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


public class 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> -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> -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> -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;
                String outputDb = "";
                String mode = "GRAPH";
                
                Getopt g = new Getopt("genDbGraph", args, "i:p:c:f:d:t: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 '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 (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 (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];

                                try {

                                        System.out.println("Getting pdb data for "+pdbCode+"_"+pdbChainCode);
                                        
                                        Pdb pdb = new PdbasePdb(pdbCode, pdbChainCode, pdbaseDb, conn);
                                        //Pdb pdb = new CiffilePdb(new File("/project/StruPPi/BiO/DBd/PDB-REMEDIATED/data/structures/unzipped/all/mmCIF/"+pdbCode+".cif"), pdbChainCode);
                                        if (!mode.equals("GRAPH")) {
                                                try {
                                                        pdb.runDssp(DSSP_EXE, DSSP_PARAMS);
                                                } catch (Exception e) {
                                                        System.err.println(e.getMessage());
                                                }
                                                try {
                                                        pdb.checkScop("1.71", false);
                                                } catch (Exception e) {
                                                        System.err.println(e.getMessage());
                                                }
                                                try {
                                                        pdb.runNaccess(NACCESS_EXE, NACCESS_PARAMS);
                                                } catch (Exception e) {
                                                        System.err.println(e.getMessage());
                                                }
                                                try {
                                                        int mistakes = pdb.checkConsurfHssp(false);
                                                        System.out.println("ConsurfHssp Mistakes:"+mistakes);
                                                } catch (Exception e) {
                                                        System.err.println(e.getMessage());
                                                }
                                                try {
                                                        pdb.checkEC(false);
                                                } catch (Exception e) {
                                                        System.err.println(e.getMessage());
                                                }
                                                try {
                                                        int mistakes = pdb.checkCSA("2.2.5", false);
                                                        System.out.println("CSA Mistakes:"+mistakes);
                                                } 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("--> graph "+edgeTypes[j]+" for cutoff "+cutoffs[j]);
                                                        
                                                        Graph graph = pdb.get_graph(edgeTypes[j], cutoffs[j]);
                                                        if (seqseps != null) {
                                                                if (seqseps[j] > 1) {
                                                                        System.out.print(" and sequence separation >= "+seqseps[j]);
                                                                        graph.restrictContactsToMinRange(seqseps[j]);
                                                                }
                                                        }
                                                        //graph.write_graph_to_db(conn,outputDb);
                                                        graph.write_graph_to_db_fast(conn,outputDb);
                                                        
                                                        System.out.println();
                                                        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);
                                }/* catch (CiffileFormatError e) {
                                        System.err.println(e.getMessage());
                                }*/

                        }

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


                } else {
                        String pdbChainCode = pdbChainCodes[0];
                        try {
                                
                                System.out.println("Getting chain "+pdbChainCode+" from pdb file "+pdbfile);
                                
                                Pdb pdb = new PdbfilePdb(pdbfile,pdbChainCode);
                                if (!pdb.hasSecondaryStructure()) {
                                        pdb.runDssp(DSSP_EXE, DSSP_PARAMS);
                                }
                                if (!mode.equals("GRAPH")) {
                                        try {
                                                pdb.runDssp(DSSP_EXE, DSSP_PARAMS);
                                        } catch (Exception e) {
                                                System.err.println(e.getMessage());
                                        }
                                        try {
                                                pdb.checkScop("1.71", false);
                                        } catch (Exception e) {
                                                System.err.println(e.getMessage());
                                        }
                                        try {
                                                pdb.runNaccess(NACCESS_EXE, NACCESS_PARAMS);
                                        } catch (Exception e) {
                                                System.err.println(e.getMessage());
                                        }
                                        try {
                                                int mistakes = pdb.checkConsurfHssp(false);
                                                System.out.println("ConsurfHssp Mistakes:"+mistakes);
                                        } catch (Exception e) {
                                                System.err.println(e.getMessage());
                                        }
                                        try {
                                                pdb.checkEC(false);
                                        } catch (Exception e) {
                                                System.err.println(e.getMessage());
                                        }
                                        try {
                                                int mistakes = pdb.checkCSA("2.2.5", false);
                                                System.out.println("CSA Mistakes:"+mistakes);
                                        } 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("--> graph "+edgeTypes[j]+" for cutoff "+cutoffs[j]);
                                                
