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, 2 months ago) by stehr
File size:	3357 byte(s)
Log Message:	added application to count grid density, suppressed warning for secondary structure reassignment
Line	User	Rev	File contents
1	stehr	250	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			}