ParaSim / Blog: Recent posts

• Included the option to report together with ParaSim results an additional (concatenated) data column (e.g. for Smiles output)
• Included the option for rdkit2parasim.py and Molecule2ParaSim.xml to generate an additional Smiles column for ParaSim reference files
• The file format does no longer expect a mandatory second column BITCOUNT. If not existing, bitcounts are calculated during file reading.
• Eliminated a major bug which slowed down ParaSim during startup
• Harmonized interfaces of rdkit2parasim.py with the other tools
• For rdkit2parasim.py and Molecule2ParaSim.xml, an ID parameter is no longer mandatory when reading from Smiles. If not set, a column 'Index' will be created.... read more

This version is an important bug fix. It corrects handling of IPC shared memory segments for keeping fingerprint data persistently in memory. So far datasets were stored in segments of the same static size of 65536 bytes which is proposed in the documentation of IPC::Sharelite as a very portable segment size. This was without principal drawbacks but for large datasets generated lots of memory segments which might lead to exhaustion of segment addresses.... read more

Most important changes:

• The headline in the input files is now mandatory and is parsed for the fingerprint type

• Non-integer, alphanumerical structure IDs allowed

• Achitecture: Shared procedures (i.e. parsers) externalized into module

• Fingerprint length deteremined from fingerprint itself (no more option -l)

• Query vs. reference fingerprint types and lengths checked to avoid mismatches