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); }
start = ResidueNumber.fromString(matcher.group(2)); start.setChainName(chain); end = ResidueNumber.fromString(matcher.group(4)); end.setChainName(chain);
/** 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; }
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)); }
g.setResidueNumber(ResidueNumber.fromString(epolseq.getNum()));