owl/trunk/reconstruct.java

import gnu.getopt.Getopt;

import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.sql.SQLException;
import java.util.Formatter;

import proteinstructure.AAinfo;
import proteinstructure.ConformationsNotSameSizeError;
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 tinker.ConstraintsMaker;
import tinker.TinkerError;
import tinker.TinkerRunner;


public class reconstruct {

        
        private static final String TINKERBINDIR = "/project/StruPPi/Software/tinker/bin";
        private static final String PRMFILE = "/project/StruPPi/Software/tinker/amber/amber99.prm";
        private static final String PRMTYPE = "amber";
        
        public static void main(String[] args) {
                
                String programName = reconstruct.class.getName();
                String help = "Usage:\n" +
                        programName+" -p <pdb code> -c <pdb chain code> -t <contact_type> [-r] -d <distance cutoff 1> -D <distance cutoff 2> -i <distance cutoff 3> -b <base name> -o <output dir> [-n <number of models>]\n"; 

                String pdbCode = "";
                String pdbChainCode = "";
                String ct = "";
                double cutoff1 = 0.0;
                double cutoff2 = 0.0;
                double cutoff3 = 0.0;
                String outputDir = "";
                String baseName = "";
                boolean cross = false;
                int n = 1;

                Getopt g = new Getopt(programName, args, "p:c:d:t:rb:o:d:D:i:n:h?");
                int c;
                while ((c = g.getopt()) != -1) {
                        switch(c){
                        case 'p':
                                pdbCode = g.getOptarg();
                                break;
                        case 'c':
                                pdbChainCode = g.getOptarg();
                                break;
                        case 't':
                                ct = g.getOptarg();
                                break;
                        case 'r':
                                cross = true;
                                break;
                        case 'd':
                                cutoff1 = Double.valueOf(g.getOptarg());
                                break;
                        case 'D':
                                cutoff2 = Double.valueOf(g.getOptarg());
                                break;
                        case 'i':
                                cutoff3 = Double.valueOf(g.getOptarg());
                                break;
                        case 'b':
                                baseName = g.getOptarg();
                                break;
                        case 'o':
                                outputDir = g.getOptarg();
                                break;
                        case 'n':
                                n = Integer.parseInt(g.getOptarg());
                                break;                          
                        case 'h':
                        case '?':
                                System.out.println(help);
                                System.exit(0);
                                break; // getopt() already printed an error
                        }
                }

                if (pdbCode.equals("") || pdbChainCode.equals("") || ct.equals("") || cutoff1==0.0 || outputDir.equals("") || baseName.equals("")){
                        System.err.println("Must specify at least -p, -c, -t, -d, -o and -b");
                        System.err.println(help);
                        System.exit(1);
                }
                
                if (baseName.contains(".")) {
                        System.err.println("Basename can't contain a dot (not allowed by tinker). Exiting");
                        System.exit(1);
                }
                
                if (!AAinfo.isValidContactType(ct) || ct.contains("ALL")) {
                        System.err.println("Invalid contact type specified. Exiting");
                        System.exit(1);
                }
                
                if (n>999) {
                        System.err.println("Maximum number of models is 999. Specify a lower value. Exiting");
                        System.exit(1);
                }
                
                boolean doublecm = false;
                String ct1 = ct;
                String ct2 = ct;
                String ct3 = null;
                if (ct.contains("_")) {
                        ct1 = ct.split("_")[0];
                        ct2 = ct.split("_")[1];
                        doublecm = true;
                }
                if (cross) {
                        ct3 = ct1+"/"+ct2;
                }
                
                if (cutoff2==0.0) {
                        cutoff2 = cutoff1;
                }
                if (cutoff3==0.0) {
                        cutoff3 = cutoff1;
                }
                
                
                Pdb pdb = null;
                try {
                        pdb = new PdbasePdb(pdbCode,pdbChainCode);
                } catch (PdbaseInconsistencyError e) {
                        System.err.println("Pdbase inconsistency for structure "+pdbCode+". Can't continue, exiting");
                        System.exit(1);
                } catch (PdbCodeNotFoundError e) {
                        System.err.println("Given pdb code "+pdbCode+" couldn't be found in pdbase. Exiting");
                        System.exit(1);
                } catch (SQLException e) {
                        System.err.println("Problems connecting to database for getting pdb data for "+pdbCode+". Exiting");
                        System.exit(1);
                } catch (PdbChainCodeNotFoundError e) {
                        System.err.println("Given pdb chain code "+pdbChainCode+" couldn't be found for pdb code "+pdbCode+". Exiting");
                        System.exit(1);
                }
                String sequence = pdb.getSequence();

