ci-lab-cz/pharmd

MD pharmacophores and virtual screening

pharmd's Issues

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)

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'

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??