Author: semor
Date: Tue Jul 8 00:24:29 2008
New Revision: 6815
URL: http://svn.gna.org/viewcvs/relax?rev=6815&view=rev
Log:
Correction for the structure.atom_add() function calls to match the variables
needed.
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=6815&r1=6814&r2=6815&view=diff
==============================================================================
--- 1.3/generic_fns/structure/geometric.py (original)
+++ 1.3/generic_fns/structure/geometric.py Tue Jul 8 00:24:29 2008
@@ -90,7 +90,7 @@
"""
# Add an atom for the cone apex.
- structure.atom_add(atom_id='Apex', record_name='HETATM',
atom_name='APX', res_name=res_name, res_num=res_num, pos=apex, element='H')
+ structure.atom_add(pdb_record='HETATM', atom_num=Apex, atom_name='APX',
res_name=res_name_vect, chain_id=chain_id, res_num=res_num, pos=apex,
segment_id=None, element='H', struct_index=None)
# Initialise the rotation matrix, atom number, etc.
if R == None:
@@ -128,7 +128,7 @@
pos = apex+vector*length
# Add the vector as a H atom of the cone residue.
- 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')
+ structure.atom_add(pdb_record='HETATM', atom_num=atom_id,
atom_name='H'+`atom_num`, res_name=res_name, chain_id=chain_id,
res_num=res_num, pos=pos, segment_id=None, element='H', struct_index=None)
# Connect across the radial array (to generate the circular cone
edge).
if i != 0:
@@ -225,7 +225,7 @@
CoM = centre_of_mass()
# Add the central atom.
- 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')
+ structure.atom_add(pdb_record='HETATM', atom_num=None,
atom_name='R'+atom_id_ext, res_name='COM', chain_id=chain_id,
res_num=res_num, pos=CoM, segment_id=None, element='C', struct_index=None)
# Increment the residue number.
res_num = res_num + 1
@@ -389,10 +389,10 @@
H_id = data.proton + end
# Add the central X atom.
- 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)
+ structure.atom_add(pdb_record='ATOM', atom_num=X_id,
atom_name=data.heteronuc, res_name=data.name, chain_id='A', res_num=data.num,
pos=R, segment_id=None, element=data.heteronuc, struct_index=None)
# Add the H atom.
- 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)
+ 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)
@@ -402,7 +402,7 @@
last_name = data.name
# The TER record.
- structure.atom_add(atom_id='TER' + '_A', record_name='TER',
res_name=last_name, chain_id='A', res_num=last_res)
+ structure.atom_add(pdb_record='TER', atom_num=None, atom_name='TER' +
'_A', res_name=last_name, chain_id='A', res_num=last.res, pos=R,
segment_id=None, element=None, struct_index=None)
# Symmetry chain.
if symmetry:
@@ -428,10 +428,10 @@
H_id = data.proton + end
# Add the central X atom.
- 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)
+ structure.atom_add(pdb_record='ATOM', atom_num=X_id + 'B',
atom_name=data.heteronuc, res_name=data.name, chain_id='B', res_num=data.num,
pos=R, segment_id=None, element=data.heteronuc, struct_index=None)
# Add the H atom.
- 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)
+ 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')
@@ -441,7 +441,7 @@
last_name = data.name
# The TER record.
- structure.atom_add(atom_id='TER' + '_B', record_name='TER',
res_name=last_name, chain_id='B', res_num=last_res)
+ structure.atom_add(pdb_record='TER', atom_num=None, atom_name='TER'
+ '_B', res_name=last_name, chain_id='B', res_num=last.res, pos=R,
segment_id=None, element=None, struct_index=None)
@@ -544,7 +544,7 @@
pos = centre + vector
# Add the vector as a H atom of the TNS residue.
- 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')
+ structure.atom_add(pdb_record='HETATM', atom_num=None,
atom_name='H'+atom_id_ext, res_name=res_name, chain_id=chain_id,
res_num=res_num, pos=pos, segment_id=None, element='H', struct_index=None)
# Connect to the previous atom (to generate the longitudinal
lines).
if j > j_min:
@@ -611,19 +611,19 @@
atom_id_ext = ''
# The origin atom.
- 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')
+ structure.atom_add(pdb_record='HETATM', atom_num='R_vect'+atom_id_ext,
atom_name=R, res_name=res_name_vect, chain_id=chain_id, res_num=res_num,
pos=origin, segment_id=None, element='C', struct_index=None)
# Create the PDB residue representing the vector.
- 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_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)
if neg:
- 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_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)
# Add another atom to allow the axis labels to be shifted just outside
of the vector itself.
- 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')
+ 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)
if neg:
- 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')
+ structure.atom_add(pdb_record='HETATM', atom_num='vect neg
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)
# Print out.
print " " + atom_name + " vector (scaled + shifted to origin): " +
`origin+vector*scale`
@@ -639,10 +639,10 @@
atom_id_ext_sim = atom_id_ext + '_sim' + `i`
# Create the PDB residue representing the vector.
- 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_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)
if neg:
- 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_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)
# Return the new residue number.
r6815 - /1.3/generic_fns/structure/geometric.py