                Graph graph1 = pdb.get_graph(ct1, cutoff1);
                Graph graph2 = null;
                Graph graph3 = null;
                if (doublecm) {
                        graph2 = pdb.get_graph(ct2, cutoff2);
                }
                if (cross) {
                        graph3 = pdb.get_graph(ct3, cutoff3);
                }

                
                // defining files
                File logFile = new File(outputDir,"tinker.log");
                File prmFile = new File(PRMFILE);
                File xyzFile = new File(outputDir,baseName+".xyz");
                File seqFile = new File(outputDir,baseName+".seq");
                File pdbFile = new File(outputDir,baseName+".pdb");
                File keyFile = new File(outputDir,baseName+".key");
                
                // creating TinkerRunner object
                TinkerRunner tr = null;
                try {
                        tr = new TinkerRunner(TINKERBINDIR,PRMFILE,logFile);
                } catch (FileNotFoundException e3) {
                        System.err.println("Couldn't find tinker bin dir "+TINKERBINDIR+". Exiting");
                        System.exit(1);
                }
                
                // 1. run tinker's protein program      
                try {
                        tr.runProtein(sequence, outputDir, baseName );
                } catch (IOException e2) {
                        System.err.println("Couldn't read file to run 'protein' "+seqFile.getAbsolutePath());
                        System.err.println("Exiting");
                        System.exit(1);                 
                } catch (TinkerError e2) {
                        System.err.println("Tinker error while running 'protein', check log file "+logFile.getAbsolutePath()+". Exiting");
                        System.exit(1);                 
                }

                // 1a. convert xyz file to pdb to be able to map atom serials after
                try {
                        tr.runXyzpdb(xyzFile, seqFile, pdbFile);
                } catch (IOException e1) {
                        System.err.println("Couldn't read files "+xyzFile.getAbsolutePath()+" or "+seqFile.getAbsolutePath()+" or write to "+pdbFile.getAbsolutePath()+" for running 'xyzpdb'");
                        System.err.println("Exiting");
                        System.exit(1);
                } catch (TinkerError e1) {
                        System.err.println("Tinker error while running xyzpdb, check log file "+logFile.getAbsolutePath()+". Exiting");
                        System.exit(1);
                }

                // 2. creating constraints into key file
                ConstraintsMaker cm = null;
                try {
                        cm = new ConstraintsMaker(pdbFile,xyzFile,prmFile,PRMTYPE,keyFile);
                } catch (IOException e3) {
                        System.err.println("Couldn't read files "+xyzFile.getAbsolutePath()+", "+pdbFile.getAbsolutePath()+" or, "+prmFile.getAbsolutePath()+" write to "+keyFile.getAbsolutePath()+" for creating distance constraints");
                        System.err.println("Exiting");
                        System.exit(1);
                } catch (PdbfileFormatError e3) {
                        System.err.println("pdb file "+pdbFile.getAbsolutePath()+" converted from "+xyzFile.getAbsolutePath()+" doesn't seem to be in the right format. Check log? ("+logFile.getAbsolutePath()+"). Exiting");
                        System.exit(1);
                } 

                cm.createConstraints(graph1);
                if (doublecm) cm.createConstraints(graph2);
                if (cross) cm.createConstraints(graph3);

                cm.closeKeyFile();

