Author: bugman
Date: Fri Jan 30 18:52:30 2015
New Revision: 27403
URL: http://svn.gna.org/viewcvs/relax?rev=27403&view=rev
Log:
Modified the data returned by
lib.structure.internal.coordinates.assemble_atomic_coordinates().
The function will now assemble simple lists of object IDs, model numbers and
molecule names with
each list element corresponding to a different structural model. This will
be very useful for
converting from the complicated pipes, models, and molecules user function
arguments into relax data
store independent flat lists.
Modified:
trunk/lib/structure/internal/coordinates.py
Modified: trunk/lib/structure/internal/coordinates.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/internal/coordinates.py?rev=27403&r1=27402&r2=27403&view=diff
==============================================================================
--- trunk/lib/structure/internal/coordinates.py (original)
+++ trunk/lib/structure/internal/coordinates.py Fri Jan 30 18:52:30 2015
@@ -45,12 +45,15 @@
@type atom_id: None or str
@keyword seq_info_flag: A flag which if True will cause the
atomic sequence information to be assembled and returned. This includes the
molecule names, residue names, residue numbers, atom names, and elements.
@type seq_info_flag: bool
- @return: The list of structure IDs for each
molecule, the atom positions per molecule and per residue, the molecule names
per molecule and per residue, the residue names per molecule and per residue,
the residue numbers per molecule and per residue, the atom names per molecule
and per residue, the atomic elements per molecule and per residue, the one
letter codes for the residue sequence, the number of molecules.
- @rtype: list of str, list of list of dict of
str, list of list of dict of str, list of list of dict of str, list of list
of dict of str, list of list of dict of str, list of list of dict of str,
list of str, int
+ @return: The list of structure IDs for each
molecule, the object ID list per molecule, the model number list per
molecule, the molecule name list per molecule, the atom positions per
molecule and per residue, the molecule names per molecule and per residue,
the residue names per molecule and per residue, the residue numbers per
molecule and per residue, the atom names per molecule and per residue, the
atomic elements per molecule and per residue, the one letter codes for the
residue sequence, the number of molecules.
+ @rtype: list of str, list of str, list of
int, list of str, list of list of dict of str, list of list of dict of str,
list of list of dict of str, list of list of dict of str, list of list of
dict of str, list of list of dict of str, list of str, int
"""
print("Assembling all atomic coordinates:")
ids = []
+ object_id_list = []
+ model_list = []
+ molecule_list = []
atom_pos = []
mol_names = []
res_names = []
@@ -60,7 +63,7 @@
one_letter_codes = []
for struct_index in range(len(objects)):
# Printout.
- print(" Data pipe: %s" % object_names[struct_index])
+ print(" Object ID: %s" % object_names[struct_index])
# Validate the models.
objects[struct_index].validate_models(verbosity=0)
@@ -96,6 +99,11 @@
# Change the current molecule name and residue number.
current_mol = mol_name
current_res = None
+
+ # Update the molecule lists.
+ object_id_list.append(object_names[struct_index])
+ model_list.append(model.num)
+ molecule_list.append(mol_name)
# Store the one letter codes for sequence alignment.
one_letter_codes.append(objects[struct_index].one_letter_codes(mol_name=mol_name))
@@ -148,7 +156,7 @@
num_mols = len(atom_names)
# Return the data.
- return ids, atom_pos, mol_names, res_names, res_nums, atom_names,
elements, one_letter_codes, num_mols
+ return ids, object_id_list, model_list, molecule_list, atom_pos,
mol_names, res_names, res_nums, atom_names, elements, one_letter_codes,
num_mols
def assemble_coord_array(objects=None, object_names=None, molecules=None,
models=None, atom_id=None, algorithm='NW70', matrix='BLOSUM62',
gap_open_penalty=1.0, gap_extend_penalty=1.0, end_gap_open_penalty=0.0,
end_gap_extend_penalty=0.0, seq_info_flag=False):
@@ -183,7 +191,7 @@
"""
# Assemble the atomic coordinates of all structures.
- ids, atom_pos, mol_names, res_names, res_nums, atom_names, elements,
one_letter_codes, num_mols = assemble_atomic_coordinates(objects=objects,
object_names=object_names, molecules=molecules, models=models,
atom_id=atom_id, seq_info_flag=seq_info_flag)
+ ids, object_id_list, model_list, molecule_list, atom_pos, mol_names,
res_names, res_nums, atom_names, elements, one_letter_codes, num_mols =
assemble_atomic_coordinates(objects=objects, object_names=object_names,
molecules=molecules, models=models, atom_id=atom_id,
seq_info_flag=seq_info_flag)
# Multiple sequence alignment.
if algorithm != None:
r27403 - /trunk/lib/structure/internal/coordinates.py