def constraint_dct(zma, const_names, var_names=()):
""" Build a dictionary of constraints
has to round the values for the filesystem
"""
# Get the list names sorted for dictionary
rnames = (name for name in const_names if 'R' in name)
anames = (name for name in const_names if 'A' in name)
dnames = (name for name in const_names if 'D' in name)
rnames = tuple(sorted(rnames, key=lambda x: int(x.split('R')[1])))
anames = tuple(sorted(anames, key=lambda x: int(x.split('A')[1])))
dnames = tuple(sorted(dnames, key=lambda x: int(x.split('D')[1])))
constraint_names = rnames + anames + dnames
# Remove the scan coordinates so they are not placed in the dict
constraint_names = tuple(name for name in constraint_names
if name not in var_names)
# Build dictionary
if constraint_names:
zma_vals = value_dictionary(zma)
zma_coords = coordinates(zma)
assert set(constraint_names) <= set(zma_coords.keys()), (
'Attempting to constrain coordinates not in zma:'
f'\n{constraint_names}\n{zma_coords}')
_dct = dict(
zip(constraint_names,
(round(zma_vals[name], 2) for name in constraint_names)))
else:
_dct = None
return _dct
def bond_key_from_idxs(zma, idxs):
"""given indices of involved bonded atoms, return bond name
"""
idxs = list(idxs)
idxs.sort(reverse=True)
idxs = tuple(idxs)
bond_key = None
coords = coordinates(zma)
for key in coords:
for coord in coords.get(key, [None]):
if idxs == coord:
bond_key = key
return bond_key
def dihedral_axis_name(zma, axis):
""" gives this name of a dihedral angle that has
the given axis atoms
"""
coords = coordinates(zma)
angles = dihedral_angle_names(zma)
name = None
for ang in angles:
_coord_idxs = coords[ang]
if (tuple(list(_coord_idxs[0])[1:3]) == axis
or tuple(list(_coord_idxs[0])[3:1:-1]) == axis):
name = ang
break
return name
def set_constraint_names(zma, tors_names, tors_model):
""" Determine the names of constraints along a torsion scan
"""
constraint_models = ('1dhrf', '1dhrfa', 'tau-1dhrf', 'tau-1dhrfa')
const_names = tuple()
if tors_names and tors_model in constraint_models:
if tors_model in ('1dhrf', 'tau-1dhrf'):
const_names = tuple(itertools.chain(*tors_names))
elif tors_model in ('1dhrfa', 'tau-1dhrfa'):
coords = list(coordinates(zma))
const_names = tuple(coord for coord in coords)
return const_names
def dihedral_axis_name(zma, axis):
""" gives this name of a dihedral angle that has
the given axis atoms
currently fails if indices of axis not in zma, i.e.
if 5,1 in zma, code fails if 1,5 given
"""
coords = coordinates(zma)
angles = dihedral_angle_names(zma)
name = None
for ang in angles:
_coord_idxs = coords[ang]
if (tuple(list(_coord_idxs[0])[1:3]) == axis
or tuple(list(_coord_idxs[0])[3:1:-1]) == axis):
name = ang
break
return name
def coord_idxs(zma, key):
"""give a bond length key, return the indices of involved bonded atoms
"""
coords = coordinates(zma)
idxs = coords.get(key, [None])
return idxs[0]
def coordinates(zma, shift=0, multi=True):
""" coordinate keys associated with each coordinate name,
as a dictionary
"""
return vmat.coordinates(vmatrix(zma), shift=shift, multi=multi)