trunk/tinker/TinkerRunner.java

package tinker;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.PrintWriter;
import java.nio.channels.FileChannel;
import java.util.Formatter;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

public class TinkerRunner {
        
        private static final String PROTEIN_PROG = "protein";
        private static final String DISTGEOM_PROG = "distgeom";
        private static final String PDBXYZ_PROG = "pdbxyz";
        private static final String XYZPDB_PROG = "xyzpdb";
        private static final String CYCLISE_PROTEIN_STR = "N";
        private static final String DGEOM_PARAMS = "Y N Y Y N N A";
        private static final String TINKER_ERROR_STR = " TINKER is Unable to Continue";
        
        private String tinkerBinDir;
        
        private String forceFieldFileName;
        
        private String proteinProg;
        private String distgeomProg;
        private String pdbxyzProg;
        private String xyzpdbProg;
        
        private File logFile;
        private PrintWriter log;
        
        // arrays for storing distgeom output data
        private int[] numUpperBoundViol;
        private int[] numLowerBoundViol;
        private double[] maxUpperBoundViol;
        private double[] maxLowerBoundViol;
        private double[] rmsBoundViol;
        private int[] numUpperViol;
        private int[] numLowerViol;
        private double[] maxUpperViol;
        private double[] maxLowerViol;
        private double[] rmsRestViol;

        
        /**
         * Constructs a TinkerRunner object by passing initial parameters
         * @param tinkerBinDir The directory where the tinker executables are
         * @param forceFieldFileName The force field file
         * @param logFile File where all tinker output will be logged to
         * @throws FileNotFoundException If logFile can't be written
         */
        public TinkerRunner(String tinkerBinDir, String forceFieldFileName, File logFile) throws FileNotFoundException {
                this.tinkerBinDir = tinkerBinDir;
                this.forceFieldFileName = forceFieldFileName;
                this.proteinProg = new File(this.tinkerBinDir,PROTEIN_PROG).getAbsolutePath();
                this.distgeomProg = new File(this.tinkerBinDir,DISTGEOM_PROG).getAbsolutePath();
                this.pdbxyzProg = new File(this.tinkerBinDir,PDBXYZ_PROG).getAbsolutePath();
                this.xyzpdbProg = new File(this.tinkerBinDir,XYZPDB_PROG).getAbsolutePath();
                
                this.logFile = logFile;
                this.log = new PrintWriter(new FileOutputStream(logFile));
        }
        
        /**
         * To get the expected File that a tinker program will output given an input file and an extension for the output files
         * The directory where the input file is will be scanned to see if it contains files of the form basename.ext, basename.ext_2, basename.ext_3 etc.
         * @param file
         * @param ext
         * @return
         */
        private File getTinkerOutputFileName(File file, String ext){
                String basename = file.getName();
                basename = basename.substring(0, basename.lastIndexOf("."));
                String dirname = file.getParent();
                
                String tinkerOutFileName = basename + "." + ext;
                
                if (new File(dirname,tinkerOutFileName).exists()) {
                        int i = 2;
                        tinkerOutFileName = basename + "." + ext + "_" + i;
                        while (new File(dirname,tinkerOutFileName).exists()) {
                                i++;
                                tinkerOutFileName = basename + "." + ext + "_" + i;
                        }
                }
                return new File(dirname,tinkerOutFileName);
        }
        
        /**
         * Runs tinker's protein program to generate an elongated protein structure given a sequence
         * @param sequence
         * @param outPath The directory where output files will be written
         * @param outBasename The base name for the output files
         * @throws IOException
         * @throws TinkerError
         */
        public void runProtein(String sequence, String outPath, String outBasename) throws IOException, TinkerError {
                boolean tinkerError = false; // to store the exit state of the tinker program
                
                if (!new File(outPath).exists()) {
                        throw new FileNotFoundException("Specified directory "+outPath+" does not exist");
                }
                File tinkerxyzout = getTinkerOutputFileName(new File(outPath,outBasename+".xyz"),"xyz");
                File tinkerintout = getTinkerOutputFileName(new File(outPath,outBasename+".int"),"int");
                tinkerintout.deleteOnExit();
                File tinkerseqout = getTinkerOutputFileName(new File(outPath,outBasename+".seq"),"seq");
                
