From: pvtroshin Date: Thu, 16 Jun 2011 14:22:06 +0000 (+0000) Subject: IUPred final touches. All test cases pass X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4d68b23381e6589b665e40dc012c66e78cd2f7a5;p=jabaws.git IUPred final touches. All test cases pass git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4274 e3abac25-378b-4346-85de-24260fe3988d --- diff --git a/conf/Executable.properties b/conf/Executable.properties index d448686..4b75730 100644 --- a/conf/Executable.properties +++ b/conf/Executable.properties @@ -91,10 +91,10 @@ globplot.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M ### IUPred configuration ### #local.iupred.bin.windows= local.iupred.bin=binaries/src/iupred/iupred -# tcoffee.bin.env=IUPred_PATH#/homes/pvtroshin/workspace/jaba2/binaries/src/iupred; +iupred.bin.env=IUPred_PATH#/homes/pvtroshin/workspace/jaba2/binaries/src/iupred cluster.iupred.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/iupred/iupred -iupred.parameters.file=conf/settings/UIPredParameters.xml -iupred.limits.file=conf/settings/UIPredLimits.xml +iupred.parameters.file=conf/settings/IUPredParameters.xml +iupred.limits.file=conf/settings/IUPredLimits.xml iupred.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M ### AACon configuration ### diff --git a/conf/settings/IUPredLimits.xml b/conf/settings/IUPredLimits.xml index 8d3a09f..1183c48 100644 --- a/conf/settings/IUPredLimits.xml +++ b/conf/settings/IUPredLimits.xml @@ -7,22 +7,7 @@ # LocalEngineExecutionLimit # - 200 + 50 400 - - Quick conservation - 10000 - 10000 - - - Slow conservation - 2000 - 1000 - - - Complete conservation - 2000 - 1000 - diff --git a/conf/settings/IUPredParameters.xml b/conf/settings/IUPredParameters.xml index 1846cad..eb485c8 100644 --- a/conf/settings/IUPredParameters.xml +++ b/conf/settings/IUPredParameters.xml @@ -1,12 +1,15 @@ - compbio.runner.disorder.Disembl + compbio.runner.disorder.IUPred Disorder type - + "Long" - for prediction of long disordered regions, "short" - for + prediction of short disordered regions ( e.g. missing residues in + X-ray structures) and "glob" for predicting globular domains. "All" for all methods short long glob + all prog_docs/iupred.txt long diff --git a/conf/settings/IUPredPresets.xml b/conf/settings/IUPredPresets.xml deleted file mode 100644 index 8cf8f44..0000000 --- a/conf/settings/IUPredPresets.xml +++ /dev/null @@ -1,16 +0,0 @@ - - - compbio.runner.disorder.IUPred - - Complete Disorder - Short, Long disorder and globular domains - - - - - - - - - - diff --git a/datamodel/compbio/data/sequence/ScoreManager.java b/datamodel/compbio/data/sequence/ScoreManager.java index 4be41d5..37e041c 100644 --- a/datamodel/compbio/data/sequence/ScoreManager.java +++ b/datamodel/compbio/data/sequence/ScoreManager.java @@ -158,6 +158,14 @@ public class ScoreManager { } return null; } + public Score getScoreByMethod(String method) { + for (Score sc : scores) { + if (method.toString().equals(sc.getMethod())) { + return sc; + } + } + return null; + } public int getNumberOfScores() { return scores.size(); } diff --git a/engine/compbio/engine/client/CommandBuilder.java b/engine/compbio/engine/client/CommandBuilder.java index 53a8c22..dae6696 100644 --- a/engine/compbio/engine/client/CommandBuilder.java +++ b/engine/compbio/engine/client/CommandBuilder.java @@ -231,6 +231,7 @@ public class CommandBuilder { + "\n Parameters to be set is " + param; first = param; commands.add(0, first); + continue; } if (param.isLast()) { assert last == null : "Attempting to set more the one parameter as LAST! " diff --git a/engine/compbio/engine/client/Executable.java b/engine/compbio/engine/client/Executable.java index 85f516a..b36bc57 100644 --- a/engine/compbio/engine/client/Executable.java +++ b/engine/compbio/engine/client/Executable.java @@ -45,6 +45,8 @@ public interface Executable { */ Executable addParameters(List parameters); + // TODO remove absolute + @Deprecated List getCreatedFiles(); String getInput(); diff --git a/runner/compbio/runner/disorder/IUPred.java b/runner/compbio/runner/disorder/IUPred.java index 30e8776..5d20829 100644 --- a/runner/compbio/runner/disorder/IUPred.java +++ b/runner/compbio/runner/disorder/IUPred.java @@ -17,6 +17,8 @@ package compbio.runner.disorder; import java.io.File; import java.io.FileNotFoundException; import java.io.IOException; +import java.util.Arrays; +import java.util.List; import java.util.Map; import java.util.Set; import java.util.TreeMap; @@ -30,6 +32,7 @@ import compbio.data.sequence.SequenceUtil; import compbio.data.sequence.UnknownFileFormatException; import compbio.engine.client.SkeletalExecutable; import compbio.metadata.ResultNotAvailableException; +import compbio.runner.msa.Mafft; /** * iupred sequenceFile @@ -41,10 +44,11 @@ import compbio.metadata.ResultNotAvailableException; public class IUPred extends SkeletalExecutable { private static Logger log = Logger.getLogger(IUPred.class); - private static final String GLOB_SUFFIX = ".glob"; - private static final String SHORT_SUFFIX = ".short"; - private static final String LONG_SUFFIX = ".long"; + private static final String GLOB_OUTPUT = "out.glob"; + private static final String SHORT_OUTPUT = "out.short"; + private static final String LONG_OUTPUT = "out.long"; + @Override @SuppressWarnings("unchecked") public ScoreManager getResults(String workDirectory) @@ -52,31 +56,27 @@ public class IUPred extends SkeletalExecutable { ScoreManager results = null; try { - - Map globScores = SequenceUtil.readIUPred(new File( - workDirectory, getOutput() + GLOB_SUFFIX)); - Map shortScores = SequenceUtil.readIUPred(new File( - workDirectory, getOutput() + SHORT_SUFFIX)); - Map longScores = SequenceUtil.readIUPred(new File( - workDirectory, getOutput() + LONG_SUFFIX)); Map> combined = new TreeMap>(); - for (String key : globScores.keySet()) { - Set all = new TreeSet(); - Score globsc = globScores.get(key); - assert globsc != null; - Score shortsc = shortScores.get(key); - assert shortsc != null; - all.add(shortsc); - Score longsc = longScores.get(key); - assert longsc != null; - all.add(longsc); - combined.put(key, all); + + File shortf = new File(workDirectory, SHORT_OUTPUT); + if(shortf.exists()) { + combineScores(combined, SequenceUtil.readIUPred(shortf)); + } + File longf = new File(workDirectory, LONG_OUTPUT); + if(longf.exists()) { + combineScores(combined, SequenceUtil.readIUPred(longf)); + } + + File glob = new File(workDirectory, GLOB_OUTPUT); + if(glob.exists()) { + combineScores(combined, SequenceUtil.readIUPred(glob)); + } + if(combined.isEmpty()) { + throw new ResultNotAvailableException("Could not find any result " + + "files for the job: " + workDirectory); } results = ScoreManager.newInstance(combined); - } 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); @@ -90,11 +90,52 @@ public class IUPred extends SkeletalExecutable { return results; } + void combineScores(Map> combined, Map scores) { + if(scores==null) { + return; + } + if (combined.isEmpty()) { + for (String key : scores.keySet()) { + Set allScores = new TreeSet(); + combined.put(key, allScores); + } + } + for (String key : scores.keySet()) { + Set allScores= combined.get(key); + assert allScores!