From 4d6083e0cf39c4989e08bdaf9384e9d44c0da607 Mon Sep 17 00:00:00 2001
From: pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Date: Thu, 3 Feb 2011 17:17:42 +0000
Subject: [PATCH] Parser for DisEMBL results and finished runner, few test
 cases. DisemblTester has all tests "green"

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3695 e3abac25-378b-4346-85de-24260fe3988d
---
 .classpath                                         |    4 +-
 build.xml                                          |   10 +-
 conf/Executable.properties                         |    2 +-
 conf/settings/DisemblParameters.xml                |    6 +-
 datamodel/compbio/data/sequence/SequenceUtil.java  |   49 +-
 runner/compbio/runner/disorder/Disembl.java        |   92 +-
 runtests.sh                                        |    4 +-
 .../compbio/data/sequence/SequenceUtilTester.java  |   28 +-
 testsrc/compbio/runner/disorder/DisemblTester.java |   59 +-
 testsrc/testdata/disembl_default.out               |   21 +
 testsrc/testdata/scores.out                        | 1568 ++++++++++++++++++++
 11 files changed, 1718 insertions(+), 125 deletions(-)
 create mode 100644 testsrc/testdata/disembl_default.out
 create mode 100644 testsrc/testdata/scores.out

diff --git a/.classpath b/.classpath
index 0ace127..4820b06 100644
--- a/.classpath
+++ b/.classpath
@@ -1,10 +1,10 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
+	<classpathentry kind="src" path="datamodel"/>
 	<classpathentry kind="src" path="engine"/>
+	<classpathentry kind="src" path="runner"/>
 	<classpathentry kind="src" path="webservices"/>
 	<classpathentry kind="src" path="testsrc"/>
-	<classpathentry kind="src" path="runner"/>
-	<classpathentry kind="src" path="datamodel"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
 	<classpathentry kind="lib" path="WEB-INF/lib/log4j-1.2.15.jar"/>
 	<classpathentry kind="lib" path="testsrc/lib/testng-5.10-jdk15.jar"/>
diff --git a/build.xml b/build.xml
index 02298e0..5597457 100644
--- a/build.xml
+++ b/build.xml
@@ -87,18 +87,18 @@
 				<compilerarg value="-Xlint:unchecked"/>
 				<classpath refid="project.classpath" />
 		</javac>
-		<!-- Complile the tests -->
-		<javac srcdir="${basedir}/testsrc" destdir="${classes}" target="1.6"
+		<!-- Complile the webservices -->
+		<javac srcdir="${basedir}/webservices" destdir="${classes}" target="1.6"
 				source="1.6" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >
 				<compilerarg value="-Xlint:unchecked"/>
 				<classpath refid="project.classpath" />
-				<classpath refid="test.classpath" />
 		</javac>
-		<!-- Complile the webservices -->
-		<javac srcdir="${basedir}/webservices" destdir="${classes}" target="1.6"
+		<!-- Complile the tests -->
+		<javac srcdir="${basedir}/testsrc" destdir="${classes}" target="1.6"
 				source="1.6" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >
 				<compilerarg value="-Xlint:unchecked"/>
 				<classpath refid="project.classpath" />
+				<classpath refid="test.classpath" />
 		</javac>
 	</target>
 
diff --git a/conf/Executable.properties b/conf/Executable.properties
index 4b1cb00..548507c 100644
--- a/conf/Executable.properties
+++ b/conf/Executable.properties
@@ -75,7 +75,7 @@ jronn.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l
 ### Disembl configuration Tisean - Disembl dependancy cannot be redistributed (!) ### 
 #local.disembl.bin.windows= 
 local.disembl.bin=binaries/src/disembl/DisEMBL.py
-cluster.disembl.bin=/homes/pvtroshin/jaba2/binaries/src/disembl/DisEMBL.py
+cluster.disembl.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/disembl/DisEMBL.py
 disembl.parameters.file=conf/settings/DisemblParameters.xml
 disembl.limits.file=conf/settings/DisemblLimits.xml
 disembl.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
diff --git a/conf/settings/DisemblParameters.xml b/conf/settings/DisemblParameters.xml
index 3820a35..676395e 100644
--- a/conf/settings/DisemblParameters.xml
+++ b/conf/settings/DisemblParameters.xml
@@ -1,5 +1,9 @@
 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
 <runnerConfig>
+<!-- 
+    Extreme variation of this parameter does not have any impact on the output
+    so irrelevant. 
+
 	<runnerClassName>compbio.runner.disorder.Disembl</runnerClassName>
 	<prmSeparator>=</prmSeparator>
 	<parameters>
@@ -14,7 +18,7 @@
 			<max>30</max>
 		</validValue>
 	</parameters>
-<!--  
+ 
  These can be supported but not recommended to change so what's the point?
  
  Manual: Normally the default parameters should not be changed.
diff --git a/datamodel/compbio/data/sequence/SequenceUtil.java b/datamodel/compbio/data/sequence/SequenceUtil.java
index 85ae95f..a636c3a 100644
--- a/datamodel/compbio/data/sequence/SequenceUtil.java
+++ b/datamodel/compbio/data/sequence/SequenceUtil.java
@@ -406,12 +406,15 @@ public final class SequenceUtil {
 	 * 
 	 * TODO complete!
 	 * 
+	 * >Sequence name
+	 * 
 	 * RESIDUE COILS REM465 HOTLOOPS
 	 * 
 	 * M 0.86010 0.88512 0.37094
 	 * 
 	 * T 0.79983 0.85864 0.44331 ....
-	 * 
+
+	 * >Next Sequence name 
 	 * RESIDUE COILS REM465 HOTLOOPS
 	 * 
 	 * M 0.86010 0.88512 0.37094
@@ -422,14 +425,14 @@ public final class SequenceUtil {
 	 * @throws IOException
 	 * @throws UnknownFileFormatException
 	 */
-	static Map<FastaSequence, Set<Score>> readDisembl(final InputStream input)
+	public static Map<FastaSequence, Set<Score>> readDisembl(final InputStream input)
 			throws IOException, UnknownFileFormatException {
 		Scanner scan = new Scanner(input);
-		scan.useDelimiter("# RESIDUE COILS REM465 HOTLOOPS\n");
+		scan.useDelimiter(">");
 		if (!scan.hasNext()) {
 			throw new UnknownFileFormatException(
-					"In Disembl score format each seqeunce score is expected to start from the line: "
-							+ "'# RESIDUE COILS REM465 HOTLOOPS\\n'."
+					"In Disembl score format each sequence score is expected " +
+					"to start from the line: >Sequence name "
 							+ " No such line was found!");
 		}
 
