public void setChainId(String chainId){ if ( resNum == null) resNum = new ResidueNumber(); resNum.setChainName(chainId); }
public ResidueRange(String chainName, String start, String end) { this.chainName = chainName; this.start = ResidueNumber.fromString(start); this.start.setChainName(chainName); this.end = ResidueNumber.fromString(end); this.end.setChainName(chainName); }
/** * {@inheritDoc} */ @Override public void setChain(Chain chain) { this.parent = chain; //TODO: setChain(), getChainName() and ResidueNumber.set/getChainName() are //duplicating functionality at present and could give different values. if (residueNumber != null) { residueNumber.setChainName(chain.getName()); } }
start.setChainName(chain); end.setChainName(chain);
residueNumber.setChainName(chainId); residueNumber.setSeqNum(resNum); residueNumber.setInsCode(insCode);
public static StructureGroup fromXML(Node n) { String chainID = getAttribute(n, "chainID"); String pdbName = getAttribute(n, "pdbName"); String insCode = getAttribute(n, "insCode"); String resN = getAttribute(n, "residueNr"); String isAminoAcid = getAttribute(n,"isAminoAcid"); ResidueNumber resNum = new ResidueNumber(); resNum.setChainName(chainID); if ( ( insCode != null) && (! insCode.equals("null")) && insCode.length() == 1) resNum.setInsCode(insCode.charAt(0)); resNum.setSeqNum(Integer.parseInt(resN)); StructureGroup g = new StructureGroup(resNum, pdbName, Boolean.valueOf(isAminoAcid)); return g; }
/** get the position of PDB residue nr X in the ato marray * * @param pdbresnum pdbresidue number * @param authId chain name * @param atoms atom array * @return */ private static int getPositionForPDBresunm(String pdbresnum, String authId , Atom[] atoms){ ResidueNumber residueNumber = ResidueNumber.fromString(pdbresnum); residueNumber.setChainName(authId); boolean blankChain = authId == null || authId.equalsIgnoreCase("null") || authId.equals("_"); for ( int i =0; i< atoms.length ;i++){ Group g = atoms[i].getGroup(); // match _ to any chain if( blankChain ) { residueNumber.setChainName(g.getChain().getName()); } //System.out.println(g.getResidueNumber() + "< ? >" + residueNumber +"<"); if ( g.getResidueNumber().equals(residueNumber)){ //System.out.println(g + " == " + residueNumber ); Chain c = g.getChain(); if ( blankChain || c.getName().equals(authId)){ return i; } } } return -1; }
resNum.setChainName(num.getChainId()); resNum.setSeqNum(num.getResidueNumber()); resNum.setInsCode(num.getInsCode());
start.setChainName(chain); end.setChainName(chain);
chainName = polyChain.getName(); if(pdbresnum1 != null) pdbresnum1.setChainName(chainName); if(pdbresnum2 != null) pdbresnum2.setChainName(chainName); chainName = polyChain.getName(); if(pdbresnum1 != null) pdbresnum1.setChainName(chainName); if(pdbresnum2 != null) pdbresnum2.setChainName(chainName); logger.warn("No chain found for {}. Interpretting it as an index, using chain {} instead",chainName,polyChain.getId()); } catch(NumberFormatException e3) {