Author: bugman
Date: Fri Oct 9 18:32:18 2009
New Revision: 9702
URL: http://svn.gna.org/viewcvs/relax?rev=9702&view=rev
Log:
The software saveframe is now being created.
This information does not need to be read from the BMRB file.
Added:
branches/bmrb/bmrblib/experimental_details/software.py
branches/bmrb/generic_fns/bmrb_saveframes.py
Modified:
branches/bmrb/bmrblib/nmr_star_dict.py
branches/bmrb/bmrblib/nmr_star_dict_v3_1.py
branches/bmrb/bmrblib/nmr_star_dict_v3_2.py
branches/bmrb/specific_fns/model_free/bmrb.py
Added: branches/bmrb/bmrblib/experimental_details/software.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/experimental_details/software.py?rev=9702&view=auto
==============================================================================
--- branches/bmrb/bmrblib/experimental_details/software.py (added)
+++ branches/bmrb/bmrblib/experimental_details/software.py Fri Oct 9
18:32:18 2009
@@ -1,0 +1,191 @@
+###############################################################################
+#
#
+# Copyright (C) 2009 Edward d'Auvergne
#
+#
#
+# This file is part of the program relax.
#
+#
#
+# relax is free software; you can redistribute it and/or modify
#
+# it under the terms of the GNU General Public License as published by
#
+# the Free Software Foundation; either version 2 of the License, or
#
+# (at your option) any later version.
#
+#
#
+# relax is distributed in the hope that it will be useful,
#
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
+# GNU General Public License for more details.
#
+#
#
+# You should have received a copy of the GNU General Public License
#
+# along with relax; if not, write to the Free Software
#
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
+#
#
+###############################################################################
+
+# Module docstring.
+"""The software saveframe category.
+
+For example, see
http://www.bmrb.wisc.edu/dictionary/3.1html_frame/frame_SaveFramePage.html#software
+"""
+
+# relax module imports.
+from bmrblib.base_classes import BaseSaveframe, TagCategory
+from bmrblib.pystarlib.SaveFrame import SaveFrame
+from bmrblib.pystarlib.TagTable import TagTable
+from bmrblib.misc import translate
+
+
+class SoftwareSaveframe(BaseSaveframe):
+ """The software saveframe class."""
+
+ 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 software programs used.
+ self.software_num = 0
+
+ # Add the specific tag category objects.
+ self.add_tag_categories()
+
+
+ def add(self, name, version=None, vendor_name=None, vendor_address=None,
vendor_eaddress=None):
+ """Add the software info to the data nodes.
+
+ @param name: The name of the software program.
+ @type name: str
+ @keyword version: The software version.
+ @type version: None or str
+ @keyword vendor_name: The vendor or developers of the software.
+ @type vendor_name: None or str
+ @keyword vendor_address: The vendor address.
+ @type vendor_address: None or str
+ @keyword vendor_eaddress: The vendor electronic address.
+ @type vendor_eaddress: None or str
+ """
+
+ # Place the args into the namespace.
+ self.program_name = name
+ self.program_version = version
+ self.vendor_name = [translate(vendor_name)]
+ self.vendor_address = [translate(vendor_address)]
+ self.vendor_eaddress = [translate(vendor_eaddress)]
+
+ # Increment the ID number.
+ self.software_num = self.software_num + 1
+ self.software_id_num = [str(translate(self.software_num))]
+
+ # The category name.
+ self.cat_name = ['Software']
+
+ # Initialise the save frame.
+ self.frame = SaveFrame(title=self.program_name)
+
+ # Create the tag categories.
+ self.Software.create()
+ self.Vendor.create()
+
+ # Add the saveframe to the data nodes.
+ self.datanodes.append(self.frame)
+
+
+ def add_tag_categories(self):
+ """Create the tag categories."""
+
+ # The tag category objects.
+ self.Software = Software(self)
+ self.Software_citation = SoftwareCitation(self)
+ self.Task = Task(self)
+ self.Vendor = Vendor(self)
+
+
+
+class Software(TagCategory):
+ """Base class for the Software tag category."""
+
+ def create(self):
+ """Create the ChemShiftAnisotropy tag category."""
+
+ # The save frame category.
+ self.sf.frame.tagtables.append(self.create_tag_table([['SfCategory',
'cat_name']], free=True))
+
+ # Software ID number.
