/**
* Test for SF bug #1309731.
*
* @cdk.bug 1309731
*/
@Test
public void testModelBuilder3D_keepChemObjectIDs() throws Exception {
ModelBuilder3D mb3d = ModelBuilder3D.getInstance();
IMolecule methanol = new org.openscience.cdk.Molecule();
IChemObjectBuilder builder = methanol.getBuilder();
IAtom carbon1 = builder.newInstance(IAtom.class, "C");
carbon1.setID("carbon1");
methanol.addAtom(carbon1);
for (int i = 0; i < 3; i++) {
IAtom hydrogen = builder.newInstance(IAtom.class, "H");
methanol.addAtom(hydrogen);
methanol.addBond(builder.newInstance(IBond.class, carbon1, hydrogen, IBond.Order.SINGLE));
}
IAtom oxygen1 = builder.newInstance(IAtom.class, "O");
oxygen1.setID("oxygen1");
methanol.addAtom(oxygen1);
methanol.addBond(builder.newInstance(IBond.class, carbon1, oxygen1, IBond.Order.SINGLE));
IAtom hydrogen = builder.newInstance(IAtom.class, "H");
methanol.addAtom(hydrogen);
methanol.addBond(builder.newInstance(IBond.class, hydrogen, oxygen1, IBond.Order.SINGLE));
Assert.assertEquals(6, methanol.getAtomCount());
Assert.assertEquals(5, methanol.getBondCount());
mb3d.generate3DCoordinates(methanol, false);
checkAverageBondLength(methanol);
Assert.assertEquals("carbon1", carbon1.getID());
Assert.assertEquals("oxygen1", oxygen1.getID());
}
/** Converts an Atom to a MSML Atom element */
protected AtomType convertAtom(IAtom atom, String parentID) {
AtomType atomElement = new AtomType();
String id = "";
if (atom.getID() != null) {
id = atom.getID();
} else {
id = Integer.toString(atom.hashCode());
}
String atomID = parentID + PREFIX_ATOM + id;
atomElement.setId(atomID);
atomElement.setCustomId("" + id);
// atom name
atomElement.setTitle(atom.getAtomTypeName());
// element name
atomElement.setElementType(atom.getSymbol());
double x, y, z;
// set choords
if (atom.getPoint3d() != null) {
x = atom.getPoint3d().x;
y = atom.getPoint3d().y;
z = atom.getPoint3d().z;
} else { // what if mol in 2d? -> has to use getPoint2d
x = atom.getPoint2d().x;
y = atom.getPoint2d().y;
z = 0.0;
}
if (atom.getFormalCharge() != null) {
atomElement.setFormalCharge(BigInteger.valueOf(atom.getFormalCharge()));
}
atomElement.setX3(new Float(x));
atomElement.setY3(new Float(y));
atomElement.setZ3(new Float(z));
return atomElement;
}
@Test
public void testBond() throws Exception {
String cmlString =
"<molecule id='m1'><atomArray><atom id='a1'/><atom id='a2'/></atomArray><bondArray><bond id='b1' atomRefs2='a1 a2'/></bondArray></molecule>";
IChemFile chemFile = parseCMLString(cmlString);
IMolecule mol = checkForSingleMoleculeFile(chemFile);
Assert.assertEquals(2, mol.getAtomCount());
Assert.assertEquals(1, mol.getBondCount());
org.openscience.cdk.interfaces.IBond bond = mol.getBond(0);
Assert.assertEquals(2, bond.getAtomCount());
IAtom atom1 = bond.getAtom(0);
IAtom atom2 = bond.getAtom(1);
Assert.assertEquals("a1", atom1.getID());
Assert.assertEquals("a2", atom2.getID());
}
@Test
public void testAtomId3() throws Exception {
String cmlString = "<molecule id='m1'><atomArray atomID='a1 a2 a3'/></molecule>";
IChemFile chemFile = parseCMLString(cmlString);
IMolecule mol = checkForSingleMoleculeFile(chemFile);
Assert.assertEquals(3, mol.getAtomCount());
IAtom atom = mol.getAtom(1);
Assert.assertEquals("a2", atom.getID());
}
/**
* Read a Reaction from a file in MDL RXN format
*
* @return The Reaction that was read from the MDL file.
