[Git][java-team/openchemlib][master] 4 commits: New upstream version 2022.1.0+dfsg
Andrius Merkys (@merkys)
gitlab at salsa.debian.org
Fri Jan 14 14:42:28 GMT 2022
Andrius Merkys pushed to branch master at Debian Java Maintainers / openchemlib
Commits:
c7483100 by Andrius Merkys at 2022-01-14T08:24:53-05:00
New upstream version 2022.1.0+dfsg
- - - - -
da9e9df2 by Andrius Merkys at 2022-01-14T08:25:04-05:00
Update upstream source from tag 'upstream/2022.1.0+dfsg'
Update to upstream version '2022.1.0+dfsg'
with Debian dir ef548b12bb364c21d8caa2976ef8cb50dadb8452
- - - - -
73e9db95 by Andrius Merkys at 2022-01-14T08:26:36-05:00
Bumping copyright years.
- - - - -
4569bc28 by Andrius Merkys at 2022-01-14T08:26:53-05:00
Update changelog for 2022.1.0+dfsg-1 release
- - - - -
14 changed files:
- debian/changelog
- debian/copyright
- pom.xml
- src/main/java/com/actelion/research/chem/AbstractDepictor.java
- src/main/java/com/actelion/research/chem/chemicalspaces/ChemicalSpaceCreator.java
- src/main/java/com/actelion/research/chem/chemicalspaces/synthon/SynthonCreator.java
- src/main/java/com/actelion/research/chem/coords/CoordinateInventor.java
- src/main/java/com/actelion/research/chem/coords/InventorFragment.java
- src/main/java/com/actelion/research/chem/descriptor/flexophore/completegraphmatcher/ObjectiveBlurFlexophoreHardMatchUncovered.java
- src/main/java/com/actelion/research/chem/descriptor/flexophore/example/MatchFlexophoreNodesMain.java
- src/main/java/com/actelion/research/chem/io/CompoundTableConstants.java
- src/main/java/com/actelion/research/chem/io/Mol2FileParser.java
- src/main/java/com/actelion/research/gui/JStructureView.java
- src/main/java/com/actelion/research/util/graph/complete/CompleteGraphMatcher.java
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+openchemlib (2022.1.0+dfsg-1) unstable; urgency=medium
+
+ * New upstream version 2022.1.0+dfsg
+ * Bumping copyright years.
+
+ -- Andrius Merkys <merkys at debian.org> Fri, 14 Jan 2022 08:26:48 -0500
+
openchemlib (2021.12.0+dfsg-1) unstable; urgency=medium
* New upstream version 2021.12.0+dfsg
=====================================
debian/copyright
=====================================
@@ -5,11 +5,11 @@ Files-Excluded:
src/main/java/info
Files: *
-Copyright: 1997-2021, Idorsia Pharmaceuticals Ltd, Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
+Copyright: 1997-2022, Idorsia Pharmaceuticals Ltd, Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
License: BSD-3-clause
Files: debian/*
-Copyright: 2020-2021, Andrius Merkys <merkys at debian.org>
+Copyright: 2020-2022, Andrius Merkys <merkys at debian.org>
License: BSD-3-clause
Files: src/main/java/com/actelion/research/calc/statistics/median/MedianStatisticFunctions.java
@@ -49,7 +49,7 @@ Files: src/main/java/com/actelion/research/calc/statistics/median/MedianStatisti
src/main/java/com/actelion/research/gui/JEditableStructureView.java
src/main/java/com/actelion/research/gui/JStructureView.java
src/main/java/com/actelion/research/gui/StructureListener.java
-Copyright: 1997-2021, Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
+Copyright: 1997-2022, Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
License: GPL-3+
License: BSD-3-clause
=====================================
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>2021.12.0</version>
+ <version>2022.1.0</version>
<name>OpenChemLib</name>
<description>Open Source Chemistry Library</description>
@@ -195,7 +195,7 @@
<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-2021.12.0</tag>
+ <tag>openchemlib-2022.1.0</tag>
</scm>
<distributionManagement>
=====================================
src/main/java/com/actelion/research/chem/AbstractDepictor.java
=====================================
@@ -162,7 +162,7 @@ public abstract class AbstractDepictor<T> {
private Rectangle2D.Double mBoundingRect = new Rectangle2D.Double();
private DepictorTransformation mTransformation;
private Point2D.Double mChiralTextLocation;
- private int[] mAtomColor;
+ private int[] mAtomColor,mAtomHiliteColor;
private String[] mAtomText;
private Point2D.Double[] mAlternativeCoords;
private Color mOverruleForeground,mOverruleBackground,mBondBGHiliteColor,mBondFGHiliteColor,
@@ -198,13 +198,6 @@ public abstract class AbstractDepictor<T> {
}
-/* @Deprecated
- public void setDefaultColor(int c) {
- mStandardForegroundColor = c;
- updateBondHiliteColor();
- }*/
-
-
/**
* If the foreground color is set, the molecule is drawn in the foreground
* color except for non carbon atoms, which are drawn in atomicNo specific
@@ -235,6 +228,16 @@ public abstract class AbstractDepictor<T> {
}
+ /**
+ * If you want this tructure view to also draw an atom background with specific colors for every atom,
+ * then you need to call this method before calling paint().