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['SoftwareID']],
tagvalues=[[str(self.sf.software_num)]]))
+
+ # The program name.
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['Name']], tagvalues=[[self.sf.program_name]]))
+
+ # The program version.
+ if self.sf.program_version:
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['Version']],
tagvalues=[[self.sf.program_version]]))
+
+
+ def tag_setup(self, tag_category_label=None, sep=None):
+ """Replacement method for setting up the tag names.
+
+ @keyword tag_category_label: The tag name prefix specific for the
tag category.
+ @type tag_category_label: None or str
+ @keyword sep: The string separating the tag name
prefix and suffix.
+ @type sep: str
+ """
+
+ # Execute the base class tag_setup() method.
+ TagCategory.tag_setup(self, tag_category_label='Software', sep=sep)
+
+ # Tag names for the relaxation data.
+ self.tag_names['SfCategory'] = 'Sf_category'
+ self.tag_names['SoftwareID'] = 'ID'
+ self.tag_names['Name'] = 'Name'
+ self.tag_names['Version'] = 'Version'
+
+
+class SoftwareCitation(TagCategory):
+ """Base class for the SoftwareCitation tag category."""
+
+
+class Task(TagCategory):
+ """Base class for the Task tag category."""
+
+
+class Vendor(TagCategory):
+ """Base class for the Vendor tag category."""
+
+ def create(self):
+ """Create the Vendor tag category."""
+
+ # Keys and objects.
+ info = [
+ ['Name', 'vendor_name'],
+ ['Address', 'vendor_address'],
+ ['ElectronicAddress', 'vendor_eaddress'],
+ ['SoftwareID', 'software_id_num']
+ ]
+
+ # Get the TabTable.
+ table = self.create_tag_table(info)
+
+ # Add the tagtable to the save frame.
+ self.sf.frame.tagtables.append(table)
+
+
+ def tag_setup(self, tag_category_label=None, sep=None):
+ """Replacement method for setting up the tag names.
+
+ @keyword tag_category_label: The tag name prefix specific for the
tag category.
+ @type tag_category_label: None or str
+ @keyword sep: The string separating the tag name
prefix and suffix.
+ @type sep: str
+ """
+
+ # Execute the base class tag_setup() method.
+ TagCategory.tag_setup(self, tag_category_label='Vendor', sep=sep)
+
+ # Tag names for the relaxation data.
+ self.tag_names['Name'] = 'Name'
+ self.tag_names['Address'] = 'Address'
+ self.tag_names['ElectronicAddress'] = 'ElectronicAddress'
+ self.tag_names['SoftwareID'] = 'SoftwareID'
Modified: branches/bmrb/bmrblib/nmr_star_dict.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/nmr_star_dict.py?rev=9702&r1=9701&r2=9702&view=diff
==============================================================================
--- branches/bmrb/bmrblib/nmr_star_dict.py (original)
+++ branches/bmrb/bmrblib/nmr_star_dict.py Fri Oct 9 18:32:18 2009
@@ -29,6 +29,7 @@
# relax module imports.
from bmrblib.assembly_supercategory.entity import EntitySaveframe
+from bmrblib.experimental_details.software import SoftwareSaveframe
from bmrblib.kinetics.relaxation import Relaxation
from bmrblib.NMR_parameters.chem_shift_anisotropy import
ChemShiftAnisotropySaveframe
from bmrblib.thermodynamics.order_parameters import OrderParameterSaveframe
@@ -61,16 +62,19 @@
def create_saveframes(self):
"""Create all the saveframe objects."""
- # Initialise the assembly_supercategory saveframe supergroup.
+ # Initialise Supergroup 3 : The molecular assembly saveframe API.
self.entity = EntitySaveframe(self.data.datanodes)
- # Initialise the NMR parameters saveframe supergroup.
+ # Initialise Supergroup 4: The experimental descriptions saveframe
API.
+ self.software = SoftwareSaveframe(self.data.datanodes)
+
+ # Initialise Supergroup 5 : The NMR parameters saveframe API.
self.chem_shift_anisotropy =
ChemShiftAnisotropySaveframe(self.data.datanodes)
- # Initialise the kinetic saveframe supergroup API.
