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("1.71", 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("2.2.5", 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("1.71", 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("2.2.5", 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:	503
Committed:	Tue Jan 8 19:51:39 2008 UTC (16 years, 9 months ago) by filippis
File size:	14412 byte(s)
Log Message:	createGraphDb: -scop_graph table added -!!!!residue serial fields (num, i_num, j_num) are changed to unsigned !!!!ProtStructGraph: -interSSE variable added -getResidueSerial abstract method added -restrictContactsBetweenSs method added !!!!AIGraph: -getResidueSerial method added RIGraph: -!!!!getResidueSerial method added -scop graphs are written to db correctly -interSSE variable taken into account for CR db field DbRIgraph: -changes made so to be able to read from db using a scop id -interSSE and minSeqSep are set now in get_db_graph_info() -!!!!FIXED BUG:fullLength in read_graph_from_db is not set to the size of the serials2nodes TreeMap instead of the maximum serial in serials2nodes. It was giving wrong result for scop graphs. testDbRIGraph added: It reads one graph from a source db based either -on pdbcode, chaincode and graph properties or -on scop id and graph properties or -on a graph id and it writes the graph to a destination db. Pdb: -unused scop regions are now removed in restrictToScopDomain -unused residues are also removed from resser2pdbresser, pdbresser2resser, resser2allrsa, resser2scrsa, resser2consurfhsspscore, resser2consurfhsspcolor, catalSiteSet -!!!!sequence is reset to scop sequence and fullLength to the length of the scop sequence CatalSiteSet: - removeCatalSiteRes(int resser) method added CatalyticSite: -remRes(int resser) method added Scop: -remove(ScopRegion e) method added genDbGraph:Comments only added to demonstrate new functionality. -comment added to show how to use restrictContactsBetweenSs -comment added to show how to use restrictToScopDomain -runDssp now is always run and not only when mode != "GRAPH". This has been changed since now the contact range might depend on the ss assignment (restrictContactsBetweenSs) and we want to ensure consistent results -runNaccess moved to the bottom so it is always run last. In this way if restrictToScopDomain is used, we don't have to run naccess twice.
Line	File contents
1	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	//import proteinstructure.CiffilePdb;
10	import proteinstructure.PdbLoadError;
11	import proteinstructure.RIGraph;
12	import proteinstructure.Pdb;
13	import proteinstructure.PdbCodeNotFoundError;
14	import proteinstructure.PdbasePdb;
15	import proteinstructure.PdbfilePdb;
16	import proteinstructure.SecStrucElement;
17	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	public static final String NACCESS_EXE = "/project/StruPPi/bin/naccess";
30	public static final String NACCESS_PARAMS = "";
31
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) 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	"\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	"\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
61	String listfile = "";
62	String[] pdbCodes = null;
63	String[] pdbChainCodes = null;
64	String pdbfile = "";
65	String pdbaseDb = PDB_DB;
66	String[] edgeTypes = null;
67	double[] cutoffs = null;
68	int[] seqseps = null;
69	boolean[] directed = null;
70	String outputDb = "";
71	String mode = "GRAPH";
72
73	Getopt g = new Getopt("genDbGraph", args, "i:p:c:f:d:t:r:s:o:D:m:h?");
74	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	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	break;
96	case 't':
97	edgeTypes = g.getOptarg().split(",");
98	break;