                // running protein program in outPath dir (so that output files are written to outPath)
                Process protProc = Runtime.getRuntime().exec(proteinProg, null, new File(outPath));
                // piping input
                PrintWriter protInput = new PrintWriter(protProc.getOutputStream());
                protInput.println(outBasename);
                protInput.println("Unfolded chain created by tinker's protein program");
                protInput.println(forceFieldFileName);
                for (int i=0;i<sequence.length();i++) {
                        // we've got to use 3 letter code for CYS, otherwise tinker takes the default CYX (which means cystein with disulfide bridge)
                        if (sequence.charAt(i)=='C') {
                                protInput.println("CYS");
                        } else {
                                protInput.println(sequence.charAt(i));
                        }
                }
                protInput.println();
                protInput.println(CYCLISE_PROTEIN_STR);
                protInput.close();
                
                // logging output
                BufferedReader protOutput = new BufferedReader(new InputStreamReader(protProc.getInputStream()));
                String line;
                while((line = protOutput.readLine()) != null) {
                        log.println(line);
                        if (line.startsWith(TINKER_ERROR_STR)) {
                                tinkerError = true;
                        }
                }
                
                tinkerxyzout.renameTo(new File(outPath,outBasename+".xyz"));
                tinkerseqout.renameTo(new File(outPath,outBasename+".seq"));
                
                if (tinkerError) {
                        log.close();
                        throw new TinkerError("Tinker error, revise log file "+logFile.getAbsolutePath());
                }
        }

        /**
         * Runs tinker's distgeom program capturing output with restrain violation statistics into member variable arrays
         * that can be retrieved using the getters: getMaxLowerBoundViol, getMaxUpperBoundViol, getMaxLowerViol etc... 
         * Two files are needed as input for distgeom: an xyz file and a key file, the latter is not passed but instead implicitely 
         * defined by xyzFile: must be in same directory and must have same basename with extension .key 
         * @param xyzFile
         * @param outPath Directory where output files will be written
         * @param outBasename Base name of the output files
         * @param n Number of models that we want distgeom to produce
         * @throws TinkerError If an error seen in tinker's output
         * @throws IOException
         */
        public void runDistgeom(File xyzFile, String outPath, String outBasename, int n) throws TinkerError, IOException {
                boolean tinkerError = false; // to store the exit state of the tinker program
                if (!new File(outPath).exists()) {
                        throw new FileNotFoundException("Specified directory "+outPath+" does not exist");
                }
                if (!xyzFile.exists()){
                        throw new FileNotFoundException("Specified xyz file "+xyzFile.getAbsolutePath()+" does not exist");
                }
                String basename = xyzFile.getName();
                basename = basename.substring(0, basename.lastIndexOf("."));
                File keyFile = new File(xyzFile.getParent(),basename+".key");
                if (! keyFile.exists()) {
                        throw new FileNotFoundException("Key file "+keyFile.getAbsolutePath()+" not present in input directory "+xyzFile.getParent());
                }
                // getting names of tinker output files
                File[] tinkerout = new File[n+1];
                for (int i=1;i<=n;i++) {
                        String ext = new Formatter().format("%03d", i).toString();
                        tinkerout[i] = getTinkerOutputFileName(xyzFile, ext);
                }
                // initialising arrays were we store captured output data
                numUpperBoundViol = new int[n+1];
                numLowerBoundViol = new int[n+1];
                maxUpperBoundViol = new double[n+1];
                maxLowerBoundViol = new double[n+1];
                rmsBoundViol = new double[n+1];
                numUpperViol = new int[n+1];
                numLowerViol = new int[n+1];
                maxUpperViol = new double[n+1];
                maxLowerViol = new double[n+1];
                rmsRestViol = new double[n+1];
                // running distgeom program
                Process dgeomProc = Runtime.getRuntime().exec(distgeomProg+" "+xyzFile.getAbsolutePath()+" "+n+" "+DGEOM_PARAMS);
                // logging and capturing output
                BufferedReader dgeomOutput = new BufferedReader(new InputStreamReader(dgeomProc.getInputStream()));
                String line;
                int i=1;
                while((line = dgeomOutput.readLine()) != null) {
                        log.println(line);
                        if (line.startsWith(TINKER_ERROR_STR)) {
                                tinkerError = true;
                        }
                        Pattern p = Pattern.compile("^ Num Upper Bound Violations :\\s+(\\d+)");
                        Matcher m = p.matcher(line);
                        if (m.find()) {
                                numUpperBoundViol[i]=Integer.parseInt(m.group(1));
                        }
                        p = Pattern.compile("^ Num Lower Bound Violations :\\s+(\\d+)");
                        m = p.matcher(line);
                        if (m.find()) {
                                numLowerBoundViol[i]=Integer.parseInt(m.group(1));
                        }
                        p = Pattern.compile("^ Max Upper Bound Violation :\\s+(\\d+\\.\\d\\d\\d\\d)");
                        m = p.matcher(line);
                        if (m.find()) {
                                maxUpperBoundViol[i]=Double.parseDouble(m.group(1));
                        }
                        p = Pattern.compile("^ Max Lower Bound Violation :\\s+(\\d+\\.\\d\\d\\d\\d)");
                        m = p.matcher(line);
                        if (m.find()) {
                                maxLowerBoundViol[i]=Double.parseDouble(m.group(1));
                        }
                        p = Pattern.compile("^ RMS Deviation from Bounds :\\s+(\\d+\\.\\d\\d\\d\\d)");
                        m = p.matcher(line);
                        if (m.find()) {
                                rmsBoundViol[i]=Double.parseDouble(m.group(1));
                        }
                        p = Pattern.compile("^ Num Upper Restraint Violations :\\s+(\\d+)");
                        m = p.matcher(line);
                        if (m.find()) {
                                numUpperViol[i]=Integer.parseInt(m.group(1));
                        }
                        p = Pattern.compile("^ Num Lower Restraint Violations :\\s+(\\d+)");
                        m = p.matcher(line);
                        if (m.find()) {
                                numLowerViol[i]=Integer.parseInt(m.group(1));
                        }
                        p = Pattern.compile("^ Max Upper Restraint Violation :\\s+(\\d+\\.\\d\\d\\d\\d)");
                        m = p.matcher(line);
                        if (m.find()) {
                                maxUpperViol[i]=Double.parseDouble(m.group(1));
                        }
                        p = Pattern.compile("^ Max Lower Restraint Violation :\\s+(\\d+\\.\\d\\d\\d\\d)");
                        m = p.matcher(line);
                        if (m.find()) {
                                maxLowerViol[i]=Double.parseDouble(m.group(1));
                        }
                        p = Pattern.compile("^ RMS Restraint Dist Violation :\\s+(\\d+\\.\\d\\d\\d\\d)");
                        m = p.matcher(line);
                        if (m.find()) {
                                rmsRestViol[i]=Double.parseDouble(m.group(1));
                                i++;
                        }
                }
                //renaming files to our chosen outBasename+ext
                for (i=1;i<=n;i++) {
                        String ext = new Formatter().format("%03d", i).toString();
                        tinkerout[i].renameTo(new File(outPath,outBasename+"."+ext));
                }
                // throwing exception if error string was caught in output
                if (tinkerError) {
                        log.close();
                        throw new TinkerError("Tinker error, revise log file "+logFile.getAbsolutePath());
                }
                
