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.Pdb;
import proteinstructure.PdbChainCodeNotFoundError;
import proteinstructure.PdbCodeNotFoundError;
import proteinstructure.PdbaseInconsistencyError;
import proteinstructure.PdbasePdb;
import proteinstructure.PdbfileFormatError;
import proteinstructure.PdbfilePdb;
import proteinstructure.RIGraph;
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
                                        RIGraph 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);
                                }
                                RIGraph 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:	424
Committed:	Fri Nov 23 14:21:33 2007 UTC (16 years, 11 months ago) by duarte
Original Path:	*branches/aglappe-jung/genGraph.java*
File size:	6774 byte(s)
Log Message:	Added last i/o method from old Graph (write to file in Ioannis network format) Using now the more correct degree, indegree, outdegree methods instead of count neighbor methods Fixed the write_graph_to_file method name in executables in default package
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			import proteinstructure.Pdb;
10			import proteinstructure.PdbChainCodeNotFoundError;
11			import proteinstructure.PdbCodeNotFoundError;
12			import proteinstructure.PdbaseInconsistencyError;
13			import proteinstructure.PdbasePdb;
14			import proteinstructure.PdbfileFormatError;
15			import proteinstructure.PdbfilePdb;
16	duarte	420	import proteinstructure.RIGraph;
17	duarte	277	import tools.MySQLConnection;
18
19
20			public class genGraph {
21			/------------------------------ constants ------------------------------/
22
23			public static final String PDB_DB = "pdbase";
24			public static final String DB_HOST = "white";
25			public static final String DB_USER = getUserName();
26			public static final String DB_PWD = "nieve";
27			public static final String DSSP_EXE = "/project/StruPPi/bin/dssp";
28			public static final String DSSP_PARAMS = "--";
29	filippis	396	public static final String NACCESS_EXE = "/project/StruPPi/bin/naccess";
30			public static final String NACCESS_PARAMS = "";
31	duarte	277
32			//public static double cutoff = 4.2;
33			//public static String edgeType = "ALL";
34
35			/---------------------------- private methods --------------------------/
36			/**
37			* Get user name from operating system (for use as database username).
38			* */
39			private static String getUserName() {
40			String user = null;
41			user = System.getProperty("user.name");
42			if(user == null) {
43			System.err.println("Could not get user name from operating system.");
44			}
45			return user;
46			}
47
48			public static void main(String[] args) throws IOException {
49
50
51			String help = "Usage, 3 options:\n" +
52			"1) genGraph -i <listfile> -d <distance_cutoff> -t <contact_type> -o <output_dir> [-D <pdbase_db>] \n" +
53			"2) genGraph -p <pdb_code> -c <chain_pdb_code> -d <distance_cutoff> -t <contact_type> -o <output_dir> [-D <pdbase_db>] \n" +
54			"3) genGraph -f <pdbfile> -c <chain_pdb_code> -d <distance_cutoff> -t <contact_type> -o <output_dir> \n" +
55			"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" +
56			"If pdbase_db not specified, the default pdbase will be used\n";
57
58			String listfile = "";
59			String[] pdbCodes = null;
60			String[] pdbChainCodes = null;
61			String pdbfile = "";
62			String pdbaseDb = PDB_DB;
63			String edgeType = "";
64			double cutoff = 0.0;
65			String outputDir = "";
66
67			Getopt g = new Getopt("genGraph", args, "i:p:c:f:d:t:o:D:h?");
68			int c;
69			while ((c = g.getopt()) != -1) {
70			switch(c){
71			case 'i':
72			listfile = g.getOptarg();
73			break;
74			case 'p':
75			pdbCodes = g.getOptarg().split(",");
76			break;
77			case 'c':
78			pdbChainCodes = g.getOptarg().split(",");
79			break;
80			case 'f':
81			pdbfile = g.getOptarg();
82			break;
83			case 'd':
84			cutoff = Double.valueOf(g.getOptarg());
85			break;
86			case 't':
87			edgeType = g.getOptarg();
88			break;
89			case 'o':
90			outputDir = g.getOptarg();
91			break;
92			case 'D':
93			pdbaseDb = g.getOptarg();
94			break;
95			case 'h':
96			case '?':
97			System.out.println(help);