@@ -438,22 +441,27 @@ public final class SequenceUtil {
 		while (scan.hasNext()) {
 			seqCounter++;
 			String singleSeq = scan.next();
-			Scanner scansingle = new Scanner(singleSeq);
+ 			Scanner scansingle = new Scanner(singleSeq);
+			if(!scansingle.hasNextLine()) {
+ 				throw new RuntimeException("The input looks like an incomplete disembl file - cannot parse!");
+ 			}
+ 			
 			StringBuffer seqbuffer = new StringBuffer();
 			ArrayList<Float> coils = new ArrayList<Float>();
 			ArrayList<Float> rem = new ArrayList<Float>();
 			ArrayList<Float> hotloops = new ArrayList<Float>();
-			FastaSequence fs = new FastaSequence(Integer.toString(seqCounter),
-					singleSeq);
-			while (scansingle.hasNextLine()) {
-				String valueLine = scansingle.nextLine();
-				Scanner values = new Scanner(valueLine);
-				seqbuffer.append(values.next());
-				coils.add(values.nextFloat());
-				rem.add(values.nextFloat());
-				hotloops.add(values.nextFloat());
-				values.close();
+
+			String sequenceName = scansingle.nextLine().trim();
+			String title =  scansingle.nextLine();
+			assert title.startsWith("# RESIDUE COILS REM465 HOTLOOPS") : ">Sequence_name must follow column title: # RESIDUE COILS REM465 HOTLOOPS!";
+ 			
+			while (scansingle.hasNext()) {
+				seqbuffer.append(scansingle.next());
+				coils.add(scansingle.nextFloat());
+				rem.add(scansingle.nextFloat());
+				hotloops.add(scansingle.nextFloat());
 			}
+			FastaSequence fs = new FastaSequence(sequenceName,seqbuffer.toString());
 			Set<Score> scores = new HashSet<Score>();
 			scores.add(new Score(DisemblResultAnnot.COILS, coils));
 			scores.add(new Score(DisemblResultAnnot.HOTLOOPS, hotloops));
@@ -466,6 +474,15 @@ public final class SequenceUtil {
 		input.close();
 		return results;
 	}
+	
+	public static  Map<String, Set<Score>> removeSequences(Map<FastaSequence, Set<Score>> disemblResults) { 
+		Map<String, Set<Score>> seqNameScores = new HashMap<String, Set<Score>>();
+		for(Map.Entry<FastaSequence,Set<Score>> dres: disemblResults.entrySet()) {
+			seqNameScores.put(dres.getKey().getId(),dres.getValue()); 
+		}
+		return seqNameScores;
+	}
+	
 	/**
 	 * Read AACon result with no alignment files. This method leaves incoming
 	 * the InputStream results open!
diff --git a/runner/compbio/runner/disorder/Disembl.java b/runner/compbio/runner/disorder/Disembl.java
index 8f4256f..337395c 100644
--- a/runner/compbio/runner/disorder/Disembl.java
+++ b/runner/compbio/runner/disorder/Disembl.java
@@ -1,6 +1,6 @@
 /*
- * Copyright (c) 2009 Peter Troshin JAva Bioinformatics Analysis Web Services
- * (JABAWS) @version: 1.0 This library is free software; you can redistribute it
+ * Copyright (c) 2011 Peter Troshin JAva Bioinformatics Analysis Web Services
+ * (JABAWS) @version: 2.0 This library is free software; you can redistribute it
  * and/or modify it under the terms of the Apache License version 2 as published
  * by the Apache Software Foundation This library is distributed in the hope
  * that it will be useful, but WITHOUT ANY WARRANTY; without even the implied
@@ -14,13 +14,22 @@
 
 package compbio.runner.disorder;
 
-import java.util.Arrays;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStream;
+
 import java.util.Map;
+import java.util.Set;
 
 import org.apache.log4j.Logger;
 
+
 import compbio.data.sequence.Score;
-import compbio.engine.client.CommandBuilder;
+import compbio.data.sequence.SequenceUtil;
+import compbio.data.sequence.UnknownFileFormatException;
+
 import compbio.engine.client.Executable;
 import compbio.engine.client.PipedExecutable;
 import compbio.engine.client.SkeletalExecutable;
@@ -30,26 +39,27 @@ import compbio.metadata.ResultNotAvailableException;
 import compbio.runner.Util;
 
 /**
- * @see DisEMBL
- * 
  *      DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops
- *      fold_rem465 sequence_file print 'A default run would be: ./DisEMBL.py 8
- *      8 4 1.2 1.4 1.2 fasta_file > out' new DisEMBL is at
- *      /homes/pvtroshin/soft/DisEMBL-1.4raw
- * 
- *      This is not a standard DisEMBL! The script has been modified! DisEMBL.py
- *      smooth_frame peak_frame join_frame fold_coils fold_hotloops fold_rem465
- *      [mode] < fasta_file > out print
- * 
- *      'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 < fasta_file'
- *      print 'Mode: "default"(nothing) or "scores" which will give scores per
- *      residue in TAB separated format'
+ *      fold_rem465 sequence_file print 
+ *      
+ *      'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out' 
+ *	 	
+ *		This version of DisEMBL is 1.4 (latest available for download in Feb 2011)
+ *		capable of outputting raw values      
+ *      
+ *      The values of the parameters are hard coded in DisEMBL.py script. 
+ *      smooth_frame=8 peak_frame=8 join_frame=4 fold_coils=1.2 fold_hotloops=1.4
+ *      fold_rem465=1.2 
+ *      
+ *       Changing these values are not recommended by developers, apart from smoothing window. 
+ *       However, 5 orders of magnitude changes in this parameter does not change the output
+ *       so allowing this change also seems pointless. Finally, the binary, DisEMBL depends on
+ *       - Tisean is not happy with arbitruary changes to these values, so changing them can 
+ *       lead to problems.
+ *        
  * 
- *      Internal parameters names are: sj
+ *      This is not a standard DisEMBL! The script has been modified! 
  * 
- *      //TODO? pw jd ct rt lt
- * 
- *      the order is preserved
  */
 public class Disembl extends SkeletalExecutable<Disembl>
 		implements
@@ -60,22 +70,41 @@ public class Disembl extends SkeletalExecutable<Disembl>
 	// Cache for Limits information
 	private static LimitsManager<Disembl> limits;
 
-	// CHECK THIS !!!
 	public static final String KEY_VALUE_SEPARATOR = Util.SPACE;
 
+	/* The parameter list there must not contain same values! */
 	public Disembl() {
 		// remove default input to prevent it to appear in the parameters list
 		// that could happen if the parameters are set first
 		// super.setInput("");
-		addParameters(Arrays.asList("8", "8", "4", "1.2", "1.4", "1.2",
-				"scores"));
 	}
 
