Author: bugman
Date: Mon Apr 7 14:00:11 2008
New Revision: 5350
URL: http://svn.gna.org/viewcvs/relax?rev=5350&view=rev
Log:
Renamed the generic_fns.structure.structure module to
generic_fns.structure.main.
Added:
1.3/generic_fns/structure/main.py
- copied unchanged from r5348, 1.3/generic_fns/structure/structure.py
Removed:
1.3/generic_fns/structure/structure.py
Removed: 1.3/generic_fns/structure/structure.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/structure.py?rev=5349&view=auto
==============================================================================
--- 1.3/generic_fns/structure/structure.py (original)
+++ 1.3/generic_fns/structure/structure.py (removed)
@@ -1,166 +1,0 @@
-###############################################################################
-#
#
-# Copyright (C) 2003-2008 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
#
-#
#
-###############################################################################
-
-# Python module imports.
-from os import F_OK, access
-from warnings import warn
-
-# relax module imports.
-from data import Data as relax_data_store
-from generic_fns import molmol
-from generic_fns.sequence import load_PDB_sequence
-from generic_fns.selection import exists_mol_res_spin_data, spin_loop
-from relax_errors import RelaxError, RelaxFileError, RelaxNoPipeError,
RelaxNoSequenceError, RelaxPdbError
-from relax_io import get_file_path
-from relax_warnings import RelaxNoPDBFileWarning
-
-
-
-def read_pdb(run=None, file=None, dir=None, model=None, load_seq=1, fail=1,
verbosity=1):
- """The pdb loading function."""
-
- # Tests.
- ########
-
- # Test if the current data pipe exists.
- if not relax_data_store.current_pipe:
- raise RelaxNoPipeError
-
- # Alias the current data pipe.
- cdp = relax_data_store[relax_data_store.current_pipe]
-
- # Test if PDB data corresponding to the run already exists.
- if hasattr(cdp, 'struct'):
- raise RelaxPdbError
-
- # Test if sequence data is loaded.
- if not load_seq and not exists_mol_res_spin_data():
- raise RelaxNoSequenceError
-
- # The file path.
- file_path = get_file_path(file, dir)
-
- # Test if the file exists.
- if not access(file_path, F_OK):
- if fail:
- raise RelaxFileError, ('PDB', file_path)
- else:
- warn(RelaxNoPDBFileWarning(file_path))
- return
-
-
- # Data creation.
- ################
-
- # File name.
- cdp.structure.file_name = file_path
-
- # Model.
- cdp.structure.model = model
-
-
- # Load the structures.
- ######################
-
- load_structures(file_path, model, verbosity)
-
-
- # Finish.
- #########
-
- # Sequence loading.
- if load_seq and not exists_mol_res_spin_data():
- load_PDB_sequence()
-
- # Load into Molmol (if running).
- molmol.open_pdb()
-
-
-def set_vector(spin=None, xh_vect=None):
- """Place the XH unit vector into the spin container object.
-
- @keyword spin: The spin container object.
- @type spin: SpinContainer instance
- @keyword xh_vect: The unit vector parallel to the XH bond.
- @type xh_vect: array of len 3
- """
-
- # Place the XH unit vector into the container.
- spin.xh_vect = xh_vect
-
-
-def vectors(heteronuc=None, proton=None, spin_id=None, verbosity=1):
- """Function for calculating/extracting the XH unit vector from the
loaded structure.
-
- @param heteronuc: The name of the heteronucleus.
- @type heteronuc: str
- @param proton: The name of the proton.
- @type proton: str
- @param spin_id: The molecule, residue, and spin identifier string.
- @type spin_id: str
- @param verbosity: The higher the value, the more information is
printed to screen.
- @type verbosity: int
- """
-
- # Alias the current data pipe.
- cdp = relax_data_store[relax_data_store.current_pipe]
-
- # Test if the PDB file has been loaded.
- if not hasattr(cdp, 'structure'):
- raise RelaxPdbError
-
- # Test if sequence data is loaded.
- if not exists_mol_res_spin_data():
- raise RelaxNoSequenceError
-
- # Test that the nuclei have been correctly set.
- if heteronuc == proton:
- raise RelaxError, "The proton and heteronucleus are set to the same
atom."
-
- # Number of structures.
- num_str = len(cdp.structure.structures)
-
- # Print out.
- if verbosity:
- if num_str > 1:
- print "\nCalculating and averaging the unit XH vectors from all
structures."
- else:
- print "\nCalculating the unit XH vectors from the structure."
-
- # Loop over the sequence.
- for spin in spin_loop(spin_id):
- # Skip unselected residues.
- if not spin.select:
- continue
-
- # Set the proton and heteronucleus names.
- spin.proton = proton
- spin.heteronuc = heteronuc
-
- # Calculate the vector.
- vector = xh_vector(spin)
-
- # Set the vector and deselect the spin if the vector doesn't exist.
- if vector != None:
- spin.xh_vect = vector
- else:
- spin.select = False
r5350 - in /1.3/generic_fns/structure: main.py structure.py