Author: bugman
Date: Sun Oct 25 22:22:09 2009
New Revision: 9782
URL: http://svn.gna.org/viewcvs/relax?rev=9782&view=rev
Log:
The software citation IDs are now handled, and all the new model-free info
supplied.
Modified:
branches/bmrb/bmrblib/experimental_details/software.py
branches/bmrb/generic_fns/exp_info.py
branches/bmrb/specific_fns/model_free/bmrb.py
Modified: branches/bmrb/bmrblib/experimental_details/software.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/experimental_details/software.py?rev=9782&r1=9781&r2=9782&view=diff
==============================================================================
--- branches/bmrb/bmrblib/experimental_details/software.py (original)
+++ branches/bmrb/bmrblib/experimental_details/software.py Sun Oct 25
22:22:09 2009
@@ -70,6 +70,8 @@
@type task: str
@keyword cite_ids: The citation ID numbers.
@type cite_ids: None or list of int
+ @return: The software ID number.
+ @rtype: int
"""
# Check.
@@ -104,6 +106,9 @@
# Add the saveframe to the data nodes.
self.datanodes.append(self.frame)
+ # Return the software ID number.
+ return self.software_num
+
def add_tag_categories(self):
"""Create the tag categories."""
Modified: branches/bmrb/generic_fns/exp_info.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/exp_info.py?rev=9782&r1=9781&r2=9782&view=diff
==============================================================================
--- branches/bmrb/generic_fns/exp_info.py (original)
+++ branches/bmrb/generic_fns/exp_info.py Sun Oct 25 22:22:09 2009
@@ -116,9 +116,13 @@
@param star: The NMR-STAR dictionary object.
@type star: NMR_STAR instance
+ @return: A list BMRB software IDs and a list of software
labels.
+ @rtype: tuple of list of int and list of str
"""
# Loop over the software.
+ software_ids = []
+ software_labels = []
if hasattr(cdp, 'exp_info') and hasattr(cdp.exp_info, 'software'):
for software in cdp.exp_info.software:
# Get the citation ID numbers.
@@ -127,11 +131,18 @@
cite_id_nums.append(cdp.exp_info.get_cite_id_num(cite))
# The program info.
- star.software.add(name=software.name, version=software.version,
vendor_name=software.vendor_name, vendor_eaddress=software.url,
task=software.tasks, cite_ids=cite_id_nums)
+ id = star.software.add(name=software.name,
version=software.version, vendor_name=software.vendor_name,
vendor_eaddress=software.url, task=software.tasks, cite_ids=cite_id_nums)
+
+ # Append the software info.
+ software_ids.append(id)
+ software_labels.append(software.name)
# relax cannot be the only program used!
else:
raise RelaxError("relax cannot be the only program used in the
analysis - spectral analysis programs, etc. must also have been used. Please
use the relevant BMRB user functions to specify these.")
+
+ # Return the software info.
+ return software_ids, software_labels
def citation(cite_id=None, authors=None, doi=None, pubmed_id=None,
full_citation=None, title=None, status=None, type=None, journal_abbrev=None,
journal_full=None, volume=None, issue=None, page_first=None, page_last=None,
year=None):
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=9782&r1=9781&r2=9782&view=diff
==============================================================================
--- branches/bmrb/specific_fns/model_free/bmrb.py (original)
+++ branches/bmrb/specific_fns/model_free/bmrb.py Sun Oct 25 22:22:09 2009
@@ -80,8 +80,36 @@
else:
star = NMR_STAR('relax_model_free_results', file_path)
+ # Global minimisation stats.
+ global_chi2 = None
+ if hasattr(cdp, 'chi2'):
+ global_chi2 = cdp.chi2
+
# Rex frq.
rex_frq = cdp.frq[0]
+
+ # The relax to BMRB model-free model name map.
