Author: han87
Date: Wed Jul 27 11:17:48 2011
New Revision: 13924
URL: http://svn.gna.org/viewcvs/relax?rev=13924&view=rev
Log:
Deleting the function 'vector_xyz' in the generic_fns/structure/main.py
The code of the function 'vector_xyz' was removed since it will be not used.
Modified:
branches/xyz/generic_fns/structure/main.py
Modified: branches/xyz/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/xyz/generic_fns/structure/main.py?rev=13924&r1=13923&r2=13924&view=diff
==============================================================================
--- branches/xyz/generic_fns/structure/main.py (original)
+++ branches/xyz/generic_fns/structure/main.py Wed Jul 27 11:17:48 2011
@@ -612,140 +612,6 @@
raise RelaxError("No vectors could be extracted.")
-def vectors_xyz(spin_id1=None, spin_id2=None, model=None, verbosity=1,
ave=True, unit=True):
- """Extract the bond vectors from the loaded structures and store them in
the spin container.
-
- @keyword attached: The spin identifier string of the atom 1.
- @type attached: str
- @keyword spin_id: The spin identifier string of the atom 2.
- @type spin_id: str
- @keyword model: The model to extract the vector from. If None,
all vectors will be
- extracted.
- @type model: str
- @keyword verbosity: The higher the value, the more information is
printed to screen.
- @type verbosity: int
- @keyword ave: A flag which if True will cause the average of
all vectors to be
- extracted.
- @type ave: bool
- @keyword unit: A flag which if True will cause the function to
calculate the unit
- vectors.
- @type unit: bool
- """
-
- # 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
-
- # Print out.
- if verbosity:
- # Number of models.
- num_models = cdp.structure.num_models()
-
- # Multiple models loaded.
- if num_models > 1:
- if model:
- print(("Extracting vectors for model '%s'." % model))
- else:
- print(("Extracting vectors for all %s models." % num_models))
- if ave:
- print("Averaging all vectors.")
-
- # Single model loaded.
- else:
- print("Extracting vectors from the single model.")
-
- # Unit vectors.
- if unit:
- print("Calculating the unit vectors.")
-
- # Loop over the spins.
- no_vectors = True
- for spin1, mol_name1, res_num1, res_name1 in
spin_loop(selection=spin_id1, full_info=True):
- # Skip deselected spins.
- if not spin.select:
- continue
-
- # The spin identification string. The residue name and spin num is
not included to allow molecules with point mutations to be used as different
models.
- id1 = generate_spin_id(res_num1=res_num1, res_name1=None,
spin_num1=res_num1)
-
- # Test that the spin number or name are set (one or both are
essential for the identification of the atom).
- if spin.num == None and spin.name == None:
- warn(RelaxWarning("Either the spin number or name must be set
for the spin " + repr(id) + " to identify the corresponding atom in the
molecule."))
- continue
-
- # The bond vector already exists.
- if hasattr(spin, object_name):
- obj = getattr(spin, object_name)
- if obj:
- warn(RelaxWarning("The bond vector for the spin " + repr(id)
+ " already exists."))
- continue
-
- # Get the bond info.
- bond_vectors, attached_name, warnings =
cdp.structure.bond_vectors(attached_atom=attached, model_num=model,
res_num=res_num, spin_name=spin.name, return_name=True, return_warnings=True)
-
- # No attached atom.
- if not bond_vectors:
- # Warning messages.
- if warnings:
- warn(RelaxWarning(warnings + " (atom ID " + repr(id) + ")."))
-
- # Skip the spin.
- continue
-
- # Set the attached atom name.
- if not hasattr(spin, 'attached_atom'):
- spin.attached_atom = attached_name
- elif spin.attached_atom != attached_name:
- raise RelaxError("The " + repr(spin.attached_atom) + " atom
already attached to the spin does not match the attached atom " +
repr(attached_name) + ".")
-
- # Initialise the average vector.
- if ave:
- ave_vector = zeros(3, float64)
-
- # Loop over the individual vectors.
- for i in xrange(len(bond_vectors)):
- # Unit vector.
- if unit:
- # Normalisation factor.
- norm_factor = norm(bond_vectors[i])
-
- # Test for zero length.
- if norm_factor == 0.0:
- warn(RelaxZeroVectorWarning(id))
-
- # Calculate the normalised vector.
- else:
- bond_vectors[i] = bond_vectors[i] / norm_factor
-
- # Sum the vectors.
- if ave:
- ave_vector = ave_vector + bond_vectors[i]
-
- # Average.
- if ave:
- vector = ave_vector / float(len(bond_vectors))
- else:
- vector = bond_vectors
-
- # Set the vector.
- setattr(spin, object_name, vector)
-
- # We have a vector!
- no_vectors = False
-
- # Print out of modified spins.
- if verbosity:
- print(("Extracted " + spin.name + "-" + attached_name + "
vectors for " + repr(id) + '.'))
-
- # Right, catch the problem of missing vectors to prevent massive user
confusion!
- if no_vectors:
- raise RelaxError("No vectors could be extracted.")
-
-
def write_pdb(file=None, dir=None, model_num=None, force=False):
"""The PDB writing function.
r13924 - /branches/xyz/generic_fns/structure/main.py