+ * @param argb values with a==0 are not considered (may be null)
+ */
+ public void setAtomHighlightColors(int[] argb) {
+ mAtomHiliteColor = argb;
+ }
+
+
public void setTransformation(DepictorTransformation t) {
mTransformation = t;
}
@@ -561,6 +564,7 @@ public abstract class AbstractDepictor<T> {
setColor(COLOR_INITIALIZE); // to initialize the color tracking mechanism
+ hiliteAtomBackgrounds();
hiliteExcludeGroups();
hiliteBondBackgrounds();
indicateQueryFeatures();
@@ -593,7 +597,7 @@ public abstract class AbstractDepictor<T> {
&& ((mDisplayMode & cDModeNoImplicitAtomLabelColors) == 0)
&& mMol.getAtomList(i) == null
&& mMol.getAtomicNo(i) < ATOM_LABEL_COLOR.length) {
- setRGBColor(getContrastColor(ATOM_LABEL_COLOR[mMol.getAtomicNo(i)]));
+ setRGBColor(getContrastColor(ATOM_LABEL_COLOR[mMol.getAtomicNo(i)], i));
mpDrawAtom(i, esrGroupMemberCount);
setColor(mStandardForegroundColor);
}
@@ -607,9 +611,10 @@ public abstract class AbstractDepictor<T> {
}
- private Color getContrastColor(int rgb) {
+ private Color getContrastColor(int rgb, int atom) {
Color bg = (mOverruleBackground != null) ? mOverruleBackground
- : (mCustomBackground != null) ? mCustomBackground : Color.WHITE;
+ : (mAtomHiliteColor != null && atom < mAtomHiliteColor.length && (mAtomHiliteColor[atom] & 0xFF000000) != 0) ? new Color(mAtomHiliteColor[atom])
+ : (mCustomBackground != null) ? mCustomBackground : Color.WHITE;
Color fg = new Color(rgb);
return ColorHelper.getContrastColor(fg, bg);
}
@@ -666,6 +671,22 @@ public abstract class AbstractDepictor<T> {
}
+ private void hiliteAtomBackgrounds() {
+ if (mAtomHiliteColor == null
+ || (mAtomHiliteColor.length < mMol.getAtoms()))
+ return;
+
+ double d = mTransformation.getScaling() * mMol.getAverageBondLength();
+ double r = d/2;
+ for (int atom=0; atom<mMol.getAtoms(); atom++) {
+ if ((mAtomHiliteColor[atom] & 0xFF000000) != 0) {
+ setColor(new Color(mAtomHiliteColor[atom]));
+ fillCircle(getAtomX(atom)-r, getAtomY(atom)-r, d);
+ }
+ }
+ }
+
+
private void hiliteBondBackgrounds() {
setLineWidth(2*mpBondHiliteRadius);
DepictorLine line = new DepictorLine();
@@ -1592,7 +1613,6 @@ public abstract class AbstractDepictor<T> {
if (!mIsValidatingView)
onDrawAtom(atom,mMol.getAtomLabel(atom), getAtomX(atom), getAtomY(atom));
-
String propStr = null;
if (mMol.getAtomCharge(atom) != 0) {
String valStr = (Math.abs(mMol.getAtomCharge(atom)) == 1) ? ""
@@ -1611,8 +1631,6 @@ public abstract class AbstractDepictor<T> {
isoStr = append(isoStr, "!a");
if ((queryFeatures & Molecule.cAtomQFMoreNeighbours) != 0)
isoStr = append(isoStr, "s");
-// if ((queryFeatures & Molecule.cAtomQFNoMoreNeighbours) != 0)
-// isoStr = append(isoStr, "!s");
if ((queryFeatures & Molecule.cAtomQFHydrogen) != 0) {
int hydrogens = (queryFeatures & Molecule.cAtomQFHydrogen);
if (hydrogens == Molecule.cAtomQFNot1Hydrogen+Molecule.cAtomQFNot2Hydrogen+Molecule.cAtomQFNot3Hydrogen)
@@ -1766,11 +1784,6 @@ public abstract class AbstractDepictor<T> {
int hydrogensToAdd = 0;
if ((mDisplayMode & cDModeNoImplicitHydrogen) == 0) {
if (mMol.isFragment()) {
-/* if ((mMol.getAtomicNo(atom) != 6
- || !mAtomIsConnected[atom]
- || mMol.getAtomCharge(atom) != 0
- || mMol.getAtomRadical(atom) != 0)
- && (mMol.getAtomQueryFeatures(atom) & Molecule.cAtomQFNoMoreNeighbours) != 0)*/
if ((mMol.getAtomQueryFeatures(atom) & Molecule.cAtomQFNoMoreNeighbours) != 0)
hydrogensToAdd = mMol.getImplicitHydrogens(atom);
}
=====================================
src/main/java/com/actelion/research/chem/chemicalspaces/ChemicalSpaceCreator.java
=====================================
@@ -82,13 +82,13 @@ public class ChemicalSpaceCreator {
}
public void create() {
+ Map<String,List<Reaction>> allSynthonTransformations = new HashMap<String,List<Reaction>>();
+ generateSynthonTransformations(reactions,allSynthonTransformations);
ConcurrentMap<String,String> processedToOrigIDCode = new ConcurrentHashMap<String,String>();
ConcurrentMap<String,List<Map<String,String>>> reactionsWithSynthons = new ConcurrentHashMap<String,List<Map<String,String>>>();
processBuildingBlocks(this.bbs,processedToOrigIDCode,functionalizations);
fps = new ConcurrentHashMap<String,long[]>();
calcFragFPs(processedToOrigIDCode.keySet(),fps);
- Map<String,List<Reaction>> allSynthonTransformations = new ConcurrentHashMap<String,List<Reaction>>();
- generateSynthonTransformations(reactions,allSynthonTransformations);
generateSynthons(reactions, processedToOrigIDCode, reactionsWithSynthons,fps,allSynthonTransformations);
generateCombinatoriaLibraries(reactionsWithSynthons, bbs, allSynthonTransformations);
}
@@ -225,8 +225,6 @@ public class ChemicalSpaceCreator {
final int ii = i;
processedToOrigIDCode.keySet().stream().forEach(processedIDcode -> {
- //for (String processedIDcode : processedToOrigIDCode.keySet()) {
- //String processedIDcode= processedToOrigIDCode.get(idcode);
StereoMolecule mol = new IDCodeParser().getCompactMolecule(processedIDcode);
if (mol != null) {
long[] fp = fps.get(processedIDcode);
@@ -309,7 +307,7 @@ public class ChemicalSpaceCreator {
functionalizations.add(rxn);
}
List<Long> sizes = new ArrayList<>();
- reactions.parallelStream().forEach(reaction -> {
+ reactions.stream().forEach(reaction -> {
if(reaction.getReactants()<2)
return;
IDCodeParser parser = new IDCodeParser();
@@ -342,16 +340,16 @@ public class ChemicalSpaceCreator {
precursorLibs.add(precursorLib);
Reaction synthonTransformation = synthonTransformations.get(libraryReaction).get(libReactantID);
