Parser for DisEMBL results and finished runner, few test cases. DisemblTester has...

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3695 e3abac25-378b-4346-85de-24260fe3988d

diff --git a/.classpath b/.classpath
index 0ace127..4820b06 100644 (file)
--- a/.classpath
+++ b/.classpath
@@ -1,10 +1,10 @@
 <?xml version="1.0" encoding="UTF-8"?>\r
 <classpath>\r
+       <classpathentry kind="src" path="datamodel"/>\r
        <classpathentry kind="src" path="engine"/>\r
+       <classpathentry kind="src" path="runner"/>\r
        <classpathentry kind="src" path="webservices"/>\r
        <classpathentry kind="src" path="testsrc"/>\r
-       <classpathentry kind="src" path="runner"/>\r
-       <classpathentry kind="src" path="datamodel"/>\r
        <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>\r
        <classpathentry kind="lib" path="WEB-INF/lib/log4j-1.2.15.jar"/>\r
        <classpathentry kind="lib" path="testsrc/lib/testng-5.10-jdk15.jar"/>\r

diff --git a/build.xml b/build.xml
index 02298e0..5597457 100644 (file)
--- a/build.xml
+++ b/build.xml
@@ -87,18 +87,18 @@
                                <compilerarg value="-Xlint:unchecked"/>\r
                                <classpath refid="project.classpath" />\r
                </javac>\r
-               <!-- Complile the tests -->\r
-               <javac srcdir="${basedir}/testsrc" destdir="${classes}" target="1.6"\r
+               <!-- Complile the webservices -->\r
+               <javac srcdir="${basedir}/webservices" destdir="${classes}" target="1.6"\r
                                source="1.6" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >\r
                                <compilerarg value="-Xlint:unchecked"/>\r
                                <classpath refid="project.classpath" />\r
-                               <classpath refid="test.classpath" />\r
                </javac>\r
-               <!-- Complile the webservices -->\r
-               <javac srcdir="${basedir}/webservices" destdir="${classes}" target="1.6"\r
+               <!-- Complile the tests -->\r
+               <javac srcdir="${basedir}/testsrc" destdir="${classes}" target="1.6"\r
                                source="1.6" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >\r
                                <compilerarg value="-Xlint:unchecked"/>\r
                                <classpath refid="project.classpath" />\r
+                               <classpath refid="test.classpath" />\r
                </javac>\r
        </target>\r
 \r

diff --git a/conf/Executable.properties b/conf/Executable.properties
index 4b1cb00..548507c 100644 (file)
--- 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 (!) ### \r
 #local.disembl.bin.windows= \r
 local.disembl.bin=binaries/src/disembl/DisEMBL.py\r
-cluster.disembl.bin=/homes/pvtroshin/jaba2/binaries/src/disembl/DisEMBL.py\r
+cluster.disembl.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/disembl/DisEMBL.py\r
 disembl.parameters.file=conf/settings/DisemblParameters.xml\r
 disembl.limits.file=conf/settings/DisemblLimits.xml\r
 disembl.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r

diff --git a/conf/settings/DisemblParameters.xml b/conf/settings/DisemblParameters.xml
index 3820a35..676395e 100644 (file)
--- a/conf/settings/DisemblParameters.xml
+++ b/conf/settings/DisemblParameters.xml
@@ -1,5 +1,9 @@
 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
 <runnerConfig>\r
+<!-- \r
+    Extreme variation of this parameter does not have any impact on the output\r
+    so irrelevant. \r
+\r
        <runnerClassName>compbio.runner.disorder.Disembl</runnerClassName>\r
        <prmSeparator>=</prmSeparator>\r
        <parameters>\r
@@ -14,7 +18,7 @@
                        <max>30</max>\r
                </validValue>\r
        </parameters>\r
-<!--  \r
+ \r
  These can be supported but not recommended to change so what's the point?\r
  \r
  Manual: Normally the default parameters should not be changed.\r

diff --git a/datamodel/compbio/data/sequence/SequenceUtil.java b/datamodel/compbio/data/sequence/SequenceUtil.java
index 85ae95f..a636c3a 100644 (file)
--- a/datamodel/compbio/data/sequence/SequenceUtil.java
+++ b/datamodel/compbio/data/sequence/SequenceUtil.java
