owl/trunk/genGraph.java

import gnu.getopt.Getopt;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.sql.SQLException;


import proteinstructure.Graph;
import proteinstructure.Pdb;
import proteinstructure.PdbChainCodeNotFoundError;
import proteinstructure.PdbCodeNotFoundError;
import proteinstructure.PdbaseInconsistencyError;
import proteinstructure.PdbasePdb;
import proteinstructure.PdbfileFormatError;
import proteinstructure.PdbfilePdb;
import tools.MySQLConnection;


public class genGraph {
        /*------------------------------ constants ------------------------------*/
        
        public static final String                      PDB_DB = "pdbase";
        public static final String                      DB_HOST = "white";                                                              
        public static final String                      DB_USER = getUserName();
        public static final String                      DB_PWD = "nieve";
        public static final String                      DSSP_EXE = "/project/StruPPi/bin/dssp";
        public static final String                      DSSP_PARAMS = "--";
        public static final String                      NACCESS_EXE = "/project/StruPPi/bin/naccess";
        public static final String                      NACCESS_PARAMS = "";

        //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 {
                
                
                String help = "Usage, 3 options:\n" +
                                "1)  genGraph -i <listfile> -d <distance_cutoff> -t <contact_type> -o <output_dir> [-D <pdbase_db>] \n" +
                                "2)  genGraph -p <pdb_code> -c <chain_pdb_code> -d <distance_cutoff> -t <contact_type> -o <output_dir> [-D <pdbase_db>] \n" +
                                "3)  genGraph -f <pdbfile> -c <chain_pdb_code> -d <distance_cutoff> -t <contact_type> -o <output_dir> \n" +
                                "In case 2) also a list of comma separated pdb codes and chain codes can be specified, e.g. -p 1bxy,1jos -c A,A\n" +
                                "If pdbase_db not specified, the default pdbase will be used\n"; 

                String listfile = "";
                String[] pdbCodes = null;
                String[] pdbChainCodes = null;
                String pdbfile = "";
                String pdbaseDb = PDB_DB;
                String edgeType = "";
                double cutoff = 0.0;
                String outputDir = "";
                
                Getopt g = new Getopt("genGraph", args, "i:p:c:f:d:t:o:D:h?");
                int c;
                while ((c = g.getopt()) != -1) {
                        switch(c){
                        case 'i':
                                listfile = g.getOptarg();
                                break;
                        case 'p':
                                pdbCodes = g.getOptarg().split(",");
                                break;
                        case 'c':
                                pdbChainCodes = g.getOptarg().split(",");
                                break;
                        case 'f':
                                pdbfile = g.getOptarg();
                                break;
                        case 'd':
                                cutoff = Double.valueOf(g.getOptarg());
                                break;
                        case 't':
                                edgeType = g.getOptarg();
                                break;
                        case 'o':
                                outputDir = g.getOptarg();
                                break;
                        case 'D':
                                pdbaseDb = g.getOptarg();
                                break;
                        case 'h':
                        case '?':
                                System.out.println(help);
                                System.exit(0);
                                break; // getopt() already printed an error
                        }
                }

                if (outputDir.equals("") || edgeType.equals("") || cutoff==0.0) {
                        System.err.println("Some missing option");
                        System.err.println(help);
                        System.exit(1);
                }
                if (listfile.equals("") && pdbCodes==null && pdbfile.equals("")){
                        System.err.println("Either a listfile, some pdb codes/chain codes or a pdbfile must be given");
                        System.err.println(help);
                        System.exit(1);
                }
                if ((!listfile.equals("") && pdbCodes!=null) || (!listfile.equals("") && !pdbfile.equals("")) || (pdbCodes!=null && !pdbfile.equals(""))) {
                        System.err.println("Options -p/-c, -i and -f/-c are exclusive. Use only one of them");
                        System.err.println(help);
                        System.exit(1);                 
                }

                
                MySQLConnection conn = null;            

                try{
                        conn = new MySQLConnection(DB_HOST, DB_USER, DB_PWD);
                } catch (Exception e) {
                        System.err.println("Error opening database connection. Exiting");
                        System.exit(1);
                }
                