        }
        
        /**
         * Runs tinker's xyzpdb program to convert a given xyzFile (needing also a seqFile) to a pdbFile
         * @param xyzFile
         * @param seqFile
         * @param pdbFile
         * @throws IOException 
         * @throws TinkerError If an error seen in tinker's output
         */
        public void runXyzpdb(File xyzFile, File seqFile, File pdbFile) throws IOException, TinkerError {
                boolean tinkerError = false; // to store the exit state of the tinker program
                if (!xyzFile.exists()){
                        throw new FileNotFoundException("Specified xyz file "+xyzFile.getAbsolutePath()+" does not exist");
                }
                if (!seqFile.exists()){
                        throw new FileNotFoundException("Specified seq file "+seqFile.getAbsolutePath()+" does not exist");
                }
                
                String basename = xyzFile.getName();
                basename = basename.substring(0, basename.lastIndexOf("."));
                File tmpSeqFile = new File(seqFile.getParent(),basename+".seq");
                                
                // if seqFile doesn't follow the naming convention (basename of xyzFile+seq extension) that tinker expects, we copy it to tmpSeqFile (which has right name) 
                if (!tmpSeqFile.equals(seqFile)) {
                        FileChannel srcChannel = new FileInputStream(seqFile).getChannel();
                        FileChannel dstChannel = new FileOutputStream(tmpSeqFile).getChannel();
                        dstChannel.transferFrom(srcChannel, 0, srcChannel.size());
                        srcChannel.close();
                        dstChannel.close();
                        // if we copied then that means tmpSeqFile is different from seqFile and thus we want to delete the tmp file on exit
                        tmpSeqFile.deleteOnExit(); 
                }
        
