owl/trunk/benchmarkGraphAlgorithm.java

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

import proteinstructure.PdbLoadError;
import proteinstructure.RIGraph;
import proteinstructure.Pdb;
import proteinstructure.PdbCodeNotFoundError;
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) throws IOException {
                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, PDB_DB, conn);
                                        pdb.load(chainCode);
                                        int length = pdb.get_length();
                                        int atoms = pdb.getNumAtoms();

                                        // get graph
                                        long start = System.currentTimeMillis();
                                        RIGraph graph = pdb.get_graph(edgeType, cutoff);
                                        long end = System.currentTimeMillis();

                                        graph.write_graph_to_file(pdbCode+chainCode+"_"+edgeType+"_"+cutoff);
                                        
                                        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 (PdbLoadError e) {
                                        System.out.println("pdb load error in " + pdbCode + chainCode+", specific error: "+e.getMessage());
                                } catch (PdbCodeNotFoundError e) {
                                        e.printStackTrace();
                                } catch (SQLException e) {
                                        e.printStackTrace();
                                }                                       
                                
                                
                        }
                        System.out.println();
                        
                } catch (SQLException e) {
                        e.printStackTrace();
                }
                
                // output results
                System.out.println("Number of structures: " + numPdbs);


        }

}
Revision:	492
Committed:	Wed Jan 2 13:18:57 2008 UTC (16 years, 8 months ago) by duarte
File size:	3331 byte(s)
Log Message:	Copied the aglappe-jung branch into trunk.
Line	User	Rev	File contents
1	duarte	254	import java.io.IOException;
2	duarte	253	import java.sql.ResultSet;
3			import java.sql.SQLException;
4			import java.sql.Statement;
5
6	duarte	441	import proteinstructure.PdbLoadError;
7	duarte	420	import proteinstructure.RIGraph;
8	duarte	253	import proteinstructure.Pdb;
9			import proteinstructure.PdbCodeNotFoundError;
10			import proteinstructure.PdbasePdb;
11			import tools.MySQLConnection;
12
13
14			public class benchmarkGraphAlgorithm {
15			/------------------------------ constants ------------------------------/
16
17			// database with a list of pdb codes and chain codes to process
18			public static String DB_NAME = "pdb_reps";
19			public static String DB_TABLE = "reps";
20			public static String DB_COL_PDB = "accession_code";
21			public static String DB_COL_CHAIN = "chain_pdb_code";
22
23			public static String PDB_DB = "pdbase_test";
24			public static String DB_HOST = "white";
25			public static String DB_USER = getUserName();
26			public static String DB_PWD = "nieve";
27
28			public static String PDB_CODE = "1tdr";
29			public static String CHAIN_CODE = "B";
30			public static double cutoff = 4.2;
31			public static String edgeType = "ALL";
32
33			/---------------------------- private methods --------------------------/
34			/**
35			* Get user name from operating system (for use as database username).
36			* */
37			private static String getUserName() {
38			String user = null;
39			user = System.getProperty("user.name");
40			if(user == null) {
41			System.err.println("Could not get user name from operating system.");
42			}
43			return user;
44			}
45
46	duarte	254	public static void main(String[] args) throws IOException {
47	duarte	253	MySQLConnection conn = null;
48			String pdbCode, chainCode;
49			int numPdbs = 0;
50
51			// read command line parameters
52
53			// read structures from database
54			try{
55			conn = new MySQLConnection(DB_HOST, DB_USER, DB_PWD);
56			} catch (Exception e) {
57			System.err.println("Error opening database connection");
58			}
59			String query = "SELECT DISTINCT " + DB_COL_PDB + "," + DB_COL_CHAIN + " FROM " + DB_NAME + "." + DB_TABLE + " LIMIT 1000;" ;
60			Statement stmt;
61			try {
62			stmt = conn.createStatement();
63			ResultSet rs = stmt.executeQuery(query);
64			while(rs.next()) {
65			pdbCode = rs.getString(1);
66			chainCode = rs.getString(2);
67
68			if(chainCode == null) {
69			chainCode = "NULL";
70			}
71
72			numPdbs++;
73			// get graphs
74
75			Pdb pdb = null;
76			try {
77	duarte	441	pdb = new PdbasePdb(pdbCode, PDB_DB, conn);
78			pdb.load(chainCode);
79	duarte	253	int length = pdb.get_length();
80			int atoms = pdb.getNumAtoms();
81	duarte	254
82			// get graph
83			long start = System.currentTimeMillis();
84	duarte	420	RIGraph graph = pdb.get_graph(edgeType, cutoff);
85	duarte	254	long end = System.currentTimeMillis();
86
87	duarte	424	graph.write_graph_to_file(pdbCode+chainCode+"_"+edgeType+"_"+cutoff);
88	duarte	253
89	duarte	254	System.out.print(pdbCode+"_"+chainCode);
90			System.out.print("\t"+length+"\t"+atoms);
91			System.out.printf("\t%4.3f",(double) (end-start)/1000);
92			System.out.println();
93
94
95	duarte	441	} catch (PdbLoadError e) {
96			System.out.println("pdb load error in " + pdbCode + chainCode+", specific error: "+e.getMessage());
97	duarte	253	} catch (PdbCodeNotFoundError e) {
98			e.printStackTrace();
99			} catch (SQLException e) {
100			e.printStackTrace();
101	duarte	441	}
102	duarte	253
103
104
105
106			}
107			System.out.println();
108
109			} catch (SQLException e) {
110			e.printStackTrace();
111			}
112
113			// output results
114			System.out.println("Number of structures: " + numPdbs);
115
116
117			}
118
119			}