Author: bugman
Date: Sun Feb 22 00:36:22 2009
New Revision: 8838
URL: http://svn.gna.org/viewcvs/relax?rev=8838&view=rev
Log:
Shifted all the pystarlib code for the relaxation data into the NMR-STAR
dictionary object.
Modified:
branches/bmrb/bmrblib/nmr_star_dict.py
branches/bmrb/specific_fns/model_free/bmrb.py
Modified: branches/bmrb/bmrblib/nmr_star_dict.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/nmr_star_dict.py?rev=8838&r1=8837&r2=8838&view=diff
==============================================================================
--- branches/bmrb/bmrblib/nmr_star_dict.py (original)
+++ branches/bmrb/bmrblib/nmr_star_dict.py Sun Feb 22 00:36:22 2009
@@ -29,6 +29,8 @@
# relax module imports.
from pystarlib.File import File
+from pystarlib.SaveFrame import SaveFrame
+from pystarlib.TagTable import TagTable
class NMR_STAR:
@@ -46,6 +48,9 @@
# Initialise the pystarlib File object.
self.data = File(title=title, filename=file_path)
+ # Initialise the objects of this class.
+ self.relax_data = Relaxation_data(self.data.datanodes)
+
def read(self):
"""Read the data from a BMRB NMR-STAR formatted file."""
@@ -59,3 +64,86 @@
# Write the contents to the STAR formatted file.
self.data.write()
+
+
+class Relaxation_data:
+ """Base class for relaxation data support."""
+
+ def __init__(self, datanodes):
+ """Initialise the class, placing the pystarlib data nodes into the
namespace.
+
+ @param datanodes: The pystarlib data nodes object.
+ @type datanodes: list
+ """
+
+ # Place the data nodes into the namespace.
+ self.datanodes = datanodes
+
+ # The number of relaxation data sets.
+ self.r1_inc = 0
+ self.r2_inc = 0
+ self.noe_inc = 0
+
+
+ def add(self, ri_label=None, frq=None, res_nums=None, res_names=None,
atom_names=None, data=None, errors=None):
+ """Add relaxation data to the data nodes.
+
+ @keyword ri_label: The relaxation data label, one of 'R1',
'R2', or 'NOE'.
+ @type ri_label: str
+ @keyword frq: The spectrometer proton frequency, in Hz.
+ @type frq: float
+ @keyword res_nums: The residue number list.
+ @type res_nums: list of int
+ @keyword res_names: The residue name list.
+ @type res_names: list of str
+ @keyword atom_names: The atom name list.
+ @type atom_names: list of str
+ @keyword data: The relaxation data.
+ @type data: list of float
+ @keyword errors: The errors associated with the relaxation
data.
+ @type errors: list of float
+ """
+
+ # Data type label.
+ if ri_label == 'R1':
+ self.r1_inc = self.r1_inc + 1
+ ri_inc = self.r1_inc
+ label = 'T1'
+ coherence = 'Nz'
+ elif ri_label == 'R2':
+ self.r2_inc = self.r2_inc + 1
+ ri_inc = self.r2_inc
+ label = 'T2'
+ coherence = 'Ny'
+ elif ri_label == 'NOE':
+ self.noe_inc = self.noe_inc + 1
+ ri_inc = self.noe_inc
+ label = 'NOE'
+
+ # Initialise the save frame.
+ frame = SaveFrame(title='heteronuclear_'+label+'_list_'+`ri_inc`)
+
+ # The save frame category.
+ frame.tagtables.append(TagTable(free=True,
tagnames=['_Saveframe_category'], tagvalues=[[label+'_relaxation']]))
+
+ # Sample info.
+ frame.tagtables.append(TagTable(free=True,
tagnames=['_Sample_label'], tagvalues=[['$sample_1']]))
+ frame.tagtables.append(TagTable(free=True,
tagnames=['_Sample_conditions_label'], tagvalues=[['$conditions_1']]))
+
+ # NMR info.
+ frame.tagtables.append(TagTable(free=True,
tagnames=['_Spectrometer_frequency_1H'], tagvalues=[[str(frq/1e6)]]))
+ if label in ['T1', 'T2']:
+ frame.tagtables.append(TagTable(free=True,
tagnames=['_'+label+'_coherence_type'], tagvalues=[[coherence]]))
+ frame.tagtables.append(TagTable(free=True,
tagnames=['_'+label+'_value_units'], tagvalues=[['1/s']]))
+
+ # The relaxation tag names.
