Author: bugman
Date: Mon Mar 18 17:25:54 2013
New Revision: 18864
URL: http://svn.gna.org/viewcvs/relax?rev=18864&view=rev
Log:
Split up the frame_order.pdb_model user function backend into three
components.
The main _pdb_model() method now consists of calls to three new methods
_pdb_ave_pos(),
_pdb_geometric_rep() and _pdb_distribution(). The _pdb_geometric_rep()
method is simply the
contents of the old _pdb_model() method and the two other methods are
currently stubs.
Modified:
branches/frame_order_testing/specific_fns/frame_order.py
Modified: branches/frame_order_testing/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/specific_fns/frame_order.py?rev=18864&r1=18863&r2=18864&view=diff
==============================================================================
--- branches/frame_order_testing/specific_fns/frame_order.py (original)
+++ branches/frame_order_testing/specific_fns/frame_order.py Mon Mar 18
17:25:54 2013
@@ -946,10 +946,224 @@
return num
+ def _pdb_ave_pos(self, file=None, dir=None, force=False):
+ """Create a PDB file of the molecule with the moving domains shifted
to the average position.
+
+ @keyword file: The name of the file for the average molecule
structure.
+ @type file: str
+ @keyword dir: The name of the directory to place the PDB file into.
+ @type dir: str
+ @keyword force: Flag which if set to True will cause any
pre-existing file to be overwritten.
+ @type force: bool
+ """
+
+
+ def _pdb_distribution(self, file=None, dir=None, force=False):
+ """Create a PDB file of a distribution of positions coving the full
dynamics of the moving domain.
+
+ @keyword file: The name of the file which will contain multiple
models spanning the full dynamics distribution of the frame order model.
+ @type file: str
+ @keyword dir: The name of the directory to place the PDB file into.
+ @type dir: str
+ @keyword force: Flag which if set to True will cause any
pre-existing file to be overwritten.
+ @type force: bool
+ """
+
+
+ def _pdb_geometric_rep(self, file=None, dir=None, size=30.0, inc=36,
force=False, neg_cone=True):
+ """Create a PDB file containing a geometric object representing the
frame order dynamics.
+
+ @keyword file: The name of the file of the PDB
representation of the frame order dynamics to create.
+ @type file: str
+ @keyword dir: The name of the directory to place the PDB
file into.
+ @type dir: str
+ @keyword size: The size of the geometric object in
Angstroms.
+ @type size: float
+ @keyword inc: The number of increments for the filling of
the cone objects.
+ @type inc: int
+ @keyword force: Flag which if set to True will cause any
pre-existing file to be overwritten.
+ @type force: bool
+ @keyword neg_cone: A flag which if True will cause the negative
cone to be added to the representation.
+ @type neg_cone: bool
+ """
+
+ # Monte Carlo simulation flag.
+ sim = False
+ num_sim = 0
+ if hasattr(cdp, 'sim_number'):
+ sim = True
+ num_sim = cdp.sim_number
+
+ # The inversion matrix.
+ inv_mat = -eye(3)
+
+ # Create the structural object.
+ structure = Internal()
+
+ # Create model for the positive and negative images.
+ model = structure.add_model(model=1)
+ if neg_cone:
+ model_neg = structure.add_model(model=2)
+
+ # Create the molecule.
+ structure.add_molecule(name=cdp.model)
+
+ # Alias the molecules.
+ mol = model.mol[0]
+ if neg_cone:
+ mol_neg = model_neg.mol[0]
+
+
+ # The pivot point.
+ ##################
+
+ # Add the pivot point.
+ structure.add_atom(mol_name=cdp.model, pdb_record='HETATM',
atom_num=1, atom_name='R', res_name='PIV', res_num=1, pos=cdp.pivot,
element='C')
+
+
+ # The axes.
+ ###########
+
+ # The spherical angles.
+ if cdp.model in ['iso cone', 'free rotor', 'iso cone, torsionless',
'iso cone, free rotor', 'rotor']:
+ # Print out.
+ print("\nGenerating the z-axis system.")
+
+ # The axis.
+ axis = zeros(3, float64)
+ spherical_to_cartesian([1.0, getattr(cdp, 'axis_theta'),
getattr(cdp, 'axis_phi')], axis)
+ print(("Central axis: %s." % axis))
+
+ # Rotations and inversions.
+ axis_pos = axis
+ axis_neg = dot(inv_mat, axis)
+
+ # Simulation central axis.
+ axis_sim_pos = None
+ axis_sim_neg = None
+ if sim:
+ # Init.
+ axis_sim = zeros((cdp.sim_number, 3), float64)
+
+ # Fill the structure.
