owl/trunk/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.PdbLoadError;
import proteinstructure.RIGraph;
import proteinstructure.Pdb;
import proteinstructure.PdbCodeNotFoundError;
import proteinstructure.PdbasePdb;

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";
        
        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>] [-m <min range>] [-M <max range>] \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;
                //double forceConstant = 100.0;
                int minRange = 0;
                int maxRange = 0;
                
                Getopt g = new Getopt(programName, args, "p:c:d:t:rb:o:d:D:i:n:m:M: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 'm':
                                minRange = Integer.parseInt(g.getOptarg());
                                break;
                        case 'M':
                                maxRange = Integer.parseInt(g.getOptarg());
                                break;                          
                        //case 'f':
                        //      forceConstant = Double.valueOf(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);
                        pdb.load(pdbChainCode);
                } catch (PdbLoadError e) {
                        System.err.println("Error while loading pdb data. Specific error "+e.getMessage());
                        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);
                }
                // 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();

                RIGraph[] graphs =null;
                RIGraph graph1 = pdb.get_graph(ct1, cutoff1);
                if (maxRange>0) graph1.restrictContactsToMaxRange(maxRange);
                if (minRange>0) graph1.restrictContactsToMinRange(minRange);
                RIGraph graph2 = null;
                RIGraph graph3 = null;
                if (doublecm) {
                        graph2 = pdb.get_graph(ct2, cutoff2);
                        if (maxRange>0) graph2.restrictContactsToMaxRange(maxRange);
                        if (minRange>0) graph2.restrictContactsToMinRange(minRange);
                        if (cross) {
                                graph3 = pdb.get_graph(ct3, cutoff3);
                                if (maxRange>0) graph3.restrictContactsToMaxRange(maxRange);
                                if (minRange>0) graph3.restrictContactsToMinRange(minRange);
                                graphs = new RIGraph[3];
                                graphs[0] = graph1;
                                graphs[1] = graph2;
                                graphs[2] = graph3;
                        } else {
                                graphs = new RIGraph[2];
                                graphs[0] = graph1;
                                graphs[1] = graph2;
                        }
                } else {
                        graphs = new RIGraph[1];
                        graphs[0] = graph1;
                }
                
                // defining files
                File reportFile = new File(outputDir,baseName+".report");
                
                // creating TinkerRunner object
                
                TinkerRunner tr = null;
                try {
                        tr = new TinkerRunner(TINKERBINDIR, PRMFILE);
                } catch (FileNotFoundException e3) {
                        System.err.println("Couldn't find tinker bin dir "+TINKERBINDIR+". Exiting");
                        System.exit(1);
                }
                
                // call reconstruction
                
                try {
                        tr.reconstruct(sequence, graphs, n, outputDir, baseName, false);
                } catch (IOException e) {
                        System.err.println("Error while running Tinker reconstruction: " + e.getMessage());
                        System.exit(1);
                } catch (TinkerError e) {
                        System.err.println("Error while running Tinker reconstruction: " + e.getMessage());
                        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();
                

                // calculate rmsds

                double[] rmsds = new double[n+1];               
                
                for (int i = 1; i<=n; i++) {
                        String ext = new Formatter().format(".%03d",i).toString();
                        File outputPdbFile = new File(outputDir, baseName+ext+".pdb");
                        try {
                                Pdb outputPdb = tr.getStructure(i);
                                rmsds[i] = pdb.rmsd(outputPdb, "Ca");
                        }
                        catch (TinkerError e) {
                                System.err.println("Error while trying to retrieve results from Tinker: "+ e.getMessage());
                        } catch (ConformationsNotSameSizeError e) {
                                System.err.println(origPdbFile.getAbsolutePath()+" and "+outputPdbFile.getAbsolutePath()+" don't have the same conformation size, can't calculate rmsd for them.");
                        }                               
                }                                       

