Author: bugman
Date: Wed Oct 26 10:25:23 2011
New Revision: 14918
URL: http://svn.gna.org/viewcvs/relax?rev=14918&view=rev
Log:
Added the centroid arg to the structure.displacement user function for
pivoted motions.
By specifying the centroid position for all structures, a pivoted motion is
assumed. All
displacements will be zero, and the angles will be that of the pivoting
motion.
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=14918&r1=14917&r2=14918&view=diff
==============================================================================
--- 1.3/generic_fns/structure/api_base.py (original)
+++ 1.3/generic_fns/structure/api_base.py Wed Oct 26 10:25:23 2011
@@ -909,7 +909,7 @@
return R
- def _calculate(self, model_from=None, model_to=None, coord_from=None,
coord_to=None):
+ def _calculate(self, model_from=None, model_to=None, coord_from=None,
coord_to=None, centroid=None):
"""Calculate the rotational and translational displacements using
the given coordinate sets.
This uses the Kabsch algorithm
(http://en.wikipedia.org/wiki/Kabsch_algorithm).
@@ -923,11 +923,17 @@
@type coord_from: numpy rank-2, Nx3 array
@keyword coord_to: The list of atomic coordinates for the
ending structure.
@type coord_to: numpy rank-2, Nx3 array
+ @keyword centroid: An alternative position of the centroid,
used for studying pivoted systems.
+ @type centroid: list of float or numpy rank-1, 3D array
"""
# Calculate the centroids.
- centroid_from = self._calc_centriod(coord_from)
- centroid_to = self._calc_centriod(coord_to)
+ if centroid != None:
+ centroid_from = centroid
+ centroid_to = centroid
+ else:
+ centroid_from = self._calc_centriod(coord_from)
+ centroid_to = self._calc_centriod(coord_to)
# The translation.
trans_vect = centroid_to - centroid_from
Modified: 1.3/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/internal.py?rev=14918&r1=14917&r2=14918&view=diff
==============================================================================
--- 1.3/generic_fns/structure/internal.py (original)
+++ 1.3/generic_fns/structure/internal.py Wed Oct 26 10:25:23 2011
@@ -781,7 +781,7 @@
return data
- def calc_displacement(self, model_from=None, model_to=None,
atom_id=None):
+ def calc_displacement(self, model_from=None, model_to=None,
atom_id=None, centroid=None):
"""Calculate the rotational and translational displacement between
two structural models.
@keyword model_from: The optional model number for the
starting position of the displacement.
@@ -790,6 +790,8 @@
@type model_to: int or None
@keyword atom_id: The molecule, residue, and atom
identifier string. This matches the spin ID string format.
@type atom_id: str or None
+ @keyword centroid: An alternative position of the centroid,
used for studying pivoted systems.
+ @type centroid: list of float or numpy rank-1, 3D array
"""
# Convert the model_from and model_to args to lists, is supplied.
@@ -828,7 +830,7 @@
coord_to.append(pos[0])
# Send to the base container for the calculations.
- self.displacements._calculate(model_from=model_from[i],
model_to=model_to[j], coord_from=array(coord_from), coord_to=array(coord_to))
+ self.displacements._calculate(model_from=model_from[i],
model_to=model_to[j], coord_from=array(coord_from), coord_to=array(coord_to),
centroid=centroid)
def delete(self):
Modified: 1.3/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/main.py?rev=14918&r1=14917&r2=14918&view=diff
==============================================================================
--- 1.3/generic_fns/structure/main.py (original)
+++ 1.3/generic_fns/structure/main.py Wed Oct 26 10:25:23 2011
@@ -61,7 +61,7 @@
del spin.xh_vect
-def displacement(model_from=None, model_to=None, atom_id=None):
+def displacement(model_from=None, model_to=None, atom_id=None,
centroid=None):
"""Calculate the rotational and translational displacement between two
structural models.
This will just redirect straight to the API.
@@ -72,9 +72,11 @@
@type model_to: int or None
@keyword atom_id: The molecule, residue, and atom identifier
string. This matches the spin ID string format.
@type atom_id: str or None
- """
-
- cdp.structure.calc_displacement(model_from=model_from,
model_to=model_to, atom_id=atom_id)
+ @keyword centroid: An alternative position of the centroid,
used for studying pivoted systems.
+ @type centroid: list of float or numpy rank-1, 3D array
+ """
+
+ cdp.structure.calc_displacement(model_from=model_from,
model_to=model_to, atom_id=atom_id, centroid=centroid)
def get_pos(spin_id=None, str_id=None, ave_pos=False):
Modified: 1.3/prompt/structure.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/structure.py?rev=14918&r1=14917&r2=14918&view=diff
==============================================================================
--- 1.3/prompt/structure.py (original)
+++ 1.3/prompt/structure.py Wed Oct 26 10:25:23 2011
@@ -195,22 +195,24 @@
_build_doc(delete)
- def displacement(self, model_from=None, model_to=None, atom_id=None):
+ def displacement(self, model_from=None, model_to=None, atom_id=None,
centroid=None):
# Function intro text.
if self._exec_info.intro:
text = self._exec_info.ps3 + "structure.displacement("
text = text + "model_from=" + repr(model_from)
text = text + ", model_to=" + repr(model_to)
- text = text + ", atom_id=" + repr(atom_id) + ")"
+ text = text + ", atom_id=" + repr(atom_id)
+ text = text + ", centroid=" + repr(centroid) + ")"
print(text)
# The argument checks.
arg_check.is_int(model_from, 'model from', can_be_none=True)
arg_check.is_int(model_to, 'model to', can_be_none=True)
arg_check.is_str(atom_id, 'atom identification string',
can_be_none=True)
-
- # Execute the functional code.
- generic_fns.structure.main.displacement(model_from=model_from,
model_to=model_to, atom_id=atom_id)
+ arg_check.is_float_array(centroid, 'centroid position',
can_be_none=True)
+
+ # Execute the functional code.
+ generic_fns.structure.main.displacement(model_from=model_from,
model_to=model_to, atom_id=atom_id, centroid=centroid)
# The function doc info.
displacement._doc_title = "Determine the rotational and translational
displacement between a set of models."
@@ -218,12 +220,15 @@
displacement._doc_args = [
["model_from", "The optional model number for the starting position
of the displacement."],
["model_to", "The optional model number for the ending position of
the displacement."],
- ["atom_id", "The atom identification string."]
+ ["atom_id", "The atom identification string."],
+ ["centroid", "The alternative position of the centroid."]
]
displacement._doc_desc = """
This user function allows the rotational and translational
displacement between two models of the same structure to be calculated. The
information will be printed out in various formats and held in the relax data
store. This is directional, so there is a starting and ending position for
each displacement. If the starting and ending models are not specified, then
the displacements in all directions between all models will be calculated.
The atom ID, which uses the same notation as the spin ID strings,
can be used to restrict the displacement calculation to certain molecules,
residues, or atoms. This is useful if studying domain motions, secondary
structure rearrangements, amino acid side chain rotations, etc.
+
+ By supplying the position of the centroid, an alternative position
than the standard rigid body centre is used as the focal point of the motion.
The allows, for example, a pivot of a rotational domain motion to be
specified. This is not a formally correct algorithm, all translations will
be zero, but does give an indication to the amplitude of the pivoting angle.
"""
displacement._doc_examples = """
To determine the rotational and translational displacements between
all sets of models, type:
r14918 - in /1.3: generic_fns/structure/ prompt/