Author: bugman
Date: Wed Feb 20 11:57:33 2008
New Revision: 5042
URL: http://svn.gna.org/viewcvs/relax?rev=5042&view=rev
Log:
All calls to generic_fns.structure.atom_connect() now have the atomic_data
object passed into it.
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=5042&r1=5041&r2=5042&view=diff
==============================================================================
--- 1.3/generic_fns/structure.py (original)
+++ 1.3/generic_fns/structure.py Wed Feb 20 11:57:33 2008
@@ -422,17 +422,17 @@
# Connect to the previous atom (to generate the longitudinal
lines).
if j != 0:
prev_id = 'T' + `i` + 'P' + `j-1` + atom_id_ext
- atom_connect(atom_id=atom_id, bonded_id=prev_id)
+ atom_connect(atomic_data=atomic_data, atom_id=atom_id,
bonded_id=prev_id)
# Connect across the radial arrays (to generate the
latitudinal lines).
if i != 0:
neighbour_id = 'T' + `i-1` + 'P' + `j` + atom_id_ext
- atom_connect(atom_id=atom_id, bonded_id=neighbour_id)
+ atom_connect(atomic_data=atomic_data, atom_id=atom_id,
bonded_id=neighbour_id)
# Connect the last radial array to the first (to zip up the
geometric object and close the latitudinal lines).
if i == inc-1:
neighbour_id = 'T' + `0` + 'P' + `j` + atom_id_ext
- atom_connect(atom_id=atom_id, bonded_id=neighbour_id)
+ atom_connect(atomic_data=atomic_data, atom_id=atom_id,
bonded_id=neighbour_id)
# Increment the atom number.
atom_num = atom_num + 1
@@ -606,7 +606,7 @@
atom_add(atomic_data=atomic_data, atom_id=H_id, record_name='ATOM',
atom_name=data.proton, res_name=data.name, chain_id='A', res_num=data.num,
pos=R+vector, element=data.proton)
# Connect the two atoms.
- atom_connect(atom_id=X_id, bonded_id=H_id)
+ atom_connect(atomic_data=atomic_data, atom_id=X_id, bonded_id=H_id)
# Store the terminate residue number for the TER record.
last_res = data.num
@@ -645,7 +645,7 @@
atom_add(atomic_data=atomic_data, atom_id=H_id + '_B',
record_name='ATOM', atom_name=data.proton, res_name=data.name, chain_id='B',
res_num=data.num, pos=R-vector, element=data.proton)
# Connect the two atoms.
- atom_connect(atom_id=X_id + '_B', bonded_id=H_id + '_B')
+ atom_connect(atomic_data=atomic_data, atom_id=X_id + '_B',
bonded_id=H_id + '_B')
# Store the terminate residue number for the TER record.
last_res = data.num
@@ -733,12 +733,12 @@
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(atom_id='Dx'+atom_id_ext, bonded_id='R_axes'+atom_id_ext)
- atom_connect(atom_id='Dy'+atom_id_ext, bonded_id='R_axes'+atom_id_ext)
- atom_connect(atom_id='Dz'+atom_id_ext, bonded_id='R_axes'+atom_id_ext)
- atom_connect(atom_id='Dx_neg'+atom_id_ext,
bonded_id='R_axes'+atom_id_ext)
- atom_connect(atom_id='Dy_neg'+atom_id_ext,
bonded_id='R_axes'+atom_id_ext)
- atom_connect(atom_id='Dz_neg'+atom_id_ext,
bonded_id='R_axes'+atom_id_ext)
+ 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:
@@ -803,8 +803,8 @@
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(atom_id='Dpar'+atom_id_ext, bonded_id='R_axes'+atom_id_ext)
- atom_connect(atom_id='Dpar_neg'+atom_id_ext,
bonded_id='R_axes'+atom_id_ext)
+ 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:
@@ -871,10 +871,10 @@
# Create the PDB residue representing the vector.
atom_add(atomic_data=atomic_data, 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)
+ atom_connect(atomic_data=atomic_data, atom_id=atom_name+atom_id_ext,
bonded_id='R_vect'+atom_id_ext)
if neg:
atom_add(atomic_data=atomic_data,
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)
+ atom_connect(atomic_data=atomic_data,
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(atomic_data=atomic_data, 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')
@@ -895,10 +895,10 @@
# Create the PDB residue representing the vector.
atom_add(atomic_data=atomic_data,
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)
+ atom_connect(atomic_data=atomic_data,
atom_id=atom_name+atom_id_ext_sim, bonded_id='R_vect'+atom_id_ext_sim)
if neg:
atom_add(atomic_data=atomic_data,
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)
+ atom_connect(atomic_data=atomic_data,
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
r5042 - /1.3/generic_fns/structure.py