owl/trunk/genDbGraph.java

import gnu.getopt.Getopt;

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


//import proteinstructure.CiffilePdb;
import proteinstructure.PdbLoadError;
import proteinstructure.RIGraph;
import proteinstructure.Pdb;
import proteinstructure.PdbCodeNotFoundError;
import proteinstructure.PdbasePdb;
import proteinstructure.PdbfilePdb;
import proteinstructure.SecStrucElement;
import tools.MySQLConnection;


public class genDbGraph {
        /*------------------------------ 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)  genDbGraph -i <listfile> -d <distance_cutoff> -t <contact_type> [-r directed] -s <seq_sep> -o <output_db> [-D <pdbase_db>] [-m <mode>] \n" +
                                "2)  genDbGraph -p <pdb_code> -c <chain_pdb_code> -d <distance_cutoff> -t <contact_type> [-r directed] -s <seq_sep> -o <output_db> [-D <pdbase_db>] [-m <mode>] \n" +
                                "3)  genDbGraph -f <pdbfile> -c <chain_pdb_code> -d <distance_cutoff> -t <contact_type> [-r directed] -s <seq_sep> -o <output_db> [-m <mode>] \n" +
                                "\nA comma separated list of contact types and distance cutoffs can be given instead of just 1, e.g. -d 8.0,8.5 -t Ca,Cb will generate the graphs for Ca at 8.0 and for Cb at 8.5\n" +
                                "If only 1 contact type given and multiple cutoffs, graphs will be generated at all the cutoffs for the one contact type\n"+
                                "\nIn 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" +
                                "\nIf pdbase_db not specified, the default pdbase will be used\n" +
                                "\nSecondary structure will be taken from pdbase database. If reading from pdb file and the pdb file is missing the secondary structure, then it will be assigned using dssp\n"; 

                String listfile = "";
                String[] pdbCodes = null;
                String[] pdbChainCodes = null;
                String pdbfile = "";
                String pdbaseDb = PDB_DB;
                String[] edgeTypes = null;
                double[] cutoffs = null;
                int[] seqseps = null;
                boolean[] directed = null; 
                String outputDb = "";
                String mode = "GRAPH";
                
                Getopt g = new Getopt("genDbGraph", args, "i:p:c:f:d:t:r:s:o:D:m: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':
                                String[] cutoffsStr = g.getOptarg().split(",");
                                cutoffs = new double[cutoffsStr.length];
                                for (int i =0;i<cutoffs.length;i++) {
                                        cutoffs[i] = Double.valueOf(cutoffsStr[i]);
                                }
                                break;
                        case 't':
                                edgeTypes = g.getOptarg().split(",");
                                break;
                        case 'r':
                                String[] directedStr = g.getOptarg().split(",");
                                directed = new boolean[directedStr.length];
                                for (int i =0;i<directed.length;i++) {
                                        directed[i] = Boolean.valueOf(directedStr[i]);
                                }
                                break;                          
                        case 's':
                                String[] seqsepsStr = g.getOptarg().split(",");
                                seqseps = new int[seqsepsStr.length];
                                for (int i=0;i<seqseps.length;i++) {
                                        seqseps[i] = Integer.valueOf(seqsepsStr[i]);
                                }
                                break;
                        case 'o':
                                outputDb = g.getOptarg();
                                break;
                        case 'D':
                                pdbaseDb = g.getOptarg();
                                break;
                        case 'm':
                                mode = g.getOptarg();
                                break;
                        case 'h':
                        case '?':
                                System.out.println(help);
                                System.exit(0);
                                break; // getopt() already printed an error
                        }
                }

                if (directed==null) {
                        // we set by default all directed to false
                        directed = new boolean[edgeTypes.length];
                }
                
                if (outputDb.equals("") || edgeTypes==null || cutoffs==null) {
                        System.err.println("Some missing option\n");
                        System.err.println(help);
                        System.exit(1);
                }
                if (edgeTypes.length!=cutoffs.length && edgeTypes.length!=1) {
                        System.err.println("Not same number of contact types as cutoffs given\n");
                        System.err.println(help);
                        System.exit(1);
                }
                if (seqseps != null && edgeTypes.length!=seqseps.length) {
                        System.err.println("Not same number of contact types as sequence separations given\n");
                        System.err.println(help);
                        System.exit(1);
                }
                if (directed != null && edgeTypes.length!=directed.length) {
                        System.err.println("Not same number of contact types as directionalities given\n");
                        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\n");
                        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\n");
                        System.err.println(help);
                        System.exit(1);                 
                }
                if (!(mode.equals("GRAPH") || mode.equals("PDB") || mode.equals("BOTH"))) {
                        System.err.println("Allowed values for mode:GRAPH,PDB,BOTH.");
                        System.err.println(help);
                        System.exit(1);                 
                }
                