 	@SuppressWarnings("unchecked")
-	public Map<String, Score> getResults(String workDirectory)
+	public Map<String, Set<Score>> getResults(String workDirectory)
 			throws ResultNotAvailableException {
 
-		return null;
+		InputStream inStream = null;
+		Map<String, Set<Score>> results= null; 
+			try {
+				inStream = new FileInputStream(new File(workDirectory,
+						getOutput()));
+				results = SequenceUtil.removeSequences(SequenceUtil.readDisembl(inStream));
+				inStream.close();
+			} catch (FileNotFoundException e) {
+				log.error(e.getMessage(), e.getCause());
+				throw new ResultNotAvailableException(e);
+			} catch (IOException e) {
+				log.error(e.getMessage(), e.getCause());
+				throw new ResultNotAvailableException(e);
+			} catch (UnknownFileFormatException e) {
+				log.error(e.getMessage(), e.getCause());
+				throw new ResultNotAvailableException(e);
+			} catch (NullPointerException e) {
+				log.error(e.getMessage(), e.getCause());
+				throw new ResultNotAvailableException(e);
+			}
+		
+		return results;
 	}
 
 	@Override
@@ -122,15 +151,4 @@ public class Disembl extends SkeletalExecutable<Disembl>
 		return this.getClass();
 	}
 
-	@Override
-	public CommandBuilder<Disembl> getParameters(ExecProvider provider) {
-		// If Savitzky-Golay smoothing parameter is specified then set it
-		String val = cbuilder.getParamValue("sg");
-		log.info("DisEMBL sav-gol value: " + val);
-		if (val != null) {
-			cbuilder.removeParam("sg");
-			cbuilder.setFirst(val);
-		}
-		return super.getParameters(provider);
-	}
 }
diff --git a/runtests.sh b/runtests.sh
index 0fc5a51..6d52d1f 100644
--- a/runtests.sh
+++ b/runtests.sh
@@ -6,7 +6,7 @@ ANT_HOME=/sw/java/ant; export ANT_HOME;
 ANT=/sw/java/ant/bin/ant; export ANT;
 
 # Re-Run tests run which was last run in IDE 
-#$ANT -f build.xml CustomTest
+$ANT -f build.xml CustomTest
 
 # Excludes cluster dependent and non-windows machine tests, 
 # so can be safely run from the development environment 
@@ -19,4 +19,4 @@ ANT=/sw/java/ant/bin/ant; export ANT;
 #$ANT -f build.xml Run_cluster_dependent_test
 
 # For running ALL tests
-$ANT -f build.xml Test
\ No newline at end of file
+#$ANT -f build.xml Test
\ No newline at end of file
diff --git a/testsrc/compbio/data/sequence/SequenceUtilTester.java b/testsrc/compbio/data/sequence/SequenceUtilTester.java
index 82aa4a3..edb57a4 100644
--- a/testsrc/compbio/data/sequence/SequenceUtilTester.java
+++ b/testsrc/compbio/data/sequence/SequenceUtilTester.java
@@ -148,27 +148,33 @@ public class SequenceUtilTester {
 
 	/**
 	 * This test tests the loading of horizontally formatted Jronn output file
+	 * 
+	 * First seq 
+	 * 
+	 * M	0.86010	0.88512	0.37094
+	 * 
+	 * T	0.79983	0.85864	0.44331
+	 * 
 	 */
 	@SuppressWarnings("unchecked")
 	@Test
-	public void testMultiAnnotatedSequence() {
+	public void testReadDisemblResults() {
 
 		FileInputStream fio;
 		try {
 			fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH
-					+ "disembl.out");
+					+ "scores.out");
 			Map<FastaSequence, Set<Score>> aseqs = SequenceUtil
 					.readDisembl(fio);
 			assertNotNull(aseqs);
-
-			/*
-			 * Map<Trial, List<Number>> val = ma.getInstance(Trial.class);
-			 * List<Number> list = new ArrayList<Number>(); list.add(new
-			 * Float(1.2)); list.add(new Double(5.662)); val.put(Trial.one,
-			 * list); val.put(Trial.two, Arrays.asList(6.22f, 1, 37.6f));
-			 * System.out.println(val); AnnotatedSequence aseq = aseqs.get(0);
-			 */
-			fio.close();
+			assertEquals(aseqs.size(), 3); 
+			System.out.println(aseqs);
+			for(FastaSequence fs: aseqs.keySet()) {
+				assertTrue(" Foobar_dundeefriends Foobar dundeefriends ".contains(fs.getId()));
+				Set<Score> scores = aseqs.get(fs); 
+				assertEquals(scores.size(),3);
+			}
+			  fio.close();
 		} catch (FileNotFoundException e) {
 			e.printStackTrace();
 			fail(e.getLocalizedMessage());
diff --git a/testsrc/compbio/runner/disorder/DisemblTester.java b/testsrc/compbio/runner/disorder/DisemblTester.java
index d77648e..133168e 100644
--- a/testsrc/compbio/runner/disorder/DisemblTester.java
+++ b/testsrc/compbio/runner/disorder/DisemblTester.java
@@ -31,6 +31,8 @@ import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.text.ParseException;
 import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
 
 import javax.xml.bind.ValidationException;
 
@@ -153,7 +155,7 @@ public class DisemblTester {
 				System.out.println("Job Status: " + status);
 				Thread.sleep(1000);
 				status = aengine.getJobStatus(jobId);
-				ConfiguredExecutable<Jronn> result = (ConfiguredExecutable<Jronn>) aengine
+				ConfiguredExecutable<Disembl> result = (ConfiguredExecutable<Disembl>) aengine
 						.getResults(jobId);
 				assertNotNull(result);
 				System.out.println("RES:" + result);
@@ -188,7 +190,7 @@ public class DisemblTester {
 			lr.executeJob();
 			ConfiguredExecutable<?> al1 = lr.waitForResult();
 			assertNotNull(al1.getResults());
-			HashSet<Score> al2 = confDisembl.getResults();
+			Map<String,Set<Score>> al2 = confDisembl.getResults();
 			assertNotNull(al2);
 			assertEquals(al2.size(), 3);
 			assertEquals(al1.getResults(), al2);
@@ -206,51 +208,7 @@ public class DisemblTester {
 
