def _prepare_asa(entities, symmetry_mode=None, crystal_mode=None, points=960, \
**kwargs):
"""Prepares the atomic solvent-accessible surface area (ASA) calculation.
Arguments:
- entities: input entities for ASA calculation (most commondly a
structure entity).
- 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
- points: number of points on atom spheres higher is slower but more
accurate.
Additional keyworded arguments are passed to the ``_run_asa`` function.
"""
# generate uniform points on the unit-sphere
spoints = sphere_points(points)
# prepare entities for asa calculation
# free-floating area mode
result = {}
atoms = einput(entities, 'A')
if not symmetry_mode and not crystal_mode:
coords = array(atoms.getData('coords', forgiving=False))
coords = array([[coords]]) # fake 3D and 4D
idx_to_id = dict(enumerate(atoms.getData('getFull_id', \
forgiving=False, method=True)))
asas = _run_asa(atoms, coords, spoints, **kwargs)
for idx in xrange(asas.shape[0]):
result[idx_to_id[idx]] = asas[idx]
# crystal-contact area mode
elif symmetry_mode in ('table', 'uc'):
structure = einput(entities, 'S').values()[0]
sh = structure.header
coords = array(atoms.getData('coords', forgiving=False))
idx_to_id = dict(enumerate(atoms.getData('getFull_id', \
forgiving=False, method=True)))
# expand to unit-cell, real 3D
coords = coords_to_symmetry(coords, \
sh[symmetry_mode + '_fmx'], \
sh[symmetry_mode + '_omx'], \
sh[symmetry_mode + '_mxs'], \
symmetry_mode)
# expand to crystal, real 4D
if crystal_mode:
coords = coords_to_crystal(coords, \
sh[symmetry_mode + '_fmx'], \
sh[symmetry_mode + '_omx'], \
crystal_mode) # real 4D
else:
coords = array([coords]) # fake 4D
asas = _run_asa(atoms, coords, spoints, **kwargs)
for idx in xrange(asas.shape[0]):
result[idx_to_id[idx]] = asas[idx]
# biological area mode
elif symmetry_mode == 'bio':
structure = einput(entities, 'S').values()[0]
chains = einput(entities, 'C')
sh = structure.header
start = 0
for chain_ids, mx_num in sh['bio_cmx']:
sel = chains.selectChildren(chain_ids, 'contains', 'id').values()
atoms = einput(sel, 'A')
coords = array(atoms.getData('coords', forgiving=False))
idx_to_id = dict(enumerate(atoms.getData('getFull_id', \
forgiving=False, method=True)))
stop = start + mx_num
coords = coords_to_symmetry(coords, \
sh['uc_fmx'], \
sh['uc_omx'], \
sh['bio_mxs'][start:stop], \
symmetry_mode)
coords = array([coords])
start = stop
asas = _run_asa(atoms, coords, spoints, **kwargs)
for idx in xrange(asas.shape[0]):
result[idx_to_id[idx]] = asas[idx]
return result
def test_sphere_points(self):
"""tests sphere points"""
self.assertEquals(sphere_points(1), array([[1., 0., 0.]]))
def _prepare_asa(entities, symmetry_mode=None, crystal_mode=None, points=960, \
**kwargs):
"""Prepares the atomic solvent-accessible surface area (ASA) calculation.
Arguments:
- entities: input entities for ASA calculation (most commondly a
structure entity).
- 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
- points: number of points on atom spheres higher is slower but more
accurate.
Additional keyworded arguments are passed to the ``_run_asa`` function.
"""
# generate uniform points on the unit-sphere
spoints = sphere_points(points)
# prepare entities for asa calculation
# free-floating area mode
result = {}
atoms = einput(entities, 'A')
if not symmetry_mode and not crystal_mode:
coords = array(atoms.getData('coords', forgiving=False))
coords = array([[coords]]) # fake 3D and 4D
idx_to_id = dict(enumerate(atoms.getData('getFull_id', \
forgiving=False, method=True)))
asas = _run_asa(atoms, coords, spoints, **kwargs)
for idx in xrange(asas.shape[0]):
result[idx_to_id[idx]] = asas[idx]
# crystal-contact area mode
elif symmetry_mode in ('table', 'uc'):
structure = einput(entities, 'S').values()[0]
sh = structure.header
coords = array(atoms.getData('coords', forgiving=False))
idx_to_id = dict(enumerate(atoms.getData('getFull_id', \
forgiving=False, method=True)))
# expand to unit-cell, real 3D
coords = coords_to_symmetry(coords, \
sh[symmetry_mode + '_fmx'], \
sh[symmetry_mode + '_omx'], \
sh[symmetry_mode + '_mxs'], \
symmetry_mode)
# expand to crystal, real 4D
if crystal_mode:
coords = coords_to_crystal(coords, \
sh[symmetry_mode + '_fmx'], \
sh[symmetry_mode + '_omx'], \
crystal_mode) # real 4D
else:
coords = array([coords]) # fake 4D
asas = _run_asa(atoms, coords, spoints, **kwargs)
for idx in xrange(asas.shape[0]):
result[idx_to_id[idx]] = asas[idx]
# biological area mode
elif symmetry_mode == 'bio':
structure = einput(entities, 'S').values()[0]
chains = einput(entities, 'C')
sh = structure.header
start = 0
for chain_ids, mx_num in sh['bio_cmx']:
sel = chains.selectChildren(chain_ids, 'contains', 'id').values()
atoms = einput(sel, 'A')
coords = array(atoms.getData('coords', forgiving=False))
idx_to_id = dict(enumerate(atoms.getData('getFull_id', \
forgiving=False, method=True)))
stop = start + mx_num
coords = coords_to_symmetry(coords, \
sh['uc_fmx'], \
sh['uc_omx'], \
sh['bio_mxs'][start:stop], \
symmetry_mode)
coords = array([coords])
start = stop
asas = _run_asa(atoms, coords, spoints, **kwargs)
for idx in xrange(asas.shape[0]):
result[idx_to_id[idx]] = asas[idx]
return result
def test_sphere_points(self):
"""tests sphere points"""
self.assertEquals(sphere_points(1), array([[ 1., 0., 0.]]))