                
                if (pdbfile.equals("")){
                        
                        if (!listfile.equals("")) {                     
                                BufferedReader fpdb = new BufferedReader(new FileReader(listfile));
                                String line = "";
                                int numLines = 0;
                                fpdb.mark(100000);
                                while ((line = fpdb.readLine() ) != null ) {
                                        if (line.length()>0) numLines++;
                                }
                                fpdb.reset();
                                pdbCodes = new String[numLines];
                                pdbChainCodes = new String[numLines];
                                numLines = 0;
                                while ((line = fpdb.readLine() ) != null ) {
                                        pdbCodes[numLines] = line.split("\\s+")[0].toLowerCase();
                                        pdbChainCodes[numLines] = line.split("\\s+")[1];
                                        numLines++;
                                }
                        }

                        int numPdbs = 0;

                        for (int i=0;i<pdbCodes.length;i++) {
                                String pdbCode = pdbCodes[i];
                                String pdbChainCode = pdbChainCodes[i];

                                try {
                                        
                                        long start = System.currentTimeMillis();
                                        
                                        Pdb pdb = new PdbasePdb(pdbCode, pdbChainCode, pdbaseDb, conn);

                                        // get graph
                                        Graph graph = pdb.get_graph(edgeType, cutoff);

                                        File outputFile = new File(outputDir,pdbCode+"_"+pdbChainCode+"_"+edgeType+"_"+cutoff+".graph");
                                        graph.write_graph_to_file(outputFile.getAbsolutePath());

                                        long end = System.currentTimeMillis();
                                        double time = (double) (end -start)/1000;

                                        System.out.println("Wrote "+outputFile.getAbsolutePath());
                                        System.out.printf("%5.3f s\n",time);
                                        
                                        numPdbs++;

                                } catch (PdbaseInconsistencyError e) {
                                        System.err.println("Inconsistency in " + pdbCode + pdbChainCode);
                                } catch (PdbCodeNotFoundError e) {
                                        System.err.println("Couldn't find pdb code "+pdbCode);
                                } catch (SQLException e) {
                                        System.err.println("SQL error for structure "+pdbCode+"_"+pdbChainCode+", error: "+e.getMessage());
                                } catch (PdbChainCodeNotFoundError e) {
                                        System.err.println("Couldn't find pdb chain code "+pdbChainCode+" for pdb code "+pdbCode);
                                }

                        }

                        // output results
                        System.out.println("Number of structures done successfully: " + numPdbs);


                } else {
                        String pdbChainCode = pdbChainCodes[0];
                        try {
                                Pdb pdb = new PdbfilePdb(pdbfile,pdbChainCode);
                                if (!pdb.hasSecondaryStructure()) {
                                        pdb.runDssp(DSSP_EXE, DSSP_PARAMS);
                                }
                                Graph graph = pdb.get_graph(edgeType, cutoff);

                                File outputFile = new File(outputDir,pdb.getPdbCode()+"_"+pdbChainCode+"_"+edgeType+"_"+cutoff+".graph");
                                graph.write_graph_to_file(outputFile.getAbsolutePath());
                                System.out.println("Wrote graph file "+outputFile.getAbsolutePath()+" from pdb file "+pdbfile);
                                
                        } catch (PdbfileFormatError e) {
                                System.err.println("pdb file "+pdbfile+" doesn't have right format");
                        } catch (PdbChainCodeNotFoundError e) {
                                System.err.println("chain code "+pdbChainCode+" wasn't found in file "+pdbfile);        
                        }
                }
        }