 	@Test(groups = {AllTestSuit.test_group_runner})
 	public void readStatistics() {
-		try {
-			ConfiguredExecutable<Disembl> confDisembl = Configurator
-					.configureExecutable(disembl, Executable.ExecProvider.Local);
-			// For local execution use relavive
-
-			AsyncExecutor sexec = Configurator.getAsyncEngine(confDisembl);
-			String jobId = sexec.submitJob(confDisembl);
-			FilePuller fw = FilePuller.newFilePuller(
-					confDisembl.getWorkDirectory() + File.separator
-							+ Jronn.getStatFile(),
-					FileWatcher.MIN_CHUNK_SIZE_BYTES);
-			int count = 0;
-			long position = 0;
-			fw.waitForFile(4);
-			JobStatus status = sexec.getJobStatus(jobId);
-			while (status != JobStatus.FINISHED) {
-				if (fw.hasMoreData()) {
-					ChunkHolder ch = fw.pull(position);
-					String chunk = ch.getChunk();
-					position = ch.getNextPosition();
-				}
-				count++;
-				// Make sure the loop is terminated if the job fails
-				if ((status == JobStatus.UNDEFINED || status == JobStatus.FAILED)) {
-					break;
-				}
-				Thread.sleep(300);
-				status = sexec.getJobStatus(jobId);
-			}
-			assertTrue(count > 1);
-			ConfiguredExecutable<?> al = sexec.getResults(jobId);
-			assertNotNull(al.getResults());
-		} catch (JobSubmissionException e) {
-			e.printStackTrace();
-			fail(e.getMessage());
-		} catch (ResultNotAvailableException e) {
-			e.printStackTrace();
-			fail(e.getMessage());
-		} catch (IOException e) {
-			e.printStackTrace();
-			fail(e.getMessage());
-		} catch (InterruptedException e) {
-			e.printStackTrace();
-			fail(e.getMessage());
-		}
+		// No execution statistics is available!
 	}
 
 	@Test(groups = {AllTestSuit.test_group_runner})
@@ -293,11 +251,11 @@ public class DisemblTester {
 			// See in details whether executables are the same
 			assertEquals(resurrectedCDisembl.getExecutable(), disembl);
 
-			ConfiguredExecutable<Disembl> resJronn = Configurator
+			ConfiguredExecutable<Disembl> resDisembl = Configurator
 					.configureExecutable(resurrectedCDisembl.getExecutable(),
 							Executable.ExecProvider.Local);
 
-			sexec = Configurator.getSyncEngine(resJronn,
+			sexec = Configurator.getSyncEngine(resDisembl,
 					Executable.ExecProvider.Local);
 			sexec.executeJob();
 			al = sexec.waitForResult();
@@ -327,7 +285,8 @@ public class DisemblTester {
 			RunnerConfig<Disembl> disemblConfig = ConfExecutable
 					.getRunnerOptions(Disembl.class);
 			assertNotNull(disemblConfig);
-			assertTrue(disemblConfig.getArguments().size() > 0);
+			// There is no disembl parameters
+			assertTrue(disemblConfig.getArguments().size() == 0);
 
