pub_soft/rdkit
3
0
Fork 0
mirror of https://github.com/rdkit/rdkit.git synced 2026-06-07 22:44:25 +08:00
Code Issues Packages Projects Releases Wiki Activity
Files
99aa358fe024a7bf198449eadbd7f2e6da3fa433
rdkit/Code/MinimalLib/tests/tests.js
Paolo Tosco 948f7d231a Expose reaction drawing and additional FPs in MinimalLib (#5277) 
* - exposed reaction drawing in MinimalLib
- fixed a typo in the error message "JSON doesn't contain 'atoms' field, or it is not an array"
- replaced RapidJson HasMember() with FindMember() to avoid a duplicate lookup in case the member exists and can be accessed
- some cosmetic style changes (avoid multiple variable declarations on a single line, use curly bracket also for one-liner if clauses, use auto where possible)
- capitalized "greg Landrum" to "Greg Landrum" (well deserved)
- exposed other FPs in addition to Morgan and Pattern FPs in MinimalLib
- added relevant tests

* - update CXSMARTS test in MinimalLib

* Changes in response to review:
- exposed reaction drawing functionality to CFFI and added relevant tests
- refactored fingerprint code to use JSON details and deprecated the Morgan/pattern fingerprint functions that used multiple parameters
- all fingerprints are now exposed to both JS and CFFI with no code duplication
- fixed a potential crash bug in the CFFI library where calling get_morgan_fp(), get_rdkit_fp() or get_pattern_fp with a NULL mol_pkl would result in dereferencing a nullptr

* removed debugging printouts committed accidentally

Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
2022-09-06 14:27:10 +02:00

899 lines
33 KiB
JavaScript
Raw Blame History

//
//
// Copyright (C) 2019 Greg Landrum
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
const assert = require('assert');
const {
performance
} = require('perf_hooks');
var initRDKitModule = require("../demo/RDKit_minimal.js");
var RDKitModule;
const fs = require('fs');
const readline = require('readline');
// the goal here isn't to be comprehensive (the RDKit has tests for that),
// just to make sure that the wrappers are working as expected
function test_basics() {
var bmol = null;
try {
bmol = RDKitModule.get_mol("c1ccccc");
assert.equal(bmol.is_valid(),0);
} catch {
assert(bmol === null);
}
var mol = RDKitModule.get_mol("c1ccccc1O");
assert.equal(mol.is_valid(),1);
assert.equal(mol.get_smiles(),"Oc1ccccc1");
assert.equal(mol.get_inchi(),"InChI=1S/C6H6O/c7-6-4-2-1-3-5-6/h1-5,7H");
assert.equal(RDKitModule.get_inchikey_for_inchi(mol.get_inchi()),"ISWSIDIOOBJBQZ-UHFFFAOYSA-N");
var mb = mol.get_molblock();
assert(mb.search("M END")>0);
var mol2 = RDKitModule.get_mol(mb);
assert.equal(mol2.is_valid(),1);
assert.equal(mol2.get_smiles(),"Oc1ccccc1");
var mjson = mol.get_json();
assert(mjson.search("commonchem")>0);
var mol3 = RDKitModule.get_mol(mjson);
assert.equal(mol3.is_valid(),1);
assert.equal(mol3.get_smiles(),"Oc1ccccc1");
var descrs = JSON.parse(mol.get_descriptors());
assert.equal(descrs.NumAromaticRings,1);
assert.equal(descrs.NumRings,1);
assert.equal(descrs.amw,94.11299);
var checkStringBinaryFpIdentity = (stringFp, binaryFp) => {
assert.equal(binaryFp.length, stringFp.length / 8);
for (var i = 0, c = 0; i < binaryFp.length; ++i) {
var byte = 0;
for (var j = 0; j < 8; ++j, ++c) {
if (stringFp[c] === "1") {
byte |= (1 << j);
}
}
assert.equal(byte, binaryFp[i]);
}
};
{
var fp1 = mol.get_morgan_fp();
assert.equal(fp1.length, 2048);
assert.equal((fp1.match(/1/g)||[]).length, 11);
var fp1Uint8Array = mol.get_morgan_fp_as_uint8array();
checkStringBinaryFpIdentity(fp1, fp1Uint8Array);
var fp2 = mol.get_morgan_fp(JSON.stringify({ radius: 0, nBits: 512 }));
assert.equal(fp2.length, 512);
assert.equal((fp2.match(/1/g)||[]).length, 3);
var fp2Uint8Array = mol.get_morgan_fp_as_uint8array(JSON.stringify({ radius: 0, nBits: 512 }));
