/**
* Gets a list of atoms that are part of a ChemComp, with bonds already formed for you.
*
* @param name the name of the ChemComp, like "ALA" or "HEM".
* @return a list of PDBAtoms that make up a ChemComp
*/
public static List<PDBAtom> getGraph(String name) {
ChemComp cc = ChemCompGroupFactory.getChemComp(name);
List<PDBAtom> atoms = new ArrayList<PDBAtom>();
List<String> atomNames = new ArrayList<String>();
for (ChemCompAtom atom : cc.getAtoms()) {
Element element = getElement(atom);
if (element.isHeavyAtom()) {
atoms.add(new PDBAtom(element, atom.getAtom_id()));
atomNames.add(atom.getAtom_id());
}
}
for (ChemCompBond bond : cc.getBonds()) {
String atomName1 = bond.getAtom_id_1();
String atomName2 = bond.getAtom_id_2();
int index1 = atomNames.indexOf(atomName1);
int index2 = atomNames.indexOf(atomName2);
if (index1 != -1 && index2 != -1) {
Atom atom1 = atoms.get(index1);
Atom atom2 = atoms.get(index2);
new Bond(atom1, atom2, bond.getNumericalBondOrder()).addSelfToAtoms();
}
}
return atoms;
}
/** Converts biojava chemical components to ResidueInfo classes */
public ResidueInfo getResidue(String monId) {
BioJavaResidueInfo ri = (BioJavaResidueInfo) cache.get(monId);
if (ri != null) return ri;
ChemComp cc = ChemCompGroupFactory.getChemComp(monId);
ri = new BioJavaResidueInfo();
ri.setChemComp(cc);
return ri;
}