                File tinkerpdbout = getTinkerOutputFileName(xyzFile, "pdb");
                
                // running tinker's xyzpdb
                // beware: it takes as a silent input the seq file seqFile (or tmpSeqFile if the input seqFile didn't have the right name) 
                Process xyzpdbProc = Runtime.getRuntime().exec(xyzpdbProg+" "+xyzFile.getAbsolutePath()+" "+forceFieldFileName);

                // logging output
                BufferedReader xyzpdbOutput = new BufferedReader(new InputStreamReader(xyzpdbProc.getInputStream()));
                String line;
                while((line = xyzpdbOutput.readLine()) != null) {
                        log.println(line);
                        if (line.startsWith(TINKER_ERROR_STR)) {
                                tinkerError = true;
                        }
                }
                
                tinkerpdbout.renameTo(pdbFile);
                
                if (tinkerError) {
                        log.close();
                        throw new TinkerError("Tinker error, revise log file "+logFile.getAbsolutePath());
                }
        }
        
        /**
         * Runs tinker's pdbxyz program to convert a pdbFile to a xyzFile
         * @param pdbFile
         * @param xyzFile
         * @throws IOException
         * @throws TinkerError If an error seen in tinker's output
         */
        public void runPdbxyz(File pdbFile, File xyzFile) throws IOException, TinkerError{
                boolean tinkerError = false; // to store the exit state of the tinker program
                if (!pdbFile.exists()){
                        throw new FileNotFoundException("Specified pdb file "+pdbFile.getAbsolutePath()+" does not exist");
                }
                File tinkerxyzout = getTinkerOutputFileName(pdbFile, "xyz");
                // running tinker's pdbxyz
                Process pdbxyzProc = Runtime.getRuntime().exec(pdbxyzProg+" "+pdbFile.getAbsolutePath()+" "+forceFieldFileName);

                // logging output
                BufferedReader pdbxyzOutput = new BufferedReader(new InputStreamReader(pdbxyzProc.getInputStream()));
                String line;
                while((line = pdbxyzOutput.readLine()) != null) {
                        log.println(line);
                        if (line.startsWith(TINKER_ERROR_STR)) {
                                tinkerError = true;
                        }
                }
                tinkerxyzout.renameTo(xyzFile);
                if (tinkerError) {
                        log.close();
                        throw new TinkerError("Tinker error, revise log file "+logFile.getAbsolutePath());
                }
        }
        
        /**
         * Closes log stream, must be called after no other tinker program will be run with this TinkerRunner object
         * (otherwise log is not flushed to file)
         */
        public void closeLog() {
                log.close();
        } 
        
        public double[] getMaxLowerBoundViol() {
                return maxLowerBoundViol;
        }

        public double[] getMaxLowerViol() {
                return maxLowerViol;
        }

        public double[] getMaxUpperBoundViol() {
                return maxUpperBoundViol;
        }

        public double[] getMaxUpperViol() {
                return maxUpperViol;
        }

        public int[] getNumLowerBoundViol() {
                return numLowerBoundViol;
        }

        public int[] getNumLowerViol() {
                return numLowerViol;
        }

        public int[] getNumUpperBoundViol() {
                return numUpperBoundViol;
        }

        public int[] getNumUpperViol() {
                return numUpperViol;
        }

        public double[] getRmsBoundViol() {
                return rmsBoundViol;
        }