                // setting edgeTypes in case only 1 was given with multiple cutoffs
                if (edgeTypes.length==1 && cutoffs.length>1) {
                        String edgeType = edgeTypes[0];
                        edgeTypes = new String[cutoffs.length];
                        for (int i=0;i<cutoffs.length;i++){
                                edgeTypes[i] = edgeType;
                        }
                }

                
                MySQLConnection conn = null;            

                try{
                        conn = new MySQLConnection(DB_HOST, DB_USER, DB_PWD);
                        conn.setSqlMode("NO_UNSIGNED_SUBTRACTION,TRADITIONAL");
                } 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++;
                                }
                                fpdb.close();
                        }

                        int numPdbs = 0;

                        for (int i=0;i<pdbCodes.length;i++) {
                                String pdbCode = pdbCodes[i];
                                String pdbChainCode = pdbChainCodes[i];
                                
                                boolean dssp = false, scop = false, naccess = false, consurf = false, ec = false, csa = false;
                                int numGraphs = 0;
                                
                                try {
                                        
                                        System.out.println("Getting pdb data for "+pdbCode+"_"+pdbChainCode);
                                        
                                        Pdb pdb = new PdbasePdb(pdbCode, pdbaseDb, conn);       
                                        //Pdb pdb = new CiffilePdb(new File("/project/StruPPi/BiO/DBd/PDB-REMEDIATED/data/structures/unzipped/all/mmCIF/"+pdbCode+".cif"), pdbChainCode);       
                                        pdb.load(pdbChainCode);                                 
                                        try {
                                                pdb.runDssp(DSSP_EXE, DSSP_PARAMS, SecStrucElement.ReducedState.THREESTATE, SecStrucElement.ReducedState.THREESTATE);
                                                //pdb.runDssp(DSSP_EXE, DSSP_PARAMS);
                                                dssp = true;
                                        } catch (Exception e) {
                                                System.err.println(e.getMessage());
                                        }
                                        if (!mode.equals("GRAPH")) {
                                                try {
                                                        pdb.checkScop("1.73", false);
                                                        scop = true;
                                                } catch (Exception e) {
                                                        System.err.println(e.getMessage());
                                                }
                                                try {
                                                        int mistakes = pdb.checkConsurfHssp(false);
                                                        System.out.println("ConsurfHssp Mistakes:"+mistakes);
                                                        if (mistakes == 0) consurf = true;
                                                } catch (Exception e) {
                                                        System.err.println(e.getMessage());
                                                }       
                                                try {
                                                        pdb.checkEC(false);
                                                        ec = true;
                                                } catch (Exception e) {
                                                        System.err.println(e.getMessage());
                                                }
                                                try {
                                                        int mistakes = pdb.checkCSA("2.2.7", false);
                                                        System.out.println("CSA Mistakes:"+mistakes);
                                                        if (mistakes == 0) csa = true;
                                                } catch (Exception e) {
                                                        System.err.println(e.getMessage());
                                                }/*
                                                pdb.restrictToScopDomain("d1pjua2");
                                                try {
                                                        pdb.runDssp(DSSP_EXE, DSSP_PARAMS, SecStrucElement.ReducedState.THREESTATE, SecStrucElement.ReducedState.THREESTATE);
                                                        //pdb.runDssp(DSSP_EXE, DSSP_PARAMS);
                                                        dssp = true;
                                                } catch (Exception e) {
                                                        System.err.println(e.getMessage());
                                                }*/                                     
                                                try {
                                                        pdb.runNaccess(NACCESS_EXE, NACCESS_PARAMS);
                                                        naccess = true;
                                                } catch (Exception e) {
                                                        System.err.println(e.getMessage());
                                                }
                                                
