amanda li

Fingerprint generation runs and fails on [Cl-].[K+] (and possibly similar molecules)

4

Fingerprint generation (using `generate.py` in serial mode) for [Cl-].[K+] raises the following catastrophic error: ``` 2017-05-16 14:51:41,242|INFO|Generating fingerprints for CHEMBL1200731. 2017-05-16 14:51:41,242|ERROR|Error generating fingerprints for CHEMBL1200731. Traceback (most recent call...

HDF5 writing errors due to previously generated conformers

4

When `conformer/generate.py` is run to a folder containing previously generated conformers, the following error appears when writing values to the file specified by `--values_file`: ``` 2017-05-19 13:05:22,864|ERROR|Problem writing values to...

Fix clobbering in output log files

1

The `$LOGFILE` produced by this call: `python e3fp/e3fp/fingerprint/generate.py $SDFDIR -o $OUTDIR -l $LOGFILE -b 4096 -p $NSLOTS --parallel_mode mpi` contains clobbered lines like this: ``` 2017-05-09 10:15:37,194|INFO|Generating fingerprints for CHEMBL1001642017-05-09...