Author: tlinnet
Date: Fri Oct 3 18:30:38 2014
New Revision: 26145
URL: http://svn.gna.org/viewcvs/relax?rev=26145&view=rev
Log:
Implemented the initial part of the API, to collect data for BMRB submission.
task #7858 (https://gna.org/task/?7858): Make it possible to submit CPMG
experiments for BMRB
Modified:
trunk/specific_analyses/relax_disp/api.py
Modified: trunk/specific_analyses/relax_disp/api.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/api.py?rev=26145&r1=26144&r2=26145&view=diff
==============================================================================
--- trunk/specific_analyses/relax_disp/api.py (original)
+++ trunk/specific_analyses/relax_disp/api.py Fri Oct 3 18:30:38 2014
@@ -25,8 +25,11 @@
"""The relaxation dispersion API object."""
# Python module imports.
+import bmrblib
from copy import deepcopy
+from numpy import int32, zeros
from re import match, search
+import string
import sys
from types import MethodType
@@ -36,9 +39,11 @@
from lib.errors import RelaxError, RelaxImplementError
from lib.text.sectioning import subsection
from multi import Processor_box
-from pipe_control import pipes, sequence
-from pipe_control.mol_res_spin import check_mol_res_spin_data, return_spin,
spin_loop
+from pipe_control import pipes, relax_data, sequence
+from pipe_control.exp_info import bmrb_write_citations, bmrb_write_methods,
bmrb_write_software
+from pipe_control.mol_res_spin import bmrb_write_entity,
check_mol_res_spin_data, get_molecule_names, return_spin, spin_loop
from pipe_control.pipes import check_pipe
+from pipe_control.spectrometer import check_spectrometer_setup
from pipe_control.sequence import return_attached_protons
from specific_analyses.api_base import API_base
from specific_analyses.api_common import API_common
@@ -120,6 +125,115 @@
# Yield the spin container and ID.
yield spin, spin_id
+
+
+ def bmrb_write(self, file_path, version=None):
+ """Write the model-free results to a BMRB NMR-STAR v3.1 formatted
file.
+
+ @param file_path: The full file path.
+ @type file_path: str
+ @keyword version: The BMRB NMR-STAR dictionary format to output to.
+ @type version: str
+ """
+
+ # Checks.
+ check_spectrometer_setup(escalate=2)
+
+ # Alias the current data pipe.
+ cdp = pipes.get_pipe()
+
+ # Initialise the NMR-STAR data object.
+ star =
bmrblib.create_nmr_star('relax_relaxation_dispersion_results', file_path,
version)
+
+ # Initialise the spin specific data lists.
+ mol_name_list = []
+ res_num_list = []
+ res_name_list = []
+ atom_name_list = []
+
+ isotope_list = []
+ element_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):
+ # Skip the protons.
+ if spin.name == 'H' or (hasattr(spin, 'element') and
spin.element == 'H'):
+ warn(RelaxWarning("Skipping the proton spin '%s'." %
spin_id))
+ continue
+
+ # Check the data for None (not allowed in BMRB!).
+ if res_num == None:
+ raise RelaxError("For the BMRB, the residue of spin '%s'
must be numbered." % spin_id)
+ if res_name == None:
+ raise RelaxError("For the BMRB, the residue of spin '%s'
must be named." % spin_id)
+ if spin.name == None:
+ raise RelaxError("For the BMRB, the spin '%s' must be
named." % spin_id)
+ if not hasattr(spin, 'isotope') or spin.isotope == None:
+ raise RelaxError("For the BMRB, the spin isotope type of
'%s' must be specified." % spin_id)
+ if not hasattr(spin, 'element') or spin.element == None:
+ raise RelaxError("For the BMRB, the spin element type of
'%s' must be specified. Please use the spin user function for setting the
element type." % spin_id)
+
+ # The molecule/residue/spin info.
+ mol_name_list.append(mol_name)
+ res_num_list.append(res_num)
+ res_name_list.append(res_name)
+ atom_name_list.append(spin.name)
+
+ # The nuclear isotope.
+ if hasattr(spin, 'isotope'):
+
isotope_list.append(int(spin.isotope.strip(string.ascii_letters)))
+ else:
+ isotope_list.append(None)
+
+ # The element.
+ if hasattr(spin, 'element'):
+ element_list.append(spin.element)
+ else:
+ element_list.append(None)
+
+ # Opt stats.
+ if hasattr(spin, 'chi2'):
+ chi2_list.append(spin.chi2)
+ else:
+ chi2_list.append(None)
+
+ # Model-free model.
+ model_list.append(spin.model)
+
+ # Convert the molecule names into the entity IDs.
+ entity_ids = zeros(len(mol_name_list), int32)
+ mol_names = get_molecule_names()
+ for i in range(len(mol_name_list)):
+ for j in range(len(mol_names)):
+ if mol_name_list[i] == mol_names[j]:
+ entity_ids[i] = j+1
+
+
+ # Create Supergroup 2 : The citations.
+ ######################################
+
+ # Generate the citations saveframe.
+ bmrb_write_citations(star)
+
+
+ # Create Supergroup 3 : The molecular assembly saveframes.
+ ##########################################################
+
+ # Generate the entity saveframe.
+ bmrb_write_entity(star)
+
+
+ # Create Supergroup 4: The experimental descriptions saveframes.
+ #################################################################
+
+ # Generate the method saveframes.
+ bmrb_write_methods(star)
+
+ # Generate the software saveframe.
+ software_ids, software_labels = bmrb_write_software(star)
def calculate(self, spin_id=None, scaling_matrix=None, verbosity=1,
sim_index=None):
r26145 - /trunk/specific_analyses/relax_disp/api.py