Author: bugman
Date: Wed Nov 25 09:44:55 2009
New Revision: 9958
URL: http://svn.gna.org/viewcvs/relax?rev=9958&view=rev
Log:
Separation of all the non-API frame order specific methods.
Modified:
1.3/specific_fns/frame_order.py
Modified: 1.3/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/frame_order.py?rev=9958&r1=9957&r2=9958&view=diff
==============================================================================
--- 1.3/specific_fns/frame_order.py (original)
+++ 1.3/specific_fns/frame_order.py Wed Nov 25 09:44:55 2009
@@ -66,6 +66,130 @@
return array([cdp.alpha, cdp.beta, cdp.gamma, cdp.theta_axis,
cdp.phi_axis, cdp.theta_cone], float64)
+ def _back_calc(self):
+ """Back-calculation of the reduced alignment tensor.
+
+ @return: The reduced alignment tensors.
+ @rtype: numpy array
+ """
+
+ # Get the parameter vector.
+ param_vector = self._assemble_param_vector()
+
+ # Get the data structures for optimisation using the tensors as base
data sets.
+ full_tensors, red_tensors, red_tensor_err, full_in_ref_frame =
self._minimise_setup_tensors()
+
+ # Set up the optimisation function.
+ target = frame_order.Frame_order(model=cdp.model,
full_tensors=full_tensors, red_tensors=red_tensors,
red_errors=red_tensor_err, full_in_ref_frame=full_in_ref_frame)
+
+ # Make a single function call. This will cause back calculation and
the data will be stored in the class instance.
+ target.func(param_vector)
+
+ # Return the reduced tensors.
+ return target.red_tensors_bc
+
+
+ def _cone_pdb(self, size=30.0, file=None, dir=None, inc=40, force=False):
+ """Create a PDB file containing a geometric object representing the
Frame Order cone models.
+
+ @param size: The size of the geometric object in Angstroms.
+ @type size: float
+ @param inc: The number of increments for the filling of the
cone objects.
+ @type inc: int
+ @param file: The name of the PDB file to create.
+ @type file: str
+ @param dir: The name of the directory to place the PDB file
into.
+ @type dir: str
+ @param force: Flag which if set to True will cause any
pre-existing file to be
+ overwritten.
+ @type force: bool
+ """
+
+ # Test if the current data pipe exists.
+ pipes.test()
+
+ # Test the model.
+ if not cdp.model in ['iso cone']:
+ raise RelaxError("A cone PDB representation of the '%s' model
cannot be made." % cdp.model)
+
+ # Test for the data structures.
+ if not hasattr(cdp, 'theta_cone'):
+ raise RelaxError("The cone angle theta_cone does not exist.")
+ if not hasattr(cdp, 'theta_axis'):
+ raise RelaxError("The cone polar angle theta_axis does not
exist.")
+ if not hasattr(cdp, 'phi_axis'):
+ raise RelaxError("The cone azimuthal angle phi_axis does not
exist.")
+ if not hasattr(cdp, 'pivot'):
+ raise RelaxError("The pivot point for the cone motion has not
been set.")
+
+ # The cone axis.
+ cone_axis = zeros(3, float64)
+ generate_vector(cone_axis, cdp.theta_axis, cdp.phi_axis)
+ print(("Cone axis: %s." % cone_axis))
+ print(("Cone angle: %s." % cdp.theta_cone))
+
+ # Cone axis from simulations.
+ num_sim = 0
+ cone_axis_sim = None
+ cone_axis_sim_new = None
+ if hasattr(cdp, 'sim_number'):
+ num_sim = cdp.sim_number
+ cone_axis_sim = zeros((num_sim, 3), float64)
+ for i in range(num_sim):
+ generate_vector(cone_axis_sim[i], cdp.theta_axis_sim[i],
cdp.phi_axis_sim[i])
+
+ # Create a positive and negative cone.
+ for factor in [-1, 1]:
+ # Negative prefix.
+ prefix = ''
+ if factor == -1:
+ prefix = 'neg_'
+
+ # The rotation matrix (rotation from the z-axis to the cone
axis).
+ R = zeros((3, 3), float64)
+ two_vect_to_R(array([0, 0, 1], float64), cone_axis, R)
+
+ # Mirroring.
+ cone_axis_new = factor*cone_axis
+ if cone_axis_sim != None:
+ cone_axis_sim_new = factor*cone_axis_sim
+ if factor == -1:
+ R = -R
+
+ # Create the structural object.