                                                //pdb.writeToDb(conn,outputDb);
                                                pdb.writeToDbFast(conn, outputDb);
                                        }
                                        // get graphs
                                        if (!mode.equals("PDB")) {
                                                for (int j = 0; j<edgeTypes.length; j++) {
                                                        System.out.print("--> "+(directed[j]?"directed":"")+" graph "+edgeTypes[j]+" for cutoff "+cutoffs[j]);
                                                        
                                                        RIGraph graph = pdb.get_graph(edgeTypes[j], cutoffs[j], directed[j]);
                                                        //graph.restrictContactsBetweenSs();
                                                        if (seqseps != null) {
                                                                if (seqseps[j] > 1) {
                                                                        System.out.print(" and sequence separation >= "+seqseps[j]);
                                                                        graph.restrictContactsToMinRange(seqseps[j]);
                                                                }
                                                        }
                                                        //graph.writeToDb(conn,outputDb);
                                                        graph.write_graph_to_db_fast(conn,outputDb);
                                                        
                                                        System.out.println();                                                   
                                                        numPdbs++;
                                                        numGraphs++;
                                                }
                                        }
                                        
                                } catch (PdbLoadError e) {
                                        System.err.println("Error loading pdb data for " + pdbCode + pdbChainCode+", specific error: "+e.getMessage());
                                } 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 (CiffileFormatError e) {
                                        System.err.println(e.getMessage());
                                }*/
                                
                                System.out.println("SUMMARY:"+pdbCode+"_"+pdbChainCode+" dssp:"+dssp+" scop:"+scop+" naccess:"+naccess+" consurf:"+consurf+" ec:"+ec+" csa:"+csa+ " graphs:"+numGraphs);

                        }

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


                } else {
                        String pdbChainCode = pdbChainCodes[0];
                        boolean dssp = false, scop = false, naccess = false, consurf = false, ec = false, csa = false;
                        int numGraphs = 0;
                        
                        try {
                                
                                System.out.println("Getting chain "+pdbChainCode+" from pdb file "+pdbfile);
                                
                                Pdb pdb = new PdbfilePdb(pdbfile);
                                pdb.load(pdbChainCode);
                                if (!pdb.hasSecondaryStructure()) {
                                        pdb.runDssp(DSSP_EXE, DSSP_PARAMS, SecStrucElement.ReducedState.THREESTATE, SecStrucElement.ReducedState.THREESTATE);
                                        //pdb.runDssp(DSSP_EXE, DSSP_PARAMS);
                                }
                                if (!mode.equals("GRAPH")) {
                                        try {
                                                pdb.runDssp(DSSP_EXE, DSSP_PARAMS, SecStrucElement.ReducedState.THREESTATE, SecStrucElement.ReducedState.THREESTATE);
                                                //pdb.runDssp(DSSP_EXE, DSSP_PARAMS);
                                                dssp = true;
                                        } catch (Exception e) {
                                                System.err.println(e.getMessage());
                                        }
                                        try {
                                                pdb.checkScop("1.73", false);
                                                scop = true;
                                        } catch (Exception e) {
                                                System.err.println(e.getMessage());
                                        }
                                        try {
                                                int mistakes = pdb.checkConsurfHssp(false);
                                                System.out.println("ConsurfHssp Mistakes:"+mistakes);
                                                if (mistakes == 0) consurf = true;
                                        } catch (Exception e) {
                                                System.err.println(e.getMessage());
                                        }
                                        try {
                                                pdb.checkEC(false);
                                                ec = true;
                                        } catch (Exception e) {
                                                System.err.println(e.getMessage());
                                        }
                                        try {
                                                int mistakes = pdb.checkCSA("2.2.7", false);
                                                System.out.println("CSA Mistakes:"+mistakes);
                                                if (mistakes == 0) csa = true;
                                        } catch (Exception e) {
                                                System.err.println(e.getMessage());
                                        }
                                        /*pdb.restrictToScopDomain("d1eaka3");
                                        try {
                                                pdb.runDssp(DSSP_EXE, DSSP_PARAMS, SecStrucElement.ReducedState.THREESTATE, SecStrucElement.ReducedState.THREESTATE);
                                                //pdb.runDssp(DSSP_EXE, DSSP_PARAMS);
                                                dssp = true;
                                        } catch (Exception e) {
                                                System.err.println(e.getMessage());
                                        }*/                                     
                                        try {
                                                pdb.runNaccess(NACCESS_EXE, NACCESS_PARAMS);
                                                naccess = true;
                                        } catch (Exception e) {
                                                System.err.println(e.getMessage());
                                        }
                                        
