owl/trunk/benchmarkGraphAlgorithm.java

import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;

import proteinstructure.Pdb;
import proteinstructure.PdbChainCodeNotFoundError;
import proteinstructure.PdbCodeNotFoundError;
import proteinstructure.PdbaseInconsistencyError;
import proteinstructure.PdbasePdb;
import tools.MySQLConnection;


public class benchmarkGraphAlgorithm {
        /*------------------------------ constants ------------------------------*/
        
        // database with a list of pdb codes and chain codes to process
        public static String                    DB_NAME = "pdb_reps";
        public static String                    DB_TABLE = "reps";
        public static String                    DB_COL_PDB = "accession_code";
        public static String                    DB_COL_CHAIN = "chain_pdb_code";        
        
        public static String                    PDB_DB = "pdbase_test";
        public static String                    DB_HOST = "white";                                                              
        public static String                    DB_USER = getUserName();
        public static String                    DB_PWD = "nieve";

        public static String                    PDB_CODE = "1tdr";
        public static String                    CHAIN_CODE = "B";
        public static double                    cutoff = 4.2;
        public static String                    edgeType = "ALL";
        
        /*---------------------------- private methods --------------------------*/
        /** 
         * Get user name from operating system (for use as database username). 
         * */
        private static String getUserName() {
                String user = null;
                user = System.getProperty("user.name");
                if(user == null) {
                        System.err.println("Could not get user name from operating system.");
                }
                return user;
        }
        
        public static void main(String[] args) {
                MySQLConnection conn = null;            
                String pdbCode, chainCode;
                int numPdbs = 0;
                
                // read command line parameters
                
                // read structures from database
                try{
                        conn = new MySQLConnection(DB_HOST, DB_USER, DB_PWD);
                } catch (Exception e) {
                        System.err.println("Error opening database connection");
                }
                String query = "SELECT DISTINCT " + DB_COL_PDB + "," + DB_COL_CHAIN + " FROM " + DB_NAME + "." + DB_TABLE + " LIMIT 1000;" ;
                Statement stmt;
                try {
                        stmt = conn.createStatement();
                        ResultSet rs = stmt.executeQuery(query);
                        while(rs.next()) {
                                pdbCode = rs.getString(1);
                                chainCode = rs.getString(2);
                                
                                if(chainCode == null) {
                                        chainCode = "NULL";
                                }
                                
                                numPdbs++;
                                // get graphs
                        
                                Pdb pdb = null;
                                try {
                                        pdb = new PdbasePdb(pdbCode, chainCode, PDB_DB, conn);
                                        int length = pdb.get_length();
                                        int atoms = pdb.getNumAtoms();
                                        if (atoms>3000) {
                                                // get graph
                                                long start = System.currentTimeMillis();
                                                pdb.get_graph(edgeType, cutoff);
                                                long end = System.currentTimeMillis();
                                                
                                                System.out.print(pdbCode+"_"+chainCode);
                                                System.out.print("\t"+length+"\t"+atoms);
                                                System.out.printf("\t%4.3f",(double) (end-start)/1000);
                                                System.out.println();
                                        }
                                        
                                } catch (PdbaseInconsistencyError e) {
                                        System.out.println("Inconsistency in " + pdbCode + chainCode);
                                } catch (PdbCodeNotFoundError e) {
                                        e.printStackTrace();
                                } catch (SQLException e) {
                                        e.printStackTrace();
                                } catch (PdbChainCodeNotFoundError e) {
                                        e.printStackTrace();
                                }
                                        
                                
                        }
                        System.out.println();
                        
                } catch (SQLException e) {
                        e.printStackTrace();
                }
                
                // output results
                System.out.println("Number of structures: " + numPdbs);


