Hello everyone, i have a little issue with molconverter, the task is to convert the csv file with smiles which contain stereochemistry to sdf:V3 file
I use cmd with c:\bin>molconvert sdf:V3 test2.csv -o test2.sdf and have an error on smile which contain stereochemistry, all others smiles are converted correctly.
Stereochemistry in smile are represented as, example: "|&1:11,16,r|"
I have an error "java.lang.ArrayIndexOutOfBoundsException: 10
at com.chemaxon.marvin.io.formats.csv.CsvRecordReader.nextRecord(CsvRecordReader.java:110)
at chemaxon.marvin.io.MRecordImporter.startReadingNext(MRecordImporter.java:1028)
at chemaxon.marvin.io.MRecordImporter.readRecord(MRecordImporter.java:672)
at chemaxon.marvin.io.MRecordImporter.readDoc0(MRecordImporter.java:479)
at chemaxon.marvin.io.MRecordImporter.readDoc(MRecordImporter.java:429)
at chemaxon.formats.MolImporter.readDoc(MolImporter.java:871)
at chemaxon.formats.MolConverter.readDoc(MolConverter.java:1202)
at chemaxon.formats.MolConverter.convert0(MolConverter.java:1029)
at chemaxon.formats.MolConverter.convert(MolConverter.java:861)
at chemaxon.formats.MolConverter.main(MolConverter.java:2132)"
Help please.
1 Comment
I
Illya Beznischenko
said
7 months ago
Problem solved through cxsmiles with tabulation, you can close the topic.
Illya Beznischenko
Hello everyone, i have a little issue with molconverter, the task is to convert the csv file with smiles which contain stereochemistry to sdf:V3 file
I use cmd with c:\bin>molconvert sdf:V3 test2.csv -o test2.sdf and have an error on smile which contain stereochemistry, all others smiles are converted correctly.
Stereochemistry in smile are represented as, example: "|&1:11,16,r|"
I have an error "java.lang.ArrayIndexOutOfBoundsException: 10
at com.chemaxon.marvin.io.formats.csv.CsvRecordReader.nextRecord(CsvRecordReader.java:110)
at chemaxon.marvin.io.MRecordImporter.startReadingNext(MRecordImporter.java:1028)
at chemaxon.marvin.io.MRecordImporter.readRecord(MRecordImporter.java:672)
at chemaxon.marvin.io.MRecordImporter.readDoc0(MRecordImporter.java:479)
at chemaxon.marvin.io.MRecordImporter.readDoc(MRecordImporter.java:429)
at chemaxon.formats.MolImporter.readDoc(MolImporter.java:871)
at chemaxon.formats.MolConverter.readDoc(MolConverter.java:1202)
at chemaxon.formats.MolConverter.convert0(MolConverter.java:1029)
at chemaxon.formats.MolConverter.convert(MolConverter.java:861)
at chemaxon.formats.MolConverter.main(MolConverter.java:2132)"
Help please.