Author: bugman
Date: Tue May 27 17:19:16 2014
New Revision: 23477
URL: http://svn.gna.org/viewcvs/relax?rev=23477&view=rev
Log:
Fixes for the lib.structure.represent.cone module.
The function arguments named 'cone' have been renamed to 'cone_obj' so that
they do not clash with
the cone() function in the module namespace.
Modified:
trunk/lib/structure/represent/cone.py
Modified: trunk/lib/structure/represent/cone.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/represent/cone.py?rev=23477&r1=23476&r2=23477&view=diff
==============================================================================
--- trunk/lib/structure/represent/cone.py (original)
+++ trunk/lib/structure/represent/cone.py Tue May 27 17:19:16 2014
@@ -27,9 +27,10 @@
from lib.geometry.rotations import two_vect_to_R
from lib.structure.angles import angles_regular, angles_uniform
from lib.structure.conversion import get_proton_name
-
-
-def cone_edge(mol=None, cone=None, res_name='CON', res_num=None,
chain_id='', apex=None, axis=None, R=None, scale=None, inc=None,
distribution='uniform', debug=False):
+from lib.structure.geometric import generate_vector_dist
+
+
+def cone_edge(mol=None, cone_obj=None, res_name='CON', res_num=None,
chain_id='', apex=None, axis=None, R=None, scale=None, inc=None,
distribution='uniform', debug=False):
"""Add a residue to the atomic data representing a cone of the given
angle.
A series of vectors totalling the number of increments and starting at
the origin are equally spaced around the cone axis. The atoms representing
neighbouring vectors will be directly bonded together. This will generate an
object representing the outer edge of a cone.
@@ -37,8 +38,8 @@
@keyword mol: The molecule container.
@type mol: MolContainer instance
- @keyword cone: The cone object. This should provide the
limit_check() method with determines the limits of the distribution accepting
two arguments, the polar angle phi and the azimuthal angle theta, and return
True if the point is in the limits or False if outside. It should also
provide the phi_max() method for returning the phi value for the given theta.
- @type cone: class instance
+ @keyword cone_obj: The cone object. This should provide the
limit_check() method with determines the limits of the distribution accepting
two arguments, the polar angle phi and the azimuthal angle theta, and return
True if the point is in the limits or False if outside. It should also
provide the phi_max() method for returning the phi value for the given theta.
+ @type cone_obj: class instance
@keyword res_name: The residue name.
@type res_name: str
@keyword res_num: The residue number.
@@ -85,7 +86,7 @@
edge_index = zeros(len(theta), int)
for i in range(len(theta)):
# Get the polar angle for the longitude edge atom.
- phi_max[i] = cone.phi_max(theta[i])
+ phi_max[i] = cone_obj.phi_max(theta[i])
# The index.
for j in range(len(phi)):
@@ -158,7 +159,7 @@
theta_max = theta[fwd_index] + 2*pi
else:
theta_max = theta[fwd_index]
- theta_max = cone.theta_max(phi_val, theta_min=theta[i],
theta_max=theta_max-1e-7)
+ theta_max = cone_obj.theta_max(phi_val, theta_min=theta[i],
theta_max=theta_max-1e-7)
# Back edge (skip when the latitude is phi max).
rev_index = i-1
@@ -174,7 +175,7 @@
# Find the theta value for this polar angle phi.
phi_val = phi[k]
- theta_max = cone.theta_max(phi_val, theta_min=theta[i-1],
theta_max=theta[i])
+ theta_max = cone_obj.theta_max(phi_val,
theta_min=theta[i-1], theta_max=theta[i])
# Skipping.
if skip:
@@ -216,13 +217,13 @@
mol.atom_connect(index1=atom_num-2, index2=origin_atom)
-def cone(mol=None, cone=None, start_res=1, apex=None, axis=None, R=None,
inc=None, scale=30.0, distribution='regular', axis_flag=True):
+def cone(mol=None, cone_obj=None, start_res=1, apex=None, axis=None, R=None,
inc=None, scale=30.0, distribution='regular', axis_flag=True):
"""Create a structural representation of the given cone object.