*/
private IReaction readReaction(IChemObjectBuilder builder) throws CDKException {
IReaction reaction = builder.newReaction();
try {
input.readLine(); // first line should be $RXN
input.readLine(); // second line
input.readLine(); // third line
input.readLine(); // fourth line
} catch (IOException exception) {
logger.debug(exception);
throw new CDKException("Error while reading header of RXN file", exception);
}
int reactantCount = 0;
int productCount = 0;
try {
String countsLine = input.readLine();
/* this line contains the number of reactants
and products */
StringTokenizer tokenizer = new StringTokenizer(countsLine);
reactantCount = Integer.valueOf(tokenizer.nextToken()).intValue();
logger.info("Expecting " + reactantCount + " reactants in file");
productCount = Integer.valueOf(tokenizer.nextToken()).intValue();
logger.info("Expecting " + productCount + " products in file");
} catch (Exception exception) {
logger.debug(exception);
throw new CDKException("Error while counts line of RXN file", exception);
}
// now read the reactants
try {
for (int i = 1; i <= reactantCount; i++) {
StringBuffer molFile = new StringBuffer();
input.readLine(); // announceMDLFileLine
String molFileLine = "";
do {
molFileLine = input.readLine();
molFile.append(molFileLine);
molFile.append(System.getProperty("line.separator"));
} while (!molFileLine.equals("M END"));
// read MDL molfile content
// Changed this to mdlv2000 reader
MDLV2000Reader reader =
new MDLV2000Reader(new StringReader(molFile.toString()), super.mode);
IMolecule reactant = (IMolecule) reader.read(builder.newMolecule());
// add reactant
reaction.addReactant(reactant);
}
} catch (CDKException exception) {
// rethrow exception from MDLReader
throw exception;
} catch (Exception exception) {
logger.debug(exception);
throw new CDKException("Error while reading reactant", exception);
}
// now read the products
try {
for (int i = 1; i <= productCount; i++) {
StringBuffer molFile = new StringBuffer();
input.readLine(); // String announceMDLFileLine =
String molFileLine = "";
do {
molFileLine = input.readLine();
molFile.append(molFileLine);
molFile.append(System.getProperty("line.separator"));
} while (!molFileLine.equals("M END"));
// read MDL molfile content
MDLV2000Reader reader = new MDLV2000Reader(new StringReader(molFile.toString()));
IMolecule product = (IMolecule) reader.read(builder.newMolecule());
// add reactant
reaction.addProduct(product);
}
} catch (CDKException exception) {
// rethrow exception from MDLReader
throw exception;
} catch (Exception exception) {
logger.debug(exception);
throw new CDKException("Error while reading products", exception);
}
// now try to map things, if wanted
logger.info("Reading atom-atom mapping from file");
// distribute all atoms over two AtomContainer's
IAtomContainer reactingSide = builder.newAtomContainer();
java.util.Iterator molecules = reaction.getReactants().molecules().iterator();
while (molecules.hasNext()) {
reactingSide.add((IMolecule) molecules.next());
}
IAtomContainer producedSide = builder.newAtomContainer();
molecules = reaction.getProducts().molecules().iterator();
while (molecules.hasNext()) {
producedSide.add((IMolecule) molecules.next());
}
// map the atoms
int mappingCount = 0;
// IAtom[] reactantAtoms = reactingSide.getAtoms();
// IAtom[] producedAtoms = producedSide.getAtoms();
for (int i = 0; i < reactingSide.getAtomCount(); i++) {
for (int j = 0; j < producedSide.getAtomCount(); j++) {
IAtom eductAtom = reactingSide.getAtom(i);
IAtom productAtom = producedSide.getAtom(j);
if (eductAtom.getID() != null && eductAtom.getID().equals(productAtom.getID())) {
reaction.addMapping(builder.newMapping(eductAtom, productAtom));
mappingCount++;
break;
}
}
}
logger.info("Mapped atom pairs: " + mappingCount);
return reaction;
}
@Override
public BoundsTree layout(IAtom atom, Graphics2D g) {
Rectangle2D idBounds;