=null; + Score score = scores.get(key); + allScores.add(score); + combined.put(key, allScores); + } + } + + + @Override public IUPred setInput(String inFile) { super.setInput(inFile); cbuilder.setFirst(inFile); return this; + } + + + @Override + public IUPred setOutput(String outFile) { + log.warn("IUpred output is predefined and cannot be set!"); + return this; + } + + UnsupportedOperationException newUnsupportedOutputException() { + return new UnsupportedOperationException("The outputs from this executable " + + "are always either of those 3 files (depending on the method called): " + GLOB_OUTPUT + ", " + + SHORT_OUTPUT + ", "+ LONG_OUTPUT); + } + @Override + public String getOutput() { + log.warn("IUpred output is predefined and is one of the three files " + + "(depending on the method called): " + GLOB_OUTPUT + ", " + + SHORT_OUTPUT + ", "+ LONG_OUTPUT); + return LONG_OUTPUT; } @SuppressWarnings("unchecked") diff --git a/testsrc/compbio/data/sequence/SequenceUtilTester.java b/testsrc/compbio/data/sequence/SequenceUtilTester.java index 7621dcc..2b2ca1a 100644 --- a/testsrc/compbio/data/sequence/SequenceUtilTester.java +++ b/testsrc/compbio/data/sequence/SequenceUtilTester.java @@ -291,17 +291,30 @@ public class SequenceUtilTester { public void testReadIUPredForShortAndLongDisorder() { try { Map scores = SequenceUtil.readIUPred(new File( - AllTestSuit.TEST_DATA_PATH, "output.long")); + AllTestSuit.TEST_DATA_PATH, "out.long")); ScoreManager man = ScoreManager.newInstanceSingleScore(scores); // man.writeOut(new PrintWriter(System.out, true)); assertNotNull(scores); - assertEquals(2, scores.size()); + assertEquals(3, scores.size()); - Score score = scores.get("P50_HUMAN"); + Score score = scores.get("Foobar_dundeefriends"); + assertNotNull(score); + assertEquals(0, score.getRanges().size()); + assertEquals(568, score.getScores().size()); + assertEquals("Long", score.getMethod()); + + score = scores.get("Foobar"); + assertNotNull(score); + assertEquals(0, score.getRanges().size()); + assertEquals(481, score.getScores().size()); + assertEquals("Long", score.getMethod()); + + score = scores.get("dundeefriends"); assertNotNull(score); assertEquals(0, score.getRanges().size()); - assertEquals(393, score.getScores().size()); + assertEquals(513, score.getScores().size()); assertEquals("Long", score.getMethod()); + } catch (IOException e) { e.printStackTrace(); fail(e.getLocalizedMessage()); diff --git a/testsrc/compbio/runner/disorder/IUPredTester.java b/testsrc/compbio/runner/disorder/IUPredTester.java index 1ef709b..d3d6e5e 100644 --- a/testsrc/compbio/runner/disorder/IUPredTester.java +++ b/testsrc/compbio/runner/disorder/IUPredTester.java @@ -38,7 +38,10 @@ import org.ggf.drmaa.JobInfo; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; +import compbio.data.sequence.Score; import compbio.data.sequence.ScoreManager; +import compbio.data.sequence.ScoreManager.ScoreHolder; +import