                                        //pdb.writeToDb(conn,outputDb);
                                        pdb.writeToDbFast(conn, outputDb);
                                }
                                
                                // get graphs
                                if (!mode.equals("PDB")) {
                                        for (int j = 0; j<edgeTypes.length; j++) {
                                                System.out.print("--> "+(directed[j]?"directed":"")+" graph "+edgeTypes[j]+" for cutoff "+cutoffs[j]);
                                                
                                                RIGraph graph = pdb.get_graph(edgeTypes[j], cutoffs[j], directed[j]);
                                                //graph.restrictContactsBetweenSs();
                                                if (seqseps != null) {
                                                        if (seqseps[j] > 1) {
                                                                System.out.print(" and sequence separation >= "+seqseps[j]);
                                                                graph.restrictContactsToMinRange(seqseps[j]);
                                                        }
                                                }
                                                //graph.writeToDb(conn,outputDb);
                                                graph.write_graph_to_db_fast(conn,outputDb);
                                                
                                                System.out.println();                                           
                                                numGraphs++;
                                        }
                                }
                                
                        } catch (SQLException e) {
                                System.err.println("Couldn't write graph to db, error: "+e.getMessage());
                        } catch (PdbLoadError e) {
                                System.err.println("Error loading from pdb file "+pdbfile+", specific error: "+e.getMessage());
                        } 
                        
                        System.out.println("SUMMARY:"+pdbfile+"_"+pdbChainCode+" dssp:"+dssp+" scop:"+scop+" naccess:"+naccess+" consurf:"+consurf+" ec:"+ec+" csa:"+csa+ " graphs:"+numGraphs);

