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, InterruptedException {
                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
                String cmdLine = distgeomProg+" "+xyzFile.getAbsolutePath()+" "+n+" "+DGEOM_PARAMS;
                Process dgeomProc = Runtime.getRuntime().exec(cmdLine);
                // 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));
                                System.out.println("Done model "+i+". Violations: "+numUpperViol[i]+" upper, "+numLowerViol[i]+" lower");
                                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());
                }
                int exitValue = dgeomProc.waitFor();
                // throwing exception if exit state is 137: happens in Linux when another instance of distgeom is running in same machine, the OS kills it with exit state 137 
                if (exitValue==137) {
                        log.close();
                        throw new TinkerError("Distgeom was killed by OS, probably another instance of distgeom is running in this computer");
                }
                if (exitValue==139) {
                        log.close();
                        throw new TinkerError("Distgeom was killed with exit code 139. Not enough memory.");
                }
                
        }
        
        /**
         * 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:	343
Committed:	Wed Oct 10 16:19:18 2007 UTC (17 years, 4 months ago) by stehr
File size:	15381 byte(s)
Log Message:	fixed bug when running distgeom, now waiting for process to exit before checking exit status
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	stehr	343	public void runDistgeom(File xyzFile, String outPath, String outBasename, int n) throws TinkerError, IOException, InterruptedException {
165	duarte	322	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	stehr	342	String cmdLine = distgeomProg+" "+xyzFile.getAbsolutePath()+" "+n+" "+DGEOM_PARAMS;
197			Process dgeomProc = Runtime.getRuntime().exec(cmdLine);
198	duarte	322	// logging and capturing output
199			BufferedReader dgeomOutput = new BufferedReader(new InputStreamReader(dgeomProc.getInputStream()));
200			String line;
201			int i=1;
202			while((line = dgeomOutput.readLine()) != null) {
203			log.println(line);
204			if (line.startsWith(TINKER_ERROR_STR)) {
205			tinkerError = true;
206			}
207			Pattern p = Pattern.compile("^ Num Upper Bound Violations :\\s+(\\d+)");
208			Matcher m = p.matcher(line);
209			if (m.find()) {
210			numUpperBoundViol[i]=Integer.parseInt(m.group(1));
211			}
212			p = Pattern.compile("^ Num Lower Bound Violations :\\s+(\\d+)");
213			m = p.matcher(line);
214			if (m.find()) {
215			numLowerBoundViol[i]=Integer.parseInt(m.group(1));
216			}
217			p = Pattern.compile("^ Max Upper Bound Violation :\\s+(\\d+\\.\\d\\d\\d\\d)");
218			m = p.matcher(line);
219			if (m.find()) {
220			maxUpperBoundViol[i]=Double.parseDouble(m.group(1));
221			}
222			p = Pattern.compile("^ Max Lower Bound Violation :\\s+(\\d+\\.\\d\\d\\d\\d)");
223			m = p.matcher(line);
224			if (m.find()) {
225			maxLowerBoundViol[i]=Double.parseDouble(m.group(1));
226			}
227			p = Pattern.compile("^ RMS Deviation from Bounds :\\s+(\\d+\\.\\d\\d\\d\\d)");
228			m = p.matcher(line);
229			if (m.find()) {
230			rmsBoundViol[i]=Double.parseDouble(m.group(1));
231			}
232			p = Pattern.compile("^ Num Upper Restraint Violations :\\s+(\\d+)");
233			m = p.matcher(line);
234			if (m.find()) {
235			numUpperViol[i]=Integer.parseInt(m.group(1));
236			}
237			p = Pattern.compile("^ Num Lower Restraint Violations :\\s+(\\d+)");
238			m = p.matcher(line);
239			if (m.find()) {
240			numLowerViol[i]=Integer.parseInt(m.group(1));
241			}
242			p = Pattern.compile("^ Max Upper Restraint Violation :\\s+(\\d+\\.\\d\\d\\d\\d)");
243			m = p.matcher(line);
244			if (m.find()) {
245			maxUpperViol[i]=Double.parseDouble(m.group(1));
246			}
247			p = Pattern.compile("^ Max Lower Restraint Violation :\\s+(\\d+\\.\\d\\d\\d\\d)");
248			m = p.matcher(line);
249			if (m.find()) {
250			maxLowerViol[i]=Double.parseDouble(m.group(1));
251			}
252			p = Pattern.compile("^ RMS Restraint Dist Violation :\\s+(\\d+\\.\\d\\d\\d\\d)");
253			m = p.matcher(line);
254			if (m.find()) {
255			rmsRestViol[i]=Double.parseDouble(m.group(1));
256	duarte	341	System.out.println("Done model "+i+". Violations: "+numUpperViol[i]+" upper, "+numLowerViol[i]+" lower");
257	duarte	322	i++;
258	duarte	341
259	duarte	322	}
260			}
261			//renaming files to our chosen outBasename+ext
262			for (i=1;i<=n;i++) {
263			String ext = new Formatter().format("%03d", i).toString();
264			tinkerout[i].renameTo(new File(outPath,outBasename+"."+ext));
265			}
266			// throwing exception if error string was caught in output
267			if (tinkerError) {
268			log.close();
269			throw new TinkerError("Tinker error, revise log file "+logFile.getAbsolutePath());
270			}
271	stehr	343	int exitValue = dgeomProc.waitFor();
272	duarte	341	// throwing exception if exit state is 137: happens in Linux when another instance of distgeom is running in same machine, the OS kills it with exit state 137