 			PresetManager<Disembl> disemblPresets = ConfExecutable
 					.getRunnerPresets(Disembl.class);
diff --git a/testsrc/testdata/disembl_default.out b/testsrc/testdata/disembl_default.out
new file mode 100644
index 0000000..78821a0
--- /dev/null
+++ b/testsrc/testdata/disembl_default.out
@@ -0,0 +1,21 @@
+> Foobar_dundeefriends_COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343, 350-391, 429-485, 497-506, 539-547
+mtadgprellqlraavrhrpqdfvawlmladaeLGMGDTTAgemavqrgLALHPGHPEavarlgrvrwtqqrhaeaavllqqASDAAPEHPgialwlghaledagqaeaaaaaytraHQLLPEEPYItaqllnwrrrlcdwraldvlsaqvraavaqgvGAVEPFAFLSedasaaeqlacartraqaiaaSVRPLAPTRVRSKGPLRVGFVSNGFGAHPTglltvalfealqrrqpdlqmhlFATSGDDGSTlrtrlaqastlhdvtalghlatakhirhhgidllFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSehvlrlQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPqsmarmlavlrevpdsvlwllsgpgeadarlrafahaQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGCPVLTTPGEtfaarvagslnHHLGLDEMNVaddaafvakavalasdpaaltalharvdvlrrESGVFEMDGfaddfgallqalarrhgwlgi
+> Foobar_dundeefriends_REM465 355-368
+mtadgprellqlraavrhrpqdfvawlmladaelgmgdttagemavqrglalhpghpeavarlgrvrwtqqrhaeaavllqqasdaapehpgialwlghaledagqaeaaaaaytrahqllpeepyitaqllnwrrrlcdwraldvlsaqvraavaqgvgavepfaflsedasaaeqlacartraqaiaasvrplaptrvrskgplrvgfvsngfgahptglltvalfealqrrqpdlqmhlfatsgddgstlrtrlaqastlhdvtalghlatakhirhhgidllfdlrgwggggrpevfalrpapvqvnwlaypgtsgapwmdyvlgdafalppalepfysehvlrlqgafqPSDTSRVVAEPPSRtqcglpeqgvvlccfnnsyklnpqsmarmlavlrevpdsvlwllsgpgeadarlrafahaqgvdaqrlvfmpklphpqylaryrhadlfldthpynahttasdalwtgcpvlttpgetfaarvagslnhhlgldemnvaddaafvakavalasdpaaltalharvdvlrresgvfemdgfaddfgallqalarrhgwlgi
+> Foobar_dundeefriends_HOTLOOPS 190-204
+mtadgprellqlraavrhrpqdfvawlmladaelgmgdttagemavqrglalhpghpeavarlgrvrwtqqrhaeaavllqqasdaapehpgialwlghaledagqaeaaaaaytrahqllpeepyitaqllnwrrrlcdwraldvlsaqvraavaqgvgavepfaflsedasaaeqlacartraqaiaASVRPLAPTRVRSKGplrvgfvsngfgahptglltvalfealqrrqpdlqmhlfatsgddgstlrtrlaqastlhdvtalghlatakhirhhgidllfdlrgwggggrpevfalrpapvqvnwlaypgtsgapwmdyvlgdafalppalepfysehvlrlqgafqpsdtsrvvaeppsrtqcglpeqgvvlccfnnsyklnpqsmarmlavlrevpdsvlwllsgpgeadarlrafahaqgvdaqrlvfmpklphpqylaryrhadlfldthpynahttasdalwtgcpvlttpgetfaarvagslnhhlgldemnvaddaafvakavalasdpaaltalharvdvlrresgvfemdgfaddfgallqalarrhgwlgi
+
+> Foobar_COILS 32-40, 65-73, 85-133, 156-165, 200-256, 263-304, 342-398, 410-419, 452-460
+mgdttagemavqrglalhqqrhaeaavllqqASDAAPEHPgialwlhaledagqaeaaaaytraHQLLPEEPYitaqllnavaqGVGAVEPFAFLSEDASAAESVRPLAPTRVRSKGPLRVGFVSNGFGAHPTglltvalfealqrrqpdlqmhlFATSGDDGSTlrtrlaqastlhdvtalghlatakhirhhgidllFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSehvlrlQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPqsmarmlavlrevpdsvlwllsgpgeadarlrafahaQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGCPVLTTPGEtfaarvagslnHHLGLDEMNVaddaafvakavalasdpaaltalharvdvlrrESGVFEMDGfaddfgallqalarrhgwlgi
+> Foobar_REM465 1-11, 268-281
+MGDTTAGEMAVqrglalhqqrhaeaavllqqasdaapehpgialwlhaledagqaeaaaaytrahqllpeepyitaqllnavaqgvgavepfaflsedasaaesvrplaptrvrskgplrvgfvsngfgahptglltvalfealqrrqpdlqmhlfatsgddgstlrtrlaqastlhdvtalghlatakhirhhgidllfdlrgwggggrpevfalrpapvqvnwlaypgtsgapwmdyvlgdafalppalepfysehvlrlqgafqPSDTSRVVAEPPSRtqcglpeqgvvlccfnnsyklnpqsmarmlavlrevpdsvlwllsgpgeadarlrafahaqgvdaqrlvfmpklphpqylaryrhadlfldthpynahttasdalwtgcpvlttpgetfaarvagslnhhlgldemnvaddaafvakavalasdpaaltalharvdvlrresgvfemdgfaddfgallqalarrhgwlgi
+> Foobar_HOTLOOPS 100-118
+mgdttagemavqrglalhqqrhaeaavllqqasdaapehpgialwlhaledagqaeaaaaytrahqllpeepyitaqllnavaqgvgavepfaflsedaSAAESVRPLAPTRVRSKGPlrvgfvsngfgahptglltvalfealqrrqpdlqmhlfatsgddgstlrtrlaqastlhdvtalghlatakhirhhgidllfdlrgwggggrpevfalrpapvqvnwlaypgtsgapwmdyvlgdafalppalepfysehvlrlqgafqpsdtsrvvaeppsrtqcglpeqgvvlccfnnsyklnpqsmarmlavlrevpdsvlwllsgpgeadarlrafahaqgvdaqrlvfmpklphpqylaryrhadlfldthpynahttasdalwtgcpvlttpgetfaarvagslnhhlgldemnvaddaafvakavalasdpaaltalharvdvlrresgvfemdgfaddfgallqalarrhgwlgi
+
+> dundeefriends_COILS 33-40, 49-57, 82-90, 99-112, 132-141, 163-192, 215-224, 259-315, 322-363, 401-457, 469-478
+mtadgprellqlraavrhrpqdvawlmladaeLGMGDTTAgemavqrgLALHPGHPEavarlgrvrwtqqrhaeaavllqqASDAAPEHPgialwlghALEDHQLLPEEPYItaqldvlsaqvraavaqgvGAVEPFAFLSedasaaeqlacartraqaiaaSVRPLAPTRVRSKGPLRVGFVSNGFGAHPTglltvalfealqrrqpdlqmhlFATSGDDGSTlrtrlaqastlhdvtalghlatakhirhhgidllFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSehvlrlQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPqsmarmlavlrevpdsvlwllsgpgeadarlrafahaQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGCPVLTTPGEtfaarvagslnHHLGLDEMNVaddaafvakavalasdpaaltalharvdvlrresi
+> dundeefriends_REM465 327-340
+mtadgprellqlraavrhrpqdvawlmladaelgmgdttagemavqrglalhpghpeavarlgrvrwtqqrhaeaavllqqasdaapehpgialwlghaledhqllpeepyitaqldvlsaqvraavaqgvgavepfaflsedasaaeqlacartraqaiaasvrplaptrvrskgplrvgfvsngfgahptglltvalfealqrrqpdlqmhlfatsgddgstlrtrlaqastlhdvtalghlatakhirhhgidllfdlrgwggggrpevfalrpapvqvnwlaypgtsgapwmdyvlgdafalppalepfysehvlrlqgafqPSDTSRVVAEPPSRtqcglpeqgvvlccfnnsyklnpqsmarmlavlrevpdsvlwllsgpgeadarlrafahaqgvdaqrlvfmpklphpqylaryrhadlfldthpynahttasdalwtgcpvlttpgetfaarvagslnhhlgldemnvaddaafvakavalasdpaaltalharvdvlrresi
+> dundeefriends_HOTLOOPS 162-176
