[Git][java-team/openchemlib][upstream] New upstream version 2021.11.0+dfsg
Andrius Merkys (@merkys)
gitlab at salsa.debian.org
Fri Nov 5 10:50:18 GMT 2021
Andrius Merkys pushed to branch upstream at Debian Java Maintainers / openchemlib
Commits:
22a8091d by Andrius Merkys at 2021-11-05T04:57:55-04:00
New upstream version 2021.11.0+dfsg
- - - - -
9 changed files:
- pom.xml
- src/main/java/com/actelion/research/chem/ExtendedMolecule.java
- src/main/java/com/actelion/research/chem/IsomericSmilesCreator.java
- src/main/java/com/actelion/research/chem/Mutator.java
- src/main/java/com/actelion/research/chem/RingCollection.java
- src/main/java/com/actelion/research/chem/SmilesParser.java
- src/main/java/com/actelion/research/chem/docking/DockingEngine.java
- src/main/java/com/actelion/research/chem/io/CompoundTableConstants.java
- src/main/java/com/actelion/research/chem/reaction/Reactor.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>2021.10.1</version>
+ <version>2021.11.0</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-2021.10.1</tag>
+ <tag>openchemlib-2021.11.0</tag>
</scm>
<distributionManagement>
=====================================
src/main/java/com/actelion/research/chem/ExtendedMolecule.java
=====================================
@@ -1664,8 +1664,9 @@ public class ExtendedMolecule extends Molecule implements Serializable {
/**
- * Converts any stereo bond attached with its pointed tip
- * to this atom into a single bond.
+ * Converts any stereo bond being attached with the pointed tip to the given potential stereocenter
+ * (TH or allene) into a single bond. For allenic stereo centers, stereo bonds at the allene end atoms
+ * are converted. Atoms with PI electrons are not touched, unless they are P,S,...
* @param atom
*/
public void convertStereoBondsToSingleBonds(int atom) {
@@ -1673,12 +1674,13 @@ public class ExtendedMolecule extends Molecule implements Serializable {
for (int i=0; i<2; i++) {
int alleneEnd = findAlleneEndAtom(atom, mConnAtom[atom][i]);
if (alleneEnd != -1)
- convertStereoBondsToSingleBonds(alleneEnd);
+ for (int j=0; j<mConnAtoms[alleneEnd];j++)
+ if (isStereoBond(mConnBond[alleneEnd][j]))
+ mBondType[mConnBond[alleneEnd][j]] = cBondTypeSingle;
}
return;
}
- // avoid flattening allene stereo bonds
if (mPi[atom] == 0 || mAtomicNo[atom] >= 15) {
for (int i=0; i<mAllConnAtoms[atom]; i++) {
int connBond = mConnBond[atom][i];
=====================================
src/main/java/com/actelion/research/chem/IsomericSmilesCreator.java
=====================================
@@ -42,6 +42,7 @@ import java.util.List;
public class IsomericSmilesCreator {
public static final int MODE_CREATE_SMARTS = 1;
public static final int MODE_INCLUDE_MAPPING = 2;
+ public static final int MODE_KEKULIZED_OUTPUT = 4; // no lower case atom labels and single/double bonds to represent aromaticity
private StereoMolecule mMol;
private Canonizer mCanonizer;
@@ -430,6 +431,7 @@ public class IsomericSmilesCreator {
if (!isAnyAtom
&& atomList == null
&& mMol.isAromaticAtom(atom)