                // 3. run tinker's distgeom
                try {
                        System.out.println("Running distgeom...");
                        tr.runDistgeom(xyzFile, outputDir, baseName, n);
                } catch (TinkerError e1) {
                        System.err.println(e1.getMessage());
                        System.err.println("Exiting");
                        System.exit(1);                 
                } catch (IOException e1) {
                        System.err.println("Couldn't read files "+xyzFile.getAbsolutePath()+" or write 'distgeom' output files to output dir "+outputDir);
                        System.err.println("Exiting");
                        System.exit(1);
                } catch(InterruptedException e) {
                        System.err.println("Distgeom was interrupted:" + e.getMessage());
                        System.err.println("Exiting.");
                        System.exit(1);
                }
                
                double[] mubv = tr.getMaxUpperBoundViol();
                double[] mlbv = tr.getMaxLowerBoundViol();
                double[] muv = tr.getMaxUpperViol();
                double[] mlv = tr.getMaxLowerViol();
                int[] nubv = tr.getNumUpperBoundViol();
                int[] nlbv = tr.getNumLowerBoundViol();
                int[] nuv = tr.getNumUpperViol();
                int[] nlv = tr.getNumLowerViol();
                double[] rbv = tr.getRmsBoundViol();
                double[] rrv = tr.getRmsRestViol();
                

                // 4. converting xyz output files to pdb files and calculating rmsds

                double[] rmsds = new double[n+1];               
                
                        for (int i = 1; i<=n; i++) {
                                String ext = new Formatter().format(".%03d",i).toString();
                                File outputXyzFile = new File(outputDir, baseName+ext);
                                File outputPdbFile = new File(outputDir, baseName+ext+".pdb");
                                try {
                                        tr.runXyzpdb(outputXyzFile, seqFile, outputPdbFile);
                                        
                                        Pdb outputPdb = new PdbfilePdb(outputPdbFile.getAbsolutePath(),"NULL");
                                        rmsds[i] = pdb.rmsd(outputPdb, "Ca");

                                } catch (IOException e) {
                                        System.err.println("Couldn't read file "+outputXyzFile.getAbsolutePath()+", or "+seqFile.getAbsolutePath()+", or write to "+outputPdbFile.getAbsolutePath()+" while converting with 'xyzpdb'");
                                        System.err.println("Can't calculate rmsd for it");
                                } catch (TinkerError e) {
                                        System.err.println("Tinker error while running 'xyzpdb' to convert"+outputXyzFile.getAbsolutePath()+", check log file "+logFile.getAbsolutePath());
                                        System.err.println("Can't calculate rmsd for it");
                                }
                                catch (PdbfileFormatError e) {
                                        System.err.println("Output pdb file "+outputPdbFile.getAbsolutePath()+" doesn't seem to be in the correcet format. Can't calculate rmsd for it");
                                } catch (PdbChainCodeNotFoundError e) {
                                        // this shouldn't happen, chain code is hard coded, we throw stack trace and continue if it happens
                                        e.printStackTrace();
                                } catch (ConformationsNotSameSizeError e) {
                                        System.err.println(pdbFile.getAbsolutePath()+" and "+outputPdbFile.getAbsolutePath()+" don't have the same conformation size, can't calculate rmsd for them.");
                                }                               
                                
                                tr.closeLog();
                        }                                       

                
                // 6. report
                System.out.println("accession_code\tchain_pdb_code\tcutoff\tcutoff2\tcutoff3\tct\tct2\tct3" +
                                "\tresult_id\tup_bound_viol\tlow_bound_viol\tmax_bound_up\tmax_bound_low\trms_bound" +
                                "\tup_viol\tlow_viol\tmax_up\tmax_low\trms_viol\trmsd_to_orig");
                
                for (int i=1;i<=n;i++){
                        System.out.println(pdbCode+"\t"+pdbChainCode+"\t"+cutoff1+"\t"+cutoff2+"\t"+cutoff3+"\t"+ct1+"\t"+ct2+"\t"+ct3+"\t"+
                                        i+"\t"+nubv[i]+"\t"+nlbv[i]+"\t"+mubv[i]+"\t"+mlbv[i]+"\t"+muv[i]+"\t"+mlv[i]+"\t"+rbv[i]+"\t"+
                                        "\t"+nuv[i]+"\t"+nlv[i]+"\t"+rrv[i]+"\t"+rmsds[i]);
                }
                
