Author: bugman
Date: Wed Nov 9 11:55:34 2011
New Revision: 14991
URL: http://svn.gna.org/viewcvs/relax?rev=14991&view=rev
Log:
Added the atom ID argument to the structure.rotate and structure.translate
user functions.
This allows subsets of molecules or models to be translated and rotated.
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=14991&r1=14990&r2=14991&view=diff
==============================================================================
--- 1.3/generic_fns/structure/api_base.py (original)
+++ 1.3/generic_fns/structure/api_base.py Wed Nov 9 11:55:34 2011
@@ -539,7 +539,7 @@
model.mol[-1].file_model = orig_model_num[i]
- def rotate(self, R=None, origin=None, model=None):
+ def rotate(self, R=None, origin=None, model=None, atom_id=None):
"""Method stub for rotating a structure.
@keyword R: The forwards rotation matrix.
@@ -548,6 +548,8 @@
@type origin: numpy 3D, rank-1 array
@keyword model: The model to rotate. If None, all models will
be rotated.
@type model: int
+ @keyword atom_id: The molecule, residue, and atom identifier
string. Only atoms matching this selection will be used.
+ @type atom_id: str or None
"""
# Raise the error.
@@ -579,13 +581,15 @@
target.append(file_root(file) + '_mol' + repr(mol_num))
- def translate(self, T=None, model=None):
+ def translate(self, T=None, model=None, atom_id=None):
"""Method stub for displacing the structural information by the
given translation vector.
@keyword T: The translation vector.
@type T: numpy 3D, rank-1 array
@keyword model: The model to rotate. If None, all models will
be rotated.
@type model: int
+ @keyword atom_id: The molecule, residue, and atom identifier
string. Only atoms matching this selection will be used.
+ @type atom_id: str or None
"""
# 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=14991&r1=14990&r2=14991&view=diff
==============================================================================
--- 1.3/generic_fns/structure/internal.py (original)
+++ 1.3/generic_fns/structure/internal.py Wed Nov 9 11:55:34 2011
@@ -1164,7 +1164,7 @@
return True
- def rotate(self, R=None, origin=None, model=None):
+ def rotate(self, R=None, origin=None, model=None, atom_id=None):
"""Rotate the structural information about the given origin.
@keyword R: The forwards rotation matrix.
@@ -1173,14 +1173,29 @@
@type origin: numpy 3D, rank-1 array
@keyword model: The model to rotate. If None, all models will
be rotated.
@type model: int
- """
+ @keyword atom_id: The molecule, residue, and atom identifier
string. Only atoms matching this selection will be used.
+ @type atom_id: str or None
+ """
+
+ # Generate the selection object.
+ sel_obj = None
+ if atom_id:
+ sel_obj = Selection(atom_id)
# Loop over the models.
for model_cont in self.model_loop(model):
# Loop over the molecules.
for mol in model_cont.mol:
+ # Skip non-matching molecules.
+ if sel_obj and not sel_obj.contains_mol(mol.mol_name):
+ continue
+
# Loop over the atoms.
for i in range(len(mol.atom_num)):
+ # Skip non-matching atoms.
+ if sel_obj and not
sel_obj.contains_spin(mol.atom_num[i], mol.atom_name[i], mol.res_num[i],
mol.res_name[i], mol.mol_name):
+ continue
+
# The origin to atom vector.
vect = array([mol.x[i], mol.y[i], mol.z[i]], float64) -
origin
@@ -1194,21 +1209,36 @@
mol.z[i] = pos[2]
- def translate(self, T=None, model=None):
+ def translate(self, T=None, model=None, atom_id=None):
"""Displace the structural information by the given translation
vector.
@keyword T: The translation vector.
@type T: numpy 3D, rank-1 array
@keyword model: The model to rotate. If None, all models will
be rotated.
@type model: int
- """
+ @keyword atom_id: The molecule, residue, and atom identifier
string. Only atoms matching this selection will be used.
+ @type atom_id: str or None
+ """
+
+ # Generate the selection object.
+ sel_obj = None
+ if atom_id:
+ sel_obj = Selection(atom_id)
# Loop over the models.
for model_cont in self.model_loop(model):
# Loop over the molecules.
for mol in model_cont.mol:
+ # Skip non-matching molecules.
+ if sel_obj and not sel_obj.contains_mol(mol.mol_name):
+ continue
+
# Loop over the atoms.
for i in range(len(mol.atom_num)):
+ # Skip non-matching atoms.