checkStringBinaryFpIdentity(fp2, fp2Uint8Array);
var fp3 = mol.get_morgan_fp(0, 512);
assert.equal(fp3.length, 512);
assert.equal((fp3.match(/1/g)||[]).length, 3);
var fp3Uint8Array = mol.get_morgan_fp_as_uint8array(0, 512);
checkStringBinaryFpIdentity(fp3, fp3Uint8Array);
}
{
var fp1 = mol.get_pattern_fp();
assert.equal(fp1.length, 2048);
assert.equal((fp1.match(/1/g)||[]).length, 73);
var fp1Uint8Array = mol.get_pattern_fp_as_uint8array();
checkStringBinaryFpIdentity(fp1, fp1Uint8Array);
var fp2 = mol.get_pattern_fp(JSON.stringify({ nBits: 256 }));
assert.equal(fp2.length, 256);
assert.equal((fp2.match(/1/g)||[]).length, 65);
var fp2Uint8Array = mol.get_pattern_fp_as_uint8array(JSON.stringify({ nBits: 256 }));
checkStringBinaryFpIdentity(fp2, fp2Uint8Array);
var fp3 = mol.get_pattern_fp(256);
assert.equal(fp3.length, 256);
assert.equal((fp3.match(/1/g)||[]).length, 65);
var fp3Uint8Array = mol.get_pattern_fp_as_uint8array(256);
checkStringBinaryFpIdentity(fp3, fp3Uint8Array);
}
{
var fp1 = mol.get_topological_torsion_fp();
assert.equal(fp1.length, 2048);
assert.equal((fp1.match(/1/g)||[]).length, 8);
var fp1Uint8Array = mol.get_topological_torsion_fp_as_uint8array();
checkStringBinaryFpIdentity(fp1, fp1Uint8Array);
var fp2 = mol.get_topological_torsion_fp(JSON.stringify({ nBits: 512 }));
assert.equal(fp2.length, 512);
assert.equal((fp2.match(/1/g)||[]).length, 8);
var fp2Uint8Array = mol.get_topological_torsion_fp_as_uint8array(JSON.stringify({ nBits: 512 }));
checkStringBinaryFpIdentity(fp2, fp2Uint8Array);
}
{
var fp1 = mol.get_rdkit_fp();
assert.equal(fp1.length, 2048);
assert.equal((fp1.match(/1/g)||[]).length, 38);
var fp1Uint8Array = mol.get_rdkit_fp_as_uint8array();
checkStringBinaryFpIdentity(fp1, fp1Uint8Array);
var fp2 = mol.get_rdkit_fp(JSON.stringify({ nBits: 512 }));
assert.equal(fp2.length, 512);
assert.equal((fp2.match(/1/g)||[]).length, 37);
var fp2Uint8Array = mol.get_rdkit_fp_as_uint8array(JSON.stringify({ nBits: 512 }));
checkStringBinaryFpIdentity(fp2, fp2Uint8Array);
var fp3 = mol.get_rdkit_fp(JSON.stringify({ nBits: 512, minPath: 2 }));
assert.equal(fp3.length, 512);
assert.equal((fp3.match(/1/g)||[]).length, 34);
var fp3Uint8Array = mol.get_rdkit_fp_as_uint8array(JSON.stringify({ nBits: 512, minPath: 2 }));
checkStringBinaryFpIdentity(fp3, fp3Uint8Array);
var fp4 = mol.get_rdkit_fp(JSON.stringify({ nBits: 512, minPath: 2, maxPath: 4 }));
assert.equal(fp4.length, 512);
assert.equal((fp4.match(/1/g)||[]).length, 16);
var fp4Uint8Array = mol.get_rdkit_fp_as_uint8array(JSON.stringify({ nBits: 512, minPath: 2, maxPath: 4 }));
checkStringBinaryFpIdentity(fp4, fp4Uint8Array);
}
{
var fp1 = mol.get_atom_pair_fp();
assert.equal(fp1.length, 2048);
assert.equal((fp1.match(/1/g)||[]).length, 19);
var fp1Uint8Array = mol.get_atom_pair_fp_as_uint8array();
checkStringBinaryFpIdentity(fp1, fp1Uint8Array);
var fp2 = mol.get_atom_pair_fp(JSON.stringify({ nBits: 512 }));
assert.equal(fp2.length, 512);
assert.equal((fp2.match(/1/g)||[]).length, 19);
var fp2Uint8Array = mol.get_atom_pair_fp_as_uint8array(JSON.stringify({ nBits: 512 }));
checkStringBinaryFpIdentity(fp2, fp2Uint8Array);
var fp3 = mol.get_atom_pair_fp(JSON.stringify({ nBits: 512, minLength: 2 }));
assert.equal(fp3.length, 512);
assert.equal((fp3.match(/1/g)||[]).length, 13);
var fp3Uint8Array = mol.get_atom_pair_fp_as_uint8array(JSON.stringify({ nBits: 512, minLength: 2 }));
checkStringBinaryFpIdentity(fp3, fp3Uint8Array);
var fp4 = mol.get_atom_pair_fp(JSON.stringify({ nBits: 512, minLength: 2, maxLength: 3 }));
assert.equal(fp4.length, 512);
assert.equal((fp4.match(/1/g)||[]).length, 12);
var fp4Uint8Array = mol.get_atom_pair_fp_as_uint8array(JSON.stringify({ nBits: 512, minLength: 2, maxLength: 3 }));
checkStringBinaryFpIdentity(fp4, fp4Uint8Array);
}
if (typeof Object.getPrototypeOf(mol).get_avalon_fp === 'function') {