        }

}
Revision:	346
Committed:	Thu Oct 11 08:38:36 2007 UTC (17 years ago) by duarte
File size:	10094 byte(s)
Log Message:	Doing more input error checks In ConstraintsMaker createConstraints won't throw Exception anymore, we only assery that ALL can't be used
Line	User	Rev	File contents
1	duarte	338	import gnu.getopt.Getopt;
2
3			import java.io.File;
4			import java.io.FileNotFoundException;
5			import java.io.IOException;
6			import java.sql.SQLException;
7			import java.util.Formatter;
8
9	duarte	346	import proteinstructure.AAinfo;
10	duarte	338	import proteinstructure.ConformationsNotSameSizeError;
11			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
20			import tinker.ConstraintsMaker;
21			import tinker.TinkerError;
22			import tinker.TinkerRunner;
23
24
25			public class reconstruct {
26
27
28			private static final String TINKERBINDIR = "/project/StruPPi/Software/tinker/bin";
29			private static final String PRMFILE = "/project/StruPPi/Software/tinker/amber/amber99.prm";
30			private static final String PRMTYPE = "amber";
31
32			public static void main(String[] args) {
33
34			String programName = reconstruct.class.getName();
35			String help = "Usage:\n" +
36			programName+" -p <pdb code> -c <pdb chain code> -t <contact_type> [-r] -d <distance cutoff 1> -D <distance cutoff 2> -i <distance cutoff 3> -b <base name> -o <output dir> [-n <number of models>]\n";
37
38			String pdbCode = "";
39			String pdbChainCode = "";
40			String ct = "";
41			double cutoff1 = 0.0;
42			double cutoff2 = 0.0;
43			double cutoff3 = 0.0;
44			String outputDir = "";
45			String baseName = "";
46			boolean cross = false;
47			int n = 1;
48
49			Getopt g = new Getopt(programName, args, "p:c:d:t:rb:o:d:D:i:n:h?");
50			int c;
51			while ((c = g.getopt()) != -1) {
52			switch(c){
53			case 'p':
54			pdbCode = g.getOptarg();
55			break;
56			case 'c':
57			pdbChainCode = g.getOptarg();
58			break;
59			case 't':
60			ct = g.getOptarg();
61			break;
62			case 'r':
63			cross = true;
64			break;
65			case 'd':
66			cutoff1 = Double.valueOf(g.getOptarg());
67			break;
68			case 'D':
69			cutoff2 = Double.valueOf(g.getOptarg());
70			break;
71			case 'i':
72			cutoff3 = Double.valueOf(g.getOptarg());
73			break;
74			case 'b':
75			baseName = g.getOptarg();
76			break;
77			case 'o':
78			outputDir = g.getOptarg();
79			break;
80			case 'n':
81			n = Integer.parseInt(g.getOptarg());
82			break;
83			case 'h':
84			case '?':
85			System.out.println(help);
86			System.exit(0);
87			break; // getopt() already printed an error
88			}
89			}
90
91			if (pdbCode.equals("") \|\| pdbChainCode.equals("") \|\| ct.equals("") \|\| cutoff1==0.0 \|\| outputDir.equals("") \|\| baseName.equals("")){
92			System.err.println("Must specify at least -p, -c, -t, -d, -o and -b");
93			System.err.println(help);
94			System.exit(1);
95			}
96
97	duarte	346	if (baseName.contains(".")) {
98			System.err.println("Basename can't contain a dot (not allowed by tinker). Exiting");
99			System.exit(1);
100			}
101
102			if (!AAinfo.isValidContactType(ct) \|\| ct.contains("ALL")) {
103			System.err.println("Invalid contact type specified. Exiting");
104			System.exit(1);
105			}
106
107			if (n>999) {
108			System.err.println("Maximum number of models is 999. Specify a lower value. Exiting");
109			System.exit(1);
110			}
111
112	duarte	338	boolean doublecm = false;
113			String ct1 = ct;
114			String ct2 = ct;
115			String ct3 = null;
116			if (ct.contains("_")) {
117			ct1 = ct.split("_")[0];
118			ct2 = ct.split("_")[1];
119			doublecm = true;
120			}
121			if (cross) {
122			ct3 = ct1+"/"+ct2;
123			}
124
125			if (cutoff2==0.0) {
126			cutoff2 = cutoff1;