StereoMolecule genericProduct = synthonTransformation.getProduct(0);
- int offset = 0;
+ int offset = 0; //offset is required to correctly mutate connector atoms
for(int a=0;a<genericProduct.getAtoms();a++) {
if(genericProduct.getAtomicNo(a)>=92)
offset++;
}
- for(Reaction reaction2 : reactions) {
- if(reaction2.getReactants()!=2)
+ for(Reaction reactionPrec : reactions) { // precursor reaction
+ if(reactionPrec.getReactants()!=2)
continue;
- String precursorReaction = reaction2.getName();
+ String precursorReaction = reactionPrec.getName();
for(int reactantID=0;reactantID<reactionsWithSynthons.get(precursorReaction).size();reactantID++) {
List<Map<String,String>> libSynthons = new ArrayList<>();
@@ -359,18 +357,17 @@ public class ChemicalSpaceCreator {
precursorName = precursorReaction + "_" + reactantID;
precursorLib.put(precursorName, libSynthons);
Map<Integer,StereoMolecule> dummyReactants = new HashMap<Integer,StereoMolecule>();
- for(int l=0;l<reaction2.getReactants();l++) {
+ for(int l=0;l<reactionPrec.getReactants();l++) {
if(l==reactantID)
continue;
else {
- dummyReactants.put(l,reaction2.getReactant(l));
+ dummyReactants.put(l,reactionPrec.getReactant(l));
}
}
for(int i=0;i<reactionsWithSynthons.get(precursorReaction).size();i++) {
Map<String,String> precursorSynthons = new HashMap<String,String>();
libSynthons.add(precursorSynthons);
- }
-
+ }
Map<String,String> twoConnectorSynthons = libSynthons.get(reactantID);
Map<String,String> synthons = reactionsWithSynthons.get(precursorReaction).get(reactantID);
@@ -378,7 +375,7 @@ public class ChemicalSpaceCreator {
StereoMolecule mol = new StereoMolecule();
String bb = synthons.get(synthon);
parser.parse(mol, synthon);
- StereoMolecule reactedBB = dummyReaction(bb,reaction2,dummyReactants,reactantID);
+ StereoMolecule reactedBB = dummyReaction(bb,reactionPrec,dummyReactants,reactantID);
if(reactedBB==null)
continue;
// we create candidate products by a "dummy reaction" and see if it still matches the substructure query of rxn1
@@ -392,7 +389,7 @@ public class ChemicalSpaceCreator {
else {
for(Reaction functionalization : functionalizations) {
- if(functionalizations.contains(reaction2))
+ if(functionalizations.contains(reactionPrec))
continue; //don't couple two functionalization reactions
SSSearcher ssearcher = new SSSearcher();
ssearcher.setFragment(functionalization.getReactant(0));
@@ -409,8 +406,7 @@ public class ChemicalSpaceCreator {
if(prod==null)
continue;
mutateConnectorAtoms(prod,offset);
- //for(int j=0;j<reactantID;j++)
- // mutateConnectorAtoms(prod,offset); //mutate again, to prevent same linker atoms appearing in A and B (C) parts of same library
+
String transformedSynthon = transformToSynthon(synthonTransformation,prod);
if(!precursorLib.containsKey(precursorName)) {
List<Map<String,String>> libSynthons2 = new ArrayList<>();
@@ -431,7 +427,6 @@ public class ChemicalSpaceCreator {
}
-
// if the BB that is used in the precursor step also matches any role of the second reaction, it is excluded (otherwise multiple products may be formed)
for(int j=0;j<reactionsWithSynthons.get(precursorReaction).size();j++) { //get synthons from rxn1 that are compatible with the two-connector synthon
if(j==reactantID) {
@@ -451,11 +446,9 @@ public class ChemicalSpaceCreator {
}
if(!compatible) //matches also role from second reaction --> don't add to library
continue;
-
mutateConnectorAtoms(mutatedSynthon,offset);
- //for(int k=0;k<reactantID;k++)
- //mutateConnectorAtoms(mutatedSynthon,offset); //mutate again, to prevent same linker atoms appearing in A and B (C) parts of same library
+
mutatedSynthons.put(mutatedSynthon.getIDCode(), compatibleSynthons.get(s));
}
libSynthons.get(j).putAll(mutatedSynthons);
@@ -470,9 +463,8 @@ public class ChemicalSpaceCreator {
}
combiLibrary.cleanup();
sizes.add(combiLibrary.getSize());
- combiLibrary.generateRandomProducts(300,productsWithSynthons,productsWithBBs,productsWithReactions);
- System.out.println("generated");
- System.out.println(productsWithSynthons.keySet().size() + " compounds");
+ System.out.println(reaction.getName());
+ combiLibrary.generateRandomProducts(1000,productsWithSynthons,productsWithBBs,productsWithReactions);
try {
writeCombinatorialLibrary(combiLibrary);
@@ -743,10 +735,12 @@ public class ChemicalSpaceCreator {
toRemove = new ArrayList<>();
}
- }
+ }
+
public long getSize() {
long sizeOneStep = 1;
+ // first calculate size of the single-step space
for(Map<String,String> synthons : bbSynthons) {
sizeOneStep*=(long)synthons.size();
}
@@ -780,12 +774,17 @@ public class ChemicalSpaceCreator {
}
+
+
+
+
+
public void generateRandomProducts(int nProducts, Map<String,List<String>> productsWithSynthons, Map<String,List<String>> productsWithBBs, Map<String,
List<String>> productsWithReactions ) {
- int count=0;
Random rnd = new Random();
IDCodeParser parser = new IDCodeParser();
- while(count<nProducts) {
+ long max = productsWithSynthons.keySet().size() + Math.min(getSize(), nProducts);
+ while(productsWithSynthons.keySet().size()<max) {
List<StereoMolecule> synthons = new ArrayList<>();
List<String> bbs = new ArrayList<>();
List<String> reactions = new ArrayList<>();
@@ -794,7 +793,8 @@ public class ChemicalSpaceCreator {
reactions.add(reaction.getName());
for(int i=0;i<reaction.getReactants();i++) {
int r = rnd.nextInt(2);
- if(r==0) { //pick commercial bb