var fp1 = mol.get_avalon_fp();
assert.equal(fp1.length, 512);
assert.equal((fp1.match(/1/g)||[]).length, 19);
var fp1Uint8Array = mol.get_avalon_fp_as_uint8array();
checkStringBinaryFpIdentity(fp1, fp1Uint8Array);
var fp2 = mol.get_avalon_fp(JSON.stringify({ nBits: 2048 }));
assert.equal(fp2.length, 2048);
assert.equal((fp2.match(/1/g)||[]).length, 20);
var fp2Uint8Array = mol.get_avalon_fp_as_uint8array(JSON.stringify({ nBits: 2048 }));
checkStringBinaryFpIdentity(fp2, fp2Uint8Array);
}
var svg = mol.get_svg();
assert(svg.search("svg")>0);
var qmol = RDKitModule.get_qmol("Oc(c)c");
assert.equal(qmol.is_valid(),1);
var match = mol.get_substruct_match(qmol);
var pmatch = JSON.parse(match);
assert.equal(pmatch.atoms.length,4);
assert.equal(pmatch.atoms[0],6);
var svg2 = mol.get_svg_with_highlights(match);
assert(svg2.search("svg")>0);
assert(svg.search("#FF7F7F")<0);
assert(svg2.search("#FF7F7F")>0);
}
function test_molblock_nostrict() {
var molblock = `
MJ201100
10 10 0 0 0 0 0 0 0 0999 V2000
-1.2946 0.5348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.0090 0.1223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.0090 -0.7027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2946 -1.1152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5801 -0.7027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5801 0.1223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5467 1.2493 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
0.1342 0.5348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5467 -0.1796 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
-0.6907 0.5348 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
6 1 1 0 0 0 0
6 8 1 0 0 0 0
7 8 1 0 0 0 0
8 9 1 0 0 0 0
8 10 1 0 0 0 0
M STY 1 1 SUP
M SAL 1 4 7 8 9 10
M SMT 1 CF3
M SBL 1 1 7
M SAP 1 1 8
M END`;
var mol = RDKitModule.get_mol(molblock);
assert.equal(mol.is_valid(),1);
var mb = mol.get_molblock();
assert.equal(mb.includes("M SAP 1 1 8 6"), true);
var qmol = RDKitModule.get_qmol(molblock);
assert.equal(qmol.is_valid(),1);
var qmb = qmol.get_molblock();
assert.equal(qmb.includes("M SAP 1 1 8 6"), true);
}
function test_molblock_rgp() {
var molblock = `
MJ190400
9 9 0 0 0 0 0 0 0 0999 V2000
-6.5623 0.3105 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
-5.8478 -0.1019 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.1333 0.3105 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-4.4188 -0.1019 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-4.4188 -0.9269 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.1333 -1.3394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.8478 -0.9269 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.7043 -1.3394 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-2.9898 -0.9268 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
3 4 4 0 0 0 0
4 5 4 0 0 0 0
5 6 4 0 0 0 0
6 7 4 0 0 0 0
2 3 4 0 0 0 0
2 7 4 0 0 0 0
5 8 1 0 0 0 0
8 9 1 0 0 0 0
1 2 1 0 0 0 0
M RGP 2 1 2 9 1
M END`;
var mol = RDKitModule.get_mol(molblock);
assert.equal(mol.is_valid(),1);
}
function test_get_aromatic_kekule_form() {
const aromRegExp = / \d \d 4 \d\n/g;
const kekRegExp = / \d \d [12] \d\n/g;
var mol = RDKitModule.get_mol("c1ccccc1");
var molblock = mol.get_molblock();
assert (molblock.match(aromRegExp) === null);
assert (molblock.match(kekRegExp).length === 6);
var molblock = mol.get_kekule_form();
assert (molblock.match(aromRegExp) === null);
assert (molblock.match(kekRegExp).length === 6);
molblock = mol.get_aromatic_form();
assert (molblock.match(aromRegExp).length === 6);
assert (molblock.match(kekRegExp) === null);
}
function test_sketcher_services() {
var mol = RDKitModule.get_mol("C[C@](F)(Cl)/C=C/C(F)Br");
assert.equal(mol.is_valid(),1);
var tags = mol.get_stereo_tags();
