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class ChangeAtomSymbol extends AbstractUndoableEdit { | |
IAtomContainer container; | |
IAtom remove, replace; | |
ChangeAtomSymbol(IAtomContainer container, | |
IAtom original, | |
String newSymbol) { | |
Atom copy = new Atom(original); // do not clone! |
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// check for wide labels | |
boolean blunt = bounds.getWidth() / bounds.getHeight() > 3; | |
// ... | |
return new RoundRectangle2D.Double(x - (width/2), y - (height/2), | |
width, height, | |
blunt ? height : width, height); |
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public double[] transformPointDouble(double xCoord, double yCoord) { | |
double[] src = new double[] {xCoord, yCoord}; | |
double[] dest = new double[2]; | |
this.transform.transform(src, 0, dest, 0, 1); | |
return dest; | |
} | |
// ... used in the bounds calculation | |
double[] p = this.transformPointDouble(x, y); |
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class CustomChemObjectBuilder implements IChemObjectBuilder { | |
private final DynamicFactory factory = new DynamicFactory(200); | |
public CustomChemObjectBuilder() { | |
// basic registration | |
factory.register(Element.class); // discovers Element is an instance of IElement, alternatively... | |
factory.register(IElement.class, Element.class); // registers Element with IElement explicitly |
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IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance(); | |
SmilesParser parser = new SmilesParser(builder); | |
IAtomContainer sodiumChloride = parser.parseSmiles("[Na+].[Cl-]"); | |
IAtomContainer adenine = parser.parseSmiles("n1c(c2c(nc1)ncn2)N"); | |
// if you want the separate parts | |
// import static org.openscience.cdk.graph.ConnectivityChecker.partitionIntoMolecules; | |
IAtomContainerSet sodiumChlorideSet = partitionIntoMolecules(sodiumChloride); | |
IAtomContainerSet adenineSet = partitionIntoMolecules(adenine); |
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IAtomContainer a = new AtomContainer(); | |
a.addAtom(new Atom("C")); | |
a.addAtom(new Atom("C")); | |
a.addBond(new Bond(a.getAtom(0), a.getAtom(1), SINGLE)); | |
// copy constructor | |
IAtomContainer b = new AtomContainer(a); | |
b.removeAtom(0); // atom at index 0 is removed from b, a is not affected | |
b.getBond(0).setOrder(DOUBLE); // bond order is change in both a and b |
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public class AdjacencyList implements Graph { | |
private final int[][] vertexes; | |
private final IAtom[] atoms; | |
private final int n; | |
public AdjacencyList(final IAtomContainer container) { | |
this.n = container.getAtomCount(); |
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private int iterate(IAtomContainer container) { | |
int total = 0; | |
for (int d = 0; d < 8; d++) { | |
for (IAtom atom : container.atoms()) { | |
for (IBond bond : container.getConnectedBondsList(atom)) { | |
IAtom other = bond.getConnectedAtom(atom); | |
total += other.getAtomicNumber(); | |
} | |
} | |
} |
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public int rotate(int value, int n){ | |
for(int i = 0; i < n; i++) | |
value = nextInt(value); | |
return value; | |
} | |
public int nextInt(int seed){ | |
// return pseudo random number from the given seed | |
} |
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public int rotate(int value, int n){ | |
for(int i = 0; i < n; i++) | |
value = nextInt(value); | |
return value; | |
} | |
public int nextInt(int seed){ | |
// return pseudo random number from the given seed | |
} |