127			}
128			if (cutoff3==0.0) {
129			cutoff3 = cutoff1;
130			}
131
132
133			Pdb pdb = null;
134			try {
135			pdb = new PdbasePdb(pdbCode,pdbChainCode);
136			} catch (PdbaseInconsistencyError e) {
137			System.err.println("Pdbase inconsistency for structure "+pdbCode+". Can't continue, exiting");
138			System.exit(1);
139			} catch (PdbCodeNotFoundError e) {
140			System.err.println("Given pdb code "+pdbCode+" couldn't be found in pdbase. Exiting");
141			System.exit(1);
142			} catch (SQLException e) {
143			System.err.println("Problems connecting to database for getting pdb data for "+pdbCode+". Exiting");
144			System.exit(1);
145			} catch (PdbChainCodeNotFoundError e) {
146			System.err.println("Given pdb chain code "+pdbChainCode+" couldn't be found for pdb code "+pdbCode+". Exiting");
147			System.exit(1);
148			}
149			String sequence = pdb.getSequence();
150
151			Graph graph1 = pdb.get_graph(ct1, cutoff1);
152			Graph graph2 = null;
153			Graph graph3 = null;
154			if (doublecm) {
155			graph2 = pdb.get_graph(ct2, cutoff2);
156			}
157			if (cross) {
158			graph3 = pdb.get_graph(ct3, cutoff3);
159			}
160
161
162			// defining files
163			File logFile = new File(outputDir,"tinker.log");
164			File prmFile = new File(PRMFILE);
165			File xyzFile = new File(outputDir,baseName+".xyz");
166			File seqFile = new File(outputDir,baseName+".seq");
167			File pdbFile = new File(outputDir,baseName+".pdb");
168			File keyFile = new File(outputDir,baseName+".key");
169
170			// creating TinkerRunner object
171			TinkerRunner tr = null;
172			try {
173			tr = new TinkerRunner(TINKERBINDIR,PRMFILE,logFile);
174			} catch (FileNotFoundException e3) {
175			System.err.println("Couldn't find tinker bin dir "+TINKERBINDIR+". Exiting");
176			System.exit(1);
177			}
178
179			// 1. run tinker's protein program
180			try {
181			tr.runProtein(sequence, outputDir, baseName );
182			} catch (IOException e2) {
183			System.err.println("Couldn't read file to run 'protein' "+seqFile.getAbsolutePath());
184			System.err.println("Exiting");
185			System.exit(1);
186			} catch (TinkerError e2) {
187			System.err.println("Tinker error while running 'protein', check log file "+logFile.getAbsolutePath()+". Exiting");
188			System.exit(1);
189			}
190
191			// 1a. convert xyz file to pdb to be able to map atom serials after
192			try {
193			tr.runXyzpdb(xyzFile, seqFile, pdbFile);
194			} catch (IOException e1) {
195			System.err.println("Couldn't read files "+xyzFile.getAbsolutePath()+" or "+seqFile.getAbsolutePath()+" or write to "+pdbFile.getAbsolutePath()+" for running 'xyzpdb'");
196			System.err.println("Exiting");
197			System.exit(1);
198			} catch (TinkerError e1) {
199			System.err.println("Tinker error while running xyzpdb, check log file "+logFile.getAbsolutePath()+". Exiting");
200			System.exit(1);
201			}
202
203			// 2. creating constraints into key file
204			ConstraintsMaker cm = null;
205			try {
206			cm = new ConstraintsMaker(pdbFile,xyzFile,prmFile,PRMTYPE,keyFile);
207			} catch (IOException e3) {
208			System.err.println("Couldn't read files "+xyzFile.getAbsolutePath()+", "+pdbFile.getAbsolutePath()+" or, "+prmFile.getAbsolutePath()+" write to "+keyFile.getAbsolutePath()+" for creating distance constraints");
209			System.err.println("Exiting");
210			System.exit(1);
211			} catch (PdbfileFormatError e3) {
212			System.err.println("pdb file "+pdbFile.getAbsolutePath()+" converted from "+xyzFile.getAbsolutePath()+" doesn't seem to be in the right format. Check log? ("+logFile.getAbsolutePath()+"). Exiting");
213			System.exit(1);
214			}
215	duarte	346
216			cm.createConstraints(graph1);
