/** * Finalize the molecule layout, primarily updating Sgroups. * * @param mol molecule being laid out */ private void finalizeLayout(IAtomContainer mol) { placeMultipleGroups(mol); placePositionalVariation(mol); placeSgroupBrackets(mol); }
/** * Create an entry for the provided container and add it to the library. * * @param container structure representation */ void add(IAtomContainer container) { add(createEntry(container)); }
private void assignStereochem(IAtomContainer molecule) { // XXX: can't check this unless we store 'unspecified' double bonds // if (!molecule.stereoElements().iterator().hasNext()) // return; // assign up/down labels, this doesn't not alter layout and could be // done on-demand (e.g. when writing a MDL Molfile) NonplanarBonds.assign(molecule); }
/** * The main method of this StructurDiagramGenerator. Assign a molecule to the * StructurDiagramGenerator, call the generateCoordinates() method and get * your molecule back. * * @param firstBondVector The vector of the first bond to lay out * @throws CDKException if an error occurs */ public void generateCoordinates(Vector2d firstBondVector) throws CDKException { generateCoordinates(firstBondVector, false, false); }
/** * Assings a molecule to be layed out. Call generateCoordinates() to do the * actual layout. * * @param molecule the molecule for which coordinates are to be generated. */ public void setMolecule(IAtomContainer molecule) { setMolecule(molecule, true); }
/** * Place ring with default start angles, using {@link #defaultAngles}. * @param ring the ring to place. * @param ringCenter center coordinates of the ring. * @param bondLength given bond length. */ public void placeRing(IRing ring, Point2d ringCenter, double bondLength) { placeRing(ring, ringCenter, bondLength, defaultAngles); }
/** * Create an empty template library. * * @return an empty template library */ static IdentityTemplateLibrary empty() { return new IdentityTemplateLibrary(); }
/** * Creates a new TemplateHandler with default templates loaded. */ public TemplateHandler(IChemObjectBuilder builder) { loadTemplates(builder); }
public AtomPair(int fst, int snd, int[] seqAt, IBond[] bndAt) { this.fst = fst; this.snd = snd; this.seqAt = seqAt; this.bndAt = bndAt; this.bndAtCode = bndCode(bndAt); }
/** * The main method of this StructurDiagramGenerator. Assign a molecule to the * StructurDiagramGenerator, call the generateCoordinates() method and get * your molecule back. * * @param firstBondVector The vector of the first bond to lay out * @throws CDKException if an error occurs */ public void generateCoordinates(Vector2d firstBondVector) throws CDKException { generateCoordinates(firstBondVector, false, false); }
/** * Assings a molecule to be layed out. Call generateCoordinates() to do the * actual layout. * * @param molecule the molecule for which coordinates are to be generated. */ public void setMolecule(IAtomContainer molecule) { setMolecule(molecule, true); }
/** * Finalize the molecule layout, primarily updating Sgroups. * * @param mol molecule being laid out */ private void finalizeLayout(IAtomContainer mol) { placeMultipleGroups(mol); placePositionalVariation(mol); placeSgroupBrackets(mol); }
private void assignStereochem(IAtomContainer molecule) { // XXX: can't check this unless we store 'unspecified' double bonds // if (!molecule.stereoElements().iterator().hasNext()) // return; // assign up/down labels, this doesn't not alter layout and could be // done on-demand (e.g. when writing a MDL Molfile) NonplanarBonds.assign(molecule); }
/** * Create an empty template library. * * @return an empty template library */ static IdentityTemplateLibrary empty() { return new IdentityTemplateLibrary(); }
/** * Creates a new TemplateHandler with default templates loaded. */ public TemplateHandler(IChemObjectBuilder builder) { loadTemplates(builder); }
public AtomPair(int fst, int snd, int[] seqAt, IBond[] bndAt) { this.fst = fst; this.snd = snd; this.seqAt = seqAt; this.bndAt = bndAt; this.bndAtCode = bndCode(bndAt); }
/** * The main method of this StructurDiagramGenerator. Assign a molecule to the * StructurDiagramGenerator, call the generateCoordinates() method and get * your molecule back. * * @throws CDKException if an error occurs */ public void generateCoordinates() throws CDKException { generateCoordinates(DEFAULT_BOND_VECTOR); }
/** * Creates an instance of this class while assigning a molecule to be layed * out. * * @param molecule The molecule to be layed out. */ public StructureDiagramGenerator(IAtomContainer molecule) { this(); setMolecule(molecule, false); }
/** * The main method of this StructurDiagramGenerator. Assign a molecule to the * StructurDiagramGenerator, call the generateCoordinates() method and get * your molecule back. * * @throws CDKException if an error occurs */ public void generateCoordinates() throws CDKException { generateCoordinates(DEFAULT_BOND_VECTOR); }
/** * Creates an instance of this class while assigning a molecule to be layed * out. * * @param molecule The molecule to be layed out. */ public StructureDiagramGenerator(IAtomContainer molecule) { this(); setMolecule(molecule, false); }