+mtadgprellqlraavrhrpqdvawlmladaelgmgdttagemavqrglalhpghpeavarlgrvrwtqqrhaeaavllqqasdaapehpgialwlghaledhqllpeepyitaqldvlsaqvraavaqgvgavepfaflsedasaaeqlacartraqaiaASVRPLAPTRVRSKGplrvgfvsngfgahptglltvalfealqrrqpdlqmhlfatsgddgstlrtrlaqastlhdvtalghlatakhirhhgidllfdlrgwggggrpevfalrpapvqvnwlaypgtsgapwmdyvlgdafalppalepfysehvlrlqgafqpsdtsrvvaeppsrtqcglpeqgvvlccfnnsyklnpqsmarmlavlrevpdsvlwllsgpgeadarlrafahaqgvdaqrlvfmpklphpqylaryrhadlfldthpynahttasdalwtgcpvlttpgetfaarvagslnhhlgldemnvaddaafvakavalasdpaaltalharvdvlrresi
+
diff --git a/testsrc/testdata/scores.out b/testsrc/testdata/scores.out
new file mode 100644
index 0000000..647759d
--- /dev/null
+++ b/testsrc/testdata/scores.out
@@ -0,0 +1,1568 @@
+> Foobar_dundeefriends
+# RESIDUE COILS REM465 HOTLOOPS
+M	0.86010	0.88512	0.37094
+T	0.79983	0.85864	0.44331
+A	0.72031	0.83329	0.42744
+D	0.62168	0.79393	0.24390
+G	0.50983	0.59080	0.11673
+P	0.25998	0.36247	0.06320
+R	0.29879	0.44037	0.06982
+E	0.25286	0.32959	0.05194
+L	0.21085	0.31715	0.04783
+L	0.17763	0.27760	0.02311
+Q	0.16044	0.27182	0.01845
+L	0.18476	0.27532	0.04620
+R	0.22259	0.29066	0.06996
+A	0.26044	0.31137	0.08420
+A	0.28021	0.31834	0.09161
+V	0.31770	0.33024	0.09771
+R	0.34459	0.33123	0.10017
+H	0.35438	0.33015	0.10042
+R	0.34941	0.31879	0.09479
+P	0.33860	0.29840	0.08436
+Q	0.31280	0.26756	0.07276
+D	0.27741	0.22690	0.06044
+F	0.25835	0.18412	0.05193
+V	0.22091	0.15604	0.03427
+A	0.19781	0.13840	0.02145
+W	0.17252	0.12069	0.00934
+L	0.16471	0.13344	0.00824
+M	0.18962	0.14399	0.02030
+L	0.20990	0.15715	0.02233
+A	0.24890	0.18675	0.02482
+D	0.30416	0.20404	0.02828
+A	0.36864	0.21878	0.03293
+E	0.42323	0.24384	0.03802
+L	0.49613	0.27329	0.04467
+G	0.54673	0.30276	0.04821
+M	0.58288	0.32961	0.05112
+G	0.58734	0.35779	0.05103
+D	0.57351	0.39639	0.04991
+T	0.54838	0.40374	0.04728
+T	0.49719	0.41796	0.04257
+A	0.44247	0.42299	0.03589
+G	0.38488	0.42355	0.03230
+E	0.32062	0.43459	0.02845
+M	0.27621	0.43599	0.02370
+A	0.24947	0.43579	0.02298
+V	0.26104	0.44630	0.02480
+Q	0.28555	0.42657	0.02998
+R	0.33863	0.41808	0.03700
+G	0.42083	0.41277	0.04747
+L	0.52012	0.40903	0.05937
+A	0.57192	0.40310	0.06615
+L	0.61014	0.39172	0.07155
+H	0.62000	0.38603	0.07143
+P	0.61420	0.38863	0.07132
+G	0.59027	0.36809	0.06880
+H	0.54439	0.37383	0.06386
+P	0.50222	0.36429	0.05768
+E	0.45498	0.35329	0.05279
+A	0.40408	0.33619	0.04550
+V	0.36729	0.33364	0.03718
+A	0.33908	0.34380	0.03627
+R	0.34141	0.35219	0.03640
+L	0.35060	0.35611	0.03942
+G	0.37329	0.36835	0.04165
+R	0.39930	0.37477	0.04556
+V	0.41249	0.38955	0.04707
+R	0.40000	0.39924	0.04544
+W	0.38778	0.41158	0.04330
+T	0.36202	0.43951	0.03890
+Q	0.32894	0.45950	0.03453
+Q	0.29139	0.46461	0.03096
+R	0.24944	0.47555	0.02594
+H	0.22078	0.46457	0.02235
+A	0.18668	0.44830	0.01686
+E	0.15893	0.41673	0.01509
+A	0.13593	0.41862	0.01529
+A	0.13590	0.41297	0.02241
+V	0.16183	0.39515	0.02782
+L	0.19353	0.40028	0.03466
+L	0.24663	0.40988	0.04213
+Q	0.31725	0.43753	0.04908
+Q	0.38948	0.45652	0.05581
+A	0.46684	0.49088	0.06222
+S	0.54056	0.51927	0.06666
+D	0.60106	0.54082	0.06870
+A	0.64620	0.53213	0.06829
+A	0.66751	0.51461	0.06782
+P	0.65871	0.48304	0.06293
+E	0.61353	0.45002	0.05575
+H	0.54564	0.40062	0.04662
+P	0.48933	0.35331	0.04148
+G	0.42808	0.30441	0.03594
+I	0.39194	0.24590	0.03330
+A	0.35118	0.18098	0.02877
+L	0.33052	0.16960	0.02819
+W	0.32568	0.16924	0.02737
+L	0.32371	0.18936	0.02656
+G	0.33488	0.20189	0.02826
+H	0.35178	0.23060	0.02991
+A	0.36475	0.26267	0.03080
+L	0.36778	0.29931	0.03102
+E	0.35647	0.34612	0.03008
+D	0.32886	0.40965	0.02761
+A	0.28835	0.44616	0.02340
+G	0.22931	0.48443	0.01894
+Q	0.19242	0.49768	0.01648
+A	0.17246	0.51975	0.01495
+E	0.14513	0.52485	0.01265
+A	0.14509	0.52733	0.01241
+A	0.13113	0.52307	0.01172
+A	0.14257	0.52022	0.00727
+A	0.15732	0.49780	0.00925
+A	0.16228	0.47742	0.01891
+Y	0.19799	0.44287	0.03106
+T	0.24619	0.40365	0.03941
+R	0.30467	0.37339	0.05366
+A	0.38077	0.34312	0.06721
+H	0.44188	0.32533	0.07549
+Q	0.49887	0.30498	0.07979
+L	0.56428	0.26520	0.08702
+L	0.60765	0.24710	0.09515
+P	0.62855	0.22427	0.09743
+E	0.61894	0.22200	0.09484
+E	0.59193	0.21352	0.08797
+P	0.55817	0.21264	0.07919
+Y	0.50412	0.20699	0.06826
+I	0.45257	0.20568	0.05530
+T	0.38361	0.21586	0.05098
+A	0.31311	0.22920	0.04859
+Q	0.25850	0.23918	0.04120
+L	0.22610	0.24305	0.03398
+L	0.20761	0.24496	0.03393
+N	0.21606	0.24725	0.03076
+W	0.21665	0.23931	0.02528
+R	0.24919	0.22444	0.02444
+R	0.29430	0.21166	0.02930
+R	0.31798	0.20457	0.03067
+L	0.33694	0.18726	0.03113
+C	0.34845	0.17414	0.03145
+D	0.36210	0.16875	0.03166
+W	0.37031	0.16887	0.03294
+R	0.37025	0.16619	0.03378
+A	0.35790	0.18814	0.03081
+L	0.33779	0.21887	0.03011
+D	0.30930	0.24621	0.02892
+V	0.26754	0.27678	0.02676
+L	0.23659	0.32224	0.02315
+S	0.20691	0.35984	0.02471
+A	0.17775	0.39641	0.02215
+Q	0.15081	0.42204	0.02329
+V	0.14823	0.43457	0.02579
+R	0.15588	0.44450	0.02810
+A	0.18517	0.44995	0.03299
+A	0.22282	0.44130	0.03871
+V	0.26328	0.41804	0.04349
+A	0.31092	0.40182	0.04799
+Q	0.35060	0.36068	0.05071
+G	0.38352	0.32101	0.05107
+V	0.42164	0.29133	0.05083
+G	0.45736	0.26373	0.05326
+A	0.49886	0.22661	0.05499
+V	0.52391	0.20562	0.05560