                // write report file
                
                try {
                        PrintWriter reportOut = new PrintWriter(new FileOutputStream(reportFile));
                        reportOut.println("run_id\tcutoff\tcutoff2\tcutoff3\tct\tct2\tct3\tnum_res" +
                                                "\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]);
                                //                         run_id                cutoff      cutoff2      cutoff3      ct1      ct2      ct3         num_res
                                reportOut.println(pdbCode+"_"+pdbChainCode+"\t"+cutoff1+"\t"+cutoff2+"\t"+cutoff3+"\t"+ct1+"\t"+ct2+"\t"+ct3+"\t"+sequence.length()+"\t"+
                                //  result_id     error_val         
                                                i + "\t" + errStr + "\t" +
                                //   up_bound_viol    low_bound_viol   max_bound_up    max_bound_low      rms_bound
                                                nubv[i] + "\t" + nlbv[i] + "\t" + mubv[i] + "\t" + mlbv[i] + "\t" + rbv[i] + "\t" +
                                //      up_viol         low_viol       max_up         max_low         rms_viol
                                                nuv[i] + "\t" + nlv[i] + "\t" + muv[i] + "\t" + mlv[i] + "\t"+ rrv[i] + "\t"+
                                //      rmsd_to_orig
                                                rmsd);
                        }
                        reportOut.close();
                } catch (FileNotFoundException e) {
                        System.err.println("Couldn't write to report file "+reportFile.getAbsolutePath() +". Error: "+e.getMessage());
                }
                