this.currentObject = atom;
String id = atom.getID();
IAtomContainer molecule = null;
if (this.parent != null) {
molecule = (IAtomContainer) this.parent.getCurrentObject();
}
this.boundsTree = new BoundsTree(atom.getID());
if (molecule == null || this.shouldDraw(atom, molecule)) {
Integer implicitHydrogenCount;
this.boundsTree.add(id + ":symbol", this.layoutAtomSymbol(atom, g));
if (this.isCharged(atom)) {
Rectangle2D chargeBounds = this.layoutCharge(atom, g);
this.boundsTree.add(id + ":charge", chargeBounds);
}
if (this.params.drawImplicitHydrogens
&& (implicitHydrogenCount = atom.getImplicitHydrogenCount()) != null
&& implicitHydrogenCount > 0) {
int align = 1;
if (molecule != null) {
GeometryTools.getBestAlignmentForLabel((IAtomContainer) molecule, (IAtom) atom);
}
LabelManager.AnnotationPosition suggestedPosition =
this.labelManager.alignmentToAnnotationPosition(align);
if (atom.getSymbol().equals("O")
&& (molecule == null || molecule.getConnectedAtomsCount(atom) == 0)) {
suggestedPosition = LabelManager.AnnotationPosition.W;
}
if (this.labelManager.isUsed(atom, suggestedPosition)) {
suggestedPosition = this.labelManager.getNextSparePosition(atom);
}
this.labelManager.setUsedPosition(atom, suggestedPosition);
Rectangle2D hBounds =
this.layoutImplicitHydrogens(atom, implicitHydrogenCount, suggestedPosition, g);
if (hBounds != null) {
this.boundsTree.add(id + ":hs", hBounds);
}
}
} else if (this.params.drawRS && this.chiralMap.containsKey(atom)) {
this.boundsTree.add(
id + ":chiral", this.layoutChiralSymbol(atom, this.chiralMap.get(atom), g));
} else {
Point2d p = atom.getPoint2d();
this.boundsTree.add(id + ":symbol", new Point2D.Double(p.x, p.y));
}
if (this.params.drawAtomID
&& molecule != null
&& (idBounds = this.layoutAtomID(atom, molecule, g)) != null) {
this.boundsTree.add(id + ":id", idBounds);
}
if (this.params.drawLonePairs && molecule != null) {
int lonePairCount = 0;
for (ILonePair lonePair : molecule.lonePairs()) {
if (!lonePair.contains(atom)) {
continue;
}
++lonePairCount;
}
if (lonePairCount > 0) {
Stroke stroke = g.getStroke();
g.setStroke(new BasicStroke(0.05f));
this.layoutElectronPairs(atom, molecule, lonePairCount, g);
g.setStroke(stroke);
}
}
return this.boundsTree;
}
public Rectangle2D layoutAtomID(IAtom atom, IAtomContainer container, Graphics2D g) {
String atomID = atom.getID();
if (atomID == null) {
return null;
}
g.setFont(this.atomSymbolFont);
Point2d p = atom.getPoint2d();
Rectangle2D atomSymbolBounds =
this.shouldDraw(atom, container)
? this.getTextBounds(g, atom.getSymbol())
: new Rectangle2D.Double(p.x, p.y, 1.0, 1.0);
g.setFont(this.atomIDFont);
Rectangle2D bounds = this.getTextBounds(g, atomID);
Point2d pID = new Point2d(p);
LabelManager.AnnotationPosition suggestedPosition =
this.labelManager.alignmentToAnnotationPosition(
GeometryTools.getBestAlignmentForLabelXY((IAtomContainer) container, (IAtom) atom));
LabelManager.AnnotationPosition pos =
this.labelManager.isUsed(atom, suggestedPosition)
? this.labelManager.getNextSparePosition(atom)
: suggestedPosition;
double aW2 = atomSymbolBounds.getWidth() / 2.0;
double bW2 = bounds.getWidth() / 2.0;
double aH2 = atomSymbolBounds.getHeight() / 2.0;
double bH2 = bounds.getHeight() / 2.0;
if (null != pos)
switch (pos) {
case N:
pID.y -= aH2 + bH2;
break;
case NE:
pID.x += aW2 + bW2;
pID.y -= aH2 + bH2;
break;
case E:
pID.x += aW2 + bW2;
break;
case SE:
pID.x += aW2 + bW2;
pID.y += aH2 + bH2;
break;
case S:
pID.y += aH2 + bH2;
break;
case SW:
pID.x -= aW2 + bW2;
pID.y += aH2 + bH2;
break;
case W:
pID.x -= aW2 + bW2;
break;
case NW:
pID.x -= aW2 + bW2;
pID.y -= aH2 + bH2;
break;
default:
pID.x += aW2 + bW2;
break;
}
if (pos != null) {
this.labelManager.setUsedPosition(atom, pos);
}
g.setFont(this.atomSymbolFont);
return new Rectangle2D.Double(
pID.x - bounds.getWidth() / 2.0,
pID.y - bounds.getHeight() / 2.0,
bounds.getWidth(),
bounds.getHeight());
}