+ Map<String,List<Map<String,String>>> libs = precursorLibs.get(i);
+ if(libs.size()<1 || r==0) { //pick commercial bb
if(bbSynthons.get(i).size()<1)
return ;
int r2 = rnd.nextInt(bbSynthons.get(i).size());
@@ -809,9 +809,6 @@ public class ChemicalSpaceCreator {
else { //create random virtual bb
//pick random precursor reaction
List<StereoMolecule> precursors = new ArrayList<>();
- Map<String,List<Map<String,String>>> libs = precursorLibs.get(i);
- if(libs.size()<1)
- return;
int reactionNr = rnd.nextInt(libs.keySet().size());
List<String> keys = new ArrayList<>(libs.keySet());
List<Map<String,String>> lib = libs.get(keys.get(reactionNr));
@@ -830,31 +827,36 @@ public class ChemicalSpaceCreator {
preCoupledSynthons.add(SynthonReactor.react(precursors));
}
catch(Exception e) {
-
+ e.printStackTrace();
+ continue;
}
}
}
- count++;
+
try {
StereoMolecule product = SynthonReactor.react(preCoupledSynthons);
List<String> bbIDCodes = synthons.stream().map(e -> e.getIDCode()).collect(Collectors.toList());
+ if(productsWithSynthons.containsKey(product.getIDCode()))
+ continue;
productsWithSynthons.put(product.getIDCode(),bbIDCodes);
productsWithBBs.put(product.getIDCode(),bbs);
productsWithReactions.put(product.getIDCode(),reactions);
}
catch(Exception e) {
+ e.printStackTrace();
-
- }
}
+ }
+
}
}
+
public static boolean matchesReactionRole(Reaction rxn, SSSearcherWithIndex[] searchers, int component, StereoMolecule reactant,
long[] index) {
boolean isMatch = true;
=====================================
src/main/java/com/actelion/research/chem/chemicalspaces/synthon/SynthonCreator.java
=====================================
@@ -13,6 +13,7 @@ import java.util.Map;
import java.util.Set;
import com.actelion.research.chem.Molecule;
+import com.actelion.research.chem.RingCollection;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.chem.coords.CoordinateInventor;
import com.actelion.research.chem.io.RXNFileCreator;
@@ -21,6 +22,12 @@ import com.actelion.research.chem.reaction.Reaction;
public class SynthonCreator {
+ /**
+ * only works for reactions with a single product
+ * @param rxn
+ * @return
+ * @throws Exception
+ */
public static Reaction[] create(Reaction rxn) throws Exception {
if(rxn.getProducts()>1)
throw new Exception("only reactions with one product are supported");
@@ -41,219 +48,112 @@ public class SynthonCreator {
}
//find bonds in products that are formed between a) atoms from different reactants or b) between an unmapped and a mapped atom
//in a properly mapped reaction, unmapped atoms stem from a reagent or solvent
- for(int p=0;p<rxn.getProducts();p++) {
- StereoMolecule product = rxn.getProduct(p);
- List<Integer> bondsToCut = new ArrayList<>();
- for(int b=0;b<product.getBonds();b++) {
- int bondAtom1 = product.getBondAtom(0, b);
- int bondAtom2 = product.getBondAtom(1, b);
- int mappedBondAtom1 = product.getAtomMapNo(bondAtom1);
- int mappedBondAtom2 = product.getAtomMapNo(bondAtom2);
- if(mappedBondAtom1==0) {
- if(mappedBondAtom2==0)
- continue;
- else
- bondsToCut.add(b);
-
- }
- else if(mappedBondAtom2==0) {
- bondsToCut.add(b);
+ StereoMolecule product = rxn.getProduct(0);
+ //detect homogeneous rings: homogeneous rings are rings that either consist of only one reactant, or
+ //one reactant and unmapped (reagent) atoms. Bonds in homogeneous rings should not be cut!
+ RingCollection rc = product.getRingSet();
+ List<Integer> homogeneousRingBonds = new ArrayList<>();
+ for(int ringNo=0;ringNo<rc.getSize();ringNo++) {
+ Set<Integer> ringReactant = new HashSet<Integer>();
+ int[] atoms = rc.getRingAtoms(ringNo);
+ for(int a : atoms) {
+ int mappedA = product.getAtomMapNo(a);
+ if(mappedA==0)
continue;
- }
- else if(mappedAtomToReactant.get(mappedBondAtom1)!=mappedAtomToReactant.get(mappedBondAtom2)) {
- bondsToCut.add(b);
- }
+ int reactant = mappedAtomToReactant.get(mappedA);
+ ringReactant.add(reactant);
}
-
- StereoMolecule decomposedProduct = new StereoMolecule(product);
- decomposedProduct.ensureHelperArrays(Molecule.cHelperCIP);
- int counter = 0;
- for(int cutBond : bondsToCut) {
- //first check if cutting this bond would result in isolating a fragment that is made of nonmapped atoms --> stem from a reagent
- //we want to assign these atoms to one of the synthons, so such a cut is forbidden
- StereoMolecule tmpMol = new StereoMolecule(decomposedProduct);
- tmpMol.ensureHelperArrays(Molecule.cHelperNeighbours);
- tmpMol.setBondType(cutBond, Molecule.cBondTypeDeleted);
- tmpMol.deleteMarkedAtomsAndBonds();
- StereoMolecule[] tmpFrags = tmpMol.getFragments();
- boolean acceptCut = true;
- for(StereoMolecule tmpFrag : tmpFrags) {
- tmpFrag.ensureHelperArrays(Molecule.cHelperNeighbours);
- int mapSum = 0;
- for(int a=0;a<tmpFrag.getAtoms();a++) {
- mapSum+=tmpFrag.getAtomMapNo(a);
- }
- if(mapSum==0) {
- acceptCut=false;
- break;
- }
- }
- if(acceptCut) {
- int bondType = decomposedProduct.getBondType(cutBond);
- decomposedProduct.setBondType(cutBond, Molecule.cBondTypeDeleted);
- int connector1 = decomposedProduct.addAtom(92+counter);
- int connector2 = decomposedProduct.addAtom(92+counter);
- int newBond1 = decomposedProduct.addBond(decomposedProduct.getBondAtom(0, cutBond), connector1);
- decomposedProduct.setBondType(newBond1, bondType);
- int newBond2 = decomposedProduct.addBond(connector2,decomposedProduct.getBondAtom(1, cutBond));
- decomposedProduct.setBondType(newBond2, bondType);
- counter++;
- }
-
+ if(ringReactant.size()==1) {//homogeneous ring!
