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use relative imports inside MDPOW #257

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Jul 2, 2023
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use relative imports inside MDPOW #257

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59ba2d1
use relative imports inside MDPOW
orbeckst Jul 2, 2023
7ce55c4
add simple test for registry
orbeckst Jul 2, 2023
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6 changes: 6 additions & 0 deletions mdpow/tests/test_workflows_registry.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
import pytest

from mdpow.workflows import registry

def test_registry():
assert list(registry.registry.keys()) == ['DihedralAnalysis']
11 changes: 3 additions & 8 deletions mdpow/workflows/base.py
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Expand Up @@ -24,8 +24,6 @@
import re
import pandas as pd

from mdpow.workflows import registry

import logging

logger = logging.getLogger('mdpow.workflows.base')
Expand Down Expand Up @@ -147,6 +145,8 @@ def automated_project_analysis(project_paths, ensemble_analysis, **kwargs):
automated_project_analysis(project_paths, ensemble_analysis='DihedralAnalysis', **kwargs)

"""
# import inside function to avoid circular imports
from .registry import registry

for row in project_paths.itertuples():
molname = row.molecule
Expand All @@ -156,24 +156,19 @@ def automated_project_analysis(project_paths, ensemble_analysis, **kwargs):
logger.info(f'starting {molname}')

try:
registry.registry[ensemble_analysis](dirname=dirname, resname=resname, molname=molname, **kwargs)

registry[ensemble_analysis](dirname=dirname, resname=resname, molname=molname, **kwargs)
logger.info(f'{molname} completed')

except KeyError as err:
msg = (f"Invalid ensemble_analysis {err}. An EnsembleAnalysis type that corresponds "
"to an existing automated workflow module must be input as a kwarg. "
"ex: ensemble_analysis='DihedralAnalysis'")
logger.error(f'{err} is an invalid selection')

raise KeyError(msg)

except TypeError as err:
msg = (f"Invalid ensemble_analysis {ensemble_analysis}. An EnsembleAnalysis type that "
"corresponds to an existing automated workflow module must be input as a kwarg. "
"ex: ensemble_analysis='DihedralAnalysis'")
logger.error(f'workflow module for {ensemble_analysis} does not exist yet')

raise TypeError(msg)

logger.info('all analyses completed')
Expand Down
107 changes: 53 additions & 54 deletions mdpow/workflows/dihedrals.py
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Expand Up @@ -7,7 +7,7 @@

:mod:`~mdpow.workflows.dihedrals` module provides functions for automated
workflows that encompass :class:`~mdpow.analysis.dihedral.DihedralAnalysis`.
See each function for requirements and examples.
See each function for requirements and examples.

Most functions can be used as standalone, individually, or in combination
depending on the desired results. Details of the completely automated workflow
Expand Down Expand Up @@ -42,12 +42,11 @@
import seaborn as sns
import matplotlib.pyplot as plt

import mdpow
from mdpow.analysis.dihedral import DihedralAnalysis

import MDAnalysis as mda
from MDAnalysis.topology.guessers import guess_atom_element

from ..analysis import ensemble, dihedral

import logging

logger = logging.getLogger('mdpow.workflows.dihedrals')
Expand Down Expand Up @@ -92,11 +91,11 @@
def build_universe(dirname):
"""Builds :class:`~MDAnalysis.core.universe.Universe` from
``water/Coulomb/0000`` topology and trajectory for the specified project.

Used by :func:`~mdpow.workflows.dihedrals.rdkit_conversion`
and :func:`~mdpow.workflows.dihedrals.dihedral_indices` to obtain atom indices
for each dihedral atom group.

:keywords:

*dirname*
Expand All @@ -108,12 +107,12 @@ def build_universe(dirname):
searches for .gro, .gro.bz2, .gro.gz, and .tpr files for topology,
and .xtc files for trajectory. It will default to using the tpr file
available.

:returns:

*u*
:class:`~MDAnalysis.core.universe.Universe` object

"""

path = pathlib.Path(dirname)
Expand All @@ -127,30 +126,30 @@ def rdkit_conversion(u, resname):
"""Converts the solute, `resname`, of the
:class:`~MDAnalysis.core.universe.Universe` to :class:`rdkit.Chem.rdchem.Mol` object
for use with a SMARTS selection string to identify dihedral atom groups.

Accepts :class:`~MDAnalysis.core.universe.Universe` object made with
:func:`~mdpow.workflows.dihedrals.build_universe` and a `resname` as input.
Uses `resname` to select the solute for conversion by
:class:`~MDAnalysis.converters.RDKit.RDKitConverter` to :class:`rdkit.Chem.rdchem.Mol`,
and will add element attributes for Hydrogen if not listed in the topology.