assert.equal(tags,'{"CIP_atoms":[[1,"(S)"],[6,"(?)"]],"CIP_bonds":[[4,5,"(E)"]]}');
}
function test_sketcher_services2() {
var mol = RDKitModule.get_mol("c1ccccc1");
assert.equal(mol.is_valid(),1);
var molb = mol.add_hs();
assert(molb.search(" H ")>0);
assert.equal((molb.match(/ H /g) || []).length,6);
var mol2 = RDKitModule.get_mol(molb);
assert.equal(mol2.is_valid(),1);
var molb2 = mol2.get_molblock();
assert(molb2.search(" H ")>0);
assert.equal((molb2.match(/ H /g) || []).length,6);
molb2 = mol2.remove_hs();
assert(molb2.search(" H ")<0);
}
function test_abbreviations() {
var bmol = RDKitModule.get_mol("C1CC(C(F)(F)F)C1");
assert.equal(bmol.is_valid(),1);
var mapping = bmol.condense_abbreviations();
assert.equal(mapping, JSON.stringify({
atoms: [0, 1, 2, 3, 4, 5, 6, 7],
bonds: [0, 1, 2, 3, 4, 5, 6, 7],
}));
assert.equal(bmol.get_cxsmiles(),"FC(F)(F)C1CCC1");
mapping = bmol.condense_abbreviations(1.0,false);
assert.equal(mapping, JSON.stringify({
atoms: [0, 1, 2, 3, 7],
bonds: [0, 1, 2, 6, 7],
}));
assert.equal(bmol.get_cxsmiles(),"*C1CCC1 |$CF3;;;;$|");
}
function test_substruct_library(done) {
done.test_substruct_library = false;
var smiReader = readline.createInterface({
input: fs.createReadStream(__dirname + '/../../GraphMol/test_data/compounds.smi')
});
var sslib = new RDKitModule.SubstructLibrary();
// var t0 = performance.now()
// console.log('Started adding trusted SMILES');
smiReader.on('line', (smi) => {
sslib.add_trusted_smiles(smi);
});
smiReader.on('close', () => {
var query = RDKitModule.get_qmol("N");
// var t1 = performance.now();
// console.log('Finished adding trusted SMILES took ' + (t1 - t0) / 1000 + ' seconds');
assert.equal(sslib.count_matches(query), 52);
assert.equal(sslib.get_matches(query), JSON.stringify([
12,13,19,22,24,30,31,32,35,36,39,41,43,44,55,56,58,64,72,80,
85,95,96,101,105,113,124,127,128,131,143,150,151,185,201,202,
203,214,215,223,232,234,238,240,241,246,258,261,263,265,266,284
]));
done.test_substruct_library = true;
});
}
function test_substruct_library_merge_hs() {
var sslib = new RDKitModule.SubstructLibrary();
var mol1 = RDKitModule.get_mol("c1ccccc1");
var mol2 = RDKitModule.get_mol("Cc1ccccc1");
sslib.add_trusted_smiles(mol1.get_smiles());
sslib.add_trusted_smiles(mol2.get_smiles());
var query = RDKitModule.get_mol(`
MJ201100 2D
6 6 0 0 0 0 0 0 0 0999 V2000
-1.0491 0.7134 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7635 0.3009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7635 -0.5241 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0491 -0.9366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3346 -0.5241 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3346 0.3009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 3 1 0 0 0 0
5 6 2 0 0 0 0
1 2 2 0 0 0 0
6 1 1 0 0 0 0
3 4 2 0 0 0 0
4 5 1 0 0 0 0
M END`);
assert.equal(sslib.get_matches(query), JSON.stringify([0, 1]));
var query_hs = RDKitModule.get_mol(query.add_hs());
assert.equal(sslib.get_matches(query_hs), JSON.stringify([]));
query_hs = RDKitModule.get_mol(query_hs.get_molblock(), JSON.stringify({ mergeQueryHs: true }));
assert.equal(sslib.get_matches(query_hs), JSON.stringify([0]));
}
function test_substruct_library_empty_mols() {
var sslib = new RDKitModule.SubstructLibrary();
var mol1 = RDKitModule.get_mol("");
var mol2 = RDKitModule.get_mol("");
sslib.add_trusted_smiles(mol1.get_smiles());
sslib.add_trusted_smiles(mol2.get_smiles());
var query = RDKitModule.get_mol("C");
assert.equal(sslib.get_matches(query), JSON.stringify([]));
var empty_query = RDKitModule.get_mol("");
assert.equal(sslib.get_matches(empty_query), JSON.stringify([]));
}
function test_substruct_library_empty_query() {
var sslib = new RDKitModule.SubstructLibrary();
var mol1 = RDKitModule.get_mol("C");
var mol2 = RDKitModule.get_mol("CC");
sslib.add_trusted_smiles(mol1.get_smiles());