+ structure = Internal()
+
+ # Add a molecule.
+ structure.add_molecule(name='iso cone')
+
+ # Alias the single molecule from the single model.
+ mol = structure.structural_data[0].mol[0]
+
+ # Add the pivot point.
+ mol.atom_add(pdb_record='HETATM', atom_num=1, atom_name='R',
res_name='PIV', res_num=1, pos=cdp.pivot, element='C')
+
+ # Generate the axis vectors.
+ print("\nGenerating the axis vectors.")
+ res_num = generate_vector_residues(mol=mol,
vector=cone_axis_new, atom_name='Axis', res_name_vect='AXE',
sim_vectors=cone_axis_sim_new, res_num=2, origin=cdp.pivot, scale=size)
+
+ # Generate the cone outer edge.
+ print("\nGenerating the cone outer edge.")
+ edge_start_atom = mol.atom_num[-1]+1
+ cone_edge(mol=mol, res_name='CON', res_num=3+num_sim,
apex=cdp.pivot, R=R, angle=cdp.theta_cone, length=size, inc=inc)
+
+ # Generate the cone cap, and stitch it to the cone edge.
+ print("\nGenerating the cone cap.")
+ cone_start_atom = mol.atom_num[-1]+1
+ generate_vector_dist(mol=mol, res_name='CON', res_num=3+num_sim,
centre=cdp.pivot, R=R, max_angle=cdp.theta_cone, scale=size, inc=inc)
+ stitch_cone_to_edge(mol=mol, cone_start=cone_start_atom,
edge_start=edge_start_atom+1, max_angle=cdp.theta_cone, inc=inc)
+
+ # Create the PDB file.
+ print("\nGenerating the PDB file.")
+ pdb_file = open_write_file(prefix+file, dir, force=force)
+ structure.write_pdb(pdb_file)
+ pdb_file.close()
+
+
def _grid_row(self, incs, lower, upper, dist_type=None):
"""Set up a row of the grid search for a given parameter.
@@ -181,6 +305,82 @@
return full_tensors, red_tensors, red_err, full_in_ref_frame
+ def _pivot(self, pivot=None):
+ """Set the pivot point for the 2 body motion.
+
+ @param pivot: The pivot point of the two bodies (domains, etc.) in
the structural
+ coordinate system.
+ @type pivot: list of num
+ """
+
+ # Test if the current data pipe exists.
+ pipes.test()
+
+ # Set the pivot point.
+ cdp.pivot = pivot
+
+ # Convert to floats.
+ for i in range(3):
+ cdp.pivot[i] = float(cdp.pivot[i])
+
+
+ def _ref_domain(self, ref=None):
+ """Set the reference domain for the frame order, multi-domain models.
+
+ @param ref: The reference domain.
+ @type ref: str
+ """
+
+ # Test if the current data pipe exists.
+ pipes.test()
+
+ # Test if the model is setup.
+ if not hasattr(cdp, 'model'):
+ raise RelaxNoModelError('Frame order')
+
+ # Test if the reference domain exists.
+ exists = False
+ for tensor_cont in cdp.align_tensors:
+ if hasattr(tensor_cont, 'domain') and tensor_cont.domain == ref:
+ exists = True
+ if not exists:
+ raise RelaxError("The reference domain cannot be found within
any of the loaded tensors.")
+
+ # Set the reference domain.
+ cdp.ref_domain = ref
+
+ # Update the model.
+ self._update_model()
+
+
+ def _select_model(self, model=None):
+ """Select the Frame Order model.
+
+ @param model: The Frame Order model. As of yet, this can only be
'iso cone'.
+ @type model: str
+ """
+
+ # Test if the current data pipe exists.
+ pipes.test()
+
+ # Test if the model is already setup.
+ if hasattr(cdp, 'model'):
+ raise RelaxModelError('Frame Order')
+
+ # Test if the model name exists.
+ if not model in ['rigid', 'iso cone']:
+ raise RelaxError("The model name " + repr(model) + " is
invalid.")
+
+ # Set the model
+ cdp.model = model
+
+ # Initialise the list of model parameters.
+ cdp.params = []
+
+ # Update the model.
+ self._update_model()
+
+
def _tensor_loop(self, red=False):
"""Generator method for looping over the full or reduced tensors.
@@ -356,14 +556,22 @@
cdp.warning = warning
- def _back_calc(self):
- """Back-calculation of the reduced alignment tensor.