}
Revision:	419
Committed:	Thu Nov 22 14:09:18 2007 UTC (16 years, 10 months ago) by duarte
Original Path:	*branches/aglappe-jung/genGraph.java*
File size:	6769 byte(s)
Log Message:	Re-branching for JUNG2 development
Line	User	Rev	File contents
1	duarte	277	import gnu.getopt.Getopt;
2
3			import java.io.BufferedReader;
4			import java.io.File;
5			import java.io.FileReader;
6			import java.io.IOException;
7			import java.sql.SQLException;
8
9
10			import proteinstructure.Graph;
11			import proteinstructure.Pdb;
12			import proteinstructure.PdbChainCodeNotFoundError;
13			import proteinstructure.PdbCodeNotFoundError;
14			import proteinstructure.PdbaseInconsistencyError;
15			import proteinstructure.PdbasePdb;
16			import proteinstructure.PdbfileFormatError;
17			import proteinstructure.PdbfilePdb;
18			import tools.MySQLConnection;
19
20
21			public class genGraph {
22			/------------------------------ constants ------------------------------/
23
24			public static final String PDB_DB = "pdbase";
25			public static final String DB_HOST = "white";
26			public static final String DB_USER = getUserName();
27			public static final String DB_PWD = "nieve";
28			public static final String DSSP_EXE = "/project/StruPPi/bin/dssp";
29			public static final String DSSP_PARAMS = "--";
30	filippis	396	public static final String NACCESS_EXE = "/project/StruPPi/bin/naccess";
31			public static final String NACCESS_PARAMS = "";
32	duarte	277
33			//public static double cutoff = 4.2;
34			//public static String edgeType = "ALL";
35
36			/---------------------------- private methods --------------------------/
37			/**
38			* Get user name from operating system (for use as database username).
39			* */
40			private static String getUserName() {
41			String user = null;
42			user = System.getProperty("user.name");
43			if(user == null) {
44			System.err.println("Could not get user name from operating system.");
45			}
46			return user;
47			}
48
49			public static void main(String[] args) throws IOException {
50
51
52			String help = "Usage, 3 options:\n" +
53			"1) genGraph -i <listfile> -d <distance_cutoff> -t <contact_type> -o <output_dir> [-D <pdbase_db>] \n" +
54			"2) genGraph -p <pdb_code> -c <chain_pdb_code> -d <distance_cutoff> -t <contact_type> -o <output_dir> [-D <pdbase_db>] \n" +
55			"3) genGraph -f <pdbfile> -c <chain_pdb_code> -d <distance_cutoff> -t <contact_type> -o <output_dir> \n" +
56			"In case 2) also a list of comma separated pdb codes and chain codes can be specified, e.g. -p 1bxy,1jos -c A,A\n" +
57			"If pdbase_db not specified, the default pdbase will be used\n";
58
59			String listfile = "";
60			String[] pdbCodes = null;
61			String[] pdbChainCodes = null;
62			String pdbfile = "";
63			String pdbaseDb = PDB_DB;
64			String edgeType = "";
65			double cutoff = 0.0;
66			String outputDir = "";
67
68			Getopt g = new Getopt("genGraph", args, "i:p:c:f:d:t:o:D:h?");
69			int c;
70			while ((c = g.getopt()) != -1) {
71			switch(c){
72			case 'i':
73			listfile = g.getOptarg();
74			break;
75			case 'p':
76			pdbCodes = g.getOptarg().split(",");
77			break;
78			case 'c':
79			pdbChainCodes = g.getOptarg().split(",");
80			break;
81			case 'f':
82			pdbfile = g.getOptarg();
83			break;
84			case 'd':
85			cutoff = Double.valueOf(g.getOptarg());
86			break;
87			case 't':
88			edgeType = g.getOptarg();
89			break;
90			case 'o':
91			outputDir = g.getOptarg();
92			break;
93			case 'D':
94			pdbaseDb = g.getOptarg();
95			break;
96			case 'h':
97			case '?':
98			System.out.println(help);
99			System.exit(0);
100			break; // getopt() already printed an error
101			}
102			}
103
104			if (outputDir.equals("") \|\| edgeType.equals("") \|\| cutoff==0.0) {
105			System.err.println("Some missing option");
106			System.err.println(help);
107			System.exit(1);