:keywords:

*u*
:class:`~MDAnalysis.core.universe.Universe` object

*resname*
`resname` for the molecule as defined in
`resname` for the molecule as defined in
the topology and trajectory

:returns:

*tuple(mol, solute)*
function call returns tuple, see below

*mol*
:class:`rdkit.Chem.rdchem.Mol` object converted from `solute`

*solute*
molecule specified by :func:`~MDAnalysis.core.groups.select_atoms`
for :class:`~MDAnalysis.core.universe.Universe` object
Expand All @@ -171,8 +170,8 @@ def rdkit_conversion(u, resname):
def dihedral_indices(dirname, resname, SMARTS=SMARTS_DEFAULT):
'''Uses a SMARTS selection string to identify indices for
relevant dihedral atom groups.
Requires an MDPOW project directory and `resname`

Requires an MDPOW project directory and `resname`
as input. With :func:`~mdpow.workflows.dihedrals.build_universe` and
:func:`~mdpow.workflows.dihedrals.rdkit_conversion`, uses the topology
and trajectory from ``water/Coulomb/0000`` and creates a
Expand All @@ -190,16 +189,16 @@ def dihedral_indices(dirname, resname, SMARTS=SMARTS_DEFAULT):
searches for .gro, .gro.bz2, .gro.gz, and .tpr files for topology,
and .xtc files for trajectory. It will default to using the tpr file
available.

*resname*
`resname` for the molecule as defined in
`resname` for the molecule as defined in
the topology and trajectory

*SMARTS*
The default SMARTS string is described in detail under :data:`SMARTS_DEFAULT`.

:returns:

*atom_group_indices*
tuple of tuples of indices for each dihedral atom group

Expand All @@ -209,15 +208,15 @@ def dihedral_indices(dirname, resname, SMARTS=SMARTS_DEFAULT):
mol = rdkit_conversion(u=u, resname=resname)[0]
pattern = Chem.MolFromSmarts(SMARTS)
atom_group_indices = mol.GetSubstructMatches(pattern)

return atom_group_indices

def dihedral_groups(dirname, resname, SMARTS=SMARTS_DEFAULT):
'''Uses the indices of the relevant dihedral atom groups determined
by :func:`~mdpow.workflows.dihedral.dihedral_indices`
and returns the names for each atom in each group.
Requires an MDPOW project directory and `resname`

Requires an MDPOW project directory and `resname`
as input. Expands upon usage of
:func:`~mdpow.workflows.dihedral.dihedral_indices`
to return an array of the names of each atom within
Expand All @@ -239,14 +238,14 @@ def dihedral_groups(dirname, resname, SMARTS=SMARTS_DEFAULT):
available.

*resname*
`resname` for the molecule as defined in
`resname` for the molecule as defined in
the topology and trajectory

*SMARTS*
The default SMARTS string is described in detail under :data:`SMARTS_DEFAULT`.

:returns:

*dihedral_groups*
list of :func:`numpy.array` for atom names in each dihedral atom group

Expand All @@ -263,12 +262,12 @@ def dihedral_groups(dirname, resname, SMARTS=SMARTS_DEFAULT):
def dihedral_groups_ensemble(dirname, atom_group_indices,
solvents=SOLVENTS_DEFAULT,
interactions=INTERACTIONS_DEFAULT,
start=None, stop=None, step=None):
start=None, stop=None, step=None):
'''Creates one :class:`~mdpow.analysis.ensemble.Ensemble` for the MDPOW
project and runs :class:`~mdpow.analysis.dihedral.DihedralAnalysis`
for each dihedral atom group identified by the SMARTS
selection string.

.. seealso::

:func:`~mdpow.workflows.dihedrals.automated_dihedral_analysis`,
Expand Down Expand Up @@ -304,30 +303,30 @@ def dihedral_groups_ensemble(dirname, atom_group_indices,
.. seealso:: :class:`~mdpow.analysis.ensemble.EnsembleAnalysis`

:returns:

*df*
:class:`pandas.DataFrame` of :class:`~mdpow.analysis.dihedral.DihedralAnalysis`
results, including all dihedral atom groups for molecule of current project

'''

dih_ens = mdpow.analysis.ensemble.Ensemble(dirname=dirname,
solvents=solvents,
interactions=interactions)
dih_ens = ensemble.Ensemble(dirname=dirname,
solvents=solvents,
interactions=interactions)
indices = atom_group_indices
all_dihedrals = [dih_ens.select_atoms(f'index {i[0]}',
f'index {i[1]}',
f'index {i[2]}',
f'index {i[3]}' ) for i in indices]

da = DihedralAnalysis(all_dihedrals)
da = dihedral.DihedralAnalysis(all_dihedrals)
da.run(start=start, stop=stop, step=step)
df = da.results

return df

def save_df(df, df_save_dir, resname=None, molname=None):
'''Takes a :class:`pandas.DataFrame` of results from
'''Takes a :class:`pandas.DataFrame` of results from
:class:`~mdpow.analysis.dihedral.DihedralAnalysis`
as input before padding the angles to optionaly save the raw
data.
Expand All @@ -349,13 +348,13 @@ def save_df(df, df_save_dir, resname=None, molname=None):
optional, path to the location to save results :class:`pandas.DataFrame`

