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Merge pull request #221 from cdk/patch/cxsmilesgen
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Patch/cxsmilesgen
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@egonw
egonw committed Aug 17, 2016
2 parents b5c9719 + a607a73 commit cf622a4
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Showing 12 changed files with 1,355 additions and 199 deletions.
32 changes: 32 additions & 0 deletions base/standard/src/main/java/org/openscience/cdk/tools/manipulator/ReactionManipulator.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -60,6 +60,10 @@ public static int getAtomCount(IReaction reaction) {
for (int i = 0; i < reactants.getAtomContainerCount(); i++) {
count += reactants.getAtomContainer(i).getAtomCount();
}
IAtomContainerSet agents = reaction.getAgents();
for (int i = 0; i < agents.getAtomContainerCount(); i++) {
count += agents.getAtomContainer(i).getAtomCount();
}
IAtomContainerSet products = reaction.getProducts();
for (int i = 0; i < products.getAtomContainerCount(); i++) {
count += products.getAtomContainer(i).getAtomCount();
Expand All @@ -73,6 +77,10 @@ public static int getBondCount(IReaction reaction) {
for (int i = 0; i < reactants.getAtomContainerCount(); i++) {
count += reactants.getAtomContainer(i).getBondCount();
}
IAtomContainerSet agents = reaction.getAgents();
for (int i = 0; i < agents.getAtomContainerCount(); i++) {
count += agents.getAtomContainer(i).getBondCount();
}
IAtomContainerSet products = reaction.getProducts();
for (int i = 0; i < products.getAtomContainerCount(); i++) {
count += products.getAtomContainer(i).getBondCount();
Expand All @@ -88,6 +96,13 @@ public static void removeAtomAndConnectedElectronContainers(IReaction reaction,
mol.removeAtomAndConnectedElectronContainers(atom);
}
}
IAtomContainerSet agents = reaction.getReactants();
for (int i = 0; i < agents.getAtomContainerCount(); i++) {
IAtomContainer mol = agents.getAtomContainer(i);
if (mol.contains(atom)) {
mol.removeAtomAndConnectedElectronContainers(atom);
}
}
IAtomContainerSet products = reaction.getProducts();
for (int i = 0; i < products.getAtomContainerCount(); i++) {
IAtomContainer mol = products.getAtomContainer(i);
Expand All @@ -105,6 +120,13 @@ public static void removeElectronContainer(IReaction reaction, IElectronContaine
mol.removeElectronContainer(electrons);
}
}
IAtomContainerSet agents = reaction.getReactants();
for (int i = 0; i < agents.getAtomContainerCount(); i++) {
IAtomContainer mol = agents.getAtomContainer(i);
if (mol.contains(electrons)) {
mol.removeElectronContainer(electrons);
}
}
IAtomContainerSet products = reaction.getProducts();
for (int i = 0; i < products.getAtomContainerCount(); i++) {
IAtomContainer mol = products.getAtomContainer(i);
Expand All @@ -124,6 +146,7 @@ public static IAtomContainerSet getAllMolecules(IReaction reaction) {
IAtomContainerSet moleculeSet = reaction.getBuilder().newInstance(IAtomContainerSet.class);

moleculeSet.add(getAllReactants(reaction));
moleculeSet.add(getAllAgents(reaction));
moleculeSet.add(getAllProducts(reaction));

return moleculeSet;
Expand Down Expand Up @@ -159,6 +182,15 @@ public static IAtomContainerSet getAllReactants(IReaction reaction) {
return moleculeSet;
}

public static IAtomContainerSet getAllAgents(IReaction reaction) {
IAtomContainerSet moleculeSet = reaction.getBuilder().newInstance(IAtomContainerSet.class);
IAtomContainerSet agents = reaction.getAgents();
for (int i = 0; i < agents.getAtomContainerCount(); i++) {
moleculeSet.addAtomContainer(agents.getAtomContainer(i));
}
return moleculeSet;
}

/**
* Returns a new Reaction object which is the reverse of the given
* Reaction.
Expand Down
88 changes: 42 additions & 46 deletions storage/smiles/src/main/java/org/openscience/cdk/smiles/CDKToBeam.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,6 @@

import com.google.common.collect.Maps;

import org.openscience.cdk.CDK;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.config.Isotopes;
import org.openscience.cdk.config.IsotopeFactory;
Expand Down Expand Up @@ -91,39 +90,33 @@ final class CDKToBeam {
* Whether to convert the molecule with isotope and stereo information -
* Isomeric SMILES.
*/
private final boolean isomeric;

/** Use aromatic flags. */
private final boolean aromatic;