+ && (mMode & MODE_KEKULIZED_OUTPUT) == 0
&& (mMol.getAtomPi(atom) != 0
|| (mMol.getAtomAbnormalValence(atom) == -1
&& mMol.getAtomRadical(atom) == Molecule.cAtomRadicalStateNone)))
@@ -461,7 +463,7 @@ public class IsomericSmilesCreator {
(!isAnyAtom && !isOrganic(mMol.getAtomicNo(atom)))
|| atomList != null
|| qualifiesForAtomParity(atom)
- || (mMol.isAromaticAtom(atom) && mMol.getAtomPi(atom) == 0)
+ || (mMol.isAromaticAtom(atom) && mMol.getAtomPi(atom) == 0 && (mMode & MODE_KEKULIZED_OUTPUT) == 0)
|| charge != 0
|| isotop != 0
|| mapNo != 0
@@ -513,13 +515,13 @@ public class IsomericSmilesCreator {
private String createMultiAtomLabel(int atom, int[] atomicNo, StringBuilder buffer) {
buffer.setLength(0);
- boolean isAromatic = mMol.isAromaticAtom(atom);
+ boolean isLowerCase = mMol.isAromaticAtom(atom) && (mMode & MODE_KEKULIZED_OUTPUT) == 0;
for (int a:atomicNo) {
if (buffer.length() != 0)
buffer.append(',');
String label = Molecule.cAtomLabel[a];
- buffer.append(isAromatic ? label.toLowerCase() : label);
+ buffer.append(isLowerCase ? label.toLowerCase() : label);
}
return buffer.toString();
@@ -740,11 +742,12 @@ public class IsomericSmilesCreator {
}
}
}
- if (startLength == builder.length() && !mMol.isAromaticBond(bond)) {
+ if (startLength == builder.length() && (!mMol.isAromaticBond(bond) || (mMode & MODE_KEKULIZED_OUTPUT) != 0)) {
int bondType = mMol.getBondType(bond) & Molecule.cBondTypeMaskSimple;
if (bondType == Molecule.cBondTypeSingle) {
if (mMol.isAromaticAtom(mMol.getBondAtom(0, bond))
- && mMol.isAromaticAtom(mMol.getBondAtom(1, bond)))
+ && mMol.isAromaticAtom(mMol.getBondAtom(1, bond))
+ && (mMode & MODE_KEKULIZED_OUTPUT) == 0)
builder.append('-');
} else if (bondType == Molecule.cBondTypeDouble)
builder.append('=');
=====================================
src/main/java/com/actelion/research/chem/Mutator.java
=====================================
@@ -1521,20 +1521,19 @@ public class Mutator {
}
private void repairStereoChemistry(StereoMolecule mol) {
+ for (int bond=0; bond<mol.getAllBonds(); bond++)
+ if (mol.isStereoBond(bond))
+ mol.setBondType(bond, Molecule.cBondTypeSingle);
+
for (int atom=0; atom<mol.getAtoms(); atom++) {
- switch (mol.getAtomParity(atom)) {
- case Molecule.cAtomParityUnknown:
- int parity = (mRandom.nextDouble() < 0.5) ? Molecule.cAtomParity1 : Molecule.cAtomParity2;
- boolean isPseudo = mol.isAtomParityPseudo(atom);
- mol.setAtomParity(atom, parity, isPseudo);
- case Molecule.cAtomParity1:
- case Molecule.cAtomParity2:
+ int parity = mol.getAtomParity(atom);
+ if (parity == Molecule.cAtomParityUnknown) {
+ parity = (mRandom.nextDouble()<0.5) ? Molecule.cAtomParity1 : Molecule.cAtomParity2;
+ boolean isPseudo = mol.isAtomParityPseudo(atom);
+ mol.setAtomParity(atom, parity, isPseudo);
+ }
+ if (parity != Molecule.cAtomParityNone)
mol.setStereoBondFromAtomParity(atom);
- break;
- case Molecule.cAtomParityNone:
- mol.convertStereoBondsToSingleBonds(atom);
- break;
- }
}
for (int bond=0; bond<mol.getBonds(); bond++) {
if (mol.isBINAPChiralityBond(bond)) {
