Author: bugman
Date: Mon Apr 7 16:53:04 2008
New Revision: 5370
URL: http://svn.gna.org/viewcvs/relax?rev=5370&view=rev
Log:
Changed the 'atomic_data' arg in all the geometric function to 'structure'.
This is because the structral data object will be passed into these functions
instead.
Modified:
1.3/generic_fns/structure/geometric.py
Modified: 1.3/generic_fns/structure/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/geometric.py?rev=5370&r1=5369&r2=5370&view=diff
==============================================================================
--- 1.3/generic_fns/structure/geometric.py (original)
+++ 1.3/generic_fns/structure/geometric.py Mon Apr 7 16:53:04 2008
@@ -56,7 +56,7 @@
return 1.8e-6
-def cone_edge(atomic_data=None, res_name='CON', res_num=None, apex=None,
axis=None, R=None, angle=None, length=None, inc=None):
+def cone_edge(structure=None, res_name='CON', res_num=None, apex=None,
axis=None, R=None, angle=None, length=None, inc=None):
"""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
@@ -64,8 +64,8 @@
bonded together. This will generate an object representing the outer
edge of a cone.
- @param atomic_data: The dictionary to place the atomic data into.
- @type atomic_data: dict
+ @param structure: The structural data object.
+ @type structure: instance of class derived from Str_object
@param res_name: The residue name.
@type res_name: str
@param res_num: The residue number.
@@ -465,7 +465,7 @@
tensor_pdb_file.close()
-def generate_vector_dist(atomic_data=None, atom_id_ext='', res_name=None,
res_num=None, chain_id='', centre=zeros(3, float64), R=eye(3), warp=eye(3),
max_angle=None, scale=1.0, inc=20):
+def generate_vector_dist(structure=None, atom_id_ext='', res_name=None,
res_num=None, chain_id='', centre=zeros(3, float64), R=eye(3), warp=eye(3),
max_angle=None, scale=1.0, inc=20):
"""Generate a uniformly distributed distribution of atoms on a warped
sphere.
The vectors from the function uniform_vect_dist_spherical_angles() are
used to generate the
@@ -474,8 +474,8 @@
centred and at the head of the vector, a proton is placed.
- @param atomic_data: The dictionary to place the atomic data into.
- @type atomic_data: dict
+ @param structure: The structural data object.
+ @type structure: instance of class derived from Str_object
@param atom_id_ext: The atom identifier extension.
@type atom_id_ext: str
@param res_name: The residue name.
@@ -569,14 +569,14 @@
atom_num = atom_num + 1
-def generate_vector_residues(atomic_data=None, vector=None, atom_name=None,
res_name_vect='AXS', sim_vectors=None, res_name_sim='SIM', chain_id='',
res_num=None, origin=None, scale=1.0, label_placement=1.1, neg=False):
+def generate_vector_residues(structure=None, vector=None, atom_name=None,
res_name_vect='AXS', sim_vectors=None, res_name_sim='SIM', chain_id='',
res_num=None, origin=None, scale=1.0, label_placement=1.1, neg=False):
"""Generate residue representations for the vector and the MC
simulationed vectors.
This is used to create a PDB representation of any vector, including its
Monte Carlo
simulations.
- @param atomic_data: The dictionary to place the atomic data into.
- @type atomic_data: dict
+ @param structure: The structural data object.
+ @type structure: instance of class derived from Str_object
@param vector: The vector to be represented in the PDB.
@type vector: numpy array, len 3
@param atom_name: The atom name used to label the atom
representing the head of the vector
@@ -654,11 +654,11 @@
return res_num
-def stitch_cap_to_cone(atomic_data=None, atom_id_ext='', max_angle=None,
inc=None):
+def stitch_cap_to_cone(structure=None, atom_id_ext='', max_angle=None,
inc=None):
"""Function for stitching the cap of a cone to the cone edge, in the PDB
representations.
- @param atomic_data: The dictionary containing the atomic data.
- @type atomic_data: dict
+ @param structure: The structural data object.
+ @type structure: instance of class derived from Str_object
@param atom_id_ext: The atom identifier extension.
@type atom_id_ext: str
@param max_angle: The maximal polar angle, in rad, after which all
vectors are skipped.
r5370 - /1.3/generic_fns/structure/geometric.py