInt = Column.Undefined(molecule.num_atoms, Column.Schema.int);
+    const atom_idTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2);
+    const atom_nameTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2);;
+    const xTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2);
+    const yTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2);    
+    const zTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2);
+    const atom_typeTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2);
+    // optionals
+    const subst_idTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2);
+    const subst_nameTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2);
+    const chargeTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2);
+    const status_bitTokens = TokenBuilder.create(tokenizer, molecule.num_atoms * 2);
+
+
+    const atom_idTokenColumn = TokenColumn(atom_idTokens);
+    const atom_nameTokenColumn = TokenColumn(atom_nameTokens);
+    const xTokenColumn = TokenColumn(xTokens);
+    const yTokenColumn = TokenColumn(yTokens);
+    const zTokenColumn = TokenColumn(zTokens);
+    const atom_typeColumn = TokenColumn(atom_typeTokens);
+    // optionals
+    const subst_idTokenColumn = TokenColumn(subst_idTokens);
+    const subst_nameTokenColumn = TokenColumn(subst_nameTokens);
+    const chargeTokenColumn = TokenColumn(chargeTokens); 
+    const status_bitTokenColumn = TokenColumn(status_bitTokens);
+     
+    
     const undefFloat = Column.Undefined(molecule.num_atoms, Column.Schema.float);
-    //const undefPooledStr = UndefinedColumn(molecule.num_atoms, ColumnType.pooledStr);
-    // created below column to pass unit tests
+    const undefInt = Column.Undefined(molecule.num_atoms, Column.Schema.int);
     const undefStr = Column.Undefined(molecule.num_atoms, Column.Schema.str);
 
+    let numOfColumn = 5;
+    if(hasSubst_id){numOfColumn++}
+    if(hasSubst_name){numOfColumn++}
+    if(hasCharge){numOfColumn++}
+    if(hasStatus_bit){numOfColumn++}
+
+    tokenizer.position = initialTokenizerPosition;
+    tokenizer.lineNumber = initialTOkenizerLineNumber;
+
+    for(let i = 0; i < molecule.num_atoms; i++){
+            let subst_idWritten = false;
+            let subst_nameWritten = false;
+            let chargeWritten = false;
+            let status_bitWritten = false;
+        for(let j = 0; j < numOfColumn; j++){
+            Tokenizer.skipWhitespace(tokenizer);
+            Tokenizer.eatValue(tokenizer);
+            switch(j){
+                case 0:
+                    TokenBuilder.addUnchecked(atom_idTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
+                case 1:
+                    TokenBuilder.addUnchecked(atom_nameTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
+                case 2:
+                    TokenBuilder.addUnchecked(xTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
+                case 3:
+                    TokenBuilder.addUnchecked(yTokens, tokenizer.tokenStart, tokenizer.tokenEnd); 
+                case 4:
+                    TokenBuilder.addUnchecked(zTokens, tokenizer.tokenStart, tokenizer.tokenEnd); 
+                case 5:
+                    TokenBuilder.addUnchecked(atom_typeTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
+                default:
+                    if(hasSubst_id == true && subst_idWritten == false){
+                        TokenBuilder.addUnchecked(subst_idTokens, tokenizer.tokenStart, tokenizer.tokenEnd); 
+                        subst_idWritten = true;
+                    }else if(hasSubst_name == true && subst_nameWritten == false){
+                        TokenBuilder.addUnchecked(subst_nameTokens, tokenizer.tokenStart, tokenizer.tokenEnd); 
+                        subst_nameWritten = true;
+                    }else if(hasCharge == true && chargeWritten == false){
+                        TokenBuilder.addUnchecked(chargeTokens, tokenizer.tokenStart, tokenizer.tokenEnd); 
+                        chargeWritten = true;
+                    }else if(hasStatus_bit == true && status_bitWritten == false){
+                        TokenBuilder.addUnchecked(status_bitTokens, tokenizer.tokenStart, tokenizer.tokenEnd); 
+                        status_bitWritten = true;
+                    }
+            }
+        }
+    }
+
     const ret = {
         count: molecule.num_atoms,
-        atom_id: col(0, 7, Column.Schema.int),
-        atom_name: col(7, 9, Column.Schema.str), 
-        x: col(16, 10, Column.Schema.float),
-        y: col(26, 10, Column.Schema.float),
-        z: col(36, 10, Column.Schema.float),
-        atom_type: col(46, 6, Column.Schema.str),
+        atom_id: atom_idTokenColumn(Column.Schema.int),
+        atom_name: atom_nameTokenColumn(Column.Schema.str), 
+        x: xTokenColumn(Column.Schema.float),
+        y: yTokenColumn(Column.Schema.float),
+        z: zTokenColumn(Column.Schema.float),
+        atom_type: atom_typeColumn(Column.Schema.str),
         // optional properties
-        subst_id: hasSubst_id ? col(52, 6, Column.Schema.int) : undefInt, 
-        subst_name: hasSubst_name ? col(58, 8, Column.Schema.str) : undefStr,
-        charge: hasCharge ? col(66, 10, Column.Schema.float) : undefFloat, 
-        status_bit: hasStatus_bit ? col(76, 100, Column.Schema.str) : undefStr, 
+        subst_id: hasSubst_id ? subst_idTokenColumn(Column.Schema.int) : undefInt, 
+        subst_name: hasSubst_name ? subst_nameTokenColumn(Column.Schema.str) : undefStr,
+        charge: hasCharge ? chargeTokenColumn(Column.Schema.float) : undefFloat, 
+        status_bit: hasStatus_bit ? status_bitTokenColumn(Column.Schema.str) : undefStr, 
 