/** Set atom class data. */
private final boolean atomClasses;
private final int flavour;

/** Create a isomeric and aromatic converter. */
CDKToBeam() {
this(true, true);
this(SmiFlavour.AtomicMass | SmiFlavour.AtomAtomMap | SmiFlavour.UseAromaticSymbols);
}

/** Create a aromatic converter specifying whether to be isomeric or not. */
CDKToBeam(boolean isomeric) {
this(isomeric, true);
CDKToBeam(int flavour) {
this.flavour = flavour;
}

/**
* Create a convert which will optionally convert isomeric and aromatic
* information from CDK data model.
*
* @param isomeric convert isomeric information
* @param aromatic convert aromatic information
*/
CDKToBeam(boolean isomeric, boolean aromatic) {
this(isomeric, aromatic, true);
Graph toBeamGraph(IAtomContainer ac) throws CDKException {
return toBeamGraph(ac, flavour);
}

CDKToBeam(boolean isomeric, boolean aromatic, boolean atomClasses) {
this.isomeric = isomeric;
this.aromatic = aromatic;
this.atomClasses = atomClasses;
Atom toBeamAtom(IAtom atom) throws CDKException {
return toBeamAtom(atom, flavour);
}

Edge toBeamEdge(IBond b, Map<IAtom, Integer> indices) throws CDKException {

checkArgument(b.getAtomCount() == 2, "Invalid number of atoms on bond");

int u = indices.get(b.getAtom(0));
int v = indices.get(b.getAtom(1));

return toBeamEdgeLabel(b, this.flavour).edge(u, v);
}

/**
Expand All @@ -134,7 +127,7 @@ final class CDKToBeam {
* @param ac an atom container instance
* @return the Beam ChemicalGraph for additional manipulation
*/
Graph toBeamGraph(IAtomContainer ac) throws CDKException {
static Graph toBeamGraph(IAtomContainer ac, int flavour) throws CDKException {

int order = ac.getAtomCount();

Expand All @@ -143,21 +136,24 @@ Graph toBeamGraph(IAtomContainer ac) throws CDKException {

for (IAtom a : ac.atoms()) {
indices.put(a, indices.size());
gb.add(toBeamAtom(a));
gb.add(toBeamAtom(a, flavour));
}

for (IBond b : ac.bonds()) {
gb.add(toBeamEdge(b, indices));
gb.add(toBeamEdge(b, flavour, indices));
}

// configure stereo-chemistry by encoding the stereo-elements
if (isomeric) {
if (SmiFlavour.isSet(flavour, SmiFlavour.Stereo)) {
for (IStereoElement se : ac.stereoElements()) {
if (se instanceof ITetrahedralChirality) {
if (SmiFlavour.isSet(flavour, SmiFlavour.StereoTetrahedral) &&
se instanceof ITetrahedralChirality) {
addTetrahedralConfiguration((ITetrahedralChirality) se, gb, indices);
} else if (se instanceof IDoubleBondStereochemistry) {
addGeometricConfiguration((IDoubleBondStereochemistry) se, gb, indices);
} else if (se instanceof ExtendedTetrahedral) {
} else if (SmiFlavour.isSet(flavour, SmiFlavour.StereoCisTrans) &&
se instanceof IDoubleBondStereochemistry) {
addGeometricConfiguration((IDoubleBondStereochemistry) se, flavour, gb, indices);
} else if (SmiFlavour.isSet(flavour, SmiFlavour.StereoExTetrahedral) &&
se instanceof ExtendedTetrahedral) {
addExtendedTetrahedralConfiguration((ExtendedTetrahedral) se, gb, indices);
}
}
Expand All @@ -177,9 +173,9 @@ Graph toBeamGraph(IAtomContainer ac) throws CDKException {
* @throws NullPointerException the atom had an undefined symbol or implicit
* hydrogen count
*/
Atom toBeamAtom(final IAtom a) {
static Atom toBeamAtom(final IAtom a, final int flavour) {

final boolean aromatic = this.aromatic && a.getFlag(CDKConstants.ISAROMATIC);
final boolean aromatic = SmiFlavour.isSet(flavour, SmiFlavour.UseAromaticSymbols) && a.getFlag(CDKConstants.ISAROMATIC);
final Integer charge = a.getFormalCharge();
final String symbol = checkNotNull(a.getSymbol(), "An atom had an undefined symbol");

Expand All @@ -199,7 +195,7 @@ Atom toBeamAtom(final IAtom a) {
if (charge != null) ab.charge(charge);

