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."); } } }
parseCAonly = params.isParseCAOnly();
if (! params.isParseCAOnly()) { logger.warn("Could not find atoms specified in LINK record: {}",linkRecord.toString()); } else {
if ( params.isParseCAOnly() ){