/**
* Testcase from Stefan.
*
* <p>- Is form a nature paper and a holo and apo form of a protein... - Testcase for an alignment
* - AND - testcase if all aminos and hetagtoms get indexed...
*/
public void testAllAgainstAll() {
int ngramSize = 17;
String pathToTargetDirOrFile = "src/test/resources/nature_paper_apo_holo/";
String pathToQueryDirOrFile = pathToTargetDirOrFile;
String outputFilePath = tempDir + File.separator + this.getClass().getSimpleName() + "/";
boolean dealOnlyWithFirstModel = true;
IFileToStringTranslator iFileToStringTranslator =
new PDBProteinTranslator(
iResidueToStringTransformer,
dealOnlyWithFirstModel,
scoringFunction,
ngramTo3DTranslator);
double thresholdOfRefinementScoreUnderWichResultIsOmitted = 0.3;
// set up and clean:
DeleteDirRecursively.deleteDir(new File(tempDir));
ProteinMatchRunner.executeSearch(
ngramSize,
iFileToStringTranslator,
iResidueToStringTransformer,
pathToTargetDirOrFile,
pathToQueryDirOrFile,
outputFilePath,
dealOnlyWithFirstModel,
thresholdOfRefinementScoreUnderWichResultIsOmitted,
1);
// check if there are two result dirs with 2 perfect matches each...
// check if there are two result dirs with 2 perfect matches each...
String[] dirNames = new File(outputFilePath).list();
// 0. check if there are 8 result dirs in general:
if (dirNames.length != 2) {
fail();
}
// 1. for each resultdir check if there are enough result files:
for (String dirName : dirNames) {
String resultDirFileName = outputFilePath + File.separator + dirName;
// System.out.println(resultDirFileName + " " + new File(resultDirFileName).list().length);
if (new File(resultDirFileName).list().length != 3) {
fail();
}
}
// tear down and clean:
// DeleteDirRecursively.deleteDir(new File(tempDir));
}
public void testLength10() {
String tempDir = "src/test/tmp";
int ngramSize = 10;
// apoform
String pathToTargetDirOrFile =
"src/test/resources/bindingsitedetection/dominic_testfall/proteine/1ABB_C.ent";
// binding site of holo
String pathToQueryDirOrFile =
"src/test/resources/bindingsitedetection/dominic_testfall/binding_sites/1H5U_A_999.ent";
String outputFilePath = "src/test/tmp/" + this.getClass().getSimpleName() + "/";
boolean dealOnlyWithFirstModel = true;
IFileToStringTranslator iFileToStringTranslator =
new PDBProteinTranslator(
iResidueToStringTransformer,
dealOnlyWithFirstModel,
scoringFunction,
ngramTo3DTranslator);
double thresholdOfRefinementScoreUnderWichResultIsOmitted = 0.6;
// set up and clean:
DeleteDirRecursively.deleteDir(new File(tempDir));
ProteinMatchRunner.executeSearch(
ngramSize,
iFileToStringTranslator,
iResidueToStringTransformer,
pathToTargetDirOrFile,
pathToQueryDirOrFile,
outputFilePath,
dealOnlyWithFirstModel,
thresholdOfRefinementScoreUnderWichResultIsOmitted,
1);
// check if there are two result dirs with 2 perfect matches each...
File chainADir = new File(outputFilePath + File.separator + "1H5U_A_999.ent-model-0-chain-A");
String[] allFiles = chainADir.list();
if (allFiles.length != 2) {
fail();
}
// tear down and clean:
// DeleteDirRecursively.deleteDir(new File(tempDir));
}