Author: bugman
Date: Tue Feb 1 20:03:23 2011
New Revision: 12491
URL: http://svn.gna.org/viewcvs/relax?rev=12491&view=rev
Log:
Shifted some of the code out of specific_fns/model_free/bmrb.py for use in
generic_fns/relax_data.py.
Modified:
branches/bmrb/generic_fns/bmrb.py
branches/bmrb/generic_fns/relax_data.py
branches/bmrb/specific_fns/model_free/bmrb.py
Modified: branches/bmrb/generic_fns/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/bmrb.py?rev=12491&r1=12490&r2=12491&view=diff
==============================================================================
--- branches/bmrb/generic_fns/bmrb.py (original)
+++ branches/bmrb/generic_fns/bmrb.py Tue Feb 1 20:03:23 2011
@@ -115,6 +115,51 @@
create_spin(spin_num=spin_nums[i], spin_name=spin_names[i],
res_num=res_nums[i], res_name=res_names[i], mol_name=mol_names[i])
+def molecule_names(data):
+ """Generate the molecule names list.
+
+ @param data: An element of data from bmrblib.
+ @type data: dict
+ @return: The list of molecule names.
+ @rtype: list of str
+ """
+
+ # The molecule index and name.
+ mol_index = []
+ for i in range(N):
+ if 'entity_ids' in keys and data['entity_ids'] != None and
data['entity_ids'][i] != None:
+ mol_index.append(int(data['entity_ids'][i]) -1 )
+ else:
+ mol_index = [0]*N
+ mol_names = []
+ for i in range(N):
+ mol_names.append(cdp.mol[mol_index[i]].name)
+
+
+def num_spins(data):
+ """Determine the number of spins in the given data.
+
+ @param data: An element of data from bmrblib.
+ @type data: dict
+ @return: The number of spins.
+ @rtype: int
+ """
+
+ # The number of spins.
+ N = 0
+ if data['data_ids']:
+ N = len(data['data_ids'])
+ elif data['entity_ids']:
+ N = len(data['entity_ids'])
+ elif data['res_nums']:
+ N = len(data['res_nums'])
+ elif data['s2']:
+ N = len(data['s2'])
+
+ # Return the number.
+ return N
+
+
def read(file=None, directory=None, version='3.1'):
"""Read the contents of a BMRB NMR-STAR formatted file."""
Modified: branches/bmrb/generic_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/relax_data.py?rev=12491&r1=12490&r2=12491&view=diff
==============================================================================
--- branches/bmrb/generic_fns/relax_data.py (original)
+++ branches/bmrb/generic_fns/relax_data.py Tue Feb 1 20:03:23 2011
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2010 Edward d'Auvergne
#
+# Copyright (C) 2003-2011 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -33,7 +33,7 @@
# relax module imports.
from data import Relax_data_store; ds = Relax_data_store()
from data.exp_info import ExpInfo
-from generic_fns.bmrb import generate_sequence
+from generic_fns import bmrb
from generic_fns.mol_res_spin import create_spin, exists_mol_res_spin_data,
find_index, generate_spin_id, get_molecule_names, return_spin,
spin_index_loop, spin_loop
from generic_fns import pipes
from generic_fns import value
@@ -242,6 +242,9 @@
# Get the relaxation data.
for data in star.relaxation.loop():
+ # Store the keys.
+ keys = data.keys()
+
# Create the labels.
ri_label = data['data_type']
frq = float(data['frq']) * 1e6
@@ -249,8 +252,18 @@
# Round the label to the nearest factor of 10.
frq_label = str(int(round(float(data['frq'])/10)*10))
+ # The number of spins.
+ N = bmrb.num_spins(data)
+
+ # No data in the saveframe.
+ if N == 0:
+ continue
+
+ # The molecule names.
+ mol_names = bmrb.molecule_names(data)
+
# Pack the data.
- pack_data(ri_label, frq_label, frq, data['data'], data['errors'],
res_nums=data['res_nums'], res_names=data['res_names'], spin_nums=None,
spin_names=data['atom_names'], gen_seq=True)
+ pack_data(ri_label, frq_label, frq, data['data'], data['errors'],
mol_names=mol_names, res_nums=data['res_nums'], res_names=data['res_names'],
spin_nums=None, spin_names=data['atom_names'], gen_seq=True)
@@ -807,7 +820,7 @@
# Generate the sequence.
if gen_seq:
- generate_sequence(N, spin_ids=spin_ids, spin_nums=spin_nums,
spin_names=spin_names, res_nums=res_nums, res_names=res_names,
mol_names=mol_names)
+ bmrb.generate_sequence(N, spin_ids=spin_ids, spin_nums=spin_nums,
spin_names=spin_names, res_nums=res_nums, res_names=res_names,
mol_names=mol_names)
# Loop over the spin data.
for i in range(N):
Modified: branches/bmrb/specific_fns/model_free/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/specific_fns/model_free/bmrb.py?rev=12491&r1=12490&r2=12491&view=diff
==============================================================================
--- branches/bmrb/specific_fns/model_free/bmrb.py (original)
+++ branches/bmrb/specific_fns/model_free/bmrb.py Tue Feb 1 20:03:23 2011
@@ -139,16 +139,8 @@
if N == 0:
continue
- # The molecule index and name.
- mol_index = []
- for i in range(N):
- if 'entity_ids' in keys and data['entity_ids'] != None and
data['entity_ids'][i] != None:
- mol_index.append(int(data['entity_ids'][i]) -1 )
- else:
- mol_index = [0]*N
- mol_names = []
- for i in range(N):
- mol_names.append(cdp.mol[mol_index[i]].name)
+ # The molecule names.
+ mol_names = bmrb.molecule_names(data)
# Generate the spin IDs.
spin_ids = []
r12491 - in /branches/bmrb: generic_fns/bmrb.py generic_fns/relax_data.py specific_fns/model_free/bmrb.py