Author: bugman
Date: Sun Mar 8 22:15:18 2009
New Revision: 8928
URL: http://svn.gna.org/viewcvs/relax?rev=8928&view=rev
Log:
Merged revisions 8920-8927 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r8925 | bugman | 2009-03-06 19:21:27 +0100 (Fri, 06 Mar 2009) | 5 lines
The read() function has been split into to for code recycling in the bmrb
branch.
The new pack_data() function has been spun off to fill the data pipe and
spin containers.
........
r8926 | bugman | 2009-03-06 19:25:21 +0100 (Fri, 06 Mar 2009) | 5 lines
Bug fix for the read() function.
The construction of the data for sending to pack_data() was failing.
........
r8927 | bugman | 2009-03-06 19:25:49 +0100 (Fri, 06 Mar 2009) | 3 lines
Spacing fix.
........
Modified:
branches/bmrb/ (props changed)
branches/bmrb/generic_fns/mol_res_spin.py
branches/bmrb/generic_fns/relax_data.py
Propchange: branches/bmrb/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Sun Mar 8 22:15:18 2009
@@ -1,1 +1,1 @@
-/1.3:1-8919
+/1.3:1-8927
Modified: branches/bmrb/generic_fns/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/mol_res_spin.py?rev=8928&r1=8927&r2=8928&view=diff
==============================================================================
--- branches/bmrb/generic_fns/mol_res_spin.py (original)
+++ branches/bmrb/generic_fns/mol_res_spin.py Sun Mar 8 22:15:18 2009
@@ -841,7 +841,6 @@
for i in xrange(len(cdp.mol)):
if cdp.mol[i].name == mol_name:
raise RelaxError, "The molecule '" + `mol_name` + "' already
exists in the relax data store."
-
# Append the molecule.
cdp.mol.add_item(mol_name=mol_name)
Modified: branches/bmrb/generic_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/relax_data.py?rev=8928&r1=8927&r2=8928&view=diff
==============================================================================
--- branches/bmrb/generic_fns/relax_data.py (original)
+++ branches/bmrb/generic_fns/relax_data.py Sun Mar 8 22:15:18 2009
@@ -29,7 +29,7 @@
# relax module imports.
from data import Relax_data_store; ds = Relax_data_store()
-from generic_fns.mol_res_spin import exists_mol_res_spin_data,
generate_spin_id_data_array, return_spin, spin_index_loop, spin_loop
+from generic_fns.mol_res_spin import create_molecule, create_residue,
create_spin, exists_mol_res_spin_data, generate_spin_id, return_spin,
spin_index_loop, spin_loop
from generic_fns import pipes
from generic_fns import value
from relax_errors import RelaxError, RelaxNoRiError, RelaxNoSequenceError,
RelaxNoSpinError, RelaxRiError
@@ -596,6 +596,65 @@
# Return the index.
return index
+
+
+def pack_data(ri_label, frq_label, frq, values, errors, mol_names=None,
res_nums=None, res_names=None, spin_nums=None, spin_names=None,
gen_seq=False):
+ """Pack the relaxation data into the data pipe and spin containers.
+
+ The values, errors, mol_names, res_nums, res_names, spin_nums, and
spin_names arguments must be
+ lists of equal length or None. Each element i corresponds to a unique
spin.
+
+ @param ri_label: The relaxation data type, ie 'R1', 'R2', or
'NOE'.
+ @type ri_label: str
+ @param frq_label: The field strength label.
+ @type frq_label: str
+ @param frq: The spectrometer proton frequency in Hz.
+ @type frq: float
+ @keyword mol_names: The list of molecule names for each spin.
+ @type mol_names: None or list of str
+ @keyword res_nums: The list of residue numbers for each spin.
+ @type res_nums: None or list of str
+ @keyword res_names: The list of residue names for each spin.
+ @type res_names: None or list of str
+ @keyword spin_nums: The list of spin numbers.
+ @type spin_nums: None or list of str
+ @keyword spin_names: The list of spin names.
+ @type spin_names: None or list of str
+ @keyword gen_seq: A flag which if True will cause the molecule,
residue, and spin sequence
+ data to be generated.
+ @type gen_seq: bool
+ """
+
+ # Get the current data pipe.
+ cdp = pipes.get_pipe()
+
+ # Initialise the global data for the current pipe if necessary.
