Source code for MDAnalysis.topology.base
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# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
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# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
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"""
Base topology reader classes --- :mod:`MDAnalysis.topology.base`
================================================================
Derive topology reader classes from the base class in this module. All
topology readers raise :exc:`IOError` upon failing to read a topology
file and :exc:`ValueError` upon failing to make sense of the read data.
Classes
-------
.. autoclass:: TopologyReaderBase
:members:
:inherited-members:
"""
from __future__ import absolute_import
import six
from six.moves import zip
# While reduce is a built-in in python 2, it is not in python 3
from functools import reduce
import itertools
import numpy as np
import warnings
from .. import _PARSERS, _PARSER_HINTS
from ..coordinates.base import IOBase
from ..lib import util
class _Topologymeta(type):
"""Internal: Topology Parser registration voodoo
When classes which inherit from TopologyReaderBase are *defined*
this metaclass makes it known to MDAnalysis. The optional `format`
attribute and `_format_hint` staticmethod are read:
- `format` defines the file extension this Parser targets.
- `_format_hint` defines a function which returns a boolean if the
Parser can process a particular object
Eg::
class ThingParser(TopologyReaderBase):
format = ['foo', 'bar']
@staticmethod
_format_hint(thing):
try:
import WeirdPackage
except ImportError:
return False
return isinstance(thing, WeirdPackage.Thing)
This way there is no strict dependency on "WeirdPackage", but if
a user supplies a WeirdPackage.Thing the "ThingParser' will be able
to step up and read it.
.. versionchanged:: 1.0.0
Added format_hint functionality
"""
def __init__(cls, name, bases, classdict):
type.__init__(type, name, bases, classdict)
try:
fmt = util.asiterable(classdict['format'])
except KeyError:
pass
else:
for fmt_name in fmt:
fmt_name = fmt_name.upper()
_PARSERS[fmt_name] = cls
if '_format_hint' in classdict:
_PARSER_HINTS[fmt_name] = classdict['_format_hint'].__func__
[docs]class TopologyReaderBase(six.with_metaclass(_Topologymeta, IOBase)):
"""Base class for topology readers
Parameters
----------
filename : str
name of the topology file
universe : Universe, optional
Supply a Universe to the Parser. This then passes it to the
atom instances that are created within parsers.
All topology readers must define a `parse` method which
returns a Topology object
Raises
------
* :exc:`IOError` upon failing to read a topology file
* :exc:`ValueError` upon failing to make sense of the read data
.. versionadded:: 0.9.0
.. versionchanged:: 0.9.2
Added keyword 'universe' to pass to Atom creation.
"""
def __init__(self, filename):
self.filename = filename
def parse(self, **kwargs): # pragma: no cover
raise NotImplementedError("Override this in each subclass")
def squash_by(child_parent_ids, *attributes):
"""Squash a child-parent relationship
Arguments
---------
child_parent_ids - array of ids (unique values that identify the parent)
*attributes - other arrays that need to follow the sorting of ids
Returns
-------
child_parents_idx - an array of len(child) which points to the index of
parent
parent_ids - len(parent) of the ids
*parent_attrs - len(parent) of the other attributes
"""
unique_resids, sort_mask, atom_idx = np.unique(
child_parent_ids, return_index=True, return_inverse=True)
return atom_idx, unique_resids, [attr[sort_mask] for attr in attributes]
def change_squash(criteria, to_squash):
"""Squash per atom data to per residue according to changes in resid
Parameters
----------
criteria : list of numpy ndarray
Arrays which when changing indicate a new residue
to_squash : list of numpy arrays
Arrays which get squashed according to the criteria arrays
Returns
-------
residx : numpy array
The Residue *index* that each Atom gets assigned to. [len(resids)]
squashed : numpy array
The to_squash arrays reduced down to per Residue values
Example
-------
resids = np.array([2, 2, 3, 3, 2, 2])
resnames = np.array(['RsA', 'RsA', 'RsB', 'RsB', 'RsC', 'RsC'])
segids = np.array(['A', 'A', 'A', 'A', 'B', 'B'])
residx, (new_resids, new_resnames, new_segids) = resid_change_squash(
(resids,), (resids, resnames, segids))
# Per atom res index
residx: [0, 0, 1, 1, 2, 2]
# Per residue record of each attribute
new_resids: [2, 3, 2]
new_resnames: ['RsA', 'RsB', 'RsC']
new_segids: ['A', 'A', 'B']
"""
def get_borders(*arrays):
"""Generator of indices to slice arrays when they change"""
borders = np.nonzero(reduce(np.logical_or,
(a[:-1] != a[1:] for a in arrays)))
# Add Nones so we can slice from start to end
return [None] + list(borders[0] + 1) + [None]
l0 = len(criteria[0])
if not all(len(other) == l0
for other in itertools.chain(criteria[1:], to_squash)):
raise ValueError("All arrays must be equally sized")
# 1) Detect where resids change
borders = get_borders(*criteria)
# Number of groups = number of changes + 1
# 2 `None`s have been added, so -1
nres = len(borders) - 1
# 2) Allocate new arrays
# Per atom record of what residue they belong to
residx = np.zeros_like(criteria[0], dtype=int)
# Per residue record of various attributes
new_others = [np.zeros(nres, dtype=o.dtype) for o in to_squash]
# 3) Slice through resids and others to find values
for i, (x, y) in enumerate(zip(borders[:-1], borders[1:])):
residx[x:y] = i # atoms between x & y are in the i'th residue
for old, new in zip(to_squash, new_others):
new[i] = old[x:y][0] # TODO: Check that x:y is the same
# Should be the same for self consistency...
return residx, new_others
def reduce_singular(values):
"""Returns the value in an array of length 1, or
the tuple of an array with a longer lengh.
Parameters
----------
values: array-like
Array to squash
Returns
-------
values: tuple or single value
"""
if len(values) == 1:
return values[0]
else:
return tuple(values)