sslib.add_trusted_smiles(mol2.get_smiles());
var query = RDKitModule.get_mol("");
assert.equal(sslib.get_matches(query), JSON.stringify([]));
}
function test_substruct_library_empty_lib() {
var sslib = new RDKitModule.SubstructLibrary();
var query = RDKitModule.get_mol("C");
assert.equal(sslib.get_matches(query), JSON.stringify([]));
var empty_query = RDKitModule.get_mol("");
assert.equal(sslib.get_matches(empty_query), JSON.stringify([]));
}
function test_generate_aligned_coords() {
var smiles = "CCC";
var mol = RDKitModule.get_mol(smiles);
var template = "CC";
var qmol = RDKitModule.get_mol(template);
assert.equal(mol.generate_aligned_coords(qmol, true), "");
}
function test_isotope_labels() {
var mol = RDKitModule.get_mol("[1*]c1cc([2*])c([3*])c[14c]1");
assert.equal(mol.is_valid(), 1);
var textIsoDummyIso = mol.get_svg_with_highlights(JSON.stringify({}));
var nLinesIsoDummyIso = textIsoDummyIso.split("\n").length;
var textNoIsoDummyIso = mol.get_svg_with_highlights(JSON.stringify({ isotopeLabels: false }));
var nLinesNoIsoDummyIso = textNoIsoDummyIso.split("\n").length;
var textIsoNoDummyIso = mol.get_svg_with_highlights(JSON.stringify({ dummyIsotopeLabels: false }));
var nLinesIsoNoDummyIso = textIsoNoDummyIso.split("\n").length;
var textNoIsoNoDummyIso = mol.get_svg_with_highlights(JSON.stringify({ isotopeLabels: false, dummyIsotopeLabels: false }));
var nLinesNoIsoNoDummyIso = textNoIsoNoDummyIso.split("\n").length;
var res = [nLinesNoIsoNoDummyIso, nLinesIsoNoDummyIso, nLinesNoIsoDummyIso, nLinesIsoDummyIso];
var resSorted = [...res];
resSorted.sort((a, b) => (a - b));
assert.ok(res.every((resItem, i) => (resItem === resSorted[i])));
}
function test_generate_aligned_coords_allow_rgroups() {
var template_molblock = `
RDKit 2D
9 9 0 0 0 0 0 0 0 0999 V2000
-0.8929 1.0942 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1919 0.3442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1919 -1.1558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8929 -1.9059 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4060 -1.1558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4060 0.3442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.4910 1.0942 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0
1.7051 1.0942 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0
-3.4910 -1.9059 0.0000 R3 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 6 2 0
6 1 1 0
6 8 1 0
3 9 1 0
2 7 1 0
M RGP 3 7 1 8 2 9 3
M END`;
var ortho_meta_smiles = 'c1ccc(-c2ccc(-c3ccccc3)c(-c3ccccc3)c2)cc1';
var ortho_smiles = 'c1ccc(-c2ccccc2-c2ccccc2)cc1';
var meta_smiles = 'c1ccc(-c2cccc(-c3ccccc3)c2)cc1';
var biphenyl_smiles = 'c1ccccc1-c1ccccc1';
var phenyl_smiles = 'c1ccccc1';
var template_ref = RDKitModule.get_mol(template_molblock);
var ortho_meta = RDKitModule.get_mol(ortho_meta_smiles);
var ortho = RDKitModule.get_mol(ortho_smiles);
var meta = RDKitModule.get_mol(meta_smiles);
var biphenyl = RDKitModule.get_mol(biphenyl_smiles);
var phenyl = RDKitModule.get_mol(phenyl_smiles);
assert.equal(JSON.parse(ortho_meta.generate_aligned_coords(
template_ref, false, true)).atoms.length, 9);
assert.equal(JSON.parse(ortho.generate_aligned_coords(
template_ref, false, true)).atoms.length, 8);
assert.equal(JSON.parse(meta.generate_aligned_coords(
template_ref, false, true)).atoms.length, 8);
assert.equal(JSON.parse(biphenyl.generate_aligned_coords(
template_ref, false, true)).atoms.length, 7);
assert.equal(JSON.parse(phenyl.generate_aligned_coords(
template_ref, false, true)).atoms.length, 6);
}
function test_accept_failure() {
var template_molblock = `
RDKit 2D
9 9 0 0 0 0 0 0 0 0999 V2000