+ for i in range(cdp.sim_number):
+ spherical_to_cartesian([1.0, getattr(cdp,
'axis_theta_sim')[i], getattr(cdp, 'axis_phi_sim')[i]], axis_sim[i])
+
+ # Inversion.
+ axis_sim_pos = axis_sim
+ axis_sim_neg = transpose(dot(inv_mat,
transpose(axis_sim_pos)))
+
+ # Generate the axis vectors.
+ print("\nGenerating the axis vectors.")
+ res_num = geometric.generate_vector_residues(mol=mol,
vector=axis_pos, atom_name='z-ax', res_name_vect='AXE',
sim_vectors=axis_sim_pos, res_num=2, origin=cdp.pivot, scale=size)
+
+ # The negative.
+ if neg_cone:
+ res_num = geometric.generate_vector_residues(mol=mol_neg,
vector=axis_neg, atom_name='z-ax', res_name_vect='AXE',
sim_vectors=axis_sim_neg, res_num=2, origin=cdp.pivot, scale=size)
+
+ # The full axis system.
+ else:
+ # Print out.
+ print("\nGenerating the full axis system.")
+
+ # The axis system.
+ axes = zeros((3, 3), float64)
+ euler_to_R_zyz(cdp.eigen_alpha, cdp.eigen_beta, cdp.eigen_gamma,
axes)
+ print(("Axis system:\n%s" % axes))
+
+ # Rotations and inversions.
+ axes_pos = axes
+ axes_neg = dot(inv_mat, axes)
+
+ # Simulations
+ axes_sim_pos = None
+ axes_sim_neg = None
+ if sim:
+ # Init.
+ axes_sim_pos = zeros((cdp.sim_number, 3, 3), float64)
+ axes_sim_neg = zeros((cdp.sim_number, 3, 3), float64)
+
+ # Fill the structure.
+ for i in range(cdp.sim_number):
+ # The positive system.
+ euler_to_R_zyz(cdp.eigen_alpha_sim[i],
cdp.eigen_beta_sim[i], cdp.eigen_gamma_sim[i], axes_sim_pos[i])
+
+ # The negative system.
+ euler_to_R_zyz(cdp.eigen_alpha_sim[i],
cdp.eigen_beta_sim[i], cdp.eigen_gamma_sim[i], axes_sim_neg[i])
+ axes_sim_neg[i] = dot(inv_mat, axes_sim_neg[i])
+
+ # Generate the axis vectors.
+ print("\nGenerating the axis vectors.")
+ label = ['x', 'y', 'z']
+ for j in range(len(label)):
+ # The simulation data.
+ axis_sim_pos = None
+ axis_sim_neg = None
+ if sim:
+ axis_sim_pos = axes_sim_pos[:,:, j]
+ axis_sim_neg = axes_sim_neg[:,:, j]
+
+ # The vectors.
+ res_num = geometric.generate_vector_residues(mol=mol,
vector=axes_pos[:, j], atom_name='%s-ax'%label[j], res_name_vect='AXE',
sim_vectors=axis_sim_pos, res_num=2, origin=cdp.pivot, scale=size)
+ if neg_cone:
+ res_num =
geometric.generate_vector_residues(mol=mol_neg, vector=axes_neg[:, j],
atom_name='%s-ax'%label[j], res_name_vect='AXE', sim_vectors=axis_sim_neg,
res_num=2, origin=cdp.pivot, scale=size)
+
+
+ # The cone object.
+ ##################
+
+ # Skip models missing a cone.
+ if cdp.model not in ['rotor', 'free rotor']:
+ # The rotation matrix (rotation from the z-axis to the cone
axis).
+ if cdp.model not in ['iso cone', 'iso cone, torsionless', 'iso
cone, free rotor']:
+ R = axes
+ else:
+ R = zeros((3, 3), float64)
+ two_vect_to_R(array([0, 0, 1], float64), axis, R)
+
+ # Average position rotation.
+ R_pos = R
+ R_neg = dot(inv_mat, R)
+
+ # The pseudo-ellipse cone object.
+ if cdp.model in ['pseudo-ellipse', 'pseudo-ellipse,
torsionless', 'pseudo-ellipse, free rotor']:
+ cone = Pseudo_elliptic(cdp.cone_theta_x, cdp.cone_theta_y)
+
+ # The isotropic cone object.
+ else:
+ # The angle.
+ if hasattr(cdp, 'cone_theta'):
+ cone_theta = cdp.cone_theta
+ elif hasattr(cdp, 'cone_s1'):
+ cone_theta =
order_parameters.iso_cone_S_to_theta(cdp.cone_s1)
+
+ # The object.
+ cone = Iso_cone(cone_theta)
+
+ # Create the positive and negative cones.