+ if sel_obj and not
sel_obj.contains_spin(mol.atom_num[i], mol.atom_name[i], mol.res_num[i],
mol.res_name[i], mol.mol_name):
+ continue
+
# Translate.
mol.x[i] = mol.x[i] + T[0]
mol.y[i] = mol.y[i] + T[1]
Modified: 1.3/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/main.py?rev=14991&r1=14990&r2=14991&view=diff
==============================================================================
--- 1.3/generic_fns/structure/main.py (original)
+++ 1.3/generic_fns/structure/main.py Wed Nov 9 11:55:34 2011
@@ -500,7 +500,7 @@
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, model=None):
+def rotate(R=None, origin=None, model=None, atom_id=None):
"""Rotate the structural data about the origin by the specified forwards
rotation.
@keyword R: The forwards rotation matrix.
@@ -509,6 +509,8 @@
@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
+ @keyword atom_id: The molecule, residue, and atom identifier string.
Only atoms matching this selection will be used.
+ @type atom_id: str or None
"""
# Test if the current data pipe exists.
@@ -527,7 +529,7 @@
origin = array(origin, float64)
# Call the specific code.
- cdp.structure.rotate(R=R, origin=origin, model=model)
+ cdp.structure.rotate(R=R, origin=origin, model=model, atom_id=atom_id)
def set_vector(spin=None, xh_vect=None):
@@ -589,13 +591,15 @@
rotate(R=R[i], origin=pivot[i], model=models[i])
-def translate(T=None, model=None):
+def translate(T=None, model=None, atom_id=None):
"""Shift the structural data by the specified translation vector.
@keyword T: The translation vector.
@type T: numpy rank-1, 3D array or list of float
@keyword model: The model to translate. If None, all models will be
rotated.
- @type model: int
+ @type model: int or None
+ @keyword atom_id: The molecule, residue, and atom identifier string.
Only atoms matching this selection will be used.
+ @type atom_id: str or None
"""
# Test if the current data pipe exists.
@@ -609,7 +613,7 @@
T = array(T, float64)
# Call the specific code.
- cdp.structure.translate(T=T, model=model)
+ cdp.structure.translate(T=T, model=model, atom_id=atom_id)
def vectors(attached=None, spin_id=None, model=None, verbosity=1, ave=True,
unit=True):
Modified: 1.3/prompt/structure.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/structure.py?rev=14991&r1=14990&r2=14991&view=diff
==============================================================================
--- 1.3/prompt/structure.py (original)
+++ 1.3/prompt/structure.py Wed Nov 9 11:55:34 2011
@@ -577,22 +577,24 @@
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, model=None):
+ def rotate(self, R=None, origin=None, model=None, atom_id=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 + ", model=" + repr(model) + ")"
+ text = text + ", model=" + repr(model)
+ text = text + ", atom_id=" + repr(atom_id) + ")"
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)
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)
+ arg_check.is_str(atom_id, 'atom identification string',
can_be_none=True)
+
+ # Execute the functional code.
+ generic_fns.structure.main.rotate(R=R, origin=origin, model=model,
atom_id=atom_id)
# The function doc info.
rotate._doc_title = "Rotate the internal structural object about the
given origin by the rotation matrix."
@@ -670,27 +672,30 @@
_build_doc(superimpose)
- def translate(self, T=None, model=None):
+ def translate(self, T=None, model=None, atom_id=None):
# Function intro text.
if self._exec_info.intro:
text = self._exec_info.ps3 + "structure.translate("
text = text + "T=" + repr(T)
- text = text + ", model=" + repr(model) + ")"
+ text = text + ", model=" + repr(model)
+ text = text + ", atom_id=" + repr(atom_id) + ")"
print(text)
# The argument checks.
arg_check.is_float_array(T, 'translation vector', size=3)
arg_check.is_int(model, 'model', can_be_none=True)
-
- # Execute the functional code.
- generic_fns.structure.main.translate(T=T, model=model)
+ arg_check.is_str(atom_id, 'atom identification string',
can_be_none=True)
+
+ # Execute the functional code.
+ generic_fns.structure.main.translate(T=T, model=model,
atom_id=atom_id)
# The function doc info.
translate._doc_title = "Laterally displace the internal structural
object by the translation vector."
translate._doc_title_short = "Structure translation."
translate._doc_args = [
["T", "The translation vector."],
- ["model", "The model to translate (which if not set will cause all
models to be translate)."]
+ ["model", "The model to translate (which if not set will cause all
models to be translate)."],
+ ["atom_id", "The atom identification string."]
]
translate._doc_desc = """
This is used to translate the internal structural data by the given
translation vector. The model argument can be used to translate specific
models.
r14991 - in /1.3: generic_fns/structure/ prompt/