-0.8929 1.0942 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1919 0.3442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1919 -1.1558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8929 -1.9059 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4060 -1.1558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4060 0.3442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.4910 1.0942 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0
1.7051 1.0942 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0
-3.4910 -1.9059 0.0000 R3 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 6 2 0
6 1 1 0
6 8 1 0
3 9 1 0
2 7 1 0
M RGP 3 7 1 8 2 9 3
M END
`;
var mol_molblock = `
RDKit 2D
9 9 0 0 0 0 0 0 0 0999 V2000
-0.8929 1.0942 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-2.1919 0.3442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1919 -1.1558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8929 -1.9059 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4060 -1.1558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4060 0.3442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.4910 1.0942 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
1.7051 1.0942 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
-3.4910 -1.9059 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 6 2 0
6 1 1 0
6 8 1 0
3 9 1 0
2 7 1 0
M END
`;
var template_ref = RDKitModule.get_mol(template_molblock);
var mol = RDKitModule.get_mol(mol_molblock);
var hasThrown = false;
try {
mol.generate_aligned_coords(template_ref, false, true, false);
} catch (e) {
hasThrown = true;
}
assert(hasThrown);
assert.equal(mol.get_molblock(), mol_molblock);
}
function test_get_mol_no_kekulize() {
var molIsValid = true;
try {
mol = RDKitModule.get_mol("c");
molIsValid = mol.is_valid();
} catch (e) {
molIsValid = false;
}
assert(!molIsValid);
mol = RDKitModule.get_mol("c", JSON.stringify({kekulize: false}));
assert(mol.is_valid());
}
function test_get_smarts() {
var mol = RDKitModule.get_mol(`
MJ201100
8 8 0 0 0 0 0 0 0 0999 V2000
-1.0491 1.5839 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7635 1.1714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7635 0.3463 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0491 -0.0661 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3346 0.3463 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3346 1.1714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3798 1.5839 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
0.3798 -0.0661 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
6 1 1 0 0 0 0
6 7 1 0 0 2 0
5 8 1 0 0 2 0
M RGP 2 7 1 8 2
M END
`);
assert(mol.is_valid());
smarts = mol.get_smarts();
assert(smarts == "[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1-&!@*)-&!@*");
}
function test_get_cxsmarts() {
var mol = RDKitModule.get_mol(`
MJ201100
8 8 0 0 0 0 0 0 0 0999 V2000
-1.0491 1.5839 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7635 1.1714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7635 0.3463 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0491 -0.0661 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3346 0.3463 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3346 1.1714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3798 1.5839 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
0.3798 -0.0661 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
6 1 1 0 0 0 0
6 7 1 0 0 2 0
5 8 1 0 0 2 0
M RGP 2 7 1 8 2
M END
`);
assert(mol.is_valid());
cxsmarts = mol.get_cxsmarts();
assert(cxsmarts == "[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1-&!@*)-&!@* |" +
"(-1.0491,1.5839,;-1.7635,1.1714,;-1.7635,0.3463,;-1.0491,-0.0661,;" +
"-0.3346,0.3463,;-0.3346,1.1714,;0.3798,1.5839,;0.3798,-0.0661,)," +
"atomProp:6.dummyLabel.R1:7.dummyLabel.R2|");
}
function test_normalize_depiction() {
var mol = RDKitModule.get_mol(`
MJ201100
9 10 0 0 0 0 0 0 0 0999 V2000
