Author: bugman
Date: Thu Jan 22 15:54:08 2009
New Revision: 8595
URL: http://svn.gna.org/viewcvs/relax?rev=8595&view=rev
Log:
Fixes for generate_vector_dist(), generate_vector_residues(), and
stitch_cap_to_cone().
These now handle the MolContainer instance.
Modified:
branches/multi_structure/generic_fns/structure/geometric.py
Modified: branches/multi_structure/generic_fns/structure/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_structure/generic_fns/structure/geometric.py?rev=8595&r1=8594&r2=8595&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/geometric.py (original)
+++ branches/multi_structure/generic_fns/structure/geometric.py Thu Jan 22
15:54:08 2009
@@ -244,7 +244,7 @@
print "\nGenerating the geometric object."
# The distribution.
- generate_vector_dist(molecule=mol, res_name='TNS', res_num=res_num,
chain_id=chain_id, centre=CoM, R=pipe.diff_tensor.rotation,
warp=pipe.diff_tensor.tensor, scale=scale, inc=20)
+ generate_vector_dist(mol=mol, res_name='TNS', res_num=res_num,
chain_id=chain_id, centre=CoM, R=pipe.diff_tensor.rotation,
warp=pipe.diff_tensor.tensor, scale=scale, inc=20)
# Increment the residue number.
res_num = res_num + 1
@@ -266,7 +266,7 @@
sim_vectors = None
# Generate the axes representation.
- res_num = generate_vector_residues(molecule=mol,
vector=pipe.diff_tensor.Dpar*pipe.diff_tensor.Dpar_unit, atom_name='Dpar',
res_name_vect='AXS', sim_vectors=sim_vectors, chain_id=chain_id,
res_num=res_num, origin=CoM, scale=scale, neg=True)
+ res_num = generate_vector_residues(mol=mol,
vector=pipe.diff_tensor.Dpar*pipe.diff_tensor.Dpar_unit, atom_name='Dpar',
res_name_vect='AXS', sim_vectors=sim_vectors, chain_id=chain_id,
res_num=res_num, origin=CoM, scale=scale, neg=True)
# Create the three axes of the ellipsoid.
@@ -286,9 +286,9 @@
sim_Dz_vectors = None
# Generate the axes representation.
- res_num = generate_vector_residues(molecule=mol,
vector=pipe.diff_tensor.Dx*pipe.diff_tensor.Dx_unit, atom_name='Dpar',
res_name_vect='AXS', sim_vectors=sim_Dx_vectors, chain_id=chain_id,
res_num=res_num, origin=CoM, scale=scale, neg=True)
- res_num = generate_vector_residues(molecule=mol,
vector=pipe.diff_tensor.Dy*pipe.diff_tensor.Dy_unit, atom_name='Dpar',
res_name_vect='AXS', sim_vectors=sim_Dy_vectors, chain_id=chain_id,
res_num=res_num, origin=CoM, scale=scale, neg=True)
- res_num = generate_vector_residues(molecule=mol,
vector=pipe.diff_tensor.Dz*pipe.diff_tensor.Dz_unit, atom_name='Dpar',
res_name_vect='AXS', sim_vectors=sim_Dz_vectors, chain_id=chain_id,
res_num=res_num, origin=CoM, scale=scale, neg=True)
+ res_num = generate_vector_residues(mol=mol,
vector=pipe.diff_tensor.Dx*pipe.diff_tensor.Dx_unit, atom_name='Dpar',
res_name_vect='AXS', sim_vectors=sim_Dx_vectors, chain_id=chain_id,
res_num=res_num, origin=CoM, scale=scale, neg=True)
+ res_num = generate_vector_residues(mol=mol,
vector=pipe.diff_tensor.Dy*pipe.diff_tensor.Dy_unit, atom_name='Dpar',
res_name_vect='AXS', sim_vectors=sim_Dy_vectors, chain_id=chain_id,
res_num=res_num, origin=CoM, scale=scale, neg=True)
+ res_num = generate_vector_residues(mol=mol,
vector=pipe.diff_tensor.Dz*pipe.diff_tensor.Dz_unit, atom_name='Dpar',
res_name_vect='AXS', sim_vectors=sim_Dz_vectors, chain_id=chain_id,
res_num=res_num, origin=CoM, scale=scale, neg=True)
# Create the PDB file.
@@ -446,7 +446,7 @@
tensor_pdb_file.close()
-def generate_vector_dist(structure=None, res_name=None, res_num=None,
chain_id='', centre=zeros(3, float64), R=eye(3), warp=eye(3), max_angle=None,
scale=1.0, inc=20):
+def generate_vector_dist(mol=None, res_name=None, res_num=None, chain_id='',
centre=zeros(3, float64), R=eye(3), warp=eye(3), max_angle=None, scale=1.0,
inc=20):
"""Generate a uniformly distributed distribution of atoms on a warped
sphere.
The vectors from the function uniform_vect_dist_spherical_angles() are
used to generate the
@@ -455,8 +455,8 @@
centred and at the head of the vector, a proton is placed.
- @keyword structure: The structural data object.
- @type structure: instance of class derived from Base_struct_API
+ @keyword mol: The molecule container.
+ @type mol: MolContainer instance
@keyword res_name: The residue name.
@type res_name: str
@keyword res_num: The residue number.