108			}
109			if (listfile.equals("") && pdbCodes==null && pdbfile.equals("")){
110			System.err.println("Either a listfile, some pdb codes/chain codes or a pdbfile must be given");
111			System.err.println(help);
112			System.exit(1);
113			}
114			if ((!listfile.equals("") && pdbCodes!=null) \|\| (!listfile.equals("") && !pdbfile.equals("")) \|\| (pdbCodes!=null && !pdbfile.equals(""))) {
115			System.err.println("Options -p/-c, -i and -f/-c are exclusive. Use only one of them");
116			System.err.println(help);
117			System.exit(1);
118			}
119
120
121			MySQLConnection conn = null;
122
123			try{
124			conn = new MySQLConnection(DB_HOST, DB_USER, DB_PWD);
125			} catch (Exception e) {
126			System.err.println("Error opening database connection. Exiting");
127			System.exit(1);
128			}
129
130
131			if (pdbfile.equals("")){
132
133			if (!listfile.equals("")) {
134			BufferedReader fpdb = new BufferedReader(new FileReader(listfile));
135			String line = "";
136			int numLines = 0;
137			fpdb.mark(100000);
138			while ((line = fpdb.readLine() ) != null ) {
139	duarte	285	if (line.length()>0) numLines++;
140	duarte	277	}
141			fpdb.reset();
142			pdbCodes = new String[numLines];
143			pdbChainCodes = new String[numLines];
144			numLines = 0;
145			while ((line = fpdb.readLine() ) != null ) {
146	duarte	285	pdbCodes[numLines] = line.split("\\s+")[0].toLowerCase();
147			pdbChainCodes[numLines] = line.split("\\s+")[1];
148	duarte	277	numLines++;
149			}
150			}
151
152			int numPdbs = 0;
153
154			for (int i=0;i<pdbCodes.length;i++) {
155			String pdbCode = pdbCodes[i];
156			String pdbChainCode = pdbChainCodes[i];
157
158			try {
159	duarte	285
160			long start = System.currentTimeMillis();
161
162	duarte	277	Pdb pdb = new PdbasePdb(pdbCode, pdbChainCode, pdbaseDb, conn);
163
164			// get graph
165			Graph graph = pdb.get_graph(edgeType, cutoff);
166
167			File outputFile = new File(outputDir,pdbCode+"_"+pdbChainCode+"_"+edgeType+"_"+cutoff+".graph");
168			graph.write_graph_to_file(outputFile.getAbsolutePath());
169
170	duarte	285	long end = System.currentTimeMillis();
171			double time = (double) (end -start)/1000;
172
173	duarte	277	System.out.println("Wrote "+outputFile.getAbsolutePath());
174	duarte	285	System.out.printf("%5.3f s\n",time);
175
176	duarte	277	numPdbs++;
177
178			} catch (PdbaseInconsistencyError e) {
179			System.err.println("Inconsistency in " + pdbCode + pdbChainCode);
180			} catch (PdbCodeNotFoundError e) {
181			System.err.println("Couldn't find pdb code "+pdbCode);
182			} catch (SQLException e) {
183	duarte	285	System.err.println("SQL error for structure "+pdbCode+"_"+pdbChainCode+", error: "+e.getMessage());
184	duarte	277	} catch (PdbChainCodeNotFoundError e) {
185			System.err.println("Couldn't find pdb chain code "+pdbChainCode+" for pdb code "+pdbCode);
186			}
187
188			}
189
190			// output results
191			System.out.println("Number of structures done successfully: " + numPdbs);
192
193
194			} else {
195			String pdbChainCode = pdbChainCodes[0];
196			try {
197			Pdb pdb = new PdbfilePdb(pdbfile,pdbChainCode);
198			if (!pdb.hasSecondaryStructure()) {
199			pdb.runDssp(DSSP_EXE, DSSP_PARAMS);
200			}
201			Graph graph = pdb.get_graph(edgeType, cutoff);
202
203			File outputFile = new File(outputDir,pdb.getPdbCode()+"_"+pdbChainCode+"_"+edgeType+"_"+cutoff+".graph");
204			graph.write_graph_to_file(outputFile.getAbsolutePath());
205			System.out.println("Wrote graph file "+outputFile.getAbsolutePath()+" from pdb file "+pdbfile);
206
207			} catch (PdbfileFormatError e) {
208			System.err.println("pdb file "+pdbfile+" doesn't have right format");
209			} catch (PdbChainCodeNotFoundError e) {
210			System.err.println("chain code "+pdbChainCode+" wasn't found in file "+pdbfile);
211			}
212			}
213			}
214
215			}