@@ -406,12 +406,15 @@ public final class SequenceUtil {
         * \r
         * TODO complete!\r
         * \r
+        * >Sequence name\r
+        * \r
         * RESIDUE COILS REM465 HOTLOOPS\r
         * \r
         * M 0.86010 0.88512 0.37094\r
         * \r
         * T 0.79983 0.85864 0.44331 ....\r
-        * \r
+\r
+        * >Next Sequence name \r
         * RESIDUE COILS REM465 HOTLOOPS\r
         * \r
         * M 0.86010 0.88512 0.37094\r
@@ -422,14 +425,14 @@ public final class SequenceUtil {
         * @throws IOException\r
         * @throws UnknownFileFormatException\r
         */\r
-       static Map<FastaSequence, Set<Score>> readDisembl(final InputStream input)\r
+       public static Map<FastaSequence, Set<Score>> readDisembl(final InputStream input)\r
                        throws IOException, UnknownFileFormatException {\r
                Scanner scan = new Scanner(input);\r
-               scan.useDelimiter("# RESIDUE COILS REM465 HOTLOOPS\n");\r
+               scan.useDelimiter(">");\r
                if (!scan.hasNext()) {\r
                        throw new UnknownFileFormatException(\r
-                                       "In Disembl score format each seqeunce score is expected to start from the line: "\r
-                                                       + "'# RESIDUE COILS REM465 HOTLOOPS\\n'."\r
+                                       "In Disembl score format each sequence score is expected " +\r
+                                       "to start from the line: >Sequence name "\r
                                                        + " No such line was found!");\r
                }\r
 \r
@@ -438,22 +441,27 @@ public final class SequenceUtil {
                while (scan.hasNext()) {\r
                        seqCounter++;\r
                        String singleSeq = scan.next();\r
-                       Scanner scansingle = new Scanner(singleSeq);\r
+                       Scanner scansingle = new Scanner(singleSeq);\r
+                       if(!scansingle.hasNextLine()) {\r
+                               throw new RuntimeException("The input looks like an incomplete disembl file - cannot parse!");\r
+                       }\r
+                       \r
                        StringBuffer seqbuffer = new StringBuffer();\r
                        ArrayList<Float> coils = new ArrayList<Float>();\r
                        ArrayList<Float> rem = new ArrayList<Float>();\r
                        ArrayList<Float> hotloops = new ArrayList<Float>();\r
-                       FastaSequence fs = new FastaSequence(Integer.toString(seqCounter),\r
-                                       singleSeq);\r
-                       while (scansingle.hasNextLine()) {\r
-                               String valueLine = scansingle.nextLine();\r
-                               Scanner values = new Scanner(valueLine);\r
-                               seqbuffer.append(values.next());\r
-                               coils.add(values.nextFloat());\r
-                               rem.add(values.nextFloat());\r
-                               hotloops.add(values.nextFloat());\r
-                               values.close();\r
+\r
+                       String sequenceName = scansingle.nextLine().trim();\r
+                       String title =  scansingle.nextLine();\r
+                       assert title.startsWith("# RESIDUE COILS REM465 HOTLOOPS") : ">Sequence_name must follow column title: # RESIDUE COILS REM465 HOTLOOPS!";\r
+                       \r
+                       while (scansingle.hasNext()) {\r
+                               seqbuffer.append(scansingle.next());\r
+                               coils.add(scansingle.nextFloat());\r
+                               rem.add(scansingle.nextFloat());\r
+                               hotloops.add(scansingle.nextFloat());\r
                        }\r
+                       FastaSequence fs = new FastaSequence(sequenceName,seqbuffer.toString());\r
                        Set<Score> scores = new HashSet<Score>();\r
                        scores.add(new Score(DisemblResultAnnot.COILS, coils));\r
