def contact_matrix(coord, cutoff=15.0, returntype="numpy", box=None):
'''Calculates a matrix of contacts within a numpy array of type float32.
There is a fast, high-memory-usage version for small systems
(*returntype* = 'numpy'), and a slower, low-memory-usage version for
larger systems (*returntype* = 'sparse').
If *box* dimensions are passed (``box = [Lx, Ly, Lz]``), then
periodic boundary conditions are applied. Only orthorhombic boxes
are currently supported.
.. versionchanged:: 0.11.0
Keyword *suppress_progmet* and *progress_meter_freq* were removed.
'''
if returntype == "numpy":
adj = (distance_array(coord, coord, box=box) < cutoff)
return adj
elif returntype == "sparse":
# Initialize square List of Lists matrix of dimensions equal to number of coordinates passed
sparse_contacts = sparse.lil_matrix((len(coord), len(coord)), dtype='bool')
if box is not None:
# if PBC
contact_matrix_pbc(coord, sparse_contacts, box, cutoff)
else:
# if no PBC
contact_matrix_no_pbc(coord, sparse_contacts, cutoff)
return sparse_contacts
def contact_matrix(coord, cutoff=15.0, returntype="numpy", box=None):
'''Calculates a matrix of contacts within a numpy array of type float32.
There is a fast, high-memory-usage version for small systems
(*returntype* = 'numpy'), and a slower, low-memory-usage version for
larger systems (*returntype* = 'sparse').
If *box* dimensions are passed (``box = [Lx, Ly, Lz]``), then
periodic boundary conditions are applied. Only orthorhombic boxes
are currently supported.
.. versionchanged:: 0.11.0
Keyword *suppress_progmet* and *progress_meter_freq* were removed.
'''
if returntype == "numpy":
adj = (distance_array(coord, coord, box=box) < cutoff)
return adj
elif returntype == "sparse":
# Initialize square List of Lists matrix of dimensions equal to number of coordinates passed
sparse_contacts = sparse.lil_matrix((len(coord), len(coord)),
dtype='bool')
if box is not None:
# if PBC
contact_matrix_pbc(coord, sparse_contacts, box, cutoff)
else:
# if no PBC
contact_matrix_no_pbc(coord, sparse_contacts, cutoff)
return sparse_contacts
def contact_matrix(coord, cutoff=15.0, returntype="numpy", box=None):
'''Calculates a matrix of contacts.
There is a fast, high-memory-usage version for small systems
(*returntype* = 'numpy'), and a slower, low-memory-usage version for
larger systems (*returntype* = 'sparse').
If *box* dimensions are passed then periodic boundary conditions
are applied.
Parameters
---------
coord : array
Array of coordinates of shape ``(N, 3)`` and dtype float32.
cutoff : float, optional, default 15
Particles within `cutoff` are considered to form a contact.
returntype : string, optional, default "numpy"
Select how the contact matrix is returned.
* ``"numpy"``: return as an ``(N. N)`` :class:`numpy.ndarray`
* ``"sparse"``: return as a :class:`scipy.sparse.lil_matrix`
box : array-like or ``None``, optional, default ``None``
Simulation cell dimensions in the form of
:attr:`MDAnalysis.trajectory.base.Timestep.dimensions` when
periodic boundary conditions should be taken into account for
the calculation of contacts.
Returns
-------
array or sparse matrix
The contact matrix is returned in a format determined by the `returntype`
keyword.
See Also
--------
:mod:`MDAnalysis.analysis.contacts` for native contact analysis
.. versionchanged:: 0.11.0
Keyword *suppress_progmet* and *progress_meter_freq* were removed.
'''
if returntype == "numpy":
adj = (distance_array(coord, coord, box=box) < cutoff)
return adj
elif returntype == "sparse":
# Initialize square List of Lists matrix of dimensions equal to number
# of coordinates passed
sparse_contacts = scipy.sparse.lil_matrix((len(coord), len(coord)),
dtype='bool')
if box is not None:
# with PBC
contact_matrix_pbc(coord, sparse_contacts, box, cutoff)
else:
# without PBC
contact_matrix_no_pbc(coord, sparse_contacts, cutoff)
return sparse_contacts
def contact_matrix(coord, cutoff=15.0, returntype="numpy", box=None):
'''Calculates a matrix of contacts.
