Author: bugman
Date: Thu Dec 7 04:33:48 2006
New Revision: 2919
URL: http://svn.gna.org/viewcvs/relax?rev=2919&view=rev
Log:
Added the method 'self.create_vector_dist()' to 'generic_fns/structure.py'.
This function currently calculates and adds the centre of mass to the PDB
file, adds the XH vectors
as protons to the 'self.atomic_data' data structure, and creates the PDB
file. The code is
incomplete as each vector is being set to the true residue name and number
and ATM record support
still needs to be added.
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=2919&r1=2918&r2=2919&view=diff
==============================================================================
--- 1.3/generic_fns/structure.py (original)
+++ 1.3/generic_fns/structure.py Thu Dec 7 04:33:48 2006
@@ -438,6 +438,111 @@
# Add the TER 'atom''.
self.atom_add(atom_id='TER' + atom_id_ext, record_name='TER',
res_name=last_res, res_num=res_num)
+
+
+ # Create the PDB file.
+ ######################
+
+ # Print out.
+ print "\nGenerating the PDB file."
+
+ # Open the PDB file for writing.
+ tensor_pdb_file = self.relax.IO.open_write_file(self.file, self.dir,
force=self.force)
+
+ # Write the data.
+ self.write_pdb_file(tensor_pdb_file)
+
+ # Close the file.
+ tensor_pdb_file.close()
+
+
+ def create_vector_dist(self, run=None, length=1.8e-6, file=None,
dir=None, force=0):
+ """Create a PDB representation of the XH vector distribution.
+
+ @param run: The run.
+ @type run: str
+ @param length: The length to set the vectors to in the PDB file.
+ @type length: 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 1 will overwrite any
pre-existing file.
+ @type force: int
+ """
+
+ # Arguments.
+ self.length = length
+ self.file = file
+ self.dir = dir
+ self.force = force
+
+ # Test if the run exists.
+ if not run in self.relax.data.run_names:
+ raise RelaxNoRunError, run
+
+ # Test if the PDB file of the macromolecule has been loaded.
+ if not self.relax.data.pdb.has_key(self.run):
+ raise RelaxNoPdbError, self.run
+
+ # Test if sequence data is loaded.
+ if not len(self.relax.data.res[self.run]):
+ raise RelaxNoSequenceError, self.run
+
+ # Test if unit vectors exist.
+ vectors = 0
+ for i in xrange(len(self.relax.data.res[self.run])):
+ if hasattr(self.relax.data.res[self.run][i], 'xh_vect'):
+ vectors = 1
+ break
+ if not vectors:
+ raise RelaxNoVectorsError, self.run
+
+
+ # Initialise.
+ #############
+
+ # Initialise the atom and atomic connections data structures.
+ self.atomic_data = {}
+
+ # Initialise the residue number.
+ res_num = 1
+
+
+ # Centre of mass.
+ #################
+
+ # Calculate the centre of mass.
+ R = self.centre_of_mass()
+
+ # Add the central atom.
+ self.atom_add(atom_id='R', record_name='HETATM', atom_name='R',
res_name='COM', chain_id='A', res_num=res_num, pos=R, element='C')
+
+ # Increment the residue number.
+ res_num = res_num + 1
+
+
+ # The XH vectors.
+ #################
+
+ # Loop over the spin systems.
+ for i in xrange(len(self.relax.data.res[self.run])):
+ # Alias the spin system data.
+ data = self.relax.data.res[self.run][i]
+
+ # Skip unselected spin systems.
+ if not data.select:
+ continue
+
+ # Skip spin systems missing the xh_vect structure.
+ if not hasattr(data, 'xh_vect'):
+ continue
+
+ # Scale the vector.
+ vector = data.xh_vect * length * 1e10
+
+ # Add the vector as a H atom of the TNS residue.
+ self.atom_add(atom_id=data.num, record_name='ATM',
atom_name='H'+`data.num`, res_name=data.name, chain_id='A', res_num=data.num,
pos=vector, element='H')
# Create the PDB file.
r2919 - /1.3/generic_fns/structure.py