+ int[] ringBonds = rc.getRingBonds(ringNo);
+ Arrays.stream(ringBonds).forEach(e -> homogeneousRingBonds.add(e));
}
- decomposedProduct.deleteMarkedAtomsAndBonds();
- decomposedProduct.ensureHelperArrays(Molecule.cHelperCIP);
- StereoMolecule[] frags = decomposedProduct.getFragments();
- for(StereoMolecule frag : frags) {
- CoordinateInventor inventor = new CoordinateInventor();
- inventor.setRandomSeed(0x1234567890L); // create reproducible coordinates
- inventor.invent(frag);
- Reaction reaction = new Reaction();
- int reactantID = -1;
- for(int a=0;a<frag.getAtoms();a++) {
- if(frag.getAtomMapNo(a)!=0) {
- reactantID = mappedAtomToReactant.get(frag.getAtomMapNo(a));
- }
-
- }
- if(reactantID==-1)
- throw new Exception("could not process reaction");
- frag.ensureHelperArrays(Molecule.cHelperCIP);
- reaction.addReactant(rxn.getReactant(reactantID));
- reaction.addProduct(frag);
- synthonTransformations[reactantID] = reaction;
- //Writer writer = new BufferedWriter(new FileWriter(rxn.getName() + "_" + i + ".rxn"));
- //new RXNFileCreator(reaction).writeRXNfile(writer);
- //writer.close();
-
-
-
-
- }
-
+
}
- return synthonTransformations;
-
-
-
-
-
- }
- /**
- * does not allow cuts through ring bonds
- * @param rxn
- * @return
- * @throws Exception
- */
- public static Reaction[] createStrict(Reaction rxn) throws Exception {
- if(rxn.getProducts()>1)
- throw new Exception("only reactions with one product are supported");
- Reaction[] synthonTransformations = new Reaction[rxn.getReactants()];
- Map<Integer,Integer> mappedAtomToReactant = new HashMap<Integer,Integer>(); //stores the information on which mapped atom in the product is contributed by which reactant
- for(int r=0;r<rxn.getReactants();r++) {
- if(rxn.getReactants()==0)
- throw new Exception("cannot create Synthons for reactions with one reactant");
- StereoMolecule reactant = rxn.getReactant(r);
- for(int a=0;a<reactant.getAtoms();a++) {
- int reactantMapNo = reactant.getAtomMapNo(a);
- if(reactantMapNo==0)
- continue;
- else {
- mappedAtomToReactant.put(reactantMapNo, r);
- }
- }
- }
- //find bonds in products that are formed between a) atoms from different reactants or b) between an unmapped and a mapped atom
- //in a properly mapped reaction, unmapped atoms stem from a reagent or solvent
- for(int p=0;p<rxn.getProducts();p++) {
- StereoMolecule product = rxn.getProduct(p);
- List<Integer> bondsToCut = new ArrayList<>();
- for(int b=0;b<product.getBonds();b++) {
- int bondAtom1 = product.getBondAtom(0, b);
- int bondAtom2 = product.getBondAtom(1, b);
- int mappedBondAtom1 = product.getAtomMapNo(bondAtom1);
- int mappedBondAtom2 = product.getAtomMapNo(bondAtom2);
- if(mappedBondAtom1==0) {
- if(mappedBondAtom2==0)
- continue;
- else
- bondsToCut.add(b);
-
- }
- else if(mappedBondAtom2==0) {
- bondsToCut.add(b);
+ List<Integer> bondsToCut = new ArrayList<>();
+ for(int b=0;b<product.getBonds();b++) {
+ if(homogeneousRingBonds.contains(b))
+ continue;
+ int bondAtom1 = product.getBondAtom(0, b);
+ int bondAtom2 = product.getBondAtom(1, b);
+ int mappedBondAtom1 = product.getAtomMapNo(bondAtom1);
+ int mappedBondAtom2 = product.getAtomMapNo(bondAtom2);
+ if(mappedBondAtom1==0) {
+ if(mappedBondAtom2==0) // both atoms unmapped
continue;
- }
- else if(mappedAtomToReactant.get(mappedBondAtom1)!=mappedAtomToReactant.get(mappedBondAtom2)) {
+ else //bond between a mapped and an unmapped atom
bondsToCut.add(b);
- }
+
+ }
+ else if(mappedBondAtom2==0) { //bond between a mapped and an umapped atom
+ bondsToCut.add(b);
+ continue;
+ }
+ else if(mappedAtomToReactant.get(mappedBondAtom1)!=mappedAtomToReactant.get(mappedBondAtom2)) { //atoms from two different reactants
+ bondsToCut.add(b);
}
+ }
- StereoMolecule decomposedProduct = new StereoMolecule(product);
- decomposedProduct.ensureHelperArrays(Molecule.cHelperCIP);
- int counter = 0;
- for(int cutBond : bondsToCut) {
- //first check if cutting this bond would result in isolating a fragment that is made of nonmapped atoms --> stem from a reagent
- //we want to assign these atoms to one of the synthons, so such a cut is forbidden
- StereoMolecule tmpMol = new StereoMolecule(decomposedProduct);
- tmpMol.ensureHelperArrays(Molecule.cHelperNeighbours);
- tmpMol.setBondType(cutBond, Molecule.cBondTypeDeleted);
- tmpMol.deleteMarkedAtomsAndBonds();
- StereoMolecule[] tmpFrags = tmpMol.getFragments();
- boolean acceptCut = true;
- for(StereoMolecule tmpFrag : tmpFrags) {
- tmpFrag.ensureHelperArrays(Molecule.cHelperNeighbours);
- int mapSum = 0;
- for(int a=0;a<tmpFrag.getAtoms();a++) {
- mapSum+=tmpFrag.getAtomMapNo(a);
- }
- if(mapSum==0) {
- acceptCut=false;
- break;
- }
+ StereoMolecule decomposedProduct = new StereoMolecule(product);
+ decomposedProduct.ensureHelperArrays(Molecule.cHelperCIP);
+ int counter = 0;
+ for(int cutBond : bondsToCut) {
+ //first check if cutting this bond would result in isolating a fragment that is made of nonmapped atoms --> stem from a reagent
+ //we want to assign these atoms to one of the synthons, so such a cut is forbidden
+ StereoMolecule tmpMol = new StereoMolecule(decomposedProduct);
+ tmpMol.ensureHelperArrays(Molecule.cHelperNeighbours);
+ tmpMol.setBondType(cutBond, Molecule.cBondTypeDeleted);
+ tmpMol.deleteMarkedAtomsAndBonds();
+ StereoMolecule[] tmpFrags = tmpMol.getFragments();
+ boolean acceptCut = true;
+ for(StereoMolecule tmpFrag : tmpFrags) {
+ tmpFrag.ensureHelperArrays(Molecule.cHelperNeighbours);
+ int mapSum = 0;
+ for(int a=0;a<tmpFrag.getAtoms();a++) {
+ mapSum+=tmpFrag.getAtomMapNo(a);
}
- if(acceptCut) {
- int bondType = decomposedProduct.getBondType(cutBond);
- decomposedProduct.setBondType(cutBond, Molecule.cBondTypeDeleted);
- int connector1 = decomposedProduct.addAtom(92+counter);
- int connector2 = decomposedProduct.addAtom(92+counter);
