Author: bugman
Date: Tue Mar 1 17:04:07 2011
New Revision: 12649
URL: http://svn.gna.org/viewcvs/relax?rev=12649&view=rev
Log:
Updated the relax_data.read() back end for the new ID string based design.
The update_data_structures_pipe() and data_init() functions have been deleted
and the pack_data()
function highly modified.
Modified:
branches/relax_data/generic_fns/relax_data.py
Modified: branches/relax_data/generic_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_data/generic_fns/relax_data.py?rev=12649&r1=12648&r2=12649&view=diff
==============================================================================
--- branches/relax_data/generic_fns/relax_data.py (original)
+++ branches/relax_data/generic_fns/relax_data.py Tue Mar 1 17:04:07 2011
@@ -559,40 +559,6 @@
update_data_structures_spin(spin_to, ri_label, frq_label, frq,
value, error)
-def data_init(container, global_flag=False):
- """Initialise the data structures for a spin container.
-
- @param container: The data pipe or spin data container
(PipeContainer or SpinContainer).
- @type container: class instance
- @keyword global_flag: A flag which if True corresponds to the pipe
specific data structures
- and if False corresponds to the spin specific
data structures.
- @type global_flag: bool
- """
-
- # Get the data names.
- data_names = get_data_names(global_flag)
-
- # Init.
- list_data = [ 'relax_data',
- 'relax_error',
- 'ri_labels',
- 'remap_table',
- 'noe_r1_table',
- 'frq_labels',
- 'frq' ]
- zero_data = [ 'num_ri', 'num_frq' ]
-
- # Loop over the data structure names.
- for name in data_names:
- # If the name is not in the container, add it as an empty array.
- if name in list_data and not hasattr(container, name):
- setattr(container, name, [])
-
- # If the name is not in the container, add it as a variable set to
zero.
- if name in zero_data and not hasattr(container, name):
- setattr(container, name, 0)
-
-
def get_data_names(global_flag=False, sim_names=False):
"""Return a list of names of data structures associated with relax_data.
@@ -785,15 +751,15 @@
return index
-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):
+def pack_data(ri_id, ri_type, 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 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
- @param frq_label: The field strength label.
- @type frq_label: str
+ @param ri_id: The relaxation data ID string.
+ @type ri_id: str
+ @param ri_type: The relaxation data type, ie 'R1', 'R2', or
'NOE'.
+ @type ri_type: str
@param frq: The spectrometer proton frequency in Hz.
@type frq: float
@keyword values: The relaxation data for each spin.
@@ -856,10 +822,17 @@
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)
+ if not hasattr(cdp, 'frq'):
+ cdp.frq = {}
+ if not hasattr(cdp, 'ri_type'):
+ cdp.ri_type = {}
+ if not hasattr(cdp, 'ri_ids'):
+ cdp.ri_ids = []
# Update the global data.
- update_data_structures_pipe(ri_label, frq_label, frq)
+ cdp.ri_ids.append(ri_id)
+ cdp.ri_type[ri_id] = ri_type
+ cdp.frq[ri_id] = frq
# Generate the sequence.
if gen_seq:
@@ -872,8 +845,15 @@
if spin == None:
raise RelaxNoSpinError(spin_ids[i])
+ # Initialise the spin data if necessary.
+ if not hasattr(cdp, 'ri_data'):
+ spin.ri_data = {}
+ if not hasattr(cdp, 'ri_data_err'):
+ spin.ri_data_err = {}
+
# Update all data structures.
- update_data_structures_spin(spin, ri_label, frq_label, frq,
values[i], errors[i])
+ spin.ri_data[ri_id] = values[i]
+ spin.ri_data_err[ri_id] = errors[i]
def peak_intensity_type(ri_label=None, frq_label=None, type=None):
@@ -911,42 +891,32 @@
cdp.exp_info.setup_peak_intensity_type(ri_label, frq_label, type)
-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):
+def read(ri_id=None, ri_type=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):
"""Read R1, R2, or NOE relaxation data from a file.
- @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 ri_id: The relaxation data ID string.
+ @type ri_id: str
+ @param ri_type: The relaxation data type, ie 'R1', 'R2', or
'NOE'.
+ @type ri_type: str
@param frq: The spectrometer proton frequency in Hz.
@type frq: float
@param file: The name of the file to open.
@type file: str
- @param dir: The directory containing the file (defaults to
the current directory
- if None).
+ @param dir: The directory containing the file (defaults to
the current directory if None).
@type dir: str or None
- @param file_data: An alternative opening a file, if the data
already exists in the
- correct format. The format is a list of lists
where the first index
- corresponds to the row and the second the column.
+ @param file_data: An alternative opening a file, if the data
already exists in the correct format. The format is a list of lists where
the first index corresponds to the row and the second the column.
@type file_data: list of lists
- @keyword spin_id_col: The column containing the spin ID strings. If
supplied, the
- mol_name_col, res_name_col, res_num_col,
spin_name_col, and spin_num_col
- arguments must be none.