@keyword mol: The molecule container.
@type mol: MolContainer instance
- @keyword cone: The cone object. This should provide the
limit_check() method with determines the limits of the distribution accepting
two arguments, the polar angle phi and the azimuthal angle theta, and return
True if the point is in the limits or False if outside. It should also
provide the theta_max() method for returning the theta value for the given
phi, the phi_max() method for returning the phi value for the given theta.
- @type cone: class instance
+ @keyword cone_obj: The cone object. This should provide the
limit_check() method with determines the limits of the distribution accepting
two arguments, the polar angle phi and the azimuthal angle theta, and return
True if the point is in the limits or False if outside. It should also
provide the theta_max() method for returning the theta value for the given
phi, the phi_max() method for returning the phi value for the given theta.
+ @type cone_obj: class instance
@keyword start_res: The starting residue number.
@type start_res: str
@keyword apex: The apex of the cone.
@@ -266,22 +267,22 @@
# Generate the cone outer edge.
print("\nGenerating the cone outer edge.")
edge_start_atom = mol.atom_num[-1]+1
- cone_edge(mol=mol, cone=cone, res_name='EDG', res_num=start_res+2,
apex=apex, R=R, scale=scale, inc=inc, distribution=distribution)
+ cone_edge(mol=mol, cone_obj=cone_obj, res_name='EDG',
res_num=start_res+2, apex=apex, R=R, scale=scale, inc=inc,
distribution=distribution)
# 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=start_res+3,
centre=apex, R=R, limit_check=cone.limit_check, scale=scale, inc=inc,
distribution=distribution)
- stitch_cone_to_edge(mol=mol, cone=cone, dome_start=cone_start_atom,
edge_start=edge_start_atom+1, scale=scale, inc=inc, distribution=distribution)
-
-
-def stitch_cone_to_edge(mol=None, cone=None, chain_id='', dome_start=None,
edge_start=None, scale=1.0, inc=None, distribution='uniform', debug=False):
+ generate_vector_dist(mol=mol, res_name='CON', res_num=start_res+3,
centre=apex, R=R, limit_check=cone_obj.limit_check, scale=scale, inc=inc,
distribution=distribution)
+ stitch_cone_to_edge(mol=mol, cone_obj=cone_obj,
dome_start=cone_start_atom, edge_start=edge_start_atom+1, scale=scale,
inc=inc, distribution=distribution)
+
+
+def stitch_cone_to_edge(mol=None, cone_obj=None, chain_id='',
dome_start=None, edge_start=None, scale=1.0, inc=None,
distribution='uniform', debug=False):
"""Function for stitching the cone dome to its edge, in the PDB
representations.
@keyword mol: The molecule container.
@type mol: MolContainer instance
- @keyword cone: The cone object. This should provide the
limit_check() method with determines the limits of the distribution accepting
two arguments, the polar angle phi and the azimuthal angle theta, and return
True if the point is in the limits or False if outside. It should also
provide the theta_max() method for returning the theta value for the given
phi.
- @type cone: class instance
+ @keyword cone_obj: The cone object. This should provide the
limit_check() method with determines the limits of the distribution accepting
two arguments, the polar angle phi and the azimuthal angle theta, and return
True if the point is in the limits or False if outside. It should also
provide the theta_max() method for returning the theta value for the given
phi.
+ @type cone_obj: class instance
@keyword chain_id: The chain identifier.
@type chain_id: str
@keyword dome_start: The starting atom number of the cone dome
residue.
@@ -307,7 +308,7 @@
edge_index = zeros(len(theta), int)
for i in range(len(theta)):
# Get the polar angle for the longitude edge atom.
- phi_max[i] = cone.phi_max(theta[i])
+ phi_max[i] = cone_obj.phi_max(theta[i])
# The index.
for j in range(len(phi)):
r23477 - /trunk/lib/structure/represent/cone.py