        public double[] getRmsRestViol() {
                return rmsRestViol;
        }
}
Revision:	338
Committed:	Fri Oct 5 11:56:28 2007 UTC (17 years, 4 months ago) by duarte
File size:	14717 byte(s)
Log Message:	Initial commit of reconstruct script. Works only sometimes!! Some others doesn't run distgeom without apparent reason! Throwing less exceptions in ConstraintsMaker
Line	User	Rev	File contents
1	duarte	323	package tinker;
2	duarte	322
3			import java.io.BufferedReader;
4			import java.io.File;
5			import java.io.FileInputStream;
6			import java.io.FileNotFoundException;
7			import java.io.FileOutputStream;
8			import java.io.IOException;
9			import java.io.InputStreamReader;
10			import java.io.PrintWriter;
11			import java.nio.channels.FileChannel;
12			import java.util.Formatter;
13			import java.util.regex.Matcher;
14			import java.util.regex.Pattern;
15
16			public class TinkerRunner {
17
18			private static final String PROTEIN_PROG = "protein";
19			private static final String DISTGEOM_PROG = "distgeom";
20			private static final String PDBXYZ_PROG = "pdbxyz";
21			private static final String XYZPDB_PROG = "xyzpdb";
22			private static final String CYCLISE_PROTEIN_STR = "N";
23			private static final String DGEOM_PARAMS = "Y N Y Y N N A";
24			private static final String TINKER_ERROR_STR = " TINKER is Unable to Continue";
25
26			private String tinkerBinDir;
27
28			private String forceFieldFileName;
29
30			private String proteinProg;
31			private String distgeomProg;
32			private String pdbxyzProg;
33			private String xyzpdbProg;
34
35			private File logFile;
36			private PrintWriter log;
37
38			// arrays for storing distgeom output data
39			private int[] numUpperBoundViol;
40			private int[] numLowerBoundViol;
41			private double[] maxUpperBoundViol;
42			private double[] maxLowerBoundViol;
43			private double[] rmsBoundViol;
44			private int[] numUpperViol;
45			private int[] numLowerViol;
46			private double[] maxUpperViol;
47			private double[] maxLowerViol;
48			private double[] rmsRestViol;
49
50
51			/**
52			* Constructs a TinkerRunner object by passing initial parameters
53			* @param tinkerBinDir The directory where the tinker executables are
54			* @param forceFieldFileName The force field file
55			* @param logFile File where all tinker output will be logged to
56			* @throws FileNotFoundException If logFile can't be written
57			*/
58			public TinkerRunner(String tinkerBinDir, String forceFieldFileName, File logFile) throws FileNotFoundException {
59			this.tinkerBinDir = tinkerBinDir;
60			this.forceFieldFileName = forceFieldFileName;
61			this.proteinProg = new File(this.tinkerBinDir,PROTEIN_PROG).getAbsolutePath();
62			this.distgeomProg = new File(this.tinkerBinDir,DISTGEOM_PROG).getAbsolutePath();
63			this.pdbxyzProg = new File(this.tinkerBinDir,PDBXYZ_PROG).getAbsolutePath();
64			this.xyzpdbProg = new File(this.tinkerBinDir,XYZPDB_PROG).getAbsolutePath();
65
66			this.logFile = logFile;
67			this.log = new PrintWriter(new FileOutputStream(logFile));
68			}
69
70			/**
71			* To get the expected File that a tinker program will output given an input file and an extension for the output files
72			* The directory where the input file is will be scanned to see if it contains files of the form basename.ext, basename.ext_2, basename.ext_3 etc.
73			* @param file
74			* @param ext
75			* @return
76			*/
77			private File getTinkerOutputFileName(File file, String ext){
78			String basename = file.getName();
79			basename = basename.substring(0, basename.lastIndexOf("."));
80			String dirname = file.getParent();
81
82			String tinkerOutFileName = basename + "." + ext;
83
84			if (new File(dirname,tinkerOutFileName).exists()) {
85			int i = 2;
86			tinkerOutFileName = basename + "." + ext + "_" + i;
87			while (new File(dirname,tinkerOutFileName).exists()) {
88			i++;
89			tinkerOutFileName = basename + "." + ext + "_" + i;
90			}
91			}
92			return new File(dirname,tinkerOutFileName);
93			}
94
95			/**
96			* Runs tinker's protein program to generate an elongated protein structure given a sequence
97			* @param sequence