        }

}
Revision:	253
Committed:	Thu Aug 9 13:24:12 2007 UTC (17 years, 1 month ago) by duarte
File size:	3290 byte(s)
Log Message:	Initial commit. Script to benchmark the graph generation algorithm
Line	User	Rev	File contents
1	duarte	253	import java.sql.ResultSet;
2			import java.sql.SQLException;
3			import java.sql.Statement;
4
5			import proteinstructure.Pdb;
6			import proteinstructure.PdbChainCodeNotFoundError;
7			import proteinstructure.PdbCodeNotFoundError;
8			import proteinstructure.PdbaseInconsistencyError;
9			import proteinstructure.PdbasePdb;
10			import tools.MySQLConnection;
11
12
13			public class benchmarkGraphAlgorithm {
14			/------------------------------ constants ------------------------------/
15
16			// database with a list of pdb codes and chain codes to process
17			public static String DB_NAME = "pdb_reps";
18			public static String DB_TABLE = "reps";
19			public static String DB_COL_PDB = "accession_code";
20			public static String DB_COL_CHAIN = "chain_pdb_code";
21
22			public static String PDB_DB = "pdbase_test";
23			public static String DB_HOST = "white";
24			public static String DB_USER = getUserName();
25			public static String DB_PWD = "nieve";
26
27			public static String PDB_CODE = "1tdr";
28			public static String CHAIN_CODE = "B";
29			public static double cutoff = 4.2;
30			public static String edgeType = "ALL";
31
32			/---------------------------- private methods --------------------------/
33			/**
34			* Get user name from operating system (for use as database username).
35			* */
36			private static String getUserName() {
37			String user = null;
38			user = System.getProperty("user.name");
39			if(user == null) {
40			System.err.println("Could not get user name from operating system.");
41			}
42			return user;
43			}
44
45			public static void main(String[] args) {
46			MySQLConnection conn = null;
47			String pdbCode, chainCode;
48			int numPdbs = 0;
49
50			// read command line parameters
51
52			// read structures from database
53			try{
54			conn = new MySQLConnection(DB_HOST, DB_USER, DB_PWD);
55			} catch (Exception e) {
56			System.err.println("Error opening database connection");
57			}
58			String query = "SELECT DISTINCT " + DB_COL_PDB + "," + DB_COL_CHAIN + " FROM " + DB_NAME + "." + DB_TABLE + " LIMIT 1000;" ;
59			Statement stmt;
60			try {
61			stmt = conn.createStatement();
62			ResultSet rs = stmt.executeQuery(query);
63			while(rs.next()) {
64			pdbCode = rs.getString(1);
65			chainCode = rs.getString(2);
66
67			if(chainCode == null) {
68			chainCode = "NULL";
69			}
70
71			numPdbs++;
72			// get graphs
73
74			Pdb pdb = null;
75			try {
76			pdb = new PdbasePdb(pdbCode, chainCode, PDB_DB, conn);
77			int length = pdb.get_length();
78			int atoms = pdb.getNumAtoms();
79			if (atoms>3000) {
80			// get graph
81			long start = System.currentTimeMillis();
82			pdb.get_graph(edgeType, cutoff);
83			long end = System.currentTimeMillis();
84
85			System.out.print(pdbCode+"_"+chainCode);
86			System.out.print("\t"+length+"\t"+atoms);
87			System.out.printf("\t%4.3f",(double) (end-start)/1000);
88			System.out.println();
89			}
90
91			} catch (PdbaseInconsistencyError e) {
92			System.out.println("Inconsistency in " + pdbCode + chainCode);
93			} catch (PdbCodeNotFoundError e) {
94			e.printStackTrace();
95			} catch (SQLException e) {
96			e.printStackTrace();
97			} catch (PdbChainCodeNotFoundError e) {
98			e.printStackTrace();
99			}
100
101
102
103
104
105			}
106			System.out.println();
107
108			} catch (SQLException e) {
109			e.printStackTrace();
110			}
111
112			// output results
113			System.out.println("Number of structures: " + numPdbs);
114
115
116			}
117
118			}