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Tweaks to disconnected component placement to try and avoid overlaps.
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@johnmay
johnmay committed Oct 5, 2016
1 parent 7041beb commit 91a92e4
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Showing 2 changed files with 185 additions and 2 deletions.
162 changes: 160 additions & 2 deletions tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@
import com.google.common.collect.HashMultimap;
import com.google.common.collect.Multimap;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.config.Elements;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.geometry.GeometryUtil;
import org.openscience.cdk.graph.ConnectedComponents;
Expand Down Expand Up @@ -54,9 +55,9 @@
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
import org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator;
import org.openscience.cdk.tools.manipulator.ReactionManipulator;
import org.openscience.cdk.tools.manipulator.RingSetManipulator;
import uk.ac.ebi.beam.Element;

import javax.vecmath.Point2d;
import javax.vecmath.Vector2d;
Expand Down Expand Up @@ -907,6 +908,88 @@ private static int countAlignedBonds(IAtomContainer mol) {
return count;
}

private final double adjustForHydrogen(IAtom atom, IAtomContainer mol) {
Integer hcnt = atom.getImplicitHydrogenCount();
if (hcnt == null || hcnt == 0)
return 0;
List<IBond> bonds = mol.getConnectedBondsList(atom);

int pos = 0; // right

// isolated atoms, HCl vs NH4+ etc
if (bonds.isEmpty()) {
Elements elem = Elements.ofNumber(atom.getAtomicNumber());
// see HydrogenPosition for canonical list
switch (elem) {
case Oxygen:
case Sulfur:
case Selenium:
case Tellurium:
case Fluorine:
case Chlorine:
case Bromine:
case Iodine:
pos = -1; // left
break;
default:
pos = +1; // right
break;
}
} else if (bonds.size() == 1) {
IAtom other = bonds.get(0).getConnectedAtom(atom);
double deltaX = atom.getPoint2d().x - other.getPoint2d().x;
if (Math.abs(deltaX) > 0.05)
pos = (int) Math.signum(deltaX);
}
return pos * (bondLength/2);
}

/**
* Similar to the method {@link GeometryUtil#getMinMax(IAtomContainer)} but considers
* heteroatoms with hydrogens.
*
* @param mol molecule
* @return the min/max x and y bounds
*/
private final double[] getAprxBounds(IAtomContainer mol) {
double maxX = -Double.MAX_VALUE;
double maxY = -Double.MAX_VALUE;
double minX = Double.MAX_VALUE;
double minY = Double.MAX_VALUE;
IAtom[] boundedAtoms = new IAtom[4];
for (int i = 0; i < mol.getAtomCount(); i++) {
IAtom atom = mol.getAtom(i);
if (atom.getPoint2d() != null) {
if (atom.getPoint2d().x < minX) {
minX = atom.getPoint2d().x;
boundedAtoms[0] = atom;
}
if (atom.getPoint2d().y < minY) {
minY = atom.getPoint2d().y;
boundedAtoms[1] = atom;
}
if (atom.getPoint2d().x > maxX) {
maxX = atom.getPoint2d().x;
boundedAtoms[2] = atom;
}
if (atom.getPoint2d().y > maxY) {
maxY = atom.getPoint2d().y;
boundedAtoms[3] = atom;
}
}
}
double[] minmax = new double[4];
minmax[0] = minX;
minmax[1] = minY;
minmax[2] = maxX;
minmax[3] = maxY;
double minXAdjust = adjustForHydrogen(boundedAtoms[0], mol);
double maxXAdjust = adjustForHydrogen(boundedAtoms[1], mol);
if (minXAdjust < 0) minmax[0] += minXAdjust;
if (maxXAdjust > 0) minmax[1] += maxXAdjust;
return minmax;
}

private void generateFragmentCoordinates(IAtomContainer mol, List<IAtomContainer> frags) throws CDKException {
final List<IBond> ionicBonds = makeIonicBonds(frags);

Expand Down Expand Up @@ -934,7 +1017,8 @@ private void generateFragmentCoordinates(IAtomContainer mol, List<IAtomContainer
for (IAtomContainer fragment : frags) {
setMolecule(fragment, false, afix, bfix);
generateCoordinates(DEFAULT_BOND_VECTOR, true, true);
limits.add(GeometryUtil.getMinMax(fragment));
lengthenIonicBonds(ionicBonds, fragment);
limits.add(getAprxBounds(fragment));
}

