Author: bugman
Date: Mon Jul 2 22:09:16 2012
New Revision: 17144
URL: http://svn.gna.org/viewcvs/relax?rev=17144&view=rev
Log:
Converted generic_fns.structure.geometric.create_vector_dist() to the
interatomic data design.
Modified:
branches/interatomic/generic_fns/structure/geometric.py
Modified: branches/interatomic/generic_fns/structure/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/generic_fns/structure/geometric.py?rev=17144&r1=17143&r2=17144&view=diff
==============================================================================
--- branches/interatomic/generic_fns/structure/geometric.py (original)
+++ branches/interatomic/generic_fns/structure/geometric.py Mon Jul 2
22:09:16 2012
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2011 Edward d'Auvergne
#
+# Copyright (C) 2003-2012 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -28,7 +28,8 @@
from warnings import warn
# relax module imports.
-from generic_fns.mol_res_spin import exists_mol_res_spin_data, spin_loop
+from generic_fns.interatomic import interatomic_loop
+from generic_fns.mol_res_spin import exists_mol_res_spin_data, return_spin,
spin_loop
from generic_fns import pipes
from generic_fns.structure.mass import centre_of_mass
from internal import Internal
@@ -582,12 +583,11 @@
def create_vector_dist(length=None, symmetry=True, file=None, dir=None,
force=False):
- """Create a PDB representation of the XH vector distribution.
+ """Create a PDB representation of the vector distribution.
@param length: The length to set the vectors to in the PDB file.
@type length: float
- @param symmetry: The symmetry flag which if set will create a second
PDB chain 'B' which
- is the same as chain 'A' but with the XH vectors reversed.
+ @param symmetry: The symmetry flag which if set will create a second
PDB chain 'B' which is the same as chain 'A' but with the vectors reversed.
@type symmetry: bool
@param file: The name of the PDB file to create.
@type file: str
@@ -609,10 +609,10 @@
raise RelaxNoSequenceError
# Test if unit vectors exist.
- vectors = 0
- for spin in spin_loop():
- if hasattr(spin, 'xh_vect'):
- vectors = 1
+ vectors = False
+ for interatom in interatomic_loop():
+ if hasattr(interatom, 'vector'):
+ vectors = True
break
if not vectors:
raise RelaxNoVectorsError
@@ -645,27 +645,31 @@
res_num = res_num + 1
- # The XH vectors.
- #################
-
- # Loop over the spin systems.
- for spin, mol_name, res_num, res_name in spin_loop(full_info=True):
+ # The vectors.
+ ##############
+
+ # Loop over the interatomic data containers.
+ for interatom in interatomic_loop():
+ # Get the spins.
+ spin1 = return_spin(interatom.spin_id1)
+ spin2 = return_spin(interatom.spin_id2)
+
# Skip deselected spin systems.
- if not spin.select:
+ if not spin1.select or not spin2.select:
continue
- # Skip spin systems missing the xh_vect structure.
- if not hasattr(spin, 'xh_vect'):
+ # Skip containers missing vectors.
+ if not hasattr(interatom, 'vector'):
continue
# Scale the vector.
- vector = spin.xh_vect * length * 1e10
-
- # Add the central X atom.
- mol.atom_add(pdb_record='ATOM', atom_num=atom_num,
atom_name=spin.name, res_name=res_name, chain_id='A', res_num=res_num, pos=R,
segment_id=None, element=spin.element)
-
- # Add the H atom.
- mol.atom_add(pdb_record='ATOM', atom_num=atom_num+1, atom_name='H',
res_name=res_name, chain_id='A', res_num=res_num, pos=R+vector,
segment_id=None, element='H')
+ vector = interatom.vector * length * 1e10
+
+ # Add the first spin as the central atom.
+ mol.atom_add(pdb_record='ATOM', atom_num=atom_num,
atom_name=spin1.name, res_name=spin1._res_name, chain_id='A',
res_num=spin1._res_num, pos=R, segment_id=None, element=spin1.element)
+
+ # Add the second spin as the end atom.
+ mol.atom_add(pdb_record='ATOM', atom_num=atom_num+1,
atom_name=spin2.name, res_name=spin2._res_name, chain_id='A',
res_num=spin2._res_num, pos=R+vector, segment_id=None, element=spin2.element)
# Connect the two atoms.
mol.atom_connect(index1=atom_num-1, index2=atom_num)
@@ -675,24 +679,28 @@
# Symmetry chain.
if symmetry:
- # Loop over the spin systems.
- for spin, mol_name, res_num, res_name in spin_loop(full_info=True):
+ # Loop over the interatomic data containers.
+ for interatom in interatomic_loop():
+ # Get the spins.
+ spin1 = return_spin(interatom.spin_id1)
+ spin2 = return_spin(interatom.spin_id2)
+
# Skip deselected spin systems.
- if not spin.select:
+ if not spin1.select or not spin2.select:
continue
- # Skip spin systems missing the xh_vect structure.
- if not hasattr(spin, 'xh_vect'):
+ # Skip containers missing vectors.
+ if not hasattr(interatom, 'vector'):
continue
# Scale the vector.
- vector = spin.xh_vect * length * 1e10
-
- # Add the central X atom.
- mol.atom_add(pdb_record='ATOM', atom_num=atom_num,
atom_name=spin.name, res_name=res_name, chain_id='B', res_num=res_num, pos=R,
segment_id=None, element=spin.element)
-
- # Add the H atom.
- mol.atom_add(pdb_record='ATOM', atom_num=atom_num+1,
atom_name='H', res_name=res_name, chain_id='B', res_num=res_num,
pos=R-vector, segment_id=None, element='H')
+ vector = interatom.vector * length * 1e10
+
+ # Add the first spin as the central atom.
+ mol.atom_add(pdb_record='ATOM', atom_num=atom_num,
atom_name=spin1.name, res_name=spin1._res_name, chain_id='B',
res_num=spin1._res_num, pos=R, segment_id=None, element=spin1.element)
+
+ # Add the second spin as the end atom.
+ mol.atom_add(pdb_record='ATOM', atom_num=atom_num+1,
atom_name=spin2.name, res_name=spin2._res_name, chain_id='B',
res_num=spin2._res_num, pos=R-vector, segment_id=None, element=spin2.element)
# Connect the two atoms.
mol.atom_connect(index1=atom_num-1, index2=atom_num)
r17144 - /branches/interatomic/generic_fns/structure/geometric.py