@@ -479,7 +479,7 @@
"""
# Initial atom number.
- origin_num = structure.structural_data[0].atom_num[-1]+1
+ origin_num = mol.atom_num[-1]+1
atom_num = origin_num
# Get the uniform vector distribution.
@@ -528,32 +528,32 @@
pos = centre + vector
# Add the vector as a H atom of the TNS residue.
- structure.atom_add(pdb_record='HETATM', atom_num=atom_num,
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)
+ mol.atom_add(pdb_record='HETATM', atom_num=atom_num,
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 to the previous atom (to generate the longitudinal
lines).
if j > j_min:
- structure.atom_connect(index1=atom_num-1, index2=atom_num-2)
+ mol.atom_connect(index1=atom_num-1, index2=atom_num-2)
# Connect across the radial arrays (to generate the latitudinal
lines).
if i != 0:
- structure.atom_connect(index1=atom_num-1,
index2=atom_num-1-j_min-2)
+ mol.atom_connect(index1=atom_num-1, index2=atom_num-1-j_min-2)
# Connect the last radial array to the first (to zip up the
geometric object and close the latitudinal lines).
if i == inc-1:
- structure.atom_connect(index1=atom_num-1,
index2=origin_num-1+j+2)
+ mol.atom_connect(index1=atom_num-1, index2=origin_num-1+j+2)
# Increment the atom number.
atom_num = atom_num + 1
-def generate_vector_residues(structure=None, vector=None, atom_name=None,
res_name_vect='AXS', sim_vectors=None, res_name_sim='SIM', chain_id='',
res_num=None, origin=None, scale=1.0, label_placement=1.1, neg=False):
+def generate_vector_residues(mol=None, vector=None, atom_name=None,
res_name_vect='AXS', sim_vectors=None, res_name_sim='SIM', chain_id='',
res_num=None, origin=None, scale=1.0, label_placement=1.1, neg=False):
"""Generate residue representations for the vector and the MC simulationed
vectors.
This is used to create a PDB representation of any vector, including its
Monte Carlo
simulations.
- @param structure: The structural data object.
- @type structure: instance of class derived from Base_struct_API
+ @keyword mol: The molecule container.
+ @type mol: MolContainer instance
@param vector: The vector to be represented in the PDB.
@type vector: numpy array, len 3
@param atom_name: The atom name used to label the atom representing
the head of the
@@ -586,24 +586,24 @@
"""
# The atom numbers (and indices).
- origin_num = structure.structural_data[0].atom_num[-1]+1
- atom_num = structure.structural_data[0].atom_num[-1]+2
- atom_neg_num = structure.structural_data[0].atom_num[-1]+3
+ origin_num = mol.atom_num[-1]+1
+ atom_num = mol.atom_num[-1]+2
+ atom_neg_num = mol.atom_num[-1]+3
# The origin atom.
- structure.atom_add(pdb_record='HETATM', atom_num=origin_num,
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)
+ mol.atom_add(pdb_record='HETATM', atom_num=origin_num, 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(pdb_record='HETATM', atom_num=atom_num,
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(index1=atom_num-1, index2=origin_num-1)
+ mol.atom_add(pdb_record='HETATM', atom_num=atom_num, 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)
+ mol.atom_connect(index1=atom_num-1, index2=origin_num-1)
if neg:
- structure.atom_add(pdb_record='HETATM', atom_num=atom_neg_num,
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(index1=atom_neg_num-1, index2=origin_num-1)
+ mol.atom_add(pdb_record='HETATM', atom_num=atom_neg_num,
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)
+ mol.atom_connect(index1=atom_neg_num-1, index2=origin_num-1)
# 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=atom_num+2,
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)
+ mol.atom_add(pdb_record='HETATM', atom_num=atom_num+2,
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(pdb_record='HETATM', atom_num=atom_neg_num+2,
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)
+ mol.atom_add(pdb_record='HETATM', atom_num=atom_neg_num+2,
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`
@@ -616,25 +616,25 @@
res_num = res_num + 1
# The atom numbers (and indices).
- atom_num = structure.structural_data[0].atom_num[-1]+1
- atom_neg_num = structure.structural_data[0].atom_num[-1]+2
+ atom_num = mol.atom_num[-1]+1
+ atom_neg_num = mol.atom_num[-1]+2
# Create the PDB residue representing the vector.
- structure.atom_add(pdb_record='HETATM', atom_num=atom_num,
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(index1=atom_num-1, index2=origin_num-1)
+ mol.atom_add(pdb_record='HETATM', atom_num=atom_num,
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)
+ mol.atom_connect(index1=atom_num-1, index2=origin_num-1)
if neg:
- structure.atom_add(pdb_record='HETATM', atom_num=atom_num+1,
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(index1=atom_neg_num-1,
index2=origin_num-1)
+ mol.atom_add(pdb_record='HETATM', atom_num=atom_num+1,
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)
+ mol.atom_connect(index1=atom_neg_num-1, index2=origin_num-1)
# Return the new residue number.
return res_num
-def stitch_cap_to_cone(structure=None, cone_start=None, cap_start=None,
max_angle=None, inc=None):
+def stitch_cap_to_cone(mol=None, cone_start=None, cap_start=None,
max_angle=None, inc=None):
"""Function for stitching the cap of a cone to the cone edge, in the PDB
representations.
- @keyword structure: The structural data object.
- @type structure: instance of class derived from Base_struct_API
+ @keyword mol: The molecule container.
+ @type mol: MolContainer instance
@keyword cone_start: The starting atom number of the cone residue.
@type cone_start: int
@keyword cap_start: The starting atom number of the cap residue.
@@ -670,7 +670,7 @@
dome_edge = cone_start + i + i*(j_min+1)
# Connect the two atoms (to stitch up the 2 objects).
- structure.atom_connect(index1=dome_edge-1, index2=cap_atom-1)
+ mol.atom_connect(index1=dome_edge-1, index2=cap_atom-1)
def uniform_vect_dist_spherical_angles(inc=20):
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