*resname*
`resname` for the molecule as defined in
`resname` for the molecule as defined in
the topology and trajectory

*molname*
molecule name to be used for labelling
plots, if different from `resname`

'''

df = df.sort_values(by=["selection",
Expand All @@ -379,13 +378,13 @@ def save_df(df, df_save_dir, resname=None, molname=None):
def periodic_angle(df, padding=45):
'''Pads the angles from the results :class:`~pandas.DataFrame`
to maintain periodicity in the violin plots.

Takes a :class:`pandas.DataFrame` of results from
:class:`~mdpow.analysis.dihedral.DihedralAnalysis`
as input and pads the angles to maintain periodicity
for properly plotting dihedral angle frequencies as KDE violins
with :func:`~mdpow.workflows.dihedrals.dihedral_violins`.
Creates two new :class:`pandas.DataFrame` based on the
Creates two new :class:`pandas.DataFrame` based on the
cutoff value specified, adds to the angle values, concatenates
all three :class:`pandas.DataFrame`, maintaining original data and
adding padding, and returns new augmented :class:`pandas.DataFrame`.
Expand All @@ -399,15 +398,15 @@ def periodic_angle(df, padding=45):
*padding*
value in degrees
default: 45

:returns:

*df_aug*
augmented results :class:`pandas.DataFrame` containing
padded dihedral angles as specified by `padding`

.. rubric:: Example

Typical Workflow::

da = DihedralAnalysis(all_dihedrals)
Expand Down Expand Up @@ -443,7 +442,7 @@ def dihedral_violins(df, width=0.9, solvents=SOLVENTS_DEFAULT):

*solvents*
The default solvents are documented under :data:`SOLVENTS_DEFAULT`.

:returns:

*violin plot*
Expand All @@ -468,7 +467,7 @@ def dihedral_violins(df, width=0.9, solvents=SOLVENTS_DEFAULT):
solv2 = 'octanol'
if solvs.size > 1:
solv2 = solvs[1]

g = sns.catplot(data=df, x="lambda", y="dihedral", hue="solvent", col="interaction",
kind="violin", split=True, width=width, inner=None, cut=0,
linewidth=0.5,
Expand Down Expand Up @@ -496,7 +495,7 @@ def dihedral_violins(df, width=0.9, solvents=SOLVENTS_DEFAULT):
def plot_violins(df, resname, figdir=None, molname=None, width=0.9, solvents=SOLVENTS_DEFAULT):
'''Coordinates plotting and optionally saving figures for all dihedral
atom groups.

Makes a subdirectory within the specified
`figdir` using `resname` or `molname` provided and saves violin plot
figur for each dihedral atom group separately.
Expand All @@ -505,15 +504,15 @@ def plot_violins(df, resname, figdir=None, molname=None, width=0.9, solvents=SOL

:func:`~mdpow.workflows.dihedrals.automated_dihedral_analysis`,
:func:`~mdpow.workflows.dihedrals.dihedral_violins`

:keywords:

*df*
augmented results :class:`pandas.DataFrame` from
:func:`~mdpow.workflows.dihedrals.periodic_angle`

*resname*
`resname` for the molecule as defined in
`resname` for the molecule as defined in
the topology and trajectory

*figdir*
Expand Down Expand Up @@ -575,7 +574,7 @@ def automated_dihedral_analysis(dirname=None, df_save_dir=None, figdir=None,
'''Runs :class:`~mdpow.analysis.dihedral.DihedralAnalysis` for a single MDPOW
project and creates violin plots of dihedral angle frequencies for each
relevant dihedral atom group.

For one MDPOW project, automatically determines all relevant dihedral atom groups
in the molecule, runs :class:`~mdpow.analysis.dihedral.DihedralAnalysis` for each group,
pads the dihedral angles from analysis results for all groups to maintain periodicity,
Expand Down Expand Up @@ -605,13 +604,13 @@ def automated_dihedral_analysis(dirname=None, df_save_dir=None, figdir=None,
optional, path to the location to save figures

*resname*
`resname` for the molecule as defined in
`resname` for the molecule as defined in
the topology and trajectory

*molname*
molecule name to be used for labelling
plots, if different from `resname`

*SMARTS*
The default SMARTS string is described in detail under :data:`SMARTS_DEFAULT`.

Expand Down Expand Up @@ -652,7 +651,7 @@ def automated_dihedral_analysis(dirname=None, df_save_dir=None, figdir=None,
relevant dihedral atom group in the molecule from the current MDPOW project

.. rubric:: Example

Typical Workflow::

import automated_dihedral_analysis as ada
Expand Down
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