private void recordUnidentifiableModifiedResidues(List<ModifiedCompound> modComps) { Set<StructureGroup> identifiedComps = new HashSet<StructureGroup>(); for (ModifiedCompound mc : modComps) { identifiedComps.addAll(mc.getGroups(true)); } // TODO: use the ModifiedAminoAcid after Andreas add that. for (Group group : residues) { if (group.getType().equals(GroupType.HETATM)) { StructureGroup strucGroup = StructureUtil.getStructureGroup( group, true); strucGroup.setChainId(group.getChainId()); if (!identifiedComps.contains(strucGroup)) { unidentifiableModifiedResidues.add(strucGroup); } } } }
public boolean hasContact(Atom atom1, Atom atom2) { return hasContact( new AtomIdentifier(atom1.getPDBserial(),atom1.getGroup().getChainId()), new AtomIdentifier(atom2.getPDBserial(),atom2.getGroup().getChainId()) ); }
/** * Returns the corresponding AtomContact or null if no contact exists between the 2 given atoms * @param atom1 * @param atom2 * @return */ public AtomContact getContact(Atom atom1, Atom atom2) { return contacts.get(new Pair<AtomIdentifier>( new AtomIdentifier(atom1.getPDBserial(),atom1.getGroup().getChainId()), new AtomIdentifier(atom2.getPDBserial(),atom2.getGroup().getChainId()) )); }
Group startG = ca[start].getGroup(); Group endG = ca[end].getGroup(); logger.debug(" Segment: " +startG.getResidueNumber() +":" + startG.getChainId() + " - " + endG.getResidueNumber()+":"+endG.getChainId() + " " + s); String j1 = startG.getResidueNumber()+""; String j2 = endG.getResidueNumber()+":"+endG.getChainId(); String script = " select " +j1 +"-" +j2 +"/1;"; script += " color [" + c1.getRed() + ","+c1.getGreen() + "," +c1.getBlue()+"];";
else buf.append(" "); buf.append(parent.getChainId()); if (parent.getChainId().length() == 1) buf.append(" ");
if (ss.type == type && chainId == g.getChainId()) { previous = g.getResidueNumber(); count++; start = g.getResidueNumber(); previous = start; chainId = g.getChainId(); count = 1; start = g.getResidueNumber(); previous = start; chainId = g.getChainId(); count = 1;
if (ss.type == type && chainId == g.getChainId()) { previous = g.getResidueNumber(); count++; start = g.getResidueNumber(); previous = start; chainId = g.getChainId(); count = 1; start = g.getResidueNumber(); previous = start; chainId = g.getChainId(); count = 1;
/** * * @param atom a {@link Atom} in structure. * @param isParentAminoAcid true if the containing group is an amino acid. * @return the {@link StructureAtom} of the atom. */ public static StructureAtom getStructureAtom(Atom atom, boolean isParentAminoAcid) { Group g = atom.getGroup(); String chainId = g.getChainId(); StructureGroup strucGroup = getStructureGroup(g, isParentAminoAcid); strucGroup.setChainId(chainId); return new StructureAtom(strucGroup, atom.getName()); }
tChain = templateAtoms[i].getGroup().getChainId(); break;
try { wasAdded = reduced.findGroup(g.getChainId(), g.getResidueNumber().toString(), toModel) != null; } catch (StructureException e) {
private Pair<AtomIdentifier> getAtomIdPairFromContact(AtomContact contact) { Pair<AtomIdentifier> pair = new Pair<AtomIdentifier>( new AtomIdentifier(contact.getPair().getFirst().getPDBserial(),contact.getPair().getFirst().getGroup().getChainId()), new AtomIdentifier(contact.getPair().getSecond().getPDBserial(),contact.getPair().getSecond().getGroup().getChainId())); return pair; }
ssbond.setChainID1(bond.getAtomA().getGroup().getChainId()); ssbond.setChainID2(bond.getAtomB().getGroup().getChainId()); ssbond.setResnum1(String.valueOf(bond.getAtomA().getGroup().getResidueNumber().getSeqNum())); ssbond.setResnum2(String.valueOf(bond.getAtomB().getGroup().getResidueNumber().getSeqNum()));
g.getChainId(), g.getResidueNumber().toString(), g.getChain().getStructure().getPDBCode() );
synchronized(s) { String chainId = g.getChainId(); assert !chainId.isEmpty(); Chain chain;