martimunicoy/peleffy issues and pull requests

#183 - Devel

Pull Request - State: closed - Opened by martimunicoy about 2 months ago

#182 - Release version 1.5.0

Pull Request - State: closed - Opened by martimunicoy 8 months ago

#181 - Release version 1.4.5

Pull Request - State: closed - Opened by martimunicoy 11 months ago - 1 comment

#180 - Alchemistry fix

Pull Request - State: closed - Opened by martimunicoy 11 months ago - 1 comment

#179 - Added from_foyer classmethod to Topology class.

Pull Request - State: open - Opened by ricardlambea over 1 year ago

#178 - Devel

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

#177 - Alchemical fixes

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

#176 - Mulliken charge selector

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

#175 - Add CodeQL workflow for GitHub code scanning

Pull Request - State: open - Opened by lgtm-com[bot] almost 2 years ago

#174 - Do not load basic config when setting log level

Pull Request - State: closed - Opened by martimunicoy about 2 years ago - 1 comment

#173 - Bump mistune from 0.8.4 to 2.0.3 in /docs

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies

#172 - peleffy 1.4.3 release

Pull Request - State: closed - Opened by martimunicoy over 2 years ago - 1 comment

#171 - Ffld error

Pull Request - State: closed - Opened by martimunicoy over 2 years ago - 1 comment

#170 - peleffy 1.4.2 release

Pull Request - State: closed - Opened by martimunicoy over 2 years ago - 1 comment

#169 - Mae compatibility

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

#168 - Ffld fixes

Pull Request - State: closed - Opened by martimunicoy over 2 years ago - 1 comment

#167 - Rotamer bug

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

#166 - Add handler managers to logger

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

#165 - Error when use_peleffy: true in both versions of pele_platform

Issue - State: open - Opened by etiur almost 3 years ago

#164 - peleffy 1.4.1 release

Pull Request - State: closed - Opened by martimunicoy almost 3 years ago

#163 - Stripped arom numbers (SAM bugfix)

Pull Request - State: closed - Opened by frumpowy almost 3 years ago

#162 - Upgrade openff-toolkit

Pull Request - State: closed - Opened by martimunicoy almost 3 years ago

#161 - peleffy 1.4.0 release

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

#160 - Alchemistry docs

Issue - State: open - Opened by martimunicoy almost 3 years ago
Labels: documentation

#159 - Bugfix: issues with long atom numbers and HET extraction

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

#158 - Fix bug and add checkers for --chain flag

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

#157 - --chain flag error when dealing with pdb containing only the ligand

Issue - State: closed - Opened by ignasipuch almost 3 years ago

#156 - Error at generating template files with peleffy

Issue - State: closed - Opened by etiur almost 3 years ago - 2 comments

#155 - Impact for amber

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

#154 - Alchemizer

Pull Request - State: closed - Opened by martimunicoy about 3 years ago - 9 comments

#153 - Fix parameters inconsistencies

Pull Request - State: closed - Opened by martimunicoy about 3 years ago

#152 - peleffy 1.3.4 release

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

#151 - Add support to OpenFF 2.0.0

Pull Request - State: closed - Opened by laumalo about 3 years ago

#150 - Extend support to openff 2.0.0 and test it

Issue - State: closed - Opened by laumalo about 3 years ago
Labels: enhancement

#149 - Error parsing ffld_output file from Schrodinger

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

#148 - Diferent Schrodinger versions causes parsing error in ffld_output

Issue - State: closed - Opened by laumalo about 3 years ago
Labels: bug

#147 - 1.3.3 Release

Pull Request - State: closed - Opened by martimunicoy over 3 years ago - 1 comment

#146 - Explicit hydrogens support

Pull Request - State: closed - Opened by martimunicoy over 3 years ago

#145 - 1.3.2 Release

Pull Request - State: closed - Opened by martimunicoy over 3 years ago - 1 comment

#144 - Migrated openforcefield imports to openff.toolkit

Pull Request - State: closed - Opened by frumpowy over 3 years ago - 1 comment

#143 - 1.3.1 Release

Pull Request - State: closed - Opened by martimunicoy over 3 years ago - 1 comment

#142 - PELE-451 Minor adjustments to facilitate platform compatibility

Pull Request - State: closed - Opened by frumpowy over 3 years ago - 1 comment

#141 - Add examples for peleffy 1.3.0

Issue - State: open - Opened by martimunicoy over 3 years ago
Labels: documentation, good first issue

#140 - 1.3.0 release

Pull Request - State: closed - Opened by martimunicoy over 3 years ago - 1 comment

#139 - Multiple molecules in the input PDB file

Issue - State: closed - Opened by laumalo over 3 years ago
Labels: enhancement

#138 - Support for python 3.8

Issue - State: closed - Opened by martimunicoy over 3 years ago

#137 - Add input module

Pull Request - State: closed - Opened by laumalo over 3 years ago - 3 comments

#136 - 1.2.1 Release

Pull Request - State: closed - Opened by laumalo over 3 years ago - 2 comments

#135 - Generate conformation libraries from BCE output

Pull Request - State: closed - Opened by cescgina over 3 years ago

#134 - Fix bug name_to_index dict

Pull Request - State: closed - Opened by laumalo over 3 years ago

#133 - Peleffy parameters for a macrocycle causes infinte loop in PELE

Issue - State: closed - Opened by cescgina over 3 years ago - 2 comments
Labels: bug

