Author: semor
Date: Tue Jul 8 00:31:15 2008
New Revision: 6816
URL: http://svn.gna.org/viewcvs/relax?rev=6816&view=rev
Log:
Corrections for the atom_connect() function calls to match the needed
variables.
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=6816&r1=6815&r2=6816&view=diff
==============================================================================
--- 1.3/generic_fns/structure/geometric.py (original)
+++ 1.3/generic_fns/structure/geometric.py Tue Jul 8 00:31:15 2008
@@ -133,15 +133,15 @@
# Connect across the radial array (to generate the circular cone
edge).
if i != 0:
neighbour_id = 'T' + `i-1`
- structure.atom_connect(atom_id=atom_id, bonded_id=neighbour_id)
+ structure.atom_connect(index1=atom_id, index2=neighbour_id)
# Connect the last radial array to the first (to zip up the circle).
if i == inc-1:
neighbour_id = 'T' + `0`
- structure.atom_connect(atom_id=atom_id, bonded_id=neighbour_id)
+ structure.atom_connect(index1=atom_id, index2=neighbour_id)
# Join the atom to the cone apex.
- structure.atom_connect(atom_id=atom_id, bonded_id='Apex')
+ structure.atom_connect(index1=atom_id, index2='Apex')
# Increment the atom number.
atom_num = atom_num + 1
@@ -395,7 +395,7 @@
structure.atom_add(pdb_record='ATOM', atom_num=H_id,
atom_name=data.proton, res_name=data.name, chain_id='A', res_num=data.num,
pos=R+vector, segment_id=None, element=data.proton, struct_index=None)
# Connect the two atoms.
- structure.atom_connect(atom_id=X_id, bonded_id=H_id)
+ structure.atom_connect(index1=X_id, index2=H_id)
# Store the terminate residue number for the TER record.
last_res = data.num
@@ -434,7 +434,7 @@
structure.atom_add(pdb_record='ATOM', atom_num=H_id + 'B',
atom_name=data.proton, res_name=data.name, chain_id='B', res_num=data.num,
pos=R+vector, segment_id=None, element=data.proton, struct_index=None)
# Connect the two atoms.
- structure.atom_connect(atom_id=X_id + '_B', bonded_id=H_id +
'_B')
+ structure.atom_connect(index1=X_id + '_B', index2=H_id + '_B')
# Store the terminate residue number for the TER record.
last_res = data.num
@@ -549,17 +549,17 @@
# Connect to the previous atom (to generate the longitudinal
lines).
if j > j_min:
prev_id = 'T' + `i` + 'P' + `j-1` + atom_id_ext
- structure.atom_connect(atom_id=atom_id, bonded_id=prev_id)
+ structure.atom_connect(index1=atom_id, index2=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
- structure.atom_connect(atom_id=atom_id,
bonded_id=neighbour_id)
+ structure.atom_connect(index1=atom_id, index2=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
- structure.atom_connect(atom_id=atom_id,
bonded_id=neighbour_id)
+ structure.atom_connect(index1=atom_id, index2=neighbour_id)
# Increment the atom number.
atom_num = atom_num + 1
@@ -615,10 +615,10 @@
# Create the PDB residue representing the vector.
structure.atom_add(pdb_record='HETATM', atom_num=atom_name+atom_id_ext,
atom_name=atom_name, res_name=res_name_vect, chain_id=chain_id,
res_num=res_num, pos=origin+vector*scale, segment_id=None, element='C',
struct_index=None)
- structure.atom_connect(atom_id=atom_name+atom_id_ext,
bonded_id='R_vect'+atom_id_ext)
+ structure.atom_connect(index1=atom_name+atom_id_ext,
index2='R_vect'+atom_id_ext)
if neg:
structure.atom_add(pdb_record='HETATM',
atom_num=atom_name+'_neg'+atom_id_ext, atom_name=atom_name,
res_name=res_name_vect, chain_id=chain_id, res_num=res_num,
pos=origin+vector*scale, segment_id=None, element='C', struct_index=None)
- structure.atom_connect(atom_id=atom_name+'_neg'+atom_id_ext,
bonded_id='R_vect'+atom_id_ext)
+ structure.atom_connect(index1=atom_name+'_neg'+atom_id_ext,
index2='R_vect'+atom_id_ext)
# Add another atom to allow the axis labels to be shifted just outside
of the vector itself.
structure.atom_add(pdb_record='HETATM', atom_num='vect
label'+atom_id_ext, atom_name=atom_name, res_name=res_name_vect,
chain_id=chain_id, res_num=res_num, pos=origin+label_placement*vector*scale,
segment_id=None, element='N', struct_index=None)
@@ -640,10 +640,10 @@
# Create the PDB residue representing the vector.
structure.atom_add(pdb_record='HETATM',
atom_num=atom_name+atom_id_ext_sim, atom_name=atom_name,
res_name=res_name_sim, chain_id=chain_id, res_num=res_num,
pos=origin+sim_vectors[i]*scale, segment_id=None, element='C',
struct_index=None)
- structure.atom_connect(atom_id=atom_name+atom_id_ext_sim,
bonded_id='R_vect'+atom_id_ext_sim)
+ structure.atom_connect(index1=atom_name+atom_id_ext_sim,
index2='R_vect'+atom_id_ext_sim)
if neg:
structure.atom_add(pdb_record='HETATM',
atom_num=atom_name+'_neg'+atom_id_ext_sim, atom_name=atom_name,
res_name=res_name_sim, chain_id=chain_id, res_num=res_num,
pos=origin-sim_vectors[i]*scale, segment_id=None, element='C',
struct_index=None)
-
structure.atom_connect(atom_id=atom_name+'_neg'+atom_id_ext_sim,
bonded_id='R_vect'+atom_id_ext_sim)
+
structure.atom_connect(index1=atom_name+'_neg'+atom_id_ext_sim,
index2='R_vect'+atom_id_ext_sim)
# Return the new residue number.
return res_num
@@ -687,7 +687,7 @@
edge_atom_id = 'T' + `i` + atom_id_ext
# Connect the two atoms (to stitch up the 2 objects).
- structure.atom_connect(atom_id=edge_atom_id, bonded_id=cap_atom_id)
+ structure.atom_connect(index1=edge_atom_id, index2=cap_atom_id)
def uniform_vect_dist_spherical_angles(inc=20):
r6816 - /1.3/generic_fns/structure/geometric.py