                }
                
                // closing db connection
                conn.close();
        }

}
Revision:	514
Committed:	Fri Jan 11 14:59:43 2008 UTC (16 years, 8 months ago) by filippis
File size:	14412 byte(s)
Log Message:	Latest scop and csa versions updated.
Line	User	Rev	File contents
1	duarte	264	import gnu.getopt.Getopt;
2
3			import java.io.BufferedReader;
4			import java.io.FileReader;
5			import java.io.IOException;
6			import java.sql.SQLException;
7
8
9	filippis	398	//import proteinstructure.CiffilePdb;
10	duarte	441	import proteinstructure.PdbLoadError;
11	duarte	420	import proteinstructure.RIGraph;
12	duarte	264	import proteinstructure.Pdb;
13			import proteinstructure.PdbCodeNotFoundError;
14			import proteinstructure.PdbasePdb;
15			import proteinstructure.PdbfilePdb;
16	filippis	412	import proteinstructure.SecStrucElement;
17	duarte	264	import tools.MySQLConnection;
18
19
20			public class genDbGraph {
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	264
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	filippis	438	"1) genDbGraph -i <listfile> -d <distance_cutoff> -t <contact_type> [-r directed] -s <seq_sep> -o <output_db> [-D <pdbase_db>] [-m <mode>] \n" +
53			"2) genDbGraph -p <pdb_code> -c <chain_pdb_code> -d <distance_cutoff> -t <contact_type> [-r directed] -s <seq_sep> -o <output_db> [-D <pdbase_db>] [-m <mode>] \n" +
54			"3) genDbGraph -f <pdbfile> -c <chain_pdb_code> -d <distance_cutoff> -t <contact_type> [-r directed] -s <seq_sep> -o <output_db> [-m <mode>] \n" +
55	duarte	359	"\nA comma separated list of contact types and distance cutoffs can be given instead of just 1, e.g. -d 8.0,8.5 -t Ca,Cb will generate the graphs for Ca at 8.0 and for Cb at 8.5\n" +
56			"If only 1 contact type given and multiple cutoffs, graphs will be generated at all the cutoffs for the one contact type\n"+
57			"\nIn 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" +
58	duarte	358	"\nIf pdbase_db not specified, the default pdbase will be used\n" +
59			"\nSecondary structure will be taken from pdbase database. If reading from pdb file and the pdb file is missing the secondary structure, then it will be assigned using dssp\n";
60	duarte	264
61			String listfile = "";
62			String[] pdbCodes = null;
63			String[] pdbChainCodes = null;
64			String pdbfile = "";
65			String pdbaseDb = PDB_DB;
66	duarte	359	String[] edgeTypes = null;
67			double[] cutoffs = null;
68	filippis	407	int[] seqseps = null;
69	filippis	438	boolean[] directed = null;
70	duarte	264	String outputDb = "";
71	filippis	396	String mode = "GRAPH";
72	duarte	264
73	filippis	438	Getopt g = new Getopt("genDbGraph", args, "i:p:c:f:d:t:r:s:o:D:m:h?");
74	duarte	264	int c;
75			while ((c = g.getopt()) != -1) {
76			switch(c){
77			case 'i':
78			listfile = g.getOptarg();
79			break;
80			case 'p':
81			pdbCodes = g.getOptarg().split(",");
82			break;
83			case 'c':
84			pdbChainCodes = g.getOptarg().split(",");
85			break;
86			case 'f':
87			pdbfile = g.getOptarg();
88			break;
89			case 'd':
90	duarte	359	String[] cutoffsStr = g.getOptarg().split(",");
91			cutoffs = new double[cutoffsStr.length];
92			for (int i =0;i<cutoffs.length;i++) {
93			cutoffs[i] = Double.valueOf(cutoffsStr[i]);
94			}
95	duarte	264	break;
96			case 't':
97	duarte	359	edgeTypes = g.getOptarg().split(",");
98	duarte	264	break;
99	filippis	438	case 'r':
100			String[] directedStr = g.getOptarg().split(",");
101			directed = new boolean[directedStr.length];
102			for (int i =0;i<directed.length;i++) {
103			directed[i] = Boolean.valueOf(directedStr[i]);
104			}
105			break;
106	filippis	407	case 's':
107			String[] seqsepsStr = g.getOptarg().split(",");
108			seqseps = new int[seqsepsStr.length];
109	filippis	503	for (int i=0;i<seqseps.length;i++) {
110	filippis	407	seqseps[i] = Integer.valueOf(seqsepsStr[i]);
111			}
112			break;
113	duarte	264	case 'o':
114			outputDb = g.getOptarg();
115			break;
