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fix pep8
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ALescoulie committed Oct 10, 2023
1 parent d7a23f0 commit d625933
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156 changes: 86 additions & 70 deletions package/MDAnalysis/analysis/nucleicacids.py
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Original file line number Diff line number Diff line change
Expand Up @@ -107,17 +107,22 @@ class NucPairDist(AnalysisBase):
Attributes
----------
results.pair_distances: numpy.ndarray
2D array of pair distances. First dimension is simulation time,
2D array of pair distances. First dimension is simulation time,
second dimension contains the pair distances for each each entry
pair in selection1 and selection2.
.. versionadded:: 2.4.0
.. note::
`results.pair_distances` is slated for deprecation in
version 3.0.0, use `results.distances` instead.
.. deprecated:: 2.7.0
`results.pair_distances` will be removed in
version 3.0.0, use :attr:`results.distances` instead.
results.distances: numpy.ndarray
stored in a 2d numpy array with first index selecting the
Residue pair, and the second index selecting the frame number
Distances are stored in a 2d numpy array with axis 0 (first index)
indexing the trajectory frame and axis 1 (second index) selecting the
Residue pair.
Expand All @@ -127,30 +132,32 @@ class NucPairDist(AnalysisBase):
times: numpy.ndarray
Simulation times for analysis.
Raises
------
ValueError
If the selections given are not the same length
ValueError
An :class:`~MDAnalysis.core.groups.AtomGroup` in one of the
An :class:`~MDAnalysis.core.groups.AtomGroup` in one of the
strands not a valid nucleic acid
ValueError
If a given residue pair from the provided strands returns an empty
:class:`~MDAnalysis.core.groups.AtomGroup` when selecting the atom
pairs used in the distance calculations
*Version Info*
.. versionchanged:: 2.5.0
The ability to access by passing selection indices to :attr:`results`
is now removed as of MDAnalysis version 2.5.0. Please use
:attr:`results.pair_distances` instead.
The :attr:`results.times` was deprecated and is now removed as of
MDAnalysis 2.5.0.
MDAnalysis 2.5.0.
Please use the class attribute :attr:`times` instead.
.. versionchanged:: 2.7.0
Added static method :attr:`select_strand_atoms` as a
Added static method :attr:`select_strand_atoms` as a
helper for selecting atom pairs for distance analysis.
"""

Expand All @@ -162,7 +169,11 @@ class NucPairDist(AnalysisBase):
def __init__(self, selection1: List[mda.AtomGroup],
selection2: List[mda.AtomGroup],
**kwargs) -> None:
super(NucPairDist, self).__init__(selection1[0].universe.trajectory, **kwargs)
super(
NucPairDist,
self).__init__(
selection1[0].universe.trajectory,
**kwargs)

if len(selection1) != len(selection2):
raise ValueError("Selections must be same length")
Expand All @@ -178,16 +189,16 @@ def __init__(self, selection1: List[mda.AtomGroup],

@staticmethod
def select_strand_atoms(
strand1: ResidueGroup, strand2: ResidueGroup,
strand1: ResidueGroup, strand2: ResidueGroup,
a1_name: str, a2_name: str, g_name: str = 'G',
a_name: str = 'A', u_name: str = 'U',
t_name: str = 'T', c_name: str = 'C'
) -> Tuple[List[mda.AtomGroup], List[mda.AtomGroup]]:
) -> Tuple[List[mda.AtomGroup], List[mda.AtomGroup]]:
r"""
A helper method for nucleic acid pair distance analyses.
A helper method for nucleic acid pair distance analyses.
Used for selecting specific atoms from two strands of nucleic acids.
Parameters
----------
strand1: List[Residue]
Expand All @@ -208,18 +219,18 @@ def select_strand_atoms(
Name of Thymine in topology, by default assigned to T
c_name: str (optional)
Name of Cytosine in topology, by default assigned to C
Returns
-------
Tuple[List[AtomGroup], List[AtomGroup]]
returns a tuple containing two lists of
returns a tuple containing two lists of
:class:`~MDAnalysis.core.groups.AtomGroup`\s
corresponding to the provided selections from each strand.
Raises
------
ValueError:
An :class:`~MDAnalysis.core.groups.AtomGroup`
An :class:`~MDAnalysis.core.groups.AtomGroup`
in one of the strands not a valid nucleic acid
ValueError:
An :class:`~MDAnalysis.core.groups.Residue` returns an empty
Expand All @@ -228,7 +239,7 @@ def select_strand_atoms(
.. versionadded:: 2.7.0
"""
"""
pyrimidines: List[str] = [c_name, t_name, u_name]
purines: List[str] = [a_name, g_name]

