branches/aglappe-jung/reconstruct.java

import gnu.getopt.Getopt;

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

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);
                }
                // we also write the file to the out dir so it can be used later for clustering rmsds etc.
                File origPdbFile = new File (outputDir,baseName+".native.pdb");
                try {
                        pdb.dump2pdbfile(origPdbFile.getAbsolutePath());
                } catch (IOException e4) {
                        System.err.println("Couldn't write original pdb file "+origPdbFile.getAbsolutePath());
                        System.err.println("Continuing without it, this is not needed for the rest of the reconstruction process but only for post processing (e.g. comparing rmsds to original)");
                }

                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,baseName+".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");
                File reportFile = new File(outputDir,baseName+".report");
                
                // 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
                try {
                        PrintWriter reportOut = new PrintWriter(new FileOutputStream(reportFile));
                        reportOut.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++){
                                String rmsd = String.format(Locale.US,"%6f",rmsds[i]);
                                reportOut.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"+
                                                nuv[i]+"\t"+nlv[i]+"\t"+rrv[i]+"\t"+rmsd);
                        }
                        reportOut.close();
                } catch (FileNotFoundException e) {
                        System.err.println("Couldn't write to report file "+reportFile.getAbsolutePath() +". Error: "+e.getMessage());
                }
                
        }

}
Revision:	367
Committed:	Wed Oct 24 13:29:15 2007 UTC (16 years, 11 months ago) by duarte
Original Path:	*trunk/reconstruct.java*
File size:	11051 byte(s)
Log Message:	Changed name of native output pdb file
Line	User	Rev	File contents
1	duarte	338	import gnu.getopt.Getopt;
2
3			import java.io.File;
4			import java.io.FileNotFoundException;
5	duarte	347	import java.io.FileOutputStream;
6	duarte	338	import java.io.IOException;
7	duarte	347	import java.io.PrintWriter;
8	duarte	338	import java.sql.SQLException;
9			import java.util.Formatter;
10	duarte	349	import java.util.Locale;
11	duarte	338
12	duarte	346	import proteinstructure.AAinfo;
13	duarte	338	import proteinstructure.ConformationsNotSameSizeError;
14			import proteinstructure.Graph;
15			import proteinstructure.Pdb;
16			import proteinstructure.PdbChainCodeNotFoundError;
17			import proteinstructure.PdbCodeNotFoundError;
18			import proteinstructure.PdbaseInconsistencyError;
19			import proteinstructure.PdbasePdb;
20			import proteinstructure.PdbfileFormatError;
21			import proteinstructure.PdbfilePdb;
22
23			import tinker.ConstraintsMaker;
24			import tinker.TinkerError;
25			import tinker.TinkerRunner;
26
27
28			public class reconstruct {
29
30
31			private static final String TINKERBINDIR = "/project/StruPPi/Software/tinker/bin";
32			private static final String PRMFILE = "/project/StruPPi/Software/tinker/amber/amber99.prm";
33			private static final String PRMTYPE = "amber";
34
35			public static void main(String[] args) {
36
37			String programName = reconstruct.class.getName();
38			String help = "Usage:\n" +