                        scores.add(new Score(DisemblResultAnnot.HOTLOOPS, hotloops));\r
@@ -466,6 +474,15 @@ public final class SequenceUtil {
                input.close();\r
                return results;\r
        }\r
+       \r
+       public static  Map<String, Set<Score>> removeSequences(Map<FastaSequence, Set<Score>> disemblResults) { \r
+               Map<String, Set<Score>> seqNameScores = new HashMap<String, Set<Score>>();\r
+               for(Map.Entry<FastaSequence,Set<Score>> dres: disemblResults.entrySet()) {\r
+                       seqNameScores.put(dres.getKey().getId(),dres.getValue()); \r
+               }\r
+               return seqNameScores;\r
+       }\r
+       \r
        /**\r
         * Read AACon result with no alignment files. This method leaves incoming\r
         * the InputStream results open!\r

diff --git a/runner/compbio/runner/disorder/Disembl.java b/runner/compbio/runner/disorder/Disembl.java
index 8f4256f..337395c 100644 (file)
--- a/runner/compbio/runner/disorder/Disembl.java
+++ b/runner/compbio/runner/disorder/Disembl.java
@@ -1,6 +1,6 @@
 /*\r
- * Copyright (c) 2009 Peter Troshin JAva Bioinformatics Analysis Web Services\r
- * (JABAWS) @version: 1.0 This library is free software; you can redistribute it\r
+ * Copyright (c) 2011 Peter Troshin JAva Bioinformatics Analysis Web Services\r
+ * (JABAWS) @version: 2.0 This library is free software; you can redistribute it\r
  * and/or modify it under the terms of the Apache License version 2 as published\r
  * by the Apache Software Foundation This library is distributed in the hope\r
  * that it will be useful, but WITHOUT ANY WARRANTY; without even the implied\r
@@ -14,13 +14,22 @@
 \r
 package compbio.runner.disorder;\r
 \r
-import java.util.Arrays;\r
+import java.io.File;\r
+import java.io.FileInputStream;\r
+import java.io.FileNotFoundException;\r
+import java.io.IOException;\r
+import java.io.InputStream;\r
+\r
 import java.util.Map;\r
+import java.util.Set;\r
 \r
 import org.apache.log4j.Logger;\r
 \r
+\r
 import compbio.data.sequence.Score;\r
-import compbio.engine.client.CommandBuilder;\r
+import compbio.data.sequence.SequenceUtil;\r
+import compbio.data.sequence.UnknownFileFormatException;\r
+\r
 import compbio.engine.client.Executable;\r
 import compbio.engine.client.PipedExecutable;\r
 import compbio.engine.client.SkeletalExecutable;\r
@@ -30,26 +39,27 @@ import compbio.metadata.ResultNotAvailableException;
 import compbio.runner.Util;\r
 \r
 /**\r
- * @see DisEMBL\r
- * \r
  *      DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops\r
- *      fold_rem465 sequence_file print 'A default run would be: ./DisEMBL.py 8\r
- *      8 4 1.2 1.4 1.2 fasta_file > out' new DisEMBL is at\r
- *      /homes/pvtroshin/soft/DisEMBL-1.4raw\r
- * \r
- *      This is not a standard DisEMBL! The script has been modified! DisEMBL.py\r
- *      smooth_frame peak_frame join_frame fold_coils fold_hotloops fold_rem465\r
- *      [mode] < fasta_file > out print\r
- * \r
- *      'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 < fasta_file'\r
- *      print 'Mode: "default"(nothing) or "scores" which will give scores per\r
- *      residue in TAB separated format'\r
+ *      fold_rem465 sequence_file print \r
+ *      \r
+ *      'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out' \r
+ *             \r
+ *             This version of DisEMBL is 1.4 (latest available for download in Feb 2011)\r
+ *             capable of outputting raw values      \r
+ *      \r
+ *      The values of the parameters are hard coded in DisEMBL.py script. \r
+ *      smooth_frame=8 peak_frame=8 join_frame=4 fold_coils=1.2 fold_hotloops=1.4\r
+ *      fold_rem465=1.2 \r
+ *      \r
+ *       Changing these values are not recommended by developers, apart from smoothing window. \r
+ *       However, 5 orders of magnitude changes in this parameter does not change the output\r
+ *       so allowing this change also seems pointless. Finally, the binary, DisEMBL depends on\r
+ *       - Tisean is not happy with arbitruary changes to these values, so changing them can \r
+ *       lead to problems.\r
+ *        \r
  * \r
- *      Internal parameters names are: sj\r
+ *      This is not a standard DisEMBL! The script has been modified! \r