Expand All @@ -243,42 +254,42 @@ def select_strand_atoms(
else:
raise ValueError(
f"AtomGroup in {pair} is not a valid nucleic acid"
)
)

ag1 = pair[0].atoms.select_atoms(f'name {a1}')
ag2 = pair[1].atoms.select_atoms(f'name {a2}')

if not all(len(ag) > 0 for ag in [ag1, ag2]):
err_info: Tuple[Residue, str] = (pair[0], a1) \
if len(ag1) == 0 else (pair[1], a2)

raise ValueError(
(
f"{err_info[0]} returns an empty AtomGroup"
"with selection string \"name {a2}\""
)
)

sel1.append(ag1)
sel1.append(ag1)
sel2.append(ag2)

return (sel1, sel2)

def _prepare(self) -> None:
self._res_array: np.ndarray = np.zeros(
[self.n_frames, self._n_sel]
)
)

def _single_frame(self) -> None:
dist: np.ndarray = calc_bonds(
self._s1.positions, self._s2.positions
)
)

self._res_array[self._frame_index, :] = dist

def _conclude(self) -> None:
self.results['distances'] = self._res_array
self.results['pair_distances'] = self.results['distances']
self.results['pair_distances'] = self.results['distances']
# TODO: remove pair_distances in 3.0.0


Expand All @@ -287,13 +298,20 @@ class WatsonCrickDist(NucPairDist):
Watson-Crick base pair distance for selected
residues over a trajectory.
Takes two :class:`~MDAnalysis.core.groups.ResidueGroup` objects
as `strand1` and `strand2` and calculates the distance between
the nitrogen atoms in the Watson-Crick hydrogen bond over the
trajectory. Bases are matched by their index in `strand1` and `strand2`
(similar to ``base_pairs = zip(strand1, strand2)``).
Therefore, `strand1` and `strand2` must contain the *same number of
residues*.
Takes two :class:`~MDAnalysis.core.groups.ResidueGroup`
objects or two lists of :class:`~MDAnalysis.core.groups.Residue`
and calculates the distance between the nitrogen atoms in the
Watson-Crick hydrogen bond over the trajectory. Bases are matched
either by their index in the two
:class:`~MDAnalysis.core.groups.ResidueGroup` provided as arguments,
or based on the indices of the provided lists of
:class:`~MDAnalysis.core.groups.Residue` objects depending
on which is provided.
.. note::
Support for :class:`~MDAnalysis.core.groups.Residue` is slated for
deprecation and will raise a warning when used. It still works but
:class:`~MDAnalysis.core.groups.ResidueGroup` is preferred.
Parameters
----------
Expand Down Expand Up @@ -326,9 +344,9 @@ class WatsonCrickDist(NucPairDist):
t_name: str (optional)
Name of Thymine in topology, by default assigned to "T"
c_name: str (optional)
Name of Cytosine in topology, by default assigned to "C"
**kwargs:
Additional keyword arguments for
Name of Cytosine in topology, by default assigned to C
**kwargs: dict
Key word arguments for
:class:`~MDAnalysis.analysis.base.AnalysisBase`
Attributes
Expand All @@ -341,7 +359,7 @@ class WatsonCrickDist(NucPairDist):
.. versionadded:: 2.7.0
results.pair_distances: numpy.ndarray
2D array of pair distances. First dimension is
2D array of pair distances. First dimension is
simulation time, second dimension contains the
pair distances for each each entry pair in
selection1 and selection2.
Expand All @@ -368,24 +386,26 @@ class WatsonCrickDist(NucPairDist):
ValueError
If `strand1` and `strand2` are not the same length
ValueError:
A :class:`~MDAnalysis.core.Residue` in one of the strands is not a
valid nucleic acid
An :class:`~MDAnalysis.core.groups.AtomGroup`
in one of the strands not a valid nucleic acid
ValueError
If a given residue pair from the provided strands returns an empty
:class:`~MDAnalysis.core.groups.AtomGroup` when selecting the atom
pairs used in the distance calculations
*Version Info*
.. versionchanged:: 2.5.0
Accessing results by passing strand indices to :attr:`results`
was deprecated and is now removed as of MDAnalysis version 2.5.0.
Please use :attr:`results.pair_distances` instead.
The :attr:`results.times` was deprecated and is now removed as of
MDAnalysis 2.5.0. Please use the class attribute
MDAnalysis 2.5.0. Please use the class attribute
:attr:`times` instead.
.. versionchanged:: 2.7.0
`strand1` and `strand2` now also accept a
`strand1` and `strand2` now also accept a
:class:`~MDAnalysis.core.groups.ResidueGroup` as input.
The previous input type, ``List[Residue]`` is still supported,
but it is **deprecated** and will be removed in release 3.0.0.
Expand All @@ -399,50 +419,48 @@ def __init__(self, strand1: ResidueClass, strand2: ResidueClass,

