Dear Colleagues,
I just installed on conda env the new rdkit version
and wanted to try mmpdb but upon testing I got the error below
reverting back to rdkit=2017.09.3.0 it works fine (I still get some errors
but it goes thrugh)
It is a bug, am I doing anything obviously wrong?
Any help will be higly appreciated.
Cheers,
Marco
#details of my environment
#conda 4.4.10
conda create --name mmpdb_env python=3.6
source activate mmpdb_env
conda install -c rdkit rdkit
git clone https://github.com/rdkit/mmpdb.git
cd mmpdb/
python setup.py install
git clone https://github.com/rogerbinns/apsw.git
cd apsw
python setup.py fetch --all build --enable-all-extensions install test
git clone https://github.com/rogerbinns/apsw.git
cd apsw
#python setup.py fetch --all build --enable-all-extensions install test
#does not fetches from where I am: use this instead (no amalgamation or
download of sqlite, for headers, etc)
python setup.py build --enable-all-extensions install test
python test.py
https://github.com/esnme/ultrajson.git
cd ultrajson
python setup.py install
mmpdb fragment test_data.smi -o test_data.fragments
Failure: file 'test_data.smi', line 1, record #1: first line is 'Oc1ccccc1
phenol'
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File
"/home/u776341/.conda/envs/mmpdb_env/lib/python3.6/multiprocessing/pool.py",
line 119, in worker
result = (True, func(*args, **kwds))
File
"/home/u776341/.conda/envs/mmpdb_env/lib/python3.6/site-packages/mmpdblib/do_fragment.py",
line 363, in _as_list
return list(method(normalized_mol, fragment_filter,
num_normalized_heavies))
File
"/home/u776341/.conda/envs/mmpdb_env/lib/python3.6/site-packages/mmpdblib/fragment_algorithm.py",
line 690, in fragment_mol
for x in _fragment_mol(mol, fragment_filter, num_heavies):
File
"/home/u776341/.conda/envs/mmpdb_env/lib/python3.6/site-packages/mmpdblib/fragment_algorithm.py",
line 722, in _fragment_mol
for fragmentation in fragmentations:
File
"/home/u776341/.conda/envs/mmpdb_env/lib/python3.6/site-packages/mmpdblib/fragment_algorithm.py",
line 368, in make_single_cut
constant_smiles_with_H = replace_wildcard_with_H(constant_smiles)
File
"/home/u776341/.conda/envs/mmpdb_env/lib/python3.6/site-packages/mmpdblib/fragment_algorithm.py",
line 302, in replace_wildcard_with_H
assert smiles.count("[*]") == 1, smiles
AssertionError: *O
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/u776341/.conda/envs/mmpdb_env/bin/mmpdb", line 10, in <module>
commandline.main()
File
"/home/u776341/.conda/envs/mmpdb_env/lib/python3.6/site-packages/mmpdblib/commandline.py",
line 988, in main
parsed_args.command(parsed_args.subparser, parsed_args)
File
"/home/u776341/.conda/envs/mmpdb_env/lib/python3.6/site-packages/mmpdblib/commandline.py",
line 173, in fragment_command
do_fragment.fragment_command(parser, args)
File
"/home/u776341/.conda/envs/mmpdb_env/lib/python3.6/site-packages/mmpdblib/do_fragment.py",
line 531, in fragment_command
writer.write_records(records)
File
"/home/u776341/.conda/envs/mmpdb_env/lib/python3.6/site-packages/mmpdblib/fragment_io.py",
line 396, in write_records
for rec in fragment_records:
File
"/home/u776341/.conda/envs/mmpdb_env/lib/python3.6/site-packages/mmpdblib/do_fragment.py",
line 433, in make_fragment_records
fragments = result.get()
File
"/home/u776341/.conda/envs/mmpdb_env/lib/python3.6/multiprocessing/pool.py",
line 644, in get
raise self._value
AssertionError: *O
#revert rdkit back
conda install -c rdkit rdkit=2017.09.3.0
python test_fragment.py
....[10:03:40] SMARTS Parse Error: syntax error for input: 'Q4'
...............[10:03:42] SMARTS Parse Error: syntax error for input: 'Q4'
........[10:03:42] SMILES Parse Error: syntax error for input:
'Oc1ccccc1O,record'
.[10:03:42] SMILES Parse Error: syntax error for input: 'Oc1ccccc1O,record'
.[10:03:42] SMILES Parse Error: syntax error for input: 'Oc1ccccc1O,record'
.[10:03:42] SMILES Parse Error: syntax error for input: 'Oc1ccccc1O,record'
...................[10:03:44] SMILES Parse Error: syntax error for input:
'Oc1ccccc1O record'
[10:03:44] SMILES Parse Error: syntax error for input: 'Nc1ccccc1C entry'
..........
----------------------------------------------------------------------
Ran 59 tests in 5.291s
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
