Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / pharmai/plip issues and pull requests

#158 - Fixing OverflowError: Python integer -1000 out of bounds for uint32

Pull Request - State: open - Opened by gmrandazzo 6 months ago - 1 comment

#153 - Fixes several mistakes in interaction detection with peptide ligands

Pull Request - State: closed - Opened by kalinni 11 months ago

#152 - Fixes mistakes in waterbridge detection and filtering

Pull Request - State: closed - Opened by kalinni 11 months ago

#151 - Fixes a mistake in hydrogen bond acceptor identification

Pull Request - State: closed - Opened by kalinni 11 months ago

#150 - fixes NumPy DeprecationWarning

Pull Request - State: closed - Opened by QY0831 12 months ago

#148 - Incorrectly indexed interacting residues

Issue - State: open - Opened by kaw97 about 1 year ago - 2 comments

#146 - MmCIF support

Issue - State: open - Opened by xrobin over 1 year ago - 1 comment

#145 - Version 2.3.0

Pull Request - State: closed - Opened by fkaiserbio over 1 year ago

#144 - Updates ImageMagick to version 7 and makes its use platform independent

Pull Request - State: closed - Opened by kalinni over 1 year ago - 3 comments

#143 - conf.NOHYDRO and aromatics

Issue - State: open - Opened by matteoferla over 1 year ago

#142 - The ligand structure is not visible.

Issue - State: open - Opened by Tangbbmc almost 2 years ago

#140 - Option not to add whitespace after trimming

Issue - State: open - Opened by baoilleach about 2 years ago

#137 - Segmentation error with pdb files:

Issue - State: open - Opened by sgrannem about 2 years ago - 1 comment

#136 - << PLIP took forever >>

Issue - State: open - Opened by icamps over 2 years ago

#135 - pymol.CmdException: Error: Object not found

Issue - State: open - Opened by Le-Phung-Hien over 2 years ago

#134 - Batch mode for protein-peptide

Issue - State: open - Opened by victorconan over 2 years ago

#131 - python module stuck in loop with some pdb files

Issue - State: open - Opened by ydzdfci over 2 years ago

#130 - Openbabel package name conflict

Issue - State: open - Opened by klsarathk over 2 years ago - 2 comments

#129 - XML filename shouldn't be `report.xml`

Issue - State: open - Opened by pslacerda almost 3 years ago - 2 comments

#128 - Interpretation of results

Issue - State: closed - Opened by JinyuanSun almost 3 years ago - 3 comments

#127 - fixes salt bridge detection for nucleic acid receptors

Pull Request - State: closed - Opened by sungekim almost 3 years ago - 2 comments

#126 - Fixes a bug when using --nofix

Pull Request - State: closed - Opened by zrt almost 3 years ago - 1 comment

#125 - Add explanation for OpenBabel atom groups to README

Issue - State: open - Opened by fkaiserbio almost 3 years ago
Labels: enhancement

#124 - Segfault again...

Issue - State: closed - Opened by DSuveges almost 3 years ago - 6 comments

#123 - Plip shows same Hydrogen Bond twice (Donor and Acceptor switched)

Issue - State: open - Opened by PhiCMS almost 3 years ago
Labels: bug

#122 - Water bridge water_angle

Issue - State: open - Opened by bernieleecy almost 3 years ago - 3 comments
Labels: bug

#121 - Is there a bug on waterbridge atom index?

Issue - State: open - Opened by freeenergylab about 3 years ago - 1 comment
Labels: enhancement

#120 - Fixes PDB file correction for multi-model structures

Pull Request - State: closed - Opened by kalinni about 3 years ago - 1 comment

#119 - interactions between protein and ligand only ??

Issue - State: closed - Opened by momarzouksobeh about 3 years ago - 3 comments

#118 - Salt Bridge recognised although it should not

Issue - State: open - Opened by i2nico over 3 years ago - 1 comment
Labels: bug, enhancement

#117 - -SO2 in the ligand group makes interaction (Salt bridge/Hbond) with protein but not captured by plip.

