Author: bugman
Date: Fri Oct 9 12:44:59 2009
New Revision: 9685
URL: http://svn.gna.org/viewcvs/relax?rev=9685&view=rev
Log:
Redesigned pack_data() to handle sequence generation.
Modified:
branches/bmrb/generic_fns/relax_data.py
Modified: branches/bmrb/generic_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/relax_data.py?rev=9685&r1=9684&r2=9685&view=diff
==============================================================================
--- branches/bmrb/generic_fns/relax_data.py (original)
+++ branches/bmrb/generic_fns/relax_data.py Fri Oct 9 12:44:59 2009
@@ -597,11 +597,10 @@
return index
-def pack_data(ri_label, frq_label, frq, values, errors, ids=None,
gen_seq=False):
+def pack_data(ri_label, frq_label, frq, values, errors, spin_ids=None,
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, and ids arguments must be lists of equal length or
None. Each element i
- corresponds to a unique spin.
+ The values, errors, and spin_ids 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
@@ -613,10 +612,19 @@
@type values: None or list of str
@keyword errors: The relaxation data errors for each spin.
@type errors: None or list of str
- @keyword ids: The list of spin ID strings.
- @type ids: list of str
- @keyword gen_seq: A flag which if True will cause the molecule,
residue, and spin sequence
- data to be generated.
+ @keyword spin_ids: The list of spin ID strings. If the other spin
identifiers are given, i.e. mol_names, res_nums, res_names, spin_nums, and/or
spin_names, then this argument is not necessary.
+ @type spin_ids: None or list of str
+ @keyword mol_names: The list of molecule names used for creating the
spin IDs (if not given) or for generating the sequence data.
+ @type mol_names: None or list of str
+ @keyword res_nums: The list of residue numbers used for creating
the spin IDs (if not given) or for generating the sequence data.
+ @type res_nums: None or list of str
+ @keyword res_names: The list of residue names used for creating the
spin IDs (if not given) or for generating the sequence data.
+ @type res_names: None or list of str
+ @keyword spin_nums: The list of spin numbers used for creating the
spin IDs (if not given) or for generating the sequence data.
+ @type spin_nums: None or list of str
+ @keyword spin_names: The list of spin names used for creating the
spin IDs (if not given) or for generating the sequence data.
+ @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
"""
@@ -626,8 +634,36 @@
# Test the data.
if len(errors) != N:
raise RelaxError("The length of the errors arg (%s) does not match
that of the value arg (%s)." % (len(errors), N))
- if len(ids) != N:
+ if spin_ids and len(spin_ids) != N:
raise RelaxError("The length of the spin ID strings arg (%s) does
not match that of the value arg (%s)." % (len(mol_names), N))
+ if mol_names and len(mol_names) != N:
+ raise RelaxError("The length of the molecule names arg (%s) does not
match that of the value arg (%s)." % (len(mol_names), N))
+ if res_nums and len(res_nums) != N:
+ raise RelaxError("The length of the residue numbers arg (%s) does
not match that of the value arg (%s)." % (len(res_nums), N))
+ if res_names and len(res_names) != N:
+ raise RelaxError("The length of the residue names arg (%s) does not
match that of the value arg (%s)." % (len(res_names), N))
+ if spin_nums and len(spin_nums) != N:
+ raise RelaxError("The length of the spin numbers arg (%s) does not
match that of the value arg (%s)." % (len(spin_nums), N))
+ if spin_names and len(spin_names) != N:
+ raise RelaxError("The length of the spin names arg (%s) does not
match that of the value arg (%s)." % (len(spin_names), N))
+
+ # Generate some empty lists.
+ if not mol_names:
+ mol_names = [None] * N
+ if not res_nums:
+ res_nums = [None] * N
+ if not res_names:
+ res_names = [None] * N
+ if not spin_nums:
+ spin_nums = [None] * N
+ if not spin_names:
+ spin_names = [None] * N
+
+ # Generate the spin IDs.
+ if not spin_ids:
+ spin_ids = []
+ for i in range(N):
+ spin_ids.append(generate_spin_id(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]))
# Initialise the global data for the current pipe if necessary.
data_init(cdp, global_flag=True)
@@ -636,22 +672,18 @@
update_data_structures_pipe(ri_label, frq_label, frq)
# Loop over the spin data.
- for value, error, id in zip(values, errors, ids):
- # Skip all rows where the value or error is None.
- if value == None or error == None:
- continue
-
+ for i in range(N):
# Get the corresponding spin container.
- spin = return_spin(id)
+ spin = return_spin(spin_ids[i])
if spin == None:
if not gen_seq:
- raise RelaxNoSpinError(id)
+ raise RelaxNoSpinError(spin_ids[i])
else:
- create_spin(spin_num=spin_num, spin_name=spin_name,
res_num=res_num, res_name=res_name, mol_name=mol_name)
- spin = return_spin(id)
+ 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])
# Update all data structures.
- update_data_structures_spin(spin, ri_label, frq_label, frq, value,
error)
+ update_data_structures_spin(spin, ri_label, frq_label, frq,
values[i], errors[i])
def read(ri_label=None, frq_label=None, frq=None, file=None, dir=None,
file_data=None, spin_id_col=None, mol_name_col=None, res_num_col=None,
res_name_col=None, spin_num_col=None, spin_name_col=None, data_col=None,
error_col=None, sep=None, spin_id=None):
r9685 - /branches/bmrb/generic_fns/relax_data.py