本文整理汇总了Java中org.openscience.cdk.interfaces.IAtomContainer.getBondCount方法的典型用法代码示例。如果您正苦于以下问题：Java IAtomContainer.getBondCount方法的具体用法？Java IAtomContainer.getBondCount怎么用？Java IAtomContainer.getBondCount使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类org.openscience.cdk.interfaces.IAtomContainer的用法示例。
在下文中一共展示了IAtomContainer.getBondCount方法的6个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Java代码示例。
示例1: isValidDoubleBondConfiguration
import org.openscience.cdk.interfaces.IAtomContainer; //导入方法依赖的package包/类
/**
* Tells if a certain bond is center of a valid double bond configuration.
*
*@param container The atomcontainer.
*@param bond The bond.
*@return true=is a potential configuration, false=is not.
*/
public boolean isValidDoubleBondConfiguration(IAtomContainer container, IBond bond)
{
IAtom atom0 = bond.getAtom(0);
IAtom atom1 = bond.getAtom(1);
List<IAtom> connectedAtoms = container.getConnectedAtomsList(atom0);
IAtom from = null;
for (IAtom connectedAtom : connectedAtoms) {
if (connectedAtom != atom1) {
from = connectedAtom;
}
}
boolean[] array = new boolean[container.getBondCount()];
for (int i = 0; i < array.length; i++)
{
array[i] = true;
}
if (isStartOfDoubleBond(container, atom0, from, array) && isEndOfDoubleBond(container, atom1, atom0, array) && !bond.getFlag(CDKConstants.ISAROMATIC))
{
return (true);
} else
{
return (false);
}
}
示例2: generateImage
import org.openscience.cdk.interfaces.IAtomContainer; //导入方法依赖的package包/类
/**
* draw image and return it as RenderedImage
*
* @param structure
* @return
* @throws CDKException
*/
public RenderedImage generateImage(final IAtomContainer structure) {
Image image = new BufferedImage(this.imageWidth, this.imageHeight, BufferedImage.TYPE_INT_ARGB);
Graphics2D g2 = (Graphics2D) image.getGraphics();
g2.setColor(new Color(1.0f, 1.0f, 1.0f, 0.0f));
g2.fillRect(0, 0, this.imageWidth, this.imageHeight);
try {
IAtomContainer moleculeToDraw = AtomContainerManipulator.removeHydrogens(structure);
Rectangle drawArea = new Rectangle(this.imageWidth, this.imageHeight);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(moleculeToDraw);
for(int i = 0; i < moleculeToDraw.getAtomCount(); i++)
moleculeToDraw.getAtom(i).setProperty(StandardGenerator.ANNOTATION_LABEL, i + "");
for(int i = 0; i < moleculeToDraw.getBondCount(); i++)
moleculeToDraw.getBond(i).setProperty(StandardGenerator.ANNOTATION_LABEL, i + "");
StructureDiagramGenerator sdg = new StructureDiagramGenerator();
sdg.setMolecule(moleculeToDraw);
sdg.generateCoordinates();
this.renderer.setup(sdg.getMolecule(), drawArea);
RendererModel rendererModel = this.renderer.getRenderer2DModel();
rendererModel.set(StandardGenerator.Visibility.class, SymbolVisibility.iupacRecommendations());
rendererModel.set(StandardGenerator.AtomColor.class, new CDK2DAtomColors());
rendererModel.set(StandardGenerator.AnnotationColor.class, new Color(0x455FFF));
rendererModel.set(StandardGenerator.StrokeRatio.class, this.strokeRatio);
Rectangle2D bounds = new Rectangle2D.Double(0, 0, this.imageWidth, this.imageHeight);
this.renderer.paint(sdg.getMolecule(), new AWTDrawVisitor(g2), bounds, true);
} catch (Exception e) {
return (RenderedImage) image;
}
return (RenderedImage) image;
}
开发者ID:c-ruttkies，项目名称:MetFragRelaunched，代码行数:42，代码来源:AnnotatedStandardSingleStructureImageGenerator.java
示例3: getBondRefs
import org.openscience.cdk.interfaces.IAtomContainer; //导入方法依赖的package包/类
public static BondRef[] getBondRefs(IAtomContainer mol) {