-1.5402 1.3161 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.2546 0.9036 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.2546 0.0785 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5402 -0.3339 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8257 0.0785 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8257 0.9036 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0411 -0.1764 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.4438 0.4909 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0410 1.1583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
6 1 1 0 0 0 0
8 9 2 0 0 0 0
6 9 1 0 0 0 0
7 8 1 0 0 0 0
5 7 1 0 0 0 0
M END
`);
const scalingFactor = mol.normalize_depiction();
assert(scalingFactor > 1.8 && scalingFactor < 1.9);
}
function test_straighten_depiction() {
var mol1 = RDKitModule.get_mol(`
MJ201900
2 1 0 0 0 0 0 0 0 0999 V2000
-0.3904 2.1535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.1049 1.7410 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 0 0 0 0
M END
`);
var mol2 = RDKitModule.get_mol(`
MJ201900
2 1 0 0 0 0 0 0 0 0999 V2000
0.1899 1.9526 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5245 1.5401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 0 0 0 0
M END
`);
mol1.normalize_depiction();
mol1.straighten_depiction();
mol2.normalize_depiction();
mol2.straighten_depiction();
assert(mol1.get_molblock() === mol2.get_molblock());
}
function test_has_coords() {
var mol = RDKitModule.get_mol('CC');
assert(!mol.has_coords());
var mol2 = RDKitModule.get_mol(mol.get_new_coords());
assert(mol2.has_coords());
assert(!mol.has_coords());
mol.set_new_coords();
assert(mol.has_coords());
}
function test_kekulize() {
const badAromaticSmiles = 'c1cccc1';
var mol = null;
try {
mol = RDKitModule.get_mol(badAromaticSmiles);
assert(!mol.is_valid());
} catch {
assert(mol === null);
}
mol = RDKitModule.get_mol(badAromaticSmiles, JSON.stringify({ kekulize: false }));
assert(mol.is_valid());
}
function test_sanitize() {
const badValenceSmiles = 'N(C)(C)(C)C';
var mol = null;
try {
mol = RDKitModule.get_mol(badValenceSmiles);
assert(!mol.is_valid());
} catch {
assert(mol === null);
}
try {
mol = RDKitModule.get_mol(badValenceSmiles, JSON.stringify({ kekulize: false }));
assert(!mol.is_valid());
} catch {
assert(mol === null);
}
mol = RDKitModule.get_mol(badValenceSmiles, JSON.stringify({ sanitize: false }));
assert(mol.is_valid());
}
function test_flexicanvas() {
var mol = RDKitModule.get_mol("CCCC");
assert.equal(mol.is_valid(),1);
var svg = mol.get_svg(-1,-1);
assert(svg.search("svg")>0);
assert(svg.search("width='95px'")>0);
assert(svg.search("height='21px'")>0);
}
function test_rxn_drawing() {
{
var rxn = RDKitModule.get_rxn("[CH3:1][OH:2]>>[CH2:1]=[OH0:2]");
var svg = rxn.get_svg();
assert(svg.search("svg") > 0);
var rxn_from_block = RDKitModule.get_rxn(`$RXN
RDKit
1 1
$MOL
RDKit 2D
2 1 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0
1.2990 0.7500 0.0000 O 0 0 0 0 0 0 0 0 0 2 0 0
1 2 6 0
V 1 [C&H3:1]
V 2 [O&H1:2]
M END
$MOL
RDKit 2D
2 1 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0
1.2990 0.7500 0.0000 O 0 0 0 0 0 0 0 0 0 2 0 0
1 2 2 0
V 1 [C&H2:1]
V 2 [O&H0:2]
M END`);
var svg_from_block = rxn_from_block.get_svg();
assert(svg_from_block.search("svg") > 0);
assert(svg.match(/<path/g).length > 0);
assert(svg.match(/<path/g).length === svg_from_block.match(/<path/g).length);
}
{
var rxn = RDKitModule.get_rxn("[cH:5]1[cH:6][c:7]2[cH:8][n:9][cH:10][cH:11][c:12]2[c:3]([cH:4]1)[C:2](=[O:1])O.[N-:13]=[N+:14]=[N-:15]>C(Cl)Cl.C(=O)(C(=O)Cl)Cl>[cH:5]1[cH:6][c:7]2[cH:8][n:9][cH:10][cH:11][c:12]2[c:3]([cH:4]1)[C:2](=[O:1])[N:13]=[N+:14]=[N-:15]",
JSON.stringify({ useSmiles: true }));
{
var svg = rxn.get_svg();
assert(svg.search("svg") > 0);
assert(svg.search("stroke-dasharray" < 0));
assert(svg.search("ellipse") < 0);
}
{
var svg = rxn.get_svg_with_highlights(JSON.stringify({ kekulize: false }));