116			case 'D':
117			pdbaseDb = g.getOptarg();
118			break;
119	filippis	396	case 'm':
120			mode = g.getOptarg();
121	filippis	398	break;
122	duarte	264	case 'h':
123			case '?':
124			System.out.println(help);
125			System.exit(0);
126			break; // getopt() already printed an error
127			}
128			}
129
130	duarte	453	if (directed==null) {
131			// we set by default all directed to false
132			directed = new boolean[edgeTypes.length];
133			}
134
135	duarte	359	if (outputDb.equals("") \|\| edgeTypes==null \|\| cutoffs==null) {
136			System.err.println("Some missing option\n");
137	duarte	264	System.err.println(help);
138			System.exit(1);
139			}
140	duarte	359	if (edgeTypes.length!=cutoffs.length && edgeTypes.length!=1) {
141			System.err.println("Not same number of contact types as cutoffs given\n");
142			System.err.println(help);
143			System.exit(1);
144			}
145	filippis	407	if (seqseps != null && edgeTypes.length!=seqseps.length) {
146			System.err.println("Not same number of contact types as sequence separations given\n");
147			System.err.println(help);
148			System.exit(1);
149			}
150	filippis	438	if (directed != null && edgeTypes.length!=directed.length) {
151			System.err.println("Not same number of contact types as directionalities given\n");
152			System.err.println(help);
153			System.exit(1);
154			}
155	duarte	264	if (listfile.equals("") && pdbCodes==null && pdbfile.equals("")){
156	duarte	359	System.err.println("Either a listfile, some pdb codes/chain codes or a pdbfile must be given\n");
157	duarte	264	System.err.println(help);
158			System.exit(1);
159			}
160			if ((!listfile.equals("") && pdbCodes!=null) \|\| (!listfile.equals("") && !pdbfile.equals("")) \|\| (pdbCodes!=null && !pdbfile.equals(""))) {
161	duarte	359	System.err.println("Options -p/-c, -i and -f/-c are exclusive. Use only one of them\n");
162	duarte	264	System.err.println(help);
163			System.exit(1);
164			}
165	filippis	396	if (!(mode.equals("GRAPH") \|\| mode.equals("PDB") \|\| mode.equals("BOTH"))) {
166			System.err.println("Allowed values for mode:GRAPH,PDB,BOTH.");
167			System.err.println(help);
168			System.exit(1);
169			}
170	duarte	359
171			// setting edgeTypes in case only 1 was given with multiple cutoffs
172			if (edgeTypes.length==1 && cutoffs.length>1) {
173			String edgeType = edgeTypes[0];
174			edgeTypes = new String[cutoffs.length];
175			for (int i=0;i<cutoffs.length;i++){
176			edgeTypes[i] = edgeType;
177			}
178			}
179	duarte	264
180
181			MySQLConnection conn = null;
182
183			try{
184			conn = new MySQLConnection(DB_HOST, DB_USER, DB_PWD);
185	filippis	407	conn.setSqlMode("NO_UNSIGNED_SUBTRACTION,TRADITIONAL");
186	duarte	264	} catch (Exception e) {
187			System.err.println("Error opening database connection. Exiting");
188			System.exit(1);
189			}
190
191
192			if (pdbfile.equals("")){
193
194			if (!listfile.equals("")) {
195			BufferedReader fpdb = new BufferedReader(new FileReader(listfile));
196			String line = "";
197			int numLines = 0;
198			fpdb.mark(100000);
199			while ((line = fpdb.readLine() ) != null ) {
200	duarte	285	if (line.length()>0) numLines++;
201	duarte	264	}
202			fpdb.reset();
203			pdbCodes = new String[numLines];
204			pdbChainCodes = new String[numLines];
205			numLines = 0;
206			while ((line = fpdb.readLine() ) != null ) {
207	duarte	285	pdbCodes[numLines] = line.split("\\s+")[0].toLowerCase();
208			pdbChainCodes[numLines] = line.split("\\s+")[1];
209	duarte	264	numLines++;
210			}
211	duarte	358	fpdb.close();
212	duarte	264	}
213
214			int numPdbs = 0;
215
216			for (int i=0;i<pdbCodes.length;i++) {
217			String pdbCode = pdbCodes[i];
218			String pdbChainCode = pdbChainCodes[i];
219	filippis	412
220			boolean dssp = false, scop = false, naccess = false, consurf = false, ec = false, csa = false;
221			int numGraphs = 0;
222
223	duarte	264	try {
224	filippis	412
225	duarte	359	System.out.println("Getting pdb data for "+pdbCode+"_"+pdbChainCode);