  * \r
- *      //TODO? pw jd ct rt lt\r
- * \r
- *      the order is preserved\r
  */\r
 public class Disembl extends SkeletalExecutable<Disembl>\r
                implements\r
@@ -60,22 +70,41 @@ public class Disembl extends SkeletalExecutable<Disembl>
        // Cache for Limits information\r
        private static LimitsManager<Disembl> limits;\r
 \r
-       // CHECK THIS !!!\r
        public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
 \r
+       /* The parameter list there must not contain same values! */\r
        public Disembl() {\r
                // remove default input to prevent it to appear in the parameters list\r
                // that could happen if the parameters are set first\r
                // super.setInput("");\r
-               addParameters(Arrays.asList("8", "8", "4", "1.2", "1.4", "1.2",\r
-                               "scores"));\r
        }\r
 \r
        @SuppressWarnings("unchecked")\r
-       public Map<String, Score> getResults(String workDirectory)\r
+       public Map<String, Set<Score>> getResults(String workDirectory)\r
                        throws ResultNotAvailableException {\r
 \r
-               return null;\r
+               InputStream inStream = null;\r
+               Map<String, Set<Score>> results= null; \r
+                       try {\r
+                               inStream = new FileInputStream(new File(workDirectory,\r
+                                               getOutput()));\r
+                               results = SequenceUtil.removeSequences(SequenceUtil.readDisembl(inStream));\r
+                               inStream.close();\r
+                       } catch (FileNotFoundException e) {\r
+                               log.error(e.getMessage(), e.getCause());\r
+                               throw new ResultNotAvailableException(e);\r
+                       } catch (IOException e) {\r
+                               log.error(e.getMessage(), e.getCause());\r
+                               throw new ResultNotAvailableException(e);\r
+                       } catch (UnknownFileFormatException e) {\r
+                               log.error(e.getMessage(), e.getCause());\r
+                               throw new ResultNotAvailableException(e);\r
+                       } catch (NullPointerException e) {\r
+                               log.error(e.getMessage(), e.getCause());\r
+                               throw new ResultNotAvailableException(e);\r
+                       }\r
+               \r
+               return results;\r
        }\r
 \r
        @Override\r
@@ -122,15 +151,4 @@ public class Disembl extends SkeletalExecutable<Disembl>
                return this.getClass();\r
        }\r
 \r
-       @Override\r
-       public CommandBuilder<Disembl> getParameters(ExecProvider provider) {\r
-               // If Savitzky-Golay smoothing parameter is specified then set it\r
-               String val = cbuilder.getParamValue("sg");\r
-               log.info("DisEMBL sav-gol value: " + val);\r
-               if (val != null) {\r
-                       cbuilder.removeParam("sg");\r
-                       cbuilder.setFirst(val);\r
-               }\r
-               return super.getParameters(provider);\r
-       }\r
 }\r

diff --git a/runtests.sh b/runtests.sh
index 0fc5a51..6d52d1f 100644 (file)
--- 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 (file)
--- a/testsrc/compbio/data/sequence/SequenceUtilTester.java
+++ b/testsrc/compbio/data/sequence/SequenceUtilTester.java
@@ -148,27 +148,33 @@ public class SequenceUtilTester {
 \r
        /**\r
         * This test tests the loading of horizontally formatted Jronn output file\r
+        * \r
+        * First seq \r
+        * \r
+        * M    0.86010 0.88512 0.37094\r
+        * \r
+        * T    0.79983 0.85864 0.44331\r
+        * \r
         */\r
        @SuppressWarnings("unchecked")\r
        @Test\r
-       public void testMultiAnnotatedSequence() {\r
+       public void testReadDisemblResults() {\r
 \r
                FileInputStream fio;\r
                try {\r
                        fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