Issue - State: open - Opened by aniketsh over 3 years ago - 4 comments
Labels: enhancement

#116 - Interactions between cocrystallized cofactor and ligand

Issue - State: open - Opened by michabirklbauer over 3 years ago - 1 comment
Labels: enhancement

#115 - Duplicate lines of code: sorted_main = sorted(main, key=lambda x: (x[1], x[2]))

Issue - State: closed - Opened by koyurion almost 4 years ago - 1 comment

#114 - Specific handling of alternative locations

Issue - State: open - Opened by koyurion almost 4 years ago - 2 comments
Labels: enhancement

#113 - HET from custom .pdb file created in PyMOL not parsed correctly by plip

Issue - State: open - Opened by fabioatuib almost 4 years ago - 6 comments
Labels: enhancement, improve PDB handling

#112 - Version 2.2.2

Pull Request - State: closed - Opened by fkaiserbio almost 4 years ago

#111 - Unicode Encoding Error (UnicodeEncodeError) on CentOS with Docker

Issue - State: closed - Opened by eblen almost 4 years ago - 1 comment

#110 - Development

Pull Request - State: closed - Opened by fkaiserbio almost 4 years ago - 3 comments

#109 - PyMol visualizations not generated

Issue - State: open - Opened by MiloszGrabski almost 4 years ago - 5 comments
Labels: bug, conda

#108 - Missing key hydrogen bond interaction in hinge region of kinases

Issue - State: open - Opened by jaimergp almost 4 years ago - 7 comments
Labels: enhancement

#107 - PLIP with multiple ligand sdf for a single pdb

Issue - State: open - Opened by dangthatsright almost 4 years ago - 1 comment

#106 - Improvements to install instructions and updates to documentation

Pull Request - State: closed - Opened by kalinni almost 4 years ago

#105 - Development

Pull Request - State: closed - Opened by fkaiserbio almost 4 years ago - 1 comment

#104 - Fixes visualizations for model flag

Pull Request - State: closed - Opened by kalinni almost 4 years ago

#103 - Version 2.1.9

Pull Request - State: closed - Opened by fkaiserbio almost 4 years ago

#102 - Open Babel problem during installation

Issue - State: closed - Opened by momarzouksobeh almost 4 years ago - 3 comments

#101 - Make --dnareceptor flag behave consistently

Pull Request - State: closed - Opened by kalinni almost 4 years ago

#100 - Version 2.1.8

Pull Request - State: closed - Opened by fkaiserbio about 4 years ago

#99 - Ligands with identical name collapse in single entity

Issue - State: closed - Opened by jaimergp about 4 years ago - 2 comments

#98 - error with the webserver

Issue - State: closed - Opened by hima111997 about 4 years ago - 7 comments

#96 - Ligand properties from PLIP differs from PubChem data

Issue - State: closed - Opened by in-seixas about 4 years ago - 3 comments
Labels: bug

#95 - Provide an instruction document to use with python

Issue - State: closed - Opened by ankit1-iitbhu about 4 years ago - 1 comment

#94 - PyPI plip wheel 2.1.7 is broken.

Issue - State: closed - Opened by zacharyrs about 4 years ago - 1 comment

#93 - Version 2.1.7

Pull Request - State: closed - Opened by fkaiserbio about 4 years ago

#92 - Analyze feature evolution through trajectory data

Issue - State: open - Opened by CoryKornowicz about 4 years ago - 4 comments
Labels: enhancement

#91 - Fixed for MacOS 11.0.1

Pull Request - State: closed - Opened by CoryKornowicz about 4 years ago

#90 - --intra option not working for all structures

Issue - State: closed - Opened by kalinni about 4 years ago - 1 comment

#89 - Visualizations faulty for models other than model 1

Issue - State: closed - Opened by kalinni about 4 years ago - 4 comments
Labels: bug