98			* @param outPath The directory where output files will be written
99			* @param outBasename The base name for the output files
100			* @throws IOException
101			* @throws TinkerError
102			*/
103			public void runProtein(String sequence, String outPath, String outBasename) throws IOException, TinkerError {
104			boolean tinkerError = false; // to store the exit state of the tinker program
105
106			if (!new File(outPath).exists()) {
107			throw new FileNotFoundException("Specified directory "+outPath+" does not exist");
108			}
109			File tinkerxyzout = getTinkerOutputFileName(new File(outPath,outBasename+".xyz"),"xyz");
110			File tinkerintout = getTinkerOutputFileName(new File(outPath,outBasename+".int"),"int");
111			tinkerintout.deleteOnExit();
112			File tinkerseqout = getTinkerOutputFileName(new File(outPath,outBasename+".seq"),"seq");
113
114			// running protein program in outPath dir (so that output files are written to outPath)
115			Process protProc = Runtime.getRuntime().exec(proteinProg, null, new File(outPath));
116			// piping input
117			PrintWriter protInput = new PrintWriter(protProc.getOutputStream());
118			protInput.println(outBasename);
119			protInput.println("Unfolded chain created by tinker's protein program");
120			protInput.println(forceFieldFileName);
121			for (int i=0;i<sequence.length();i++) {
122			// we've got to use 3 letter code for CYS, otherwise tinker takes the default CYX (which means cystein with disulfide bridge)
123			if (sequence.charAt(i)=='C') {
124			protInput.println("CYS");
125			} else {
126			protInput.println(sequence.charAt(i));
127			}
128			}
129			protInput.println();
130			protInput.println(CYCLISE_PROTEIN_STR);
131			protInput.close();
132
133			// logging output
134			BufferedReader protOutput = new BufferedReader(new InputStreamReader(protProc.getInputStream()));
135			String line;
136			while((line = protOutput.readLine()) != null) {
137			log.println(line);
138			if (line.startsWith(TINKER_ERROR_STR)) {
139			tinkerError = true;
140			}
141			}
142
143			tinkerxyzout.renameTo(new File(outPath,outBasename+".xyz"));
144			tinkerseqout.renameTo(new File(outPath,outBasename+".seq"));
145
146			if (tinkerError) {
147			log.close();
148			throw new TinkerError("Tinker error, revise log file "+logFile.getAbsolutePath());
149			}
150			}
151
152			/**
153			* Runs tinker's distgeom program capturing output with restrain violation statistics into member variable arrays
154			* that can be retrieved using the getters: getMaxLowerBoundViol, getMaxUpperBoundViol, getMaxLowerViol etc...
155	duarte	338	* Two files are needed as input for distgeom: an xyz file and a key file, the latter is not passed but instead implicitely
156			* defined by xyzFile: must be in same directory and must have same basename with extension .key
157	duarte	322	* @param xyzFile
158			* @param outPath Directory where output files will be written
159			* @param outBasename Base name of the output files
160			* @param n Number of models that we want distgeom to produce
161			* @throws TinkerError If an error seen in tinker's output
162			* @throws IOException
163			*/
164			public void runDistgeom(File xyzFile, String outPath, String outBasename, int n) throws TinkerError, IOException {
165			boolean tinkerError = false; // to store the exit state of the tinker program
166			if (!new File(outPath).exists()) {
167			throw new FileNotFoundException("Specified directory "+outPath+" does not exist");
168			}
169			if (!xyzFile.exists()){
170			throw new FileNotFoundException("Specified xyz file "+xyzFile.getAbsolutePath()+" does not exist");
171			}
172			String basename = xyzFile.getName();
173			basename = basename.substring(0, basename.lastIndexOf("."));
174			File keyFile = new File(xyzFile.getParent(),basename+".key");
175			if (! keyFile.exists()) {
176			throw new FileNotFoundException("Key file "+keyFile.getAbsolutePath()+" not present in input directory "+xyzFile.getParent());
177			}
178			// getting names of tinker output files
179			File[] tinkerout = new File[n+1];
180			for (int i=1;i<=n;i++) {
181			String ext = new Formatter().format("%03d", i).toString();
