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feat: update OCL to 2024.5.0 (#203)
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@targos
targos committed May 10, 2024
1 parent d63ec13 commit 802d12d
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Showing 9 changed files with 150 additions and 81 deletions.
2 changes: 1 addition & 1 deletion openchemlib
Submodule openchemlib updated 29 files
+2 −2 pom.xml
+55 −53 src/main/java/com/actelion/research/chem/AbstractDepictor.java
+61 −9 src/main/java/com/actelion/research/chem/ExtendedDepictor.java
+13 −4 src/main/java/com/actelion/research/chem/ExtendedMolecule.java
+2 −2 src/main/java/com/actelion/research/chem/Molecule.java
+7 −1 src/main/java/com/actelion/research/chem/StereoMolecule.java
+0 −57 src/main/java/com/actelion/research/chem/combinatorialspace/Synthon.java
+1 −1 src/main/java/com/actelion/research/chem/descriptor/DescriptorHelper.java
+18 −30 src/main/java/com/actelion/research/chem/descriptor/flexophore/MolDistHist.java
+36 −21 src/main/java/com/actelion/research/chem/descriptor/flexophore/MolDistHistHelper.java
+27 −0 src/main/java/com/actelion/research/chem/descriptor/flexophore/MolDistHistVizHelper.java
+18 −3 src/main/java/com/actelion/research/chem/descriptor/flexophore/PPNodeVizHelper.java
+33 −0 src/main/java/com/actelion/research/chem/descriptor/flexophore/PPNodeVizMultCoord.java
+9 −0 src/main/java/com/actelion/research/chem/descriptor/flexophore/SlidingWindowDistHist.java
+48 −0 src/main/java/com/actelion/research/chem/descriptor/flexophore/generator/SubFlexophoreExtractorHelper.java
+15 −9 src/main/java/com/actelion/research/chem/docking/DockingEngine.java
+5 −24 src/main/java/com/actelion/research/chem/docking/LigandPose.java
+1 −8 src/main/java/com/actelion/research/chem/docking/receptorpharmacophore/NegativeReceptorImageCreator.java
+176 −85 src/main/java/com/actelion/research/chem/docking/scoring/ChemPLP.java
+15 −15 src/main/java/com/actelion/research/chem/docking/scoring/ProbeScanning.java
+36 −33 src/main/java/com/actelion/research/chem/docking/scoring/chemscore/HBTerm.java
+56 −35 src/main/java/com/actelion/research/chem/docking/scoring/chemscore/MetalTerm.java
+28 −20 src/main/java/com/actelion/research/chem/docking/scoring/chemscore/SimpleMetalTerm.java
+1 −2 src/main/java/com/actelion/research/chem/docking/scoring/plp/PLPTerm.java
+10 −9 src/main/java/com/actelion/research/chem/reaction/Reactor.java
+3 −3 src/main/java/com/actelion/research/util/CommandLineParser.java
+12 −15 src/main/java/com/actelion/research/util/StringFunctions.java
+5 −0 src/main/java/com/actelion/research/util/graph/complete/CompleteGraphMatcher.java
+3 −3 src/main/java/com/actelion/research/util/graph/complete/SolutionCompleteGraph.java
1 change: 0 additions & 1 deletion scripts/openchemlib/classes.js
View file
Original file line number Diff line number Diff line change
Expand Up @@ -94,7 +94,6 @@ const removed = [
'chem/AtomTypeList.java',
'chem/chemicalspaces',
'chem/Clusterer.java',
'chem/combinatorialspace',
'chem/conf/BondRotationHelper.java',
'chem/conf/ConformerSetGenerator.java',
'chem/conf/MolecularFlexibilityCalculator.java',
Expand Down
108 changes: 55 additions & 53 deletions src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/AbstractDepictor.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -203,7 +203,7 @@ public void setAtomText(String[] atomText) {

/**
* If the foreground color is set (!=0), then molecule is drawn in the foreground
* color except for non carbon atoms, which are drawn in atomicNo specific
* color except for non-carbon atoms, which are drawn in atomicNo specific
* colors. If a background color is given (!=0), then atom coloring and highlighting
* is optimized to achieve good contrasts.
* @param foreground null (black) or color to be used for molecule drawing
Expand All @@ -217,7 +217,7 @@ public void setForegroundColor(Color foreground, Color background) {