There is a fast, high-memory-usage version for small systems
(*returntype* = 'numpy'), and a slower, low-memory-usage version for
larger systems (*returntype* = 'sparse').
If *box* dimensions are passed then periodic boundary conditions
are applied.
Parameters
---------
coord : array
Array of coordinates of shape ``(N, 3)`` and dtype float32.
cutoff : float, optional, default 15
Particles within `cutoff` are considered to form a contact.
returntype : string, optional, default "numpy"
Select how the contact matrix is returned.
* ``"numpy"``: return as an ``(N. N)`` :class:`numpy.ndarray`
* ``"sparse"``: return as a :class:`scipy.sparse.lil_matrix`
box : array-like or ``None``, optional, default ``None``
Simulation cell dimensions in the form of
:attr:`MDAnalysis.trajectory.base.Timestep.dimensions` when
periodic boundary conditions should be taken into account for
the calculation of contacts.
Returns
-------
array or sparse matrix
The contact matrix is returned in a format determined by the `returntype`
keyword.
See Also
--------
:mod:`MDAnalysis.analysis.contacts` for native contact analysis
.. versionchanged:: 0.11.0
Keyword *suppress_progmet* and *progress_meter_freq* were removed.
'''
if returntype == "numpy":
adj = (distance_array(coord, coord, box=box) < cutoff)
return adj
elif returntype == "sparse":
# Initialize square List of Lists matrix of dimensions equal to number
# of coordinates passed
sparse_contacts = scipy.sparse.lil_matrix((len(coord), len(coord)), dtype='bool')
if box is not None:
# with PBC
contact_matrix_pbc(coord, sparse_contacts, box, cutoff)
else:
# without PBC
contact_matrix_no_pbc(coord, sparse_contacts, cutoff)
return sparse_contacts
def contact_matrix(coord, cutoff=15.0, returntype="numpy", box=None):
'''Calculates a matrix of contacts.
There is a fast, high-memory-usage version for small systems
(*returntype* = 'numpy'), and a slower, low-memory-usage version for
larger systems (*returntype* = 'sparse').
If *box* dimensions are passed then periodic boundary conditions
are applied.
Parameters
---------
coord : array
Array of coordinates of shape ``(N, 3)`` and dtype float32.
cutoff : float, optional, default 15
Particles within `cutoff` are considered to form a contact.
returntype : string, optional, default "numpy"
Select how the contact matrix is returned.
* ``"numpy"``: return as an ``(N. N)`` :class:`numpy.ndarray`
* ``"sparse"``: return as a :class:`scipy.sparse.lil_matrix`
box : array-like or ``None``, optional, default ``None``
Simulation cell dimensions in the form of
:attr:`MDAnalysis.trajectory.base.Timestep.dimensions` when
periodic boundary conditions should be taken into account for
the calculation of contacts.
Returns
-------
array or sparse matrix
The contact matrix is returned in a format determined by the `returntype`
keyword.
Note
----
:module:`scipy.sparse` is require for using *sparse* matrices; if it cannot
be imported then an `ImportError` is raised.
.. versionchanged:: 0.11.0
Keyword *suppress_progmet* and *progress_meter_freq* were removed.
'''
if returntype == "numpy":
adj = (distance_array(coord, coord, box=box) < cutoff)
return adj
elif returntype == "sparse":
if sparse is None:
# hack: if we are running with minimal dependencies then scipy was
# not imported and we have to bail here (see scipy import at top)
raise ImportError("For sparse matrix functionality you need to "
"import scipy.")
# Initialize square List of Lists matrix of dimensions equal to number
# of coordinates passed
sparse_contacts = sparse.lil_matrix((len(coord), len(coord)), dtype='bool')
if box is not None:
# with PBC
contact_matrix_pbc(coord, sparse_contacts, box, cutoff)
else:
# without PBC
contact_matrix_no_pbc(coord, sparse_contacts, cutoff)
return sparse_contacts