39			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";
40
41			String pdbCode = "";
42			String pdbChainCode = "";
43			String ct = "";
44			double cutoff1 = 0.0;
45			double cutoff2 = 0.0;
46			double cutoff3 = 0.0;
47			String outputDir = "";
48			String baseName = "";
49			boolean cross = false;
50			int n = 1;
51
52			Getopt g = new Getopt(programName, args, "p:c:d:t:rb:o:d:D:i:n:h?");
53			int c;
54			while ((c = g.getopt()) != -1) {
55			switch(c){
56			case 'p':
57			pdbCode = g.getOptarg();
58			break;
59			case 'c':
60			pdbChainCode = g.getOptarg();
61			break;
62			case 't':
63			ct = g.getOptarg();
64			break;
65			case 'r':
66			cross = true;
67			break;
68			case 'd':
69			cutoff1 = Double.valueOf(g.getOptarg());
70			break;
71			case 'D':
72			cutoff2 = Double.valueOf(g.getOptarg());
73			break;
74			case 'i':
75			cutoff3 = Double.valueOf(g.getOptarg());
76			break;
77			case 'b':
78			baseName = g.getOptarg();
79			break;
80			case 'o':
81			outputDir = g.getOptarg();
82			break;
83			case 'n':
84			n = Integer.parseInt(g.getOptarg());
85			break;
86			case 'h':
87			case '?':
88			System.out.println(help);
89			System.exit(0);
90			break; // getopt() already printed an error
91			}
92			}
93
94			if (pdbCode.equals("") \|\| pdbChainCode.equals("") \|\| ct.equals("") \|\| cutoff1==0.0 \|\| outputDir.equals("") \|\| baseName.equals("")){
95			System.err.println("Must specify at least -p, -c, -t, -d, -o and -b");
96			System.err.println(help);
97			System.exit(1);
98			}
99
100	duarte	346	if (baseName.contains(".")) {
101			System.err.println("Basename can't contain a dot (not allowed by tinker). Exiting");
102			System.exit(1);
103			}
104
105			if (!AAinfo.isValidContactType(ct) \|\| ct.contains("ALL")) {
106			System.err.println("Invalid contact type specified. Exiting");
107			System.exit(1);
108			}
109
110			if (n>999) {
111			System.err.println("Maximum number of models is 999. Specify a lower value. Exiting");
112			System.exit(1);
113			}
114
115	duarte	338	boolean doublecm = false;
116			String ct1 = ct;
117			String ct2 = ct;
118			String ct3 = null;
119			if (ct.contains("_")) {
120			ct1 = ct.split("_")[0];
121			ct2 = ct.split("_")[1];
122			doublecm = true;
123			}
124			if (cross) {
125			ct3 = ct1+"/"+ct2;
126			}
127
128			if (cutoff2==0.0) {
129			cutoff2 = cutoff1;
130			}
131			if (cutoff3==0.0) {
132			cutoff3 = cutoff1;
133			}
134
135			Pdb pdb = null;
136			try {
137			pdb = new PdbasePdb(pdbCode,pdbChainCode);
138			} catch (PdbaseInconsistencyError e) {
139			System.err.println("Pdbase inconsistency for structure "+pdbCode+". Can't continue, exiting");
140			System.exit(1);
141			} catch (PdbCodeNotFoundError e) {
142			System.err.println("Given pdb code "+pdbCode+" couldn't be found in pdbase. Exiting");
143			System.exit(1);
144			} catch (SQLException e) {
145			System.err.println("Problems connecting to database for getting pdb data for "+pdbCode+". Exiting");
146			System.exit(1);
147			} catch (PdbChainCodeNotFoundError e) {
148			System.err.println("Given pdb chain code "+pdbChainCode+" couldn't be found for pdb code "+pdbCode+". Exiting");
149			System.exit(1);
150			}
151	duarte	349	// we also write the file to the out dir so it can be used later for clustering rmsds etc.
152	duarte	367	File origPdbFile = new File (outputDir,baseName+".native.pdb");
153	duarte	349	try {
154			pdb.dump2pdbfile(origPdbFile.getAbsolutePath());
155			} catch (IOException e4) {
156			System.err.println("Couldn't write original pdb file "+origPdbFile.getAbsolutePath());