99	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	case 's':
107	String[] seqsepsStr = g.getOptarg().split(",");
108	seqseps = new int[seqsepsStr.length];
109	for (int i=0;i<seqseps.length;i++) {
110	seqseps[i] = Integer.valueOf(seqsepsStr[i]);
111	}
112	break;
113	case 'o':
114	outputDb = g.getOptarg();
115	break;
116	case 'D':
117	pdbaseDb = g.getOptarg();
118	break;
119	case 'm':
120	mode = g.getOptarg();
121	break;
122	case 'h':
123	case '?':
124	System.out.println(help);
125	System.exit(0);
126	break; // getopt() already printed an error
127	}
128	}
129
130	if (directed==null) {
131	// we set by default all directed to false
132	directed = new boolean[edgeTypes.length];
133	}
134
135	if (outputDb.equals("") \|\| edgeTypes==null \|\| cutoffs==null) {
136	System.err.println("Some missing option\n");
137	System.err.println(help);
138	System.exit(1);
139	}
140	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	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	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	if (listfile.equals("") && pdbCodes==null && pdbfile.equals("")){
156	System.err.println("Either a listfile, some pdb codes/chain codes or a pdbfile must be given\n");
157	System.err.println(help);
158	System.exit(1);
159	}
160	if ((!listfile.equals("") && pdbCodes!=null) \|\| (!listfile.equals("") && !pdbfile.equals("")) \|\| (pdbCodes!=null && !pdbfile.equals(""))) {
161	System.err.println("Options -p/-c, -i and -f/-c are exclusive. Use only one of them\n");
162	System.err.println(help);
163	System.exit(1);
164	}
165	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
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
180
181	MySQLConnection conn = null;
182
183	try{
184	conn = new MySQLConnection(DB_HOST, DB_USER, DB_PWD);
185	conn.setSqlMode("NO_UNSIGNED_SUBTRACTION,TRADITIONAL");
186	} 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	if (line.length()>0) numLines++;
201	}
202	fpdb.reset();
203	pdbCodes = new String[numLines];
204	pdbChainCodes = new String[numLines];
205	numLines = 0;
206	while ((line = fpdb.readLine() ) != null ) {
207	pdbCodes[numLines] = line.split("\\s+")[0].toLowerCase();
208	pdbChainCodes[numLines] = line.split("\\s+")[1];
209	numLines++;
210	}
211	fpdb.close();
212	}
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
220	boolean dssp = false, scop = false, naccess = false, consurf = false, ec = false, csa = false;
221	int numGraphs = 0;
222
223	try {
224
225	System.out.println("Getting pdb data for "+pdbCode+"_"+pdbChainCode);
226
227	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	if (!mode.equals("GRAPH")) {
238	try {
239	pdb.checkScop("1.71", false);
240	scop = true;
241	} 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	if (mistakes == 0) consurf = true;
248	} catch (Exception e) {
249	System.err.println(e.getMessage());
250	}
251	try {
252	pdb.checkEC(false);
253	ec = true;
254	} catch (Exception e) {
255	System.err.println(e.getMessage());
256	}
257	try {
258	int mistakes = pdb.checkCSA("2.2.5", false);
259	System.out.println("CSA Mistakes:"+mistakes);
260	if (mistakes == 0) csa = true;
261	} catch (Exception e) {
262	System.err.println(e.getMessage());
263	}/*
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	}
278
279	//pdb.writeToDb(conn,outputDb);
280	pdb.writeToDbFast(conn, outputDb);
281	}
282	// get graphs
283	if (!mode.equals("PDB")) {
284	for (int j = 0; j<edgeTypes.length; j++) {
285	System.out.print("--> "+(directed[j]?"directed":"")+" graph "+edgeTypes[j]+" for cutoff "+cutoffs[j]);
286
287	RIGraph graph = pdb.get_graph(edgeTypes[j], cutoffs[j], directed[j]);
288	//graph.restrictContactsBetweenSs();
289	if (seqseps != null) {
290	if (seqseps[j] > 1) {
291	System.out.print(" and sequence separation >= "+seqseps[j]);
