public int getResidueNumber() { return resNum.getSeqNum(); }
@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) {
int resnum = parent.getResidueNumber().getSeqNum(); if (resnum < 10) buf.append(" ");
int seqResPos = atomResNum.getSeqNum();
if (seqresG.getResidueNumber().getSeqNum() == internalNr ) { seqResGroups.set(seqResPos, atomG); found = true;
public void setAa1(AminoAcid aa) { setPdbId(aa.getChain().getStructure().getPDBCode()); pdbChainId1 = aa.getChainId(); aaPos1 = aa.getResidueNumber().getSeqNum() - 1; aa1 = aa.getChemComp().getOne_letter_code().charAt(0); }
start = new ResidueNumber(chain,start.getSeqNum(),start.getInsCode()); end = new ResidueNumber(chain,end.getSeqNum(),end.getInsCode()); if( !key.getChainName().equals(chain) ) continue; if( start.getSeqNum() <= key.getSeqNum() ) { start = key; startIndex = getPosition(key); if( end.getSeqNum() >= key.getSeqNum() ) { end = key; endIndex = value;
public void setAa2(AminoAcid aa) { setPdbId(aa.getChain().getStructure().getPDBCode()); pdbChainId2 = aa.getChainId(); aaPos2 = aa.getResidueNumber().getSeqNum() - 1; aa2 = aa.getChemComp().getOne_letter_code().charAt(0); }
/** * 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()); } }
if (group instanceof AminoAcid) { AminoAcid aa = (AminoAcid) group; int aaPos = aa.getResidueNumber().getSeqNum() - 1; if (aaPos < 0) continue; // I don't know why some PDB coordinates are negative...
serial = g.getResidueNumber().getSeqNum();
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()));
/** * 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; }
singleLetterCode = chemComp.getOne_letter_code().charAt(0); mmtfDecoderInterface.setGroupInfo(group.getPDBName(), group.getResidueNumber().getSeqNum(), insCode.charValue(), chemComp.getType().toUpperCase(), atomsInGroup.size(), MmtfUtils.getNumBondsInGroup(atomsInGroup), singleLetterCode, sequenceGroups.indexOf(group), MmtfUtils.getSecStructType(group));
String labelSeqId = Integer.toString(g.getResidueNumber().getSeqNum()); if (g.getChain()!=null && g.getChain().getEntityInfo()!=null) { entityId = Integer.toString(g.getChain().getEntityInfo().getMolId()); atomSite.setOccupancy(FileConvert.d2.format(a.getOccupancy())); atomSite.setB_iso_or_equiv(FileConvert.d2.format(a.getTempFactor())); atomSite.setAuth_seq_id(Integer.toString(g.getResidueNumber().getSeqNum())); atomSite.setAuth_comp_id(g.getPDBName()); atomSite.setAuth_asym_id(chainName);