final int numAtoms = mol.getAtomCount();
final int numBonds = mol.getBondCount();
BondRef[] bonds = new BondRef[numBonds];
final Map<IAtom, AtomRef> atomCache = new IdentityHashMap<>(mol.getAtomCount());
for (int i = 0; i < numAtoms; i++) {
final IAtom atom = mol.getAtom(i);
final AtomRef atomrf = new AtomRef(i,
atom,
new ArrayList<BondRef>());
atomCache.put(atomrf.atom, atomrf);
}
for (int i = 0; i < numBonds; i++) {
final IBond bond = mol.getBond(i);
AtomRef beg = atomCache.get(bond.getAtom(0));
AtomRef end = atomCache.get(bond.getAtom(1));
final BondRef bondref = new BondRef(bond, i, beg, end);
beg.bonds.add(bondref);
end.bonds.add(bondref);
bonds[i] = bondref;
}
return bonds;
}
示例4: getAtomRefs
import org.openscience.cdk.interfaces.IAtomContainer; //导入方法依赖的package包/类
public static AtomRef[] getAtomRefs(IAtomContainer mol) {
final int numAtoms = mol.getAtomCount();
final int numBonds = mol.getBondCount();
AtomRef[] atoms = new AtomRef[numAtoms];
final Map<IAtom, AtomRef> atomCache = new IdentityHashMap<>(mol.getAtomCount());
for (int i = 0; i < numAtoms; i++) {
final IAtom atom = mol.getAtom(i);
final AtomRef atomrf = new AtomRef(i,
atom,
new ArrayList<BondRef>());
atomCache.put(atomrf.atom, atomrf);
atoms[i] = atomrf;
}
for (int i = 0; i < numBonds; i++) {
final IBond bond = mol.getBond(i);
AtomRef beg = atomCache.get(bond.getAtom(0));
AtomRef end = atomCache.get(bond.getAtom(1));
final BondRef bondref = new BondRef(bond, i, beg, end);
beg.bonds.add(bondref);
end.bonds.add(bondref);
}
return atoms;
}
示例5: setScale
import org.openscience.cdk.interfaces.IAtomContainer; //导入方法依赖的package包/类
private void setScale(IAtomContainer container) {
if (container.getBondCount() > 0) {
double bondLength = GeometryUtil.getBondLengthMedian(container);
if (bondLength < 0.001)
setScaleForBondLength(0.826);
else
setScaleForBondLength(bondLength);
}
else {
setScaleForBondLength(0.826);
}
}
示例6: main
import org.openscience.cdk.interfaces.IAtomContainer; //导入方法依赖的package包/类
public static void main(String[] args) throws InvalidSmilesException, IOException {
//SmilesParser sp = new SmilesParser(SilentChemObjectBuilder.getInstance());
//IAtomContainer m = sp.parseSmiles("CC(C)c1ccc(cc1)S(=O)(=O)O");
IAtomContainer m = null;
try {
m = MoleculeFunctions.getAtomContainerFromInChI("InChI=1S/C10H22N2/c1-9(2)4-8(12)5-10(3,6-9)7-11/h8H,4-7,11-12H2,1-3H3");
MoleculeFunctions.prepareAtomContainer(m, false);
} catch (Exception e) {
e.printStackTrace();
}
HighlightSubStructureImageGenerator s = new HighlightSubStructureImageGenerator(new Font("Verdana", Font.BOLD, 18));
s.setImageHeight(500);
s.setImageWidth(500);
s.setStrokeRation(1.5);
BitArray bitArrayAtoms = new BitArray(m.getAtomCount());
BitArray bitArrayBonds = new BitArray(m.getBondCount());
bitArrayAtoms.set(0, true);
bitArrayAtoms.set(1, true);
bitArrayAtoms.set(2, true);
bitArrayAtoms.set(3, true);
bitArrayAtoms.set(4, true);
bitArrayAtoms.set(5, true);
bitArrayAtoms.set(6, true);
bitArrayAtoms.set(7, true);
bitArrayAtoms.set(8, true);
bitArrayAtoms.set(9, true);
bitArrayBonds.set(0, true);
bitArrayBonds.set(1, true);
bitArrayBonds.set(2, true);
bitArrayBonds.set(3, true);
bitArrayBonds.set(4, true);
bitArrayBonds.set(5, true);
bitArrayBonds.set(6, true);
bitArrayBonds.set(7, true);
bitArrayBonds.set(8, true);
bitArrayBonds.set(9, true);
RenderedImage img = s.generateImage(bitArrayAtoms, bitArrayBonds, m);
ImageIO.write((RenderedImage) img, "PNG", new java.io.File("/tmp/file.png"));
}