Author: bugman
Date: Wed Mar 20 17:25:24 2013
New Revision: 18926
URL: http://svn.gna.org/viewcvs/relax?rev=18926&view=rev
Log:
Merged revisions 18923-18925 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r18923 | bugman | 2013-03-20 17:06:40 +0100 (Wed, 20 Mar 2013) | 5 lines
Split the generic_fns.structure.geometric.create_rotor_pdb() function.
The non-relax specific code has been shifted into the rotor_pdb() function.
........
r18924 | bugman | 2013-03-20 17:09:55 +0100 (Wed, 20 Mar 2013) | 3 lines
Initialised the lib.structure package - this is currently empty.
........
r18925 | bugman | 2013-03-20 17:24:22 +0100 (Wed, 20 Mar 2013) | 8 lines
Shifted the rotor creation components from generic_fns.structure.geometric
to lib.structure.rotor.
The create_rotor_pdb() function remains in place as this is the user
function backend which checks
for data pipes and updates the status object, but the rotor_pdb() and
create_rotor_propellers()
functions have been moved into the relax library. The
create_rotor_propellers() function has been
renamed to lib.structure.rotor.rotor_propellers().
........
Added:
branches/frame_order_testing/lib/structure/
- copied from r18925, trunk/lib/structure/
Modified:
branches/frame_order_testing/ (props changed)
branches/frame_order_testing/generic_fns/structure/geometric.py
Propchange: branches/frame_order_testing/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Wed Mar 20 17:25:24 2013
@@ -1,1 +1,1 @@
-/trunk:1-18919
+/trunk:1-18925
Modified: branches/frame_order_testing/generic_fns/structure/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/structure/geometric.py?rev=18926&r1=18925&r2=18926&view=diff
==============================================================================
--- branches/frame_order_testing/generic_fns/structure/geometric.py (original)
+++ branches/frame_order_testing/generic_fns/structure/geometric.py Wed Mar
20 17:25:24 2013
@@ -21,21 +21,20 @@
# Python module imports.
from math import cos, pi, sin
-from numpy import arccos, array, cross, dot, eye, float64, transpose, zeros
-from numpy.linalg import norm
+from numpy import arccos, array, dot, eye, float64, transpose, zeros
from os import getcwd
from string import ascii_uppercase
from warnings import warn
# relax module imports.
from generic_fns.interatomic import interatomic_loop
-from generic_fns.mol_res_spin import exists_mol_res_spin_data, return_spin,
spin_loop
+from generic_fns.mol_res_spin import exists_mol_res_spin_data, return_spin
from generic_fns import pipes
from generic_fns.structure.internal import Internal
from generic_fns.structure.mass import centre_of_mass
-from lib.geometry.lines import closest_point_ax
-from maths_fns.rotation_matrix import axis_angle_to_R, two_vect_to_R
-from relax_errors import RelaxError, RelaxNoPdbError, RelaxNoSequenceError,
RelaxNoTensorError, RelaxNoVectorsError
+from lib.structure.rotor import rotor_pdb
+from maths_fns.rotation_matrix import two_vect_to_R
+from relax_errors import RelaxNoPdbError, RelaxNoSequenceError,
RelaxNoTensorError, RelaxNoVectorsError
from relax_io import get_file_path, open_write_file
from relax_warnings import RelaxWarning
from status import Status; status = Status()
@@ -610,48 +609,14 @@
@type staggered: bool
"""
- # Convert the arguments to numpy arrays, radians and Angstrom.
- axis = array(axis, float64)
- axis_pt = array(axis_pt, float64)
- centre = array(centre, float64)
- rotor_angle = rotor_angle / 360.0 * 2.0 * pi
- span = span * 1e10
- blade_length = blade_length * 1e10
-
- # Normalise.
- axis_norm = axis / norm(axis)
-
# Test if the current pipe exists.
pipes.test()
# Create the structural object.
structure = Internal()
- # Add a structure.
- structure.add_molecule(name='rotor')
-
- # Alias the single molecule from the single model.
- mol = structure.get_molecule('rotor')
-
- # The central point.
- mid_point = closest_point_ax(line_pt=axis_pt, axis=axis, point=centre)
- mol.atom_add(pdb_record='HETATM', atom_num=1, atom_name='CTR',
res_name='AX', res_num=1, pos=mid_point, element='PT')
-
- # Centre of the propellers.
- prop1 = mid_point + axis_norm * span
- prop1_index = 1
- mol.atom_add(pdb_record='HETATM', atom_num=2, atom_name='PRP',
res_name='PRC', res_num=2, pos=prop1, element='O')
- mol.atom_connect(index1=0, index2=prop1_index)
-
- # Centre of the propellers.
- prop2 = mid_point - axis_norm * span
- prop2_index = 2
- mol.atom_add(pdb_record='HETATM', atom_num=3, atom_name='PRP',
res_name='PRC', res_num=3, pos=prop2, element='O')
- mol.atom_connect(index1=0, index2=prop2_index)
-
- # Create the rotor propellers.
