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[] err = tr.getErrorFunctionVal();
                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("run_id\tcutoff\tcutoff2\tcutoff3\tct\tct2\tct3" +
                                                "\tresult_id\terror_val\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,"%6.3f",rmsds[i]);
                                String errStr = String.format(Locale.US, "%6.3f", err[i]);
                                reportOut.println(pdbCode+"_"+pdbChainCode+"\t"+cutoff1+"\t"+cutoff2+"\t"+cutoff3+"\t"+ct1+"\t"+ct2+"\t"+ct3+"\t"+
                                                i+"\t"+errStr+"\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:	368
Committed:	Thu Oct 25 09:38:02 2007 UTC (16 years, 11 months ago) by duarte
Original Path:	*trunk/reconstruct.java*
File size:	11157 byte(s)
Log Message:	Now parsing tinker's error function value, changed report file format (again!!)
Line	File contents
1	import gnu.getopt.Getopt;
2
3	import java.io.File;
4	import java.io.FileNotFoundException;
5	import java.io.FileOutputStream;
6	import java.io.IOException;
7	import java.io.PrintWriter;
8	import java.sql.SQLException;
9	import java.util.Formatter;
10	import java.util.Locale;
11
12	import proteinstructure.AAinfo;
13	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	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	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	// we also write the file to the out dir so it can be used later for clustering rmsds etc.
152	File origPdbFile = new File (outputDir,baseName+".native.pdb");
153	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	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	File logFile = new File(outputDir,baseName+".tinker.log");
175	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	File reportFile = new File(outputDir,baseName+".report");
181
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
228	cm.createConstraints(graph1);
229	if (doublecm) cm.createConstraints(graph2);
230	if (cross) cm.createConstraints(graph3);
231
232	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	System.err.println(e1.getMessage());
240	System.err.println("Exiting");
241	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	} catch(InterruptedException e) {
247	System.err.println("Distgeom was interrupted:" + e.getMessage());
248	System.err.println("Exiting.");
249	System.exit(1);
250	}
251
252	double[] err = tr.getErrorFunctionVal();
253	double[] mubv = tr.getMaxUpperBoundViol();
254	double[] mlbv = tr.getMaxLowerBoundViol();
255	double[] muv = tr.getMaxUpperViol();
256	double[] mlv = tr.getMaxLowerViol();
257	int[] nubv = tr.getNumUpperBoundViol();
258	int[] nlbv = tr.getNumLowerBoundViol();
259	int[] nuv = tr.getNumUpperViol();
260	int[] nlv = tr.getNumLowerViol();
261	double[] rbv = tr.getRmsBoundViol();
262	double[] rrv = tr.getRmsRestViol();
263
264
265	// 4. converting xyz output files to pdb files and calculating rmsds
266
267	double[] rmsds = new double[n+1];
268
269	for (int i = 1; i<=n; i++) {
270	String ext = new Formatter().format(".%03d",i).toString();
271	File outputXyzFile = new File(outputDir, baseName+ext);
272	File outputPdbFile = new File(outputDir, baseName+ext+".pdb");
273	try {
274	tr.runXyzpdb(outputXyzFile, seqFile, outputPdbFile);
275
276	Pdb outputPdb = new PdbfilePdb(outputPdbFile.getAbsolutePath(),"NULL");
277	rmsds[i] = pdb.rmsd(outputPdb, "Ca");
278
279	} catch (IOException e) {
280	System.err.println("Couldn't read file "+outputXyzFile.getAbsolutePath()+", or "+seqFile.getAbsolutePath()+", or write to "+outputPdbFile.getAbsolutePath()+" while converting with 'xyzpdb'");
281	System.err.println("Can't calculate rmsd for it");
282	} catch (TinkerError e) {
283	System.err.println("Tinker error while running 'xyzpdb' to convert"+outputXyzFile.getAbsolutePath()+", check log file "+logFile.getAbsolutePath());
284	System.err.println("Can't calculate rmsd for it");
285	}
286	catch (PdbfileFormatError e) {
287	System.err.println("Output pdb file "+outputPdbFile.getAbsolutePath()+" doesn't seem to be in the correcet format. Can't calculate rmsd for it");
288	} catch (PdbChainCodeNotFoundError e) {
289	// this shouldn't happen, chain code is hard coded, we throw stack trace and continue if it happens
290	e.printStackTrace();
291	} catch (ConformationsNotSameSizeError e) {
292	System.err.println(pdbFile.getAbsolutePath()+" and "+outputPdbFile.getAbsolutePath()+" don't have the same conformation size, can't calculate rmsd for them.");
293	}
294
295	tr.closeLog();
296	}
297
298
299	// 6. report
300	try {
301	PrintWriter reportOut = new PrintWriter(new FileOutputStream(reportFile));
302	reportOut.println("run_id\tcutoff\tcutoff2\tcutoff3\tct\tct2\tct3" +
303	"\tresult_id\terror_val\tup_bound_viol\tlow_bound_viol\tmax_bound_up\tmax_bound_low\trms_bound" +
304	"\tup_viol\tlow_viol\tmax_up\tmax_low\trms_viol\trmsd_to_orig");
305
306	for (int i=1;i<=n;i++){
307	String rmsd = String.format(Locale.US,"%6.3f",rmsds[i]);
308	String errStr = String.format(Locale.US, "%6.3f", err[i]);
309	reportOut.println(pdbCode+"_"+pdbChainCode+"\t"+cutoff1+"\t"+cutoff2+"\t"+cutoff3+"\t"+ct1+"\t"+ct2+"\t"+ct3+"\t"+
310	i+"\t"+errStr+"\t"+nubv[i]+"\t"+nlbv[i]+"\t"+mubv[i]+"\t"+mlbv[i]+"\t"+muv[i]+"\t"+mlv[i]+"\t"+rbv[i]+"\t"+
311	nuv[i]+"\t"+nlv[i]+"\t"+rrv[i]+"\t"+rmsd);
312	}
313	reportOut.close();
314	} catch (FileNotFoundException e) {
315	System.err.println("Couldn't write to report file "+reportFile.getAbsolutePath() +". Error: "+e.getMessage());
316	}
317
318	}
319
320	}