owl/trunk/benchmarkGraphAlgorithm.java

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

import proteinstructure.RIGraph;
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();
                                        RIGraph graph = pdb.get_graph(edgeType, cutoff);
                                        long end = System.currentTimeMillis();

                                        graph.writeToFile(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:	420
Committed:	Thu Nov 22 17:27:44 2007 UTC (16 years, 11 months ago) by duarte
Original Path:	*branches/aglappe-jung/benchmarkGraphAlgorithm.java*
File size:	3417 byte(s)
Log Message:	First implementation of the new graph framework using JUNG2. Still a few classes to fix, but all basic functionality is there. NOTE: at the moment ProtStructGraph is a SparseGraph which doesn't guarantee that the graph has no parallel or loop edges (I thought that would be solved by using the SimpleGraph interface but it doesn't, that's only a marker interface)
Line	File contents
1	import java.io.IOException;
2	import java.sql.ResultSet;
3	import java.sql.SQLException;
4	import java.sql.Statement;
5
6	import proteinstructure.RIGraph;
7	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	public static void main(String[] args) throws IOException {
48	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
82	// get graph
83	long start = System.currentTimeMillis();
84	RIGraph graph = pdb.get_graph(edgeType, cutoff);
85	long end = System.currentTimeMillis();
86
87	graph.writeToFile(pdbCode+chainCode+"_"+edgeType+"_"+cutoff);
88
89	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	} 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	}