public int pdbend = 0;\r
public int seqstart = 0;\r
public int seqend = 0;\r
+ public int [] seqMapping;\r
\r
//public DrawableSequence ds;\r
public PDBChain(String id) {\r
return tmp;\r
}\r
\r
- public void makeCaBondList() {\r
- for (int i = 0; i < (residues.size() - 1); i++) {\r
+ public void makeCaBondList()\r
+ {\r
+ for (int i = 0; i < (residues.size() - 1); i++)\r
+ {\r
Residue tmpres = (Residue) residues.elementAt(i);\r
Residue tmpres2 = (Residue) residues.elementAt(i + 1);\r
Atom at1 = tmpres.findAtom("CA");\r
Atom at2 = tmpres2.findAtom("CA");\r
\r
- if ((at1 != null) && (at2 != null)) {\r
- if (at1.chain.equals(at2.chain)) {\r
+ if ((at1 != null) && (at2 != null))\r
+ {\r
+ if (at1.chain.equals(at2.chain))\r
+ {\r
makeBond(at1, at2);\r
}\r
}\r
\r
public void makeResidueList() {\r
int count = 0;\r
- String seq = "";\r
+ StringBuffer seq = new StringBuffer();\r
\r
- for (int i = 0; i < atoms.size(); i++) {\r
+ int i, iSize = atoms.size()-1;\r
+ for (i = 0; i < iSize; i++)\r
+ {\r
Atom tmp = (Atom) atoms.elementAt(i);\r
- //String resName = tmp.resName;\r
int resNumber = tmp.resNumber;\r
int res = resNumber;\r
\r
Atom tmpat = (Atom) tmpres.atoms.elementAt(0);\r
\r
// Keep totting up the sequence\r
- if (ResidueProperties.getAA3Hash().get(tmpat.resName) == null) {\r
- System.err.println("PDBReader:Null aa3Hash for " +\r
- tmpat.resName);\r
+ if (ResidueProperties.getAA3Hash().get(tmpat.resName) == null)\r
+ {\r
+ seq.append("X") ;\r
+ // System.err.println("PDBReader:Null aa3Hash for " +\r
+ // tmpat.resName);\r
} else {\r
- String tmpres2 = ResidueProperties.aa[((Integer) ResidueProperties.getAA3Hash()\r
- .get(tmpat.resName)).intValue()];\r
- seq = seq + tmpres2;\r
+\r
+ seq.append(ResidueProperties.aa[((Integer) ResidueProperties.getAA3Hash()\r
+ .get(tmpat.resName)).intValue()]);\r
}\r
}\r
\r
if(id.length()<1 || id.equals(" "))\r
id = "_";\r
\r
- sequence = new Sequence(id, seq, 1, seq.length());\r
- // System.out.println("PDB Sequence is :\nSequence = " + seq);\r
+ sequence = new Sequence(id, seq.toString(), 1, seq.length());\r
+ // System.out.println("PDB Sequence is :\nSequence = " + seq);\r
// System.out.println("No of residues = " + residues.size());\r
}\r
\r