assert(svg.search("svg") > 0);
assert(svg.search("stroke-dasharray" > 0));
assert(svg.search("ellipse") < 0);
}
{
var svg = rxn.get_svg_with_highlights(JSON.stringify({ highlightByReactant: true }));
assert(svg.search("svg") > 0);
assert(svg.search("stroke-dasharray" < 0));
assert(svg.search("ellipse") > 0);
assert(svg.search("#BCD6ED") < 0);
assert(svg.search("#A8D08D") < 0);
}
{
var svg = rxn.get_svg_with_highlights(JSON.stringify({
highlightColorsReactants: [[.741, .843, .933], [.659, .816, .553]]
}));
assert(svg.search("svg") > 0);
assert(svg.search("stroke-dasharray" < 0));
assert(svg.search("ellipse") < 0);
}
{
var svg = rxn.get_svg_with_highlights(JSON.stringify({
highlightByReactant: true,
highlightColorsReactants: [[.741, .843, .933], [.659, .816, .553]]
}));
assert(svg.search("svg") > 0);
assert(svg.search("stroke-dasharray" < 0));
assert(svg.search("ellipse") > 0);
assert(svg.search("#BCD6ED") > 0);
assert(svg.search("#A8D08D") > 0);
}
rxn.delete();
}
{
var rxn = RDKitModule.get_rxn("[cH:5]1[cH:6][c:7]2[cH:8][n:9][cH:10][cH:11][c:12]2[c:3]([cH:4]1)[C:2](=[O:1])O.[N-:13]=[N+:14]=[N-:15]>C(Cl)Cl.C(=O)(C(=O)Cl)Cl>[cH:5]1[cH:6][c:7]2[cH:8][n:9][cH:10][cH:11][c:12]2[c:3]([cH:4]1)[C:2](=[O:1])[N:13]=[N+:14]=[N-:15]");
var hasThrown = false;
var isAromatic = false;
// if the code is built with exception support it will not throw
// but rather display molecules in their aromatic form rather
// than kekulized
try {
var svg = rxn.get_svg();
isAromatic = svg.search("stroke-dasharray" > 0);
} catch {
hasThrown = true;
}
assert(isAromatic || hasThrown);
}
}
function test_legacy_stereochem() {
RDKitModule.use_legacy_stereo_perception(true);
var mol = RDKitModule.get_mol("C[C@H]1CCC2(CC1)CC[C@H](C)C(C)C2");
assert.equal(mol.is_valid(),1);
assert.equal(mol.get_smiles(),"CC1CCC2(CC1)CC[C@H](C)C(C)C2");
RDKitModule.use_legacy_stereo_perception(false);
mol = RDKitModule.get_mol("C[C@H]1CCC2(CC1)CC[C@H](C)C(C)C2");
assert.equal(mol.is_valid(),1);
//assert.equal(mol.get_smiles(),"CC1CC2(CC[C@H](C)CC2)CC[C@@H]1C");
}
function test_prop() {
var mol = RDKitModule.get_mol(`
MJ201900
2 1 0 0 0 0 0 0 0 0999 V2000
0.1899 1.9526 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5245 1.5401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 0 0 0 0
M END
`);
assert.equal(mol.has_prop("test1"), false);
assert.equal(mol.set_prop("test1","val"), true);
assert.equal(mol.has_prop("test1"), true);
assert.equal(mol.get_prop("test1"),"val");
assert.equal(mol.set_prop("test2","val"), true);
props = mol.get_prop_list(false, false);
assert.equal(props.get(0), "test1");
assert.equal(props.get(1), "test2");
}
initRDKitModule().then(function(instance) {
var done = {};
const waitAllTestsFinished = () => {
const poll = resolve => {
if (Object.values(done).every(v => v)) {
resolve();
} else {
setTimeout(() => poll(resolve), 100);
}
}
return new Promise(poll);
}
RDKitModule = instance;
console.log(RDKitModule.version());
test_basics();
test_molblock_nostrict();
test_molblock_rgp();
test_get_aromatic_kekule_form();
test_sketcher_services();
test_sketcher_services2();
test_abbreviations();
test_substruct_library(done);
test_substruct_library_merge_hs();
test_substruct_library_empty_mols();
test_substruct_library_empty_lib();
test_substruct_library_empty_query();
test_generate_aligned_coords();
test_isotope_labels();
test_generate_aligned_coords_allow_rgroups();
test_accept_failure();
test_get_mol_no_kekulize();
test_get_smarts();
test_get_cxsmarts();
test_has_coords();
test_kekulize();
test_sanitize();
test_normalize_depiction();
test_straighten_depiction();
test_flexicanvas();
test_rxn_drawing();
test_legacy_stereochem();
test_prop();
waitAllTestsFinished().then(() =>
console.log("Tests finished successfully")
);
});
Reference in New Issue View Git Blame Copy Permalink