        }

}
Revision:	485
Committed:	Wed Dec 19 15:42:46 2007 UTC (16 years, 9 months ago) by duarte
Original Path:	*branches/aglappe-jung/reconstruct.java*
File size:	8846 byte(s)
Log Message:	Now exiting upon distgeom error
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	duarte	441	import proteinstructure.PdbLoadError;
15	duarte	420	import proteinstructure.RIGraph;
16	duarte	338	import proteinstructure.Pdb;
17			import proteinstructure.PdbCodeNotFoundError;
18			import proteinstructure.PdbasePdb;
19
20			import tinker.TinkerError;
21			import tinker.TinkerRunner;
22
23
24			public class reconstruct {
25
26			private static final String TINKERBINDIR = "/project/StruPPi/Software/tinker/bin";
27			private static final String PRMFILE = "/project/StruPPi/Software/tinker/amber/amber99.prm";
28
29			public static void main(String[] args) {
30
31			String programName = reconstruct.class.getName();
32			String help = "Usage:\n" +
33	duarte	471	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>] [-m <min range>] [-M <max range>] \n";
34	duarte	338
35			String pdbCode = "";
36			String pdbChainCode = "";
37			String ct = "";
38			double cutoff1 = 0.0;
39			double cutoff2 = 0.0;
40			double cutoff3 = 0.0;
41			String outputDir = "";
42			String baseName = "";
43			boolean cross = false;
44			int n = 1;
45	duarte	393	//double forceConstant = 100.0;
46	duarte	471	int minRange = 0;
47			int maxRange = 0;
48	duarte	393
49	duarte	471	Getopt g = new Getopt(programName, args, "p:c:d:t:rb:o:d:D:i:n:m:M:h?");
50	duarte	338	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	duarte	393	break;
83	duarte	471	case 'm':
84			minRange = Integer.parseInt(g.getOptarg());
85			break;
86			case 'M':
87			maxRange = Integer.parseInt(g.getOptarg());
88			break;
89	duarte	393	//case 'f':
90			// forceConstant = Double.valueOf(g.getOptarg());
91			// break;
92	duarte	338	case 'h':
93			case '?':
94			System.out.println(help);
95			System.exit(0);
96			break; // getopt() already printed an error
97			}
98			}
99
100			if (pdbCode.equals("") \|\| pdbChainCode.equals("") \|\| ct.equals("") \|\| cutoff1==0.0 \|\| outputDir.equals("") \|\| baseName.equals("")){
101			System.err.println("Must specify at least -p, -c, -t, -d, -o and -b");
102			System.err.println(help);
103			System.exit(1);
104			}
105
106	duarte	346	if (baseName.contains(".")) {
107			System.err.println("Basename can't contain a dot (not allowed by tinker). Exiting");
108			System.exit(1);
109			}
110
111			if (!AAinfo.isValidContactType(ct) \|\| ct.contains("ALL")) {
112			System.err.println("Invalid contact type specified. Exiting");
113			System.exit(1);
114			}
115
116			if (n>999) {
117			System.err.println("Maximum number of models is 999. Specify a lower value. Exiting");
118			System.exit(1);
119			}
120
121	duarte	338	boolean doublecm = false;
122			String ct1 = ct;
123			String ct2 = ct;
124			String ct3 = null;
125			if (ct.contains("_")) {
126			ct1 = ct.split("_")[0];
127			ct2 = ct.split("_")[1];
128			doublecm = true;
129			}
130			if (cross) {
131			ct3 = ct1+"/"+ct2;
132			}
133
134			if (cutoff2==0.0) {
135			cutoff2 = cutoff1;
136			}
137			if (cutoff3==0.0) {
138			cutoff3 = cutoff1;
139			}
140
141			Pdb pdb = null;
142			try {
143	duarte	441	pdb = new PdbasePdb(pdbCode);
144			pdb.load(pdbChainCode);
145			} catch (PdbLoadError e) {
146			System.err.println("Error while loading pdb data. Specific error "+e.getMessage());
147	duarte	338	System.exit(1);
148			} catch (PdbCodeNotFoundError e) {
149			System.err.println("Given pdb code "+pdbCode+" couldn't be found in pdbase. Exiting");
150			System.exit(1);
151			} catch (SQLException e) {
152			System.err.println("Problems connecting to database for getting pdb data for "+pdbCode+". Exiting");
153			System.exit(1);
154			}
155	duarte	349	// we also write the file to the out dir so it can be used later for clustering rmsds etc.
156	duarte	367	File origPdbFile = new File (outputDir,baseName+".native.pdb");
157	duarte	349	try {
158			pdb.dump2pdbfile(origPdbFile.getAbsolutePath());
159			} catch (IOException e4) {
160			System.err.println("Couldn't write original pdb file "+origPdbFile.getAbsolutePath());
161			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)");
162			}
163
164	duarte	338	String sequence = pdb.getSequence();
165
166	duarte	420	RIGraph[] graphs =null;
167			RIGraph graph1 = pdb.get_graph(ct1, cutoff1);
168	duarte	471	if (maxRange>0) graph1.restrictContactsToMaxRange(maxRange);
169			if (minRange>0) graph1.restrictContactsToMinRange(minRange);
