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

#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

#182 - Saving position of ligand interactor on metadata

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

#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

#168 - Run fingerprint over multiple conformations of the same molecule

Issue - State: open - Opened by forcefield 7 months ago - 2 comments
Labels: enhancement

#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

#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

#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

#102 - Add CodeQL workflow for GitHub code scanning

Pull Request - State: closed - Opened by lgtm-com[bot] over 1 year ago - 1 comment

#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

#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