Author: bugman
Date: Wed Feb 20 14:20:43 2008
New Revision: 5045
URL: http://svn.gna.org/viewcvs/relax?rev=5045&view=rev
Log:
Deleted the generate_spheroid_axes() and generate_ellipsoid_axes() fns.
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=5045&r1=5044&r2=5045&view=diff
==============================================================================
--- 1.3/generic_fns/structure.py (original)
+++ 1.3/generic_fns/structure.py Wed Feb 20 14:20:43 2008
@@ -675,154 +675,6 @@
# Close the file.
tensor_pdb_file.close()
-
-
-def generate_ellipsoid_axes(chain_id=None, res_num=None, R=None, i=None):
- """Generate the AXS and SIM residues of the ellipsoidal PDB tensor
representation.
-
- @param chain_id: The chain identification code.
- @type chain_id: str
- @param res_num: The residue number.
- @type res_num: int
- @param R: The centre of mass.
- @type R: numpy array (float64)
- @param i: The Monte Carlo simulation index.
- @type i: int
- @return: None
- """
-
- # Alias the relevant data.
- scale = scale
- if i == None:
- Dx = relax_data_store.diff[run].Dx
- Dy = relax_data_store.diff[run].Dy
- Dz = relax_data_store.diff[run].Dz
- Dx_unit = relax_data_store.diff[run].Dx_unit
- Dy_unit = relax_data_store.diff[run].Dy_unit
- Dz_unit = relax_data_store.diff[run].Dz_unit
- res_name = 'AXS'
- atom_id_ext = '_' + chain_id
- else:
- Dx = relax_data_store.diff[run].Dx_sim[i]
- Dy = relax_data_store.diff[run].Dy_sim[i]
- Dz = relax_data_store.diff[run].Dz_sim[i]
- Dx_unit = relax_data_store.diff[run].Dx_unit_sim[i]
- Dy_unit = relax_data_store.diff[run].Dy_unit_sim[i]
- Dz_unit = relax_data_store.diff[run].Dz_unit_sim[i]
- res_name = 'SIM'
- atom_id_ext = '_' + chain_id + '_sim' + `i`
-
- # The Dx, Dy, and Dz vectors.
- Dx_vect = Dx_unit * Dx * scale
- Dy_vect = Dy_unit * Dy * scale
- Dz_vect = Dz_unit * Dz * scale
-
- # The negative Dx, Dy, and Dz vectors.
- Dx_vect_neg = -Dx_vect
- Dy_vect_neg = -Dy_vect
- Dz_vect_neg = -Dz_vect
-
- # Positions relative to the centre of mass.
- Dx_vect = R + Dx_vect
- Dy_vect = R + Dy_vect
- Dz_vect = R + Dz_vect
- Dx_vect_neg = R + Dx_vect_neg
- Dy_vect_neg = R + Dy_vect_neg
- Dz_vect_neg = R + Dz_vect_neg
-
- # Create the 'AXS' residue.
- atom_add(atomic_data=atomic_data, atom_id='R_axes'+atom_id_ext,
record_name='HETATM', atom_name='R', res_name=res_name, chain_id=chain_id,
res_num=res_num, pos=R, element='C')
- atom_add(atomic_data=atomic_data, atom_id='Dx'+atom_id_ext,
record_name='HETATM', atom_name='Dx', res_name=res_name, chain_id=chain_id,
res_num=res_num, pos=Dx_vect, element='C')
- atom_add(atomic_data=atomic_data, atom_id='Dy'+atom_id_ext,
record_name='HETATM', atom_name='Dy', res_name=res_name, chain_id=chain_id,
res_num=res_num, pos=Dy_vect, element='C')
- atom_add(atomic_data=atomic_data, atom_id='Dz'+atom_id_ext,
record_name='HETATM', atom_name='Dz', res_name=res_name, chain_id=chain_id,
res_num=res_num, pos=Dz_vect, element='C')
- atom_add(atomic_data=atomic_data, atom_id='Dx_neg'+atom_id_ext,
record_name='HETATM', atom_name='Dx', res_name=res_name, chain_id=chain_id,
res_num=res_num, pos=Dx_vect_neg, element='C')
- atom_add(atomic_data=atomic_data, atom_id='Dy_neg'+atom_id_ext,
record_name='HETATM', atom_name='Dy', res_name=res_name, chain_id=chain_id,
res_num=res_num, pos=Dy_vect_neg, element='C')
- atom_add(atomic_data=atomic_data, atom_id='Dz_neg'+atom_id_ext,
record_name='HETATM', atom_name='Dz', res_name=res_name, chain_id=chain_id,
res_num=res_num, pos=Dz_vect_neg, element='C')
- atom_connect(atomic_data=atomic_data, atom_id='Dx'+atom_id_ext,
bonded_id='R_axes'+atom_id_ext)
- atom_connect(atomic_data=atomic_data, atom_id='Dy'+atom_id_ext,
bonded_id='R_axes'+atom_id_ext)
- atom_connect(atomic_data=atomic_data, atom_id='Dz'+atom_id_ext,
bonded_id='R_axes'+atom_id_ext)
- atom_connect(atomic_data=atomic_data, atom_id='Dx_neg'+atom_id_ext,
bonded_id='R_axes'+atom_id_ext)
- atom_connect(atomic_data=atomic_data, atom_id='Dy_neg'+atom_id_ext,
bonded_id='R_axes'+atom_id_ext)
- atom_connect(atomic_data=atomic_data, atom_id='Dz_neg'+atom_id_ext,
bonded_id='R_axes'+atom_id_ext)
-
- # Add six more atoms to allow the axis labels to be shifted just outside
of the geometric object.
