From 2735ab4555573ed2e40487e15be9295314a5baa1 Mon Sep 17 00:00:00 2001
From: Zepei Xu <xuzepei19950617@gmail.com>
Date: Sat, 21 Oct 2017 23:08:03 -0700
Subject: [PATCH] complete mol2 parser, and its unit tests
---
src/reader/mol2/parser.ts | 167 ++++++++---------
src/reader/mol2/schema.d.ts | 1 -
src/reader/spec/gro.spec.ts | 1 -
src/reader/spec/mol2.spec.ts | 340 +++++++++++++++++++++++++++++++++--
4 files changed, 412 insertions(+), 97 deletions(-)
diff --git a/src/reader/mol2/parser.ts b/src/reader/mol2/parser.ts
index 035f1f5da..87a22cbf7 100644
--- a/src/reader/mol2/parser.ts
+++ b/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;
\ No newline at end of file
diff --git a/src/reader/mol2/schema.d.ts b/src/reader/mol2/schema.d.ts
index a34dc9f9e..7f1e73fb2 100644
--- a/src/reader/mol2/schema.d.ts
+++ b/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 {
diff --git a/src/reader/spec/gro.spec.ts b/src/reader/spec/gro.spec.ts
index 8f78668d5..9f74a7960 100644
--- a/src/reader/spec/gro.spec.ts
+++ b/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];
diff --git a/src/reader/spec/mol2.spec.ts b/src/reader/spec/mol2.spec.ts
index 675f41a69..2a04c751f 100644
--- a/src/reader/spec/mol2.spec.ts
+++ b/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);
--
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