public String printFull() { final String chain = chainName==null? "" : chainName; return chain + "_" + toString(); }
/** * {@inheritDoc} * */ @Override public Group getGroupByPDB(ResidueNumber resNum) throws StructureException { String pdbresnum = resNum.toString(); if ( pdbResnumMap.containsKey(pdbresnum)) { Integer pos = pdbResnumMap.get(pdbresnum); return groups.get(pos); } else { throw new StructureException("unknown PDB residue number " + pdbresnum + " in chain " + authId); } }
if ( g1 != null){ aa3 = g1.getPDBName(); res1 = g1.getResidueNumber().toString(); Chain ch1 = g1.getChain(); if (ch1 != null)
for (ResidueNumber residueNumber : linkedGroups) { String pdbCode = residueNumber.toString(); String chain = residueNumber.getChainName();
ResidueNumber resNum = group.getResidueNumber(); if ( resNum != null) pdbResnum = resNum.toString(); if ( pdbResnum != null) { Integer pos = groups.size() - 1;
private void getPdbRegions(Atom[] ca1, Atom[] ca2){ pdbresnum1 = new String[idx1.length]; pdbresnum2 = new String[idx2.length]; for (int i =0 ; i < idx1.length;i++){ Atom a1 = ca1[idx1[i]]; Atom a2 = ca2[idx2[i]]; Group p1 = a1.getGroup(); Group p2 = a2.getGroup(); Chain c1 = p1.getChain(); Chain c2 = p2.getChain(); String cid1 = c1.getId(); String cid2 = c2.getId(); String pdb1 = p1.getResidueNumber().toString(); String pdb2 = p2.getResidueNumber().toString(); if ( ! cid1.equals(" ")) pdb1 += ":" + cid1; if ( ! cid2.equals(" ")) pdb2 += ":" + cid2; pdbresnum1[i] = pdb1; pdbresnum2[i] = pdb2; } }
private static CharSequence getPDBPos(Atom atom) { Group g = atom.getGroup(); if ( g!= null){ Chain c = g.getChain(); if (c != null){ return g.getResidueNumber().toString()+":" + c.getName() ; //return g.getPDBCode()+":" + c.getName() + "." + getOneLetter(g) ; } } return "!"; }
String pdbcode = g.getResidueNumber().toString();
String rnum = g.getResidueNumber().toString();
Atom atom2 = ca2[ optAln[block][1][i] ]; pairs.append(atom1.getGroup().getResidueNumber().toString()); pairs.append('\t'); pairs.append(atom1.getGroup().getChain().getName()); pairs.append(atom1.getGroup().getPDBName()); pairs.append('\t'); pairs.append(atom2.getGroup().getResidueNumber().toString()); pairs.append('\t'); pairs.append(atom2.getGroup().getChain().getName());
.toString()); residueGroup.append('\t'); residueGroup.append(atom.getGroup().getChain()
ResidueNumber rn2 = ca2[res2].getGroup().getResidueNumber(); String node1 = name1+rn1.getChainName()+rn1.toString(); String node2 = name2+rn2.getChainName()+rn2.toString(); String last = name1+rn.getChainName()+rn.toString(); for(int i=1;i<ca1.length;i++) { rn = ca1[i].getGroup().getResidueNumber(); String curr = name1+rn.getChainName()+rn.toString(); out.write(String.format("%s\t%s\t%s\n",last, backboneInteraction, curr)); last = curr; !ca1[0].getGroup().getResidueNumber().equals(ca2[0].getGroup().getResidueNumber()) ) ) { rn = ca2[0].getGroup().getResidueNumber(); last = name2+rn.getChainName()+rn.toString(); for(int i=1;i<ca2.length;i++) { rn = ca2[i].getGroup().getResidueNumber(); String curr = name2+rn.getChainName()+rn.toString(); out.write(String.format("%s\t%s\t%s\n",last, backboneInteraction, curr)); last = curr;
g.getResidueNumber().toString(), toModel) != null; } catch (StructureException e) {
public static void printXMLEQRInferPositions(PrettyXMLWriter xml, AFPChain afpChain, int bk, Atom[] ca1, Atom[] ca2) throws IOException{ int[] optLen = afpChain.getOptLen(); if ( optLen == null) return; int[][][] optAln = afpChain.getOptAln(); for ( int pos=0;pos< optLen[bk];pos++){ int pos1 = optAln[bk][0][pos]; int pos2 = optAln[bk][1][pos]; xml.openTag("eqr"); xml.attribute("eqrNr", String.valueOf(pos)); xml.attribute("pdbres1",ca1[pos1].getGroup().getResidueNumber().toString()); xml.attribute("chain1", ca1[pos1].getGroup().getChain().getName()); xml.attribute("pdbres2",ca2[pos2].getGroup().getResidueNumber().toString()); xml.attribute("chain2", ca2[pos2].getGroup().getChain().getName()); xml.closeTag("eqr"); //System.out.println("aligned position: " + pos1 + ":" + pos2 + //" pdbresnum " + ca1[pos1].getGroup().getResidueNumber().toString() + " " + //ca1[pos1].getParent().getPDBName()+":" + //ca2[pos2].getGroup().getResidueNumber().toString() + " " + ca2[pos2].getParent().getPDBName()); } }
g.getResidueNumber().toString(), g.getChain().getStructure().getPDBCode() ); continue;
String rnum = g.getResidueNumber().toString();
xw.attribute("name",gr.getPDBName()); xw.attribute("type",gr.getType().toString()); xw.attribute("groupID",gr.getResidueNumber().toString());