+E	0.53303	0.20165	0.05326
+P	0.53975	0.20063	0.05487
+F	0.52385	0.20385	0.05015
+A	0.50639	0.22752	0.05004
+F	0.48741	0.26114	0.04785
+L	0.46674	0.28999	0.04586
+S	0.43909	0.33263	0.04388
+E	0.39696	0.36707	0.03940
+D	0.35208	0.41809	0.03515
+A	0.30408	0.46253	0.03007
+S	0.24901	0.46649	0.02454
+A	0.19867	0.47834	0.01929
+A	0.16075	0.50072	0.01365
+E	0.13788	0.50748	0.01122
+Q	0.13506	0.50876	0.01368
+L	0.12169	0.51337	0.01547
+A	0.12136	0.51136	0.01598
+C	0.13259	0.50633	0.01649
+A	0.13448	0.48088	0.01786
+R	0.13417	0.48245	0.02171
+T	0.14810	0.47380	0.02092
+R	0.15594	0.46796	0.02898
+A	0.16180	0.47356	0.03389
+Q	0.19117	0.47436	0.04219
+A	0.22511	0.46346	0.05995
+I	0.26575	0.46364	0.06867
+A	0.31723	0.44786	0.08230
+A	0.37505	0.45856	0.10196
+S	0.43341	0.46499	0.12734
+V	0.50181	0.46517	0.14401
+R	0.55621	0.45469	0.15645
+P	0.60375	0.45290	0.17581
+L	0.64486	0.44417	0.18570
+A	0.66990	0.43379	0.19070
+P	0.68382	0.41168	0.18878
+T	0.70233	0.41020	0.18048
+R	0.72070	0.40484	0.16987
+V	0.71180	0.39972	0.16069
+R	0.71532	0.37964	0.14413
+S	0.70293	0.35656	0.12867
+K	0.67155	0.32107	0.11402
+G	0.63844	0.31759	0.08838
+P	0.61151	0.28482	0.07748
+L	0.58165	0.26357	0.07057
+R	0.56607	0.23944	0.06683
+V	0.55583	0.20985	0.05244
+G	0.54798	0.18271	0.04783
+F	0.54729	0.18625	0.06066
+V	0.56353	0.19115	0.06687
+S	0.58514	0.20302	0.07328
+N	0.61899	0.21760	0.07727
+G	0.64417	0.24094	0.08164
+F	0.66852	0.25410	0.08724
+G	0.67113	0.26439	0.08635
+A	0.65329	0.26395	0.08354
+H	0.59906	0.25471	0.07613
+P	0.53852	0.23852	0.06676
+T	0.46756	0.23838	0.05520
+G	0.39638	0.22887	0.04532
+L	0.32435	0.21985	0.03424
+L	0.25959	0.20622	0.02455
+T	0.21092	0.19002	0.01454
+V	0.16286	0.18984	0.00874
+A	0.13222	0.19663	0.01040
+L	0.13718	0.21327	0.01176
+F	0.15922	0.22668	0.01421
+E	0.19287	0.25014	0.01571
+A	0.24795	0.27481	0.02231
+L	0.30912	0.29319	0.02781
+Q	0.36600	0.31761	0.03436
+R	0.40904	0.32357	0.04039
+R	0.44641	0.31944	0.04550
+Q	0.47387	0.31066	0.04911
+P	0.48015	0.30088	0.05001
+D	0.46585	0.27977	0.04718
+L	0.43848	0.26224	0.04029
+Q	0.41204	0.24283	0.03653
+M	0.40286	0.22376	0.03416
+H	0.38445	0.22935	0.04559
+L	0.40616	0.24686	0.05506
+F	0.44756	0.28038	0.07106
+A	0.47610	0.30637	0.08409
+T	0.52735	0.35044	0.09517
+S	0.56587	0.38896	0.10535
+G	0.57757	0.43154	0.10837
+D	0.58300	0.46681	0.10980
+D	0.55714	0.47586	0.10507
+G	0.52225	0.46343	0.09636
+S	0.49037	0.44504	0.08443
+T	0.44095	0.43528	0.06889
+L	0.37153	0.42133	0.04888
+R	0.31143	0.39708	0.03105
+T	0.27726	0.37781	0.01676
+R	0.27155	0.36109	0.01414
+L	0.28212	0.36818	0.02699
+A	0.32672	0.37349	0.03457
+Q	0.37520	0.37718	0.04759
+A	0.40565	0.37791	0.05522
+S	0.43709	0.38006	0.06145
+T	0.42865	0.37978	0.06213
+L	0.42653	0.37779	0.06203
+H	0.41799	0.35467	0.06181
+D	0.40044	0.33312	0.05776
+V	0.40150	0.31093	0.05556
+T	0.41246	0.30646	0.05349
+A	0.40495	0.29640	0.05083
+L	0.38425	0.29841	0.04063
+G	0.37341	0.31172	0.03907
+H	0.37246	0.32334	0.03285
+L	0.38933	0.33516	0.04222
+A	0.38737	0.36073	0.05225
+T	0.39737	0.37986	0.06044
+A	0.39716	0.39982	0.06460
+K	0.37829	0.40866	0.06597
+H	0.35046	0.39889	0.06465
+I	0.32903	0.38932	0.06095
+R	0.31342	0.37365	0.05668
+H	0.28853	0.35140	0.05380
+H	0.27629	0.33450	0.04777
+G	0.29822	0.30711	0.04648
+I	0.31666	0.28368	0.04202
+D	0.33323	0.24918	0.03960
+L	0.35823	0.24361	0.03424
+L	0.39797	0.22750	0.04012
+F	0.44639	0.21384	0.04190
+D	0.50116	0.22639	0.05091
+L	0.55514	0.24972	0.05808
+R	0.61133	0.27218	0.06250
+G	0.66599	0.28765	0.06599
+W	0.70960	0.29860	0.06791
+G	0.73011	0.30278	0.06742
+G	0.72946	0.30915	0.06371
+G	0.71108	0.30904	0.06168
+G	0.68003	0.30934	0.05571
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+V	0.62287	0.23817	0.06756
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+L	0.72402	0.22164	0.06056
+E	0.69564	0.22568	0.05896
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+L	0.34704	0.33592	0.03225
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+S	0.72130	0.54316	0.08945
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+P	0.78245	0.55519	0.07148
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+C	0.43433	0.09879	0.03559
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+N	0.57712	0.12335	0.05514
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+T	0.61727	0.40648	0.07578
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+A	0.20346	0.22812	0.01511
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+A	0.38886	0.33013	0.08340
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+D	0.25029	0.15580	0.03139
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+L	0.07925	0.21160	0.01748
+L	0.06858	0.24220	0.00433
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+R	0.24695	0.44230	0.05018
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+L	0.47985	0.62475	0.12977
+G	0.69681	0.58187	0.22957
+I	0.79530	0.62112	0.21132
+> Foobar
+# RESIDUE COILS REM465 HOTLOOPS
+M	0.79892	0.92921	0.40349
+G	0.74423	0.81900	0.43658
+D	0.60842	0.82833	0.08939
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+G	0.26586	0.62069	0.02838
+E	0.28016	0.66860	0.07984