-
- @return: The reduced alignment tensors.
- @rtype: numpy array
- """
-
- # Get the parameter vector.
+ def base_data_loop(self):
+ """Generator method for looping nothing.
+
+ The loop essentially consists of a single element.
+
+ @return: Nothing.
+ @rtype: None
+ """
+
+ yield None
+
+
+ def calculate(self, verbosity=None):
+ """Calculate the chi-squared value for the current parameter
values."""
+
+ # Assemble the parameter vector.
param_vector = self._assemble_param_vector()
# Get the data structures for optimisation using the tensors as base
data sets.
@@ -373,142 +581,10 @@
target = frame_order.Frame_order(model=cdp.model,
full_tensors=full_tensors, red_tensors=red_tensors,
red_errors=red_tensor_err, full_in_ref_frame=full_in_ref_frame)
# Make a single function call. This will cause back calculation and
the data will be stored in the class instance.
- target.func(param_vector)
-
- # Return the reduced tensors.
- return target.red_tensors_bc
-
-
- def base_data_loop(self):
- """Generator method for looping nothing.
-
- The loop essentially consists of a single element.
-
- @return: Nothing.
- @rtype: None
- """
-
- yield None
-
-
- def calculate(self, verbosity=None):
- """Calculate the chi-squared value for the current parameter
values."""
-
- # Assemble the parameter vector.
- param_vector = self._assemble_param_vector()
-
- # Get the data structures for optimisation using the tensors as base
data sets.
- full_tensors, red_tensors, red_tensor_err, full_in_ref_frame =
self._minimise_setup_tensors()
-
- # Set up the optimisation function.
- target = frame_order.Frame_order(model=cdp.model,
full_tensors=full_tensors, red_tensors=red_tensors,
red_errors=red_tensor_err, full_in_ref_frame=full_in_ref_frame)
-
- # Make a single function call. This will cause back calculation and
the data will be stored in the class instance.
chi2 = target.func(param_vector)
# Set the chi2.
cdp.chi2 = chi2
-
-
- def cone_pdb(self, size=30.0, file=None, dir=None, inc=40, force=False):
- """Create a PDB file containing a geometric object representing the
Frame Order cone models.
-
- @param size: The size of the geometric object in Angstroms.
- @type size: float
- @param inc: The number of increments for the filling of the
cone objects.
- @type inc: int
- @param file: The name of the PDB file to create.
- @type file: str
- @param dir: The name of the directory to place the PDB file
into.
- @type dir: str
- @param force: Flag which if set to True will cause any
pre-existing file to be
- overwritten.
- @type force: bool
- """
-
- # Test if the current data pipe exists.
- pipes.test()
-
- # Test the model.
- if not cdp.model in ['iso cone']:
- raise RelaxError("A cone PDB representation of the '%s' model
cannot be made." % cdp.model)
-
- # Test for the data structures.
- if not hasattr(cdp, 'theta_cone'):
- raise RelaxError("The cone angle theta_cone does not exist.")
- if not hasattr(cdp, 'theta_axis'):
- raise RelaxError("The cone polar angle theta_axis does not
exist.")
- if not hasattr(cdp, 'phi_axis'):
- raise RelaxError("The cone azimuthal angle phi_axis does not
exist.")
- if not hasattr(cdp, 'pivot'):
- raise RelaxError("The pivot point for the cone motion has not
been set.")
-
- # The cone axis.
- cone_axis = zeros(3, float64)
- generate_vector(cone_axis, cdp.theta_axis, cdp.phi_axis)
- print(("Cone axis: %s." % cone_axis))
- print(("Cone angle: %s." % cdp.theta_cone))
-
- # Cone axis from simulations.
- num_sim = 0
- cone_axis_sim = None
- cone_axis_sim_new = None
- if hasattr(cdp, 'sim_number'):
- num_sim = cdp.sim_number
- cone_axis_sim = zeros((num_sim, 3), float64)
- for i in range(num_sim):
- generate_vector(cone_axis_sim[i], cdp.theta_axis_sim[i],
cdp.phi_axis_sim[i])
-
- # Create a positive and negative cone.
- for factor in [-1, 1]:
- # Negative prefix.
- prefix = ''
- if factor == -1:
- prefix = 'neg_'
-
- # The rotation matrix (rotation from the z-axis to the cone
axis).