#132 - Parents order altered

Issue - State: closed - Opened by carlesperez94 over 3 years ago

#131 - Load parameters from JSON file

Pull Request - State: closed - Opened by laumalo over 3 years ago - 2 comments

#130 - Load parameters from JSON

Issue - State: closed - Opened by laumalo over 3 years ago
Labels: enhancement

#129 - Fix API documentation links

Pull Request - State: closed - Opened by laumalo over 3 years ago

#128 - Fix documentation API links

Issue - State: closed - Opened by laumalo over 3 years ago
Labels: bug, documentation

#127 - 1.2.0 Release

Pull Request - State: closed - Opened by martimunicoy over 3 years ago - 1 comment

#126 - Solvent class with multiple topologies

Pull Request - State: closed - Opened by laumalo over 3 years ago - 1 comment

#125 - Fix bug PDB index

Pull Request - State: closed - Opened by laumalo over 3 years ago - 1 comment

#124 - Error in peleffy.topology.molecule.Molecule._pdb_checkup()

Issue - State: closed - Opened by carlesperez94 over 3 years ago - 2 comments
Labels: bug

#123 - Add CLI option for mae charges

Issue - State: closed - Opened by martimunicoy over 3 years ago - 1 comment
Labels: enhancement

#122 - Solvent class compatible with multiple topologies

Issue - State: closed - Opened by martimunicoy over 3 years ago - 1 comment
Labels: enhancement

#121 - Enhancements

Pull Request - State: closed - Opened by laumalo over 3 years ago - 1 comment

#120 - Openforcefield-0.8.3 upgrade

Issue - State: closed - Opened by martimunicoy over 3 years ago - 1 comment
Labels: enhancement, good first issue

#119 - Explanatory error messages when using an invalid Impact template

Issue - State: closed - Opened by martimunicoy over 3 years ago
Labels: enhancement

#118 - Method from_impact_template()

Pull Request - State: closed - Opened by laumalo over 3 years ago - 5 comments

#117 - Assignment of external partial charges

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

#116 - Create new molecule silently

Issue - State: closed - Opened by cescgina almost 4 years ago - 5 comments
Labels: enhancement

#115 - Write molecule tag not name

Pull Request - State: closed - Opened by martimunicoy almost 4 years ago
Labels: bug

#114 - Expose charge calculator types to main for consitency

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

#113 - Different names for charge methods in forcefield selector and main for OPLS

Issue - State: closed - Opened by cescgina almost 4 years ago

#112 - PDB fixer

Pull Request - State: closed - Opened by martimunicoy almost 4 years ago - 1 comment
Labels: enhancement

#111 - No matching found when assigning connectivity through template

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

#110 - Report the basic guideline of the Impact template in the documentation

Issue - State: open - Opened by martimunicoy almost 4 years ago
Labels: documentation

#109 - Rotamer libraries write molecule's name not tag

Issue - State: closed - Opened by martimunicoy almost 4 years ago
Labels: bug

#108 - Invalid atom ordering in Impact template

Issue - State: closed - Opened by martimunicoy almost 4 years ago - 1 comment
Labels: bug

#107 - Fix graph issues

Pull Request - State: closed - Opened by martimunicoy almost 4 years ago
Labels: bug

#106 - Mol from rdkit

Pull Request - State: closed - Opened by martimunicoy almost 4 years ago - 1 comment
Labels: enhancement

#105 - Add RDKit initializer for Molecule class

Issue - State: closed - Opened by martimunicoy almost 4 years ago

#104 - Add tests for solvent writers

Issue - State: closed - Opened by martimunicoy almost 4 years ago - 2 comments
Labels: testing

#103 - Change openff output for PELE

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

#102 - Support OpenFF's constraints

Issue - State: open - Opened by martimunicoy almost 4 years ago

#101 - Support OpenFF's LibraryCharges

Issue - State: open - Opened by martimunicoy almost 4 years ago

#100 - Add writer of OBC parameters template

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

#99 - peleffy 1.1.0 release

Pull Request - State: closed - Opened by martimunicoy almost 4 years ago - 21 comments

#98 - Improve parameterization API

Issue - State: closed - Opened by martimunicoy almost 4 years ago
Labels: enhancement

#97 - Parameterization api change

Pull Request - State: closed - Opened by martimunicoy almost 4 years ago - 3 comments
Labels: enhancement

#96 - Add individual tests for the RDKit toolkit

Issue - State: open - Opened by martimunicoy almost 4 years ago
Labels: testing

#95 - Correction of bad geometries

Issue - State: open - Opened by carlesperez94 almost 4 years ago - 1 comment

#94 - New method for the OPLS OBC parameters

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

#93 - Load parameters from an Impact file

Issue - State: closed - Opened by martimunicoy almost 4 years ago - 3 comments
Labels: enhancement

#92 - Stereochemistry

Pull Request - State: closed - Opened by martimunicoy almost 4 years ago
Labels: enhancement

#91 - Compatibility with OpenFF allow_undefined_stereo parameter

Issue - State: closed - Opened by martimunicoy almost 4 years ago
Labels: enhancement

#90 - Add support to openff 1.3.0

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

#89 - Add support to openff 1.3.0

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

#88 - Number of bonds

Pull Request - State: closed - Opened by martimunicoy almost 4 years ago
Labels: enhancement

#87 - Extend support to openff-1.3.0 and test it

Issue - State: closed - Opened by martimunicoy almost 4 years ago
Labels: enhancement, testing

#86 - PDB checking

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

#83 - Missing dummy propers in OPLS

Issue - State: closed - Opened by martimunicoy almost 4 years ago
Labels: bug

#80 - Allow the assignment of external partial charges

Issue - State: closed - Opened by martimunicoy almost 4 years ago - 2 comments
Labels: enhancement

GitHub / martimunicoy/peleffy issues and pull requests