170	duarte	420	RIGraph graph2 = null;
171			RIGraph graph3 = null;
172	duarte	338	if (doublecm) {
173	duarte	471	graph2 = pdb.get_graph(ct2, cutoff2);
174			if (maxRange>0) graph2.restrictContactsToMaxRange(maxRange);
175			if (minRange>0) graph2.restrictContactsToMinRange(minRange);
176	stehr	379	if (cross) {
177			graph3 = pdb.get_graph(ct3, cutoff3);
178	duarte	471	if (maxRange>0) graph3.restrictContactsToMaxRange(maxRange);
179			if (minRange>0) graph3.restrictContactsToMinRange(minRange);
180	duarte	420	graphs = new RIGraph[3];
181	stehr	379	graphs[0] = graph1;
182			graphs[1] = graph2;
183			graphs[2] = graph3;
184			} else {
185	duarte	420	graphs = new RIGraph[2];
186	stehr	379	graphs[0] = graph1;
187			graphs[1] = graph2;
188			}
189			} else {
190	duarte	420	graphs = new RIGraph[1];
191	stehr	379	graphs[0] = graph1;
192	duarte	338	}
193
194			// defining files
195	duarte	347	File reportFile = new File(outputDir,baseName+".report");
196	duarte	338
197			// creating TinkerRunner object
198	stehr	379
199	duarte	338	TinkerRunner tr = null;
200			try {
201	stehr	379	tr = new TinkerRunner(TINKERBINDIR, PRMFILE);
202	duarte	338	} catch (FileNotFoundException e3) {
203			System.err.println("Couldn't find tinker bin dir "+TINKERBINDIR+". Exiting");
204			System.exit(1);
205			}
206
207	stehr	379	// call reconstruction
208
209	duarte	338	try {
210	stehr	379	tr.reconstruct(sequence, graphs, n, outputDir, baseName, false);
211			} catch (IOException e) {
212			System.err.println("Error while running Tinker reconstruction: " + e.getMessage());
213	duarte	485	System.exit(1);
214	stehr	379	} catch (TinkerError e) {
215			System.err.println("Error while running Tinker reconstruction: " + e.getMessage());
216	duarte	485	System.exit(1);
217	duarte	338	}
218	stehr	379
219	duarte	368	double[] err = tr.getErrorFunctionVal();
220	duarte	338	double[] mubv = tr.getMaxUpperBoundViol();
221			double[] mlbv = tr.getMaxLowerBoundViol();
222			double[] muv = tr.getMaxUpperViol();
223			double[] mlv = tr.getMaxLowerViol();
224			int[] nubv = tr.getNumUpperBoundViol();
225			int[] nlbv = tr.getNumLowerBoundViol();
226			int[] nuv = tr.getNumUpperViol();
227			int[] nlv = tr.getNumLowerViol();
228			double[] rbv = tr.getRmsBoundViol();
229			double[] rrv = tr.getRmsRestViol();
230
231
232	stehr	379	// calculate rmsds
233	duarte	338
234			double[] rmsds = new double[n+1];
235
236	duarte	347	for (int i = 1; i<=n; i++) {
237			String ext = new Formatter().format(".%03d",i).toString();
238			File outputPdbFile = new File(outputDir, baseName+ext+".pdb");
239			try {
240	stehr	379	Pdb outputPdb = tr.getStructure(i);
241	duarte	347	rmsds[i] = pdb.rmsd(outputPdb, "Ca");
242			}
243	stehr	379	catch (TinkerError e) {
244	duarte	471	System.err.println("Error while trying to retrieve results from Tinker: "+ e.getMessage());
245	duarte	347	} catch (ConformationsNotSameSizeError e) {
246	stehr	379	System.err.println(origPdbFile.getAbsolutePath()+" and "+outputPdbFile.getAbsolutePath()+" don't have the same conformation size, can't calculate rmsd for them.");
247	duarte	347	}
248			}
249
250	stehr	379	// write report file
251	duarte	338
252	duarte	347	try {
253			PrintWriter reportOut = new PrintWriter(new FileOutputStream(reportFile));
254	duarte	373	reportOut.println("run_id\tcutoff\tcutoff2\tcutoff3\tct\tct2\tct3\tnum_res" +
255			"\tresult_id\terror_val" +
256			"\tup_bound_viol\tlow_bound_viol\tmax_bound_up\tmax_bound_low\trms_bound" +
257	duarte	347	"\tup_viol\tlow_viol\tmax_up\tmax_low\trms_viol\trmsd_to_orig");
258
259			for (int i=1;i<=n;i++){
260	duarte	368	String rmsd = String.format(Locale.US,"%6.3f",rmsds[i]);
261			String errStr = String.format(Locale.US, "%6.3f", err[i]);
262	duarte	373	// run_id cutoff cutoff2 cutoff3 ct1 ct2 ct3 num_res
263			reportOut.println(pdbCode+"_"+pdbChainCode+"\t"+cutoff1+"\t"+cutoff2+"\t"+cutoff3+"\t"+ct1+"\t"+ct2+"\t"+ct3+"\t"+sequence.length()+"\t"+
264			// result_id error_val
265			i + "\t" + errStr + "\t" +
266			// up_bound_viol low_bound_viol max_bound_up max_bound_low rms_bound
267			nubv[i] + "\t" + nlbv[i] + "\t" + mubv[i] + "\t" + mlbv[i] + "\t" + rbv[i] + "\t" +
268			// up_viol low_viol max_up max_low rms_viol
269			nuv[i] + "\t" + nlv[i] + "\t" + muv[i] + "\t" + mlv[i] + "\t"+ rrv[i] + "\t"+
270			// rmsd_to_orig
271			rmsd);
272	duarte	347	}
273			reportOut.close();
274			} catch (FileNotFoundException e) {
275			System.err.println("Couldn't write to report file "+reportFile.getAbsolutePath() +". Error: "+e.getMessage());
276	duarte	338	}
277
278			}
279
280			}