217			if (doublecm) cm.createConstraints(graph2);
218			if (cross) cm.createConstraints(graph3);
219
220	duarte	338	cm.closeKeyFile();
221
222			// 3. run tinker's distgeom
223			try {
224			System.out.println("Running distgeom...");
225			tr.runDistgeom(xyzFile, outputDir, baseName, n);
226			} catch (TinkerError e1) {
227	duarte	340	System.err.println(e1.getMessage());
228			System.err.println("Exiting");
229	duarte	338	System.exit(1);
230			} catch (IOException e1) {
231			System.err.println("Couldn't read files "+xyzFile.getAbsolutePath()+" or write 'distgeom' output files to output dir "+outputDir);
232			System.err.println("Exiting");
233			System.exit(1);
234	stehr	344	} catch(InterruptedException e) {
235			System.err.println("Distgeom was interrupted:" + e.getMessage());
236			System.err.println("Exiting.");
237			System.exit(1);
238	duarte	338	}
239
240			double[] mubv = tr.getMaxUpperBoundViol();
241			double[] mlbv = tr.getMaxLowerBoundViol();
242			double[] muv = tr.getMaxUpperViol();
243			double[] mlv = tr.getMaxLowerViol();
244			int[] nubv = tr.getNumUpperBoundViol();
245			int[] nlbv = tr.getNumLowerBoundViol();
246			int[] nuv = tr.getNumUpperViol();
247			int[] nlv = tr.getNumLowerViol();
248			double[] rbv = tr.getRmsBoundViol();
249			double[] rrv = tr.getRmsRestViol();
250
251
252			// 4. converting xyz output files to pdb files and calculating rmsds
253
254			double[] rmsds = new double[n+1];
255
256			for (int i = 1; i<=n; i++) {
257			String ext = new Formatter().format(".%03d",i).toString();
258			File outputXyzFile = new File(outputDir, baseName+ext);
259			File outputPdbFile = new File(outputDir, baseName+ext+".pdb");
260			try {
261			tr.runXyzpdb(outputXyzFile, seqFile, outputPdbFile);
262
263			Pdb outputPdb = new PdbfilePdb(outputPdbFile.getAbsolutePath(),"NULL");
264			rmsds[i] = pdb.rmsd(outputPdb, "Ca");
265
266			} catch (IOException e) {
267			System.err.println("Couldn't read file "+outputXyzFile.getAbsolutePath()+", or "+seqFile.getAbsolutePath()+", or write to "+outputPdbFile.getAbsolutePath()+" while converting with 'xyzpdb'");
268			System.err.println("Can't calculate rmsd for it");
269			} catch (TinkerError e) {
270			System.err.println("Tinker error while running 'xyzpdb' to convert"+outputXyzFile.getAbsolutePath()+", check log file "+logFile.getAbsolutePath());
271			System.err.println("Can't calculate rmsd for it");
272			}
273			catch (PdbfileFormatError e) {
274			System.err.println("Output pdb file "+outputPdbFile.getAbsolutePath()+" doesn't seem to be in the correcet format. Can't calculate rmsd for it");
275			} catch (PdbChainCodeNotFoundError e) {
276			// this shouldn't happen, chain code is hard coded, we throw stack trace and continue if it happens
277			e.printStackTrace();
278			} catch (ConformationsNotSameSizeError e) {
279			System.err.println(pdbFile.getAbsolutePath()+" and "+outputPdbFile.getAbsolutePath()+" don't have the same conformation size, can't calculate rmsd for them.");
280			}
281
282			tr.closeLog();
283			}
284
285
286			// 6. report
287			System.out.println("accession_code\tchain_pdb_code\tcutoff\tcutoff2\tcutoff3\tct\tct2\tct3" +
288			"\tresult_id\tup_bound_viol\tlow_bound_viol\tmax_bound_up\tmax_bound_low\trms_bound" +
289			"\tup_viol\tlow_viol\tmax_up\tmax_low\trms_viol\trmsd_to_orig");
290
291			for (int i=1;i<=n;i++){
292			System.out.println(pdbCode+"\t"+pdbChainCode+"\t"+cutoff1+"\t"+cutoff2+"\t"+cutoff3+"\t"+ct1+"\t"+ct2+"\t"+ct3+"\t"+
293	duarte	340	i+"\t"+nubv[i]+"\t"+nlbv[i]+"\t"+mubv[i]+"\t"+mlbv[i]+"\t"+muv[i]+"\t"+mlv[i]+"\t"+rbv[i]+"\t"+
294	duarte	338	"\t"+nuv[i]+"\t"+nlv[i]+"\t"+rrv[i]+"\t"+rmsds[i]);
295			}
296
297			}
298
299			}