#88 - MacOS : resource

Issue - State: closed - Opened by t-kimber about 4 years ago - 6 comments
Labels: bug

#87 - --model doesn't take an argument

Issue - State: closed - Opened by kalinni about 4 years ago - 1 comment
Labels: bug

#86 - Development

Pull Request - State: closed - Opened by fkaiserbio over 4 years ago

#85 - Version 2.1.5

Pull Request - State: closed - Opened by fkaiserbio over 4 years ago

#84 - variable hetatoms on the preparation.py file on the master branch is wrong

Issue - State: closed - Opened by chrisxu2016 over 4 years ago - 1 comment

#83 - Interactions between ligands in the same binding site.

Issue - State: open - Opened by snbolz over 4 years ago - 2 comments
Labels: enhancement

#82 - HET record that is part of a biological polymer is recognized as ligand

Issue - State: open - Opened by snbolz over 4 years ago - 1 comment
Labels: bug, enhancement, improve PDB handling

#81 - add requirements for correct PDB files to README

Issue - State: open - Opened by fkaiserbio over 4 years ago
Labels: enhancement

#80 - Sometimes run well but sometimes raised an error while submiting a same command

Issue - State: closed - Opened by zhangshd over 4 years ago - 4 comments
Labels: bug

#79 - Something abnormal while using pdb file prepared by pymol

Issue - State: closed - Opened by zhangshd over 4 years ago - 4 comments

#78 - handle insertion codes

Issue - State: open - Opened by fkaiserbio over 4 years ago
Labels: bug, enhancement, improve PDB handling

#77 - Include API in dockerized PLIP

Issue - State: open - Opened by ssalentin over 4 years ago - 1 comment
Labels: enhancement

#76 - Results as JSON

Issue - State: open - Opened by ssalentin over 4 years ago - 1 comment
Labels: enhancement

#75 - Usermanual

Issue - State: closed - Opened by e-mayo over 4 years ago - 1 comment

#74 - Update README.md

Pull Request - State: closed - Opened by fkaiserbio over 4 years ago

#73 - Different results between web and command line

Issue - State: closed - Opened by xrobin over 4 years ago - 6 comments

#72 - Update issue templates

Pull Request - State: closed - Opened by fkaiserbio over 4 years ago

#71 - Merge Development for Dependency Fix

Pull Request - State: closed - Opened by fkaiserbio over 4 years ago

#70 - PyMol in setup.py requirements

Issue - State: closed - Opened by jaimergp over 4 years ago

#69 - How does PLIP handle multiple models in a PDB structure?

Issue - State: closed - Opened by koyurion over 4 years ago - 2 comments
Labels: enhancement

#68 - Change methods not using its bound instance to staticmethods

Pull Request - State: closed - Opened by cleberecht over 4 years ago
Labels: enhancement

#67 - Deepsource fixes to remove unused variables and change methods

Pull Request - State: closed - Opened by navanchauhan over 4 years ago - 2 comments

#66 - Update Master to Development

Pull Request - State: closed - Opened by fkaiserbio over 4 years ago

#65 - Create ARM compatible docker images

Issue - State: closed - Opened by navanchauhan over 4 years ago - 8 comments

#64 - Update Web Server's Download link

Issue - State: closed - Opened by navanchauhan over 4 years ago - 2 comments

#63 - Is this a bug from PLIP v2.1.0-beta?

Issue - State: closed - Opened by binfen almost 5 years ago - 15 comments

#62 - conda forge package

Issue - State: closed - Opened by hadim almost 5 years ago - 2 comments

#61 - Use setuptools.find_packages()

Pull Request - State: closed - Opened by xrobin almost 5 years ago - 1 comment

#60 - ModuleNotFoundError: No module named 'plip.basic'

Issue - State: closed - Opened by xrobin almost 5 years ago - 1 comment

#59 - ValueError: inchikey is not a recognised Open Babel format

Issue - State: closed - Opened by koyurion almost 5 years ago - 6 comments