@@ -1547,10 +1546,6 @@ public class Mutator {
case Molecule.cBondParityZor2:
mol.setStereoBondFromBondParity(bond);
break;
- case Molecule.cBondParityNone:
- mol.convertStereoBondsToSingleBonds(mol.getBondAtom(0, bond));
- mol.convertStereoBondsToSingleBonds(mol.getBondAtom(1, bond));
- break;
}
}
}
=====================================
src/main/java/com/actelion/research/chem/RingCollection.java
=====================================
@@ -50,6 +50,7 @@ public class RingCollection {
public static final int MODE_SMALL_AND_LARGE_RINGS_AND_AROMATICITY = MODE_SMALL_RINGS
| MODE_LARGE_RINGS
| MODE_AROMATICITY;
+ public static final int MODE_INCLUDE_TAUTOMERIC_BONDS = 8;
private ExtendedMolecule mMol;
private ArrayList<int[]> mRingAtomSet;
@@ -171,7 +172,7 @@ public class RingCollection {
mIsAromatic = new boolean[mRingAtomSet.size()];
mIsDelocalized = new boolean[mRingAtomSet.size()];
mHeteroPosition = new int[mRingAtomSet.size()];
- determineAromaticity(mIsAromatic, mIsDelocalized, mHeteroPosition, false);
+ determineAromaticity(mIsAromatic, mIsDelocalized, mHeteroPosition, (mode & MODE_INCLUDE_TAUTOMERIC_BONDS) != 0);
}
// find large rings by examining every potential ring bond
@@ -729,7 +730,7 @@ public class RingCollection {
public boolean qualifiesAsAmideTypeBond(int bond) {
for (int i=0; i<2; i++) {
int atom1 = mMol.getBondAtom(i, bond);
- if (mMol.getAtomicNo(atom1) == 7
+ if ((mMol.getAtomicNo(atom1) == 7)
&& mMol.getConnAtoms(atom1) == 2) {
int atom2 = mMol.getBondAtom(1-i, bond);
if (mMol.getAtomicNo(atom2) == 6) {
=====================================
src/main/java/com/actelion/research/chem/SmilesParser.java
=====================================
@@ -54,7 +54,7 @@ public class SmilesParser {
private static final int INITIAL_CONNECTIONS = 16;
private static final int MAX_CONNECTIONS = 100; // largest allowed one in SMILES is 99
- private static final int MAX_BRACKET_LEVELS = 64;
+ private static final int BRACKET_LEVELS = 32;
private static final int MAX_AROMATIC_RING_SIZE = 15;
private static final int HYDROGEN_ANY = -1;
@@ -239,7 +239,7 @@ public class SmilesParser {
TreeMap<Integer,THParity> parityMap = null;
- int[] baseAtom = new int[MAX_BRACKET_LEVELS];
+ int[] baseAtom = new int[BRACKET_LEVELS];
baseAtom[0] = -1;
int[] ringClosureAtom = new int[INITIAL_CONNECTIONS];
@@ -857,8 +857,10 @@ public class SmilesParser {
if (theChar == '(') {
if (baseAtom[bracketLevel] == -1)
throw new Exception("Smiles with leading parenthesis are not supported");
- baseAtom[bracketLevel+1] = baseAtom[bracketLevel];
bracketLevel++;
+ if (baseAtom.length == bracketLevel)
+ baseAtom = Arrays.copyOf(baseAtom, baseAtom.length + BRACKET_LEVELS);
+ baseAtom[bracketLevel] = baseAtom[bracketLevel-1];
continue;
}
@@ -1213,6 +1215,22 @@ public class SmilesParser {
} while (qualifyingBondFound);
}
+ /* Some SMILES still contain kekulized aromatic rings with lowercase hetero atoms, e.g. C1=CC=C[se]1
+ // If we recognize those rings to be aromatic, we remove the aromaticity marker from all ring atoms.