// use the mass number to specify isotope?
if (isomeric) {
if (SmiFlavour.isSet(flavour, SmiFlavour.AtomicMass)) {
Integer massNumber = a.getMassNumber();
if (massNumber != null) {
// XXX: likely causing some overhead but okay for now
Expand All @@ -214,7 +210,7 @@ Atom toBeamAtom(final IAtom a) {
}

Integer atomClass = a.getProperty(ATOM_ATOM_MAPPING);
if (atomClasses && atomClass != null) {
if (SmiFlavour.isSet(flavour, SmiFlavour.AtomAtomMap) && atomClass != null) {
ab.atomClass(atomClass);
}

Expand All @@ -231,14 +227,14 @@ Atom toBeamAtom(final IAtom a) {
* unsupported order
* @throws NullPointerException the bond order was undefined
*/
Edge toBeamEdge(IBond b, Map<IAtom, Integer> indices) throws CDKException {
static Edge toBeamEdge(IBond b, int flavour, Map<IAtom, Integer> indices) throws CDKException {

checkArgument(b.getAtomCount() == 2, "Invalid number of atoms on bond");

int u = indices.get(b.getAtom(0));
int v = indices.get(b.getAtom(1));

return toBeamEdgeLabel(b).edge(u, v);
return toBeamEdgeLabel(b, flavour).edge(u, v);
}

/**
Expand All @@ -250,9 +246,9 @@ Edge toBeamEdge(IBond b, Map<IAtom, Integer> indices) throws CDKException {
* not-aromatic
* @throws IllegalArgumentException the bond order could not be converted
*/
private Bond toBeamEdgeLabel(IBond b) throws CDKException {
private static Bond toBeamEdgeLabel(IBond b, int flavour) throws CDKException {

if (this.aromatic && b.getFlag(CDKConstants.ISAROMATIC)) return Bond.AROMATIC;
if (SmiFlavour.isSet(flavour, SmiFlavour.UseAromaticSymbols) && b.getFlag(CDKConstants.ISAROMATIC)) return Bond.AROMATIC;

if (b.getOrder() == null) throw new CDKException("A bond had undefined order, possible query bond?");

Expand All @@ -268,7 +264,7 @@ private Bond toBeamEdgeLabel(IBond b) throws CDKException {
case QUADRUPLE:
return Bond.QUADRUPLE;
default:
if (!this.aromatic && b.getFlag(CDKConstants.ISAROMATIC))
if (!SmiFlavour.isSet(flavour, SmiFlavour.UseAromaticSymbols) && b.getFlag(CDKConstants.ISAROMATIC))
throw new CDKException("Cannot write Kekulé SMILES output due to aromatic bond with unset bond order - molecule should be Kekulized");
throw new CDKException("Unsupported bond order: " + order);
}
Expand All @@ -281,13 +277,13 @@ private Bond toBeamEdgeLabel(IBond b) throws CDKException {
* @param gb the current graph builder
* @param indices atom indices
*/
private void addGeometricConfiguration(IDoubleBondStereochemistry dbs, GraphBuilder gb, Map<IAtom, Integer> indices) {
private static void addGeometricConfiguration(IDoubleBondStereochemistry dbs, int flavour, GraphBuilder gb, Map<IAtom, Integer> indices) {

IBond db = dbs.getStereoBond();
IBond[] bs = dbs.getBonds();

// don't try to set a configuration on aromatic bonds
if (this.aromatic && db.getFlag(CDKConstants.ISAROMATIC)) return;
if (SmiFlavour.isSet(flavour, SmiFlavour.UseAromaticSymbols) && db.getFlag(CDKConstants.ISAROMATIC)) return;

int u = indices.get(db.getAtom(0));
int v = indices.get(db.getAtom(1));
Expand All @@ -310,7 +306,7 @@ private void addGeometricConfiguration(IDoubleBondStereochemistry dbs, GraphBuil
* @param gb the current graph builder
* @param indices atom indices
*/
private void addTetrahedralConfiguration(ITetrahedralChirality tc, GraphBuilder gb, Map<IAtom, Integer> indices) {
private static void addTetrahedralConfiguration(ITetrahedralChirality tc, GraphBuilder gb, Map<IAtom, Integer> indices) {

IAtom[] ligands = tc.getLigands();

Expand All @@ -329,7 +325,7 @@ private void addTetrahedralConfiguration(ITetrahedralChirality tc, GraphBuilder
* @param gb the current graph builder
* @param indices atom indices
*/
private void addExtendedTetrahedralConfiguration(ExtendedTetrahedral et, GraphBuilder gb,
private static void addExtendedTetrahedralConfiguration(ExtendedTetrahedral et, GraphBuilder gb,
Map<IAtom, Integer> indices) {

IAtom[] ligands = et.peripherals();
Expand Down
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