/**
* If the foreground color is set (!=0), then molecule is drawn in the foreground
* color except for non carbon atoms, which are drawn in atomicNo specific
* color except for non-carbon atoms, which are drawn in atomicNo specific
* colors. If a background color is given (!=0), then atom coloring and highlighting
* is optimized to achieve good contrasts.
* @param foreground 0 or ARGB values of color to be used for molecule drawing
Expand Down Expand Up @@ -628,7 +628,7 @@ public synchronized void paint(T context) {
mAtomColor[atom] = Molecule.cAtomColorMagenta;
}

setColor_(COLOR_INITIALIZE); // to initialize the color tracking mechanism
setColorCode(COLOR_INITIALIZE); // to initialize the color tracking mechanism

if (mAtomHiliteColor != null && (mAtomHiliteColor.length >= mMol.getAtoms()))
hiliteAtomBackgrounds(mAtomHiliteColor, mAtomHiliteRadius);
Expand All @@ -641,7 +641,7 @@ public synchronized void paint(T context) {
mpSetNormalLabelSize();
setLineWidth(mpLineWidth);

setColor_(mStandardForegroundColor);
setColorCode(mStandardForegroundColor);
markIsolatedAtoms();

mpDot.clear();
Expand All @@ -656,25 +656,27 @@ public synchronized void paint(T context) {

for (int i=0; i<mMol.getAllAtoms(); i++) {
if (isHighlightedAtom(i)) {
setColor_(COLOR_HILITE_BOND_FG);
setColorCode(COLOR_HILITE_BOND_FG);
mpDrawAtom(i, esrGroupMemberCount);
setColor_(mStandardForegroundColor);
setColorCode(mStandardForegroundColor);
}
else if (mAtomColor[i] != 0) {
setColor_(mAtomColor[i]);
setColorCode(mAtomColor[i]);
mpDrawAtom(i, esrGroupMemberCount);
setColor_(mStandardForegroundColor);
setColorCode(mStandardForegroundColor);
}
else if (!explicitAtomColors
&& mMol.getMoleculeColor() != Molecule.cMoleculeColorNeutral
&& mMol.getAtomicNo(i) != 1
&& mMol.getAtomicNo(i) != 6
&& ((mDisplayMode & cDModeNoImplicitAtomLabelColors) == 0)
&& mMol.getAtomList(i) == null
&& mMol.getAtomicNo(i) < ATOM_LABEL_COLOR.length) {
setRGBColor(getContrastColor(ATOM_LABEL_COLOR[mMol.getAtomicNo(i)], i));
&& mMol.getAtomicNo(i) < ATOM_LABEL_COLOR.length
&& ATOM_LABEL_COLOR[mMol.getAtomicNo(i)] != 0) {
int rgb = ATOM_LABEL_COLOR[mMol.getAtomicNo(i)];
setRGBColor(getContrastColor(rgb, i));
mpDrawAtom(i, esrGroupMemberCount);
setColor_(mStandardForegroundColor);
setColorCode(mStandardForegroundColor);
}
else {
mpDrawAtom(i, esrGroupMemberCount);
Expand Down Expand Up @@ -751,7 +753,7 @@ private void addChiralInfo() {

setTextSize((int)mChiralTextSize);
if (mMol.getMoleculeColor() != Molecule.cMoleculeColorNeutral)
setColor_(COLOR_CHIRALITY_TEXT);
setColorCode(COLOR_CHIRALITY_TEXT);
drawString(chiralText, mChiralTextLocation.x, mChiralTextLocation.y+0.3f*mChiralTextSize);
}
}
Expand Down Expand Up @@ -792,7 +794,7 @@ private void hiliteBondBackgrounds() {
line.y1 = getAtomY(atom1);
line.x2 = getAtomX(atom2);
line.y2 = getAtomY(atom2);
setColor_(COLOR_HILITE_BOND_BG);
setColorCode(COLOR_HILITE_BOND_BG);
drawBlackLine(line);
}
}
Expand All @@ -802,7 +804,7 @@ private void hiliteBondBackgrounds() {
private void hiliteExcludeGroups() {
if (mMol.isFragment()) {
double radius = mpExcludeGroupRadius;
setColor_(COLOR_EXCLUDE_GROUP_BG);
setColorCode(COLOR_EXCLUDE_GROUP_BG);
for (int atom = 0; atom < mMol.getAtoms(); atom++)
if ((mMol.getAtomQueryFeatures(atom) & Molecule.cAtomQFExcludeGroup) != 0)
fillCircle(getAtomX(atom)-radius, getAtomY(atom)-radius, 2*radius);
Expand All @@ -827,7 +829,7 @@ private void hiliteExcludeGroups() {

