owl/trunk/calculateGridDensity.java

import java.sql.*;
import java.util.*;
import proteinstructure.*;
import tools.MySQLConnection;


public class calculateGridDensity {

        /*------------------------------ 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";
        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 = 4.0;
        public static String                    edgeType = "Ca";
        
        /*---------------------------- 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;
        }
        
        private static void calcDensity(String pdbCode, String chainCode, double cutoff, String egdeType, MySQLConnection conn, Map<Integer, Integer> densityCount) {
                Pdb pdb = null;
                try {
                        pdb = new PdbasePdb(pdbCode, chainCode, PDB_DB, conn);
                        // add to density count vector
                        pdb.calcGridDensity(edgeType, cutoff, densityCount);
                        
                } 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();
                }
                        
        }
        
        public static void printValues(Map<Integer, Integer> v) {
                int atoms = 0;
                for(int size:v.keySet()) {
                        System.out.println(size + ": " + v.get(size));
                        atoms += size*v.get(size);
                }
                System.out.println("Atoms: " + atoms);
        }
        
        public static void main(String[] args) {
                MySQLConnection conn = null;
                Map<Integer, Integer> densityCount = new TreeMap<Integer,Integer>();            
                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 + ";" ;
                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++;
                                // calculate statistics
                                calcDensity(pdbCode, chainCode, cutoff, edgeType, conn, densityCount); // will add to densityCount
                                System.out.print(".");
                                
                                // for each protein write to db: pdb, chain, num_res, volume, max_density
                        }
                        System.out.println();
                        
                } catch (SQLException e) {
                        e.printStackTrace();
                }
                
                // output results
                System.out.println("Number of structures: " + numPdbs);
                printValues(densityCount);

        }

}
Revision:	250
Committed:	Mon Aug 6 14:48:37 2007 UTC (17 years, 1 month ago) by stehr
File size:	3357 byte(s)
Log Message:	added application to count grid density, suppressed warning for secondary structure reassignment
Line	File contents
1	import java.sql.*;
2	import java.util.*;
3	import proteinstructure.*;
4	import tools.MySQLConnection;
5
6
7	public class calculateGridDensity {
8
9	/------------------------------ constants ------------------------------/
10
11	// database with a list of pdb codes and chain codes to process
12	public static String DB_NAME = "pdb_reps";
13	public static String DB_TABLE = "reps";
14	public static String DB_COL_PDB = "accession_code";
15	public static String DB_COL_CHAIN = "chain_pdb_code";
16
17	public static String PDB_DB = "pdbase";
18	public static String DB_HOST = "white";
19	public static String DB_USER = getUserName();
20	public static String DB_PWD = "nieve";
21
22	public static String PDB_CODE = "1tdr";
23	public static String CHAIN_CODE = "B";
24	public static double cutoff = 4.0;
25	public static String edgeType = "Ca";
26
27	/---------------------------- private methods --------------------------/
28	/**
29	* Get user name from operating system (for use as database username).
30	* */
31	private static String getUserName() {
32	String user = null;
33	user = System.getProperty("user.name");
34	if(user == null) {
35	System.err.println("Could not get user name from operating system.");
36	}
37	return user;
38	}
39
40	private static void calcDensity(String pdbCode, String chainCode, double cutoff, String egdeType, MySQLConnection conn, Map<Integer, Integer> densityCount) {
41	Pdb pdb = null;
42	try {
43	pdb = new PdbasePdb(pdbCode, chainCode, PDB_DB, conn);
44	// add to density count vector
45	pdb.calcGridDensity(edgeType, cutoff, densityCount);
46
47	} catch (PdbaseInconsistencyError e) {
48	System.out.println("Inconsistency in " + pdbCode + chainCode);
49	} catch (PdbCodeNotFoundError e) {
50	e.printStackTrace();
51	} catch (SQLException e) {
52	e.printStackTrace();
53	} catch (PdbChainCodeNotFoundError e) {
54	e.printStackTrace();
55	}
56
57	}
58
59	public static void printValues(Map<Integer, Integer> v) {
60	int atoms = 0;
61	for(int size:v.keySet()) {
62	System.out.println(size + ": " + v.get(size));
63	atoms += size*v.get(size);
64	}
65	System.out.println("Atoms: " + atoms);
66	}
67
68	public static void main(String[] args) {
69	MySQLConnection conn = null;
70	Map<Integer, Integer> densityCount = new TreeMap<Integer,Integer>();
71	String pdbCode, chainCode;
72	int numPdbs = 0;
73
74	// read command line parameters
75
76	// read structures from database
77	try{
78	conn = new MySQLConnection(DB_HOST, DB_USER, DB_PWD);
79	} catch (Exception e) {
80	System.err.println("Error opening database connection");
81	}
82	String query = "SELECT DISTINCT " + DB_COL_PDB + "," + DB_COL_CHAIN + " FROM " + DB_NAME + "." + DB_TABLE + ";" ;
83	Statement stmt;
84	try {
85	stmt = conn.createStatement();
86	ResultSet rs = stmt.executeQuery(query);
87	while(rs.next()) {
88	pdbCode = rs.getString(1);
89	chainCode = rs.getString(2);
90
91	if(chainCode == null) {
92	chainCode = "NULL";
93	}
94
95	numPdbs++;
96	// calculate statistics
97	calcDensity(pdbCode, chainCode, cutoff, edgeType, conn, densityCount); // will add to densityCount
98	System.out.print(".");
99
100	// for each protein write to db: pdb, chain, num_res, volume, max_density
101	}
102	System.out.println();
103
104	} catch (SQLException e) {
105	e.printStackTrace();
106	}
107
108	// output results
109	System.out.println("Number of structures: " + numPdbs);
110	printValues(densityCount);
111
112	}
113
114	}