Author: bugman
Date: Wed Jul 27 17:54:24 2011
New Revision: 13932
URL: http://svn.gna.org/viewcvs/relax?rev=13932&view=rev
Log:
Redesign of the structure.load_spins user function back end.
This redesign is required due to problems encountered by Han in the xyz
branch. See the thread
starting at https://mail.gna.org/public/relax-devel/2011-07/msg00021.html.
This commit consists of a number of changes:
- The combine_models argument has been removed as it is a relic, and
isn't used at all.
- The spins are now created in the standard way via the
generic_fns.mol_res_spin.create_spin()
function, eliminating all of the issues and complications of the old code.
- The atomic positions are now converted to numpy arrays.
- Only the created spins are included in the print out, and not
replicated for each model.
Modified:
1.3/generic_fns/structure/main.py
1.3/prompt/structure.py
1.3/sample_scripts/n_state_model/conformation_analysis_rdc+pcs.py
1.3/test_suite/shared_data/align_data/population_model/generate.py
1.3/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py
1.3/test_suite/system_tests/scripts/n_state_model/missing_data_test.py
1.3/test_suite/system_tests/scripts/n_state_model/populations.py
1.3/test_suite/system_tests/scripts/n_state_model/vector_loading.py
Modified: 1.3/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/main.py?rev=13932&r1=13931&r2=13932&view=diff
==============================================================================
--- 1.3/generic_fns/structure/main.py (original)
+++ 1.3/generic_fns/structure/main.py Wed Jul 27 17:54:24 2011
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2010 Edward d'Auvergne
#
+# Copyright (C) 2003-2011 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -22,7 +22,7 @@
# Python module imports.
from math import sqrt
-from numpy import dot, float64, ndarray, zeros
+from numpy import array, dot, float64, ndarray, zeros
from numpy.linalg import norm
from os import F_OK, access
from re import search
@@ -32,7 +32,7 @@
# relax module imports.
from generic_fns import molmol, relax_re
-from generic_fns.mol_res_spin import exists_mol_res_spin_data,
generate_spin_id, linear_ave, return_molecule, return_residue, return_spin,
spin_loop
+from generic_fns.mol_res_spin import create_spin, exists_mol_res_spin_data,
generate_spin_id, linear_ave, return_molecule, return_residue, return_spin,
spin_loop
from generic_fns import pipes
from generic_fns.structure.internal import Internal
from generic_fns.structure.scientific import Scientific_data
@@ -159,19 +159,14 @@
spin.pos = ave[0]
-def load_spins(spin_id=None, str_id=None, combine_models=True,
ave_pos=False):
+def load_spins(spin_id=None, str_id=None, ave_pos=False):
"""Load the spins from the structural object into the relax data store.
@keyword spin_id: The molecule, residue, and spin identifier
string.
@type spin_id: str
- @keyword str_id: The structure identifier. This can be the
file name, model number,
- or structure number.
+ @keyword str_id: The structure identifier. This can be the
file name, model number, or structure number.
@type str_id: int or str
- @keyword combine_models: A flag specifying if spins from only one
structure of the ensemble
- or from all should be loaded.
- @type combine_models: bool
- @keyword ave_pos: A flag specifying if the average atom
position or the atom position
- from all loaded structures is loaded into
the SpinContainer.
+ @keyword ave_pos: A flag specifying if the average atom
position or the atom position from all loaded structures is loaded into the
SpinContainer.
@type ave_pos: bool
"""
@@ -192,9 +187,11 @@
spin_nums = []
spin_names = []
+ # Initialise data for the atom loop.
+ model_index = -1
+ last_model = 1000000
+
# Loop over all atoms of the spin_id selection.
- model_index = -1
- last_model = None
for model_num, mol_name, res_num, res_name, atom_num, atom_name,
element, pos in cdp.structure.atom_loop(atom_id=spin_id, str_id=str_id,
model_num_flag=True, mol_name_flag=True, res_num_flag=True,
res_name_flag=True, atom_num_flag=True, atom_name_flag=True,
element_flag=True, pos_flag=True, ave=ave_pos):
# Update the model info.
if last_model != model_num:
@@ -209,84 +206,48 @@
if atom_name and search('\+', atom_name):
atom_name = replace(atom_name, '+', '')
- # Initialise the identification string.