private void indicateQueryFeatures() {
if (mMol.isFragment()) {
setColor_(Molecule.cAtomColorOrange);
setColorCode(Molecule.cAtomColorOrange);
if (((mDisplayMode & cDModeHiliteAllQueryFeatures) != 0))
for (int atom=0; atom<mMol.getAtoms(); atom++)
if ((mMol.getAtomQueryFeatures(atom) & ~Molecule.cAtomQFExcludeGroup) != 0)
Expand All @@ -853,7 +855,7 @@ private void mpDrawAllBonds(int[][] esrGroupMemberCount) {
if ((mDisplayMode & cDModeDrawBondsInGray) != 0) {
mStandardForegroundColor = COLOR_CUSTOM_FOREGROUND;
mCustomForeground = 0xFF808080;
setColor_(cColorGray);
setColorCode(cColorGray);
}

mAlternativeCoords = new GenericPoint[mMol.getAllAtoms()];
Expand Down Expand Up @@ -894,7 +896,7 @@ private void mpDrawAllBonds(int[][] esrGroupMemberCount) {

if (cipStr != null) {
mpSetSmallLabelSize();
setColor_(mMol.isBondForegroundHilited(i) ? COLOR_HILITE_BOND_FG :
setColorCode(mMol.isBondForegroundHilited(i) ? COLOR_HILITE_BOND_FG :
(mMol.getMoleculeColor() == Molecule.cMoleculeColorNeutral || (mDisplayMode & cDModeNoColorOnESRAndCIP) != 0) ?
mStandardForegroundColor : COLOR_CIP_LETTER);
int atom1 = mMol.getBondAtom(0,i);
Expand All @@ -904,7 +906,7 @@ private void mpDrawAllBonds(int[][] esrGroupMemberCount) {
double dx = (getAtomX(atom1) - getAtomX(atom2)) / 3;
double dy = (getAtomY(atom1) - getAtomY(atom2)) / 3;
mpDrawString(x+dy,y-dx, cipStr,true);
setColor_(mStandardForegroundColor);
setColorCode(mStandardForegroundColor);
mpSetNormalLabelSize();
}
}
Expand All @@ -913,7 +915,7 @@ private void mpDrawAllBonds(int[][] esrGroupMemberCount) {

if ((mDisplayMode & cDModeBondNo) != 0) {
mpSetSmallLabelSize();
setColor_(Molecule.cAtomColorDarkGreen);
setColorCode(Molecule.cAtomColorDarkGreen);
for (int i=0; i<mMol.getAllBonds(); i++) {
int atom1 = mMol.getBondAtom(0,i);
int atom2 = mMol.getBondAtom(1,i);
Expand All @@ -923,7 +925,7 @@ private void mpDrawAllBonds(int[][] esrGroupMemberCount) {
double y = (getAtomY(atom1) + getAtomY(atom2)) / 2;
mpDrawString(x,y,type+String.valueOf(i),true);
}
setColor_(mStandardForegroundColor);
setColorCode(mStandardForegroundColor);
mpSetNormalLabelSize();
}

Expand Down Expand Up @@ -951,7 +953,7 @@ private void mpDrawBond(int bnd) {
&& !mMol.isSelectedAtom(atom2)
&& ((mMol.getAtomQueryFeatures(atom1)
| mMol.getAtomQueryFeatures(atom2)) & Molecule.cAtomQFExcludeGroup) != 0)
setColor_(COLOR_EXCLUDE_GROUP_FG);
setColorCode(COLOR_EXCLUDE_GROUP_FG);

if (mAlternativeCoords[atom1] == null) {
theLine.x1 = getAtomX(atom1);
Expand All @@ -973,7 +975,7 @@ private void mpDrawBond(int bnd) {

if ((mMol.getBondQueryFeatures(bnd) & Molecule.cBondQFBridge) != 0) {
mpHandleDottedLine(theLine, atom1, atom2);
setColor_(COLOR_RESTORE_PREVIOUS);
setColorCode(COLOR_RESTORE_PREVIOUS);
return;
}

