Author: bugman
Date: Sun Mar 24 16:58:38 2013
New Revision: 19122
URL: http://svn.gna.org/viewcvs/relax?rev=19122&view=rev
Log:
Shifted the lib.structure.rotor module to lib.structure.represent.rotor.
Added:
trunk/lib/structure/represent/rotor.py
- copied unchanged from r19118, trunk/lib/structure/rotor.py
Removed:
trunk/lib/structure/rotor.py
Modified:
trunk/lib/structure/__init__.py
trunk/lib/structure/represent/__init__.py
trunk/pipe_control/structure/geometric.py
trunk/specific_analyses/frame_order.py
Modified: trunk/lib/structure/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/__init__.py?rev=19122&r1=19121&r2=19122&view=diff
==============================================================================
--- trunk/lib/structure/__init__.py (original)
+++ trunk/lib/structure/__init__.py Sun Mar 24 16:58:38 2013
@@ -27,7 +27,6 @@
'mass',
'pdb_read',
'pdb_write',
- 'rotor',
'statistics',
'superimpose'
]
Modified: trunk/lib/structure/represent/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/represent/__init__.py?rev=19122&r1=19121&r2=19122&view=diff
==============================================================================
--- trunk/lib/structure/represent/__init__.py (original)
+++ trunk/lib/structure/represent/__init__.py Sun Mar 24 16:58:38 2013
@@ -26,5 +26,5 @@
"""
__all__ = [
- ''
+ 'rotor'
]
Removed: trunk/lib/structure/rotor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/rotor.py?rev=19121&view=auto
==============================================================================
--- trunk/lib/structure/rotor.py (original)
+++ trunk/lib/structure/rotor.py (removed)
@@ -1,186 +1,0 @@
-###############################################################################
-#
#
-# Copyright (C) 2003-2013 Edward d'Auvergne
#
-#
#
-# This file is part of the program relax (http://www.nmr-relax.com).
#
-#
#
-# This program is free software: you can redistribute it and/or modify
#
-# it under the terms of the GNU General Public License as published by
#
-# the Free Software Foundation, either version 3 of the License, or
#
-# (at your option) any later version.
#
-#
#
-# This program is distributed in the hope that it will be useful,
#
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
-# GNU General Public License for more details.
#
-#
#
-# You should have received a copy of the GNU General Public License
#
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
-#
#
-###############################################################################
-
-# Module docstring.
-"""Representations of a mechanical rotor."""
-
-# Python module imports.
-from math import pi
-from numpy import array, cross, dot, float64, transpose, zeros
-from numpy.linalg import norm
-
-# relax module imports.
-from lib.geometry.lines import closest_point_ax
-from lib.geometry.rotations import axis_angle_to_R
-
-
-def rotor_pdb(structure=None, rotor_angle=None, axis=None, axis_pt=True,
centre=None, span=2e-9, blade_length=5e-10, model=None, staggered=False):
- """Create a PDB representation of a rotor motional model.
-
- @keyword structure: The internal structural object instance to add
the rotor to as a molecule.
- @type structure: pipe_control.structure.internal.Internal instance
- @keyword rotor_angle: The angle of the rotor motion in radian.
- @type rotor_angle: float
- @keyword axis: The vector defining the rotor axis.
- @type axis: numpy rank-1, 3D array
- @keyword axis_pt: A point lying anywhere on the rotor axis. This
is used to define the position of the axis in 3D space.
- @type axis_pt: numpy rank-1, 3D array
- @keyword centre: The central point of the representation. If
this point is not on the rotor axis, then the closest point on the axis will
be used for the centre.
- @type centre: numpy rank-1, 3D array
- @keyword span: The distance from the central point to the rotor
blades (meters).
- @type span: float
- @keyword blade_length: The length of the representative rotor blades.
- @type blade_length: float
- @keyword model: The structural model number to add the rotor to.
If not supplied, the same rotor structure will be added to all models.
- @type model: int or None
- @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
- """
-
- # Convert the arguments to numpy arrays, radians and Angstrom.
- axis = array(axis, float64)
- axis_pt = array(axis_pt, float64)
- centre = array(centre, float64)
- span = span * 1e10
- blade_length = blade_length * 1e10
-
- # Normalise.
- axis_norm = axis / norm(axis)
-
- # Add a structure.
- structure.add_molecule(name='rotor')
-
- # Loop over the models.
- for model in structure.model_loop(model):
- # Alias the single molecule from the single model.
- mol = structure.get_molecule('rotor', model=model.num)
-
- # 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.
- rotor_propellers(mol=mol, rotor_angle=rotor_angle, centre=prop1,
axis=axis, blade_length=blade_length, staggered=staggered)
- rotor_propellers(mol=mol, rotor_angle=rotor_angle, centre=prop2,
axis=-axis, blade_length=blade_length, staggered=staggered)
-
-
-def 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
Modified: trunk/pipe_control/structure/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/geometric.py?rev=19122&r1=19121&r2=19122&view=diff
==============================================================================
--- trunk/pipe_control/structure/geometric.py (original)
+++ trunk/pipe_control/structure/geometric.py Sun Mar 24 16:58:38 2013
@@ -32,7 +32,7 @@
from pipe_control import pipes
from pipe_control.structure.internal import Internal
from pipe_control.structure.mass import centre_of_mass
-from lib.structure.rotor import rotor_pdb
+from lib.structure.representation.rotor import rotor_pdb
from lib.geometry.rotations import two_vect_to_R
from lib.errors import RelaxNoPdbError, RelaxNoSequenceError,
RelaxNoTensorError, RelaxNoVectorsError
from lib.io import get_file_path, open_write_file
Modified: trunk/specific_analyses/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order.py?rev=19122&r1=19121&r2=19122&view=diff
==============================================================================
--- trunk/specific_analyses/frame_order.py (original)
+++ trunk/specific_analyses/frame_order.py Sun Mar 24 16:58:38 2013
@@ -43,7 +43,7 @@
from pipe_control.structure.mass import centre_of_mass
from pipe_control.structure.internal import Internal
from lib.structure.cones import Iso_cone, Pseudo_elliptic
-from lib.structure.rotor import rotor_pdb
+from lib.structure.representation.rotor import rotor_pdb
from lib.text.sectioning import subsection
from target_functions import frame_order
from lib.geometry.coord_transform import spherical_to_cartesian
r19122 - in /trunk: lib/structure/ lib/structure/represent/ pipe_control/structure/ specific_analyses/