                                                Graph graph = pdb.get_graph(edgeTypes[j], cutoffs[j]);
                                                if (seqseps != null) {
                                                        if (seqseps[j] > 1) {
                                                                System.out.print(" and sequence separation >= "+seqseps[j]);
                                                                graph.restrictContactsToMinRange(seqseps[j]);
                                                        }
                                                }
                                                //graph.write_graph_to_db(conn,outputDb);
                                                graph.write_graph_to_db_fast(conn,outputDb);
                                                
                                                System.out.println();
                                        }
                                }
                                
                        } catch (SQLException e) {
                                System.err.println("Couldn't write graph to db, error: "+e.getMessage());
                        } 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);        
                        }
                }
                
                // closing db connection
                conn.close();
        }

}
Revision:	411
Committed:	Tue Nov 20 19:41:16 2007 UTC (16 years, 10 months ago) by filippis
File size:	11869 byte(s)
Log Message:	minor changes
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			//import proteinstructure.CiffileFormatError;
11	duarte	264	import proteinstructure.Graph;
12			import proteinstructure.Pdb;
13			import proteinstructure.PdbChainCodeNotFoundError;
14			import proteinstructure.PdbCodeNotFoundError;
15			import proteinstructure.PdbaseInconsistencyError;
16			import proteinstructure.PdbasePdb;
17			import proteinstructure.PdbfileFormatError;
18			import proteinstructure.PdbfilePdb;
19			import tools.MySQLConnection;
20
21
22			public class genDbGraph {
23			/------------------------------ constants ------------------------------/
24
25			public static final String PDB_DB = "pdbase";
26			public static final String DB_HOST = "white";
27			public static final String DB_USER = getUserName();
28			public static final String DB_PWD = "nieve";
29			public static final String DSSP_EXE = "/project/StruPPi/bin/dssp";
30			public static final String DSSP_PARAMS = "--";
31	filippis	396	public static final String NACCESS_EXE = "/project/StruPPi/bin/naccess";
32			public static final String NACCESS_PARAMS = "";
33	duarte	264
34			//public static double cutoff = 4.2;
35			//public static String edgeType = "ALL";
36
37			/---------------------------- private methods --------------------------/
38			/**
39			* Get user name from operating system (for use as database username).
40			* */
41			private static String getUserName() {
42			String user = null;
43			user = System.getProperty("user.name");
44			if(user == null) {
45			System.err.println("Could not get user name from operating system.");
46			}
47			return user;
48			}
49
50			public static void main(String[] args) throws IOException {
51
52
53			String help = "Usage, 3 options:\n" +
54	filippis	407	"1) genDbGraph -i <listfile> -d <distance_cutoff> -t <contact_type> -s <seq_sep> -o <output_db> [-D <pdbase_db>] [-m <mode>] \n" +
55			"2) genDbGraph -p <pdb_code> -c <chain_pdb_code> -d <distance_cutoff> -t <contact_type> -s <seq_sep> -o <output_db> [-D <pdbase_db>] [-m <mode>] \n" +