Expand Down Expand Up @@ -1028,9 +1030,9 @@ private void mpDrawBond(int bnd) {
aLine.x2 = theLine.x1 + i*xdiff/17 + i*ydiff/128;
aLine.y2 = theLine.y1 + i*ydiff/17 - i*xdiff/128;
if (mpProperLine(aLine)) {
setColor_((i<9) ? color1 : color2);
setColorCode((i<9) ? color1 : color2);
drawBlackLine(aLine);
setColor_(mStandardForegroundColor);
setColorCode(mStandardForegroundColor);
}
}
break;
Expand Down Expand Up @@ -1178,7 +1180,7 @@ else if ((mAtomLabelDisplayed[atom1] || mMol.getAtomPi(atom1) == 2)
}

if (mCurrentColor == COLOR_EXCLUDE_GROUP_FG)
setColor_(COLOR_RESTORE_PREVIOUS);
setColorCode(COLOR_RESTORE_PREVIOUS);
}


Expand Down Expand Up @@ -1952,7 +1954,7 @@ else if (mMol.getAtomicNo(atom) != 6
double labelWidth = 0.0;

if (!mMol.isSelectedAtom(atom) & (mMol.getAtomQueryFeatures(atom) & Molecule.cAtomQFExcludeGroup) != 0)
setColor_(COLOR_EXCLUDE_GROUP_FG);
setColorCode(COLOR_EXCLUDE_GROUP_FG);

if (atomStr != null) {
labelWidth = getStringWidth(atomStr);
Expand Down Expand Up @@ -1990,9 +1992,9 @@ else if (mpAlleneCenter(atom))
y = getAtomY(atom) + ((getTextSize()*4+4)/8);
int theColor = mCurrentColor;
if (mMol.getMoleculeColor() != Molecule.cMoleculeColorNeutral && (mDisplayMode & cDModeNoColorOnESRAndCIP) == 0)
setColor_(COLOR_CIP_LETTER);
setColorCode(COLOR_CIP_LETTER);
mpDrawString(x,y,cipStr,false);
setColor_(theColor);
setColorCode(theColor);
mpSetNormalLabelSize();
}

Expand All @@ -2001,9 +2003,9 @@ else if (mpAlleneCenter(atom))
x = getAtomX(atom) + ((labelWidth + getStringWidth(mapStr)) / 2.0 + 1);
y = getAtomY(atom) + ((getTextSize()*4+4)/8);
int theColor = mCurrentColor;
setColor_(mMol.isAutoMappedAtom(atom) ? Molecule.cAtomColorDarkGreen : Molecule.cAtomColorDarkRed);
setColorCode(mMol.isAutoMappedAtom(atom) ? Molecule.cAtomColorDarkGreen : Molecule.cAtomColorDarkRed);
mpDrawString(x,y,mapStr,true);
setColor_(theColor);
setColorCode(theColor);
mpSetNormalLabelSize();
}

Expand All @@ -2014,15 +2016,15 @@ else if (mpAlleneCenter(atom))
y = getAtomY(atom) + 0.7*getTextSize()*Math.cos(angle);
int theColor = mCurrentColor;
if (!mIsValidatingView && mMol.getMoleculeColor() != Molecule.cMoleculeColorNeutral)
setColor_(getESRColor(atom));
setColorCode(getESRColor(atom));
mpDrawString(x,y,esrStr,false);
setColor_(theColor);
setColorCode(theColor);
mpSetNormalLabelSize();
}

if (hydrogensToAdd == 0 && unpairedElectrons == 0) {
if (mCurrentColor == COLOR_EXCLUDE_GROUP_FG)
setColor_(COLOR_RESTORE_PREVIOUS);
setColorCode(COLOR_RESTORE_PREVIOUS);
return;
}

Expand Down Expand Up @@ -2189,7 +2191,7 @@ else if (hindrance[i] == minHindrance) {
}

if (mCurrentColor == COLOR_EXCLUDE_GROUP_FG)
setColor_(COLOR_RESTORE_PREVIOUS);
setColorCode(COLOR_RESTORE_PREVIOUS);
}

private String createRingSizeText(long queryFeatures) {
Expand Down Expand Up @@ -2307,10 +2309,10 @@ private void mpDrawDot(double x, double y, int atm) {

private void mpDrawAllDots() {
for (DepictorDot dot:mpDot) {
setColor_(dot.color);
setColorCode(dot.color);
drawDot(dot.x, dot.y);
}
setColor_(mStandardForegroundColor);
setColorCode(mStandardForegroundColor);
}