- id = ''
-
- # Get the molecule container corresponding to the molecule name.
- mol_cont = None
- if mol_name:
- # Update the ID string.
- id = id + '#' + mol_name
-
- # The container.
- mol_cont = return_molecule(id)
-
- # Add the molecule if it doesn't exist.
- if mol_cont == None:
- # Get the unnamed molecule, assuming there is only one.
- mol_cont = return_molecule()
-
- # Got something!
- if mol_cont != None:
- # Rename the molecule container if the mol name is given and
the sole container is unnamed.
- if mol_cont.name == None and mol_name:
- # Print out.
- print(("Renaming the unnamed sole molecule container to
'%s'." % mol_name))
-
- # Set the name.
- mol_cont.name = mol_name
-
- # Nothing exists yet.
- else:
- # Add the molecule.
- cdp.mol.add_item(mol_name=mol_name)
-
- # Get the container.
- mol_cont = cdp.mol[-1]
-
- # Add the residue number to the ID string (residue name is ignored
because only the number is unique).
- id = id + ':' + repr(res_num)
-
- # Get the corresponding residue container.
- res_cont = return_residue(id)
-
- # Add the residue if it doesn't exist.
- if res_cont == None:
- # Add the residue.
- mol_cont.res.add_item(res_name=res_name, res_num=res_num)
-
- # Get the container.
- res_cont = mol_cont.res[-1]
-
- # Add the atom number to the ID string (atom name is ignored because
only the number is unique).
- id = id + '@' + repr(atom_num)
-
- # Get the corresponding spin container.
- spin_cont = return_spin(id)
-
- # Add the spin if it doesn't exist.
- if spin_cont == None:
- # Add the spin.
- res_cont.spin.add_item(spin_name=atom_name, spin_num=atom_num)
-
- # Get the container.
- spin_cont = res_cont.spin[-1]
-
- # Append all the spin ID info.
+ # Generate a spin ID for the current atom.
+ id = generate_spin_id(mol_name=mol_name, res_num=res_num,
res_name=res_name, spin_num=atom_num, spin_name=atom_name)
+
+ # Create the spin.
+ try:
+ spin_cont = create_spin(mol_name=mol_name, res_num=res_num,
res_name=res_name, spin_num=atom_num, spin_name=atom_name)
+ except RelaxError:
+ # Throw a warning if still on the first model.
+ if not model_index:
+ warn(RelaxWarning("The spin '%s' already exists." % id))
+ continue
+
+ # Otherwise, get the spin container.
+ spin_cont = return_spin(id)
+
+ # Append all the spin ID info for the first model for printing later.
+ if model_index == 0:
mol_names.append(mol_name)
res_nums.append(res_num)
res_names.append(res_name)
spin_nums.append(atom_num)
spin_names.append(atom_name)
- # Add the position vector and element type to the spin container.
+ # Convert the position vector to a numpy array.
+ pos = array(pos, float64)
+
+ # Average position vector (already averaged across models in the
atom_loop).
if ave_pos:
spin_cont.pos = pos
+
+ # All positions.
else:
+ # Initialise.
if not hasattr(spin_cont, 'pos'):
spin_cont.pos = []
+
+ # Add the current model's position.
spin_cont.pos.append(pos)
- spin_cont.element = element
+
+ # Add the element.
+ if not model_index:
+ spin_cont.element = element
# Catch no data.
if len(mol_names) == 0:
Modified: 1.3/prompt/structure.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/structure.py?rev=13932&r1=13931&r2=13932&view=diff
==============================================================================
--- 1.3/prompt/structure.py (original)
+++ 1.3/prompt/structure.py Wed Jul 27 17:54:24 2011
@@ -277,15 +277,13 @@
generic_fns.structure.main.delete()
- def load_spins(self, spin_id=None, combine_models=True, ave_pos=True):
+ def load_spins(self, spin_id=None, ave_pos=True):
"""Load spins from the structure into the relax data store.