+ # Initialise Supergroup 6 : The kinetic data saveframe API.
self.relaxation = Relaxation(self.data.datanodes)
- # Initialise the thermodynamics saveframe supergroup.
+ # Initialise Supergroup 7 : The thermodynamics saveframe API.
self.order_parameters = OrderParameterSaveframe(self.data.datanodes)
Modified: branches/bmrb/bmrblib/nmr_star_dict_v3_1.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/nmr_star_dict_v3_1.py?rev=9702&r1=9701&r2=9702&view=diff
==============================================================================
--- branches/bmrb/bmrblib/nmr_star_dict_v3_1.py (original)
+++ branches/bmrb/bmrblib/nmr_star_dict_v3_1.py Fri Oct 9 18:32:18 2009
@@ -29,6 +29,7 @@
# relax module imports.
from bmrblib.assembly_supercategory.entity_v3_1 import EntitySaveframe_v3_1
+from bmrblib.experimental_details.software import SoftwareSaveframe
from bmrblib.kinetics.relaxation import Relaxation_v3_1
from bmrblib.NMR_parameters.chem_shift_anisotropy_v3_1 import
ChemShiftAnisotropySaveframe_v3_1
from bmrblib.thermodynamics.order_parameters_v3_1 import
OrderParameterSaveframe_v3_1
@@ -45,14 +46,17 @@
def create_saveframes(self):
"""Create all the saveframe objects."""
- # Initialise the assembly_supercategory saveframe supergroup.
+ # Initialise Supergroup 3 : The molecular assembly saveframe API.
self.entity = EntitySaveframe_v3_1(self.data.datanodes)
- # Initialise the NMR parameters saveframe supergroup.
+ # Initialise Supergroup 4: The experimental descriptions saveframe
API.
+ self.software = SoftwareSaveframe(self.data.datanodes)
+
+ # Initialise Supergroup 5 : The NMR parameters saveframe API.
self.chem_shift_anisotropy =
ChemShiftAnisotropySaveframe_v3_1(self.data.datanodes)
- # Initialise the kinetic saveframe supergroup API.
+ # Initialise Supergroup 6 : The kinetic data saveframe API.
self.relaxation = Relaxation_v3_1(self.data.datanodes)
- # Initialise the thermodynamics saveframe supergroup.
+ # Initialise Supergroup 7 : The thermodynamics saveframe API.
self.order_parameters =
OrderParameterSaveframe_v3_1(self.data.datanodes)
Modified: branches/bmrb/bmrblib/nmr_star_dict_v3_2.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/nmr_star_dict_v3_2.py?rev=9702&r1=9701&r2=9702&view=diff
==============================================================================
--- branches/bmrb/bmrblib/nmr_star_dict_v3_2.py (original)
+++ branches/bmrb/bmrblib/nmr_star_dict_v3_2.py Fri Oct 9 18:32:18 2009
@@ -29,6 +29,7 @@
# relax module imports.
from bmrblib.assembly_supercategory.entity_v3_1 import EntitySaveframe_v3_1
+from bmrblib.experimental_details.software import SoftwareSaveframe
from bmrblib.kinetics.relaxation import Relaxation_v3_2
from bmrblib.NMR_parameters.chem_shift_anisotropy_v3_1 import
ChemShiftAnisotropySaveframe_v3_1
from bmrblib.thermodynamics.order_parameters_v3_1 import
OrderParameterSaveframe_v3_1
@@ -45,14 +46,17 @@
def create_saveframes(self):
"""Create all the saveframe objects."""
- # Initialise the assembly_supercategory saveframe supergroup.
+ # Initialise Supergroup 3 : The molecular assembly saveframe API.
self.entity = EntitySaveframe_v3_1(self.data.datanodes)
- # Initialise the NMR parameters saveframe supergroup.
+ # Initialise Supergroup 4: The experimental descriptions saveframe
API.
+ self.software = SoftwareSaveframe(self.data.datanodes)
+
+ # Initialise Supergroup 5 : The NMR parameters saveframe API.
self.chem_shift_anisotropy =
ChemShiftAnisotropySaveframe_v3_1(self.data.datanodes)
- # Initialise the kinetic saveframe supergroup API.
+ # Initialise Supergroup 6 : The kinetic data saveframe API.
self.relaxation = Relaxation_v3_2(self.data.datanodes)
- # Initialise the thermodynamics saveframe supergroup.
