Author: bugman
Date: Wed Oct 1 13:39:36 2008
New Revision: 7471
URL: http://svn.gna.org/viewcvs/relax?rev=7471&view=rev
Log:
Converted the create_vector_dist() function to the new design.
Again the problem was identified by looking at incorrect usage of the relax
data store.
Modified:
branches/pipe_refs/generic_fns/structure/geometric.py
Modified: branches/pipe_refs/generic_fns/structure/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/branches/pipe_refs/generic_fns/structure/geometric.py?rev=7471&r1=7470&r2=7471&view=diff
==============================================================================
--- branches/pipe_refs/generic_fns/structure/geometric.py (original)
+++ branches/pipe_refs/generic_fns/structure/geometric.py Wed Oct 1 13:39:36
2008
@@ -305,11 +305,9 @@
tensor_pdb_file.close()
-def create_vector_dist(run=None, length=None, symmetry=1, file=None,
dir=None, force=False):
+def create_vector_dist(length=None, symmetry=1, file=None, dir=None,
force=False):
"""Create a PDB representation of the XH vector distribution.
- @param run: The run.
- @type run: str
@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
@@ -320,31 +318,31 @@
@param dir: The name of the directory to place the PDB file into.
@type dir: str
@param force: Flag which if set will overwrite any pre-existing
file.
- @type force: int
+ @type force: bool
"""
-
- # Arguments.
- run = run
# Test if the current pipe exists.
pipes.test()
- # Test if the PDB file of the macromolecule has been loaded.
- if not ds.pdb.has_key(run):
- raise RelaxNoPdbError, run
+ # Get the data pipe.
+ cdp = pipes.get_pipe()
+
+ # Test if a structure has been loaded.
+ if not hasattr(cdp, 'structure') or not cdp.structure.num > 0:
+ raise RelaxNoPdbError
# Test if sequence data is loaded.
- if not len(ds.res[run]):
- raise RelaxNoSequenceError, run
+ if not exists_mol_res_spin_data():
+ raise RelaxNoSequenceError
# Test if unit vectors exist.
vectors = 0
- for i in xrange(len(ds.res[run])):
- if hasattr(ds.res[run][i], 'xh_vect'):
+ for spin in spin_loop():
+ if hasattr(spin, 'xh_vect'):
vectors = 1
break
if not vectors:
- raise RelaxNoVectorsError, run
+ raise RelaxNoVectorsError
# Initialise.
@@ -353,8 +351,9 @@
# Create the structural object.
structure = Internal()
- # Initialise the residue number.
+ # Initialise the residue and atom numbers.
res_num = 1
+ atom_num = 1
# Centre of mass.
@@ -371,81 +370,53 @@
#################
# Loop over the spin systems.
- for i in xrange(len(ds.res[run])):
- # Alias the spin system data.
- data = ds.res[run][i]
-
+ for spin in spin_loop():
# Skip deselected spin systems.
- if not data.select:
+ if not spin.select:
continue
# Skip spin systems missing the xh_vect structure.
- if not hasattr(data, 'xh_vect'):
+ if not hasattr(spin, 'xh_vect'):
continue
# Scale the vector.
- vector = data.xh_vect * length * 1e10
-
- # The atom ids.
- end = '_' + `data.num` + '_' + data.name
- X_id = data.heteronuc + end
- H_id = data.proton + end
+ vector = spin.xh_vect * length * 1e10
# Add the central X atom.
- 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)
+ structure.atom_add(pdb_record='ATOM', atom_num=atom_num,
atom_name=spin.heteronuc, res_name=spin.name, chain_id='A', res_num=spin.num,
pos=R, segment_id=None, element=spin.heteronuc, struct_index=None)
# Add the H atom.
- 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)
+ structure.atom_add(pdb_record='ATOM', atom_num=atom_num+1,
atom_name=spin.proton, res_name=spin.name, chain_id='A', res_num=spin.num,
pos=R+vector, segment_id=None, element=spin.proton, struct_index=None)
# Connect the two atoms.
- structure.atom_connect(index1=X_id, index2=H_id)
-
- # Store the terminate residue number for the TER record.
- last_res = data.num
- last_name = data.name
-
- # The TER record.
- 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)
+ structure.atom_connect(index1=atom_num-1, index2=atom_num)
+
+ # Increment the atom number.
+ atom_num = atom_num + 2
# Symmetry chain.
if symmetry:
# Loop over the spin systems.
- for i in xrange(len(ds.res[run])):
- # Alias the spin system data.
- data = ds.res[run][i]
-
+ for spin in spin_loop():
# Skip deselected spin systems.
- if not data.select:
+ if not spin.select:
continue
# Skip spin systems missing the xh_vect structure.
- if not hasattr(data, 'xh_vect'):
+ if not hasattr(spin, 'xh_vect'):
continue
# Scale the vector.
- vector = data.xh_vect * length * 1e10
-
- # The atom ids.
- end = '_' + `data.num` + '_' + data.name
- X_id = data.heteronuc + end
- H_id = data.proton + end
+ vector = spin.xh_vect * length * 1e10
# Add the central X atom.
- 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)
+ structure.atom_add(pdb_record='ATOM', atom_num=atom_num,
atom_name=spin.heteronuc, res_name=spin.name, chain_id='B', res_num=spin.num,
pos=R, segment_id=None, element=spin.heteronuc, struct_index=None)
# Add the H atom.
- 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)
+ structure.atom_add(pdb_record='ATOM', atom_num=atom_num+1,
atom_name=spin.proton, res_name=spin.name, chain_id='B', res_num=spin.num,
pos=R+vector, segment_id=None, element=spin.proton, struct_index=None)
# Connect the two atoms.
- structure.atom_connect(index1=X_id + '_B', index2=H_id + '_B')
-
- # Store the terminate residue number for the TER record.
- last_res = data.num
- last_name = data.name
-
- # The TER record.
- 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)
-
+ structure.atom_connect(index1=atom_num-1, index2=atom_num)
# Create the PDB file.
r7471 - /branches/pipe_refs/generic_fns/structure/geometric.py