diff --git a/src/mol-io/reader/mol2/parser.ts b/src/mol-io/reader/mol2/parser.ts
index e856a87e89194796c20ee35ff5994dfc3c5cc5f6..9f40147fb008e9f0cd4c5bbab97adc87830d7499 100644
--- a/src/mol-io/reader/mol2/parser.ts
+++ b/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;