Author: bugman
Date: Mon Jul 2 19:59:32 2012
New Revision: 17135
URL: http://svn.gna.org/viewcvs/relax?rev=17135&view=rev
Log:
More BMRB fixes for the interatomic data design.
Modified:
branches/interatomic/generic_fns/bmrb.py
branches/interatomic/generic_fns/relax_data.py
branches/interatomic/specific_fns/model_free/bmrb.py
Modified: branches/interatomic/generic_fns/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/generic_fns/bmrb.py?rev=17135&r1=17134&r2=17135&view=diff
==============================================================================
--- branches/interatomic/generic_fns/bmrb.py (original)
+++ branches/interatomic/generic_fns/bmrb.py Mon Jul 2 19:59:32 2012
@@ -32,7 +32,7 @@
from data.exp_info import ExpInfo
import dep_check
from generic_fns import exp_info
-from generic_fns.mol_res_spin import create_spin, generate_spin_id,
return_residue, return_spin
+from generic_fns.mol_res_spin import create_spin, generate_spin_id,
return_residue, return_spin, set_spin_element, set_spin_isotope
from generic_fns.pipes import cdp_name
from info import Info_box
from relax_errors import RelaxError, RelaxFileError,
RelaxFileOverwriteError, RelaxNoModuleInstallError, RelaxNoPipeError
@@ -53,7 +53,7 @@
write(file=sys.stdout, version=version)
-def generate_sequence(N=0, spin_ids=None, spin_nums=None, spin_names=None,
res_nums=None, res_names=None, mol_names=None):
+def generate_sequence(N=0, spin_ids=None, spin_nums=None, spin_names=None,
res_nums=None, res_names=None, mol_names=None, isotopes=None, elements=None):
"""Generate the sequence data from the BRMB information.
@keyword N: The number of spins.
@@ -70,6 +70,10 @@
@type res_names: list of str or None
@keyword mol_names: The list of molecule names.
@type mol_names: list of str or None
+ @keyword isotopes: The optional list of isotope types.
+ @type isotopes: list of str or None
+ @keyword elements: The optional list of element types.
+ @type elements: list of str or None
"""
# The blank data.
@@ -97,7 +101,15 @@
continue
# Create the spin.
- 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])
+ spin = 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])
+
+ # Set the spin isotope and element.
+ spin_id = spin._spin_ids[0]
+ if elements:
+ set_spin_element(spin_id=spin_id, element=elements[i],
force=True)
+ if isotopes and elements:
+ isotope = "%s%s" % (isotopes[i], elements[i])
+ set_spin_isotope(spin_id=spin_id, isotope=isotope, force=True)
def list_sample_conditions(star):
Modified: branches/interatomic/generic_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/generic_fns/relax_data.py?rev=17135&r1=17134&r2=17135&view=diff
==============================================================================
--- branches/interatomic/generic_fns/relax_data.py (original)
+++ branches/interatomic/generic_fns/relax_data.py Mon Jul 2 19:59:32 2012
@@ -34,7 +34,7 @@
# relax module imports.
from data import Relax_data_store; ds = Relax_data_store()
from data.exp_info import ExpInfo
-from generic_fns import bmrb
+from generic_fns import bmrb, dipole_pair
from generic_fns.interatomic import create_interatom, return_interatom,
return_interatom_list
from generic_fns.mol_res_spin import Selection, create_spin,
exists_mol_res_spin_data, find_index, generate_spin_id, get_molecule_names,
return_spin, return_spin_from_selection, spin_index_loop, spin_loop
from generic_fns import pipes
@@ -175,7 +175,25 @@
mol_names = bmrb.molecule_names(data, N)
# Generate the sequence if needed.
- bmrb.generate_sequence(N, spin_names=data['atom_names'],
res_nums=data['res_nums'], res_names=data['res_names'], mol_names=mol_names)
+ bmrb.generate_sequence(N, spin_names=data['atom_names'],
res_nums=data['res_nums'], res_names=data['res_names'], mol_names=mol_names,
isotopes=data['isotope'], elements=data['atom_types'])
+
+ # The attached protons.
+ if data.has_key('atom_names_2'):
+ # Generate the proton spins.
+ bmrb.generate_sequence(N, spin_names=data['atom_names_2'],
res_nums=data['res_nums'], res_names=data['res_names'], mol_names=mol_names,
isotopes=data['isotope_2'], elements=data['atom_types_2'])
+
+ # Define the dipolar interaction.
+ for i in range(len(data['atom_names'])):
+ # The spin IDs.
+ spin_id1 = generate_spin_id(spin_name=data['atom_names'][i],
res_num=data['res_nums'][i], res_name=data['res_names'][i],
mol_name=mol_names[i])
+ spin_id2 =
generate_spin_id(spin_name=data['atom_names_2'][i],
res_num=data['res_nums'][i], res_name=data['res_names'][i],
mol_name=mol_names[i])
+
+ # Check if the container exists.
+ if return_interatom(spin_id1=spin_id1, spin_id2=spin_id2):
+ continue
+
+ # Define.
+ dipole_pair.define(spin_id1=spin_id1, spin_id2=spin_id2,
verbose=False)
# The data and error.
vals = data['data']
@@ -212,7 +230,7 @@
errors[i] = errors[i] * vals[i]**2
# Pack the data.
- pack_data(ri_id, ri_type, frq, vals, 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)
+ pack_data(ri_id, ri_type, frq, vals, 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, verbose=False)
# Store the temperature calibration and control.
if data['temp_calibration']:
Modified: branches/interatomic/specific_fns/model_free/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/specific_fns/model_free/bmrb.py?rev=17135&r1=17134&r2=17135&view=diff
==============================================================================
--- branches/interatomic/specific_fns/model_free/bmrb.py (original)
+++ branches/interatomic/specific_fns/model_free/bmrb.py Mon Jul 2 19:59:32
2012
@@ -440,7 +440,7 @@
# Store the spin specific data in lists for later use.
for spin, mol_name, res_num, res_name, spin_id in
spin_loop(full_info=True, return_id=True):
# Skip the protons.
- if spin.name == 'H':
+ if spin.name == 'H' or (hasattr(spin, 'element') and
spin.element == 'H'):
warn(RelaxWarning("Skipping the proton spin '%s'." %
spin_id))
continue
@@ -451,7 +451,7 @@
raise RelaxError("For the BMRB, the residue of spin '%s'
must be named." % spin_id)
if spin.name == None:
raise RelaxError("For the BMRB, the spin '%s' must be
named." % spin_id)
- if spin.isotope == None:
+ if not hasattr(spin, 'isotope') or spin.isotope == None:
raise RelaxError("For the BMRB, the spin isotope type of
'%s' must be specified." % spin_id)
if not hasattr(spin, 'element') or spin.element == None:
raise RelaxError("For the BMRB, the spin element type of
'%s' must be specified. Please use the spin user function for setting the
element type." % spin_id)
r17135 - in /branches/interatomic: generic_fns/bmrb.py generic_fns/relax_data.py specific_fns/model_free/bmrb.py