def select_model(model=None):
"""Select the Frame Order model.
@param model: The Frame Order model. This can be one of 'pseudo-ellipse', 'pseudo-ellipse, torsionless', 'pseudo-ellipse, free rotor', 'iso cone', 'iso cone, torsionless', 'iso cone, free rotor', 'rotor', 'rigid', 'free rotor', 'double rotor'.
@type model: str
"""
# Test if the current data pipe exists.
check_pipe()
# Test if the model name exists.
if not model in MODEL_LIST:
raise RelaxError("The model name '%s' is invalid, it must be one of %s." % (model, MODEL_LIST))
# Set the model
cdp.model = model
# Initialise the list of model parameters.
cdp.params = []
# Set the integration method if needed.
if not hasattr(cdp, 'quad_int'):
# Scipy quadratic numerical integration.
if cdp.model in []:
cdp.quad_int = True
# Quasi-random numerical integration.
else:
cdp.quad_int = False
# Update the model.
update_model()
def select_model(model=None):
"""Select the Frame Order model.
@param model: The Frame Order model. This can be one of 'pseudo-ellipse', 'pseudo-ellipse, torsionless', 'pseudo-ellipse, free rotor', 'iso cone', 'iso cone, torsionless', 'iso cone, free rotor', 'rotor', 'rigid', 'free rotor', 'double rotor'.
@type model: str
"""
# Test if the current data pipe exists.
check_pipe()
# Test if the model name exists.
if not model in MODEL_LIST:
raise RelaxError(
"The model name '%s' is invalid, it must be one of %s." %
(model, MODEL_LIST))
# Set the model
cdp.model = model
# Initialise the list of model parameters.
cdp.params = []
# Set the integration method if needed.
if not hasattr(cdp, 'quad_int'):
# Scipy quadratic numerical integration.
if cdp.model in []:
cdp.quad_int = True
# Quasi-random numerical integration.
else:
cdp.quad_int = False
# Update the model.
update_model()
def get_param_names(self, model_info=None):
"""Return a vector of parameter names.
@keyword model_info: The model information from model_loop(). This is unused.
@type model_info: None
@return: The vector of parameter names.
@rtype: list of str
"""
# First update the model, if needed.
update_model(verbosity=0)
# Return the parameter list object.
return cdp.params
def get_param_names(self, model_info=None):
"""Return a vector of parameter names.
@keyword model_info: The model information from model_loop(). This is unused.
@type model_info: None
@return: The vector of parameter names.
@rtype: list of str
"""
# First update the model, if needed.
update_model(verbosity=0)
# Return the parameter list object.
return cdp.params
def pivot(pivot=None, order=1, fix=False):
"""Set the pivot point for the 2 body motion.
@keyword pivot: The pivot point of the two bodies (domains, etc.) in the structural coordinate system.
@type pivot: list of num
@keyword order: The ordinal number of the pivot point. The value of 1 is for the first pivot point, the value of 2 for the second pivot point, and so on.
@type order: int
@keyword fix: A flag specifying if the pivot point should be fixed during optimisation.
@type fix: bool
"""
# Test if the current data pipe exists.
check_pipe()
# Store the fixed flag.
cdp.pivot_fixed = fix
# No pivot given, so update the model if needed and quit.
if pivot is None:
if hasattr(cdp, 'model'):
update_model()
return
# Convert the pivot to a numpy array.
pivot = array(pivot, float64)
# Check the pivot validity.
is_float_array(pivot, name='pivot point', size=3)
# Store the pivot point and fixed flag.
if order == 1:
cdp.pivot_x = pivot[0]
cdp.pivot_y = pivot[1]
cdp.pivot_z = pivot[2]
else:
# The variable names.
name_x = 'pivot_x_%i' % order
name_y = 'pivot_y_%i' % order
name_z = 'pivot_z_%i' % order
# Store the variables.
setattr(cdp, name_x, pivot[0])
setattr(cdp, name_y, pivot[1])
setattr(cdp, name_z, pivot[2])
# Update the model.
if hasattr(cdp, 'model'):
update_model()
def pivot(pivot=None, order=1, fix=False):
"""Set the pivot point for the 2 body motion.
@keyword pivot: The pivot point of the two bodies (domains, etc.) in the structural coordinate system.
@type pivot: list of num
@keyword order: The ordinal number of the pivot point. The value of 1 is for the first pivot point, the value of 2 for the second pivot point, and so on.
@type order: int
@keyword fix: A flag specifying if the pivot point should be fixed during optimisation.
@type fix: bool
"""
# Test if the current data pipe exists.
check_pipe()
# Store the fixed flag.
cdp.pivot_fixed = fix
# No pivot given, so update the model if needed and quit.
if pivot is None:
if hasattr(cdp, 'model'):
update_model()
return
# Convert the pivot to a numpy array.
pivot = array(pivot, float64)
# Check the pivot validity.
is_float_array(pivot, name='pivot point', size=3)
# Store the pivot point and fixed flag.
if order == 1:
cdp.pivot_x = pivot[0]
cdp.pivot_y = pivot[1]
cdp.pivot_z = pivot[2]
else:
# The variable names.
name_x = 'pivot_x_%i' % order
name_y = 'pivot_y_%i' % order
name_z = 'pivot_z_%i' % order
# Store the variables.
setattr(cdp, name_x, pivot[0])
setattr(cdp, name_y, pivot[1])
setattr(cdp, name_z, pivot[2])
# Update the model.
if hasattr(cdp, 'model'):
update_model()
def ref_domain(ref=None):
"""Set the reference domain for the frame order, multi-domain models.
@param ref: The reference domain.
@type ref: str
"""
# Checks.
check_pipe()
check_domain(domain=ref, escalate=0)
# Set the reference domain.
cdp.ref_domain = ref
# Update the model.
if hasattr(cdp, 'model'):
update_model()
def ref_domain(ref=None):
"""Set the reference domain for the frame order, multi-domain models.
@param ref: The reference domain.
@type ref: str
"""
# Checks.
check_pipe()
check_domain(domain=ref, escalate=0)
# Set the reference domain.
cdp.ref_domain = ref
# Update the model.
if hasattr(cdp, 'model'):
update_model()