Keyword Arguments
~~~~~~~~~~~~~~~~~
spin_id: The spin identification string.
-
- combine_models: A flag which specifies if spins from separate
models should be combined.
ave_pos: A flag specifying if the position of the atom is to be
averaged across models.
@@ -298,9 +296,6 @@
is used to select which molecules, which residues, and which atoms
will be recognised as
spin systems within relax. If spin_id is left as None, then all
molecules, residues, and
atoms will be placed within the data store.
-
- If the combine_models flag is True, then the spins from only a
single structure from the
- ensemble of models will be taken. If False, then spins will be
loaded for each model.
If the ave_pos flag is True, the average position of all models will
be loaded into the spin
container. If False, then the positions from all models will be
loaded.
@@ -340,17 +335,15 @@
if self._exec_info.intro:
text = self._exec_info.ps3 + "structure.load_spins("
text = text + "spin_id=" + repr(spin_id)
- text = text + ", combine_models=" + repr(combine_models)
text = text + ", ave_pos=" + repr(ave_pos) + ")"
print(text)
# The argument checks.
arg_check.is_str(spin_id, 'spin identification string',
can_be_none=True)
- arg_check.is_bool(combine_models, 'model combining flag')
arg_check.is_bool(ave_pos, 'average position flag')
# Execute the functional code.
- generic_fns.structure.main.load_spins(spin_id=spin_id,
combine_models=combine_models, ave_pos=ave_pos)
+ generic_fns.structure.main.load_spins(spin_id=spin_id,
ave_pos=ave_pos)
def read_pdb(self, file=None, dir=None, read_mol=None,
set_mol_name=None, read_model=None, set_model_num=None, parser='internal'):
Modified: 1.3/sample_scripts/n_state_model/conformation_analysis_rdc+pcs.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/n_state_model/conformation_analysis_rdc%2Bpcs.py?rev=13932&r1=13931&r2=13932&view=diff
==============================================================================
--- 1.3/sample_scripts/n_state_model/conformation_analysis_rdc+pcs.py
(original)
+++ 1.3/sample_scripts/n_state_model/conformation_analysis_rdc+pcs.py Wed Jul
27 17:54:24 2011
@@ -106,7 +106,7 @@
structure.read_pdb(file='LactoseMCMM4_'+`i+1`,
dir='../../../structures/tag_1000/080704_MCMM4_aligned-forEd1000',
parser='internal', set_model_num=i+1, set_mol_name='tag')
# Load the lanthanide atoms.
-structure.load_spins(spin_id=':4@C1', combine_models=False, ave_pos=False)
+structure.load_spins(spin_id=':4@C1', ave_pos=False)
# Switch back to the main analysis data pipe.
pipe.switch('lactose')
Modified: 1.3/test_suite/shared_data/align_data/population_model/generate.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/align_data/population_model/generate.py?rev=13932&r1=13931&r2=13932&view=diff
==============================================================================
--- 1.3/test_suite/shared_data/align_data/population_model/generate.py
(original)
+++ 1.3/test_suite/shared_data/align_data/population_model/generate.py Wed
Jul 27 17:54:24 2011
@@ -24,8 +24,8 @@
structure.read_pdb(file='lactose_MCMM4_S1_%i.pdb' % i, dir=str_path,
set_model_num=i, set_mol_name='LE')
# Load the sequence information.
-structure.load_spins(spin_id=':UNK@C*', combine_models=False, ave_pos=False)
-structure.load_spins(spin_id=':UNK@H*', combine_models=False, ave_pos=False)
+structure.load_spins(spin_id=':UNK@C*', ave_pos=False)
+structure.load_spins(spin_id=':UNK@H*', ave_pos=False)
# Deselect the CH2 protons (the rotation of these doesn't work in the model,
but the carbon doesn't move).