- int newBond1 = decomposedProduct.addBond(decomposedProduct.getBondAtom(0, cutBond), connector1);
- decomposedProduct.setBondType(newBond1, bondType);
- int newBond2 = decomposedProduct.addBond(connector2,decomposedProduct.getBondAtom(1, cutBond));
- decomposedProduct.setBondType(newBond2, bondType);
- counter++;
+ if(mapSum==0) {
+ acceptCut=false;
+ break;
}
-
}
- decomposedProduct.deleteMarkedAtomsAndBonds();
- decomposedProduct.ensureHelperArrays(Molecule.cHelperCIP);
- StereoMolecule[] frags = decomposedProduct.getFragments();
- for(StereoMolecule frag : frags) {
- CoordinateInventor inventor = new CoordinateInventor();
- inventor.setRandomSeed(0x1234567890L); // create reproducible coordinates
- inventor.invent(frag);
- Reaction reaction = new Reaction();
- int reactantID = -1;
- for(int a=0;a<frag.getAtoms();a++) {
- if(frag.getAtomMapNo(a)!=0) {
- reactantID = mappedAtomToReactant.get(frag.getAtomMapNo(a));
- }
-
+ if(acceptCut) {
+ int bondType = decomposedProduct.getBondType(cutBond);
+ decomposedProduct.setBondType(cutBond, Molecule.cBondTypeDeleted);
+ int connector1 = decomposedProduct.addAtom(92+counter);
+ int connector2 = decomposedProduct.addAtom(92+counter);
+ int newBond1 = decomposedProduct.addBond(decomposedProduct.getBondAtom(0, cutBond), connector1);
+ decomposedProduct.setBondType(newBond1, bondType);
+ int newBond2 = decomposedProduct.addBond(connector2,decomposedProduct.getBondAtom(1, cutBond));
+ decomposedProduct.setBondType(newBond2, bondType);
+ counter++;
+ }
+
+ }
+ decomposedProduct.deleteMarkedAtomsAndBonds();
+ decomposedProduct.ensureHelperArrays(Molecule.cHelperCIP);
+ StereoMolecule[] frags = decomposedProduct.getFragments();
+ for(StereoMolecule frag : frags) {
+ CoordinateInventor inventor = new CoordinateInventor();
+ inventor.setRandomSeed(0x1234567890L); // create reproducible coordinates
+ inventor.invent(frag);
+ Reaction reaction = new Reaction();
+ int reactantID = -1;
+ for(int a=0;a<frag.getAtoms();a++) {
+ if(frag.getAtomMapNo(a)!=0) {
+ reactantID = mappedAtomToReactant.get(frag.getAtomMapNo(a));
}
- if(reactantID==-1)
- throw new Exception("could not process reaction");
- frag.ensureHelperArrays(Molecule.cHelperCIP);
- reaction.addReactant(rxn.getReactant(reactantID));
- reaction.addProduct(frag);
- synthonTransformations[reactantID] = reaction;
- //Writer writer = new BufferedWriter(new FileWriter(rxn.getName() + "_" + i + ".rxn"));
- //new RXNFileCreator(reaction).writeRXNfile(writer);
- //writer.close();
-
-
-
-
+
}
+ if(reactantID==-1)
+ throw new Exception("could not process reaction");
+ frag.ensureHelperArrays(Molecule.cHelperCIP);
+ reaction.addReactant(rxn.getReactant(reactantID));
+ reaction.addProduct(frag);
+ synthonTransformations[reactantID] = reaction;
+ Writer writer = new BufferedWriter(new FileWriter(rxn.getName() + "_" + reactantID + ".rxn"));
+ new RXNFileCreator(reaction).writeRXNfile(writer);
+ writer.close();
+
}
return synthonTransformations;
@@ -264,7 +164,6 @@ public class SynthonCreator {
}
-
/*
public static void main(String[] args) {
List<Reaction> htmcReactions = ReactionList.INSTANCE.getReactionsHTMC();
=====================================
src/main/java/com/actelion/research/chem/coords/CoordinateInventor.java
=====================================
@@ -108,12 +108,13 @@ public class CoordinateInventor {
/**
- * By providing a custom template list containing substructures with predefined atom
- * coordinates, any occurence of any of these substructures will receive the
- * relative atom coordinates of the provided template, unless the substructure
- * shares more than one atom with a previously found substructure or the substructure
- * shares more than one atom with the non marked atoms and mode is
- * MODE_????_MARKED_ATOM_COORDS.
+ * A custom template list contains substructures with predefined atom coordinates.
+ * When such a list is provided, and if a molecules contains one of the list's substructures,
+ * then the matching atoms will receive the relative atom coordinates of the provided template,
+ * unless the substructure shares two or more atoms with another earlier found template or
+ * if mode is MODE_????_MARKED_ATOM_COORDS and the substructure match contains two or more
+ * non-marked (and therefore untouchable) atoms. If a template substructure contains an E- or Z-
+ * double bound, then the query feature 'match EZ-parity' should be set.
* @param templateList
*/
public void setCustomTemplateList(List<InventorTemplate> templateList) {
=====================================
src/main/java/com/actelion/research/chem/coords/InventorFragment.java
=====================================
@@ -195,7 +195,8 @@ public class InventorFragment {
boolean coreOnSide = false;
boolean coreOffSide = false;
for (int i = 0; i< mGlobalAtom.length; i++) {
- if (mMol.isMarkedAtom(mGlobalAtom[i])) {
+ int atom = mGlobalAtom[i];
+ if (mMol.isMarkedAtom(atom) && atom != atom1 && atom != atom2) {
if (isOnSide[mGlobalAtom[i]])
coreOnSide = true;
else
=====================================
src/main/java/com/actelion/research/chem/descriptor/flexophore/completegraphmatcher/ObjectiveBlurFlexophoreHardMatchUncovered.java
=====================================
@@ -511,6 +511,56 @@ public class ObjectiveBlurFlexophoreHardMatchUncovered implements IObjectiveComp
}
+ /**
+ *
+ * @param solution a valid solution for IMolDistHis base and IMolDistHis query. Query and base must be set before
+ * starting the similarity calculation.
+ * @param indexHeap heap index of the node for which the histogram similarities to all other nodes will be calculated.
+ * indexHeap is the index from the list of matching query and base nodes.
+ * @return histogram similarity for a single node. Calculated as average from the sum of histogram similarities.
