ci-lab-cz/pharmd

MD pharmacophores and virtual screening

pharmd's Issues

no module name 'plip.modules'

Dear peers,
I am facing a problem while executing the command 'md2pharm'.
The terminal was appeared as- no module name 'Philip.modules'.
How can I solve the issue??

Installation problem related to obabel

I tried to install pharmd in Ubuntu 20.04 but received an error related to openbabel.
So I specified the locations of Include and Library as the error message suggested:
python setup.py build_ext -I/usr/local/include/openbabel3 -L/usr/local/lib
python setup.py install
but received the same error message.
I have installed Cython (pip install Cython) when asked for.
I'd appreciate your help.

(Solved)
#4 (comment)

problem with pmapper

Hi,

I bought a new laptop.. and tried to install the packages..this time it does not work..
again the message appears "TypeError: _get_features_atom_ids() missing 1 required positional argument: 'smarts_features'"

I tried to see what is wrong.. I think there is sth wrong with pmapper may be because this function is from it. it requires 3 arguments : self, mol, smart_features..

is there any solution to this ?

TypeError: _get_features_atom_ids() missing 1 required positional argument: 'smarts_features'

Hi,

I managed to install the package, but when i run md2pharm using the command

md2pharm -i md_center.xtc -t pharmd.pdb -s 10 -g LIG -o pharmaco/frames.pdb

i got the message:

File "/home/tu/tu_tu/tu_zxolr16/.conda/envs/pharmd/bin/md2pharm", line 8, in
sys.exit(entry_point())
File "/home/tu/tu_tu/tu_zxolr16/.conda/envs/pharmd/lib/python3.9/site-packages/pharmd/md2pharm.py", line 220, in entry_point
for i, p in enumerate(get_pharmacophores(pdb_input, args.lig_id)):
File "/home/tu/tu_tu/tu_zxolr16/.conda/envs/pharmd/lib/python3.9/site-packages/pharmd/md2pharm.py", line 113, in get_pharmacophores
features = Pharmacophore._get_features_atom_ids(rdkit_lig, smarts)
TypeError: _get_features_atom_ids() missing 1 required positional argument: 'smarts_features'

problem with get_scores

it seems that pharmd installs psearch from the masters branch. so, when I did the get_scores, it said that
"no module named psearch.database".

I tried to play around, and found that the psearch@gen_pharms branch has a database.py file which is not present in the masters branch, I took it and placed it in the psearch folder installed when installing Pharma.

However, the following message appears when trying to get scores using cca approach

return mod.open(file, flag, mode)

_dbm.error: [Errno 79] Inappropriate file type or format: 'compounds'

P.S. compounds is the name of the db file generated from prepare_db.py

and when I tried CHA approach,

File "parsers.pyx", line 838, in pandas._libs.parsers.TextReader.read_low_memory
File "parsers.pyx", line 921, in pandas._libs.parsers.TextReader._read_rows
File "parsers.pyx", line 983, in pandas._libs.parsers.TextReader._convert_column_data
pandas.errors.ParserError: Too many columns specified: expected 3 and found 2