owl/trunk/benchmarkGraphAlgorithm.java

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

import proteinstructure.Graph;
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) 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, chainCode, PDB_DB, conn);
                                        int length = pdb.get_length();
                                        int atoms = pdb.getNumAtoms();

                                        // get graph
                                        long start = System.currentTimeMillis();
                                        Graph 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 (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:	254
Committed:	Thu Aug 9 13:28:02 2007 UTC (17 years, 1 month ago) by duarte
File size:	3421 byte(s)
Log Message:	Also writing graph to file
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	254	import proteinstructure.Graph;
7	duarte	253	import proteinstructure.Pdb;
8			import proteinstructure.PdbChainCodeNotFoundError;
9			import proteinstructure.PdbCodeNotFoundError;
10			import proteinstructure.PdbaseInconsistencyError;
11			import proteinstructure.PdbasePdb;
12			import tools.MySQLConnection;
13
14
15			public class benchmarkGraphAlgorithm {
16			/------------------------------ constants ------------------------------/
17
18			// database with a list of pdb codes and chain codes to process
19			public static String DB_NAME = "pdb_reps";
20			public static String DB_TABLE = "reps";
21			public static String DB_COL_PDB = "accession_code";
22			public static String DB_COL_CHAIN = "chain_pdb_code";
23
24			public static String PDB_DB = "pdbase_test";
25			public static String DB_HOST = "white";
26			public static String DB_USER = getUserName();
27			public static String DB_PWD = "nieve";
28
29			public static String PDB_CODE = "1tdr";
30			public static String CHAIN_CODE = "B";
31			public static double cutoff = 4.2;
32			public static String edgeType = "ALL";
33
34			/---------------------------- private methods --------------------------/
35			/**
36			* Get user name from operating system (for use as database username).
37			* */
38			private static String getUserName() {
39			String user = null;
40			user = System.getProperty("user.name");
41			if(user == null) {
42			System.err.println("Could not get user name from operating system.");
43			}
44			return user;
45			}
46
47	duarte	254	public static void main(String[] args) throws IOException {
48	duarte	253	MySQLConnection conn = null;
49			String pdbCode, chainCode;
50			int numPdbs = 0;
51
52			// read command line parameters
53
54			// read structures from database
55			try{
56			conn = new MySQLConnection(DB_HOST, DB_USER, DB_PWD);
57			} catch (Exception e) {
58			System.err.println("Error opening database connection");
59			}
60			String query = "SELECT DISTINCT " + DB_COL_PDB + "," + DB_COL_CHAIN + " FROM " + DB_NAME + "." + DB_TABLE + " LIMIT 1000;" ;
61			Statement stmt;
62			try {
63			stmt = conn.createStatement();
64			ResultSet rs = stmt.executeQuery(query);
65			while(rs.next()) {
66			pdbCode = rs.getString(1);
67			chainCode = rs.getString(2);
68
69			if(chainCode == null) {
70			chainCode = "NULL";
71			}
72
73			numPdbs++;
74			// get graphs
75
76			Pdb pdb = null;
77			try {
78			pdb = new PdbasePdb(pdbCode, chainCode, PDB_DB, conn);
79			int length = pdb.get_length();
80			int atoms = pdb.getNumAtoms();
81	duarte	254
82			// get graph
83			long start = System.currentTimeMillis();
84			Graph graph = pdb.get_graph(edgeType, cutoff);
85			long end = System.currentTimeMillis();
86
87			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	253	} catch (PdbaseInconsistencyError e) {
96			System.out.println("Inconsistency in " + pdbCode + chainCode);
97			} catch (PdbCodeNotFoundError e) {
98			e.printStackTrace();
99			} catch (SQLException e) {
100			e.printStackTrace();
101			} catch (PdbChainCodeNotFoundError e) {
102			e.printStackTrace();
103			}
104
105
106
107
108
109			}
110			System.out.println();
111
112			} catch (SQLException e) {
113			e.printStackTrace();
114			}
115
116			// output results
117			System.out.println("Number of structures: " + numPdbs);
118
119
120			}
121
122			}