compbio.data.sequence.SequenceUtil; import compbio.engine.AsyncExecutor; import compbio.engine.Configurator; import compbio.engine.SyncExecutor; @@ -58,18 +61,17 @@ import compbio.metadata.LimitsManager; import compbio.metadata.PresetManager; import compbio.metadata.ResultNotAvailableException; import compbio.metadata.RunnerConfig; +import compbio.runner.msa.Mafft; import compbio.util.SysPrefs; public class IUPredTester { - public static String test_outfile = "output"; - private IUPred iupred; @BeforeMethod(alwaysRun = true) void init() { iupred = new IUPred(); - iupred.setInput(AllTestSuit.test_input).setOutput(test_outfile); + iupred.setInput(AllTestSuit.test_input); } @Test(groups = {AllTestSuit.test_group_cluster, @@ -173,6 +175,31 @@ public class IUPredTester { } } + + @Test(enabled = false, groups = {AllTestSuit.test_group_runner}) + public void testSetParameter() { + assertEquals(iupred.getInput(), AllTestSuit.test_input); + assertTrue(iupred.getParameters(null).getCommandString().trim().endsWith(AllTestSuit.test_input)); + iupred.setParameter("all"); + assertEquals(iupred.getInput(), AllTestSuit.test_input); + String cmd = iupred.getParameters(null).getCommandString().trim(); + assertTrue(cmd.endsWith("all")); + assertTrue(cmd.contains(AllTestSuit.test_input)); + } + + + @Test(groups = {AllTestSuit.test_group_runner}) + public void testReadResults() { + ScoreManager scoreMan; + try { + scoreMan = iupred.getResults(AllTestSuit.TEST_DATA_PATH_ABSOLUTE); + System.out.println(scoreMan.asMap()); + } catch (ResultNotAvailableException e) { + e.printStackTrace(); + fail(e.getMessage()); + } + } + @Test(groups = {AllTestSuit.test_group_runner}) public void testRunLocally() { try { @@ -187,7 +214,17 @@ public class IUPredTester { ScoreManager al2 = confIUPred.getResults(); assertNotNull(al2); assertEquals(al2.asMap().size(), 3); + assertEquals(al2.getNumberOfSeq(),3); + ScoreHolder sch = al2.getAnnotationForSequence("Foobar"); + Score sc = sch.getScoreByMethod("Long"); + + assertEquals(sc.getMethod(), "Long"); + assertTrue(sc.getRanges().isEmpty()); + assertNotNull(sc.getScores()); + assertEquals(sc.getScores().size(), 481); assertEquals(al1.getResults(), al2); + + } catch (JobSubmissionException e) { e.printStackTrace(); fail(e.getLocalizedMessage()); @@ -200,22 +237,55 @@ public class IUPredTester { } } - @Test(groups = {AllTestSuit.test_group_runner}) - public void readStatistics() { - // No execution statistics is available! + @Test(enabled=false, groups = {AllTestSuit.test_group_runner}) + public void testRunLocallyWithParams() { + try { + iupred.setParameter("all"); + ConfiguredExecutable confIUPred = Configurator + .configureExecutable(iupred, Executable.ExecProvider.Local); + + // For local execution use relative + LocalRunner lr = new LocalRunner(confIUPred); + lr.executeJob(); + ConfiguredExecutable al1 = lr.waitForResult(); + assertNotNull(al1.getResults()); + ScoreManager al2 = confIUPred.getResults(); + + System.out.println("!!!"