Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / chemosim-lab/ProLIF issues and pull requests
#205 - Handle edge case in `utils.py`
Pull Request -
State: closed - Opened by amorehead about 1 month ago
- 2 comments
#204 - Ignoring interactions that occur below a certain threshold of the simulation frame in barcode plots
Issue -
State: closed - Opened by elizagg about 2 months ago
- 1 comment
#203 - Hydrogen atom recognition problem
Issue -
State: closed - Opened by williambrown3 about 2 months ago
- 2 comments
#202 - Fixing ligand connectivity on the fly
Issue -
State: open - Opened by asiomchen 3 months ago
- 1 comment
#196 - plf.display_residues(protein_mol)
Issue -
State: closed - Opened by milenamlakic 3 months ago
- 2 comments
#195 - Interactions vs Time
Issue -
State: closed - Opened by Anujkumarp 3 months ago
- 1 comment
#194 - Random result of ifp?
Issue -
State: open - Opened by tom832 4 months ago
- 3 comments
#193 - Fix build test
Pull Request -
State: closed - Opened by cbouy 4 months ago
- 1 comment
#192 - Error when trying to use fp.to_dataframe() for a single PDB structure
Issue -
State: closed - Opened by SampurnaM 4 months ago
- 2 comments
#190 - New acceptor SMARTS for halogen bond
Pull Request -
State: closed - Opened by asiomchen 4 months ago
- 3 comments
#189 - Default halogen bond SMARTS ignores carbonyles
Issue -
State: closed - Opened by asiomchen 4 months ago
#188 - Fix inclusion of tests in source dist
Pull Request -
State: closed - Opened by exs-cbouy 4 months ago
- 1 comment
#187 - Fingerprint fails on single frame trajectory
Issue -
State: closed - Opened by nezix 4 months ago
- 1 comment
#186 - Residue Numbers
Issue -
State: closed - Opened by Anujkumarp 5 months ago
- 2 comments
#185 - Saving interaction map / ligand network
Issue -
State: open - Opened by nezix 5 months ago
- 4 comments
#184 - how can i filter the results of fp
Issue -
State: closed - Opened by hima111997 5 months ago
- 1 comment
#183 - Getting blured plot of Interactions Fingerprint and 2-D Interactions network.
Issue -
State: closed - Opened by Anujkumarp 6 months ago
- 3 comments
#182 - Saving position of ligand interactor on metadata
Issue -
State: closed - Opened by jparcon 6 months ago
- 2 comments
#181 - TypeError: Fingerprint.to_dataframe() got an unexpected keyword argument 'return_atoms'
Issue -
State: closed - Opened by theabhijitdn 6 months ago
- 2 comments
#180 - Get dataframe with specific protein interactors (atoms instead of residues) as column headers
Issue -
State: closed - Opened by jparcon 6 months ago
- 2 comments
#178 - Issue on page /source/modules/plotting.html barcode plot error
Issue -
State: closed - Opened by crisslind 7 months ago
- 1 comment
#175 - Empty Dataframe (no interaction detected warning) but fp object shows 11 interaction
Issue -
State: closed - Opened by SampurnaM 7 months ago
- 2 comments
#174 - Multiple Residues > 1 ligand?
Issue -
State: closed - Opened by ONISniperOne 7 months ago
- 2 comments
#173 - sns plotting hangs
Issue -
State: closed - Opened by pipitoludovico 7 months ago
- 2 comments
#169 - raise RunRequiredError( prolif.exceptions.RunRequiredError: Please run the fingerprint analysis before attempting to display results.
Issue -
State: closed - Opened by tjrong123 7 months ago
- 4 comments
#168 - Run fingerprint over multiple conformations of the same molecule
Issue -
State: open - Opened by forcefield 7 months ago
- 2 comments
Labels: enhancement
#167 - Using compound names instead of pose number as X axis of interaction barcode.
