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Dihedral Plots: RDKit Mol Object #243

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Jul 4, 2023
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b4aeb11
new PR
cadeduckworth Feb 21, 2023
cc17a6b
update mol object methods, change dihedral_indices naming convention …
cadeduckworth Feb 21, 2023
30ad175
add get_bond_indices
cadeduckworth Feb 21, 2023
8d67d81
reflect name change in tests from dihedrals automated workflow
cadeduckworth Feb 21, 2023
59f32a5
missed name change in test
cadeduckworth Feb 21, 2023
9a7c25a
fix bond highlighting and add low resolution plotting function for di…
cadeduckworth Feb 21, 2023
b6f66c2
add atom_indices to titles of plot columns
cadeduckworth Feb 21, 2023
2f8c042
add atom_indices to label Mol object on plots
cadeduckworth Feb 21, 2023
844b29f
cleaner plot titles
cadeduckworth Feb 21, 2023
5fa5f11
current best plot resolution/proportion
cadeduckworth Feb 21, 2023
82cbaa2
add svgutils and cairosvg methods to plot svg mol object
cadeduckworth Mar 4, 2023
d26d9f1
reimplement DF input option and fix most tests to reflect name change…
cadeduckworth Mar 4, 2023
d80ae4c
add svgutils and cairosvg to dependencies, install, requirements list…
cadeduckworth Mar 4, 2023
a8f5b5e
remove unneccessary import
cadeduckworth Mar 4, 2023
2522b5c
remove import
cadeduckworth Mar 4, 2023
d54cd86
remove temp svg files and build, convert, and save as pdf through mem
cadeduckworth Mar 21, 2023
193dc84
fix legend issue when plotting one solvent
cadeduckworth Mar 21, 2023
dbabc62
Merge branch 'develop' into plot-Mol
cadeduckworth Mar 25, 2023
9ba26ee
Merge branch 'develop' into plot-Mol
orbeckst Mar 28, 2023
fda3206
cleanup
cadeduckworth Mar 28, 2023
e5a440e
move title setting and cleanup
cadeduckworth Mar 28, 2023
c71d3d8
split plot_violins into new build_svg function
cadeduckworth Mar 28, 2023
19973ea
merge updates from develop
cadeduckworth Mar 28, 2023
cc673fe
change, better function names for dihedrals workflow module
cadeduckworth Apr 2, 2023
348495d
cleanup
cadeduckworth Apr 2, 2023
4ad68bb
docs and cleanup, plot width docs, dict comprehension for ab_pairs
cadeduckworth Apr 3, 2023
9609022
cleanup and add list and dict comprehension methods for get_paired_in…
cadeduckworth Apr 3, 2023
42847f8
intersphinx mapping
cadeduckworth Apr 3, 2023
60ec522
remove assert method for notebook test
cadeduckworth Apr 3, 2023
5279161
tests: new fixtures and tests for bond_indices and ab_pairs
cadeduckworth Apr 3, 2023
181c012
tests: new fixtures and tests for bond_indices and ab_pairs, skip 3.7
cadeduckworth Apr 3, 2023
a69f4da
test_build_universe method
cadeduckworth Apr 3, 2023
4df1d88
confirm build universe test
cadeduckworth Apr 3, 2023
c53cd1a
fix df input test
cadeduckworth Apr 3, 2023
8135b51
Update dihedrals.py
cadeduckworth Apr 3, 2023
5d8f960
Merge branch 'develop' into plot-Mol
orbeckst Apr 4, 2023
bf1b05d
remove unused kwargs and update docs for new functions
cadeduckworth Apr 15, 2023
97267ac
rewrite docs to cover new functions and kwarg changes
cadeduckworth Apr 15, 2023
a25c97d
fix tests to accommodate kwarg updates in dihedrals module
cadeduckworth Apr 15, 2023
9175fda
explanation of why figdir is a kwarg at top level of dihedrals module…
cadeduckworth Apr 15, 2023
45cf29d
reorder positional and key word args
cadeduckworth Apr 15, 2023
71da645
accommodation for figdir kwarg
cadeduckworth Apr 15, 2023
2c21a7c
docs typo
cadeduckworth Apr 15, 2023
83c4c63
docs typos
cadeduckworth Apr 15, 2023
60636b4
temporary fix for figdir issue which should currently be a positional…
cadeduckworth Apr 15, 2023
473abaf
upcoming CHANGES
cadeduckworth Apr 15, 2023
6660c98
update to specify where enhancements are occurring
cadeduckworth Jun 9, 2023
554bdd3
remove dafault scope specification for defined functions
cadeduckworth Jun 9, 2023
9de6a4d
reimplement try/except method for rdkit conversion topology element g…
cadeduckworth Jun 9, 2023
d620619
generate combined plots pdf for automated dihedral analysis
cadeduckworth Jun 11, 2023
bd02eb7
updates for implementation of pypdf in workflows dihedrals module: CH…
cadeduckworth Jun 11, 2023
ba05311
intersphinx mapping, docs
cadeduckworth Jun 11, 2023
f435207
fix solute kwarg description for workflows dihedrals module
cadeduckworth Jun 11, 2023
3a85dde
fix ab_pairs kwarg description for workflows dihedrals module
cadeduckworth Jun 11, 2023
7f32b93
documentation for dihedral_violins function in workflows dihedrals mo…
cadeduckworth Jun 11, 2023
87f3930
documentation for get_paired_indices function in workflows dihedrals …
cadeduckworth Jun 11, 2023
34c63ec
documentation and kwarg definition for get_paired_indices function an…