+M	0.24572	0.57265	0.03040
+A	0.22255	0.54504	0.02639
+V	0.21635	0.52145	0.04038
+Q	0.21690	0.49944	0.03196
+R	0.23267	0.49259	0.03377
+G	0.24055	0.47293	0.03344
+L	0.26254	0.46643	0.03835
+A	0.26420	0.46640	0.03487
+L	0.26992	0.46901	0.03649
+H	0.26850	0.47559	0.03522
+Q	0.25527	0.49484	0.03185
+Q	0.24162	0.49611	0.02721
+R	0.20784	0.50172	0.02291
+H	0.18286	0.48178	0.01972
+A	0.15578	0.46002	0.01334
+E	0.14728	0.43253	0.01101
+A	0.13705	0.43489	0.01111
+A	0.13657	0.42917	0.01404
+V	0.16021	0.41154	0.01697
+L	0.19843	0.40639	0.02186
+L	0.25843	0.42716	0.02856
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+Q	0.39430	0.47343	0.04065
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+A	0.66685	0.50589	0.05977
+P	0.65775	0.47456	0.05758
+E	0.61771	0.43295	0.05223
+H	0.55706	0.38420	0.04516
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+G	0.42702	0.26643	0.03560
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+L	0.23802	0.16403	0.02028
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+Q	0.19947	0.47713	0.01644
+A	0.18363	0.51138	0.01469
+E	0.17932	0.51322	0.01509
+A	0.17237	0.50800	0.01518
+A	0.17338	0.49921	0.01566
+A	0.17388	0.49185	0.01698
+A	0.16234	0.46450	0.01724
+Y	0.18601	0.43144	0.02005
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+L	0.55983	0.26400	0.05140
+L	0.60053	0.24016	0.05413
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+E	0.60399	0.22079	0.05307
+E	0.57819	0.22202	0.04989
+P	0.53272	0.20311	0.04573
+Y	0.46895	0.19427	0.04013
+I	0.39975	0.19714	0.03277
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+A	0.24217	0.21072	0.02151
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+L	0.17882	0.23839	0.01623
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+A	0.37329	0.30590	0.03585
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+G	0.49950	0.24672	0.04205
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+A	0.51830	0.21316	0.05248
+F	0.51521	0.23772	0.05631
+L	0.51271	0.28019	0.05970
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+E	0.51042	0.40157	0.06786
+D	0.50605	0.45548	0.07396
+A	0.51565	0.50970	0.08190
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+A	0.51350	0.54811	0.09539
+A	0.53026	0.56442	0.09821
+E	0.54403	0.57520	0.10208
+S	0.57221	0.57416	0.10983
+V	0.57841	0.57213	0.10431
+R	0.60075	0.54032	0.09786
+P	0.62011	0.51067	0.11639
+L	0.63932	0.46748	0.12785
+A	0.64699	0.43929	0.13600
+P	0.65559	0.41463	0.14158
+T	0.67237	0.41278	0.14389
+R	0.68444	0.41621	0.14370
+V	0.68674	0.40699	0.15192
+R	0.69802	0.38662	0.14650
+S	0.69242	0.36595	0.14032
+K	0.66442	0.32203	0.12958
+G	0.63516	0.30503	0.11619
+P	0.61231	0.27691	0.09939
+L	0.58285	0.26232	0.08426
+R	0.57239	0.24178	0.06952
+V	0.55583	0.21093	0.04775
+G	0.54798	0.18271	0.03550
+F	0.54729	0.18625	0.05813
+V	0.56353	0.19115	0.06508
+S	0.58514	0.20302	0.07226
+N	0.61899	0.21760	0.07689
+G	0.64417	0.24094	0.08339
+F	0.66852	0.25410	0.08740
+G	0.67113	0.26439	0.08673
+A	0.65329	0.26395	0.08359
+H	0.59906	0.25471	0.07593
+P	0.53852	0.23852	0.06676
+T	0.46756	0.23838	0.05520
+G	0.39638	0.22887	0.04532
+L	0.32435	0.21985	0.03424
+L	0.25959	0.20622	0.02455
+T	0.21092	0.19002	0.01454
+V	0.16286	0.18984	0.00874
+A	0.13222	0.19663	0.01040
+L	0.13718	0.21327	0.01176
+F	0.15922	0.22668	0.01421
+E	0.19287	0.25014	0.01571
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+L	0.07925	0.21160	0.01748
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+L	0.47985	0.62475	0.12977
+G	0.69681	0.58187	0.22957
+I	0.79530	0.62112	0.21132
+> dundeefriends
+# RESIDUE COILS REM465 HOTLOOPS
+M	0.86010	0.88512	0.37094
+T	0.79983	0.85864	0.44331
+A	0.72031	0.83329	0.43668
+D	0.62168	0.79393	0.27484
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+L	0.20943	0.31797	0.04618
+L	0.17624	0.28671	0.01931
+Q	0.15219	0.27288	0.01291
+L	0.17077	0.27141	0.04418
+R	0.20773	0.29874	0.07215
+A	0.24652	0.32640	0.08449
+A	0.27945	0.33948	0.09399
+V	0.31413	0.35494	0.09834
+R	0.34058	0.35621	0.10360
+H	0.35819	0.36011	0.10861
+R	0.36170	0.35006	0.10579
+P	0.35340	0.32859	0.09729
+Q	0.33982	0.30310	0.09009
+D	0.31390	0.25550	0.07910
+V	0.29248	0.20603	0.06265
+A	0.25978	0.18203	0.04295
+W	0.23700	0.16252	0.03059
+L	0.20659	0.15437	0.01799
+M	0.19746	0.16052	0.01739
+L	0.22270	0.16616	0.03081
+A	0.26055	0.19292	0.03190
+D	0.30598	0.20791	0.03292
+A	0.36133	0.22227	0.03452
+E	0.41353	0.24276	0.03721
+L	0.48565	0.27072	0.04690
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+M	0.57647	0.32767	0.05319
+G	0.58650	0.35718	0.05304
+D	0.57401	0.39529	0.05115
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+T	0.49998	0.41707	0.04147
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+Q	0.29139	0.46461	0.03096
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+H	0.22078	0.46457	0.02235
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+A	0.13590	0.41297	0.02226
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+A	0.46684	0.49088	0.06182
+S	0.54056	0.51927	0.06564
+D	0.60106	0.54082	0.06724
+A	0.64620	0.53373	0.06663
+A	0.66884	0.51613	0.06630
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-- 
1.7.10.2