Issue -
State: closed - Opened by Le-Phung-Hien 8 months ago
- 1 comment
#165 - fp.ifp[0].keys() does not return a list of keys
Issue -
State: closed - Opened by forcefield 9 months ago
- 1 comment
#164 - Interface to retrieve atoms in interactions
Issue -
State: closed - Opened by forcefield 9 months ago
- 1 comment
#163 - Saving interaction JS to file
Issue -
State: open - Opened by richardjgowers 9 months ago
- 1 comment
Labels: enhancement, visualization
#162 - Error import prolif
Issue -
State: closed - Opened by groponp 9 months ago
- 2 comments
#161 - Error tutorial files instalation on MacOs
Issue -
State: closed - Opened by groponp 9 months ago
- 2 comments
#159 - Intramolecular Pi-hbond between the N-H of a peptide bond and residues with pi systems
Issue -
State: closed - Opened by DipBobDar 10 months ago
- 2 comments
#158 - New interaction (Backbone NH-Pi )
Issue -
State: closed - Opened by DipBobDar 10 months ago
- 2 comments
#157 - Interaction fingerprint show only VdW interaction
Issue -
State: closed - Opened by Le-Phung-Hien 10 months ago
- 5 comments
#156 - Getting interaction barcode
Issue -
State: closed - Opened by Le-Phung-Hien 10 months ago
- 1 comment
#155 - Getting error when calculating fingerprint
Issue -
State: closed - Opened by Le-Phung-Hien 10 months ago
- 3 comments
#154 - Problem using the last version of Prolif
Issue -
State: closed - Opened by xavgit 10 months ago
- 5 comments
#152 - Problem with visualizing the ligand with gromacs file
Issue -
State: closed - Opened by yousefymohammad 10 months ago
- 5 comments
#151 - Barcode visualization
Issue -
State: closed - Opened by AhmedHassanin-IPB 10 months ago
- 2 comments
#150 - Tutorials overhaul
Pull Request -
State: closed - Opened by cbouy 10 months ago
- 1 comment
#148 - add py3dmol plot
Pull Request -
State: closed - Opened by cbouy 10 months ago
- 1 comment
#147 - Add barcode plot
Pull Request -
State: closed - Opened by cbouy 10 months ago
- 1 comment
#146 - Analyze Autodock Vina poses.
Issue -
State: closed - Opened by Le-Phung-Hien 11 months ago
- 2 comments
#145 - Can interaction fingerprints indicate which residues are involved
Issue -
State: closed - Opened by syedzayyan 11 months ago
- 5 comments
#144 - HBA/HBD not showing
Issue -
State: closed - Opened by JenkeScheen 11 months ago
- 4 comments
#143 - Interaction Atom map
Issue -
State: open - Opened by cbouy 11 months ago
Labels: visualization
#142 - Investigate possible use of InteractionDrawer as an alternative to LigNetwork
Issue -
State: open - Opened by cbouy 11 months ago
Labels: visualization
#140 - Problem with computing PLIFS from docking results
Issue -
State: closed - Opened by Sumbul1631 11 months ago
- 1 comment
#139 - Plotting interaction graphs from docking results
Issue -
State: closed - Opened by Sumbul1631 11 months ago
- 1 comment
#138 - Get the following error when I try and run a fingerprint calculation
Issue -
State: closed - Opened by HannibaltheArrow 11 months ago
- 6 comments
#137 - Plotting ligand interaction network from molecular docking results.
Issue -
State: closed - Opened by Sumbul1631 12 months ago
- 4 comments
#135 - Fix pickle properties for Windows
Pull Request -
State: closed - Opened by cbouy 12 months ago
- 1 comment
#134 - Docked structure in SMINA problems
Issue -
State: closed - Opened by syedzayyan about 1 year ago
- 5 comments
Labels: awaiting-feedback
#133 - Unable to get coloured graph.
Issue -
State: closed - Opened by varundewaker about 1 year ago
- 7 comments
#132 - /RDKit.py:990: UserWarning: The standardization could not be completed within a reasonable number of iterations
Issue -
State: closed - Opened by H-EKE about 1 year ago
- 2 comments
#131 - Documentation redirects to unreleased master branch instead of latest release
Issue -
State: closed - Opened by cbouy about 1 year ago
- 1 comment
Labels: documentation
#129 - Count fingerprint
Pull Request -
State: closed - Opened by cbouy about 1 year ago
- 1 comment
#128 - Swap mp backend and update interaction parameters easily
Pull Request -
State: closed - Opened by cbouy about 1 year ago
- 1 comment
#127 - Ignore backbone for protein
Issue -
State: closed - Opened by cbouy about 1 year ago
Labels: enhancement
#126 - Command line
Issue -
State: open - Opened by cbouy about 1 year ago
Labels: enhancement
#125 - Account for resonance forms during substructure search
Issue -
State: open - Opened by cbouy about 1 year ago
Labels: enhancement
#124 - Count fingerprint
Issue -
State: closed - Opened by cbouy about 1 year ago
Labels: enhancement
#123 - Tutorials improvements
Issue -
State: closed - Opened by cbouy about 1 year ago
Labels: documentation
#122 - Export to "flareplot"
Issue -
State: open - Opened by cbouy about 1 year ago
Labels: visualization
#121 - LigNetwork improvements