-                                       + "disembl.out");\r
+                                       + "scores.out");\r
                        Map<FastaSequence, Set<Score>> aseqs = SequenceUtil\r
                                        .readDisembl(fio);\r
                        assertNotNull(aseqs);\r
-\r
-                       /*\r
-                        * Map<Trial, List<Number>> val = ma.getInstance(Trial.class);\r
-                        * List<Number> list = new ArrayList<Number>(); list.add(new\r
-                        * Float(1.2)); list.add(new Double(5.662)); val.put(Trial.one,\r
-                        * list); val.put(Trial.two, Arrays.asList(6.22f, 1, 37.6f));\r
-                        * System.out.println(val); AnnotatedSequence aseq = aseqs.get(0);\r
-                        */\r
-                       fio.close();\r
+                       assertEquals(aseqs.size(), 3); \r
+                       System.out.println(aseqs);\r
+                       for(FastaSequence fs: aseqs.keySet()) {\r
+                               assertTrue(" Foobar_dundeefriends Foobar dundeefriends ".contains(fs.getId()));\r
+                               Set<Score> scores = aseqs.get(fs); \r
+                               assertEquals(scores.size(),3);\r
+                       }\r
+                         fio.close();\r
                } catch (FileNotFoundException e) {\r
                        e.printStackTrace();\r
                        fail(e.getLocalizedMessage());\r

diff --git a/testsrc/compbio/runner/disorder/DisemblTester.java b/testsrc/compbio/runner/disorder/DisemblTester.java
index d77648e..133168e 100644 (file)
--- 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;\r
 import java.text.ParseException;\r
 import java.util.HashSet;\r
+import java.util.Map;\r
+import java.util.Set;\r
 \r
 import javax.xml.bind.ValidationException;\r
 \r
@@ -153,7 +155,7 @@ public class DisemblTester {
                                System.out.println("Job Status: " + status);\r
                                Thread.sleep(1000);\r
                                status = aengine.getJobStatus(jobId);\r
-                               ConfiguredExecutable<Jronn> result = (ConfiguredExecutable<Jronn>) aengine\r
+                               ConfiguredExecutable<Disembl> result = (ConfiguredExecutable<Disembl>) aengine\r
                                                .getResults(jobId);\r
                                assertNotNull(result);\r
                                System.out.println("RES:" + result);\r
@@ -188,7 +190,7 @@ public class DisemblTester {
                        lr.executeJob();\r
                        ConfiguredExecutable<?> al1 = lr.waitForResult();\r
                        assertNotNull(al1.getResults());\r
-                       HashSet<Score> al2 = confDisembl.getResults();\r
+                       Map<String,Set<Score>> al2 = confDisembl.getResults();\r
                        assertNotNull(al2);\r
                        assertEquals(al2.size(), 3);\r
                        assertEquals(al1.getResults(), al2);\r
@@ -206,51 +208,7 @@ public class DisemblTester {
 \r
        @Test(groups = {AllTestSuit.test_group_runner})\r
        public void readStatistics() {\r
-               try {\r
-                       ConfiguredExecutable<Disembl> confDisembl = Configurator\r
-                                       .configureExecutable(disembl, Executable.ExecProvider.Local);\r
-                       // For local execution use relavive\r
-\r
-                       AsyncExecutor sexec = Configurator.getAsyncEngine(confDisembl);\r
-                       String jobId = sexec.submitJob(confDisembl);\r
-                       FilePuller fw = FilePuller.newFilePuller(\r
-                                       confDisembl.getWorkDirectory() + File.separator\r
-                                                       + Jronn.getStatFile(),\r
-                                       FileWatcher.MIN_CHUNK_SIZE_BYTES);\r
-                       int count = 0;\r
-                       long position = 0;\r
-                       fw.waitForFile(4);\r
-                       JobStatus status = sexec.getJobStatus(jobId);\r
