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import java.io.IOException; |
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import java.sql.ResultSet; |
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import java.sql.SQLException; |
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import java.sql.Statement; |
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|
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import proteinstructure.PdbLoadError; |
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import proteinstructure.RIGraph; |
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import proteinstructure.Pdb; |
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import proteinstructure.PdbCodeNotFoundError; |
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import proteinstructure.PdbasePdb; |
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import tools.MySQLConnection; |
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public class benchmarkGraphAlgorithm { |
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/*------------------------------ constants ------------------------------*/ |
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|
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// database with a list of pdb codes and chain codes to process |
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public static String DB_NAME = "pdb_reps"; |
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public static String DB_TABLE = "reps"; |
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public static String DB_COL_PDB = "accession_code"; |
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public static String DB_COL_CHAIN = "chain_pdb_code"; |
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|
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public static String PDB_DB = "pdbase_test"; |
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public static String DB_HOST = "white"; |
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public static String DB_USER = getUserName(); |
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public static String DB_PWD = "nieve"; |
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|
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public static String PDB_CODE = "1tdr"; |
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public static String CHAIN_CODE = "B"; |
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public static double cutoff = 4.2; |
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public static String edgeType = "ALL"; |
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|
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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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|
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public static void main(String[] args) throws IOException { |
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MySQLConnection conn = null; |
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String pdbCode, chainCode; |
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int numPdbs = 0; |
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|
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// read command line parameters |
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|
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// read structures from database |
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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"); |
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} |
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String query = "SELECT DISTINCT " + DB_COL_PDB + "," + DB_COL_CHAIN + " FROM " + DB_NAME + "." + DB_TABLE + " LIMIT 1000;" ; |
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Statement stmt; |
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try { |
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stmt = conn.createStatement(); |
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ResultSet rs = stmt.executeQuery(query); |
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while(rs.next()) { |
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pdbCode = rs.getString(1); |
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chainCode = rs.getString(2); |
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|
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if(chainCode == null) { |
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chainCode = "NULL"; |
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} |
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|
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numPdbs++; |
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// get graphs |
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|
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Pdb pdb = null; |
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try { |
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pdb = new PdbasePdb(pdbCode, PDB_DB, conn); |
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pdb.load(chainCode); |
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int length = pdb.get_length(); |
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int atoms = pdb.getNumAtoms(); |
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|
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// get graph |
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long start = System.currentTimeMillis(); |
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RIGraph graph = pdb.get_graph(edgeType, cutoff); |
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long end = System.currentTimeMillis(); |
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|
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graph.write_graph_to_file(pdbCode+chainCode+"_"+edgeType+"_"+cutoff); |
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|
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System.out.print(pdbCode+"_"+chainCode); |
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System.out.print("\t"+length+"\t"+atoms); |
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System.out.printf("\t%4.3f",(double) (end-start)/1000); |
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System.out.println(); |
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|
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|
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} catch (PdbLoadError e) { |
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System.out.println("pdb load error in " + pdbCode + chainCode+", specific error: "+e.getMessage()); |
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} catch (PdbCodeNotFoundError e) { |
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e.printStackTrace(); |
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} catch (SQLException e) { |
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e.printStackTrace(); |
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} |
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|
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} |
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System.out.println(); |
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|
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} catch (SQLException e) { |
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e.printStackTrace(); |
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} |
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|
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// output results |
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System.out.println("Number of structures: " + numPdbs); |
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|
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|
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} |
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|
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} |
