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duarte |
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import java.io.File; |
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import proteinstructure.Pdb; |
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import proteinstructure.PdbfilePdb; |
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import proteinstructure.Residue; |
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/** |
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* Executable class to check the chirality of amino acids of a given PDB file |
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* @author duarte |
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* |
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*/ |
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public class checkChirality { |
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public static void main(String[] args) throws Exception { |
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if (args.length==0) { |
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System.err.println("Usage: checkChirality <pdb_file_name>"); |
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System.exit(1); |
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} |
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File file = new File(args[0]); |
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Pdb pdb = new PdbfilePdb(file.getAbsolutePath()); |
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String[] chains = pdb.getChains(); |
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for (String chain:chains) { |
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System.out.println("Chain "+chain+". D-form residues:"); |
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pdb.load(chain); |
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int dcount=0; |
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int lcount=0; |
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int ucount=0; |
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for (int resser:pdb.getAllSortedResSerials()) { |
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Residue res = pdb.getResidue(resser); |
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Residue.Chirality chir = res.getChirality(); |
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if (chir == Residue.Chirality.D) { |
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//System.out.println(res+" "+chir.getAbbrev()); |
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dcount++; |
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} else if (chir == Residue.Chirality.L) { |
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lcount++; |
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} else if (chir == Residue.Chirality.U) { |
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ucount++; |
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} |
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} |
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System.out.println("L-form: "+lcount+" D-form: "+dcount+" Undetermined: "+ucount); |
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} |
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} |
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} |