157			System.err.println("Continuing without it, this is not needed for the rest of the reconstruction process but only for post processing (e.g. comparing rmsds to original)");
158			}
159
160	duarte	338	String sequence = pdb.getSequence();
161
162			Graph graph1 = pdb.get_graph(ct1, cutoff1);
163			Graph graph2 = null;
164			Graph graph3 = null;
165			if (doublecm) {
166			graph2 = pdb.get_graph(ct2, cutoff2);
167			}
168			if (cross) {
169			graph3 = pdb.get_graph(ct3, cutoff3);
170			}
171
172
173			// defining files
174	duarte	348	File logFile = new File(outputDir,baseName+".tinker.log");
175	duarte	338	File prmFile = new File(PRMFILE);
176			File xyzFile = new File(outputDir,baseName+".xyz");
177			File seqFile = new File(outputDir,baseName+".seq");
178			File pdbFile = new File(outputDir,baseName+".pdb");
179			File keyFile = new File(outputDir,baseName+".key");
180	duarte	347	File reportFile = new File(outputDir,baseName+".report");
181	duarte	338
182			// creating TinkerRunner object
183			TinkerRunner tr = null;
184			try {
185			tr = new TinkerRunner(TINKERBINDIR,PRMFILE,logFile);
186			} catch (FileNotFoundException e3) {
187			System.err.println("Couldn't find tinker bin dir "+TINKERBINDIR+". Exiting");
188			System.exit(1);
189			}
190
191			// 1. run tinker's protein program
192			try {
193			tr.runProtein(sequence, outputDir, baseName );
194			} catch (IOException e2) {
195			System.err.println("Couldn't read file to run 'protein' "+seqFile.getAbsolutePath());
196			System.err.println("Exiting");
197			System.exit(1);
198			} catch (TinkerError e2) {
199			System.err.println("Tinker error while running 'protein', check log file "+logFile.getAbsolutePath()+". Exiting");
200			System.exit(1);
201			}
202
203			// 1a. convert xyz file to pdb to be able to map atom serials after
204			try {
205			tr.runXyzpdb(xyzFile, seqFile, pdbFile);
206			} catch (IOException e1) {
207			System.err.println("Couldn't read files "+xyzFile.getAbsolutePath()+" or "+seqFile.getAbsolutePath()+" or write to "+pdbFile.getAbsolutePath()+" for running 'xyzpdb'");
208			System.err.println("Exiting");
209			System.exit(1);
210			} catch (TinkerError e1) {
211			System.err.println("Tinker error while running xyzpdb, check log file "+logFile.getAbsolutePath()+". Exiting");
212			System.exit(1);
213			}
214
215			// 2. creating constraints into key file
216			ConstraintsMaker cm = null;
217			try {
218			cm = new ConstraintsMaker(pdbFile,xyzFile,prmFile,PRMTYPE,keyFile);
219			} catch (IOException e3) {
220			System.err.println("Couldn't read files "+xyzFile.getAbsolutePath()+", "+pdbFile.getAbsolutePath()+" or, "+prmFile.getAbsolutePath()+" write to "+keyFile.getAbsolutePath()+" for creating distance constraints");
221			System.err.println("Exiting");
222			System.exit(1);
223			} catch (PdbfileFormatError e3) {
224			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");
225			System.exit(1);
226			}
227	duarte	346
228			cm.createConstraints(graph1);
229			if (doublecm) cm.createConstraints(graph2);
230			if (cross) cm.createConstraints(graph3);
231
232	duarte	338	cm.closeKeyFile();
233
234			// 3. run tinker's distgeom
235			try {
236			System.out.println("Running distgeom...");
237			tr.runDistgeom(xyzFile, outputDir, baseName, n);
238			} catch (TinkerError e1) {
239	duarte	340	System.err.println(e1.getMessage());
240			System.err.println("Exiting");
241	duarte	338	System.exit(1);
242			} catch (IOException e1) {
243			System.err.println("Couldn't read files "+xyzFile.getAbsolutePath()+" or write 'distgeom' output files to output dir "+outputDir);