- if i == None:
- # A slightly longer vector (by 3 Angstrom).
- Dx_vect = Dx_unit * (Dx * scale + 3.0)
- Dy_vect = Dy_unit * (Dy * scale + 3.0)
- Dz_vect = Dz_unit * (Dz * scale + 3.0)
-
- # Add the atoms.
- atom_add(atomic_data=atomic_data, atom_id='Dx label'+atom_id_ext,
record_name='HETATM', atom_name='Dx', res_name=res_name, chain_id=chain_id,
res_num=res_num, pos=R+Dx_vect, element='N')
- atom_add(atomic_data=atomic_data, atom_id='Dx neg
label'+atom_id_ext, record_name='HETATM', atom_name='Dx', res_name=res_name,
chain_id=chain_id, res_num=res_num, pos=R-Dx_vect, element='N')
- atom_add(atomic_data=atomic_data, atom_id='Dy label'+atom_id_ext,
record_name='HETATM', atom_name='Dy', res_name=res_name, chain_id=chain_id,
res_num=res_num, pos=R+Dy_vect, element='N')
- atom_add(atomic_data=atomic_data, atom_id='Dy neg
label'+atom_id_ext, record_name='HETATM', atom_name='Dy', res_name=res_name,
chain_id=chain_id, res_num=res_num, pos=R-Dy_vect, element='N')
- atom_add(atomic_data=atomic_data, atom_id='Dz label'+atom_id_ext,
record_name='HETATM', atom_name='Dz', res_name=res_name, chain_id=chain_id,
res_num=res_num, pos=R+Dz_vect, element='N')
- atom_add(atomic_data=atomic_data, atom_id='Dz neg
label'+atom_id_ext, record_name='HETATM', atom_name='Dz', res_name=res_name,
chain_id=chain_id, res_num=res_num, pos=R-Dz_vect, element='N')
-
- # Print out.
- if i == None:
- print " Dx vector (scaled + shifted to R): " + `Dx_vect`
- print " Dy vector (scaled + shifted to R): " + `Dy_vect`
- print " Dz vector (scaled + shifted to R): " + `Dz_vect`
-
-
-def generate_spheroid_axes(chain_id=None, res_num=None, R=None, i=None):
- """Generate the AXS and SIM residues of the spheroid PDB tensor
representation.
-
- @param chain_id: The chain identification code.
- @type chain_id: str
- @param res_num: The residue number.
- @type res_num: int
- @param R: The centre of mass.
- @type R: numpy array (float64)
- @param i: The Monte Carlo simulation index.
- @type i: int
- @return: None
- """
-
- # Alias the relevant data.
- scale = scale
- if i == None:
- Dpar = relax_data_store.diff[run].Dpar
- Dpar_unit = relax_data_store.diff[run].Dpar_unit
- res_name = 'AXS'
- atom_id_ext = '_' + chain_id
- else:
- Dpar = relax_data_store.diff[run].Dpar_sim[i]
- Dpar_unit = relax_data_store.diff[run].Dpar_unit_sim[i]
- res_name = 'SIM'
- atom_id_ext = '_' + chain_id + '_sim' + `i`
-
- # The Dpar vector.
- Dpar_vect = Dpar_unit * Dpar * scale
-
- # The negative Dpar vector.
- Dpar_vect_neg = -Dpar_vect
-
- # Position of both vectors relative to the centre of mass.
- Dpar_vect = R + Dpar_vect
- Dpar_vect_neg = R + Dpar_vect_neg
-
- # Create the 'AXS' residue.
- atom_add(atomic_data=atomic_data, atom_id='R_axes'+atom_id_ext,
record_name='HETATM', atom_name='R', res_name=res_name, chain_id=chain_id,
res_num=res_num, pos=R, element='C')
- atom_add(atomic_data=atomic_data, atom_id='Dpar'+atom_id_ext,
record_name='HETATM', atom_name='Dpar', res_name=res_name, chain_id=chain_id,
res_num=res_num, pos=Dpar_vect, element='C')
- atom_add(atomic_data=atomic_data, atom_id='Dpar_neg'+atom_id_ext,
record_name='HETATM', atom_name='Dpar', res_name=res_name, chain_id=chain_id,
res_num=res_num, pos=Dpar_vect_neg, element='C')
- atom_connect(atomic_data=atomic_data, atom_id='Dpar'+atom_id_ext,
bonded_id='R_axes'+atom_id_ext)
- atom_connect(atomic_data=atomic_data, atom_id='Dpar_neg'+atom_id_ext,
bonded_id='R_axes'+atom_id_ext)
-
- # Add two more atoms to allow the axis labels to be shifted just outside
of the geometric object.
- if i == None:
- # A slightly longer vector (by 3 Angstrom).
- vect = Dpar_unit * (Dpar * scale + 3.0)
-
- # Add the atoms.
- atom_add(atomic_data=atomic_data, atom_id='Dpar label'+atom_id_ext,
record_name='HETATM', atom_name='Dpar', res_name=res_name, chain_id=chain_id,
res_num=res_num, pos=R+vect, element='N')
- atom_add(atomic_data=atomic_data, atom_id='Dpar neg
label'+atom_id_ext, record_name='HETATM', atom_name='Dpar',
res_name=res_name, chain_id=chain_id, res_num=res_num, pos=R-vect,
element='N')
-
- # 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):
r5045 - /1.3/generic_fns/structure.py