Author: bugman
Date: Wed Feb 20 11:03:41 2008
New Revision: 5040
URL: http://svn.gna.org/viewcvs/relax?rev=5040&view=rev
Log:
Created the new function generic_fns.structure.generate_vector_residues().
This new function should allow greater flexibility for creating PDB
representations of any type of
vector (and its MC sims). It will also replace the generate_spheroid_axes()
and
generate_ellipsoid_axes() functions.
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=5040&r1=5039&r2=5040&view=diff
==============================================================================
--- 1.3/generic_fns/structure.py (original)
+++ 1.3/generic_fns/structure.py Wed Feb 20 11:03:41 2008
@@ -818,6 +818,90 @@
# Print out.
if i == None:
print " Dpar vector (scaled + shifted to R): " + `Dpar_vect`
+
+
+def generate_vector_residues(atomic_data=None, vector=None, atom_name=None,
res_name_vect='AXS', sim_vectors=None, res_name_sim='SIM', chain_id=None,
res_num=None, origin=None, scale=1.0, label_placement=1.1, neg=False):
+ """Generate residue representations for the vector and the MC
simulationed vectors.
+
+ This is used to create a PDB representation of any vector, including its
Monte Carlo
+ simulations.
+
+ @param atomic_data: The dictionary to place the atomic data into.
+ @type atomic_data: dict
+ @param vector: The vector to be represented in the PDB.
+ @type vector: numpy array, len 3
+ @param atom_name: The atom name used to label the atom
representing the head of the vector
+ and also used as the first part of the atom
identifier key in the
+ atomic_data dictionary.
+ @type atom_name: str
+ @param res_name_vect: The 3 letter PDB residue code used to represent
the vector.
+ @type res_name_vect: str
+ @param sim_vectors: The optional Monte Carlo simulation vectors to
be represented in the
+ PDB.
+ @type sim_vectors: list of numpy array, each len 3
+ @param res_name_sim: The 3 letter PDB residue code used to represent
the Monte Carlo
+ simulation vectors.
+ @type res_name_sim: str
+ @param chain_id: The chain identification code.
+ @type chain_id: str
+ @param res_num: The residue number.
+ @type res_num: int
+ @param origin: The origin for the axis.
+ @type origin: numpy array, len 3
+ @param scale: The scaling factor to stretch the vectors by.
+ @type scale: float
+ @param label_placement: A scaling factor to multiply the pre-scaled
vector by. This is used to
+ place the vector labels a little further out
from the vector itself.
+ @type label_placement: float
+ @param neg: If True, then the negative vector positioned at
the origin will also be
+ included.
+ @type neg: bool
+ @return: The new residue number.
+ @rtype: int
+ """
+
+ # The atom ID extension.
+ if chain_id:
+ atom_id_ext = '_' + chain_id
+ else:
+ atom_id_ext = ''
+
+ # The origin atom.
+ atom_add(atom_id='R_vect'+atom_id_ext, record_name='HETATM',
atom_name='R', res_name=res_name_vect, chain_id=chain_id, res_num=res_num,
pos=origin, element='C')
+
+ # Create the PDB residue representing the vector.
+ atom_add(atom_id=atom_name+atom_id_ext, record_name='HETATM',
atom_name=atom_name, res_name=res_name_vect, chain_id=chain_id,
res_num=res_num, pos=origin+vector*scale, element='C')
+ atom_connect(atom_id=atom_name+atom_id_ext,
bonded_id='R_vect'+atom_id_ext)
+ if neg:
+ atom_add(atom_id=atom_name+'_neg'+atom_id_ext, record_name='HETATM',
atom_name=atom_name, res_name=res_name_vect, chain_id=chain_id,
res_num=res_num, pos=origin-vector*scale, element='C')
+ atom_connect(atom_id=atom_name+'_neg'+atom_id_ext,
bonded_id='R_vect'+atom_id_ext)
+
+ # Add another atom to allow the axis labels to be shifted just outside
of the vector itself.
+ atom_add(atom_id='vect label'+atom_id_ext, record_name='HETATM',
atom_name=atom_name, res_name=res_name_vect, chain_id=chain_id,
res_num=res_num, pos=origin+label_placement*vector*scale, element='N')
+ if neg:
+ atom_add(atom_id='vect neg label'+atom_id_ext, record_name='HETATM',
atom_name=atom_name, res_name=res_name_vect, chain_id=chain_id,
res_num=res_num, pos=origin-label_placement*vector*scale, element='N')
+
+ # Print out.
+ print " Vector (scaled + shifted to origin): " + `pdb_vect`
+
+ # Monte Carlo simulations.
+ if sim_vectors:
+ for i in xrange(sim_vectors):
+ # Increment the residue number, so each simulation is a new
residue.
+ res_num = res_num + 1
+
+ # Modify the atom_id for each simulation.
+ atom_id_ext_sim = atom_id_ext + '_sim' + `i`
+
+ # Create the PDB residue representing the vector.
+ atom_add(atom_id=atom_name+atom_id_ext_sim,
record_name='HETATM', atom_name=atom_name, res_name=res_name_sim,
chain_id=chain_id, res_num=res_num, pos=origin+sim_vectors[i]*scale,
element='C')
+ atom_connect(atom_id=atom_name+atom_id_ext_sim,
bonded_id='R_vect'+atom_id_ext_sim)
+ if neg:
+ atom_add(atom_id=atom_name+'_neg'+atom_id_ext_sim,
record_name='HETATM', atom_name=atom_name, res_name=res_name_sim,
chain_id=chain_id, res_num=res_num, pos=origin-sim_vectors[i]*scale,
element='C')
+ atom_connect(atom_id=atom_name+'_neg'+atom_id_ext_sim,
bonded_id='R_vect'+atom_id_ext_sim)
+
+ # Return the new residue number.
+ return res_num
def get_chemical_name(hetID):
r5040 - /1.3/generic_fns/structure.py