+ data_init(cdp, global_flag=True)
+
+ # Update the global data.
+ update_data_structures_pipe(ri_label, frq_label, frq)
+
+ # Loop over the spin data.
+ for value, error, mol_name, res_num, res_name, spin_num, spin_name in
zip(values, errors, mol_names, res_nums, res_names, spin_nums, spin_names):
+ # Generate the spin identification string.
+ id = generate_spin_id(mol_name=mol_name, res_num=res_num,
res_name=res_name, spin_num=spin_num, spin_name=spin_name)
+
+ # Skip all rows where the value or error is None.
+ if value == None or error == None:
+ continue
+
+ # Get the corresponding spin container.
+ spin = return_spin(id)
+ if spin == None:
+ if not gen_seq:
+ raise RelaxNoSpinError, id
+ else:
+ create_molecule(mol_name)
+ create_residue(res_num, res_name,
mol_id=generate_spin_id(mol_name=mol_name))
+ create_spin(spin_num, spin_name,
res_id=generate_spin_id(mol_name=mol_name, res_num=res_num,
res_name=res_name))
+
+ # Update all data structures.
+ update_data_structures_spin(spin, ri_label, frq_label, frq, value,
error)
def read(ri_label=None, frq_label=None, frq=None, file=None, dir=None,
file_data=None, mol_name_col=None, res_num_col=0, res_name_col=1,
spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None):
@@ -633,9 +692,6 @@
# Test if the current data pipe exists.
pipes.test()
- # Get the current data pipe.
- cdp = pipes.get_pipe()
-
# Test if sequence data exists.
if not exists_mol_res_spin_data():
raise RelaxNoSequenceError
@@ -688,44 +744,47 @@
except ValueError:
raise RelaxError, "The relaxation data in the line " +
`file_data[i]` + " is invalid."
-
- # Global (non-residue specific) data.
- #####################################
-
- # Initialise the global data for the current pipe if necessary.
- data_init(cdp, global_flag=True)
-
- # Update the global data.
- update_data_structures_pipe(ri_label, frq_label, frq)
-
-
- # Residue specific data.
- ########################
-
- # Loop over the relaxation data.
+ # Loop over the file data to create the data structures for packing.
+ values = []
+ errors = []
+ mol_names = []
+ res_nums = []
+ res_names = []
+ spin_nums = []
+ spin_names = []
for i in xrange(len(file_data)):
# Skip missing data.
if len(file_data[i]) <= min_col_num:
continue
- # Generate the spin identification string.
- id = generate_spin_id_data_array(data=file_data[i],
mol_name_col=mol_name_col, res_num_col=res_num_col,
res_name_col=res_name_col, spin_num_col=spin_num_col,
spin_name_col=spin_name_col)
+ # Pack the spin ID info.
+ if mol_name_col != None:
+ mol_names.append(file_data[i][mol_name_col])
+ else:
+ mol_names.append(None)
+ if res_num_col != None:
+ res_nums.append(file_data[i][res_num_col])
+ else:
+ res_nums.append(None)
+ if res_name_col != None:
+ res_names.append(file_data[i][res_name_col])
+ else:
+ res_names.append(None)
+ if spin_num_col != None:
+ spin_nums.append(file_data[i][spin_num_col])
+ else:
+ spin_nums.append(None)
+ if spin_name_col != None:
+ spin_names.append(file_data[i][spin_name_col])
+ else:
+ spin_names.append(None)
# Convert the data.
- value = eval(file_data[i][data_col])
- error = eval(file_data[i][error_col])
-
- # Skip all rows where the value or error is None.
- if value == None or error == None:
- continue
-
- # Get the corresponding spin container.
- spin = return_spin(id)
- if spin == None:
- raise RelaxNoSpinError, id
-
- # Update all data structures.
- update_data_structures_spin(spin, ri_label, frq_label, frq, value,
error)
+ values.append(eval(file_data[i][data_col]))
+ errors.append(eval(file_data[i][error_col]))
+
+ # Pack the data.
+ pack_data(ri_label, frq_label, frq, values, errors, mol_names, res_nums,
res_names, spin_nums, spin_names)
def return_data_desc(name):
r8928 - in /branches/bmrb: ./ generic_fns/mol_res_spin.py generic_fns/relax_data.py