Author: bugman
Date: Tue May 27 15:51:39 2014
New Revision: 23469
URL: http://svn.gna.org/viewcvs/relax?rev=23469&view=rev
Log:
Merged revisions 23468 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r23468 | bugman | 2014-05-27 15:51:08 +0200 (Tue, 27 May 2014) | 6 lines
Shifted some functions from lib.structure.geometric into their own modules.
The angles_regular() and angles_uniform() functions are now in the
lib.structure.angles module, and
the get_proton_names in lib.structure.conversion.
........
Added:
branches/frame_order_cleanup/lib/structure/angles.py
- copied unchanged from r23468, trunk/lib/structure/angles.py
branches/frame_order_cleanup/lib/structure/conversion.py
- copied unchanged from r23468, trunk/lib/structure/conversion.py
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/lib/structure/__init__.py
branches/frame_order_cleanup/lib/structure/geometric.py
branches/frame_order_cleanup/lib/structure/represent/cone.py
Propchange: branches/frame_order_cleanup/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Tue May 27 15:51:39 2014
@@ -1 +1 @@
-/trunk:1-23453
+/trunk:1-23468
Modified: branches/frame_order_cleanup/lib/structure/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/structure/__init__.py?rev=23469&r1=23468&r2=23469&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/structure/__init__.py (original)
+++ branches/frame_order_cleanup/lib/structure/__init__.py Tue May 27
15:51:39 2014
@@ -23,7 +23,9 @@
"""The relax-lib structure package - a library of functions handling
structural information."""
__all__ = [
+ 'angles',
'cones',
+ 'conversion',
'geometric',
'mass',
'pdb_read',
Modified: branches/frame_order_cleanup/lib/structure/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/structure/geometric.py?rev=23469&r1=23468&r2=23469&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/structure/geometric.py (original)
+++ branches/frame_order_cleanup/lib/structure/geometric.py Tue May 27
15:51:39 2014
@@ -23,70 +23,9 @@
from math import cos, pi, sin
from numpy import arccos, array, dot, eye, float64, zeros
-
-def angles_regular(inc=None):
- """Determine the spherical angles for a regular sphere point
distribution.
-
- @keyword inc: The number of increments in the distribution.
- @type inc: int
- @return: The phi angle array and the theta angle array.
- @rtype: array of float, array of float
- """
-
- # Generate the increment values of u.
- u = zeros(inc, float64)
- val = 1.0 / float(inc)
- for i in range(inc):
- u[i] = float(i) * val
-
- # Generate the increment values of v.
- v = zeros(inc/2+1, float64)
- val = 1.0 / float(inc/2)
- for i in range(int(inc/2+1)):
- v[i] = float(i) * val
-
- # Generate the distribution of spherical angles theta.
- theta = 2.0 * pi * u
-
- # Generate the distribution of spherical angles phi (from bottom to top).
- phi = zeros(len(v), float64)
- for i in range(len(v)):
- phi[len(v)-1-i] = pi * v[i]
-
- # Return the angle arrays.
- return phi, theta
-
-
-def angles_uniform(inc=None):
- """Determine the spherical angles for a uniform sphere point
distribution.
-
- @keyword inc: The number of increments in the distribution.
- @type inc: int
- @return: The phi angle array and the theta angle array.
- @rtype: array of float, array of float
- """
-
- # Generate the increment values of u.
- u = zeros(inc, float64)
- val = 1.0 / float(inc)
- for i in range(inc):
- u[i] = float(i) * val
-
- # Generate the increment values of v.
- v = zeros(inc/2+2, float64)
- val = 1.0 / float(inc/2)
- for i in range(1, int(inc/2)+1):
- v[i] = float(i-1) * val + val/2.0
- v[-1] = 1.0
-
- # Generate the distribution of spherical angles theta.
- theta = 2.0 * pi * u
-
- # Generate the distribution of spherical angles phi.
- phi = arccos(2.0 * v - 1.0)
-
- # Return the angle arrays.
- return phi, theta
+# relax module imports.
+from lib.structure.angles import angles_regular, angles_uniform
+from lib.structure.conversion import get_proton_name
def generate_vector_dist(mol=None, res_name=None, res_num=None, chain_id='',
centre=zeros(3, float64), R=eye(3), warp=eye(3), limit_check=None, scale=1.0,
inc=20, distribution='uniform', debug=False):
@@ -307,26 +246,6 @@
return res_num
-def get_proton_name(atom_num):
- """Return a valid PDB atom name of <4 characters.
-
- @param atom_num: The number of the atom.
- @type atom_num: int
- @return: The atom name to use in the PDB.
- @rtype: str
- """
-
- # Init the proton first letters and the atom number folding limits.
- names = ['H', 'I', 'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q']
- lims = [0, 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, 10000]
-
- # Loop over the proton names.
- for i in range(len(names)):
- # In the bounds.
- if atom_num >= lims[i] and atom_num < lims[i+1]:
- return names[i] + repr(atom_num - lims[i])
-
-
def vect_dist_spherical_angles(inc=20, distribution='uniform'):
"""Create a distribution of vectors on a sphere using a distribution of
spherical angles.
Modified: branches/frame_order_cleanup/lib/structure/represent/cone.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/structure/represent/cone.py?rev=23469&r1=23468&r2=23469&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/structure/represent/cone.py
(original)
+++ branches/frame_order_cleanup/lib/structure/represent/cone.py Tue
May 27 15:51:39 2014
@@ -25,7 +25,8 @@
# relax module imports.
from lib.geometry.rotations import two_vect_to_R
-from lib.structure.geometric import angles_uniform, get_proton_name
+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):
r23469 - in /branches/frame_order_cleanup: ./ lib/structure/ lib/structure/represent/