56			"3) genDbGraph -f <pdbfile> -c <chain_pdb_code> -d <distance_cutoff> -t <contact_type> -s <seq_sep> -o <output_db> [-m <mode>] \n" +
57	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" +
58			"If only 1 contact type given and multiple cutoffs, graphs will be generated at all the cutoffs for the one contact type\n"+
59			"\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" +
60	duarte	358	"\nIf pdbase_db not specified, the default pdbase will be used\n" +
61			"\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";
62	duarte	264
63			String listfile = "";
64			String[] pdbCodes = null;
65			String[] pdbChainCodes = null;
66			String pdbfile = "";
67			String pdbaseDb = PDB_DB;
68	duarte	359	String[] edgeTypes = null;
69			double[] cutoffs = null;
70	filippis	407	int[] seqseps = null;
71	duarte	264	String outputDb = "";
72	filippis	396	String mode = "GRAPH";
73	duarte	264
74	filippis	407	Getopt g = new Getopt("genDbGraph", args, "i:p:c:f:d:t:s:o:D:m:h?");
75	duarte	264	int c;
76			while ((c = g.getopt()) != -1) {
77			switch(c){
78			case 'i':
79			listfile = g.getOptarg();
80			break;
81			case 'p':
82			pdbCodes = g.getOptarg().split(",");
83			break;
84			case 'c':
85			pdbChainCodes = g.getOptarg().split(",");
86			break;
87			case 'f':
88			pdbfile = g.getOptarg();
89			break;
90			case 'd':
91	duarte	359	String[] cutoffsStr = g.getOptarg().split(",");
92			cutoffs = new double[cutoffsStr.length];
93			for (int i =0;i<cutoffs.length;i++) {
94			cutoffs[i] = Double.valueOf(cutoffsStr[i]);
95			}
96	duarte	264	break;
97			case 't':
98	duarte	359	edgeTypes = g.getOptarg().split(",");
99	duarte	264	break;
100	filippis	407	case 's':
101			String[] seqsepsStr = g.getOptarg().split(",");
102			seqseps = new int[seqsepsStr.length];
103			for (int i =0;i<seqseps.length;i++) {
104			seqseps[i] = Integer.valueOf(seqsepsStr[i]);
105			}
106			break;
107	duarte	264	case 'o':
108			outputDb = g.getOptarg();
109			break;
110			case 'D':
111			pdbaseDb = g.getOptarg();
112			break;
113	filippis	396	case 'm':
114			mode = g.getOptarg();
115	filippis	398	break;
116	duarte	264	case 'h':
117			case '?':
118			System.out.println(help);
119			System.exit(0);
120			break; // getopt() already printed an error
121			}
122			}
123
124	duarte	359	if (outputDb.equals("") \|\| edgeTypes==null \|\| cutoffs==null) {
125			System.err.println("Some missing option\n");
126	duarte	264	System.err.println(help);
127			System.exit(1);
128			}
129	duarte	359	if (edgeTypes.length!=cutoffs.length && edgeTypes.length!=1) {
130			System.err.println("Not same number of contact types as cutoffs given\n");
131			System.err.println(help);
132			System.exit(1);
133			}
134	filippis	407	if (seqseps != null && edgeTypes.length!=seqseps.length) {
135			System.err.println("Not same number of contact types as sequence separations given\n");
136			System.err.println(help);
137			System.exit(1);
138			}
139	duarte	264	if (listfile.equals("") && pdbCodes==null && pdbfile.equals("")){
140	duarte	359	System.err.println("Either a listfile, some pdb codes/chain codes or a pdbfile must be given\n");
141	duarte	264	System.err.println(help);
142			System.exit(1);
143			}
144			if ((!listfile.equals("") && pdbCodes!=null) \|\| (!listfile.equals("") && !pdbfile.equals("")) \|\| (pdbCodes!=null && !pdbfile.equals(""))) {
145	duarte	359	System.err.println("Options -p/-c, -i and -f/-c are exclusive. Use only one of them\n");
146	duarte	264	System.err.println(help);
147			System.exit(1);
148			}
149	filippis	396	if (!(mode.equals("GRAPH") \|\| mode.equals("PDB") \|\| mode.equals("BOTH"))) {
150			System.err.println("Allowed values for mode:GRAPH,PDB,BOTH.");