def verify_strand(strand: ResidueClass) -> ResidueGroup:
# Helper method to verify the strands

if isinstance(strand, list): # Checking if a list is given
# verify list is only Residues
if not all(isinstance(resid, Residue) for resid in strand):
raise TypeError(f"{strand} contains non-Residue elements")
if not all(isinstance(resid, Residue) for resid in strand):
raise TypeError(f"{strand} contains non-Residue elements")

warnings.warn(
DeprecationWarning(
(
f"ResidueGroup should be used for {strand} instead"
"of giving a Residue list"
)
)
)

)
# Convert to a ResidueGroup
strand: ResidueGroup = ResidueGroup(strand)
strand: ResidueGroup = ResidueGroup(strand)

return strand

strand1: ResidueGroup = verify_strand(strand1)
strand1: ResidueGroup = verify_strand(strand1)
strand2: ResidueGroup = verify_strand(strand2)

strand_atomgroups: Tuple[List[mda.AtomGroup], List[mda.AtomGroup]] = \
self.select_strand_atoms(
strand1, strand2, n1_name, n3_name,
strand1, strand2, n1_name, n3_name,
g_name=g_name, a_name=a_name,
t_name=t_name, u_name=u_name, c_name=c_name
)
)

super(WatsonCrickDist, self).__init__(
strand_atomgroups[0], strand_atomgroups[1], **kwargs
)

)


class MinorPairDist(NucPairDist):
r"""Minor-Pair basepair distance for selected residues over a trajectory.
Takes two :class:`~MDAnalysis.core.groups.ResidueGroup` objects
as `strand1` and `strand2` and calculates the Minor-groove hydrogen
bond length between the nitrogen and oxygen atoms over the trajectory.
Bases are matched by their index in `strand1` and `strand2` (similar
``base_pairs = zip(strand1, strand2)``).
Takes two :class:`~MDAnalysis.core.groups.ResidueGroup` objects and
calculates the Minor-groove hydrogen bond length between the
nitrogen and oxygen atoms over the trajectory. Bases are
matched by their index in the two
:class:`~MDAnalysis.core.groups.ResidueGroup` provided as arguments.
Parameters
----------
Expand Down Expand Up @@ -478,17 +496,15 @@ class MinorPairDist(NucPairDist):
Attributes
----------
results.distances: numpy.ndarray
Distances are stored in a 2d numpy array with axis 0 (first index)
indexing the trajectory frame and axis 1 (second index) selecting the
Residue pair.
stored in a 2d numpy array with first index selecting
the Residue pair, and the second index selecting the frame number
times: numpy.ndarray
Simulation times for analysis.
Raises
------
ValueError
If the selections given are not the same length
ValueError:
A :class:`~MDAnalysis.core.Residue` in
one of the strands not a valid nucleic acid
ValueError
Expand All @@ -511,16 +527,16 @@ def __init__(self, strand1: ResidueGroup, strand2: ResidueGroup,
strand1, strand2, c2_name, o2_name,
g_name=g_name, a_name=a_name,
t_name=t_name, u_name=u_name, c_name=c_name
)
)

super(MinorPairDist, self).__init__(
selections[0], selections[1], **kwargs
)

)


class MajorPairDist(NucPairDist):
r"""Minor-Pair base pair distance for selected residues over a trajectory.
r"""Minor-Pair base pair distance for
selected residues over a trajectory.
Takes two :class:`~MDAnalysis.core.groups.ResidueGroup` objects and
calculates the Major-groove hydrogen bond length between the nitrogen
Expand Down Expand Up @@ -588,14 +604,14 @@ def __init__(self, strand1: ResidueGroup, strand2: ResidueGroup,
g_name: str = 'G', a_name: str = 'A', u_name: str = 'U',
t_name: str = 'T', c_name: str = 'C',
**kwargs) -> None:

selections: Tuple[List[mda.AtomGroup], List[mda.AtomGroup]] = \
self.select_strand_atoms(
strand1, strand2, o6_name, n4_name, g_name=g_name,
self.select_strand_atoms(
strand1, strand2, o6_name, n4_name, g_name=g_name,
a_name=a_name, t_name=t_name, u_name=u_name,
c_name=c_name
)
)

super(MajorPairDist, self).__init__(
selections[0], selections[1], **kwargs
)
selections[0], selections[1], **kwargs
)
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