     };
-
     return ret;
 }
 
@@ -146,32 +232,64 @@ async function handleBonds(state: State): Promise<Schema.Bonds> {
     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){
+
+    const initialTokenizerPosition = tokenizer.position;
+    const initialTokenizerLineNumber = tokenizer.lineNumber;
+    const firstLine = Tokenizer.readLine(tokenizer);
+    const firstLineArray = firstLine.trim().split(/\s+/g)
+    const firstLineLength = firstLineArray.length;
+    if(firstLineLength == 5){
         hasStatus_bit = true;
     }
 
-    const col = FixedColumn(lines);
-    //const undefPooledStr = UndefinedColumn(molecule.num_bonds, ColumnType.pooledStr);
-    // created below column to pass unit tests
-    const undefStr = Column.Undefined(molecule.num_atoms, Column.Schema.str);
-
-    // if don't want to assume a fixed format, we can access a value of a column at a certain row by 
-    // parse out the whole line at row x, then split the line, and return the yth value that is at the 
-    // index of wanted value.
+    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);
+
+    const undefStr = Column.Undefined(molecule.num_bonds, Column.Schema.str);
+
+    let numberOfColumn = 4;
+    if(hasStatus_bit){numberOfColumn++}
+
+    tokenizer.position = initialTokenizerPosition;
+    tokenizer.lineNumber = initialTokenizerLineNumber;
+
+    for(let i = 0; i < molecule.num_bonds; i++){
+        for(let j = 0; j < numberOfColumn; j++){
+            Tokenizer.skipWhitespace(tokenizer);
+            Tokenizer.eatValue(tokenizer);
+            switch(j){
+                case 0:
+                    TokenBuilder.addUnchecked(bond_idTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
+                case 1:
+                    TokenBuilder.addUnchecked(origin_bond_idTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
+                case 2:
+                    TokenBuilder.addUnchecked(target_bond_idTokens, tokenizer.tokenStart, tokenizer.tokenEnd);
+                case 3:
+                    TokenBuilder.addUnchecked(bondTypeTokens, tokenizer.tokenStart, tokenizer.tokenEnd); 
+                default:
+                    TokenBuilder.addUnchecked(status_bitTokens, tokenizer.tokenStart, tokenizer.tokenEnd); 
+            }
+        }
+    }
 
     const ret = {
         count: molecule.num_bonds,
-        bond_id: col(0, 6, Column.Schema.int),
-        origin_atom_id: col(6, 6, Column.Schema.int), 
-        target_atom_id: col(12, 6, Column.Schema.int),
-        bond_type: col(18, 5, Column.Schema.str), 
-        // optional properties
-        // 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, Column.Schema.str) : undefStr, 
+        bond_id: bond_idTokenColumn(Column.Schema.int),
+        origin_atom_id: origin_bond_idTokenColumn(Column.Schema.int), 
+        target_atom_id: target_bond_idTokenColumn(Column.Schema.int),
+        bond_type: bondTypeTokenColumn(Column.Schema.str), 
+        status_bits: hasStatus_bit ? status_bitTokenColumn(Column.Schema.str) : undefStr, 
     };
 
     return ret;