-                       while (status != JobStatus.FINISHED) {\r
-                               if (fw.hasMoreData()) {\r
-                                       ChunkHolder ch = fw.pull(position);\r
-                                       String chunk = ch.getChunk();\r
-                                       position = ch.getNextPosition();\r
-                               }\r
-                               count++;\r
-                               // Make sure the loop is terminated if the job fails\r
-                               if ((status == JobStatus.UNDEFINED || status == JobStatus.FAILED)) {\r
-                                       break;\r
-                               }\r
-                               Thread.sleep(300);\r
-                               status = sexec.getJobStatus(jobId);\r
-                       }\r
-                       assertTrue(count > 1);\r
-                       ConfiguredExecutable<?> al = sexec.getResults(jobId);\r
-                       assertNotNull(al.getResults());\r
-               } catch (JobSubmissionException e) {\r
-                       e.printStackTrace();\r
-                       fail(e.getMessage());\r
-               } catch (ResultNotAvailableException e) {\r
-                       e.printStackTrace();\r
-                       fail(e.getMessage());\r
-               } catch (IOException e) {\r
-                       e.printStackTrace();\r
-                       fail(e.getMessage());\r
-               } catch (InterruptedException e) {\r
-                       e.printStackTrace();\r
-                       fail(e.getMessage());\r
-               }\r
+               // No execution statistics is available!\r
        }\r
 \r
        @Test(groups = {AllTestSuit.test_group_runner})\r
@@ -293,11 +251,11 @@ public class DisemblTester {
                        // See in details whether executables are the same\r
                        assertEquals(resurrectedCDisembl.getExecutable(), disembl);\r
 \r
-                       ConfiguredExecutable<Disembl> resJronn = Configurator\r
+                       ConfiguredExecutable<Disembl> resDisembl = Configurator\r
                                        .configureExecutable(resurrectedCDisembl.getExecutable(),\r
                                                        Executable.ExecProvider.Local);\r
 \r
-                       sexec = Configurator.getSyncEngine(resJronn,\r
+                       sexec = Configurator.getSyncEngine(resDisembl,\r
                                        Executable.ExecProvider.Local);\r
                        sexec.executeJob();\r
                        al = sexec.waitForResult();\r
@@ -327,7 +285,8 @@ public class DisemblTester {
                        RunnerConfig<Disembl> disemblConfig = ConfExecutable\r
                                        .getRunnerOptions(Disembl.class);\r
                        assertNotNull(disemblConfig);\r
-                       assertTrue(disemblConfig.getArguments().size() > 0);\r
+                       // There is no disembl parameters\r
+                       assertTrue(disemblConfig.getArguments().size() == 0);\r
 \r
                        PresetManager<Disembl> disemblPresets = ConfExecutable\r
                                        .getRunnerPresets(Disembl.class);\r

diff --git a/testsrc/testdata/disembl_default.out b/testsrc/testdata/disembl_default.out
new file mode 100644 (file)
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 (file)
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
+R      0.66061 0.29289 0.04656
+P      0.64635 0.27540 0.05550
+E      0.62499 0.25806 0.06154
+V      0.62287 0.23817 0.06756
+F      0.61060 0.22593 0.07470
+A      0.59656 0.21864 0.08205
+L      0.60330 0.21961 0.08723
+R      0.62421 0.23110 0.09194
+P      0.63973 0.23597 0.09437
+A      0.63254 0.24152 0.09269
+P      0.63711 0.23203 0.08998
+V      0.62232 0.23166 0.08314
+Q      0.60255 0.21849 0.07443
+V      0.59309 0.19996 0.06600
+N      0.59586 0.18959 0.05853
+W      0.59987 0.19889 0.04827
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+I      0.79530 0.62112 0.21132
+> Foobar
+# RESIDUE COILS REM465 HOTLOOPS
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+R      0.27155 0.36109 0.01414