+ # Initialise Supergroup 7 : The thermodynamics saveframe API.
self.order_parameters =
OrderParameterSaveframe_v3_1(self.data.datanodes)
Added: branches/bmrb/generic_fns/bmrb_saveframes.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/bmrb_saveframes.py?rev=9702&view=auto
==============================================================================
--- branches/bmrb/generic_fns/bmrb_saveframes.py (added)
+++ branches/bmrb/generic_fns/bmrb_saveframes.py Fri Oct 9 18:32:18 2009
@@ -1,0 +1,38 @@
+###############################################################################
+#
#
+# Copyright (C) 2009 Edward d'Auvergne
#
+#
#
+# This file is part of the program relax.
#
+#
#
+# relax is free software; you can redistribute it and/or modify
#
+# it under the terms of the GNU General Public License as published by
#
+# the Free Software Foundation; either version 2 of the License, or
#
+# (at your option) any later version.
#
+#
#
+# relax is distributed in the hope that it will be useful,
#
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
+# GNU General Public License for more details.
#
+#
#
+# You should have received a copy of the GNU General Public License
#
+# along with relax; if not, write to the Free Software
#
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
+#
#
+###############################################################################
+
+# Module docstring.
+"""Module containing read/write functions for miscellaneous BMRB NMR-STAR
saveframes."""
+
+# relax module imports.
+from version import version
+
+
+def write_relax(star):
+ """Generate the Software saveframe records for relax.
+
+ @param star: The NMR-STAR dictionary object.
+ @type star: NMR_STAR instance
+ """
+
+ # The relax info.
+ star.software.add(name='relax', version=version, vendor_name='The relax
development team', vendor_eaddress='http://nmr-relax.com')
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=9702&r1=9701&r2=9702&view=diff
==============================================================================
--- branches/bmrb/specific_fns/model_free/bmrb.py (original)
+++ branches/bmrb/specific_fns/model_free/bmrb.py Fri Oct 9 18:32:18 2009
@@ -28,7 +28,7 @@
from bmrblib.nmr_star_dict import NMR_STAR
from bmrblib.nmr_star_dict_v3_1 import NMR_STAR_v3_1
from bmrblib.nmr_star_dict_v3_2 import NMR_STAR_v3_2
-from generic_fns import mol_res_spin, pipes, relax_data
+from generic_fns import bmrb_saveframes, mol_res_spin, pipes, relax_data
from generic_fns.mol_res_spin import spin_loop
@@ -79,12 +79,6 @@
star = NMR_STAR_v3_1('relax_model_free_results', file_path)
else:
star = NMR_STAR('relax_model_free_results', file_path)
-
- # Generate the entity saveframe.
- mol_res_spin.bmrb_write_entity(star)
-
- # Generate the relaxation data saveframes.
- relax_data.bmrb_write(star)
# Rex frq.
rex_frq = cdp.frq[0]
@@ -168,11 +162,41 @@
# Opt stats.
chi2_list.append(spin.chi2)
+
+ # Create Supergroup 3 : The molecular assembly saveframes.
+ ##########################################################
+
+ # Generate the entity saveframe.
+ mol_res_spin.bmrb_write_entity(star)
+
+
+ # Create Supergroup 4: The experimental descriptions saveframes.
+ #################################################################
+
+ # Generate the software saveframe.
+ bmrb_saveframes.write_relax(star)
+
+
+ # Create Supergroup 5 : The NMR parameters saveframes.
+ ######################################################
+
# Generate the CSA saveframe.
star.chem_shift_anisotropy.add(res_nums=res_num_list,
res_names=res_name_list, atom_names=atom_name_list, isotope=isotope_list,
csa=csa_list)
+
+ # Create Supergroup 6 : The kinetic data saveframes.
+ ####################################################
+
+ # Generate the relaxation data saveframes.
+ relax_data.bmrb_write(star)
+
+
+ # Create Supergroup 7 : The thermodynamics saveframes.
+ ######################################################
+
# Generate the model-free data saveframe.
star.order_parameters.add(res_nums=res_num_list,
res_names=res_name_list, atom_names=atom_name_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)
+
# Write the contents to the STAR formatted file.
star.write()
r9702 - in /branches/bmrb: bmrblib/ bmrblib/experimental_details/ generic_fns/ specific_fns/model_free/