Issue -
State: closed - Opened by cbouy about 1 year ago
Labels: visualization
#120 - Include "barcode" plot in codebase
Issue -
State: closed - Opened by cbouy about 1 year ago
Labels: visualization
#119 - Include py3Dmol script in codebase
Issue -
State: closed - Opened by cbouy about 1 year ago
Labels: visualization
#118 - Pass interaction parameters to `Fingerprint` at initialization
Issue -
State: closed - Opened by cbouy about 1 year ago
Labels: enhancement
#117 - Change multiprocessing backend
Issue -
State: closed - Opened by cbouy about 1 year ago
Labels: multiprocessing
#116 - Interactions with metadata
Pull Request -
State: closed - Opened by cbouy about 1 year ago
- 1 comment
#115 - Hints to use the visualization section of the documentation in the case of "Working with docking poses instead of MD simulations"
Issue -
State: closed - Opened by xavgit about 1 year ago
- 2 comments
Labels: documentation, question
#114 - Maintenance improvements
Pull Request -
State: closed - Opened by cbouy about 1 year ago
- 1 comment
#113 - Rene hamburger1993 patch 1
Pull Request -
State: closed - Opened by ReneHamburger1993 about 1 year ago
- 3 comments
#112 - fp.to_dataframe(return_atoms=True,drop_empty=True) still slow
Issue -
State: closed - Opened by ReneHamburger1993 about 1 year ago
- 1 comment
#111 - fp.run error when try docking pose with PDBQT File
Issue -
State: closed - Opened by anpham2209 over 1 year ago
- 8 comments
#110 - speed issue with fp.run()
Issue -
State: closed - Opened by JenkeScheen over 1 year ago
- 7 comments
#109 - error with charged ligand
Issue -
State: closed - Opened by gokulalgates over 1 year ago
- 1 comment
#108 - rdkit-pypi replaced by rdkit on pypi
Pull Request -
State: closed - Opened by IAlibay over 1 year ago
- 6 comments
#103 - FP.run_from_iterable() give error of incomplete pickle to calculate fingerprint protein-ligand complex from docking simulation.How to solve this error in
Issue -
State: closed - Opened by ravishankar1307 over 1 year ago
- 3 comments
Labels: bug
#102 - Add CodeQL workflow for GitHub code scanning
Pull Request -
State: closed - Opened by lgtm-com[bot] over 1 year ago
- 1 comment
#101 - The `elements` attribute is required for the RDKitConverter but is not present in this AtomGroup. Please refer to the documentation to guess elements from other attributes or type `help(MDAnalysis.topology.guessers)`
Issue -
State: closed - Opened by vvithurshan over 1 year ago
- 2 comments
#100 - Formatting with black and isort
Pull Request -
State: closed - Opened by cbouy over 1 year ago
- 1 comment
#99 - Fix PDBQT supplier
Pull Request -
State: closed - Opened by cbouy over 1 year ago
- 1 comment
#98 - Fix pi stacking
Pull Request -
State: closed - Opened by cbouy over 1 year ago
- 1 comment
#97 - Pi-stacking fix
Pull Request -
State: closed - Opened by cbouy over 1 year ago
- 1 comment
#96 - Only showing hydrophobic interactions
Issue -
State: closed - Opened by davidcooper7 over 1 year ago
- 3 comments
#89 - fp.to_dataframe(): local variable 'has_atom_indices' referenced before assignment
Issue -
State: closed - Opened by linminhtoo over 1 year ago
- 3 comments
#87 - Empty dataframe output when generating interaction fingerprints
Issue -
State: closed - Opened by shinoxide over 1 year ago
- 7 comments
#86 - Error when overwriting new interactions
Issue -
State: closed - Opened by i2nico over 1 year ago
- 1 comment
Labels: bug
#85 - Segmentation Fault ( Core Dumped ) in Molecule
Issue -
State: closed - Opened by akhilmedvolt over 1 year ago
- 1 comment
#84 - Interaction changes
Pull Request -
State: closed - Opened by cbouy over 1 year ago
- 1 comment
#83 - Pass parameters to the RDKitConverter from MDAnalysis
Pull Request -
State: closed - Opened by cbouy almost 2 years ago
- 1 comment
#82 - Problem when loading two trajectory files
Issue -
State: closed - Opened by ayyildizm almost 2 years ago
- 1 comment
#81 - How to analysis the trajectory from MD simulation
Issue -
State: closed - Opened by tanshy17 almost 2 years ago
- 3 comments
#80 - How to extract the list of interacting Amino Acid Residues between the protein and the ligand through PDBQT
Issue -
State: closed - Opened by eschoo almost 2 years ago
- 3 comments
Labels: how-to-use
#79 - AttributeError: module 'prolif' has no attribute 'datafiles'
Issue -
State: closed - Opened by MarcAmil30 almost 2 years ago
- 2 comments
#78 - Plot prot-prot interactions as prot-lig fingerprint
Issue -
State: closed - Opened by MatiasMarambio almost 2 years ago
- 4 comments
Labels: documentation
#76 - KeyError: 'PiStacking'
Issue -
State: closed - Opened by amir-tagh almost 2 years ago
- 4 comments
Labels: invalid
#75 - fix quickstart link
Pull Request -
State: closed - Opened by radifar almost 2 years ago
- 2 comments