- create_rotor_propellers(mol=mol, rotor_angle=rotor_angle, centre=prop1,
axis=axis, blade_length=blade_length, staggered=staggered)
- create_rotor_propellers(mol=mol, rotor_angle=rotor_angle, centre=prop2,
axis=-axis, blade_length=blade_length, staggered=staggered)
+ # Generate the rotor object.
+ rotor_pdb(structure=structure, rotor_angle=rotor_angle, axis=axis,
axis_pt=axis_pt, centre=centre, span=span, blade_length=blade_length,
staggered=staggered)
# Print out.
print("\nGenerating the PDB file.")
@@ -672,98 +637,6 @@
dir = getcwd()
cdp.result_files.append(['diff_tensor_pdb', 'Diffusion tensor PDB',
get_file_path(file, dir)])
status.observers.result_file.notify()
-
-
-def create_rotor_propellers(mol=None, rotor_angle=None, centre=None,
axis=None, blade_length=5.0, staggered=False):
- """Create a PDB representation of a rotor motional model.
-
- @keyword mol: The internal structural object molecule
container to add the atoms to.
- @type mol: MolContainer instance
- @keyword rotor_angle: The angle of the rotor motion in radians.
- @type rotor_angle: float
- @keyword centre: The central point of the propeller.
- @type centre: numpy rank-1, 3D array
- @keyword axis: The vector defining the rotor axis.
- @type axis: numpy rank-1, 3D array
- @keyword blade_length: The length of the representative rotor blades in
Angstrom.
- @type blade_length: float
- @keyword staggered: A flag which if True will cause the rotor blades
to be staggered. This is used to avoid blade overlap.
- @type staggered: bool
- """
-
- # Init.
- step_angle = 2.0 / 360.0 * 2.0 * pi
- R = zeros((3, 3), float64)
- res_num = mol.last_residue() + 1
-
- # Blade vectors.
- blades = zeros((4, 3), float64)
- if abs(dot(axis, array([0, 0, 1], float64))) == 1.0: # Avoid failures
in artificial situations.
- blades[0] = cross(axis, array([1, 0, 0], float64))
- else:
- blades[0] = cross(axis, array([0, 0, 1], float64))
- blades[0] = blades[0] / norm(blades[0])
- blades[1] = cross(axis, blades[0])
- blades[1] = blades[1] / norm(blades[1])
- blades[2] = -blades[0]
- blades[3] = -blades[1]
-
- # Create the 4 blades.
- for i in range(len(blades)):
- # Staggering.
- if staggered and i % 2:
- blade_origin = centre - axis * 2
-
- # Non-staggered.
- else:
- blade_origin = centre
-
- # Add an atom for the blage origin.
- blade_origin_index = mol.atom_add(pdb_record='HETATM',
atom_name='BLO', res_name='PRB', res_num=res_num, pos=blade_origin,
element='O')
-
- # The centre edge point of the blade.
- mid_point = blade_origin + blades[i] * blade_length
- mid_pt_index = mol.atom_add(pdb_record='HETATM', atom_name='BLD',
res_name='PRB', res_num=res_num, pos=mid_point, element='N')
- mol.atom_connect(index1=mid_pt_index, index2=blade_origin_index)
-
- # Build the blade.
- angle = 0.0
- pos_last_index = mid_pt_index
- neg_last_index = mid_pt_index
- while True:
- # Increase the angle.
- angle += step_angle
-
- # The edge rotation.
- if angle > rotor_angle:
- axis_angle_to_R(axis, rotor_angle, R)
-
- # The normal rotation matrix.
- else:
- axis_angle_to_R(axis, angle, R)
-
- # The positive edge.
- pos_point = dot(R, mid_point - blade_origin) + blade_origin
- pos_index = mol.atom_add(pdb_record='HETATM', atom_name='BLD',
res_name='PRB', res_num=res_num, pos=pos_point, element='N')
- mol.atom_connect(index1=pos_index, index2=pos_last_index)
- mol.atom_connect(index1=pos_index, index2=blade_origin_index)
-
- # The negative edge.
- neg_point = dot(transpose(R), mid_point - blade_origin) +
blade_origin
- neg_index = mol.atom_add(pdb_record='HETATM', atom_name='BLD',
res_name='PRB', res_num=res_num, pos=neg_point, element='N')
- mol.atom_connect(index1=neg_index, index2=neg_last_index)
- mol.atom_connect(index1=neg_index, index2=blade_origin_index)
-
- # Update the indices.
- pos_last_index = pos_index
- neg_last_index = neg_index
-
- # Finish.
- if angle > rotor_angle:
- break
-
- # Increment the residue number.
- res_num += 1
def create_vector_dist(length=None, symmetry=True, file=None, dir=None,
force=False):
r18926 - in /branches/frame_order_testing: ./ generic_fns/structure/geometric.py lib/structure/