+ geometric.create_cone_pdb(mol=mol, cone=cone,
start_res=mol.res_num[-1]+1, apex=cdp.pivot, R=R_pos, inc=inc,
distribution='regular', axis_flag=False)
+
+ # The negative.
+ if neg_cone:
+ geometric.create_cone_pdb(mol=mol_neg, cone=cone,
start_res=mol_neg.res_num[-1]+1, apex=cdp.pivot, R=R_neg, inc=inc,
distribution='regular', axis_flag=False)
+
+
+ # Create the PDB file.
+ ######################
+
+ # Print out.
+ print("\nGenerating the PDB file.")
+
+ # Write the file.
+ pdb_file = open_write_file(file, dir, force=force)
+ structure.write_pdb(pdb_file)
+ pdb_file.close()
+
+
def _pdb_model(self, ave_pos_file="ave_pos.pdb",
rep_file="frame_order.pdb", dist_file="domain_distribution.pdb", dir=None,
size=30.0, inc=36, force=False, neg_cone=True):
- """Create a PDB file containing a geometric object representing the
Frame Order cone models.
-
- @keyword ave_pos_file: The name of the file for the average
molecule structure.
+ """Create 3 different PDB files for representing the frame order
dynamics of the system.
+
+ @keyword ave_pos_file: The name of the file for the average
molecule structure.
@type ave_pos_file: str
@keyword rep_file: The name of the file of the PDB
representation of the frame order dynamics to create.
@type rep_file: str
@@ -970,180 +1184,18 @@
# Test if the current data pipe exists.
pipes.test()
- # Negative cone flag.
- neg_cone = True
-
- # Monte Carlo simulation flag.
- sim = False
- num_sim = 0
- if hasattr(cdp, 'sim_number'):
- sim = True
- num_sim = cdp.sim_number
-
- # The inversion matrix.
- inv_mat = -eye(3)
-
- # Create the structural object.
- structure = Internal()
-
- # Create model for the positive and negative images.
- model = structure.add_model(model=1)
- if neg_cone:
- model_neg = structure.add_model(model=2)
-
- # Create the molecule.
- structure.add_molecule(name=cdp.model)
-
- # Alias the molecules.
- mol = model.mol[0]
- if neg_cone:
- mol_neg = model_neg.mol[0]
-
-
- # The pivot point.
- ##################
-
- # Add the pivot point.
- structure.add_atom(mol_name=cdp.model, pdb_record='HETATM',
atom_num=1, atom_name='R', res_name='PIV', res_num=1, pos=cdp.pivot,
element='C')
-
-
- # The axes.
- ###########
-
- # The spherical angles.
- if cdp.model in ['iso cone', 'free rotor', 'iso cone, torsionless',
'iso cone, free rotor', 'rotor']:
- # Print out.
- print("\nGenerating the z-axis system.")
-
- # The axis.
- axis = zeros(3, float64)
- spherical_to_cartesian([1.0, getattr(cdp, 'axis_theta'),
getattr(cdp, 'axis_phi')], axis)
- print(("Central axis: %s." % axis))
-
- # Rotations and inversions.
- axis_pos = axis
- axis_neg = dot(inv_mat, axis)
-
- # Simulation central axis.
- axis_sim_pos = None
- axis_sim_neg = None
- if sim:
- # Init.
- axis_sim = zeros((cdp.sim_number, 3), float64)
-
- # Fill the structure.
- for i in range(cdp.sim_number):
- spherical_to_cartesian([1.0, getattr(cdp,
'axis_theta_sim')[i], getattr(cdp, 'axis_phi_sim')[i]], axis_sim[i])
-
- # Inversion.
- axis_sim_pos = axis_sim
- axis_sim_neg = transpose(dot(inv_mat,
transpose(axis_sim_pos)))
-
- # Generate the axis vectors.
- print("\nGenerating the axis vectors.")
- res_num = geometric.generate_vector_residues(mol=mol,
vector=axis_pos, atom_name='z-ax', res_name_vect='AXE',
sim_vectors=axis_sim_pos, res_num=2, origin=cdp.pivot, scale=size)
-
- # The negative.
- if neg_cone:
- res_num = geometric.generate_vector_residues(mol=mol_neg,
vector=axis_neg, atom_name='z-ax', res_name_vect='AXE',
sim_vectors=axis_sim_neg, res_num=2, origin=cdp.pivot, scale=size)
-
- # The full axis system.
- else:
- # Print out.
- print("\nGenerating the full axis system.")
-
- # The axis system.
- axes = zeros((3, 3), float64)
- euler_to_R_zyz(cdp.eigen_alpha, cdp.eigen_beta, cdp.eigen_gamma,
axes)
- print(("Axis system:\n%s" % axes))
-
- # Rotations and inversions.