+ if (mAromaticAtoms != 0) {
+ RingCollection daylightTypeRingSet = new RingCollection(mMol, RingCollection.MODE_SMALL_RINGS_AND_AROMATICITY | RingCollection.MODE_INCLUDE_TAUTOMERIC_BONDS);
+ for (int ring=0; ring<daylightTypeRingSet.getSize(); ring++) {
+ if (daylightTypeRingSet.isAromatic(ring)) {
+ int[] ringAtom = daylightTypeRingSet.getRingAtoms(ring);
+ for (int atom:ringAtom)
+ if (mMol.isMarkedAtom(atom)) {
+ mMol.setAtomMarker(atom, false);
+ mAromaticAtoms--;
+ }
+ }
+ }
+ } taken out, because OpenChemLib should not start interpreting invalid SMILES; TLS 20-Oct-2021 */
+
while (mAromaticAtoms >= 2)
if (!connectConjugatedRadicalPairs(isAromaticBond))
break;
=====================================
src/main/java/com/actelion/research/chem/docking/DockingEngine.java
=====================================
@@ -90,8 +90,11 @@ public class DockingEngine {
public DockingEngine(StereoMolecule rec, StereoMolecule nativeLig, int mcSteps, int startPositions,
- ScoringFunction scoringFunction) {
-
+ ScoringFunction scoringFunction) throws DockingFailedException {
+ for(int ra=0;ra<rec.getAtoms();ra++) {
+ if(rec.getImplicitHydrogens(ra)>0)
+ throw new DockingFailedException("please add hydrogen atoms to receptor structure!");
+ }
nativeLigand = new Molecule3D(nativeLig);
nativeLigand.ensureHelperArrays(Molecule.cHelperCIP);
Molecule3D receptor = new Molecule3D(rec);
@@ -128,7 +131,7 @@ public class DockingEngine {
}
- public DockingEngine(StereoMolecule receptor, StereoMolecule nativeLigand) {
+ public DockingEngine(StereoMolecule receptor, StereoMolecule nativeLigand) throws DockingFailedException {
this(receptor,nativeLigand,DEFAULT_NR_MC_STEPS,DEFAULT_START_POSITIONS,ScoringFunction.CHEMPLP);
}
=====================================
src/main/java/com/actelion/research/chem/io/CompoundTableConstants.java
=====================================
@@ -173,6 +173,8 @@ public interface CompoundTableConstants {
String cColumnPropertyReferenceTypeTopDown = "topdown"; // a connection is only referenced from top record
String cColumnPropertyFormula = "formula";
String cColumnPropertySuperposeMolecule = "superposeMol"; // idcode+coords to be displayed in every cell
+ String cColumnPropertyProteinCavity = "proteinCavity"; // idcode+coords of protein cavity to be displayed in every cell
+ String cColumnPropertyNaturalLigand = "naturalLigand"; // idcode+coords of natural ligand, if proteinCavity is given (not shown, used for surface creation)
String cColumnPropertySuperpose = "superpose"; // cSuperposeValueReferenceRow or null
String cColumnPropertySuperposeAlign = "align"; // cSuperposeAlignValueShape or null
String cColumnPropertyCommentUploadStatus = "commentUploadStatus";
=====================================
src/main/java/com/actelion/research/chem/reaction/Reactor.java
=====================================
@@ -270,7 +270,7 @@ public class Reactor {
StereoMolecule genericReactant = mGenericReaction.getReactant(no);
mSSSearcher.setMol(genericReactant, mReactant[no]);
- int matchMode = SSSearcher.cMatchDBondToDelocalized + (mAllowChargeCorrections ? 0 : SSSearcher.cMatchAtomCharge);
+ int matchMode = SSSearcher.cDefaultMatchMode + (mAllowChargeCorrections ? 0 : SSSearcher.cMatchAtomCharge);
if (mSSSearcher.findFragmentInMolecule(SSSearcher.cCountModeRigorous, matchMode) == 0) {
mMatchList[no] = new ArrayList<>();
mReactantMatchCombinationCount = 0;
View it on GitLab: https://salsa.debian.org/java-team/openchemlib/-/commit/22a8091d1e0be92c7f1ef4c65c7cf754bac2680a
--
View it on GitLab: https://salsa.debian.org/java-team/openchemlib/-/commit/22a8091d1e0be92c7f1ef4c65c7cf754bac2680a
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