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1.3.0 release #140

Merged
merged 59 commits into from
Apr 20, 2021
Merged

1.3.0 release #140

merged 59 commits into from
Apr 20, 2021

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martimunicoy
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@martimunicoy martimunicoy commented Apr 20, 2021 •
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cescgina and others added 30 commits October 27, 2020 11:19
@cescgina
Add helper methods to Dihedral object
2d62238
@cescgina
Add options to main to run dihedral calculations
fff3969
@cescgina
Add default path to dihedral library file
f0e2a72
@cescgina
Add module to calculate dihedral angles
6717f0c
@cescgina
Move rdkit dependencies into its toolkit
93fee12
@cescgina
Change units of dihedral calculation to rad
d7ebbe1
@cescgina
Merge branch 'devel' into calc_dihedrals
0b74674
@cescgina
Merge branch 'devel' into calc_dihedrals
69ceffb
@cescgina
Remove duplicated method from merge
4720fe8
@cescgina
Fix discrepancy in name of OPLS charges option
8a3b62a
@cescgina
Udpate format of Dihedral library due to new changes
23bdca8
@cescgina
Revert changes in dihedral library format
588e8ec 
By using the topology instead of the molecule we can retain the same
format as before
@cescgina
Sort the output of glob to get consistent output
c2c666a 
This will produce the exact same dihedral library in all machines
@cescgina
Merge branch 'devel' into calc_dihedrals
0724711
@cescgina
Expose charge calculator types to main for consitency
3b6bea3
@cescgina
Merge branch 'devel' into calc_dihedrals
dcb2e19
@cescgina
Merge branch 'devel' into calc_dihedrals
c2ec73b
@cescgina
Add function to calculate RMSD in RDKIT toolkit
4e1aff9
@cescgina
Modify logger level inside BCEDihedrals
24a0386
@cescgina
Add new mode in BCEDihedrals
9122c85 
In this new mode, the different clusters are ordered so that the jump
between two subsequent clusters involves the minimum structural
difference. This is done heuristically, and it is not guaranteed to be
optimal
@cescgina
Raise more informative error for missing BCEDihedrals
39e8c40
@cescgina
Avoid calculating rotamer libraries with BCE
8677dda
@cescgina
Avoid logging rotamer library if not calculated
0bc8193
@cescgina
Do not avoid reading dihedrals with hydrogens
06140f6
@cescgina
Merge branch 'devel' into calc_dihedrals
f2139b3
@cescgina
Add tests for outputHandler in the dihedral library
f0dfa8f
@cescgina
Pass dihedrals_mode argument to main
8d1b214
@cescgina
Test parsing dihedral library parameters in main
9662430
@cescgina
Add tests for new functions in rdkit toolkit
88754d3
@cescgina
Add tests for BCEDihedrals module
d118a9b
cescgina and others added 25 commits April 7, 2021 12:24
@cescgina
Use parameterize_opls2005 function to avoid errors
a074110
@laumalo
Add input module
89dc2f1
@laumalo
Minor format error fixed
c683664
@laumalo
Add main option, tests and rotamers option
613bd0d
@laumalo
Allow allow_undefined_stereo to be modified by the user
c6b668d
@laumalo
Fix missing flag
978723a
@laumalo
Fix HOH error
652b75e
@laumalo
Add tests
1f350e0
@laumalo
Fix minor error tests
31a682a
@laumalo
Update releasehistory.rst
f26d594
@laumalo
Update usage.rst
de6a75f
@laumalo
Allow multiple molecules same chain
aa80251
@laumalo
Merge branch 'pdb_class' of https://github.com/martimunicoy/peleffy i…
37f1cbb 
…nto pdb_class
@laumalo
Fix alert LGTM
e69cc64
@laumalo
Fix strip spaces output path
5bf8718
@martimunicoy
Merge pull request #135 from cescgina/calc_dihedrals
8411682 
Generate conformation libraries from BCE output
@laumalo
Update usage.rst
d6c9c26
@laumalo
Supprt ligand core constraints + minor changes
500b274
@laumalo
Merge branch 'pdb_class' of https://github.com/martimunicoy/peleffy i…
cfc2b9e 
…nto pdb_class
@laumalo
Solve merge conflics
8d10b45
@martimunicoy
Styling and minor improvements on BCE conformers
8c96c19
@laumalo
Solve conflits
9443b0c
@martimunicoy
Return consistent molecules list and other minor issues
f4d050b
@martimunicoy
Merge pull request #137 from martimunicoy/pdb_class
d5165bb 
Add input module
@martimunicoy
Update releasehistory.rst
7c62ed1
@codecov-commenter
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Codecov Report

Merging #140 (7c62ed1) into master (de108f4) will decrease coverage by 1.51%.
The diff coverage is 69.46%.

This was linked to issues Apr 20, 2021
Support for python 3.8 #138
Closed
Multiple molecules in the input PDB file #139
Closed
@martimunicoy martimunicoy merged commit ba7cad2 into master Apr 20, 2021
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Successfully merging this pull request may close these issues.

Multiple molecules in the input PDB file Support for python 3.8
4 participants
@martimunicoy @codecov-commenter @laumalo @cescgina