182			tinkerout[i] = getTinkerOutputFileName(xyzFile, ext);
183			}
184			// initialising arrays were we store captured output data
185			numUpperBoundViol = new int[n+1];
186			numLowerBoundViol = new int[n+1];
187			maxUpperBoundViol = new double[n+1];
188			maxLowerBoundViol = new double[n+1];
189			rmsBoundViol = new double[n+1];
190			numUpperViol = new int[n+1];
191			numLowerViol = new int[n+1];
192			maxUpperViol = new double[n+1];
193			maxLowerViol = new double[n+1];
194			rmsRestViol = new double[n+1];
195			// running distgeom program
196			Process dgeomProc = Runtime.getRuntime().exec(distgeomProg+" "+xyzFile.getAbsolutePath()+" "+n+" "+DGEOM_PARAMS);
197			// logging and capturing output
198			BufferedReader dgeomOutput = new BufferedReader(new InputStreamReader(dgeomProc.getInputStream()));
199			String line;
200			int i=1;
201			while((line = dgeomOutput.readLine()) != null) {
202			log.println(line);
203			if (line.startsWith(TINKER_ERROR_STR)) {
204			tinkerError = true;
205			}
206			Pattern p = Pattern.compile("^ Num Upper Bound Violations :\\s+(\\d+)");
207			Matcher m = p.matcher(line);
208			if (m.find()) {
209			numUpperBoundViol[i]=Integer.parseInt(m.group(1));
210			}
211			p = Pattern.compile("^ Num Lower Bound Violations :\\s+(\\d+)");
212			m = p.matcher(line);
213			if (m.find()) {
214			numLowerBoundViol[i]=Integer.parseInt(m.group(1));
215			}
216			p = Pattern.compile("^ Max Upper Bound Violation :\\s+(\\d+\\.\\d\\d\\d\\d)");
217			m = p.matcher(line);
218			if (m.find()) {
219			maxUpperBoundViol[i]=Double.parseDouble(m.group(1));
220			}
221			p = Pattern.compile("^ Max Lower Bound Violation :\\s+(\\d+\\.\\d\\d\\d\\d)");
222			m = p.matcher(line);
223			if (m.find()) {
224			maxLowerBoundViol[i]=Double.parseDouble(m.group(1));
225			}
226			p = Pattern.compile("^ RMS Deviation from Bounds :\\s+(\\d+\\.\\d\\d\\d\\d)");
227			m = p.matcher(line);
228			if (m.find()) {
229			rmsBoundViol[i]=Double.parseDouble(m.group(1));
230			}
231			p = Pattern.compile("^ Num Upper Restraint Violations :\\s+(\\d+)");
232			m = p.matcher(line);
233			if (m.find()) {
234			numUpperViol[i]=Integer.parseInt(m.group(1));
235			}
236			p = Pattern.compile("^ Num Lower Restraint Violations :\\s+(\\d+)");
237			m = p.matcher(line);
238			if (m.find()) {
239			numLowerViol[i]=Integer.parseInt(m.group(1));
240			}
241			p = Pattern.compile("^ Max Upper Restraint Violation :\\s+(\\d+\\.\\d\\d\\d\\d)");
242			m = p.matcher(line);
243			if (m.find()) {
244			maxUpperViol[i]=Double.parseDouble(m.group(1));
245			}
246			p = Pattern.compile("^ Max Lower Restraint Violation :\\s+(\\d+\\.\\d\\d\\d\\d)");
247			m = p.matcher(line);
248			if (m.find()) {
249			maxLowerViol[i]=Double.parseDouble(m.group(1));
250			}
251			p = Pattern.compile("^ RMS Restraint Dist Violation :\\s+(\\d+\\.\\d\\d\\d\\d)");
252			m = p.matcher(line);
253			if (m.find()) {
254			rmsRestViol[i]=Double.parseDouble(m.group(1));
255			i++;
256			}
257			}
258			//renaming files to our chosen outBasename+ext
259			for (i=1;i<=n;i++) {
260			String ext = new Formatter().format("%03d", i).toString();
261			tinkerout[i].renameTo(new File(outPath,outBasename+"."+ext));
262			}
263			// throwing exception if error string was caught in output
264			if (tinkerError) {
265			log.close();
266			throw new TinkerError("Tinker error, revise log file "+logFile.getAbsolutePath());
267			}
268
269			}
270
271			/**
272			* Runs tinker's xyzpdb program to convert a given xyzFile (needing also a seqFile) to a pdbFile
273			* @param xyzFile
274			* @param seqFile
275			* @param pdbFile
276			* @throws IOException
277			* @throws TinkerError If an error seen in tinker's output
278			*/
279			public void runXyzpdb(File xyzFile, File seqFile, File pdbFile) throws IOException, TinkerError {
280			boolean tinkerError = false; // to store the exit state of the tinker program
281			if (!xyzFile.exists()){
282			throw new FileNotFoundException("Specified xyz file "+xyzFile.getAbsolutePath()+" does not exist");
283			}
284			if (!seqFile.exists()){