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+Q      0.37520 0.37718 0.04759
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+S      0.43709 0.38006 0.06145
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+A      0.65515 0.21571 0.05698
+Y      0.69371 0.23266 0.05857
+P      0.73439 0.25305 0.06008
+G      0.74188 0.26312 0.06422
+T      0.75123 0.27052 0.06498
+S      0.76951 0.26451 0.06622
+G      0.76779 0.25325 0.06613
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+C      0.43433 0.09879 0.03559
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+L      0.59979 0.15882 0.05418
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+H      0.69816 0.38328 0.06584
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+A      0.59280 0.40090 0.08299
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+G      0.64088 0.20701 0.07736
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+D      0.25029 0.15580 0.03139
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+L      0.07925 0.21160 0.01748
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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
+> dundeefriends
+# RESIDUE COILS REM465 HOTLOOPS
+M      0.86010 0.88512 0.37094
+T      0.79983 0.85864 0.44331
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+L      0.17624 0.28671 0.01931
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+L      0.17077 0.27141 0.04418
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+A      0.24652 0.32640 0.08449
+A      0.27945 0.33948 0.09399
+V      0.31413 0.35494 0.09834
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+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
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+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
+G      0.53935 0.30076 0.05086
+M      0.57647 0.32767 0.05319
+G      0.58650 0.35718 0.05304
+D      0.57401 0.39529 0.05115
+T      0.54811 0.40315 0.04712
+T      0.49998 0.41707 0.04147
+A      0.44247 0.42420 0.03617
+G      0.38488 0.42355 0.03242
+E      0.32062 0.43459 0.02860
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+A      0.33908 0.34380 0.03627
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+Q      0.29139 0.46461 0.03096
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+A      0.66884 0.51613 0.06630
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+E      0.61097 0.44778 0.05391
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+P      0.48380 0.33950 0.03971
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+I      0.38661 0.24310 0.03176
+A      0.33624 0.19820 0.02728
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+L      0.32331 0.19389 0.02797
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+A      0.45252 0.22923 0.03818
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+H      0.66654 0.25873 0.05491
+Q      0.69000 0.25600 0.05661
+L      0.72697 0.23892 0.05926
+L      0.73889 0.23497 0.06031
+P      0.72907 0.23147 0.05950
+E      0.69616 0.23346 0.05658
+E      0.64188 0.22949 0.05192
+P      0.59731 0.24316 0.04866
+Y      0.53010 0.23475 0.04373
+I      0.45703 0.24154 0.03800
+T      0.39436 0.24885 0.03356
+A      0.33742 0.25605 0.02930
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+L      0.25054 0.29481 0.02221
+D      0.22341 0.31236 0.02035
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+L      0.20065 0.36268 0.01701
+S      0.20526 0.38583 0.01910
+A      0.19260 0.41144 0.01877
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+V      0.16434 0.45274 0.01846
+R      0.17026 0.45505 0.01889
+A      0.20301 0.45055 0.02301
+A      0.23514 0.45000 0.02681
+V      0.26802 0.41894 0.03061
+A      0.31174 0.40011 0.03490
+Q      0.35250 0.36345 0.03870
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+V      0.42079 0.29097 0.04295
+G      0.45491 0.26034 0.04537
+A      0.49886 0.22657 0.04895
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+F      0.52385 0.20385 0.05161
+A      0.50639 0.22752 0.04984
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+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
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