151			System.err.println(help);
152			System.exit(1);
153			}
154	duarte	359
155			// setting edgeTypes in case only 1 was given with multiple cutoffs
156			if (edgeTypes.length==1 && cutoffs.length>1) {
157			String edgeType = edgeTypes[0];
158			edgeTypes = new String[cutoffs.length];
159			for (int i=0;i<cutoffs.length;i++){
160			edgeTypes[i] = edgeType;
161			}
162			}
163	duarte	264
164
165			MySQLConnection conn = null;
166
167			try{
168			conn = new MySQLConnection(DB_HOST, DB_USER, DB_PWD);
169	filippis	407	conn.setSqlMode("NO_UNSIGNED_SUBTRACTION,TRADITIONAL");
170	duarte	264	} catch (Exception e) {
171			System.err.println("Error opening database connection. Exiting");
172			System.exit(1);
173			}
174
175
176			if (pdbfile.equals("")){
177
178			if (!listfile.equals("")) {
179			BufferedReader fpdb = new BufferedReader(new FileReader(listfile));
180			String line = "";
181			int numLines = 0;
182			fpdb.mark(100000);
183			while ((line = fpdb.readLine() ) != null ) {
184	duarte	285	if (line.length()>0) numLines++;
185	duarte	264	}
186			fpdb.reset();
187			pdbCodes = new String[numLines];
188			pdbChainCodes = new String[numLines];
189			numLines = 0;
190			while ((line = fpdb.readLine() ) != null ) {
191	duarte	285	pdbCodes[numLines] = line.split("\\s+")[0].toLowerCase();
192			pdbChainCodes[numLines] = line.split("\\s+")[1];
193	duarte	264	numLines++;
194			}
195	duarte	358	fpdb.close();
196	duarte	264	}
197
198			int numPdbs = 0;
199
200			for (int i=0;i<pdbCodes.length;i++) {
201			String pdbCode = pdbCodes[i];
202			String pdbChainCode = pdbChainCodes[i];
203
204			try {
205	duarte	359
206			System.out.println("Getting pdb data for "+pdbCode+"_"+pdbChainCode);
207	duarte	285
208	duarte	277	Pdb pdb = new PdbasePdb(pdbCode, pdbChainCode, pdbaseDb, conn);
209	filippis	398	//Pdb pdb = new CiffilePdb(new File("/project/StruPPi/BiO/DBd/PDB-REMEDIATED/data/structures/unzipped/all/mmCIF/"+pdbCode+".cif"), pdbChainCode);
210	filippis	396	if (!mode.equals("GRAPH")) {
211	filippis	398	try {
212			pdb.runDssp(DSSP_EXE, DSSP_PARAMS);
213			} catch (Exception e) {
214			System.err.println(e.getMessage());
215			}
216			try {
217			pdb.checkScop("1.71", false);
218			} catch (Exception e) {
219			System.err.println(e.getMessage());
220			}
221			try {
222			pdb.runNaccess(NACCESS_EXE, NACCESS_PARAMS);
223			} catch (Exception e) {
224			System.err.println(e.getMessage());
225			}
226			try {
227			int mistakes = pdb.checkConsurfHssp(false);
228			System.out.println("ConsurfHssp Mistakes:"+mistakes);
229			} catch (Exception e) {
230			System.err.println(e.getMessage());
231			}
232			try {
233			pdb.checkEC(false);
234			} catch (Exception e) {
235			System.err.println(e.getMessage());
236			}
237			try {
238			int mistakes = pdb.checkCSA("2.2.5", false);
239			System.out.println("CSA Mistakes:"+mistakes);
240			} catch (Exception e) {
241			System.err.println(e.getMessage());
242			}
243	filippis	407	//pdb.writeToDb(conn,outputDb);
244			pdb.writeToDbFast(conn, outputDb);
245	filippis	396	}
246	duarte	359	// get graphs
247	filippis	396	if (!mode.equals("PDB")) {
248			for (int j = 0; j<edgeTypes.length; j++) {
249	filippis	411	System.out.print("--> graph "+edgeTypes[j]+" for cutoff "+cutoffs[j]);
250	filippis	396
251			Graph graph = pdb.get_graph(edgeTypes[j], cutoffs[j]);
252	filippis	407	if (seqseps != null) {
253			if (seqseps[j] > 1) {
254	filippis	411	System.out.print(" and sequence separation >= "+seqseps[j]);
255	filippis	407	graph.restrictContactsToMinRange(seqseps[j]);
256			}
257			}
258			//graph.write_graph_to_db(conn,outputDb);