deselect.spin(spin_id=':UNK@H6')
Modified: 1.3/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py?rev=13932&r1=13931&r2=13932&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py
(original)
+++ 1.3/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py Wed
Jul 27 17:54:24 2011
@@ -27,8 +27,8 @@
structure.read_pdb(file='lactose_MCMM4_S1_'+repr(i+1), dir=str_path,
parser='internal', set_model_num=i+1, set_mol_name='lactose_MCMM4_S1')
# Load the sequence information.
-structure.load_spins(spin_id=':UNK@C*', combine_models=False, ave_pos=False)
-structure.load_spins(spin_id=':UNK@H*', combine_models=False, ave_pos=False)
+structure.load_spins(spin_id=':UNK@C*', ave_pos=False)
+structure.load_spins(spin_id=':UNK@H*', ave_pos=False)
# Deselect the CH2 protons (the rotation of these doesn't work in the model,
but the carbon doesn't move).
deselect.spin(spin_id=':UNK@H6')
@@ -74,7 +74,7 @@
structure.read_pdb(file='tag_MCMM4_'+repr(i+1), dir=str_path,
parser='internal', set_model_num=i+1, set_mol_name='tag')
# Load the lanthanide atoms.
-structure.load_spins(spin_id='@C1', combine_models=False, ave_pos=False)
+structure.load_spins(spin_id='@C1', ave_pos=False)
# Switch back to the main analysis data pipe.
pipe.switch('lactose')
Modified:
1.3/test_suite/system_tests/scripts/n_state_model/missing_data_test.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/n_state_model/missing_data_test.py?rev=13932&r1=13931&r2=13932&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/scripts/n_state_model/missing_data_test.py
(original)
+++ 1.3/test_suite/system_tests/scripts/n_state_model/missing_data_test.py
Wed Jul 27 17:54:24 2011
@@ -18,8 +18,8 @@
structure.read_pdb(file='LE_trunc.pdb', dir=str_path, set_mol_name='LE')
# Load the sequence information.
-structure.load_spins(spin_id='@C*', combine_models=False, ave_pos=False)
-structure.load_spins(spin_id='@H*', combine_models=False, ave_pos=False)
+structure.load_spins(spin_id='@C*', ave_pos=False)
+structure.load_spins(spin_id='@H*', ave_pos=False)
# Load the CH vectors for the C atoms.
structure.vectors(spin_id='@C*', attached='H*', ave=False)
Modified: 1.3/test_suite/system_tests/scripts/n_state_model/populations.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/n_state_model/populations.py?rev=13932&r1=13931&r2=13932&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/scripts/n_state_model/populations.py
(original)
+++ 1.3/test_suite/system_tests/scripts/n_state_model/populations.py Wed Jul
27 17:54:24 2011
@@ -23,8 +23,8 @@
i += 1
# Load the sequence information.
-structure.load_spins(spin_id=':UNK@C*', combine_models=False, ave_pos=False)
-structure.load_spins(spin_id=':UNK@H*', combine_models=False, ave_pos=False)
+structure.load_spins(spin_id=':UNK@C*', ave_pos=False)
+structure.load_spins(spin_id=':UNK@H*', ave_pos=False)
# Deselect the CH2 protons (the rotation of these doesn't work in the model,
but the carbon doesn't move).
deselect.spin(spin_id=':UNK@H6')
Modified: 1.3/test_suite/system_tests/scripts/n_state_model/vector_loading.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/n_state_model/vector_loading.py?rev=13932&r1=13931&r2=13932&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/scripts/n_state_model/vector_loading.py
(original)
+++ 1.3/test_suite/system_tests/scripts/n_state_model/vector_loading.py Wed
Jul 27 17:54:24 2011
@@ -20,7 +20,7 @@
structure.read_pdb(file='lactose_MCMM4_S1_%i.pdb' %
(ds.order_struct[i]+1), dir=str_path, set_model_num=ds.order_model[i]+1,
set_mol_name='LE')
# Load the sequence information.
-structure.load_spins(spin_id=':UNK@C1', combine_models=False, ave_pos=False)
+structure.load_spins(spin_id=':UNK@C1', ave_pos=False)
# Load the CH vectors for the C atoms.
structure.vectors(spin_id='@C*', attached='H*', ave=False)
r13932 - in /1.3: generic_fns/structure/ prompt/ sample_scripts/n_state_model/ test_suite/shared_data/align_data/population_...