+al2.asMap()); + + /* + assertNotNull(al2); + assertEquals(al2.asSet().size(), 1); + assertEquals(al2.getNumberOfSeq(),1); + Score sc = al2.asSet().iterator().next(); + assertEquals(sc.getMethod(), "Long"); + assertTrue(sc.getRanges().isEmpty()); + assertNotNull(sc.getScores()); + assertEquals(sc.getScores().size(), 568); + assertEquals(al1.getResults(), al2); +*/ + } catch (JobSubmissionException e) { + e.printStackTrace(); + fail(e.getLocalizedMessage()); + } catch (ResultNotAvailableException e) { + e.printStackTrace(); + fail(e.getLocalizedMessage()); + } catch (JobExecutionException e) { + e.printStackTrace(); + fail(e.getLocalizedMessage()); + } } @Test(groups = {AllTestSuit.test_group_runner}) public void testPersistance() { try { - IUPred disembl = new IUPred(); - disembl.setError("errrr.txt").setInput(AllTestSuit.test_input) - .setOutput("outtt.txt"); - assertEquals(disembl.getInput(), AllTestSuit.test_input); - assertEquals(disembl.getError(), "errrr.txt"); - assertEquals(disembl.getOutput(), "outtt.txt"); + IUPred iupred = new IUPred(); + iupred.setError("errrr.txt").setInput(AllTestSuit.test_input); + assertEquals(iupred.getInput(), AllTestSuit.test_input); + assertEquals(iupred.getError(), "errrr.txt"); + ConfiguredExecutable cIUPred = Configurator - .configureExecutable(disembl, Executable.ExecProvider.Local); + .configureExecutable(iupred, Executable.ExecProvider.Local); SyncExecutor sexec = Configurator.getSyncEngine(cIUPred); sexec.executeJob(); @@ -240,10 +310,9 @@ public class IUPredTester { AllTestSuit.test_input); assertEquals(resurrectedCIUPred.getExecutable().getError(), "errrr.txt"); - assertEquals(resurrectedCIUPred.getExecutable().getOutput(), - "outtt.txt"); + // See in details whether executables are the same - assertEquals(resurrectedCIUPred.getExecutable(), disembl); + assertEquals(resurrectedCIUPred.getExecutable(), iupred); ConfiguredExecutable resIUPred = Configurator .configureExecutable(resurrectedCIUPred.getExecutable(), @@ -276,24 +345,22 @@ public class IUPredTester { @Test(groups = {AllTestSuit.test_group_runner}) public void testConfigurationLoading() { try { - RunnerConfig disemblConfig = ConfExecutable + RunnerConfig iupredConfig = ConfExecutable .getRunnerOptions(IUPred.class); - // There is no disembl parameters - assertNull(disemblConfig); - // If there were a IUPredParameter.xml file and reference to it, - // it would be like that - // assertTrue(disemblConfig.getArguments().size() == 0); + assertNotNull(iupredConfig); + + assertTrue(iupredConfig.getArguments().size() != 0); - PresetManager disemblPresets = ConfExecutable + PresetManager iupredPresets = ConfExecutable .getRunnerPresets(IUPred.class); - assertNull(disemblPresets); // there is no presets + assertNull(iupredPresets); // there is no presets - LimitsManager disemblLimits = ConfExecutable + LimitsManager iupredLimits = ConfExecutable .getRunnerLimits(IUPred.class); - assertNotNull(disemblLimits); - assertTrue(disemblLimits.getLimits().size() > 0); - disemblLimits.validate(disemblPresets); + assertNotNull(iupredLimits); + assertTrue(iupredLimits.getLimits().size() > 0); + iupredLimits.validate(iupredPresets); } catch (FileNotFoundException e) { e.printStackTrace(); diff --git a/testsrc/testdata/out.long b/testsrc/testdata/out.long new file mode 100644 index 0000000..3d54661 --- /dev/null +++ b/testsrc/testdata/out.long @@ -0,0 +1,1565 @@ +# Foobar_dundeefriends + 1 M 0.4507 + 2 T 0.4685 + 3 A 0.4582 + 4 D 0.4476 + 5 G 0.3840 + 6 P 0.4017 + 7 R 0.4409 + 8 E 0.4541 + 9 L 0.5139 + 10 L 0.5456 + 11 Q 0.5807 + 12 L 0.5055 + 13 R 0.4330 + 14 A 0.4330 + 15 A 0.3286 + 16 V 0.2541 + 17 R 0.1852 + 18 H 0.1275 + 19 R 0.1007 + 20 P 0.1643 + 21 Q 0.2094 + 22 D 0.2164 + 23 