292	graph.restrictContactsToMinRange(seqseps[j]);
293	}
294	}
295	//graph.writeToDb(conn,outputDb);
296	graph.write_graph_to_db_fast(conn,outputDb);
297
298	System.out.println();
299	numPdbs++;
300	numGraphs++;
301	}
302	}
303
304	} catch (PdbLoadError e) {
305	System.err.println("Error loading pdb data for " + pdbCode + pdbChainCode+", specific error: "+e.getMessage());
306	} catch (PdbCodeNotFoundError e) {
307	System.err.println("Couldn't find pdb code "+pdbCode);
308	} catch (SQLException e) {
309	System.err.println("SQL error for structure "+pdbCode+"_"+pdbChainCode+", error: "+e.getMessage());
310	}
311	/* catch (CiffileFormatError e) {
312	System.err.println(e.getMessage());
313	}*/
314
315	System.out.println("SUMMARY:"+pdbCode+"_"+pdbChainCode+" dssp:"+dssp+" scop:"+scop+" naccess:"+naccess+" consurf:"+consurf+" ec:"+ec+" csa:"+csa+ " graphs:"+numGraphs);
316
317	}
318
319	// output results
320	System.out.println("Number of graphs loaded successfully: " + numPdbs);
321
322
323	} else {
324	String pdbChainCode = pdbChainCodes[0];
325	boolean dssp = false, scop = false, naccess = false, consurf = false, ec = false, csa = false;
326	int numGraphs = 0;
327
328	try {
329
330	System.out.println("Getting chain "+pdbChainCode+" from pdb file "+pdbfile);
331
332	Pdb pdb = new PdbfilePdb(pdbfile);
333	pdb.load(pdbChainCode);
334	if (!pdb.hasSecondaryStructure()) {
335	pdb.runDssp(DSSP_EXE, DSSP_PARAMS, SecStrucElement.ReducedState.THREESTATE, SecStrucElement.ReducedState.THREESTATE);
336	//pdb.runDssp(DSSP_EXE, DSSP_PARAMS);
337	}
338	if (!mode.equals("GRAPH")) {
339	try {
340	pdb.runDssp(DSSP_EXE, DSSP_PARAMS, SecStrucElement.ReducedState.THREESTATE, SecStrucElement.ReducedState.THREESTATE);
341	//pdb.runDssp(DSSP_EXE, DSSP_PARAMS);
342	dssp = true;
343	} catch (Exception e) {
344	System.err.println(e.getMessage());
345	}
346	try {
347	pdb.checkScop("1.71", false);
348	scop = true;
349	} 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	if (mistakes == 0) consurf = true;
356	} catch (Exception e) {
357	System.err.println(e.getMessage());
358	}
359	try {
360	pdb.checkEC(false);
361	ec = true;
362	} catch (Exception e) {
363	System.err.println(e.getMessage());
364	}
365	try {
366	int mistakes = pdb.checkCSA("2.2.5", false);
367	System.out.println("CSA Mistakes:"+mistakes);
368	if (mistakes == 0) csa = true;
369	} catch (Exception e) {
370	System.err.println(e.getMessage());
371	}
372	/*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	//pdb.writeToDb(conn,outputDb);
388	pdb.writeToDbFast(conn, outputDb);
389	}
390
391	// get graphs
392	if (!mode.equals("PDB")) {
393	for (int j = 0; j<edgeTypes.length; j++) {
394	System.out.print("--> "+(directed[j]?"directed":"")+" graph "+edgeTypes[j]+" for cutoff "+cutoffs[j]);
395
396	RIGraph graph = pdb.get_graph(edgeTypes[j], cutoffs[j], directed[j]);
397	//graph.restrictContactsBetweenSs();
398	if (seqseps != null) {
399	if (seqseps[j] > 1) {
400	System.out.print(" and sequence separation >= "+seqseps[j]);
401	graph.restrictContactsToMinRange(seqseps[j]);
402	}
403	}
404	//graph.writeToDb(conn,outputDb);
405	graph.write_graph_to_db_fast(conn,outputDb);
406
407	System.out.println();
408	numGraphs++;
409	}
410	}
411
412	} catch (SQLException e) {
413	System.err.println("Couldn't write graph to db, error: "+e.getMessage());
414	} catch (PdbLoadError e) {
415	System.err.println("Error loading from pdb file "+pdbfile+", specific error: "+e.getMessage());
416	}
417
418	System.out.println("SUMMARY:"+pdbfile+"_"+pdbChainCode+" dssp:"+dssp+" scop:"+scop+" naccess:"+naccess+" consurf:"+consurf+" ec:"+ec+" csa:"+csa+ " graphs:"+numGraphs);
419
420	}
421
422	// closing db connection
423	conn.close();
424	}
425
426	}