- axes_pos = axes
- axes_neg = dot(inv_mat, axes)
-
- # Simulations
- axes_sim_pos = None
- axes_sim_neg = None
- if sim:
- # Init.
- axes_sim_pos = zeros((cdp.sim_number, 3, 3), float64)
- axes_sim_neg = zeros((cdp.sim_number, 3, 3), float64)
-
- # Fill the structure.
- for i in range(cdp.sim_number):
- # The positive system.
- euler_to_R_zyz(cdp.eigen_alpha_sim[i],
cdp.eigen_beta_sim[i], cdp.eigen_gamma_sim[i], axes_sim_pos[i])
-
- # The negative system.
- euler_to_R_zyz(cdp.eigen_alpha_sim[i],
cdp.eigen_beta_sim[i], cdp.eigen_gamma_sim[i], axes_sim_neg[i])
- axes_sim_neg[i] = dot(inv_mat, axes_sim_neg[i])
-
- # Generate the axis vectors.
- print("\nGenerating the axis vectors.")
- label = ['x', 'y', 'z']
- for j in range(len(label)):
- # The simulation data.
- axis_sim_pos = None
- axis_sim_neg = None
- if sim:
- axis_sim_pos = axes_sim_pos[:,:, j]
- axis_sim_neg = axes_sim_neg[:,:, j]
-
- # The vectors.
- res_num = geometric.generate_vector_residues(mol=mol,
vector=axes_pos[:, j], atom_name='%s-ax'%label[j], res_name_vect='AXE',
sim_vectors=axis_sim_pos, res_num=2, origin=cdp.pivot, scale=size)
- if neg_cone:
- res_num =
geometric.generate_vector_residues(mol=mol_neg, vector=axes_neg[:, j],
atom_name='%s-ax'%label[j], res_name_vect='AXE', sim_vectors=axis_sim_neg,
res_num=2, origin=cdp.pivot, scale=size)
-
-
- # The cone object.
- ##################
-
- # Skip models missing a cone.
- if cdp.model not in ['rotor', 'free rotor']:
- # The rotation matrix (rotation from the z-axis to the cone
axis).
- if cdp.model not in ['iso cone', 'iso cone, torsionless', 'iso
cone, free rotor']:
- R = axes
- else:
- R = zeros((3, 3), float64)
- two_vect_to_R(array([0, 0, 1], float64), axis, R)
-
- # Average position rotation.
- R_pos = R
- R_neg = dot(inv_mat, R)
-
- # The pseudo-ellipse cone object.
- if cdp.model in ['pseudo-ellipse', 'pseudo-ellipse,
torsionless', 'pseudo-ellipse, free rotor']:
- cone = Pseudo_elliptic(cdp.cone_theta_x, cdp.cone_theta_y)
-
- # The isotropic cone object.
- else:
- # The angle.
- if hasattr(cdp, 'cone_theta'):
- cone_theta = cdp.cone_theta
- elif hasattr(cdp, 'cone_s1'):
- cone_theta =
order_parameters.iso_cone_S_to_theta(cdp.cone_s1)
-
- # The object.
- cone = Iso_cone(cone_theta)
-
- # Create the positive and negative cones.
- geometric.create_cone_pdb(mol=mol, cone=cone,
start_res=mol.res_num[-1]+1, apex=cdp.pivot, R=R_pos, inc=inc,
distribution='regular', axis_flag=False)
-
- # The negative.
- if neg_cone:
- geometric.create_cone_pdb(mol=mol_neg, cone=cone,
start_res=mol_neg.res_num[-1]+1, apex=cdp.pivot, R=R_neg, inc=inc,
distribution='regular', axis_flag=False)
-
-
- # Create the PDB file.
- ######################
-
- # Print out.
- print("\nGenerating the PDB file.")
-
- # Write the file.
- pdb_file = open_write_file(file, dir, force=force)
- structure.write_pdb(pdb_file)
- pdb_file.close()
+ # Create the average position structure.
+ self._pdb_ave_pos(file=ave_pos_file, dir=dir, force=force)
+
+ # Nothing more to do for the rigid model.
+ if cdp.model == 'rigid':
+ return
+
+ # Create the geometric representation.
+ self._pdb_geometric_rep(file=rep_file, dir=dir, size=size, inc=inc,
force=force, neg_cone=neg_cone)
+
+ # Create the distribution.
+ self._pdb_distribution(file=dist_file, dir=dir, force=force)
def _pivot(self, pivot=None, fix=None):
r18864 - /branches/frame_order_testing/specific_fns/frame_order.py