Expand Down Expand Up @@ -2375,17 +2377,17 @@ else if ((mMol.getBondQueryFeatures(bond) & Molecule.cBondQFRingState) != 0) {

private void drawLine(DepictorLine theLine, int atom1, int atom2) {
if (mMol.isBondForegroundHilited(mMol.getBond(atom1, atom2))) {
setColor_(COLOR_HILITE_BOND_FG);
setColorCode(COLOR_HILITE_BOND_FG);
drawBlackLine(theLine);
setColor_(mStandardForegroundColor);
setColorCode(mStandardForegroundColor);
}
else if (mAtomColor[atom1] != mAtomColor[atom2]) {
drawColorLine(theLine, atom1, atom2);
}
else if (mAtomColor[atom1] != Molecule.cAtomColorNone) {
setColor_(mAtomColor[atom1]);
setColorCode(mAtomColor[atom1]);
drawBlackLine(theLine);
setColor_(mStandardForegroundColor);
setColorCode(mStandardForegroundColor);
}
else {
drawBlackLine(theLine);
Expand All @@ -2405,14 +2407,14 @@ private void drawColorLine(DepictorLine theLine,int atm1,int atm2) {
line2.x2 = theLine.x2;
line2.y2 = theLine.y2;
if (mpProperLine(line1)) {
setColor_(mAtomColor[atm1]);
setColorCode(mAtomColor[atm1]);
drawBlackLine(line1);
}
if (mpProperLine(line2)) {
setColor_(mAtomColor[atm2]);
setColorCode(mAtomColor[atm2]);
drawBlackLine(line2);
}
setColor_(mStandardForegroundColor);
setColorCode(mStandardForegroundColor);
}


Expand All @@ -2432,7 +2434,7 @@ private void drawDashedLine(DepictorLine theLine, int atom1, int atom2) {
color2 = mAtomColor[atom2];
}

setColor_(color1);
setColorCode(color1);
aLine.x1 = theLine.x1;
aLine.y1 = theLine.y1;
aLine.x2 = theLine.x1 + xinc * 2;
Expand All @@ -2444,7 +2446,7 @@ private void drawDashedLine(DepictorLine theLine, int atom1, int atom2) {
aLine.y2 = theLine.y1 + yinc * 5;
drawBlackLine(aLine);

setColor_(color2);
setColorCode(color2);
aLine.x1 = theLine.x1 + xinc * 5;
aLine.y1 = theLine.y1 + yinc * 5;
aLine.x2 = theLine.x1 + xinc * 6;
Expand All @@ -2456,7 +2458,7 @@ private void drawDashedLine(DepictorLine theLine, int atom1, int atom2) {
aLine.y2 = theLine.y2;
drawBlackLine(aLine);

setColor_(mStandardForegroundColor);
setColorCode(mStandardForegroundColor);
}


Expand All @@ -2482,21 +2484,21 @@ private void drawShortDashedLine(DepictorLine theLine, int atom1, int atom2) {
double x = theLine.x1 - mpLineWidth/2;
double y = theLine.y1 - mpLineWidth/2;

setColor_(color1);
setColorCode(color1);
for (int i=0; i<points/2; i++) {
fillCircle(x, y, mpLineWidth);
x += xinc;
y += yinc;
}

setColor_(color2);
setColorCode(color2);
for (int i=0; i<points/2; i++) {
fillCircle(x, y, mpLineWidth);
x += xinc;
y += yinc;
}

setColor_(mStandardForegroundColor);
setColorCode(mStandardForegroundColor);
}


Expand Down Expand Up @@ -2537,11 +2539,11 @@ private void drawWedge(DepictorLine theWedge,int atom1, int atom2) {
}
}

setColor_(color1);
setColorCode(color1);
drawPolygon(p1);
setColor_(color2);
setColorCode(color2);
drawPolygon(p2);
setColor_(mStandardForegroundColor);
setColorCode(mStandardForegroundColor);
}


Expand All @@ -2565,7 +2567,7 @@ private void setRGBColor(int rgb) {
}


private void setColor_(int theColor) {
private void setColorCode(int theColor) {
if (mIsValidatingView)
return;

Expand Down

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