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Fixed SD files not being imported completely #12

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merged 4 commits into from
Feb 21, 2024
Merged

Fixed SD files not being imported completely #12

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0deaff5
Fixed SD files not being imported in their entire length if structure…
SamuelBehr Aug 10, 2023
dc7a095
Additional comments;
JonasSchaub Feb 21, 2024
0184148
More specific log messages;
JonasSchaub Feb 21, 2024
8ef93bb
Merge branch 'production' into SDF_Import_fix
JonasSchaub Feb 21, 2024
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24 changes: 21 additions & 3 deletions src/main/java/de/unijena/cheminf/mortar/model/io/Importer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -255,7 +255,8 @@ else if(tmpFormat.getFormatName().equalsIgnoreCase(MDLV3000Format.getInstance().
}
//
/**
* Imports an SD file.
* Imports an SD file. If no name can be detected for a structure, the file name extended with the index of the
* structure in the file is used as name of the structure.
*
* @param aFile sdf
* @return the imported molecules in an IAtomContainerSet
Expand All @@ -266,15 +267,32 @@ private IAtomContainerSet importSDFile(File aFile) throws FileNotFoundException
IteratingSDFReader tmpSDFReader = new IteratingSDFReader(new FileInputStream(aFile),
SilentChemObjectBuilder.getInstance());
int tmpCounter = 0;
while(!Thread.currentThread().isInterrupted() && tmpSDFReader.hasNext()){
while(!Thread.currentThread().isInterrupted()){
if (!tmpSDFReader.hasNext()) {
tmpSDFReader.setSkip(true);
if (!tmpSDFReader.hasNext()) {
// there is no next
break;
}
// molecule just could not be read and has therefore been skipped
tmpSDFReader.setSkip(false);
Importer.LOGGER.info("Import failed for structure:\t" + tmpCounter + " (index of structure in file).");
tmpCounter++;
}
IAtomContainer tmpAtomContainer = tmpSDFReader.next();
String tmpName = this.findMoleculeName(tmpAtomContainer);
if(tmpName == null || tmpName.isBlank() || tmpName.isEmpty())
if(tmpName == null || tmpName.isBlank())
// the counter here equals the index of the structure in the file
tmpName = FileUtil.getFileNameWithoutExtension(aFile) + tmpCounter;
tmpAtomContainer.setProperty(Importer.MOLECULE_NAME_PROPERTY_KEY, tmpName);
tmpAtomContainerSet.addAtomContainer(tmpAtomContainer);
tmpCounter++;
}
int tmpFailedImportsCount = tmpCounter - tmpAtomContainerSet.getAtomContainerCount();
if (tmpFailedImportsCount > 0) {
Importer.LOGGER.warning("The import from SD file failed for a total of " + tmpFailedImportsCount +
" structure(s).");
}
return tmpAtomContainerSet;
}
//
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