Author: bugman
Date: Wed Feb 20 11:56:31 2008
New Revision: 5041
URL: http://svn.gna.org/viewcvs/relax?rev=5041&view=rev
Log:
All calls to generic_fns.structure.atom_add() 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=5041&r1=5040&r2=5041&view=diff
==============================================================================
--- 1.3/generic_fns/structure.py (original)
+++ 1.3/generic_fns/structure.py Wed Feb 20 11:56:31 2008
@@ -374,7 +374,7 @@
R = centre_of_mass()
# Add the central atom.
- atom_add(atom_id='R'+atom_id_ext, record_name='HETATM',
atom_name='R', res_name='COM', chain_id=chain_id, res_num=res_num, pos=R,
element='C')
+ atom_add(atomic_data=atomic_data, atom_id='R'+atom_id_ext,
record_name='HETATM', atom_name='R', res_name='COM', chain_id=chain_id,
res_num=res_num, pos=R, element='C')
# Increment the residue number.
res_num = res_num + 1
@@ -417,7 +417,7 @@
pos = R + vector
# Add the vector as a H atom of the TNS residue.
- atom_add(atom_id=atom_id, record_name='HETATM',
atom_name='H'+`atom_num`, res_name='TNS', chain_id=chain_id, res_num=res_num,
pos=pos, element='H')
+ atom_add(atomic_data=atomic_data, atom_id=atom_id,
record_name='HETATM', atom_name='H'+`atom_num`, res_name='TNS',
chain_id=chain_id, res_num=res_num, pos=pos, element='H')
# Connect to the previous atom (to generate the longitudinal
lines).
if j != 0:
@@ -493,7 +493,7 @@
last_res = atomic_arrays[-1][3]
# Add the TER 'atom'.
- atom_add(atom_id='TER' + atom_id_ext, record_name='TER',
res_name=last_res, res_num=res_num)
+ atom_add(atomic_data=atomic_data, atom_id='TER' + atom_id_ext,
record_name='TER', res_name=last_res, res_num=res_num)
# Create the PDB file.
@@ -600,10 +600,10 @@
H_id = data.proton + end
# Add the central X atom.
- atom_add(atom_id=X_id, record_name='ATOM', atom_name=data.heteronuc,
res_name=data.name, chain_id='A', res_num=data.num, pos=R,
element=data.heteronuc)
+ atom_add(atomic_data=atomic_data, atom_id=X_id, record_name='ATOM',
atom_name=data.heteronuc, res_name=data.name, chain_id='A', res_num=data.num,
pos=R, element=data.heteronuc)
# Add the H atom.
- atom_add(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)
+ 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)
@@ -613,7 +613,7 @@
last_name = data.name
# The TER record.
- atom_add(atom_id='TER' + '_A', record_name='TER', res_name=last_name,
chain_id='A', res_num=last_res)
+ atom_add(atomic_data=atomic_data, atom_id='TER' + '_A',
record_name='TER', res_name=last_name, chain_id='A', res_num=last_res)
# Symmetry chain.
if symmetry:
@@ -639,10 +639,10 @@
H_id = data.proton + end
# Add the central X atom.
- atom_add(atom_id=X_id + '_B', record_name='ATOM',
atom_name=data.heteronuc, res_name=data.name, chain_id='B', res_num=data.num,
pos=R, element=data.heteronuc)
+ atom_add(atomic_data=atomic_data, atom_id=X_id + '_B',
record_name='ATOM', atom_name=data.heteronuc, res_name=data.name,
chain_id='B', res_num=data.num, pos=R, element=data.heteronuc)
# Add the H atom.
- atom_add(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)
+ 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')
@@ -652,7 +652,7 @@
last_name = data.name
# The TER record.
- atom_add(atom_id='TER' + '_B', record_name='TER',
res_name=last_name, chain_id='B', res_num=last_res)
+ atom_add(atomic_data=atomic_data, atom_id='TER' + '_B',
record_name='TER', res_name=last_name, chain_id='B', res_num=last_res)
@@ -726,13 +726,13 @@
Dz_vect_neg = R + Dz_vect_neg
# Create the 'AXS' residue.
- atom_add(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(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(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(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(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(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(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_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(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)
@@ -748,12 +748,12 @@
Dz_vect = Dz_unit * (Dz * scale + 3.0)
# Add the atoms.
- atom_add(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(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(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(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(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(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')
+ 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:
@@ -800,9 +800,9 @@
Dpar_vect_neg = R + Dpar_vect_neg
# Create the 'AXS' residue.
- atom_add(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(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(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_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)
@@ -812,8 +812,8 @@
vect = Dpar_unit * (Dpar * scale + 3.0)
# Add the atoms.
- atom_add(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(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')
+ 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:
@@ -867,19 +867,19 @@
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')
+ atom_add(atomic_data=atomic_data, 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_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)
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_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)
# 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')
+ 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')
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')
+ atom_add(atomic_data=atomic_data, 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`
@@ -894,10 +894,10 @@
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_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)
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_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)
# Return the new residue number.
r5041 - /1.3/generic_fns/structure.py