public Character getInsCode() { return resNum.getInsCode(); }
@Override public String toString() { StringBuilder sb = new StringBuilder(); sb.append(pdbName); sb.append('\t'); sb.append(resNum.getChainName()); sb.append('\t'); sb.append(resNum.getSeqNum()); if (resNum.getInsCode() != null) sb.append(resNum.getInsCode()); sb.append('\t'); return sb.toString(); }
pos1 = residueNumber.getSeqNum(); boolean hasInsertionCode = false; if ( residueNumber.getInsCode() != null) { hasInsertionCode = true; Character insCode = g.getResidueNumber().getInsCode(); if ( insCode != null) header2.append(insCode);
buf.append(" "); buf.append(resnum); Character insCode = parent.getResidueNumber().getInsCode(); if (insCode != null) buf.append(insCode);
/** * Auxiliary method to reset chain ids of residue numbers in a chain. * Used when cloning chains and resetting their ids: one needs to take care of * resetting the ids within residue numbers too. * @param c * @param newChainName */ private static void setChainIdsInResidueNumbers(Chain c, String newChainName) { for (Group g:c.getAtomGroups()) { g.setResidueNumber(newChainName, g.getResidueNumber().getSeqNum(), g.getResidueNumber().getInsCode()); } for (Group g:c.getSeqResGroups()) { if (g.getResidueNumber()==null) continue; g.setResidueNumber(newChainName, g.getResidueNumber().getSeqNum(), g.getResidueNumber().getInsCode()); } }
ssbond.setResnum2(String.valueOf(bond.getAtomB().getGroup().getResidueNumber().getSeqNum())); Character iCode1 = bond.getAtomA().getGroup().getResidueNumber().getInsCode(); if (iCode1 == null) iCode1 = ' '; Character iCode2 = bond.getAtomB().getGroup().getResidueNumber().getInsCode(); if (iCode2 == null) iCode2 = ' ';
/** * The method will return a new reference to a Chain with any consecutive groups * having same residue numbers removed. * This is necessary to solve the microheterogeneity issue in entries like 3u7t (see github issue #160) * @param c * @return */ private static Chain removeSeqResHeterogeneity(Chain c) { Chain trimmedChain = new ChainImpl(); ResidueNumber lastResNum = null; for (Group g:c.getAtomGroups()) { // note we have to deep copy this, otherwise they stay linked and would get altered in addGroup(g) ResidueNumber currentResNum = new ResidueNumber( g.getResidueNumber().getChainName(), g.getResidueNumber().getSeqNum(), g.getResidueNumber().getInsCode()); if (lastResNum == null || !lastResNum.equals(currentResNum) ) { trimmedChain.addGroup(g); } else { logger.debug("Removing seqres group because it seems to be repeated in entity_poly_seq, most likely has hetero='y': "+g); } lastResNum = currentResNum; } return trimmedChain; }
start = new ResidueNumber(chain,start.getSeqNum(),start.getInsCode()); end = new ResidueNumber(chain,end.getSeqNum(),end.getInsCode());
List<Atom> atomsInGroup = MmtfUtils.getAtomsForGroup(group); ChemComp chemComp = group.getChemComp(); Character insCode = group.getResidueNumber().getInsCode(); if(insCode==null || insCode.equals(' ')){ insCode=MmtfStructure.UNAVAILABLE_CHAR_VALUE;
if (g.getResidueNumber().getInsCode()!=null ) { insCode = Character.toString(g.getResidueNumber().getInsCode());