Author: bugman
Date: Mon Apr 7 16:57:03 2008
New Revision: 5371
URL: http://svn.gna.org/viewcvs/relax?rev=5371&view=rev
Log:
Updated all the calls to atom_add() and atom_connect() to use the API methods
instead.
Modified:
1.3/generic_fns/structure/geometric.py
Modified: 1.3/generic_fns/structure/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/geometric.py?rev=5371&r1=5370&r2=5371&view=diff
==============================================================================
--- 1.3/generic_fns/structure/geometric.py (original)
+++ 1.3/generic_fns/structure/geometric.py Mon Apr 7 16:57:03 2008
@@ -88,7 +88,7 @@
"""
# Add an atom for the cone apex.
- atom_add(atomic_data=atomic_data, atom_id='Apex', record_name='HETATM',
atom_name='APX', res_name=res_name, res_num=res_num, pos=apex, element='H')
+ structure.atom_add(atom_id='Apex', record_name='HETATM',
atom_name='APX', res_name=res_name, res_num=res_num, pos=apex, element='H')
# Initialise the rotation matrix, atom number, etc.
if R == None:
@@ -126,20 +126,20 @@
pos = apex+vector*length
# Add the vector as a H atom of the cone residue.
- atom_add(atomic_data=atomic_data, atom_id=atom_id,
record_name='HETATM', atom_name='H'+`atom_num`, res_name=res_name,
res_num=res_num, pos=pos, element='H')
+ structure.atom_add(atom_id=atom_id, record_name='HETATM',
atom_name='H'+`atom_num`, res_name=res_name, res_num=res_num, pos=pos,
element='H')
# Connect across the radial array (to generate the circular cone
edge).
if i != 0:
neighbour_id = 'T' + `i-1`
- atom_connect(atomic_data=atomic_data, atom_id=atom_id,
bonded_id=neighbour_id)
+ structure.atom_connect(atom_id=atom_id, bonded_id=neighbour_id)
# Connect the last radial array to the first (to zip up the circle).
if i == inc-1:
neighbour_id = 'T' + `0`
- atom_connect(atomic_data=atomic_data, atom_id=atom_id,
bonded_id=neighbour_id)
+ structure.atom_connect(atom_id=atom_id, bonded_id=neighbour_id)
# Join the atom to the cone apex.
- atom_connect(atomic_data=atomic_data, atom_id=atom_id,
bonded_id='Apex')
+ structure.atom_connect(atom_id=atom_id, bonded_id='Apex')
# Increment the atom number.
atom_num = atom_num + 1
@@ -223,7 +223,7 @@
CoM = centre_of_mass()
# Add the central atom.
- 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=CoM, element='C')
+ structure.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=CoM,
element='C')
# Increment the residue number.
res_num = res_num + 1
@@ -393,20 +393,20 @@
H_id = data.proton + end
# Add the central X atom.
- 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)
+ structure.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)
# Add the H atom.
- 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)
+ structure.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)
# Connect the two atoms.
- atom_connect(atomic_data=atomic_data, atom_id=X_id, bonded_id=H_id)
+ structure.atom_connect(atom_id=X_id, bonded_id=H_id)
# Store the terminate residue number for the TER record.
last_res = data.num
last_name = data.name
# The TER record.
- atom_add(atomic_data=atomic_data, atom_id='TER' + '_A',
record_name='TER', res_name=last_name, chain_id='A', res_num=last_res)
+ structure.atom_add(atom_id='TER' + '_A', record_name='TER',
res_name=last_name, chain_id='A', res_num=last_res)
# Symmetry chain.
if symmetry:
@@ -432,20 +432,20 @@
H_id = data.proton + end
# Add the central X atom.
- 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)
+ structure.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)
# Add the H atom.
- 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)
+ structure.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)
# Connect the two atoms.
- atom_connect(atomic_data=atomic_data, atom_id=X_id + '_B',
bonded_id=H_id + '_B')
+ structure.atom_connect(atom_id=X_id + '_B', bonded_id=H_id +
'_B')
# Store the terminate residue number for the TER record.
last_res = data.num
last_name = data.name
# The TER record.
- atom_add(atomic_data=atomic_data, atom_id='TER' + '_B',
record_name='TER', res_name=last_name, chain_id='B', res_num=last_res)
+ structure.atom_add(atom_id='TER' + '_B', record_name='TER',
res_name=last_name, chain_id='B', res_num=last_res)
@@ -548,22 +548,22 @@
pos = centre + vector
# Add the vector as a H atom of the TNS residue.
- atom_add(atomic_data=atomic_data, atom_id=atom_id,
record_name='HETATM', atom_name='H'+`atom_num`, res_name=res_name,
chain_id=chain_id, res_num=res_num, pos=pos, element='H')
+ structure.atom_add(atom_id=atom_id, record_name='HETATM',
atom_name='H'+`atom_num`, res_name=res_name, chain_id=chain_id,
res_num=res_num, pos=pos, element='H')
# Connect to the previous atom (to generate the longitudinal
lines).
if j > j_min:
prev_id = 'T' + `i` + 'P' + `j-1` + atom_id_ext
- atom_connect(atomic_data=atomic_data, atom_id=atom_id,
bonded_id=prev_id)
+ structure.atom_connect(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(atomic_data=atomic_data, atom_id=atom_id,
bonded_id=neighbour_id)
+ structure.atom_connect(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(atomic_data=atomic_data, atom_id=atom_id,
bonded_id=neighbour_id)
+ structure.atom_connect(atom_id=atom_id,
bonded_id=neighbour_id)
# Increment the atom number.
atom_num = atom_num + 1
@@ -616,19 +616,19 @@
atom_id_ext = ''
# The origin atom.
- 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')
+ structure.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(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(atomic_data=atomic_data, atom_id=atom_name+atom_id_ext,
bonded_id='R_vect'+atom_id_ext)
+ structure.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')
+ structure.atom_connect(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(atomic_data=atomic_data,
atom_id=atom_name+'_neg'+atom_id_ext, bonded_id='R_vect'+atom_id_ext)
+ structure.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')
+ structure.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(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')
+ structure.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(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')
+ structure.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 " " + atom_name + " vector (scaled + shifted to origin): " +
`origin+vector*scale`
@@ -644,11 +644,11 @@
atom_id_ext_sim = atom_id_ext + '_sim' + `i`
# 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(atomic_data=atomic_data,
atom_id=atom_name+atom_id_ext_sim, bonded_id='R_vect'+atom_id_ext_sim)
+ structure.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')
+ structure.atom_connect(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(atomic_data=atomic_data,
atom_id=atom_name+'_neg'+atom_id_ext_sim, bonded_id='R_vect'+atom_id_ext_sim)
+ structure.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')
+
structure.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
@@ -692,7 +692,7 @@
edge_atom_id = 'T' + `i` + atom_id_ext
# Connect the two atoms (to stitch up the 2 objects).
- atom_connect(atomic_data=atomic_data, atom_id=edge_atom_id,
bonded_id=cap_atom_id)
+ structure.atom_connect(atom_id=edge_atom_id, bonded_id=cap_atom_id)
def uniform_vect_dist_spherical_angles(inc=20):
r5371 - /1.3/generic_fns/structure/geometric.py