Author: bugman
Date: Mon Jan 31 15:38:28 2011
New Revision: 12465
URL: http://svn.gna.org/viewcvs/relax?rev=12465&view=rev
Log:
Shifted the sequence generation code into the BMRB specific
generate_sequence() function.
This is to allow for strangeness in the BMRB entries :S
Modified:
branches/bmrb/generic_fns/bmrb.py
branches/bmrb/generic_fns/relax_data.py
Modified: branches/bmrb/generic_fns/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/bmrb.py?rev=12465&r1=12464&r2=12465&view=diff
==============================================================================
--- branches/bmrb/generic_fns/bmrb.py (original)
+++ branches/bmrb/generic_fns/bmrb.py Mon Jan 31 15:38:28 2011
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2008-2009 Edward d'Auvergne
#
+# Copyright (C) 2008-2011 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -31,10 +31,11 @@
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 info import Info_box
from relax_errors import RelaxError, RelaxFileError,
RelaxFileOverwriteError, RelaxNoModuleInstallError, RelaxNoPipeError
from relax_io import get_file_path, mkdir_nofail
-from specific_fns.setup import get_specific_fn
+import specific_fns
from version import version_full
@@ -50,10 +51,49 @@
raise RelaxNoPipeError
# Specific results writing function.
- write_function = get_specific_fn('bmrb_write',
ds[ds.current_pipe].pipe_type, raise_error=False)
+ write_function = specific_fns.setup.get_specific_fn('bmrb_write',
ds[ds.current_pipe].pipe_type, raise_error=False)
# Write the results.
write_function(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):
+ """Generate the sequence data from the BRMB information.
+
+ @keyword N: The number of spins.
+ @type N: int
+ @keyword spin_ids: The list of spin IDs.
+ @type spin_ids: list of str
+ @keyword spin_nums: The list of spin numbers.
+ @type spin_nums: list of int or None
+ @keyword spin_names: The list of spin names.
+ @type spin_names: list of str or None
+ @keyword res_nums: The list of residue numbers.
+ @type res_nums: list of int or None
+ @keyword res_names: The list of residue names.
+ @type res_names: list of str or None
+ @keyword mol_names: The list of molecule names.
+ @type mol_names: list of str or None
+ """
+
+ print cdp.mol[0].res
+ # Loop over the spin data.
+ for i in range(N):
+ # The spin already exists.
+ spin = return_spin(spin_ids[i])
+ if spin:
+ continue
+
+ # The spin container needs to be named.
+ res_cont = return_residue(generate_spin_id(mol_name=mol_names[i],
res_num=res_nums[i], res_name=res_names[i]))
+ if res_cont and len(res_cont.spin) == 1 and res_cont.spin[0].name ==
None and res_cont.spin[0].num == None:
+ # Name and number the spin.
+ res_cont.spin[0].name = spin_names[i]
+ res_cont.spin[0].num = spin_nums[i]
+ 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])
def read(file=None, directory=None, version='3.1'):
@@ -79,7 +119,7 @@
raise RelaxFileError(file_path)
# Specific results reading function.
- read_function = get_specific_fn('bmrb_read',
ds[ds.current_pipe].pipe_type)
+ read_function = specific_fns.setup.get_specific_fn('bmrb_read',
ds[ds.current_pipe].pipe_type)
# Read the results.
read_function(file_path, version=version)
@@ -101,7 +141,7 @@
directory = ds.current_pipe
# Specific results writing function.
- write_function = get_specific_fn('bmrb_write',
ds[ds.current_pipe].pipe_type)
+ write_function = specific_fns.setup.get_specific_fn('bmrb_write',
ds[ds.current_pipe].pipe_type)
# Get the full file path.
file_path = get_file_path(file, directory)
Modified: branches/bmrb/generic_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/relax_data.py?rev=12465&r1=12464&r2=12465&view=diff
==============================================================================
--- branches/bmrb/generic_fns/relax_data.py (original)
+++ branches/bmrb/generic_fns/relax_data.py Mon Jan 31 15:38:28 2011
@@ -33,6 +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.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
@@ -800,16 +801,16 @@
# Update the global data.
update_data_structures_pipe(ri_label, frq_label, frq)
+ # 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)
+
# Loop over the spin data.
for i in range(N):
# Get the corresponding spin container.
spin = return_spin(spin_ids[i])
if spin == None:
- if not gen_seq:
- raise RelaxNoSpinError(spin_ids[i])
- else:
- 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 = return_spin(spin_ids[i])
+ raise RelaxNoSpinError(spin_ids[i])
# Update all data structures.
update_data_structures_spin(spin, ri_label, frq_label, frq,
values[i], errors[i])
r12465 - in /branches/bmrb/generic_fns: bmrb.py relax_data.py