Author: bugman
Date: Wed Nov 25 18:38:14 2015
New Revision: 28108
URL: http://svn.gna.org/viewcvs/relax?rev=28108&view=rev
Log:
Modified the assemble_structural_coordinates() method to return more
information.
This is from the pipe_control.structure.main module. The 'lists' boolean
argument is now accepted
which will cause the function to additionally return the object ID list per
molecule, the model
number list per molecule, and the molecule name list per molecule.
Modified:
trunk/pipe_control/structure/main.py
Modified: trunk/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/main.py?rev=28108&r1=28107&r2=28108&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py (original)
+++ trunk/pipe_control/structure/main.py Wed Nov 25 18:38:14 2015
@@ -112,7 +112,7 @@
print("Created the empty model number %s." % model_num)
-def assemble_structural_coordinates(pipes=None, models=None, molecules=None,
atom_id=None):
+def assemble_structural_coordinates(pipes=None, models=None, molecules=None,
atom_id=None, lists=False):
"""Assemble the common atomic coordinates taking sequence alignments into
account.
@keyword pipes: The data pipes to assemble the coordinates from.
@@ -123,6 +123,8 @@
@type molecules: None or list of lists of str
@keyword atom_id: The molecule, residue, and atom identifier string.
This matches the spin ID string format.
@type atom_id: str or None
+ @keyword lists: A flag which if true will cause the object ID list per
molecule, the model number list per molecule, and the molecule name list per
molecule to also be returned.
+ @type lists: bool
@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 common list of molecule names; the common list of residue names;
the common list of residue numbers; the common list of atom names; the common
list of element names.
@rtype: numpy rank-3 float64 array, list of str, list of str,
list of str, list of int, list of str, list of str
"""
@@ -196,7 +198,10 @@
# Assemble and return the atomic coordinates and common atom information.
coord, mol_name_common, res_name_common, res_num_common, atom_name_common,
element_common = assemble_coord_array(atom_pos=atom_pos, mol_names=mol_names,
res_names=res_names, res_nums=res_nums, atom_names=atom_names,
elements=elements, sequences=one_letter_codes, skip=skip)
- return coord, ids, mol_name_common, res_name_common, res_num_common,
atom_name_common, element_common
+ if lists:
+ return coord, ids, object_id_list, model_list, molecule_list,
mol_name_common, res_name_common, res_num_common, atom_name_common,
element_common
+ else:
+ return coord, ids, mol_name_common, res_name_common, res_num_common,
atom_name_common, element_common
def assemble_structural_objects(pipes=None, models=None, molecules=None):
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