Author: bugman
Date: Mon Oct 24 15:01:05 2011
New Revision: 14897
URL: http://svn.gna.org/viewcvs/relax?rev=14897&view=rev
Log:
The structure.rotate user function can now operate in individual structural
models.
The model keyword argument has been added to allow this.
Modified:
1.3/generic_fns/structure/api_base.py
1.3/generic_fns/structure/internal.py
1.3/generic_fns/structure/main.py
1.3/prompt/structure.py
Modified: 1.3/generic_fns/structure/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/api_base.py?rev=14897&r1=14896&r2=14897&view=diff
==============================================================================
--- 1.3/generic_fns/structure/api_base.py (original)
+++ 1.3/generic_fns/structure/api_base.py Mon Oct 24 15:01:05 2011
@@ -459,13 +459,15 @@
model.mol[-1].file_model = orig_model_num[i]
- def rotate(self, R=None, origin=None):
+ def rotate(self, R=None, origin=None, model=None):
"""Method stub for rotating a structure.
@keyword R: The forwards rotation matrix.
@type R: numpy 3D, rank-2 array
@keyword origin: The origin of the rotation.
@type origin: numpy 3D, rank-1 array
+ @keyword model: The model to rotate. If None, all models will
be rotated.
+ @type model: int
"""
# Raise the error.
Modified: 1.3/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/internal.py?rev=14897&r1=14896&r2=14897&view=diff
==============================================================================
--- 1.3/generic_fns/structure/internal.py (original)
+++ 1.3/generic_fns/structure/internal.py Mon Oct 24 15:01:05 2011
@@ -1020,19 +1020,21 @@
return True
- def rotate(self, R=None, origin=None):
+ def rotate(self, R=None, origin=None, model=None):
"""Rotate the structural information about the given origin.
@keyword R: The forwards rotation matrix.
@type R: numpy 3D, rank-2 array
@keyword origin: The origin of the rotation.
@type origin: numpy 3D, rank-1 array
+ @keyword model: The model to rotate. If None, all models will
be rotated.
+ @type model: int
"""
# Loop over the models.
- for model in self.model_loop():
+ for model_cont in self.model_loop(model):
# Loop over the molecules.
- for mol in model.mol:
+ for mol in model_cont.mol:
# Loop over the atoms.
for i in range(len(mol.atom_num)):
# The origin to atom vector.
Modified: 1.3/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/main.py?rev=14897&r1=14896&r2=14897&view=diff
==============================================================================
--- 1.3/generic_fns/structure/main.py (original)
+++ 1.3/generic_fns/structure/main.py Mon Oct 24 15:01:05 2011
@@ -387,13 +387,15 @@
cdp.structure.load_xyz(file_path, read_mol=read_mol,
set_mol_name=set_mol_name, read_model=read_model,
set_model_num=set_model_num, verbosity=verbosity)
-def rotate(R=None, origin=None):
+def rotate(R=None, origin=None, model=None):
"""Rotate the structural data about the origin by the specified forwards
rotation.
@keyword R: The forwards rotation matrix.
@type R: numpy 3D, rank-2 array or a 3x3 list of floats
@keyword origin: The origin of the rotation. If not supplied, the
origin will be set to [0, 0, 0].
@type origin: numpy 3D, rank-1 array or list of len 3 or None
+ @keyword model: The model to rotate. If None, all models will be
rotated.
+ @type model: int
"""
# Test if the current data pipe exists.
@@ -412,7 +414,7 @@
origin = array(origin, float64)
# Call the specific code.
- cdp.structure.rotate(R=R, origin=origin)
+ cdp.structure.rotate(R=R, origin=origin, model=model)
def set_vector(spin=None, xh_vect=None):
Modified: 1.3/prompt/structure.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/structure.py?rev=14897&r1=14896&r2=14897&view=diff
==============================================================================
--- 1.3/prompt/structure.py (original)
+++ 1.3/prompt/structure.py Mon Oct 24 15:01:05 2011
@@ -438,30 +438,33 @@
generic_fns.structure.main.read_xyz(file=file, dir=dir,
read_mol=read_mol, set_mol_name=set_mol_name, read_model=read_model,
set_model_num=set_model_num)
- def rotate(self, R=None, origin=None):
+ def rotate(self, R=None, origin=None, model=None):
# Function intro text.
if self._exec_info.intro:
text = self._exec_info.ps3 + "structure.rotate("
text = text + "R=" + repr(R)
- text = text + ", origin=" + repr(origin) + ")"
+ text = text + ", origin=" + repr(origin)
+ text = text + ", model=" + repr(model) + ")"
print(text)
# The argument checks.
arg_check.is_float_matrix(R, 'rotation matrix', dim=(3,3))
arg_check.is_float_array(origin, 'origin of rotation', size=3,
can_be_none=True)
-
- # Execute the functional code.
- generic_fns.structure.main.rotate(R=R, origin=origin)
+ arg_check.is_int(model, 'model', can_be_none=True)
+
+ # Execute the functional code.
+ generic_fns.structure.main.rotate(R=R, origin=origin, model=model)
# The function doc info.
rotate._doc_title = "Rotate the internal structural object about the
given origin by the rotation matrix."
rotate._doc_title_short = "Structure rotation."
rotate._doc_args = [
["R", "The rotation matrix in forwards rotation notation."],
- ["origin", "The origin or pivot of the rotation."]
+ ["origin", "The origin or pivot of the rotation."],
+ ["model", "The model to rotate (which if not set will cause all
models to be rotated)."]
]
rotate._doc_desc = """
- This is used to rotate the internal structural data by the given
rotation matrix. If the origin is supplied, then this will act as the pivot
of the rotation. Otherwise, all structural data will be rotated about the
point [0, 0, 0].
+ This is used to rotate the internal structural data by the given
rotation matrix. If the origin is supplied, then this will act as the pivot
of the rotation. Otherwise, all structural data will be rotated about the
point [0, 0, 0]. The model argument can be used to rotate only specific
models.
"""
_build_doc(rotate)
r14897 - in /1.3: generic_fns/structure/ prompt/