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Fix a corner case in repeat crossing bonds when we have variable atta… #835

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Merged
merged 3 commits into from
Feb 12, 2022
Merged

Fix a corner case in repeat crossing bonds when we have variable atta… #835

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e9f7ab0
Fix a corner case in repeat crossing bonds when we have variable atta…
johnmay Feb 9, 2022
ae9ffee
Additional null check needed
johnmay Feb 9, 2022
82ebded
Fix copyright
johnmay Feb 9, 2022
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20 changes: 18 additions & 2 deletions storage/smiles/src/main/java/org/openscience/cdk/smiles/SmilesParser.java
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Original file line number Diff line number Diff line change
Expand Up @@ -652,8 +652,24 @@ else if (amol != mol)

for (IAtom atom : atomset) {
for (IBond bond : mol.getConnectedBondsList(atom)) {
if (!atomset.contains(bond.getOther(atom)))
sgroup.addBond(bond);
IAtom nbor = bond.getOther(atom);
if (!atomset.contains(nbor)) {
boolean crossing = true;

// check for variable attachments see https://github.com/cdk/depict/issues/36
if (cxstate.positionVar != null) {
List<Integer> ends = cxstate.positionVar.get(mol.indexOf(nbor));
if (ends != null) {
for (Integer end : ends) {
if (atomset.contains(mol.getAtom(end)))
crossing = false;
}
}
}

if (crossing)
sgroup.addBond(bond);
}
}
sgroup.addAtom(atom);
}
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21 changes: 21 additions & 0 deletions storage/smiles/src/test/java/org/openscience/cdk/smiles/CxSmilesParserTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -25,14 +25,18 @@

import org.hamcrest.BaseMatcher;
import org.hamcrest.Description;
import org.junit.Assert;
import org.junit.Test;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.exception.InvalidSmilesException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IPseudoAtom;
import org.openscience.cdk.interfaces.IReaction;
import org.openscience.cdk.interfaces.IStereoElement;
import org.openscience.cdk.sgroup.Sgroup;
import org.openscience.cdk.sgroup.SgroupType;
import org.openscience.cdk.silent.SilentChemObjectBuilder;
import org.openscience.cdk.tools.manipulator.ReactionManipulator;

Expand Down Expand Up @@ -370,6 +374,23 @@ public void hydrogenAndCoordinationBondingSkipped() {
is("R1"));
}

@Test public void variableAttachCrossingBonds() throws CDKException {
SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
IAtomContainer mol = smipar.parseSmiles("[H]OCCO.C* |lp:1:2,4:2,m:6:3.2,Sg:n:1,2,3,5::ht|");
List<Sgroup> sgroups = mol.getProperty(CDKConstants.CTAB_SGROUPS);
Sgroup sru = null;
for (Sgroup sgroup : sgroups) {
if (sgroup.getType() == SgroupType.CtabStructureRepeatUnit) {
sru = sgroup;
break;
}
}
Assert.assertNotNull(sru);
Assert.assertEquals(4, sru.getAtoms().size());
Assert.assertEquals(2, sru.getBonds().size());
}


/**
* Custom matcher for checking an array of doubles closely matches (epsilon=0.01)
* an expected value.
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