226	duarte	285
227	filippis	503	Pdb pdb = new PdbasePdb(pdbCode, pdbaseDb, conn);
228			//Pdb pdb = new CiffilePdb(new File("/project/StruPPi/BiO/DBd/PDB-REMEDIATED/data/structures/unzipped/all/mmCIF/"+pdbCode+".cif"), pdbChainCode);
229			pdb.load(pdbChainCode);
230			try {
231			pdb.runDssp(DSSP_EXE, DSSP_PARAMS, SecStrucElement.ReducedState.THREESTATE, SecStrucElement.ReducedState.THREESTATE);
232			//pdb.runDssp(DSSP_EXE, DSSP_PARAMS);
233			dssp = true;
234			} catch (Exception e) {
235			System.err.println(e.getMessage());
236			}
237	filippis	396	if (!mode.equals("GRAPH")) {
238	filippis	398	try {
239	filippis	514	pdb.checkScop("1.73", false);
240	filippis	412	scop = true;
241	filippis	398	} catch (Exception e) {
242			System.err.println(e.getMessage());
243			}
244			try {
245			int mistakes = pdb.checkConsurfHssp(false);
246			System.out.println("ConsurfHssp Mistakes:"+mistakes);
247	filippis	412	if (mistakes == 0) consurf = true;
248	filippis	398	} catch (Exception e) {
249			System.err.println(e.getMessage());
250	filippis	503	}
251	filippis	398	try {
252			pdb.checkEC(false);
253	filippis	412	ec = true;
254	filippis	398	} catch (Exception e) {
255			System.err.println(e.getMessage());
256			}
257			try {
258	filippis	514	int mistakes = pdb.checkCSA("2.2.7", false);
259	filippis	398	System.out.println("CSA Mistakes:"+mistakes);
260	filippis	412	if (mistakes == 0) csa = true;
261	filippis	398	} catch (Exception e) {
262			System.err.println(e.getMessage());
263	filippis	503	}/*
264			pdb.restrictToScopDomain("d1pjua2");
265			try {
266			pdb.runDssp(DSSP_EXE, DSSP_PARAMS, SecStrucElement.ReducedState.THREESTATE, SecStrucElement.ReducedState.THREESTATE);
267			//pdb.runDssp(DSSP_EXE, DSSP_PARAMS);
268			dssp = true;
269			} catch (Exception e) {
270			System.err.println(e.getMessage());
271			}*/
272			try {
273			pdb.runNaccess(NACCESS_EXE, NACCESS_PARAMS);
274			naccess = true;
275			} catch (Exception e) {
276			System.err.println(e.getMessage());
277	filippis	398	}
278	filippis	503
279	filippis	407	//pdb.writeToDb(conn,outputDb);
280			pdb.writeToDbFast(conn, outputDb);
281	filippis	396	}
282	duarte	359	// get graphs
283	filippis	396	if (!mode.equals("PDB")) {
284			for (int j = 0; j<edgeTypes.length; j++) {
285	filippis	438	System.out.print("--> "+(directed[j]?"directed":"")+" graph "+edgeTypes[j]+" for cutoff "+cutoffs[j]);
286	filippis	396
287	filippis	438	RIGraph graph = pdb.get_graph(edgeTypes[j], cutoffs[j], directed[j]);
288	filippis	503	//graph.restrictContactsBetweenSs();
289	filippis	407	if (seqseps != null) {
290			if (seqseps[j] > 1) {
291	filippis	411	System.out.print(" and sequence separation >= "+seqseps[j]);
292	filippis	407	graph.restrictContactsToMinRange(seqseps[j]);
293			}
294			}
295	duarte	420	//graph.writeToDb(conn,outputDb);
296	filippis	407	graph.write_graph_to_db_fast(conn,outputDb);
297	filippis	396
298	duarte	420	System.out.println();
299	filippis	396	numPdbs++;
300	filippis	412	numGraphs++;
301	filippis	396	}
302	duarte	359	}
303	duarte	285
304	duarte	441	} catch (PdbLoadError e) {
305			System.err.println("Error loading pdb data for " + pdbCode + pdbChainCode+", specific error: "+e.getMessage());
306	duarte	264	} catch (PdbCodeNotFoundError e) {
307	duarte	277	System.err.println("Couldn't find pdb code "+pdbCode);
308	duarte	264	} catch (SQLException e) {
309	duarte	285	System.err.println("SQL error for structure "+pdbCode+"_"+pdbChainCode+", error: "+e.getMessage());
310	duarte	441	}
311			/* catch (CiffileFormatError e) {
312	filippis	398	System.err.println(e.getMessage());
313			}*/
314	filippis	412
315			System.out.println("SUMMARY:"+pdbCode+"_"+pdbChainCode+" dssp:"+dssp+" scop:"+scop+" naccess:"+naccess+" consurf:"+consurf+" ec:"+ec+" csa:"+csa+ " graphs:"+numGraphs);
316	duarte	264
317			}
318
319			// output results
320	duarte	359	System.out.println("Number of graphs loaded successfully: " + numPdbs);
321	duarte	264
322
