[Git][java-team/openchemlib][upstream] New upstream version 2020.11.3+dfsg
Andrius Merkys
gitlab at salsa.debian.org
Mon Nov 23 11:21:52 GMT 2020
Andrius Merkys pushed to branch upstream at Debian Java Maintainers / openchemlib
Commits:
8089473a by Andrius Merkys at 2020-11-23T05:39:28-05:00
New upstream version 2020.11.3+dfsg
- - - - -
9 changed files:
- pom.xml
- src/main/java/com/actelion/research/chem/IDCodeParserWithoutCoordinateInvention.java
- src/main/java/com/actelion/research/chem/Molecule.java
- src/main/java/com/actelion/research/chem/alignment3d/PheSAAlignmentOptimizer.java
- src/main/java/com/actelion/research/chem/descriptor/flexophore/DistHistHelper.java
- src/main/java/com/actelion/research/chem/descriptor/flexophore/completegraphmatcher/ObjectiveFlexophoreHardMatchUncovered.java
- src/main/java/com/actelion/research/chem/descriptor/flexophore/generator/ConstantsFlexophoreGenerator.java
- src/main/java/com/actelion/research/chem/descriptor/flexophore/generator/SubFlexophoreGenerator.java
- src/main/java/com/actelion/research/chem/phesa/pharmacophore/PharmacophoreCalculator.java
Changes:
=====================================
pom.xml
=====================================
@@ -8,7 +8,7 @@
Please follow the naming scheme YEAR.MONTH.RELEASE_NO_OF_MONTH
(eg. 2016.4.1 for second release in Apr 2016)
-->
- <version>2020.11.2</version>
+ <version>2020.11.3</version>
<name>OpenChemLib</name>
<description>Open Source Chemistry Library</description>
@@ -98,7 +98,7 @@
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
- <version>4.9</version>
+ <version>4.13.1</version>
<scope>test</scope>
</dependency>
</dependencies>
@@ -189,7 +189,7 @@
<connection>scm:git:git at github.com:Actelion/openchemlib.git</connection>
<developerConnection>scm:git:git at github.com:Actelion/openchemlib.git</developerConnection>
<url>https://github.com/Actelion/openchemlib</url>
- <tag>openchemlib-2020.11.2</tag>
+ <tag>openchemlib-2020.11.3</tag>
</scm>
<distributionManagement>
=====================================
src/main/java/com/actelion/research/chem/IDCodeParserWithoutCoordinateInvention.java
=====================================
@@ -936,7 +936,7 @@ public class IDCodeParserWithoutCoordinateInvention {
}
public void parseMapping(byte[] mapping, int mappingStart) {
- if (mapping == null || mapping.length <= mappingStart)
+ if (mapping == null || mapping.length <= mappingStart || mapping[mappingStart] < 0x40)
return;
decodeBitsStart(mapping, mappingStart);
=====================================
src/main/java/com/actelion/research/chem/Molecule.java
=====================================
@@ -2446,7 +2446,7 @@ public class Molecule implements Serializable {
for (int i=0; i<original.length; i++) {
if (original[i] != null) {
copy[i] = new int[original[i].length];
- System.arraycopy(original[i], 0, copy, 0, original[i].length);
+ System.arraycopy(original[i], 0, copy[i], 0, original[i].length);
}
}
return copy;
@@ -2456,7 +2456,7 @@ public class Molecule implements Serializable {
for (int i=0; i<original.length; i++) {
if (original[i] != null) {
copy[i] = new byte[original[i].length];
- System.arraycopy(original[i], 0, copy, 0, original[i].length);
+ System.arraycopy(original[i], 0, copy[i], 0, original[i].length);
}
}
return copy;
=====================================
src/main/java/com/actelion/research/chem/alignment3d/PheSAAlignmentOptimizer.java
=====================================
@@ -146,7 +146,7 @@ public class PheSAAlignmentOptimizer {
double[] bestTransformPMI = new double[7];
MolecularVolume[] bestPairPMI = new MolecularVolume[2];
double similarity = 0.0;
- if(bestScoreTriangle>=0.0) {
+ if(bestScoreTriangle>0.0) {
similarity = bestScoreTriangle;
result[0] = similarity;
result[1] = triangleRes[1];
=====================================
src/main/java/com/actelion/research/chem/descriptor/flexophore/DistHistHelper.java
=====================================
@@ -36,6 +36,28 @@ import java.util.List;
*/
public class DistHistHelper {
+ public static int getMedianBin(byte [] a){
+
+ int medianBin=-1;
+
+ int sum = 0;
+ for (byte b : a) {
+ sum+=b;
+ }
+ sum /= 2;
+
+ int s2=0;
+ for (int i = 0; i < a.length; i++) {
+ s2+=a[i];
+ if(s2>=sum){
+ medianBin=i;
+ break;
+ }
+ }
+
+ return medianBin;
+ }
+
public static RangeStatistics getRangeStatistics(MolDistHist mdh){