98			System.exit(0);
99			break; // getopt() already printed an error
100			}
101			}
102
103			if (outputDir.equals("") \|\| edgeType.equals("") \|\| cutoff==0.0) {
104			System.err.println("Some missing option");
105			System.err.println(help);
106			System.exit(1);
107			}
108			if (listfile.equals("") && pdbCodes==null && pdbfile.equals("")){
109			System.err.println("Either a listfile, some pdb codes/chain codes or a pdbfile must be given");
110			System.err.println(help);
111			System.exit(1);
112			}
113			if ((!listfile.equals("") && pdbCodes!=null) \|\| (!listfile.equals("") && !pdbfile.equals("")) \|\| (pdbCodes!=null && !pdbfile.equals(""))) {
114			System.err.println("Options -p/-c, -i and -f/-c are exclusive. Use only one of them");
115			System.err.println(help);
116			System.exit(1);
117			}
118
119
120			MySQLConnection conn = null;
121
122			try{
123			conn = new MySQLConnection(DB_HOST, DB_USER, DB_PWD);
124			} catch (Exception e) {
125			System.err.println("Error opening database connection. Exiting");
126			System.exit(1);
127			}
128
129
130			if (pdbfile.equals("")){
131
132			if (!listfile.equals("")) {
133			BufferedReader fpdb = new BufferedReader(new FileReader(listfile));
134			String line = "";
135			int numLines = 0;
136			fpdb.mark(100000);
137			while ((line = fpdb.readLine() ) != null ) {
138	duarte	285	if (line.length()>0) numLines++;
139	duarte	277	}
140			fpdb.reset();
141			pdbCodes = new String[numLines];
142			pdbChainCodes = new String[numLines];
143			numLines = 0;
144			while ((line = fpdb.readLine() ) != null ) {
145	duarte	285	pdbCodes[numLines] = line.split("\\s+")[0].toLowerCase();
146			pdbChainCodes[numLines] = line.split("\\s+")[1];
147	duarte	277	numLines++;
148			}
149			}
150
151			int numPdbs = 0;
152
153			for (int i=0;i<pdbCodes.length;i++) {
154			String pdbCode = pdbCodes[i];
155			String pdbChainCode = pdbChainCodes[i];
156
157			try {
158	duarte	285
159			long start = System.currentTimeMillis();
160
161	duarte	277	Pdb pdb = new PdbasePdb(pdbCode, pdbChainCode, pdbaseDb, conn);
162
163			// get graph
164	duarte	420	RIGraph graph = pdb.get_graph(edgeType, cutoff);
165	duarte	277
166			File outputFile = new File(outputDir,pdbCode+"_"+pdbChainCode+"_"+edgeType+"_"+cutoff+".graph");
167	duarte	424	graph.write_graph_to_file(outputFile.getAbsolutePath());
168	duarte	277
169	duarte	285	long end = System.currentTimeMillis();
170			double time = (double) (end -start)/1000;
171
172	duarte	277	System.out.println("Wrote "+outputFile.getAbsolutePath());
173	duarte	285	System.out.printf("%5.3f s\n",time);
174
175	duarte	277	numPdbs++;
176
177			} catch (PdbaseInconsistencyError e) {
178			System.err.println("Inconsistency in " + pdbCode + pdbChainCode);
179			} catch (PdbCodeNotFoundError e) {
180			System.err.println("Couldn't find pdb code "+pdbCode);
181			} catch (SQLException e) {
182	duarte	285	System.err.println("SQL error for structure "+pdbCode+"_"+pdbChainCode+", error: "+e.getMessage());
183	duarte	277	} catch (PdbChainCodeNotFoundError e) {
184			System.err.println("Couldn't find pdb chain code "+pdbChainCode+" for pdb code "+pdbCode);
185			}
186
187			}
188
189			// output results
190			System.out.println("Number of structures done successfully: " + numPdbs);
191
192
193			} else {
194			String pdbChainCode = pdbChainCodes[0];
195			try {
196			Pdb pdb = new PdbfilePdb(pdbfile,pdbChainCode);
197			if (!pdb.hasSecondaryStructure()) {
198			pdb.runDssp(DSSP_EXE, DSSP_PARAMS);
199			}
200	duarte	420	RIGraph graph = pdb.get_graph(edgeType, cutoff);
201	duarte	277
202			File outputFile = new File(outputDir,pdb.getPdbCode()+"_"+pdbChainCode+"_"+edgeType+"_"+cutoff+".graph");
203	duarte	424	graph.write_graph_to_file(outputFile.getAbsolutePath());
204	duarte	277	System.out.println("Wrote graph file "+outputFile.getAbsolutePath()+" from pdb file "+pdbfile);
205
206			} catch (PdbfileFormatError e) {
207			System.err.println("pdb file "+pdbfile+" doesn't have right format");
208			} catch (PdbChainCodeNotFoundError e) {
209			System.err.println("chain code "+pdbChainCode+" wasn't found in file "+pdbfile);
210			}
211			}
212			}
213
214			}