@Override public void setChainInfo(String chainId, String chainName, int groupCount) { // First check to see if the chain exists Map<String, Chain> modelChainMap = chainMap.get(modelNumber); if(modelChainMap.containsKey(chainId)){ chain = modelChainMap.get(chainId); } // If we need to set a new chain do this else{ chain = new ChainImpl(); chain.setId(chainId.trim()); chain.setName(chainName); chain.setAtomGroups(new ArrayList<>(groupCount)); modelChainMap.put(chainId, chain); chainList.add(chain); } }
/** * Adds a chain to the given structure to form a biological assembly, * adding the symmetry-expanded chains as new chains with renamed * chain ids and names (in the form originalAsymId_transformId and originalAuthId_transformId). * @param s * @param newChain * @param transformId */ private void addChainFlattened(Structure s, Chain newChain, String transformId) { newChain.setId(newChain.getId()+"_"+transformId); newChain.setName(newChain.getName()+"_"+transformId); s.addChain(newChain); }
currentChain.setName(chainID);
newChain.setName(parentC.getName()); model.add(newChain);
newChain.setName(parentC.getName()); model.add(newChain);
currentChain.setName(chainName);
String newChainName = cOrigName+(iOperator+1)+NCS_CHAINID_SUFFIX_CHAR; clonedChain.setId(newChainId); clonedChain.setName(newChainName);
newChain = new ChainImpl(); newChain.setId(parentC.getId()); newChain.setName(parentC.getName()); model.add(newChain);
chain.setName(group.getChain().getName()); chain.setId(group.getChain().getId()); if (currentChain == null || !currentChain.getId().equals(chain.getId())) { chain.setSwissprotId(group.getChain().getSwissprotId()); chain.setId(group.getChain().getId()); chain.setName(group.getChain().getName()); currentChain = chain;
newchain.setName(c.getName());
Chain orig = a.getGroup().getChain(); c.setId(orig.getId()); c.setName(orig.getName()); } else { Chain orig = a.getGroup().getChain(); c = new ChainImpl(); c.setId(orig.getId()); c.setName(orig.getName()); Chain orig = a.getGroup().getChain(); c.setId(orig.getId()); c.setName(orig.getName()); } else { Chain orig = a.getGroup().getChain(); c = new ChainImpl(); c.setId(orig.getId()); c.setName(orig.getName());
newChain = new ChainImpl(); newChain.setId(chain.getId()); newChain.setName(chain.getName()); newChain.setEntityInfo(chain.getEntityInfo()); structure.addChain(newChain);
newChain.setName(chain.getName()); newChain.setEntityInfo(chain.getEntityInfo()); newChain.setSwissprotId(chain.getSwissprotId());
chain.setName(oldChain.getName());
c1.setName(c.getName()); c1.setEntityInfo(c.getEntityInfo()); s.addChain(c1);