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import gnu.getopt.Getopt; |
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import java.io.BufferedReader; |
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import java.io.File; |
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import java.io.FileReader; |
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import java.io.IOException; |
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import java.sql.SQLException; |
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import proteinstructure.Graph; |
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import proteinstructure.Pdb; |
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import proteinstructure.PdbChainCodeNotFoundError; |
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import proteinstructure.PdbCodeNotFoundError; |
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import proteinstructure.PdbaseInconsistencyError; |
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import proteinstructure.PdbasePdb; |
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import proteinstructure.PdbfileFormatError; |
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import proteinstructure.PdbfilePdb; |
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import tools.MySQLConnection; |
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public class genGraph { |
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/*------------------------------ constants ------------------------------*/ |
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public static final String PDB_DB = "pdbase"; |
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public static final String DB_HOST = "white"; |
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public static final String DB_USER = getUserName(); |
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public static final String DB_PWD = "nieve"; |
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public static final String DSSP_EXE = "/project/StruPPi/bin/dssp"; |
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public static final String DSSP_PARAMS = "--"; |
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public static final String NACCESS_EXE = "/project/StruPPi/bin/naccess"; |
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public static final String NACCESS_PARAMS = ""; |
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//public static double cutoff = 4.2; |
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//public static String edgeType = "ALL"; |
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/*---------------------------- private methods --------------------------*/ |
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/** |
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* Get user name from operating system (for use as database username). |
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* */ |
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private static String getUserName() { |
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String user = null; |
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user = System.getProperty("user.name"); |
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if(user == null) { |
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System.err.println("Could not get user name from operating system."); |
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} |
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return user; |
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} |
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public static void main(String[] args) throws IOException { |
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String help = "Usage, 3 options:\n" + |
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"1) genGraph -i <listfile> -d <distance_cutoff> -t <contact_type> -o <output_dir> [-D <pdbase_db>] \n" + |
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"2) genGraph -p <pdb_code> -c <chain_pdb_code> -d <distance_cutoff> -t <contact_type> -o <output_dir> [-D <pdbase_db>] \n" + |
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"3) genGraph -f <pdbfile> -c <chain_pdb_code> -d <distance_cutoff> -t <contact_type> -o <output_dir> \n" + |
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"In case 2) also a list of comma separated pdb codes and chain codes can be specified, e.g. -p 1bxy,1jos -c A,A\n" + |
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"If pdbase_db not specified, the default pdbase will be used\n"; |
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String listfile = ""; |
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String[] pdbCodes = null; |
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String[] pdbChainCodes = null; |
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String pdbfile = ""; |
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String pdbaseDb = PDB_DB; |
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String edgeType = ""; |
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double cutoff = 0.0; |
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String outputDir = ""; |
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Getopt g = new Getopt("genGraph", args, "i:p:c:f:d:t:o:D:h?"); |
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int c; |
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while ((c = g.getopt()) != -1) { |
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switch(c){ |
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case 'i': |
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listfile = g.getOptarg(); |
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break; |
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case 'p': |
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pdbCodes = g.getOptarg().split(","); |
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break; |
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case 'c': |
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pdbChainCodes = g.getOptarg().split(","); |
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break; |
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case 'f': |
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pdbfile = g.getOptarg(); |
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break; |
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case 'd': |
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cutoff = Double.valueOf(g.getOptarg()); |
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break; |
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case 't': |
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edgeType = g.getOptarg(); |
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break; |
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case 'o': |
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outputDir = g.getOptarg(); |
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break; |
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case 'D': |
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pdbaseDb = g.getOptarg(); |
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break; |
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case 'h': |
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case '?': |
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System.out.println(help); |
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System.exit(0); |
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break; // getopt() already printed an error |
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} |
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} |
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if (outputDir.equals("") || edgeType.equals("") || cutoff==0.0) { |