285			throw new FileNotFoundException("Specified seq file "+seqFile.getAbsolutePath()+" does not exist");
286			}
287
288			String basename = xyzFile.getName();
289			basename = basename.substring(0, basename.lastIndexOf("."));
290			File tmpSeqFile = new File(seqFile.getParent(),basename+".seq");
291
292			// if seqFile doesn't follow the naming convention (basename of xyzFile+seq extension) that tinker expects, we copy it to tmpSeqFile (which has right name)
293			if (!tmpSeqFile.equals(seqFile)) {
294			FileChannel srcChannel = new FileInputStream(seqFile).getChannel();
295			FileChannel dstChannel = new FileOutputStream(tmpSeqFile).getChannel();
296			dstChannel.transferFrom(srcChannel, 0, srcChannel.size());
297			srcChannel.close();
298			dstChannel.close();
299			// if we copied then that means tmpSeqFile is different from seqFile and thus we want to delete the tmp file on exit
300			tmpSeqFile.deleteOnExit();
301			}
302
303			File tinkerpdbout = getTinkerOutputFileName(xyzFile, "pdb");
304
305			// running tinker's xyzpdb
306			// beware: it takes as a silent input the seq file seqFile (or tmpSeqFile if the input seqFile didn't have the right name)
307			Process xyzpdbProc = Runtime.getRuntime().exec(xyzpdbProg+" "+xyzFile.getAbsolutePath()+" "+forceFieldFileName);
308
309			// logging output
310			BufferedReader xyzpdbOutput = new BufferedReader(new InputStreamReader(xyzpdbProc.getInputStream()));
311			String line;
312			while((line = xyzpdbOutput.readLine()) != null) {
313			log.println(line);
314			if (line.startsWith(TINKER_ERROR_STR)) {
315			tinkerError = true;
316			}
317			}
318
319			tinkerpdbout.renameTo(pdbFile);
320
321			if (tinkerError) {
322			log.close();
323			throw new TinkerError("Tinker error, revise log file "+logFile.getAbsolutePath());
324			}
325			}
326
327			/**
328			* Runs tinker's pdbxyz program to convert a pdbFile to a xyzFile
329			* @param pdbFile
330			* @param xyzFile
331			* @throws IOException
332			* @throws TinkerError If an error seen in tinker's output
333			*/
334			public void runPdbxyz(File pdbFile, File xyzFile) throws IOException, TinkerError{
335			boolean tinkerError = false; // to store the exit state of the tinker program
336			if (!pdbFile.exists()){
337			throw new FileNotFoundException("Specified pdb file "+pdbFile.getAbsolutePath()+" does not exist");
338			}
339			File tinkerxyzout = getTinkerOutputFileName(pdbFile, "xyz");
340			// running tinker's pdbxyz
341			Process pdbxyzProc = Runtime.getRuntime().exec(pdbxyzProg+" "+pdbFile.getAbsolutePath()+" "+forceFieldFileName);
342
343			// logging output
344			BufferedReader pdbxyzOutput = new BufferedReader(new InputStreamReader(pdbxyzProc.getInputStream()));
345			String line;
346			while((line = pdbxyzOutput.readLine()) != null) {
347			log.println(line);
348			if (line.startsWith(TINKER_ERROR_STR)) {
349			tinkerError = true;
350			}
351			}
352			tinkerxyzout.renameTo(xyzFile);
353			if (tinkerError) {
354			log.close();
355			throw new TinkerError("Tinker error, revise log file "+logFile.getAbsolutePath());
356			}
357			}
358
359			/**
360			* Closes log stream, must be called after no other tinker program will be run with this TinkerRunner object
361			* (otherwise log is not flushed to file)
362			*/
363			public void closeLog() {
364			log.close();
365			}
366
367			public double[] getMaxLowerBoundViol() {
368			return maxLowerBoundViol;
369			}
370
371			public double[] getMaxLowerViol() {
372			return maxLowerViol;
373			}
374
375			public double[] getMaxUpperBoundViol() {
376			return maxUpperBoundViol;
377			}
378
379			public double[] getMaxUpperViol() {
380			return maxUpperViol;
381			}
382
383			public int[] getNumLowerBoundViol() {
384			return numLowerBoundViol;
385			}
386
387			public int[] getNumLowerViol() {
388			return numLowerViol;
389			}
390
391			public int[] getNumUpperBoundViol() {
392			return numUpperBoundViol;
393			}
394
395			public int[] getNumUpperViol() {
396			return numUpperViol;
397			}
398
399			public double[] getRmsBoundViol() {
400			return rmsBoundViol;
401			}
402
403			public double[] getRmsRestViol() {
404			return rmsRestViol;
405			}
406			}