Author: bugman
Date: Wed Oct 26 11:51:44 2011
New Revision: 14924
URL: http://svn.gna.org/viewcvs/relax?rev=14924&view=rev
Log:
Shifted the structural API calc_displacement() method into the main module.
Modified:
1.3/generic_fns/structure/api_base.py
1.3/generic_fns/structure/internal.py
1.3/generic_fns/structure/main.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=14924&r1=14923&r2=14924&view=diff
==============================================================================
--- 1.3/generic_fns/structure/api_base.py (original)
+++ 1.3/generic_fns/structure/api_base.py Wed Oct 26 11:51:44 2011
@@ -184,21 +184,6 @@
raise RelaxImplementError
- def calc_displacement(self, model_from=None, model_to=None,
atom_id=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.
- @type model_from: int or None
- @keyword model_to: The optional model number for the ending
position of the displacement.
- @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
- """
-
- # Raise the error.
- raise RelaxImplementError
-
-
def delete(self):
"""Prototype method stub for deleting all structural data from the
current data pipe."""
Modified: 1.3/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/internal.py?rev=14924&r1=14923&r2=14924&view=diff
==============================================================================
--- 1.3/generic_fns/structure/internal.py (original)
+++ 1.3/generic_fns/structure/internal.py Wed Oct 26 11:51:44 2011
@@ -781,58 +781,6 @@
return data
- 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.
- @type model_from: int or None
- @keyword model_to: The optional model number for the ending
position of the displacement.
- @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.
- if model_from != None:
- model_from = [model_from]
- if model_to != None:
- model_to = [model_to]
-
- # Create a list of all models.
- models = []
- for model in self.model_loop():
- models.append(model.num)
-
- # Set model_from or model_to to all models if None.
- if model_from == None:
- model_from = models
- if model_to == None:
- model_to = models
-
- # Initialise the data structure.
- if not hasattr(self, 'displacements'):
- self.displacements = Displacements()
-
- # Loop over the starting models.
- for i in range(len(model_from)):
- # Assemble the atomic coordinates.
- coord_from = []
- for pos in self.atom_loop(atom_id=atom_id,
model_num=model_from[i], pos_flag=True):
- coord_from.append(pos[0])
-
- # Loop over the ending models.
- for j in range(len(model_to)):
- # Assemble the atomic coordinates.
- coord_to = []
- for pos in self.atom_loop(atom_id=atom_id,
model_num=model_to[j], pos_flag=True):
- 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),
centroid=centroid)
-
-
def delete(self):
"""Delete all the structural information."""
Modified: 1.3/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/main.py?rev=14924&r1=14923&r2=14924&view=diff
==============================================================================
--- 1.3/generic_fns/structure/main.py (original)
+++ 1.3/generic_fns/structure/main.py Wed Oct 26 11:51:44 2011
@@ -34,6 +34,7 @@
from generic_fns import molmol, relax_re
from generic_fns.mol_res_spin import create_spin, exists_mol_res_spin_data,
generate_spin_id, linear_ave, return_molecule, return_residue, return_spin,
spin_loop
from generic_fns import pipes
+from generic_fns.structure.api_base import Displacements
from generic_fns.structure.internal import Internal
from generic_fns.structure.scientific import Scientific_data
from relax_errors import RelaxError, RelaxFileError, RelaxNoPdbError,
RelaxNoSequenceError
@@ -63,8 +64,6 @@
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.
@keyword model_from: The optional model number for the starting
position of the displacement.
@type model_from: int or None
@@ -76,7 +75,43 @@
@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)
+ # Convert the model_from and model_to args to lists, is supplied.
+ if model_from != None:
+ model_from = [model_from]
+ if model_to != None:
+ model_to = [model_to]
+
+ # Create a list of all models.
+ models = []
+ for model in cdp.structure.model_loop():
+ models.append(model.num)
+
+ # Set model_from or model_to to all models if None.
+ if model_from == None:
+ model_from = models
+ if model_to == None:
+ model_to = models
+
+ # Initialise the data structure.
+ if not hasattr(cdp.structure, 'displacements'):
+ cdp.structure.displacements = Displacements()
+
+ # Loop over the starting models.
+ for i in range(len(model_from)):
+ # Assemble the atomic coordinates.
+ coord_from = []
+ for pos in cdp.structure.atom_loop(atom_id=atom_id,
model_num=model_from[i], pos_flag=True):
+ coord_from.append(pos[0])
+
+ # Loop over the ending models.
+ for j in range(len(model_to)):
+ # Assemble the atomic coordinates.
+ coord_to = []
+ for pos in cdp.structure.atom_loop(atom_id=atom_id,
model_num=model_to[j], pos_flag=True):
+ coord_to.append(pos[0])
+
+ # Send to the base container for the calculations.
+ cdp.structure.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 get_pos(spin_id=None, str_id=None, ave_pos=False):
r14924 - in /1.3/generic_fns/structure: api_base.py internal.py main.py