private Chain getEntityChain(String entity_id){ for (Chain chain : entityChains) { if ( chain.getId().equals(entity_id)){ return chain; } } // does not exist yet, so create... Chain chain = new ChainImpl(); chain.setId(entity_id); entityChains.add(chain); return chain; }
/** * Assign asym ids following the rules used by the PDB to assign asym ids in mmCIF files * @param polys * @param nonPolys * @param waters */ private void assignAsymIds(List<List<Chain>> polys, List<List<Chain>> nonPolys, List<List<Chain>> waters) { for (int i=0; i<polys.size(); i++) { String asymId = "A"; for (Chain poly:polys.get(i)) { poly.setId(asymId); asymId = getNextAsymId(asymId); } for (Chain nonPoly:nonPolys.get(i)) { nonPoly.setId(asymId); asymId = getNextAsymId(asymId); } for (Chain water:waters.get(i)) { water.setId(asymId); asymId = getNextAsymId(asymId); } } }
@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.setId(chainID); currentChain.setName(chainID);
/** get an artificial List of chains containing the Atoms and groups. * Does NOT rotate anything. * @param ca * @return a list of Chains that is built up from the Atoms in the ca array * @throws StructureException */ public static final List<Chain> getAlignedModel(Atom[] ca){ List<Chain> model = new ArrayList<Chain>(); for ( Atom a: ca){ Group g = a.getGroup(); Chain parentC = g.getChain(); Chain newChain = null; for ( Chain c : model) { if ( c.getId().equals(parentC.getId())){ newChain = c; break; } } if ( newChain == null){ newChain = new ChainImpl(); newChain.setId(parentC.getId()); model.add(newChain); } newChain.addGroup(g); } return model; }
/** * Create and set a new structure from a given atom array. * @param atoms */ public void setAtoms(Atom[] atoms){ Structure s = new StructureImpl(); Chain c = new ChainImpl(); c.setId("A"); for (Atom a: atoms){ c.addGroup(a.getGroup()); } s.addChain(c); setStructure(s); }
currentChain.setId(chainName); currentChain.setName(chainName);
String newChainId = cOrigId+(iOperator+1)+NCS_CHAINID_SUFFIX_CHAR; String newChainName = cOrigName+(iOperator+1)+NCS_CHAINID_SUFFIX_CHAR; clonedChain.setId(newChainId); clonedChain.setName(newChainName);
public static void main(String[] args){ Chain c = new ChainImpl(); c.setId("X"); Group g = new AminoAcidImpl(); g.setResidueNumber(ResidueNumber.fromString("1A")); try { g.setPDBName("ALA"); } catch (Exception e){} Atom a = new AtomImpl(); a.setName("CA"); g.addAtom(a); c.addGroup(g); System.out.println(getPdbInfo(a)); }
newChain.setId(parentC.getId()); newChain.setName(parentC.getName()); model.add(newChain);
chain.setId(group.getChain().getId()); if (currentChain == null || !currentChain.getId().equals(chain.getId())) { structure.addChain(chain); chain.setStructure(structure); chain.setSwissprotId(group.getChain().getSwissprotId()); chain.setId(group.getChain().getId()); chain.setName(group.getChain().getName()); currentChain = chain;
seqres.setId(asym.getId()); if (asymId2authorId.get(asym.getId()) !=null ){ seqres.setName(asymId2authorId.get(asym.getId()));
c = new ChainImpl(); Chain orig = a.getGroup().getChain(); c.setId(orig.getId()); c.setName(orig.getName()); } else { if (!orig.getId().equals(prevChainId)) { c = new ChainImpl(); c.setId(orig.getId()); c.setName(orig.getName()); c = new ChainImpl(); Chain orig = a.getGroup().getChain(); c.setId(orig.getId()); c.setName(orig.getName()); } else { if (!orig.getId().equals(prevChainId)) { c = new ChainImpl(); c.setId(orig.getId()); c.setName(orig.getName());
if (! structure.hasNonPolyChain(chain.getId())) { newChain = new ChainImpl(); newChain.setId(chain.getId()); newChain.setName(chain.getName()); newChain.setEntityInfo(chain.getEntityInfo());
newChain.setId(chain.getId()); newChain.setName(chain.getName()); newChain.setEntityInfo(chain.getEntityInfo());
chain.setId(chainId);
c1.setId(c.getId()); c1.setName(c.getName()); c1.setEntityInfo(c.getEntityInfo());