259			graph.write_graph_to_db_fast(conn,outputDb);
260	filippis	396
261	filippis	411	System.out.println();
262	filippis	396	numPdbs++;
263			}
264	duarte	359	}
265	duarte	285
266	duarte	264	} catch (PdbaseInconsistencyError e) {
267	duarte	277	System.err.println("Inconsistency in " + pdbCode + pdbChainCode);
268	duarte	264	} catch (PdbCodeNotFoundError e) {
269	duarte	277	System.err.println("Couldn't find pdb code "+pdbCode);
270	duarte	264	} catch (SQLException e) {
271	duarte	285	System.err.println("SQL error for structure "+pdbCode+"_"+pdbChainCode+", error: "+e.getMessage());
272	duarte	264	} catch (PdbChainCodeNotFoundError e) {
273	duarte	277	System.err.println("Couldn't find pdb chain code "+pdbChainCode+" for pdb code "+pdbCode);
274	filippis	398	}/* catch (CiffileFormatError e) {
275			System.err.println(e.getMessage());
276			}*/
277	duarte	264
278			}
279
280			// output results
281	duarte	359	System.out.println("Number of graphs loaded successfully: " + numPdbs);
282	duarte	264
283
284			} else {
285			String pdbChainCode = pdbChainCodes[0];
286			try {
287	duarte	359
288			System.out.println("Getting chain "+pdbChainCode+" from pdb file "+pdbfile);
289
290	duarte	264	Pdb pdb = new PdbfilePdb(pdbfile,pdbChainCode);
291			if (!pdb.hasSecondaryStructure()) {
292			pdb.runDssp(DSSP_EXE, DSSP_PARAMS);
293			}
294	filippis	396	if (!mode.equals("GRAPH")) {
295	filippis	398	try {
296			pdb.runDssp(DSSP_EXE, DSSP_PARAMS);
297			} catch (Exception e) {
298			System.err.println(e.getMessage());
299			}
300			try {
301			pdb.checkScop("1.71", false);
302			} catch (Exception e) {
303			System.err.println(e.getMessage());
304			}
305			try {
306			pdb.runNaccess(NACCESS_EXE, NACCESS_PARAMS);
307			} catch (Exception e) {
308			System.err.println(e.getMessage());
309			}
310			try {
311			int mistakes = pdb.checkConsurfHssp(false);
312			System.out.println("ConsurfHssp Mistakes:"+mistakes);
313			} catch (Exception e) {
314			System.err.println(e.getMessage());
315			}
316			try {
317			pdb.checkEC(false);
318			} catch (Exception e) {
319			System.err.println(e.getMessage());
320			}
321			try {
322			int mistakes = pdb.checkCSA("2.2.5", false);
323			System.out.println("CSA Mistakes:"+mistakes);
324			} catch (Exception e) {
325			System.err.println(e.getMessage());
326			}
327	filippis	396	pdb.writeToDb(conn,outputDb);
328	filippis	411	pdb.writeToDbFast(conn, outputDb);
329	filippis	396	}
330	duarte	359
331			// get graphs
332	filippis	396	if (!mode.equals("PDB")) {
333			for (int j = 0; j<edgeTypes.length; j++) {
334	filippis	411	System.out.print("--> graph "+edgeTypes[j]+" for cutoff "+cutoffs[j]);
335	filippis	396
336			Graph graph = pdb.get_graph(edgeTypes[j], cutoffs[j]);
337	filippis	407	if (seqseps != null) {
338			if (seqseps[j] > 1) {
339	filippis	411	System.out.print(" and sequence separation >= "+seqseps[j]);
340	filippis	407	graph.restrictContactsToMinRange(seqseps[j]);
341			}
342			}
343			//graph.write_graph_to_db(conn,outputDb);
344			graph.write_graph_to_db_fast(conn,outputDb);
345	filippis	411
346			System.out.println();
347	filippis	396	}
348	duarte	264	}
349
350	duarte	359	} catch (SQLException e) {
351			System.err.println("Couldn't write graph to db, error: "+e.getMessage());
352	duarte	264	} catch (PdbfileFormatError e) {
353			System.err.println("pdb file "+pdbfile+" doesn't have right format");
354			} catch (PdbChainCodeNotFoundError e) {
355			System.err.println("chain code "+pdbChainCode+" wasn't found in file "+pdbfile);
356			}
357			}
358	duarte	358
359			// closing db connection
360			conn.close();
361	duarte	264	}
362
363			}