cadeduckworth Jun 11, 2023
bf98c23
kwarg definition for plot_title for dihedral_violins function in work…
cadeduckworth Jun 11, 2023
a3bcddc
move in-line comments explaining figdir kward for workflows dihedrals…
cadeduckworth Jun 11, 2023
c0f9550
reorganize kwargs for plot_dihedral_violins in top-level automated_di…
cadeduckworth Jun 11, 2023
c47e055
add assert method to make figdir kwarg required in workflows dihedral…
cadeduckworth Jun 11, 2023
5376eea
temporarily remove figdir required assertion
cadeduckworth Jun 22, 2023
110b3f9
change MDA guess_atom_element to MDA guess_types for RDKit conversion…
cadeduckworth Jun 22, 2023
f5ead51
fix registry import error for workflows base, close #245
cadeduckworth Jun 22, 2023
a744033
remove guess_atom_element import
cadeduckworth Jun 22, 2023
228b7c0
fix registry import for workflows base module
cadeduckworth Jun 22, 2023
7c9f669
reimplement assert figdir reuired for workflows dihedrals module
cadeduckworth Jun 22, 2023
b8236a6
require RDKit>=2023 for testing environment to investigate failed tes…
cadeduckworth Jun 22, 2023
f45f073
require RDKit<2023 for testing environment to investigate failed test…
cadeduckworth Jun 22, 2023
adcecc6
require RDKit<=2022.09.1 for testing environment to investigate faile…
cadeduckworth Jun 22, 2023
bf6884a
Merge branch 'develop' into plot-Mol
orbeckst Jun 27, 2023
e002845
Merge branch 'develop' into plot-Mol
cadeduckworth Jun 30, 2023
9f751a8
fix function name in dihedral workflows tests
cadeduckworth Jun 30, 2023
13231a2
fix variable reference in dihedral workflows test
cadeduckworth Jun 30, 2023
0db3c5a
fix fixture call and variable assignment in dihedral groups test for …
cadeduckworth Jun 30, 2023
c540c8b
modify workflows base test for assertion of figure directory requirem…
cadeduckworth Jun 30, 2023
eca078a
add name_index pairing tests for dihedral workflows atom indices cons…
cadeduckworth Jun 30, 2023
34f3e18
modify workflows base test for dihedral workflow figure directory req…
cadeduckworth Jul 1, 2023
2b5d7af
add pypdf to setup.py install_requires for dihedrals workflow
cadeduckworth Jul 1, 2023
b6d4f61
Merge branch 'develop' into plot-Mol
cadeduckworth Jul 2, 2023
7843fce
change imports to follow PEP 8
cadeduckworth Jul 2, 2023
0cb2ddc
modify dihedrals workflow docs to explain figdir kwarg requirement
cadeduckworth Jul 2, 2023
84aed57
use first solvent specified to build MDAnalysis Universe
cadeduckworth Jul 2, 2023
d231b45
Merge branch 'develop' into plot-Mol
cadeduckworth Jul 2, 2023
9a7d385
Merge branch 'develop' into plot-Mol
orbeckst Jul 2, 2023
2970b24
modify single solvent plotting method, add solvent count assertion
cadeduckworth Jul 3, 2023
9801848
comment expected fixture scope changes, reference issue #235
cadeduckworth Jul 3, 2023
4ebf3c0
remove solute.unwrap, not needed
cadeduckworth Jul 3, 2023
292a8bd
reference issue #260 to fix jupyter notebook figure output
cadeduckworth Jul 3, 2023
4af6de6
finalize single solvent figure modifications and add test
cadeduckworth Jul 4, 2023
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tests: new fixtures and tests for bond_indices and ab_pairs, skip 3.7
cadeduckworth committed Apr 3, 2023
commit 181c012e69ff49d490170363a68bfc73c511b92d
10 changes: 10 additions & 0 deletions mdpow/tests/test_automated_dihedral_analysis.py
Original file line number Diff line number Diff line change
@@ -183,6 +183,11 @@ def test_dihedral_indices(self, atom_indices):
atom_group_indices, _ = atom_indices
assert atom_group_indices == self.check_atom_group_indices

# the following 'reason' affects every downstream function that relies
# on the atom indices returned for dihedral atom group selections
# issue raised (#239) to identify and resolve exact package/version responsible
@pytest.mark.skipif(sys.version_info < (3, 8), reason='pytest=7.2.0, build=py37h89c1867_0, '
'returns incorrect atom_indices for dihedral atom group selections')
def test_bond_indices(self, bond_indices):
bix = bond_indices
assert bix == self.check_bond_indices
@@ -208,6 +213,11 @@ def test_dihedral_groups(self, dihedral_groups):
assert groups[i].all() == self.check_groups[i].all()
i+=1

# the following 'reason' affects every downstream function that relies
# on the atom indices returned for dihedral atom group selections
# issue raised (#239) to identify and resolve exact package/version responsible
@pytest.mark.skipif(sys.version_info < (3, 8), reason='pytest=7.2.0, build=py37h89c1867_0, '
'returns incorrect atom_indices for dihedral atom group selections')
def test_ab_pairs(self, atom_indices, bond_indices, dihedral_groups):
aix, _ = atom_indices
bix = bond_indices