IAlibay/MDRestraintsGenerator issues and pull requests

#46 - Error while running the BoreschRestraintGMX.py script

Issue - State: open - Opened by Shubhangi1397 2 months ago

#45 - Go for a 0.2.1 bugfix release

Pull Request - State: closed - Opened by IAlibay about 2 years ago

#44 - Switch from using default bond/angle/dihedral values to using lib.distance calls.

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

#43 - Don't use selection strings for finding bonded atoms

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

#42 - Start 0.3.0

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

#41 - Regression failure for scipy>1.8

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

#40 - pass start/stop/step to `find_ligand_atoms` + don't always transfer to memory

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

#39 - gromacs: avoid dihedrals close to 180/-180 periodicity

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

#38 - Add powered by MDAnalysis badge

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

#37 - Adds the option of using harmonic restraints

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

#36 - Adds flat bottom restraint support

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

#35 - Adds box argument to capped_distance search

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

#34 - Renaming workflow - aesthetics

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

#33 - Add git actions CI

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

#32 - Add checks for expected topology attributes

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

#31 - Support terminal AA CN expansion

Pull Request - State: closed - Opened by IAlibay about 4 years ago - 1 comment

#30 - CN selection will fail if picking on a terminal AA

Issue - State: closed - Opened by IAlibay about 4 years ago

#29 - Enables path-to-file writing

Pull Request - State: closed - Opened by IAlibay about 4 years ago - 1 comment

#28 - Adds more tests

Pull Request - State: closed - Opened by IAlibay about 4 years ago - 1 comment

#27 - Skip linux for some tests on Travis

Pull Request - State: closed - Opened by IAlibay about 4 years ago - 2 comments

#26 - Adds protein search

Pull Request - State: closed - Opened by IAlibay about 4 years ago - 2 comments

#25 - Adds multi-frame search for finding protein anchor atoms

Pull Request - State: closed - Opened by IAlibay about 4 years ago - 2 comments

#24 - Switch to astropy's ci-helpers to avoid segfaults

Pull Request - State: closed - Opened by IAlibay about 4 years ago - 2 comments
Labels: testing

#23 - Remove double in-memory

Pull Request - State: closed - Opened by IAlibay about 4 years ago - 2 comments
Labels: bug, testing

#22 - Travis segfaults on Linux

Issue - State: closed - Opened by IAlibay about 4 years ago

#21 - Adds ligand search and separates search from restraints

Pull Request - State: closed - Opened by IAlibay about 4 years ago - 2 comments

#20 - Adds boresch analytical restraint + colinear restrictions

Pull Request - State: closed - Opened by IAlibay about 4 years ago - 1 comment

#19 - Move ligand and protein pickers outside of FindBoreschRestraint

Issue - State: closed - Opened by IAlibay about 4 years ago

#18 - Add proper documentation

Issue - State: open - Opened by IAlibay about 4 years ago - 1 comment

#17 - tests + fixes png naming and legend issue

Pull Request - State: closed - Opened by IAlibay about 4 years ago - 1 comment

#16 - Add legend to plots

Issue - State: closed - Opened by IAlibay about 4 years ago

#15 - plotting is broken

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

#14 - Add options to write to a given path

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

#13 - Refactor write to be in restraint class instead

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

#12 - Remove offset npz files & gitignore

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

#11 - Can we get badges and codecov to work?

Pull Request - State: closed - Opened by IAlibay over 4 years ago - 1 comment

#10 - Get travis working

Pull Request - State: closed - Opened by IAlibay over 4 years ago - 1 comment

#9 - Refactor for MDA.AnalysisBase and cookiecutter

Pull Request - State: closed - Opened by IAlibay over 4 years ago - 1 comment

#8 - Add options for AMBER TI restraints

Issue - State: open - Opened by IAlibay over 5 years ago

#7 - Output the analytical restraint energy

Issue - State: closed - Opened by IAlibay over 5 years ago - 1 comment
Labels: enhancement

#6 - Add the "closest frame" value to the histogram plots

Issue - State: closed - Opened by IAlibay over 5 years ago - 1 comment

#5 - Implement interactive restraint picking

Issue - State: open - Opened by IAlibay over 5 years ago

#4 - Add the ability to generate BoreschRestraints via the pull code

Issue - State: open - Opened by IAlibay over 5 years ago - 1 comment
Labels: enhancement

#3 - Extend capabilities: Ligand picker

Issue - State: closed - Opened by IAlibay over 5 years ago
Labels: enhancement

#2 - QQ plot will fail if distribution goes over the periodicity range

Issue - State: open - Opened by IAlibay over 5 years ago - 3 comments

#1 - Needs tests / examples

Issue - State: closed - Opened by IAlibay over 5 years ago - 2 comments

GitHub / IAlibay/MDRestraintsGenerator issues and pull requests