+ */
+ public float getSimilarityHistogramsForNode(SolutionCompleteGraph solution, int indexHeap) {
+ int heap = solution.getSizeHeap();
+
+ //
+ // the query must hit with all pharmacophore nodes
+ //
+ if(modeQuery) {
+ if (nodesQuery != heap) {
+ return 0;
+ }
+ }
+
+ double sumPairwiseMapping = 0;
+
+ int indexNode1Query = solution.getIndexQueryFromHeap(indexHeap);
+
+ int indexNode1Base = solution.getIndexCorrespondingBaseNode(indexNode1Query);
+
+ for (int i = 0; i < heap; i++) {
+ if(indexHeap==i)
+ continue;
+
+ int indexNode2Query = solution.getIndexQueryFromHeap(i);
+
+ int indexNode2Base = solution.getIndexCorrespondingBaseNode(indexNode2Query);
+
+ double simHists = getSimilarityHistogram(indexNode1Query, indexNode2Query, indexNode1Base, indexNode2Base);
+
+ sumPairwiseMapping += simHists;
+
+ if(verbose) {
+ System.out.println("scorePairwiseMapping " + Formatter.format2(simHists));
+ }
+ }
+
+ double mappings = heap-1;
+
+ double avrPairwiseMapping = sumPairwiseMapping/mappings;
+
+ return (float)avrPairwiseMapping;
+ }
+
public long getDeltaNanoQueryBlur() {
return deltaNanoQueryBlur;
}
@@ -835,12 +885,10 @@ public class ObjectiveBlurFlexophoreHardMatchUncovered implements IObjectiveComp
double simHists = getSimilarityHistogram(indexNode1Query, indexNode2Query, indexNode1Base, indexNode2Base);
- if(simHists==0){
-
- System.out.println("ObjectiveFlexophoreHardMatchUncovered getScorePairwiseMapping(int indexNode1Query, int indexNode2Query, int indexNode1Base, int indexNode2Base)");
-
- System.out.println("Sim hists = 0");
- }
+// if(simHists==0){
+// System.out.println("ObjectiveFlexophoreHardMatchUncovered getScorePairwiseMapping(int indexNode1Query, int indexNode2Query, int indexNode1Base, int indexNode2Base)");
+// System.out.println("Sim hists = 0");
+// }
if(verbose){
System.out.println("simHists " + Formatter.format2(simHists));
=====================================
src/main/java/com/actelion/research/chem/descriptor/flexophore/example/MatchFlexophoreNodesMain.java
=====================================
@@ -7,8 +7,13 @@ import com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore;
import com.actelion.research.chem.descriptor.flexophore.ModelSolutionSimilarity;
import com.actelion.research.chem.descriptor.flexophore.MolDistHistViz;
import com.actelion.research.chem.descriptor.flexophore.PPNodeViz;
+import com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered;
+import com.actelion.research.gui.table.ChemistryRenderPanel;
+import com.actelion.research.util.ArrayUtils;
import com.actelion.research.util.Formatter;
+import javax.swing.*;
+
public class MatchFlexophoreNodesMain {
@@ -26,45 +31,61 @@ public class MatchFlexophoreNodesMain {
pairMatch(idcode, idcodeQuery);
}
- public static void pairMatch(String idcode, String idcodeQuery) {
+ public static void pairMatch(String idcodeBase, String idcodeQuery) {
DescriptorHandlerFlexophore dhFlexophore = new DescriptorHandlerFlexophore();
+
+ ObjectiveBlurFlexophoreHardMatchUncovered objectiveBlurFlexophoreHardMatchUncovered = dhFlexophore.getObjectiveCompleteGraph();
+
IDCodeParser parser = new IDCodeParser();
- MolDistHistViz mdh = create(parser, dhFlexophore, idcode);
+ MolDistHistViz mdhvBase = create(parser, dhFlexophore, idcodeBase);
+
- System.out.println("Num pp nodes base " + mdh.getNumPPNodes());
- MolDistHistViz mdhQuery = create(parser, dhFlexophore, idcodeQuery);
- System.out.println("Num pp nodes query " + mdhQuery.getNumPPNodes());
- System.out.println(mdh.toString());
- System.out.println(mdhQuery.toString());
+ System.out.println("Num pp nodes base " + mdhvBase.getNumPPNodes());
- ModelSolutionSimilarity modelSolutionSimilarity = dhFlexophore.getBestMatch(mdh, mdhQuery);
+ MolDistHistViz mdhvQuery = create(parser, dhFlexophore, idcodeQuery);
+ System.out.println("Num pp nodes query " + mdhvQuery.getNumPPNodes());
+
+ System.out.println(mdhvBase.toString());
+ System.out.println(mdhvQuery.toString());
+
+ ModelSolutionSimilarity modelSolutionSimilarity = dhFlexophore.getBestMatch(mdhvBase, mdhvQuery);
int heap = modelSolutionSimilarity.getSizeHeap();
// System.out.println(Formatter.format3(sim) + "\t" + Formatter.format3(simDH));
// System.out.println(Formatter.format3(sim) +"\t"+ Formatter.format3(simNormalized));
+ objectiveBlurFlexophoreHardMatchUncovered.setBase(mdhvBase);
+ objectiveBlurFlexophoreHardMatchUncovered.setQuery(mdhvQuery);
+
for (int i = 0; i <heap; i++) {
int indexQuery = modelSolutionSimilarity.getIndexQueryFromHeap(i);
int indexBase = modelSolutionSimilarity.getIndexBaseFromHeap(i);
- PPNodeViz ppv = mdh.getNode(indexBase);
- PPNodeViz ppvQuery = mdhQuery.getNode(indexQuery);
- System.out.println(ppv.toString());
+ PPNodeViz ppvBase = mdhvBase.getNode(indexBase);
+
+ int [] arrAtomIndexBase = ArrayUtils.toIntArray(ppvBase.getListIndexOriginalAtoms());
+
+ PPNodeViz ppvQuery = mdhvQuery.getNode(indexQuery);
+
+ int [] arrAtomIndexQuery = ArrayUtils.toIntArray(ppvQuery.getListIndexOriginalAtoms());
+
+ System.out.println(ppvBase.toString());
System.out.println(ppvQuery.toString());
// System.out.println(Formatter.format3((double)ppv.getSimilarityMappingNodes()) + "\t" + Formatter.format3((double)ppvQuery.getSimilarityMappingNodes()));
- System.out.println(Formatter.format3((double)modelSolutionSimilarity.getSimilarityNode(indexQuery)));
+
+ float simHistogram = objectiveBlurFlexophoreHardMatchUncovered.getSimilarityHistogramsForNode(modelSolutionSimilarity, i);
+
+ System.out.println("Node similarity " + Formatter.format3((double)modelSolutionSimilarity.getSimilarityNode(indexQuery)) + ", histogram similarity " + Formatter.format3((double)simHistogram) + ".");
System.out.println();
}
System.out.println("Un-normalized similarity " + Formatter.format3(modelSolutionSimilarity.getSimilarity()));
-
-
}
=====================================
src/main/java/com/actelion/research/chem/io/CompoundTableConstants.java
=====================================
@@ -181,6 +181,7 @@ public interface CompoundTableConstants {
String cColumnProperty3DFragmentSplit = "split3D"; // if "true": unconnected fragments of 3D-structure are shown as differently colored V3DMolecules
