Author: bugman
Date: Wed Feb 20 12:11:34 2008
New Revision: 5043
URL: http://svn.gna.org/viewcvs/relax?rev=5043&view=rev
Log:
Converted the generic_fns.structure.create_diff_tensor_pdb() to the new relax
design.
Modified:
1.3/generic_fns/structure.py
Modified: 1.3/generic_fns/structure.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure.py?rev=5043&r1=5042&r2=5043&view=diff
==============================================================================
--- 1.3/generic_fns/structure.py (original)
+++ 1.3/generic_fns/structure.py Wed Feb 20 12:11:34 2008
@@ -36,7 +36,7 @@
from generic_fns.selection import exists_mol_res_spin_data, return_molecule,
return_residue, return_spin, spin_loop
from physical_constants import ArH, ArC, ArN, ArO, ArS
from relax_errors import RelaxError, RelaxFileError, RelaxNoPdbChainError,
RelaxNoPdbError, RelaxNoResError, RelaxNoPipeError, RelaxNoSequenceError,
RelaxNoTensorError, RelaxNoVectorsError, RelaxPdbError, RelaxPdbLoadError,
RelaxRegExpError
-from relax_io import get_file_path
+from relax_io import get_file_path, open_write_file
from relax_warnings import RelaxNoAtomWarning, RelaxNoPDBFileWarning,
RelaxWarning, RelaxZeroVectorWarning
@@ -303,52 +303,59 @@
return R
-def create_diff_tensor_pdb(run=None, scale=1.8e-6, file=None, dir=None,
force=0):
- """Create the PDB representation of the diffusion tensor."""
+def create_diff_tensor_pdb(scale=1.8e-6, file=None, dir=None, force=False):
+ """Create the PDB representation of the diffusion tensor.
+
+ @param scale: The scaling factor for the diffusion tensor.
+ @type scale: float
+ @param file: The name of the PDB file to create.
+ @type file: str
+ @param dir: The name of the directory to place the PDB file into.
+ @type dir: str
+ @param force: Flag which if set to True will overwrite any
pre-existing file.
+ @type force: bool
+ """
# Arguments.
- scale = scale
- file = file
- dir = dir
- force = force
if scale == 'mass':
scale = autoscale_tensor(scale)
+
+ # 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]
+
+ # Create an array of data pipes to loop over (hybrid support).
+ if cdp.pipe_type == 'hybrid':
+ pipes = cdp.hybrid_pipes
else:
- scale = scale
-
- # Test if the run exists.
- if not run in relax_data_store.run_names:
- raise RelaxNoPipeError, run
-
- # Create an array of runs to loop over (hybrid support).
- if relax_data_store.run_types[relax_data_store.run_names.index(run)] ==
'hybrid':
- runs = relax_data_store.hybrid_runs[run]
- else:
- runs = [run]
+ pipes = [relax_data_store.current_pipe]
# Initialise the atom and atomic connections data structures.
atomic_data = {}
- # Loop over the runs.
- for run_index in xrange(len(runs)):
- # Place the run into 'self'.
- run = runs[run_index]
+ # Loop over the pipes.
+ for pipe_index in xrange(len(pipes)):
+ # Alias the pipe container.
+ pipe = relax_data_store[pipes[pipe_index]]
# Tests.
########
# Test if the diffusion tensor data is loaded.
- if not relax_data_store.diff.has_key(run):
+ if not hasattr(pipe, 'diff'):
raise RelaxNoTensorError, 'diffusion'
- # Test if the PDB file of the macromolecule has been loaded.
- if not relax_data_store.pdb.has_key(run):
- raise RelaxNoPdbError, run
+ # Test if a structure has been loaded.
+ if not hasattr(cdp.structure, 'structures'):
+ raise RelaxNoPdbError
# Test if sequence data is loaded.
- if not len(relax_data_store.res[run]):
- raise RelaxNoSequenceError, run
+ if not exists_mol_res_spin_data():
+ raise RelaxNoSequenceError
# Initialise.
@@ -358,7 +365,7 @@
res_num = 1
# The chain identifier.
- chain_id = ascii_uppercase[run_index]
+ chain_id = ascii_uppercase[pipe_index]
# Atom ID extension (allow for multiple chains for hybrid runs).
atom_id_ext = '_' + chain_id
@@ -405,10 +412,10 @@
atom_id = 'T' + `i` + 'P' + `j` + atom_id_ext
# Rotate the vector into the diffusion frame.
- vector = dot(relax_data_store.diff[run].rotation,
vectors[index])
+ vector = dot(pipe.diff.rotation, vectors[index])
# Set the length of the vector to its diffusion rate within
the diffusion tensor geometric object.
- vector = dot(relax_data_store.diff[run].tensor, vector)
+ vector = dot(pipe.diff.tensor, vector)
# Scale the vector.
vector = vector * scale
@@ -445,7 +452,7 @@
#####################
# Create the unique axis of the spheroid.
- if relax_data_store.diff[run].type == 'spheroid':
+ if pipe.diff.type == 'spheroid':
# Print out.
print "\nGenerating the unique axis of the diffusion tensor."
print " Scaling factor: " + `scale`
@@ -454,18 +461,18 @@
generate_spheroid_axes(chain_id=chain_id, res_num=res_num, R=R)
# Simulations.
- if hasattr(relax_data_store.diff[run], 'tm_sim'):
+ if hasattr(pipe.diff, 'tm_sim'):
# Print out.
print " Creating the MC simulation axes."
# Create each MC simulation axis as a new residue.
- for i in xrange(len(relax_data_store.diff[run].tm_sim)):
+ for i in xrange(len(pipe.diff.tm_sim)):
res_num = res_num + 1
generate_spheroid_axes(chain_id=chain_id,
res_num=res_num, R=R, i=i)
# Create the three axes of the ellipsoid.
- if relax_data_store.diff[run].type == 'ellipsoid':
+ if pipe.diff.type == 'ellipsoid':
# Print out.
print "Generating the three axes of the ellipsoid."
print " Scaling factor: " + `scale`
@@ -474,12 +481,12 @@
generate_ellipsoid_axes(chain_id=chain_id, res_num=res_num, R=R)
# Simulations.
- if hasattr(relax_data_store.diff[run], 'tm_sim'):
+ if hasattr(pipe.diff, 'tm_sim'):
# Print out.
print " Creating the MC simulation axes."
# Create each MC simulation axis as a new residue.
- for i in xrange(len(relax_data_store.diff[run].tm_sim)):
+ for i in xrange(len(pipe.diff.tm_sim)):
res_num = res_num + 1
generate_ellipsoid_axes(chain_id=chain_id,
res_num=res_num, R=R, i=i)
@@ -503,7 +510,7 @@
print "\nGenerating the PDB file."
# Open the PDB file for writing.
- tensor_pdb_file = relax.IO.open_write_file(file, dir, force=force)
+ tensor_pdb_file = open_write_file(file, dir, force=force)
# Write the data.
write_pdb_file(tensor_pdb_file)
r5043 - /1.3/generic_fns/structure.py