// restore
Expand Down Expand Up @@ -993,6 +1077,80 @@ private void generateFragmentCoordinates(IAtomContainer mol, List<IAtomContainer
finalizeLayout(mol);
}

private void lengthenIonicBonds(List<IBond> ionicBonds, IAtomContainer fragment) {

final IChemObjectBuilder bldr = fragment.getBuilder();

if (ionicBonds.isEmpty())
return;

IAtomContainer newfrag = bldr.newInstance(IAtomContainer.class);
IAtom[] atoms = new IAtom[fragment.getAtomCount()];
for (int i = 0; i < atoms.length; i++)
atoms[i] = fragment.getAtom(i);
newfrag.setAtoms(atoms);

for (IBond bond : fragment.bonds()) {
if (!ionicBonds.contains(bond)) {
newfrag.addBond(bond);
} else {
Integer numBegIonic = bond.getAtom(0).getProperty("ionicDegree");
Integer numEndIonic = bond.getAtom(1).getProperty("ionicDegree");
if (numBegIonic == null) numBegIonic = 0;
if (numEndIonic == null) numEndIonic = 0;
numBegIonic++;
numEndIonic++;
bond.getAtom(0).setProperty("ionicDegree", numBegIonic);
bond.getAtom(1).setProperty("ionicDegree", numEndIonic);
}
}

if (newfrag.getBondCount() == fragment.getBondCount())
return;

IAtomContainerSet subfragments = ConnectivityChecker.partitionIntoMolecules(newfrag);
Map<IAtom, IAtomContainer> atomToFrag = new HashMap<>();

// index atom->fragment
for (IAtomContainer subfragment : subfragments.atomContainers())
for (IAtom atom : subfragment.atoms())
atomToFrag.put(atom, subfragment);

for (IBond bond : ionicBonds) {
IAtom beg = bond.getAtom(0);
IAtom end = bond.getAtom(1);

// select which bond to stretch from
Integer numBegIonic = bond.getAtom(0).getProperty("ionicDegree");
Integer numEndIonic = bond.getAtom(1).getProperty("ionicDegree");
if (numBegIonic == null || numEndIonic == null)
continue;
if (numBegIonic > numEndIonic) {
IAtom tmp = beg;
beg = end;
end = tmp;
} else if (numBegIonic == numEndIonic && numBegIonic > 1) {
// can't stretch these
continue;
}

IAtomContainer begFrag = atomToFrag.get(beg);
IAtomContainer endFrags = bldr.newInstance(IAtomContainer.class);
if (begFrag == null)
continue;
for (IAtomContainer mol : subfragments.atomContainers()) {
if (mol != begFrag)
endFrags.add(mol);
}
double dx = end.getPoint2d().x - beg.getPoint2d().x;
double dy = end.getPoint2d().y - beg.getPoint2d().y;
Vector2d bondVec = new Vector2d(dx, dy);
bondVec.normalize();
bondVec.scale(bondLength/2); // 1.5 bond length
GeometryUtil.translate2D(endFrags, bondVec);
}
}

/**
* Property to cache the charge of a fragment.
*/
Expand Down
25 changes: 25 additions & 0 deletions tool/sdg/src/test/java/org/openscience/cdk/layout/StructureDiagramGeneratorTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -67,6 +67,7 @@
import static org.hamcrest.CoreMatchers.not;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.closeTo;
import static org.hamcrest.Matchers.greaterThan;
import static org.hamcrest.Matchers.lessThan;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
Expand Down Expand Up @@ -1215,4 +1216,28 @@ public void disconnectedMultigroupPlacement() throws Exception {
0.01);
}
}

/**
* These molecules are laid out 'H2N=NH2.H2N=NH2', ensure we give them more space than
* usual (bond length)
*/
@Test
public void dihydroazine() throws Exception {
SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
IAtomContainer mol = smipar.parseSmiles("N=N.N=N");
layout(mol);
assertThat(mol.getAtom(2).getPoint2d().x - mol.getAtom(1).getPoint2d().x,
is(greaterThan(SDG.getBondLength())));

}

@Test
public void NH4OH() throws Exception {
SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
IAtomContainer mol = smipar.parseSmiles("[NH4+].[OH-]");
layout(mol);
assertThat(mol.getAtom(1).getPoint2d().x - mol.getAtom(0).getPoint2d().x,
is(greaterThan(SDG.getBondLength())));

}
}

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