"""Classes and functions for computing and manipulating accessible
surface areas (ASA)."""
from cogent.struct.selection import einput
from cogent.struct.annotation import xtradata
from cogent.maths.geometry import coords_to_symmetry, \
coords_to_crystal
from _contact import cnt_loop
from collections import defaultdict
from numpy import array, r_, sqrt, int64
__author__ = "Marcin Cieslik"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Marcin Cieslik"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Marcin Cieslik"
__email__ = "mpc4p@virginia.edu"
__status__ = "Development"
def _prepare_contacts(query, model=None, level='A', search_limit=6.0, \
contact_mode='diff_chain', symmetry_mode=None, \
crystal_mode=None, **kwargs):
"""Prepares distance contact calculations.
Arguments:
- query(entitie[s]): query entitie[s] for contact calculation
(most commonly a structure entity).
- model(entity): a Model entity which will be transformed according to
symmetry_mode and crystal_mode. (most commonly it is the same as the
query)
- level(str): The level in the hierarchy at which distances will be
calculated (most commonly 'A' for atoms)
- search_limit(float): maximum distance in Angstrom's
- contact_mode(str): One of "diff_cell", "diff_sym", "diff_chain".
Defines the allowed contacts i.e. requires that contacts are by
entities, which have: "diff_cell" different unit cells; "diff_sym"
different symmetry operators (if in the same unit cell) "diff_chain"
with different chain ids (if in the same unit cell and symmetry).
- symmetry_mode (str): One of 'uc', 'bio' or 'table'. This defines the
transformations of applied to the coordinates of the input entities.
It is one of 'bio', 'uc' or 'table'. Where 'bio' and 'uc' are
transformations to create the biological molecule or unit-cell from
the PDB header. The 'table' uses transformation matrices derived from
space-group information only using crystallographic tables(requires
``cctbx``).
- crystal_mode (int): Defines the number of unit-cells to expand the
initial unit-cell into. The number of unit cells in each direction
i.e. 1 is makes a total of 27 unit cells: (-1, 0, 1) == 3, 3^3 == 27
Additional arguments are passed to the ``cnt_loop`` Cython function.
"""
contact_mode = {'diff_asu' :0,
'diff_sym' :1,
'diff_chain':2 }[contact_mode]
# determine unique structure
structure = einput(query, 'S').values()[0]
sh = structure.header
# if not specified otherwise the lattice is the first model
lattice = model or structure[(0,)]
lents = einput(lattice, level)
lents_ids = lents.getData('getFull_id', forgiving=False, method=True)
lcoords = array(lents.getData('coords', forgiving=False))
qents = einput(query, level)
qents_ids = qents.getData('getFull_id', forgiving=False, method=True)
qcoords = array(qents.getData('coords', forgiving=False))
if symmetry_mode:
if symmetry_mode == 'table':
lcoords = coords_to_symmetry(lcoords, \
sh['table_fmx'], \
sh['table_omx'], \
sh['table_mxs'], \
symmetry_mode)
elif symmetry_mode == 'uc':
lcoords = coords_to_symmetry(lcoords, \
sh['uc_fmx'], \
sh['uc_omx'], \
sh['uc_mxs'], \
symmetry_mode)
elif symmetry_mode == 'bio':
# TODO see asa
raise ValueError("Unsupported symmetry_mode: %s" % symmetry_mode)
else:
raise ValueError("Unsupported symmetry_mode: %s" % symmetry_mode)
else:
lcoords = array([lcoords]) # fake 3D
if crystal_mode:
zero_tra = {1:13, 2:62, 3:171}[crystal_mode]
# 0,0,0 translation is: Thickened cube numbers:
# a(n)=n*(n^2+(n-1)^2)+(n-1)*2*n*(n-1).
# 1, 14, 63, 172, 365, 666, 1099, 1688, 2457, 3430, 4631, 6084, 7813 ...
if symmetry_mode == 'table':
lcoords = coords_to_crystal(lcoords, \
sh['table_fmx'], \
sh['table_omx'], \
crystal_mode)
elif symmetry_mode == 'uc':
lcoords = coords_to_crystal(lcoords, \
sh['uc_fmx'], \
sh['uc_omx'], \
crystal_mode)
else:
raise ValueError('crystal_mode not possible for "bio" symmetry')
else:
zero_tra = 0
lcoords = array([lcoords]) # fake 4D
shape = lcoords.shape
lcoords = lcoords.reshape((shape[0] * shape[1] * shape[2], shape[3]))
box = r_[qcoords.min(axis=0) - search_limit, \
qcoords.max(axis=0) + search_limit]
lc = [] # lattice chain
qc = [] # query chain
lchains = [i[2] for i in lents_ids]
qchains = [i[2] for i in qents_ids]
allchains = set()
allchains.update(lchains)
allchains.update(qchains)
chain2id = dict(zip(allchains, range(len(allchains))))
for lent_id in lents_ids:
lc.append(chain2id[lent_id[2]])
for qent_id in qents_ids:
qc.append(chain2id[qent_id[2]])
lc = array(lc, dtype=int64)
qc = array(qc, dtype=int64)
# here we leave python
(idxc, n_src, n_asu, n_sym, n_tra, n_dst) = cnt_loop(\
qcoords, lcoords, qc, lc, shape[1], shape[2], \
zero_tra, contact_mode, search_limit, box, \
**kwargs)
result = defaultdict(dict)
for contact in xrange(idxc):
qent_id = qents_ids[n_src[contact]]
lent_id = lents_ids[n_asu[contact]]
result[qent_id][lent_id] = (sqrt(n_dst[contact]), n_tra[contact], n_sym[contact])
return result
def contacts_xtra(query, xtra_key=None, **cnt_kwargs):
"""Finds distance contacts between entities. This function searches for
contacts for query entities (query) either within the asymmetric unit,
biological molecule, unit-cell or crystal.
Arguments:
- query (entitie[s]): query entity or sequence entities
- xtra_key (str): name of the key
Additional keyworded arguments are passed to the ``_prepare_contacts``
functon.
"""
xtra_key = xtra_key or 'CONTACTS'
structures = einput(query, 'S')
if len(structures.values()) > 1:
raise ValueError('Entities from multiple structures are not supported.')
result = _prepare_contacts(query, **cnt_kwargs) # calculate CONTACTS
result = dict([(id, {xtra_key:v}) for id, v in result.iteritems()])
xtradata(result, structures)
return result