244			System.err.println("Exiting");
245			System.exit(1);
246	stehr	344	} catch(InterruptedException e) {
247			System.err.println("Distgeom was interrupted:" + e.getMessage());
248			System.err.println("Exiting.");
249			System.exit(1);
250	duarte	338	}
251
252			double[] mubv = tr.getMaxUpperBoundViol();
253			double[] mlbv = tr.getMaxLowerBoundViol();
254			double[] muv = tr.getMaxUpperViol();
255			double[] mlv = tr.getMaxLowerViol();
256			int[] nubv = tr.getNumUpperBoundViol();
257			int[] nlbv = tr.getNumLowerBoundViol();
258			int[] nuv = tr.getNumUpperViol();
259			int[] nlv = tr.getNumLowerViol();
260			double[] rbv = tr.getRmsBoundViol();
261			double[] rrv = tr.getRmsRestViol();
262
263
264			// 4. converting xyz output files to pdb files and calculating rmsds
265
266			double[] rmsds = new double[n+1];
267
268	duarte	347	for (int i = 1; i<=n; i++) {
269			String ext = new Formatter().format(".%03d",i).toString();
270			File outputXyzFile = new File(outputDir, baseName+ext);
271			File outputPdbFile = new File(outputDir, baseName+ext+".pdb");
272			try {
273			tr.runXyzpdb(outputXyzFile, seqFile, outputPdbFile);
274	duarte	338
275	duarte	347	Pdb outputPdb = new PdbfilePdb(outputPdbFile.getAbsolutePath(),"NULL");
276			rmsds[i] = pdb.rmsd(outputPdb, "Ca");
277	duarte	338
278	duarte	347	} catch (IOException e) {
279			System.err.println("Couldn't read file "+outputXyzFile.getAbsolutePath()+", or "+seqFile.getAbsolutePath()+", or write to "+outputPdbFile.getAbsolutePath()+" while converting with 'xyzpdb'");
280			System.err.println("Can't calculate rmsd for it");
281			} catch (TinkerError e) {
282			System.err.println("Tinker error while running 'xyzpdb' to convert"+outputXyzFile.getAbsolutePath()+", check log file "+logFile.getAbsolutePath());
283			System.err.println("Can't calculate rmsd for it");
284			}
285			catch (PdbfileFormatError e) {
286			System.err.println("Output pdb file "+outputPdbFile.getAbsolutePath()+" doesn't seem to be in the correcet format. Can't calculate rmsd for it");
287			} catch (PdbChainCodeNotFoundError e) {
288			// this shouldn't happen, chain code is hard coded, we throw stack trace and continue if it happens
289			e.printStackTrace();
290			} catch (ConformationsNotSameSizeError e) {
291			System.err.println(pdbFile.getAbsolutePath()+" and "+outputPdbFile.getAbsolutePath()+" don't have the same conformation size, can't calculate rmsd for them.");
292			}
293
294			tr.closeLog();
295			}
296
297	duarte	338
298			// 6. report
299	duarte	347	try {
300			PrintWriter reportOut = new PrintWriter(new FileOutputStream(reportFile));
301			reportOut.println("accession_code\tchain_pdb_code\tcutoff\tcutoff2\tcutoff3\tct\tct2\tct3" +
302			"\tresult_id\tup_bound_viol\tlow_bound_viol\tmax_bound_up\tmax_bound_low\trms_bound" +
303			"\tup_viol\tlow_viol\tmax_up\tmax_low\trms_viol\trmsd_to_orig");
304
305			for (int i=1;i<=n;i++){
306	duarte	349	String rmsd = String.format(Locale.US,"%6f",rmsds[i]);
307	duarte	347	reportOut.println(pdbCode+"\t"+pdbChainCode+"\t"+cutoff1+"\t"+cutoff2+"\t"+cutoff3+"\t"+ct1+"\t"+ct2+"\t"+ct3+"\t"+
308			i+"\t"+nubv[i]+"\t"+nlbv[i]+"\t"+mubv[i]+"\t"+mlbv[i]+"\t"+muv[i]+"\t"+mlv[i]+"\t"+rbv[i]+"\t"+
309	duarte	349	nuv[i]+"\t"+nlv[i]+"\t"+rrv[i]+"\t"+rmsd);
310	duarte	347	}
311			reportOut.close();
312			} catch (FileNotFoundException e) {
313			System.err.println("Couldn't write to report file "+reportFile.getAbsolutePath() +". Error: "+e.getMessage());
314	duarte	338	}
315
316			}
317
318			}