String cColumnPropertyCommentUploadStatus = "commentUploadStatus";
String cColumnPropertyCommentDepartment = "commentDepartment";
+ String cColumnPropertyCalculated = "calculated"; //for columns that can be calculated by a task
String cSuperposeValueReferenceRow = "refRow"; // "reference" or null
String cSuperposeAlignValueShape = "shape"; // "reference" or null
=====================================
src/main/java/com/actelion/research/chem/io/Mol2FileParser.java
=====================================
@@ -4,31 +4,14 @@
*/
package com.actelion.research.chem.io;
-import java.io.File;
+import com.actelion.research.chem.*;
+
import java.io.LineNumberReader;
import java.io.Reader;
import java.io.Writer;
import java.text.DecimalFormat;
import java.text.NumberFormat;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.StringTokenizer;
-import java.util.TreeMap;
-
-import com.actelion.research.chem.AromaticityResolver;
-import com.actelion.research.chem.Canonizer;
-import com.actelion.research.chem.ExtendedMolecule;
-import com.actelion.research.chem.Molecule3D;
-import com.actelion.research.chem.Molecule;
-import com.actelion.research.chem.SmilesCreator;
-import com.actelion.research.chem.StereoMolecule;
-import com.actelion.research.chem.io.pdb.converter.BondsCalculator;
-import com.actelion.research.chem.io.AbstractParser;
+import java.util.*;
/**
*
@@ -87,8 +70,7 @@ public class Mol2FileParser extends AbstractParser {
for (int i=0; i<mol.getBonds(); i++) {
m.setBondOrder(i, mol.getBondOrder(bondMap[i]));
}
-
- }
+ }
/*
else {
//Use BondsCalculator.aromatize
@@ -105,7 +87,6 @@ public class Mol2FileParser extends AbstractParser {
m.setAllAtomFlag(Molecule3D.LIGAND, true);
res.add(m);
-
}
private void assignCharges(Molecule3D mol) {
@@ -140,9 +121,7 @@ public class Mol2FileParser extends AbstractParser {
public static String getChargeType(int type) {
-
if(hmIndex_CHARGETYPE==null){
-
hmIndex_CHARGETYPE = new HashMap<Integer, String>();
hmIndex_CHARGETYPE.put(iNO_CHARGES, sNO_CHARGES);
hmIndex_CHARGETYPE.put(iDEL_RE, sDEL_RE);
@@ -163,8 +142,7 @@ public class Mol2FileParser extends AbstractParser {
/**
- * @see com.actelion.research.chem.parsers.AbstractParser#parse(java.io.Reader,
- * com.actelion.research.chem.Molecule3D)
+ * @see com.actelion.research.chem.io.AbstractParser#loadGroup(String, java.io.Reader, int, int)
*/
@Override
public List<Molecule3D> loadGroup(String fileName, Reader in, int from, int to) throws Exception {
@@ -303,11 +281,8 @@ public class Mol2FileParser extends AbstractParser {
} else {
throw new RuntimeException("Unknown bond type " + order + ".");
}
-
}
-
-
int a1 = i1.intValue();
int a2 = i2.intValue();
int b = m.addBond(a1, a2,order);
@@ -356,9 +331,7 @@ public class Mol2FileParser extends AbstractParser {
*/
public void save(List<Molecule3D> mols, int chargeType, Writer writer) throws Exception {
DecimalFormat df = new DecimalFormat("0.0000");
-
-
-
+
for (Molecule3D mol : mols) {
//Count the number of bonds and atoms (except lone pairs)
@@ -373,8 +346,7 @@ public class Mol2FileParser extends AbstractParser {
if(mol.getAtomicNo(mol.getBondAtom(1, i))<=0) continue;
nBonds++;
}
-
-
+
// Write the molecule
writer.write("@<TRIPOS>MOLECULE" + NEWLINE);
writer.write(mol.getName() + NEWLINE);
@@ -423,10 +395,8 @@ public class Mol2FileParser extends AbstractParser {
writer.write(NEWLINE);
}
}
-
}
-
public static void main(String[] args) throws Exception {
List<Molecule3D> res = new Mol2FileParser().loadGroup("c:/mopac11971.mol2");
@@ -434,7 +404,4 @@ public class Mol2FileParser extends AbstractParser {
System.out.println("models=" +res.size()+" atm="+res.get(0).getAllAtoms()+" "+res.get(0).getAtoms());
//new Mol2FileParser().save(res.get(0), "c:/t.mol2");
}
-
-
-
}
=====================================
src/main/java/com/actelion/research/gui/JStructureView.java
=====================================
@@ -65,6 +65,7 @@ public class JStructureView extends JComponent implements ActionListener,MouseLi
protected int mAllowedDragAction;
protected int mAllowedDropAction;
private String mWarningMessage;
+ private int[] mAtomHiliteColor;
public JStructureView() {
this(null);
@@ -216,6 +217,15 @@ public class JStructureView extends JComponent implements ActionListener,MouseLi
mAllowFragmentStatusChangeOnPasteOrDrop = allow;
}
+ /**
+ * If you want this tructure view to also draw an atom background with specific colors for every atom,
+ * then you need to call this method before or just after one of the structureChanged() calls.
+ * @param argb values with a==0 are not considered (may be null)
+ */
+ public void setAtomHighlightColors(int[] argb) {
+ mAtomHiliteColor = argb;
+ }
+
public boolean canDrop() {
return mIsEditable && isEnabled() && !mIsDraggingThis;
}
@@ -257,6 +267,7 @@ public class JStructureView extends JComponent implements ActionListener,MouseLi
mDepictor = new GenericDepictor(mDisplayMol);
mDepictor.setDisplayMode(mDisplayMode);
mDepictor.setAtomText(mAtomText);
+ mDepictor.setAtomHighlightColors(mAtomHiliteColor);
if (!isEnabled())
mDepictor.setOverruleColor(ColorHelper.getContrastColor(Color.GRAY, bg), bg);
=====================================
src/main/java/com/actelion/research/util/graph/complete/CompleteGraphMatcher.java
=====================================
@@ -153,7 +153,6 @@ public class CompleteGraphMatcher<T extends ICompleteGraph> {
initSearch();
if(nodesBase==1 && nodesQuery==1) {
- SolutionCompleteGraph solution = liliSolution.get(1).get(0);
double sim = objectiveCompleteGraph.getSimilarityNodes(0,0);
return sim;
}
View it on GitLab: https://salsa.debian.org/java-team/openchemlib/-/compare/eaa5350449d28a28c22c3592b6579017ac1b6822...4569bc2804db071f8f402d61d54cc259ee7da279
--
View it on GitLab: https://salsa.debian.org/java-team/openchemlib/-/compare/eaa5350449d28a28c22c3592b6579017ac1b6822...4569bc2804db071f8f402d61d54cc259ee7da279
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/pkg-java-commits/attachments/20220114/9b929086/attachment.htm>
More information about the pkg-java-commits
mailing list