+ @keyword spin_id_col: The column containing the spin ID strings. If
supplied, the mol_name_col, res_name_col, res_num_col, spin_name_col, and
spin_num_col arguments must be none.
@type spin_id_col: int or None
- @keyword mol_name_col: The column containing the molecule name
information. If supplied,
- spin_id_col must be None.
+ @keyword mol_name_col: The column containing the molecule name
information. If supplied, spin_id_col must be None.
@type mol_name_col: int or None
- @keyword res_name_col: The column containing the residue name
information. If supplied,
- spin_id_col must be None.
+ @keyword res_name_col: The column containing the residue name
information. If supplied, spin_id_col must be None.
@type res_name_col: int or None
- @keyword res_num_col: The column containing the residue number
information. If supplied,
- spin_id_col must be None.
+ @keyword res_num_col: The column containing the residue number
information. If supplied, spin_id_col must be None.
@type res_num_col: int or None
- @keyword spin_name_col: The column containing the spin name information.
If supplied,
- spin_id_col must be None.
+ @keyword spin_name_col: The column containing the spin name information.
If supplied, spin_id_col must be None.
@type spin_name_col: int or None
- @keyword spin_num_col: The column containing the spin number
information. If supplied,
- spin_id_col must be None.
+ @keyword spin_num_col: The column containing the spin number
information. If supplied, spin_id_col must be None.
@type spin_num_col: int or None
@keyword data_col: The column containing the relaxation data.
@type data_col: int or None
@@ -954,8 +924,7 @@
@type error_col: int or None
@keyword sep: The column separator which, if None, defaults to
whitespace.
@type sep: str or None
- @keyword spin_id: The spin ID string used to restrict data loading
to a subset of all
- spins.
+ @keyword spin_id: The spin ID string used to restrict data loading
to a subset of all spins.
@type spin_id: None or str
"""
@@ -965,6 +934,10 @@
# Test if sequence data exists.
if not exists_mol_res_spin_data():
raise RelaxNoSequenceError
+
+ # Test if the ri_id already exists.
+ if hasattr(cdp, 'ri_ids') and ri_id in cdp.ri_ids:
+ raise RelaxError("The relaxation ID string '%s' already exists." %
ri_id)
# Loop over the file data to create the data structures for packing.
values = []
@@ -989,7 +962,7 @@
errors.append(error)
# Pack the data.
- pack_data(ri_label, frq_label, frq, values, errors, ids)
+ pack_data(ri_id, ri_type, frq, values, errors, ids)
def return_data_desc(name):
@@ -1149,68 +1122,6 @@
return False
-def update_data_structures_pipe(ri_label=None, frq_label=None, frq=None):
- """Update all relaxation data structures in the current data pipe.
-
- @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
- """
-
- # Initialise the relaxation data structures (if needed).
- data_init(cdp, global_flag=True)
-
- # The index.
- i = len(cdp.ri_labels) - 1
-
- # Update the number of relaxation data points.
- cdp.num_ri = cdp.num_ri + 1
-
- # Add ri_label to the data types.
- cdp.ri_labels.append(ri_label)
-
- # Find if the frequency has already been loaded.
- remap = len(cdp.frq)
- flag = 0
- for j in xrange(len(cdp.frq)):
- if frq == cdp.frq[j]:
- remap = j
- flag = 1
-
- # Update the remap table.
- cdp.remap_table.append(remap)
-
- # Update the data structures which have a length equal to the number of
field strengths.
- if not flag:
- # Update the number of frequencies.
- cdp.num_frq = cdp.num_frq + 1
-
- # Update the frequency labels.
- cdp.frq_labels.append(frq_label)
-
- # Update the frequency array.
- cdp.frq.append(frq)
-
- # Update the NOE R1 translation table.
- cdp.noe_r1_table.append(None)
-
- # If the data corresponds to 'NOE', try to find if the corresponding R1
data.
- if ri_label == 'NOE':
- for j in xrange(cdp.num_ri):
- if cdp.ri_labels[j] == 'R1' and frq_label ==
cdp.frq_labels[cdp.remap_table[j]]:
- cdp.noe_r1_table[cdp.num_ri - 1] = j
-
- # Update the NOE R1 translation table.
- # If the data corresponds to 'R1', try to find if the corresponding NOE
data.
- if ri_label == 'R1':
- for j in xrange(cdp.num_ri):
- if cdp.ri_labels[j] == 'NOE' and frq_label ==
cdp.frq_labels[cdp.remap_table[j]]:
- cdp.noe_r1_table[j] = cdp.num_ri - 1
-
-
def update_data_structures_spin(spin=None, ri_label=None, frq_label=None,
frq=None, value=None, error=None):
"""Update all relaxation data structures of the given spin container.
r12649 - /branches/relax_data/generic_fns/relax_data.py