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Generate conformation libraries from BCE output #135

Merged
merged 34 commits into from
Apr 19, 2021
Merged

Generate conformation libraries from BCE output #135

merged 34 commits into from
Apr 19, 2021

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cescgina
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@cescgina cescgina commented Mar 30, 2021 •
edited by martimunicoy

This PR introduces code to generate a Conformation library to use with PELE, from a set of pdb files.

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
Switch from calculating dihedrals to translations
68e206c 
In this new mode, the tranlation from each atom to the root atom of the
template is calculated instead of the dihedral angle
@cescgina
Update test for BCEConformations
fc85440
@cescgina
Merge branch 'devel' into calc_dihedrals
d1565ee
martimunicoy
martimunicoy reviewed Apr 9, 2021
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All ok! I think we only need to add some examples and a general explanation to docs.

@martimunicoy martimunicoy merged commit 8411682 into martimunicoy:devel Apr 19, 2021
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@martimunicoy martimunicoy martimunicoy left review comments

@laumalo laumalo Awaiting requested review from laumalo

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@cescgina @martimunicoy