F 0.2129 + 24 V 0.2193 + 25 A 0.2064 + 26 W 0.2292 + 27 L 0.3053 + 28 M 0.3182 + 29 L 0.3182 + 30 A 0.2988 + 31 D 0.2645 + 32 A 0.2680 + 33 E 0.2164 + 34 L 0.2918 + 35 G 0.2884 + 36 M 0.3215 + 37 G 0.4051 + 38 D 0.4831 + 39 T 0.4369 + 40 T 0.4901 + 41 A 0.4330 + 42 G 0.4220 + 43 E 0.4831 + 44 M 0.4619 + 45 A 0.5577 + 46 V 0.5992 + 47 Q 0.6755 + 48 R 0.6375 + 49 G 0.5342 + 50 L 0.4940 + 51 A 0.4801 + 52 L 0.4186 + 53 H 0.4186 + 54 P 0.3948 + 55 G 0.3667 + 56 H 0.3840 + 57 P 0.3566 + 58 E 0.3529 + 59 A 0.3704 + 60 V 0.3774 + 61 A 0.4507 + 62 R 0.4831 + 63 L 0.5456 + 64 G 0.5533 + 65 R 0.4864 + 66 V 0.4582 + 67 R 0.3840 + 68 W 0.2715 + 69 T 0.1791 + 70 Q 0.2094 + 71 Q 0.2849 + 72 R 0.2817 + 73 H 0.2849 + 74 A 0.3807 + 75 E 0.3529 + 76 A 0.3356 + 77 A 0.4330 + 78 V 0.4582 + 79 L 0.5707 + 80 L 0.6043 + 81 Q 0.5951 + 82 Q 0.4725 + 83 A 0.4541 + 84 S 0.3667 + 85 D 0.3053 + 86 A 0.2094 + 87 A 0.2364 + 88 P 0.2715 + 89 E 0.3087 + 90 H 0.3087 + 91 P 0.4017 + 92 G 0.4087 + 93 I 0.3704 + 94 A 0.3983 + 95 L 0.4087 + 96 W 0.3667 + 97 L 0.4087 + 98 G 0.4087 + 99 H 0.3460 + 100 A 0.3053 + 101 L 0.2680 + 102 E 0.2094 + 103 D 0.1298 + 104 A 0.2129 + 105 G 0.2328 + 106 Q 0.2849 + 107 A 0.3807 + 108 E 0.4725 + 109 A 0.3872 + 110 A 0.2988 + 111 A 0.3566 + 112 A 0.4541 + 113 A 0.4541 + 114 Y 0.4766 + 115 T 0.4051 + 116 R 0.3117 + 117 A 0.3117 + 118 H 0.3117 + 119 Q 0.3053 + 120 L 0.2541 + 121 L 0.2002 + 122 P 0.2364 + 123 E 0.1823 + 124 E 0.2034 + 125 P 0.2988 + 126 Y 0.2849 + 127 I 0.2129 + 128 T 0.1702 + 129 A 0.1759 + 130 Q 0.1028 + 131 L 0.1583 + 132 L 0.2064 + 133 N 0.1162 + 134 W 0.1137 + 135 R 0.0690 + 136 R 0.0327 + 137 R 0.0592 + 138 L 0.0870 + 139 C 0.0888 + 140 D 0.0704 + 141 W 0.0662 + 142 R 0.0909 + 143 A 0.1251 + 144 L 0.0780 + 145 D 0.1137 + 146 V 0.1184 + 147 L 0.1206 + 148 S 0.0835 + 149 A 0.1323 + 150 Q 0.1702 + 151 V 0.1092 + 152 R 0.1914 + 153 A 0.2224 + 154 A 0.1554 + 155 V 0.2034 + 156 A 0.1115 + 157 Q 0.1048 + 158 G 0.1611 + 159 V 0.1759 + 160 G 0.2129 + 161 A 0.1791 + 162 V 0.2364 + 163 E 0.2094 + 164 P 0.2064 + 165 F 0.2503 + 166 A 0.3215 + 167 F 0.2715 + 168 L 0.2364 + 169 S 0.1643 + 170 E 0.2002 + 171 D 0.1969 + 172 A 0.2258 + 173 S 0.2918 + 174 A 0.2503 + 175 A 0.2258 + 176 E 0.3019 + 177 Q 0.2364 + 178 L 0.3117 + 179 A 0.3599 + 180 C 0.3566 + 181 A 0.2752 + 182 R 0.2609 + 183 T 0.3215 + 184 R 0.2436 + 185 A 0.2436 + 186 Q 0.3053 + 187 A 0.2918 + 188 I 0.2849 + 189 A 0.2988 + 190 A 0.3249 + 191 S 0.3983 + 192 V 0.4256 + 193 R 0.4256 + 194 P 0.4541 + 195 L 0.3704 + 196 A 0.3983 + 197 P 0.3215 + 198 T 0.3494 + 199 R 0.3321 + 200 V 0.2988 + 201 R 0.3215 + 202 S 0.3392 + 203 K 0.4087 + 204 G 0.3019 + 205 P 0.2715 + 206 L 0.3249 + 207 R 0.3566 + 208 V 0.3566 + 209 G 0.3566 + 210 F 0.3599 + 211 V 0.3426 + 212 S 0.2609 + 213 N 0.2715 + 214 G 0.2064 + 215 F 0.1823 + 216 G 0.0967 + 217 A 0.0835 + 218 H 0.0909 + 219 P 0.1115 + 220 T 0.0676 + 221 G 0.1349 + 222 L 0.1852 + 223 L 0.1881 + 224 T 0.1852 + 225 V 0.2129 + 226 A 0.3321 + 227 L 0.2470 + 228 F 0.2884 + 229 E 0.2436 + 230 A 0.2164 + 231 L 0.1424 + 232 Q 0.0734 + 233 R 0.1007 + 234 R 0.1643 + 235 Q 0.1554 + 236 P 0.2164 + 237 D 0.2541 + 238 L 0.3460 + 239 Q 0.4582 + 240 M 0.4409 + 241 H 0.4801 + 242 L 0.4801 + 243 F 0.4685 + 244 A 0.4766 + 245 T 0.4801 + 246 S 0.3840 + 247 G 0.3215 + 248 D 0.3249 + 249 D 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