RangeStatistics rangeStatisticsTotal = new RangeStatistics();
=====================================
src/main/java/com/actelion/research/chem/descriptor/flexophore/completegraphmatcher/ObjectiveFlexophoreHardMatchUncovered.java
=====================================
@@ -421,6 +421,15 @@ public class ObjectiveFlexophoreHardMatchUncovered implements IObjectiveComplete
int heap = solution.getSizeHeap();
+ //
+ // the query must hit with all pharmacophore nodes
+ //
+ if(modeQuery) {
+ if (nodesQuery != heap) {
+ return 0;
+ }
+ }
+
double sumPairwiseMapping = 0;
// double productPairwiseMapping = 0;
@@ -462,7 +471,7 @@ public class ObjectiveFlexophoreHardMatchUncovered implements IObjectiveComplete
double ratioNodesMatchBase = Math.min(heap, nodesBase) / (double)Math.max(heap, nodesBase);
if(modeQuery) {
- similarity = avrPairwiseMappingScaled * coverageQuery * ratioNodesMatchQuery;
+ similarity = avrPairwiseMappingScaled * coverageQuery * coverageQuery * ratioNodesMatchQuery * ratioNodesMatchQuery;
} else {
similarity = avrPairwiseMappingScaled * coverage * ratioNodesMatchQuery * ratioNodesMatchBase;
}
=====================================
src/main/java/com/actelion/research/chem/descriptor/flexophore/generator/ConstantsFlexophoreGenerator.java
=====================================
@@ -27,10 +27,14 @@ public class ConstantsFlexophoreGenerator {
* Filter for sliding window to blurr distance histograms
* 07.04.2020
*/
- // public static final double [] FILTER = {0.25,0.5,0.25};
+ public static final double [] FILTER_SUB = {0.25,0.5,0.25};
// public static final double [] FILTER = {0.125, 0.25,0.25,0.25, 0.125};
// public static final double [] FILTER = {0.06, 0.125, 0.19,0.25,0.19, 0.125, 0.06};
+
+ /**
+ *
+ */
public static final double [] FILTER = {0.125, 0.125, 0.125,0.25,0.125, 0.125, 0.125};
=====================================
src/main/java/com/actelion/research/chem/descriptor/flexophore/generator/SubFlexophoreGenerator.java
=====================================
@@ -15,7 +15,6 @@ import java.util.List;
* This software is the proprietary information of Actelion Pharmaceuticals, Ltd.
* Use is subject to license terms.</p>
* @author Modest von Korff
- * @version 1.0
* Oct 12, 2012 MvK: Start implementation
*/
public class SubFlexophoreGenerator {
@@ -154,9 +153,7 @@ public class SubFlexophoreGenerator {
for (int size = minNumPPPoints; size < maxNumPPPointsReal; size++) {
List<MolDistHistViz> liMDHVSub = generateSubPharmacophores(mdhv, size);
-
liHsMolDistHistViz.get(size).addAll(liMDHVSub);
-
}
List<MolDistHistViz> liMDHVSubAll = new ArrayList<MolDistHistViz>();
=====================================
src/main/java/com/actelion/research/chem/phesa/pharmacophore/PharmacophoreCalculator.java
=====================================
@@ -68,7 +68,7 @@ public class PharmacophoreCalculator {
if(interactionClass<0) {
continue;
}
- if(mol.getAtomicNo(i)==8 && neighbours==1 && (mol.getConnBondOrder(i, 0)==2 || AtomFunctionAnalyzer.isAcidicOxygen(mol, i) )) {
+ if(mol.getAtomicNo(i)==8 && neighbours==1 && (mol.getConnBondOrder(i, 0)==2 || AtomFunctionAnalyzer.isAcidicOxygen(mol, i) || mol.getAtomCharge(i)==-1 )) {
int a1 = mol.getConnAtom(i,0);
if(!(mol.getAtomicNo(a1)==16 || mol.getAtomicNo(a1)==15)) {
int aa1 = mol.getConnAtom(a1,0);
@@ -76,6 +76,7 @@ public class PharmacophoreCalculator {
aa1 = mol.getConnAtom(a1,1);
neighbourList.add(aa1);
AcceptorPoint ap = new AcceptorPoint(mol,i,neighbourList,interactionClass,1);
+
ppPoints.add(ap);
List<Integer> neighbourList2 = new ArrayList<Integer>();
for(int neighbour : neighbourList) {
@@ -83,6 +84,7 @@ public class PharmacophoreCalculator {
}
ap = new AcceptorPoint(mol,i,neighbourList2,interactionClass,2);
ppPoints.add(ap);
+
}
else {
AcceptorPoint ap = new AcceptorPoint(mol,i,neighbourList,interactionClass);
@@ -93,6 +95,7 @@ public class PharmacophoreCalculator {
else {
AcceptorPoint ap = new AcceptorPoint(mol,i,neighbourList,interactionClass);
ppPoints.add(ap);
+
}
}
}
View it on GitLab: https://salsa.debian.org/java-team/openchemlib/-/commit/8089473afb60abe4596694df2be2f540fce06bc5
--
View it on GitLab: https://salsa.debian.org/java-team/openchemlib/-/commit/8089473afb60abe4596694df2be2f540fce06bc5
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