@Override public SSBondImpl clone() { SSBondImpl nbond = new SSBondImpl(); nbond.setChainID1(chainID1); nbond.setChainID2(chainID2); nbond.setResnum1(resnum1); nbond.setResnum2(resnum2); return nbond; }
icode2 = ""; SSBondImpl ssbond = new SSBondImpl(); ssbond.setChainID1(chain1); ssbond.setResnum1(seqNum1); ssbond.setChainID2(chain2); ssbond.setResnum2(seqNum2); ssbond.setInsCode1(icode1); ssbond.setInsCode2(icode2); ssbonds.add(ssbond);
private void formDisulfideBond(SSBondImpl disulfideBond) { try { Map<Integer, Atom> a = getAtomFromRecord("SG", "", "CYS", disulfideBond.getChainID1(), disulfideBond.getResnum1(), disulfideBond.getInsCode1()); Map<Integer, Atom> b = getAtomFromRecord("SG", "", "CYS", disulfideBond.getChainID2(), disulfideBond.getResnum2(), disulfideBond.getInsCode2()); for(int i=0; i<structure.nrModels(); i++){ if(a.containsKey(i) && b.containsKey(i)){ // TODO determine what the actual bond order of this bond is; for // now, we're assuming they're single bonds if(!a.get(i).equals(b.get(i))){ Bond ssbond = new BondImpl(a.get(i), b.get(i), 1); structure.addSSBond(ssbond); } } } } catch (StructureException e) { // Note, in Calpha only mode the CYS SG's are not present. if (! params.isParseCAOnly()) { logger.warn("Could not find atoms specified in SSBOND record: {}",disulfideBond.toString()); } else { logger.debug("Could not find atoms specified in SSBOND record while parsing in parseCAonly mode."); } } }
List<SSBondImpl> ssbonds = SSBondImpl.getSsBondListFromBondList(structure.getSSBonds()); for (SSBondImpl ssbond : ssbonds){ ssbond.toPDB(str); str.append(newline);
SSBondImpl ssbond = new SSBondImpl(); 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())); if (iCode2 == null) iCode2 = ' '; ssbond.setInsCode1(String.valueOf(iCode1)); ssbond.setInsCode2(String.valueOf(iCode2));