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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
73 lines
2.2 KiB
Java
73 lines
2.2 KiB
Java
/*
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*
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* Copyright (c) 2019 Greg Landrum and T5 Informatics GmbH
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* All rights reserved.
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*
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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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package org.RDKit;
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import static org.junit.Assert.*;
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import org.junit.*;
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public class AbbreviationsTests extends GraphMolTest {
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@Before public void setUp() {
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}
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@Test
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public void test1Basics() {
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AbbreviationDefinition_Vect abbrevs = RDKFuncs.getDefaultAbbreviations();
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RWMol mol = RWMol.MolFromSmiles("C1CCC1C(F)(F)F");
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assertEquals(mol.getNumAtoms(),8);
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RDKFuncs.condenseMolAbbreviations(mol,abbrevs);
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// no changes here due to the threshold
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assertEquals(mol.getNumAtoms(),8);
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RDKFuncs.condenseMolAbbreviations(mol,abbrevs, 1.0);
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assertEquals(mol.getNumAtoms(),5);
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assertEquals(RDKFuncs.MolToCXSmiles(mol),"*C1CCC1 |$CF3;;;;$|");
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}
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@Test
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public void test2LinkerBasics() {
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AbbreviationDefinition_Vect abbrevs = RDKFuncs.getDefaultLinkers();
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RWMol mol = RWMol.MolFromSmiles("COCCOCCOCCOCCCl");
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assertEquals(mol.getNumAtoms(),14);
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RDKFuncs.condenseMolAbbreviations(mol,abbrevs);
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// no changes here due to the threshold
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assertEquals(mol.getNumAtoms(),14);
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RDKFuncs.condenseMolAbbreviations(mol,abbrevs, 1.0);
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assertEquals(mol.getNumAtoms(),3);
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assertEquals(RDKFuncs.MolToCXSmiles(mol),"C*Cl |$;PEG4;$|");
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}
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@Test
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public void test3Matching() {
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AbbreviationDefinition_Vect abbrevs = RDKFuncs.getDefaultAbbreviations();
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RWMol mol = RWMol.MolFromSmiles("C1CCC1C(F)(F)F");
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assertEquals(mol.getNumAtoms(),8);
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AbbreviationMatch_Vect matches = RDKFuncs.findApplicableAbbreviationMatches(mol,abbrevs,1.0);
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assertEquals(matches.size(),1);
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assertEquals(matches.get(0).getAbbrev().getLabel(),"CF3");
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RDKFuncs.applyMatches(mol,matches);
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assertEquals(mol.getNumAtoms(),5);
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assertEquals(RDKFuncs.MolToCXSmiles(mol),"*C1CCC1 |$CF3;;;;$|");
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}
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public static void main(String args[]) {
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org.junit.runner.JUnitCore.main("org.RDKit.AbbreviationsTests");
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}
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}
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