- R = zeros((3, 3), float64)
- two_vect_to_R(array([0, 0, 1], float64), cone_axis, R)
-
- # Mirroring.
- cone_axis_new = factor*cone_axis
- if cone_axis_sim != None:
- cone_axis_sim_new = factor*cone_axis_sim
- if factor == -1:
- R = -R
-
- # Create the structural object.
- structure = Internal()
-
- # Add a molecule.
- structure.add_molecule(name='iso cone')
-
- # Alias the single molecule from the single model.
- mol = structure.structural_data[0].mol[0]
-
- # Add the pivot point.
- mol.atom_add(pdb_record='HETATM', atom_num=1, atom_name='R',
res_name='PIV', res_num=1, pos=cdp.pivot, element='C')
-
- # Generate the axis vectors.
- print("\nGenerating the axis vectors.")
- res_num = generate_vector_residues(mol=mol,
vector=cone_axis_new, atom_name='Axis', res_name_vect='AXE',
sim_vectors=cone_axis_sim_new, res_num=2, origin=cdp.pivot, scale=size)
-
- # Generate the cone outer edge.
- print("\nGenerating the cone outer edge.")
- edge_start_atom = mol.atom_num[-1]+1
- cone_edge(mol=mol, res_name='CON', res_num=3+num_sim,
apex=cdp.pivot, R=R, angle=cdp.theta_cone, length=size, inc=inc)
-
- # Generate the cone cap, and stitch it to the cone edge.
- print("\nGenerating the cone cap.")
- cone_start_atom = mol.atom_num[-1]+1
- generate_vector_dist(mol=mol, res_name='CON', res_num=3+num_sim,
centre=cdp.pivot, R=R, max_angle=cdp.theta_cone, scale=size, inc=inc)
- stitch_cone_to_edge(mol=mol, cone_start=cone_start_atom,
edge_start=edge_start_atom+1, max_angle=cdp.theta_cone, inc=inc)
-
- # Create the PDB file.
- print("\nGenerating the PDB file.")
- pdb_file = open_write_file(prefix+file, dir, force=force)
- structure.write_pdb(pdb_file)
- pdb_file.close()
def create_mc_data(self, spin_id=None):
@@ -889,54 +965,6 @@
return k, n, chi2
- def pivot(self, pivot=None):
- """Set the pivot point for the 2 body motion.
-
- @param pivot: The pivot point of the two bodies (domains, etc.) in
the structural
- coordinate system.
- @type pivot: list of num
- """
-
- # Test if the current data pipe exists.
- pipes.test()
-
- # Set the pivot point.
- cdp.pivot = pivot
-
- # Convert to floats.
- for i in range(3):
- cdp.pivot[i] = float(cdp.pivot[i])
-
-
- def ref_domain(self, ref=None):
- """Set the reference domain for the frame order, multi-domain models.
-
- @param ref: The reference domain.
- @type ref: str
- """
-
- # Test if the current data pipe exists.
- pipes.test()
-
- # Test if the model is setup.
- if not hasattr(cdp, 'model'):
- raise RelaxNoModelError('Frame order')
-
- # Test if the reference domain exists.
- exists = False
- for tensor_cont in cdp.align_tensors:
- if hasattr(tensor_cont, 'domain') and tensor_cont.domain == ref:
- exists = True
- if not exists:
- raise RelaxError("The reference domain cannot be found within
any of the loaded tensors.")
-
- # Set the reference domain.
- cdp.ref_domain = ref
-
- # Update the model.
- self._update_model()
-
-
def return_data_name(self, param):
"""Return a unique identifying string for the Frame order parameter.
@@ -1017,34 +1045,6 @@
return 'rad'
- def select_model(self, model=None):
- """Select the Frame Order model.
-
- @param model: The Frame Order model. As of yet, this can only be
'iso cone'.
- @type model: str
- """
-
- # Test if the current data pipe exists.
- pipes.test()
-
- # Test if the model is already setup.
- if hasattr(cdp, 'model'):
- raise RelaxModelError('Frame Order')
-
- # Test if the model name exists.
- if not model in ['rigid', 'iso cone']:
- raise RelaxError("The model name " + repr(model) + " is
invalid.")
-
- # Set the model
- cdp.model = model
-
- # Initialise the list of model parameters.
- cdp.params = []
-
- # Update the model.
- self._update_model()
-
-
def set_error(self, nothing, index, error):
"""Set the parameter errors.
r9958 - /1.3/specific_fns/frame_order.py