Error when using "--out mmpa" about mmpdb HOT 4 CLOSED

It's a legacy text format that should probably be removed.

Looks like it came from when the environment fingerprint table grew to include links from r+1 to r. It shows me no one uses that format.

Could you try using https://github.com/adalke/mmpdb/tree/v3-dev ? That's the latest dev version, mostly waiting for feedback before final release.

The current version of that section is:

    def add_environment_fingerprint(self, fp_idx, smarts, pseudosmiles, parent_smarts):
        if parent_smarts is None:
            parent_smarts = ""
        self._W("FINGERPRINT\t%d\t%s\t%s\t%s\n" % (fp_idx, smarts,  pseudosmiles, parent_smarts))

from mmpdb.

That works, but with the new version --out csv doesn't work (which I do need).

  File "/home/export/noel.oboyle/Tools/conda/miniconda3/envs/mmpdb-test/lib/python3.9/site-packages/mmpdblib/index_writers.py", line 1174, in open
    return self.opener(destination, compression,
  File "/home/export/noel.oboyle/Tools/conda/miniconda3/envs/mmpdb-test/lib/python3.9/site-packages/mmpdblib/index_writers.py", line 849, in _open_csv
    outfile = _open_output(destination, compressionf)
NameError: name 'compressionf' is not defined

from mmpdb.

Okay, fixed the typo. Seems to work.

You might also be interested in the "csvd" output format, which saves all of the tables to separate CSV files in a named directory, along with drivers to import the data into SQLite and Postgres. ("csvd" = "csv directory")

from mmpdb.

Works for me now. I note that cvsd is not (yet?) documented under "mmpdb index --help". Sounds interesting, but not for me right now.

from mmpdb.