273	stehr	343	if (exitValue==137) {
274	duarte	341	log.close();
275			throw new TinkerError("Distgeom was killed by OS, probably another instance of distgeom is running in this computer");
276			}
277	stehr	343	if (exitValue==139) {
278	stehr	342	log.close();
279			throw new TinkerError("Distgeom was killed with exit code 139. Not enough memory.");
280			}
281	duarte	322
282			}
283
284			/**
285			* Runs tinker's xyzpdb program to convert a given xyzFile (needing also a seqFile) to a pdbFile
286			* @param xyzFile
287			* @param seqFile
288			* @param pdbFile
289			* @throws IOException
290			* @throws TinkerError If an error seen in tinker's output
291			*/
292			public void runXyzpdb(File xyzFile, File seqFile, File pdbFile) throws IOException, TinkerError {
293			boolean tinkerError = false; // to store the exit state of the tinker program
294			if (!xyzFile.exists()){
295			throw new FileNotFoundException("Specified xyz file "+xyzFile.getAbsolutePath()+" does not exist");
296			}
297			if (!seqFile.exists()){
298			throw new FileNotFoundException("Specified seq file "+seqFile.getAbsolutePath()+" does not exist");
299			}
300
301			String basename = xyzFile.getName();
302			basename = basename.substring(0, basename.lastIndexOf("."));
303			File tmpSeqFile = new File(seqFile.getParent(),basename+".seq");
304
305			// 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)
306			if (!tmpSeqFile.equals(seqFile)) {
307			FileChannel srcChannel = new FileInputStream(seqFile).getChannel();
308			FileChannel dstChannel = new FileOutputStream(tmpSeqFile).getChannel();
309			dstChannel.transferFrom(srcChannel, 0, srcChannel.size());
310			srcChannel.close();
311			dstChannel.close();
312			// if we copied then that means tmpSeqFile is different from seqFile and thus we want to delete the tmp file on exit
313			tmpSeqFile.deleteOnExit();
314			}
315
316			File tinkerpdbout = getTinkerOutputFileName(xyzFile, "pdb");
317
318			// running tinker's xyzpdb
319			// beware: it takes as a silent input the seq file seqFile (or tmpSeqFile if the input seqFile didn't have the right name)
320			Process xyzpdbProc = Runtime.getRuntime().exec(xyzpdbProg+" "+xyzFile.getAbsolutePath()+" "+forceFieldFileName);
321
322			// logging output
323			BufferedReader xyzpdbOutput = new BufferedReader(new InputStreamReader(xyzpdbProc.getInputStream()));
324			String line;
325			while((line = xyzpdbOutput.readLine()) != null) {
326			log.println(line);
327			if (line.startsWith(TINKER_ERROR_STR)) {
328			tinkerError = true;
329			}
330			}
331
332			tinkerpdbout.renameTo(pdbFile);
333
334			if (tinkerError) {
335			log.close();
336			throw new TinkerError("Tinker error, revise log file "+logFile.getAbsolutePath());
337			}
338			}
339
340			/**
341			* Runs tinker's pdbxyz program to convert a pdbFile to a xyzFile
342			* @param pdbFile
343			* @param xyzFile
344			* @throws IOException
345			* @throws TinkerError If an error seen in tinker's output
346			*/
347			public void runPdbxyz(File pdbFile, File xyzFile) throws IOException, TinkerError{
348			boolean tinkerError = false; // to store the exit state of the tinker program
349			if (!pdbFile.exists()){
350			throw new FileNotFoundException("Specified pdb file "+pdbFile.getAbsolutePath()+" does not exist");
351			}
352			File tinkerxyzout = getTinkerOutputFileName(pdbFile, "xyz");
353			// running tinker's pdbxyz
354			Process pdbxyzProc = Runtime.getRuntime().exec(pdbxyzProg+" "+pdbFile.getAbsolutePath()+" "+forceFieldFileName);
355
356			// logging output
357			BufferedReader pdbxyzOutput = new BufferedReader(new InputStreamReader(pdbxyzProc.getInputStream()));
358			String line;
359			while((line = pdbxyzOutput.readLine()) != null) {
360			log.println(line);
361			if (line.startsWith(TINKER_ERROR_STR)) {
362			tinkerError = true;
363			}
364			}
365			tinkerxyzout.renameTo(xyzFile);
366			if (tinkerError) {
367			log.close();
368			throw new TinkerError("Tinker error, revise log file "+logFile.getAbsolutePath());
369			}
370			}
371
372			/**
373			* Closes log stream, must be called after no other tinker program will be run with this TinkerRunner object
374			* (otherwise log is not flushed to file)
375			*/
376			public void closeLog() {
377			log.close();
378			}
379
380			public double[] getMaxLowerBoundViol() {
381			return maxLowerBoundViol;
382			}
383
384			public double[] getMaxLowerViol() {
385			return maxLowerViol;
386			}
387
388			public double[] getMaxUpperBoundViol() {
389			return maxUpperBoundViol;
390			}
391
392			public double[] getMaxUpperViol() {
393			return maxUpperViol;
394			}
395
396			public int[] getNumLowerBoundViol() {
397			return numLowerBoundViol;
398			}
399
400			public int[] getNumLowerViol() {
401			return numLowerViol;
402			}
403
404			public int[] getNumUpperBoundViol() {
405			return numUpperBoundViol;
406			}
407
408			public int[] getNumUpperViol() {
409			return numUpperViol;
410			}
411
412			public double[] getRmsBoundViol() {
413			return rmsBoundViol;
414			}
415
416			public double[] getRmsRestViol() {
417			return rmsRestViol;
418			}
419			}