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Fix stereo bug #19

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Fix stereo bug #19

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9827d07
fixed CIP stereo bug
tylerperyea Dec 4, 2023
195a7a3
added missing files
tylerperyea Dec 4, 2023
aae01f1
updated to use siMolecules CIP rules
tylerperyea Dec 8, 2023
cfaa462
removed accidental file
tylerperyea Dec 8, 2023
2fdfa07
incremented version
tylerperyea Dec 8, 2023
e1f1cf3
incremented molwitch core version
tylerperyea Dec 8, 2023
9ff9d22
Merge branch 'master' into fixStereoBug
tylerperyea Dec 8, 2023
2c964b1
added missing file back
tylerperyea Dec 8, 2023
26992cb
Merge branch 'fixStereoBug' of github.com:tylerperyea/molwitch-cdk in…
tylerperyea Dec 8, 2023
f72c2b0
ignore test that doesn't work yet
tylerperyea Dec 8, 2023
e6b37ee
upodated stereo detector
tylerperyea Dec 11, 2023
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31 changes: 29 additions & 2 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@

<groupId>gov.nih.ncats</groupId>
<artifactId>molwitch-cdk</artifactId>
<version>1.0.14</version>
<version>1.0.15-SNAPSHOT</version>
<name>molwitch-cdk</name>

<url>https://github.com/ncats/molwitch-cdk/</url>
Expand All @@ -18,6 +18,7 @@

<properties>
<cdk.version>2.9</cdk.version>
<centres.version>1.2.1</centres.version>
</properties>
<repositories>
<repository>
Expand All @@ -30,6 +31,16 @@
<enabled>true</enabled>
</snapshots>
</repository>
<repository>
<id>oss.sonatype.org</id>
<url>https://repo1.maven.org/maven2/</url>
<releases>
<enabled>true</enabled>
</releases>
<snapshots>
<enabled>false</enabled>
</snapshots>
</repository>
</repositories>

<developers>
Expand Down Expand Up @@ -73,7 +84,7 @@
<dependency>
<groupId>gov.nih.ncats</groupId>
<artifactId>molwitch</artifactId>
<version>0.6.5</version>
<version>0.6.6-SNAPSHOT</version>
<exclusions>
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
Expand Down Expand Up @@ -112,6 +123,22 @@
<artifactId>cdk-jniinchi-support</artifactId>
<version>${cdk.version}</version>
</dependency>


<dependency>
<groupId>com.simolecule.centres</groupId>
<artifactId>centres-core</artifactId>
<version>${centres.version}</version>
</dependency>

<dependency>
<groupId>com.simolecule.centres</groupId>
<artifactId>centres-cdk</artifactId>
<version>${centres.version}</version>
</dependency>



<!-- <dependency>-->
<!-- <groupId>org.openscience.cdk</groupId>-->
<!-- <artifactId>cdk-valencycheck</artifactId>-->
Expand Down
61 changes: 56 additions & 5 deletions src/main/java/gov/nih/ncats/molwitch/cdk/CdkAtom.java
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Original file line number Diff line number Diff line change
Expand Up @@ -306,16 +306,31 @@ public void setAtomCoordinates(AtomCoordinates atomCoordinates) {
public Chirality getChirality() {
if(!parent.cahnIngoldPrelogSupplier.hasRun()) {
//forces running CIP rules

parent.getTetrahedrals();
}
String value = atom.getProperty(CDKConstants.CIP_DESCRIPTOR);
String value= Optional.ofNullable(atom.getProperty(CDKConstants.CIP_DESCRIPTOR))
.map(t->t.toString())
.orElse(null);

if("R".equals(value)) {
// if(dd!=nu)
// String value = atom.getProperty(CDKConstants.CIP_DESCRIPTOR);
//
if("R".equals(value) || "M".equals(value)) {
return Chirality.R;
}
if("S".equals(value)) {
if("r".equals(value)) {
return Chirality.r;
}

if("S".equals(value) || "P".equals(value)) {
return Chirality.S;
}

if("s".equals(value)) {
return Chirality.s;
}

if("EITHER".equals(value)) {
return Chirality.Parity_Either;
}
Expand All @@ -327,8 +342,10 @@ public Chirality getChirality() {
public void setChirality(Chirality chirality) {
Chirality chir=getChirality();
if(chir==chirality)return;
if((chirality==Chirality.R && chir==Chirality.S) ||
(chirality==Chirality.S && chir==Chirality.R)

//simple inversion
if(((chirality==Chirality.R || chirality==Chirality.r) && (chir==Chirality.S||chir==Chirality.s)) ||
((chirality==Chirality.S || chirality==Chirality.s) && (chir==Chirality.R||chir==Chirality.r))
) {
this.getBonds().stream()
.filter(b->b.getBondType().equals(BondType.SINGLE))
Expand All @@ -345,6 +362,8 @@ public void setChirality(Chirality chirality) {
atom.setProperty(CDKConstants.CIP_DESCRIPTOR,chirality.toString());
// atom.setStereoParity((atom.getStereoParity()+1)%2);
// parent.getContainer().setStereoElements(new ArrayList<>());

//simple removal
}else if(chirality.equals(Chirality.Parity_Either)) {
this.getBonds().stream()
.filter(b->b.getBondType().equals(BondType.SINGLE))
Expand All @@ -359,7 +378,39 @@ public void setChirality(Chirality chirality) {
});

atom.setProperty(CDKConstants.CIP_DESCRIPTOR,"EITHER");
}else if(chirality.isDefined() && (chir.isEither() || chir == Chirality.Non_Chiral)) {

Optional<? extends Bond> sBond = this.getBonds().stream()
.filter(b->b.getBondType().equals(BondType.SINGLE))
.filter(b->b.getStereo().equals(Stereo.NONE))
.findFirst();


sBond.ifPresent(b->{
if(b.getAtom1().getAtomIndexInParent()==this.getAtomIndexInParent()){
b.setStereo(Stereo.UP);
}else {
b.setStereo(Stereo.UP_INVERTED);
}
});


parent.cahnIngoldPrelogSupplier.resetCache();
Chirality co=this.getChirality();
if((co.isRForm() && chirality.isRForm()) ||
(co.isSForm() && chirality.isSForm())
) {
//do nothing
}else if((co.isSForm() && chirality.isRForm()) ||
(co.isRForm() && chirality.isSForm())
) {
setChirality(chirality);
}else {
//could not set
}

}

// parent.cahnIngoldPrelogSupplier.resetCache();
}

Expand Down
6 changes: 2 additions & 4 deletions src/main/java/gov/nih/ncats/molwitch/cdk/CdkBond.java
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Original file line number Diff line number Diff line change
Expand Up @@ -22,15 +22,13 @@
package gov.nih.ncats.molwitch.cdk;


import java.util.ArrayList;
import java.util.List;
import java.util.Optional;

import org.openscience.cdk.BondRef;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IBond.Order;
import org.openscience.cdk.interfaces.IStereoElement;
import org.openscience.cdk.isomorphism.matchers.IQueryBond;

import gov.nih.ncats.common.sneak.Sneak;
Expand Down Expand Up @@ -224,7 +222,7 @@ public DoubleBondStereo getDoubleBondStereo() {
return null;
}
parent.cahnIngoldPrelogSupplier.get();
String value = bond.getProperty(CDKConstants.CIP_DESCRIPTOR);
String value = Optional.ofNullable(bond.getProperty(CDKConstants.CIP_DESCRIPTOR)).map(bt->bt.toString()).orElse(null);
if("Z".equals(value)) {
return DoubleBondStereo.Z_CIS;
}
Expand Down
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