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System.err.println("Some missing option"); |
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System.err.println(help); |
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System.exit(1); |
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} |
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if (listfile.equals("") && pdbCodes==null && pdbfile.equals("")){ |
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System.err.println("Either a listfile, some pdb codes/chain codes or a pdbfile must be given"); |
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System.err.println(help); |
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System.exit(1); |
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} |
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if ((!listfile.equals("") && pdbCodes!=null) || (!listfile.equals("") && !pdbfile.equals("")) || (pdbCodes!=null && !pdbfile.equals(""))) { |
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System.err.println("Options -p/-c, -i and -f/-c are exclusive. Use only one of them"); |
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System.err.println(help); |
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System.exit(1); |
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} |
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MySQLConnection conn = null; |
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try{ |
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conn = new MySQLConnection(DB_HOST, DB_USER, DB_PWD); |
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} catch (Exception e) { |
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System.err.println("Error opening database connection. Exiting"); |
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System.exit(1); |
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} |
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if (pdbfile.equals("")){ |
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if (!listfile.equals("")) { |
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BufferedReader fpdb = new BufferedReader(new FileReader(listfile)); |
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String line = ""; |
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int numLines = 0; |
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fpdb.mark(100000); |
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while ((line = fpdb.readLine() ) != null ) { |
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if (line.length()>0) numLines++; |
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} |
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fpdb.reset(); |
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pdbCodes = new String[numLines]; |
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pdbChainCodes = new String[numLines]; |
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numLines = 0; |
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while ((line = fpdb.readLine() ) != null ) { |
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pdbCodes[numLines] = line.split("\\s+")[0].toLowerCase(); |
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pdbChainCodes[numLines] = line.split("\\s+")[1]; |
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numLines++; |
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} |
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} |
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int numPdbs = 0; |
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for (int i=0;i<pdbCodes.length;i++) { |
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String pdbCode = pdbCodes[i]; |
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String pdbChainCode = pdbChainCodes[i]; |
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try { |
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long start = System.currentTimeMillis(); |
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Pdb pdb = new PdbasePdb(pdbCode, pdbChainCode, pdbaseDb, conn); |
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// get graph |
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Graph graph = pdb.get_graph(edgeType, cutoff); |
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File outputFile = new File(outputDir,pdbCode+"_"+pdbChainCode+"_"+edgeType+"_"+cutoff+".graph"); |
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graph.write_graph_to_file(outputFile.getAbsolutePath()); |
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long end = System.currentTimeMillis(); |
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double time = (double) (end -start)/1000; |
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System.out.println("Wrote "+outputFile.getAbsolutePath()); |
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System.out.printf("%5.3f s\n",time); |
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numPdbs++; |
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} catch (PdbaseInconsistencyError e) { |
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System.err.println("Inconsistency in " + pdbCode + pdbChainCode); |
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} catch (PdbCodeNotFoundError e) { |
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System.err.println("Couldn't find pdb code "+pdbCode); |
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} catch (SQLException e) { |
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System.err.println("SQL error for structure "+pdbCode+"_"+pdbChainCode+", error: "+e.getMessage()); |
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} catch (PdbChainCodeNotFoundError e) { |
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System.err.println("Couldn't find pdb chain code "+pdbChainCode+" for pdb code "+pdbCode); |
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} |
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} |
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// output results |
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System.out.println("Number of structures done successfully: " + numPdbs); |
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} else { |
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String pdbChainCode = pdbChainCodes[0]; |
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try { |
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Pdb pdb = new PdbfilePdb(pdbfile,pdbChainCode); |
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if (!pdb.hasSecondaryStructure()) { |
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pdb.runDssp(DSSP_EXE, DSSP_PARAMS); |
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} |
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Graph graph = pdb.get_graph(edgeType, cutoff); |
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File outputFile = new File(outputDir,pdb.getPdbCode()+"_"+pdbChainCode+"_"+edgeType+"_"+cutoff+".graph"); |
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graph.write_graph_to_file(outputFile.getAbsolutePath()); |
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System.out.println("Wrote graph file "+outputFile.getAbsolutePath()+" from pdb file "+pdbfile); |
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} catch (PdbfileFormatError e) { |
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System.err.println("pdb file "+pdbfile+" doesn't have right format"); |
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} catch (PdbChainCodeNotFoundError e) { |
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System.err.println("chain code "+pdbChainCode+" wasn't found in file "+pdbfile); |
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} |
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} |
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} |
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} |