+ model_map = {'m0': '',
+ 'm1': 'S2',
+ 'm2': 'S2, te',
+ 'm3': 'S2, Rex',
+ 'm4': 'S2, te, Rex',
+ 'm5': 'S2f, S2, ts',
+ 'm6': 'S2f, tf, S2, ts',
+ 'm7': 'S2f, S2, ts, Rex',
+ 'm8': 'S2f, tf, S2, ts, Rex',
+ 'm9': 'Rex',
+ 'tm0': 'tm',
+ 'tm1': 'tm, S2',
+ 'tm2': 'tm, S2, te',
+ 'tm3': 'tm, S2, Rex',
+ 'tm4': 'tm, S2, te, Rex',
+ 'tm5': 'tm, S2f, S2, ts',
+ 'tm6': 'tm, S2f, tf, S2, ts',
+ 'tm7': 'tm, S2f, S2, ts, Rex',
+ 'tm8': 'tm, S2f, tf, S2, ts, Rex',
+ 'tm9': 'tm, Rex'
+ }
# Initialise the spin specific data lists.
res_num_list = []
@@ -93,6 +121,7 @@
isotope_list = []
element_list = []
+ local_tm_list = []
s2_list = []
s2f_list = []
s2s_list = []
@@ -101,6 +130,7 @@
ts_list = []
rex_list = []
+ local_tm_err_list = []
s2_err_list = []
s2f_err_list = []
s2s_err_list = []
@@ -110,6 +140,7 @@
rex_err_list = []
chi2_list = []
+ model_list = []
# Store the spin specific data in lists for later use.
for spin, mol_name, res_num, res_name, spin_id in
spin_loop(full_info=True, return_id=True):
@@ -140,6 +171,10 @@
element_list.append(spin.element)
else:
element_list.append(None)
+
+ # Diffusion tensor.
+ local_tm_list.append(spin.local_tm)
+ local_tm_err_list.append(spin.local_tm_err)
# Model-free data.
s2_list.append(spin.s2)
@@ -167,6 +202,9 @@
# Opt stats.
chi2_list.append(spin.chi2)
+ # Model-free model.
+ model_list.append(model_map[spin.model])
+
# Create Supergroup 2 : The citations.
######################################
@@ -186,7 +224,7 @@
#################################################################
# Generate the software saveframe.
- exp_info.bmrb_write_software(star)
+ software_ids, software_labels = exp_info.bmrb_write_software(star)
# Create Supergroup 5 : The NMR parameters saveframes.
@@ -206,8 +244,13 @@
# Create Supergroup 7 : The thermodynamics saveframes.
######################################################
+ # Get the relax software id.
+ for i in range(len(software_ids)):
+ if software_labels[i] == 'relax':
+ software_id = software_ids[i]
+
# Generate the model-free data saveframe.
- star.model_free.add(res_nums=res_num_list, res_names=res_name_list,
atom_names=atom_name_list, atom_types=element_list, s2=s2_list, s2f=s2f_list,
s2s=s2s_list, te=te_list, tf=tf_list, ts=ts_list, rex=rex_list,
s2_err=s2_err_list, s2f_err=s2f_err_list, s2s_err=s2s_err_list,
te_err=te_err_list, tf_err=tf_err_list, ts_err=ts_err_list,
rex_err=rex_err_list, rex_frq=rex_frq, chi2=chi2_list)
+ star.model_free.add(global_chi2=global_chi2,
software_ids=[software_id], software_labels=['relax'], res_nums=res_num_list,
res_names=res_name_list, atom_names=atom_name_list, atom_types=element_list,
local_tc=local_tm_list, s2=s2_list, s2f=s2f_list, s2s=s2s_list, te=te_list,
tf=tf_list, ts=ts_list, rex=rex_list, local_tc_err=local_tm_err_list,
s2_err=s2_err_list, s2f_err=s2f_err_list, s2s_err=s2s_err_list,
te_err=te_err_list, tf_err=tf_err_list, ts_err=ts_err_list,
rex_err=rex_err_list, rex_frq=rex_frq, chi2=chi2_list, model_fit=model_list)
# Write the contents to the STAR formatted file.
r9782 - in /branches/bmrb: bmrblib/experimental_details/software.py generic_fns/exp_info.py specific_fns/model_free/bmrb.py