323			} else {
324			String pdbChainCode = pdbChainCodes[0];
325	filippis	412	boolean dssp = false, scop = false, naccess = false, consurf = false, ec = false, csa = false;
326			int numGraphs = 0;
327
328	duarte	264	try {
329	duarte	359
330			System.out.println("Getting chain "+pdbChainCode+" from pdb file "+pdbfile);
331
332	duarte	441	Pdb pdb = new PdbfilePdb(pdbfile);
333			pdb.load(pdbChainCode);
334	duarte	264	if (!pdb.hasSecondaryStructure()) {
335	filippis	503	pdb.runDssp(DSSP_EXE, DSSP_PARAMS, SecStrucElement.ReducedState.THREESTATE, SecStrucElement.ReducedState.THREESTATE);
336			//pdb.runDssp(DSSP_EXE, DSSP_PARAMS);
337	duarte	264	}
338	filippis	396	if (!mode.equals("GRAPH")) {
339	filippis	398	try {
340	filippis	412	pdb.runDssp(DSSP_EXE, DSSP_PARAMS, SecStrucElement.ReducedState.THREESTATE, SecStrucElement.ReducedState.THREESTATE);
341			//pdb.runDssp(DSSP_EXE, DSSP_PARAMS);
342			dssp = true;
343	filippis	398	} catch (Exception e) {
344			System.err.println(e.getMessage());
345			}
346			try {
347	filippis	514	pdb.checkScop("1.73", false);
348	filippis	412	scop = true;
349	filippis	398	} catch (Exception e) {
350			System.err.println(e.getMessage());
351			}
352			try {
353			int mistakes = pdb.checkConsurfHssp(false);
354			System.out.println("ConsurfHssp Mistakes:"+mistakes);
355	filippis	412	if (mistakes == 0) consurf = true;
356	filippis	398	} catch (Exception e) {
357			System.err.println(e.getMessage());
358			}
359			try {
360			pdb.checkEC(false);
361	filippis	412	ec = true;
362	filippis	398	} catch (Exception e) {
363			System.err.println(e.getMessage());
364			}
365			try {
366	filippis	514	int mistakes = pdb.checkCSA("2.2.7", false);
367	filippis	398	System.out.println("CSA Mistakes:"+mistakes);
368	filippis	412	if (mistakes == 0) csa = true;
369	filippis	398	} catch (Exception e) {
370			System.err.println(e.getMessage());
371			}
372	filippis	503	/*pdb.restrictToScopDomain("d1eaka3");
373			try {
374			pdb.runDssp(DSSP_EXE, DSSP_PARAMS, SecStrucElement.ReducedState.THREESTATE, SecStrucElement.ReducedState.THREESTATE);
375			//pdb.runDssp(DSSP_EXE, DSSP_PARAMS);
376			dssp = true;
377			} catch (Exception e) {
378			System.err.println(e.getMessage());
379			}*/
380			try {
381			pdb.runNaccess(NACCESS_EXE, NACCESS_PARAMS);
382			naccess = true;
383			} catch (Exception e) {
384			System.err.println(e.getMessage());
385			}
386
387	filippis	412	//pdb.writeToDb(conn,outputDb);
388	filippis	411	pdb.writeToDbFast(conn, outputDb);
389	filippis	396	}
390	duarte	359
391			// get graphs
392	filippis	396	if (!mode.equals("PDB")) {
393			for (int j = 0; j<edgeTypes.length; j++) {
394	filippis	438	System.out.print("--> "+(directed[j]?"directed":"")+" graph "+edgeTypes[j]+" for cutoff "+cutoffs[j]);
395	filippis	396
396	filippis	438	RIGraph graph = pdb.get_graph(edgeTypes[j], cutoffs[j], directed[j]);
397	filippis	503	//graph.restrictContactsBetweenSs();
398	filippis	407	if (seqseps != null) {
399			if (seqseps[j] > 1) {
400	filippis	411	System.out.print(" and sequence separation >= "+seqseps[j]);
401	filippis	407	graph.restrictContactsToMinRange(seqseps[j]);
402			}
403			}
404	duarte	420	//graph.writeToDb(conn,outputDb);
405	filippis	407	graph.write_graph_to_db_fast(conn,outputDb);
406	filippis	411
407	filippis	412	System.out.println();
408			numGraphs++;
409	filippis	396	}
410	duarte	264	}
411
412	duarte	359	} catch (SQLException e) {
413			System.err.println("Couldn't write graph to db, error: "+e.getMessage());
414	duarte	441	} catch (PdbLoadError e) {
415			System.err.println("Error loading from pdb file "+pdbfile+", specific error: "+e.getMessage());
416			}
417	filippis	412
418			System.out.println("SUMMARY:"+pdbfile+"_"+pdbChainCode+" dssp:"+dssp+" scop:"+scop+" naccess:"+naccess+" consurf:"+consurf+" ec:"+ec+" csa:"+csa+ " graphs:"+numGraphs);
419
420	duarte	264	}
421	duarte	358
422			// closing db connection
423			conn.close();
424	duarte	264	}
425
426			}