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https://github.com/rdkit/rdkit.git
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d2d87909de
* support read-only access to cstates from python * expose GetBrackets * expose getAttachPoints too remove vestigial SubstanceGroupCState_VECT * backup * backup * basics working * backup * add label_mol_abbreviations * fix a bug in the chirality handling * add linkers, needs more testing * add another peptide test * sanitize results by default * just need rings * getting started with the C++ form of abbreviations * a bit of error handling * add findApplicableMatches * actually apply the abbreviations * make the getDefault functions more efficient * add labeling (creating s groups) * docs * basic python wrappers (maybe this is enough?) * add _displayLabel and _displayLabelW support to MolDraw2D update the docs for that * use displayLabel props * add more default abbrevs * change default linker defns add parseLinkers convenience function * make sure attachment point atoms aren't aromatic * change the color of dummies to be darker gray * remove python implementation * support abbreviations in the java wrappers * add abbreviations to the csharp wrappers * add abbreviations to the js wrappers * add molParity to the list of atom props not written to CXSMILES * support condensing SUP substance groups * add that to the python wrappers * Update testAbbreviations.py * clear ring info if we added it * document that the molecules with abbreviations removed have not been sanitized
105 lines
3.2 KiB
JavaScript
105 lines
3.2 KiB
JavaScript
//
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//
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// Copyright (C) 2019 Greg Landrum
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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const assert = require('assert');
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const Module = require("../demo/RDKit_minimal.js");
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// the goal here isn't to be comprehensive (the RDKit has tests for that),
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// just to make sure that the wrappers are working as expected
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function test_basics(){
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var bmol = Module.get_mol("c1ccccc");
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assert.equal(bmol.is_valid(),0);
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var mol = Module.get_mol("c1ccccc1O");
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assert.equal(mol.is_valid(),1);
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assert.equal(mol.get_smiles(),"Oc1ccccc1");
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assert.equal(mol.get_inchi(),"InChI=1S/C6H6O/c7-6-4-2-1-3-5-6/h1-5,7H");
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assert.equal(Module.get_inchikey_for_inchi(mol.get_inchi()),"ISWSIDIOOBJBQZ-UHFFFAOYSA-N");
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var mb = mol.get_molblock();
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assert(mb.search("M END")>0);
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var mol2 = Module.get_mol(mb);
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assert.equal(mol2.is_valid(),1);
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assert.equal(mol2.get_smiles(),"Oc1ccccc1");
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var descrs = JSON.parse(mol.get_descriptors());
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assert.equal(descrs.NumAromaticRings,1);
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assert.equal(descrs.NumRings,1);
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assert.equal(descrs.amw,94.11299);
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var fp1 = mol.get_morgan_fp();
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assert.equal(fp1.length,2048);
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assert.equal((fp1.match(/1/g)||[]).length,11);
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var fp2 = mol.get_morgan_fp(0,512);
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assert.equal(fp2.length,512);
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assert.equal((fp2.match(/1/g)||[]).length,3);
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var svg = mol.get_svg();
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assert(svg.search("svg")>0);
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var qmol = Module.get_qmol("Oc(c)c");
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assert.equal(qmol.is_valid(),1);
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var match = mol.get_substruct_match(qmol);
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var pmatch = JSON.parse(match);
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assert.equal(pmatch.atoms.length,4);
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assert.equal(pmatch.atoms[0],6);
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var svg2 = mol.get_svg_with_highlights(match);
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assert(svg2.search("svg")>0);
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assert(svg.search("#FF7F7F")<0);
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assert(svg2.search("#FF7F7F")>0);
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}
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function test_sketcher_services(){
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var mol = Module.get_mol("C[C@](F)(Cl)/C=C/C(F)Br");
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assert.equal(mol.is_valid(),1);
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var tags = mol.get_stereo_tags();
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assert.equal(tags,'{"CIP_atoms":[[1,"(S)"],[6,"(?)"]],"CIP_bonds":[[4,5,"(E)"]]}');
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}
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function test_sketcher_services2(){
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var mol = Module.get_mol("c1ccccc1");
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assert.equal(mol.is_valid(),1);
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var molb = mol.add_hs();
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assert(molb.search(" H ")>0);
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assert.equal((molb.match(/ H /g) || []).length,6);
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var mol2 = Module.get_mol(molb);
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assert.equal(mol2.is_valid(),1);
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var molb2 = mol2.get_molblock();
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assert(molb2.search(" H ")>0);
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assert.equal((molb2.match(/ H /g) || []).length,6);
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molb2 = mol2.remove_hs();
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assert(molb2.search(" H ")<0);
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}
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function test_abbreviations(){
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var bmol = Module.get_mol("C1CCC1C(F)(F)F");
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assert.equal(bmol.is_valid(),1);
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bmol.condense_abbreviations();
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assert.equal(bmol.get_cxsmiles(),"FC(F)(F)C1CCC1");
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bmol.condense_abbreviations(1.0,false);
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assert.equal(bmol.get_cxsmiles(),"*C1CCC1 |$CF3;;;;$|");
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}
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Module.onRuntimeInitialized = () => {
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console.log(Module.version());
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test_basics();
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test_sketcher_services();
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test_sketcher_services2();
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test_abbreviations();
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console.log("Tests finished successfully");
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};
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