Author: bugman
Date: Thu Dec 11 10:20:56 2014
New Revision: 27073
URL: http://svn.gna.org/viewcvs/relax?rev=27073&view=rev
Log:
The coordinate assembly function now returns list of unique IDs.
This is for each structural object, model and molecule.
Modified:
trunk/lib/structure/internal/coordinates.py
trunk/pipe_control/structure/main.py
Modified: trunk/lib/structure/internal/coordinates.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/internal/coordinates.py?rev=27073&r1=27072&r2=27073&view=diff
==============================================================================
--- trunk/lib/structure/internal/coordinates.py (original)
+++ trunk/lib/structure/internal/coordinates.py Thu Dec 11 10:20:56 2014
@@ -39,12 +39,13 @@
@type molecules: None or list of lists of str
@keyword atom_id: The molecule, residue, and atom identifier string
of the coordinates of interest. This matches the spin ID string format.
@type atom_id: None or str
- @return: The array of atomic coordinates (first dimension
is the model and/or molecule, the second are the atoms, and the third are the
coordinates), and the list of element names for each atom (if the elements flag
is set).
- @rtype: numpy rank-3 float64 array, list of str
+ @return: The array of atomic coordinates (first dimension
is the model and/or molecule, the second are the atoms, and the third are the
coordinates); a list of unique IDs for each structural object, model, and
molecule; the list of element names for each atom (if the elements flag is set).
+ @rtype: numpy rank-3 float64 array, list of str, list of
str
"""
# Assemble the atomic coordinates of all structures.
print("Assembling all atomic coordinates:")
+ ids = []
atom_ids = []
atom_pos = []
atom_elem = []
@@ -94,6 +95,12 @@
atom_pos.append({})
atom_elem.append({})
+ # Create a new structure ID.
+ if model.num != None:
+ ids.append("%s, %i, %s" % (object_names[struct_index],
model.num, mol_name))
+ else:
+ ids.append("%s, %s" % (object_names[struct_index],
mol_name))
+
# A unique identifier.
if molecules != None:
id = ":%s&%s@%s" % (res_num, res_name, atom_name)
@@ -135,6 +142,6 @@
# Return the information.
if elements_flag:
- return coord, elements
+ return coord, ids, elements
else:
- return coord
+ return coord, ids
Modified: trunk/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/main.py?rev=27073&r1=27072&r2=27073&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py (original)
+++ trunk/pipe_control/structure/main.py Thu Dec 11 10:20:56 2014
@@ -136,7 +136,7 @@
raise RelaxError("The superimposition centre type '%s' is unknown. It
must be one of %s." % (centre_type, allowed))
# Assemble the atomic coordinates and obtain the corresponding element
information.
- coord, elements = assemble_coordinates(pipes=pipes, molecules=molecules,
models=models, atom_id=atom_id, elements_flag=True)
+ coord, ids, elements = assemble_coordinates(pipes=pipes,
molecules=molecules, models=models, atom_id=atom_id, elements_flag=True)
# The different algorithms.
if method == 'fit to mean':
@@ -195,8 +195,8 @@
@type molecules: None or list of lists of str
@keyword atom_id: The molecule, residue, and atom identifier string
of the coordinates of interest. This matches the spin ID string format.
@type atom_id: None or str
- @return: The array of atomic coordinates (first dimension
is the model and/or molecule, the second are the atoms, and the third are the
coordinates), and the list of element names for each atom (if the elements flag
is set).
- @rtype: numpy rank-3 float64 array, list of str
+ @return: The array of atomic coordinates (first dimension
is the model and/or molecule, the second are the atoms, and the third are the
coordinates); a list of unique IDs for each pipe, model, and molecule; the list
of element names for each atom (if the elements flag is set).
+ @rtype: numpy rank-3 float64 array, list of str, list of
str
"""
# The data pipes to use.
@@ -557,7 +557,7 @@
init_pos = array(init_pos)
# Assemble the atomic coordinates.
- coord = assemble_coordinates(pipes=pipes, molecules=molecules,
models=models, atom_id=atom_id)
+ coord, ids = assemble_coordinates(pipes=pipes, molecules=molecules,
models=models, atom_id=atom_id)
# Linear constraints for the pivot position (between -1000 and 1000
Angstrom).
A = zeros((6, 3), float64)
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