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 (16 years, 11 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	File contents
1	package tinker;
2
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	* 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	* @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	}