+ tag_names = ['_Residue_seq_code', '_Residue_label', '_Atom_name',
'_'+label+'_value', '_'+label+'_value_error']
+
+ # Add the data.
+ table = TagTable(tagnames=tag_names, tagvalues=[res_nums, res_names,
atom_names, data, errors])
+
+ # Add the tag table to the save frame.
+ frame.tagtables.append(table)
+
+ # Add the relaxation data save frame.
+ self.datanodes.append(frame)
Modified: branches/bmrb/specific_fns/model_free/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/specific_fns/model_free/bmrb.py?rev=8838&r1=8837&r2=8838&view=diff
==============================================================================
--- branches/bmrb/specific_fns/model_free/bmrb.py (original)
+++ branches/bmrb/specific_fns/model_free/bmrb.py Sun Feb 22 00:36:22 2009
@@ -24,8 +24,6 @@
from bmrblib.nmr_star_dict import NMR_STAR
from generic_fns.mol_res_spin import spin_loop
from generic_fns.pipes import get_pipe
-from pystarlib.SaveFrame import SaveFrame
-from pystarlib.TagTable import TagTable
class Bmrb:
@@ -84,54 +82,9 @@
relax_data_list[i].append(str(spin.relax_data[i]))
relax_error_list[i].append(str(spin.relax_error[i]))
- # Relaxation data save frames.
- r1_inc = 0
- r2_inc = 0
- noe_inc = 0
+ # Add the relaxation data.
for i in range(cdp.num_ri):
- # Data type labels.
- if cdp.ri_labels[i] == 'R1':
- r1_inc = r1_inc + 1
- ri_inc = r1_inc
- ri_label = 'T1'
- coherence = 'Nz'
- elif cdp.ri_labels[i] == 'R2':
- r2_inc = r2_inc + 1
- ri_inc = r2_inc
- ri_label = 'T2'
- coherence = 'Ny'
- elif cdp.ri_labels[i] == 'NOE':
- noe_inc = noe_inc + 1
- ri_inc = noe_inc
- ri_label = 'NOE'
-
- # Initialise the save frame.
- frame =
SaveFrame(title='heteronuclear_'+ri_label+'_list_'+`ri_inc`)
-
- # The save frame category.
- frame.tagtables.append(TagTable(free=True,
tagnames=['_Saveframe_category'], tagvalues=[[ri_label+'_relaxation']]))
-
- # Sample info.
- frame.tagtables.append(TagTable(free=True,
tagnames=['_Sample_label'], tagvalues=[['$sample_1']]))
- frame.tagtables.append(TagTable(free=True,
tagnames=['_Sample_conditions_label'], tagvalues=[['$conditions_1']]))
-
- # NMR info.
- frame.tagtables.append(TagTable(free=True,
tagnames=['_Spectrometer_frequency_1H'],
tagvalues=[[str(cdp.frq[cdp.remap_table[i]]/1e6)]]))
- if ri_label in ['T1', 'T2']:
- frame.tagtables.append(TagTable(free=True,
tagnames=['_'+ri_label+'_coherence_type'], tagvalues=[[coherence]]))
- frame.tagtables.append(TagTable(free=True,
tagnames=['_'+ri_label+'_value_units'], tagvalues=[['1/s']]))
-
- # The relaxation tag names.
- tag_names = ['_Residue_seq_code', '_Residue_label',
'_Atom_name', '_'+ri_label+'_value', '_'+ri_label+'_value_error']
-
- # Add the data.
- table = TagTable(tagnames=tag_names, tagvalues=[res_num_list,
res_name_list, atom_name_list, relax_data_list[i], relax_error_list[i]])
-
- # Add the tag table to the save frame.
- frame.tagtables.append(table)
-
- # Add the relaxation data save frame.
- star.data.datanodes.append(frame)
+ star.relax_data.add(ri_label=cdp.ri_labels[i],
frq=cdp.frq[cdp.remap_table[i]], res_nums=res_num_list,
res_names=res_name_list, atom_names=atom_name_list, data=relax_data_list[i],
errors=relax_error_list[i])
# Write the contents to the STAR formatted file.
star.write()
r8838 - in /branches/bmrb: bmrblib/nmr_star_dict.py specific_fns/model_free/bmrb.py