pharmai / plip

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294

http://plip.biotec.tu-dresden.de

pharmai/plip Issues

OverflowError: Python integer -1000 out of bounds for uint32 int32_to_negative(int32) in supplemental.py
Updated 3 months ago
Request for Official PLIP User Manual and Python Usage Documentation
Updated 4 months ago
Question about function plip.structure.detection.halogen
Updated 6 months ago
How to get Information on sidechain/backbone hydrogen bond type in command options?
Updated 8 months ago
Openbabel package name conflict
Updated 8 months ago2
Is there any parameters which can control the report results only include the lig interaction within protein instead of some residue interaction in protein?
Closed 9 months ago10
Incorrectly indexed interacting residues
Updated 9 months ago2
MmCIF support
Updated 10 months ago1
XML filename shouldn't be `report.xml`
Updated a year ago2
Extract interaction specifically for RNA-small molecule ligand and exclude other interactions in the output
Updated a year ago
Duplicate lines of code: sorted_main = sorted(main, key=lambda x: (x[1], x[2]))
Closed a year ago1
conf.NOHYDRO and aromatics
Updated a year ago
The ligand structure is not visible.
Updated 2 years ago
Interpretation of results
Closed 2 years ago3
supplemental.py:90: RuntimeWarning: invalid value encountered in arccos
Updated 2 years ago
Open Babel problem during installation
Closed 4 years ago3
Option not to add whitespace after trimming
Updated 2 years ago
Generated RST file missing blank line after section titles
Updated 2 years ago
HET from custom .pdb file created in PyMOL not parsed correctly by plip
Updated 2 years ago6
Calculate and report interactions for just one amino acid residue
Updated 2 years ago
Segmentation error with pdb files:
Updated 2 years ago1
<< PLIP took forever >>
Updated 2 years ago
pymol.CmdException: Error: Object not found
Updated 2 years ago
Batch mode for protein-peptide
Updated 2 years ago
How to go about finding interacting Amino Acid Residues of ~1 billion compounds (In PDBQT)
Updated 2 years ago1
Traceback (most recent call last): File "/plip/plip/plipcmd.py", line 16, in <module> from plip.basic import config, logger ModuleNotFoundError: No module named 'plip'
Updated 2 years ago1
python module stuck in loop with some pdb files
Updated 2 years ago
Missing key hydrogen bond interaction in hinge region of kinases
Updated 3 years ago7
PyMol visualizations not generated
Updated 3 years ago5
Specific handling of alternative locations
Updated 3 years ago2
-SO2 in the ligand group makes interaction (Salt bridge/Hbond) with protein but not captured by plip.
Updated 3 years ago4
Salt Bridge recognised although it should not
Updated 3 years ago1
Is there a bug on waterbridge atom index?
Updated 3 years ago1
Water bridge water_angle
Updated 3 years ago3
Plip shows same Hydrogen Bond twice (Donor and Acceptor switched)
Updated 3 years ago
Add explanation for OpenBabel atom groups to README
Updated 3 years ago
Segfault again...
Closed 3 years ago6
interactions between protein and ligand only ??
Closed 3 years ago3
PLIP with multiple ligand sdf for a single pdb
Updated 3 years ago1
Interactions between cocrystallized cofactor and ligand
Updated 3 years ago1
Unicode Encoding Error (UnicodeEncodeError) on CentOS with Docker
Closed 4 years ago1
error with the webserver
Closed 4 years ago7
Provide an instruction document to use with python
Closed 4 years ago1
PyPI plip wheel 2.1.7 is broken.
Closed 4 years ago1
Ligand properties from PLIP differs from PubChem data
Closed 4 years ago3
Would it be possible to include peptide-protein interactions for the python library. Example: PDBComplex().load_pdb("file.pdb",peptide="chain")
Closed 4 years ago1
Ligands with identical name collapse in single entity
Closed 4 years ago2
Visualizations faulty for models other than model 1
Closed 4 years ago4
Analyze feature evolution through trajectory data
Updated 4 years ago4
--intra option not working for all structures
Closed 4 years ago1