Author: bugman
Date: Tue Jul 1 12:51:23 2014
New Revision: 24374
URL: http://svn.gna.org/viewcvs/relax?rev=24374&view=rev
Log:
Renamed the lib.structure.represent.rotor.rotor_pdb() function to rotor().
This function is not PDB specific and it just creates a 3D structural
representation of a rotor
object.
Modified:
branches/frame_order_cleanup/lib/structure/represent/rotor.py
branches/frame_order_cleanup/pipe_control/structure/geometric.py
branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/system_create.py
Modified: branches/frame_order_cleanup/lib/structure/represent/rotor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/structure/represent/rotor.py?rev=24374&r1=24373&r2=24374&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/structure/represent/rotor.py
(original)
+++ branches/frame_order_cleanup/lib/structure/represent/rotor.py Tue
Jul 1 12:51:23 2014
@@ -32,7 +32,7 @@
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):
+def rotor(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.
Modified: branches/frame_order_cleanup/pipe_control/structure/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/structure/geometric.py?rev=24374&r1=24373&r2=24374&view=diff
==============================================================================
--- branches/frame_order_cleanup/pipe_control/structure/geometric.py
(original)
+++ branches/frame_order_cleanup/pipe_control/structure/geometric.py Tue
Jul 1 12:51:23 2014
@@ -27,7 +27,7 @@
from lib.errors import RelaxNoPdbError, RelaxNoSequenceError,
RelaxNoVectorsError
from lib.io import get_file_path, open_write_file
from lib.structure.internal.object import Internal
-from lib.structure.represent.rotor import rotor_pdb
+from lib.structure.represent.rotor import rotor
from pipe_control import pipes
from pipe_control.interatomic import interatomic_loop
from pipe_control.mol_res_spin import exists_mol_res_spin_data, return_spin
@@ -70,7 +70,7 @@
structure = Internal()
# 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)
+ rotor(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.")
Modified:
branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py?rev=24374&r1=24373&r2=24374&view=diff
==============================================================================
--- branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
(original)
+++ branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
Tue Jul 1 12:51:23 2014
@@ -37,7 +37,7 @@
from lib.structure.geometric import generate_vector_residues
from lib.structure.internal.object import Internal
from lib.structure.represent.cone import cone
-from lib.structure.represent.rotor import rotor_pdb
+from lib.structure.represent.rotor import rotor
from lib.text.sectioning import subsection
from pipe_control.structure.mass import pipe_centre_of_mass
from specific_analyses.frame_order.data import domain_moving, generate_pivot
@@ -340,7 +340,7 @@
# Add each rotor to the structure as a new molecule.
for i in range(len(axis)):
- rotor_pdb(structure=structure, rotor_angle=rotor_angle[i],
axis=axis[i], axis_pt=pivot[i], centre=com[i], span=span[i],
blade_length=5e-10, staggered=staggered[i])
+ rotor(structure=structure, rotor_angle=rotor_angle[i], axis=axis[i],
axis_pt=pivot[i], centre=com[i], span=span[i], blade_length=5e-10,
staggered=staggered[i])
def create_ave_pos(format='PDB', file=None, dir=None, force=False):
Modified:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/system_create.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/system_create.py?rev=24374&r1=24373&r2=24374&view=diff
==============================================================================
---
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/system_create.py
(original)
+++
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/system_create.py
Tue Jul 1 12:51:23 2014
@@ -6,7 +6,7 @@
# relax module imports.
from lib.geometry.vectors import unit_vector_from_2point
-from lib.structure.represent.rotor import rotor_pdb
+from lib.structure.represent.rotor import rotor
# The two CoMs.
@@ -43,8 +43,8 @@
structure.connect_atom(index1=0, index2=1)
# Create a PDB representation of the rotors.
-rotor_pdb(structure=cdp.structure, rotor_angle=radians(10.5), axis=axis1,
axis_pt=pos1, centre=COM_N, span=2e-9, blade_length=5e-10, staggered=False)
-rotor_pdb(structure=cdp.structure, rotor_angle=radians(11.5), axis=axis2,
axis_pt=pos2, centre=COM_C, span=2e-9, blade_length=5e-10, staggered=False)
+rotor(structure=cdp.structure, rotor_angle=radians(10.5), axis=axis1,
axis_pt=pos1, centre=COM_N, span=2e-9, blade_length=5e-10, staggered=False)
+rotor(structure=cdp.structure, rotor_angle=radians(11.5), axis=axis2,
axis_pt=pos2, centre=COM_C, span=2e-9, blade_length=5e-10, staggered=False)
# Write out the system.
state.save('system', force=True)
r24374 - in /branches/frame_order_cleanup: lib/structure/represent/ pipe_control/structure/ specific_analyses/frame_order/ t...