Author: bugman
Date: Tue Oct 27 20:22:12 2009
New Revision: 9812
URL: http://svn.gna.org/viewcvs/relax?rev=9812&view=rev
Log:
Merged revisions 9794,9799-9800 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r9794 | bugman | 2009-10-27 10:59:25 +0100 (Tue, 27 Oct 2009) | 7 lines
Added user variable checking to the full_analysis.py script.
This is in response to Tiago Pais's <tpais att itqb dot unl dot pt> post at
https://mail.gna.org/public/relax-users/2009-10/msg00009.html (Message-id:
<E45CDDF4A4E54B34A36BFBA62E6BFF20@Mercurio>).
........
r9799 | bugman | 2009-10-27 15:24:25 +0100 (Tue, 27 Oct 2009) | 3 lines
Fix for the frame order grid search.
........
r9800 | bugman | 2009-10-27 15:25:08 +0100 (Tue, 27 Oct 2009) | 3 lines
Created the structure.get_pos() user function for extracting atomic
positions.
........
Modified:
branches/bmrb/ (props changed)
branches/bmrb/generic_fns/structure/main.py
branches/bmrb/prompt/structure.py
branches/bmrb/sample_scripts/full_analysis.py
branches/bmrb/specific_fns/frame_order.py
Propchange: branches/bmrb/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Tue Oct 27 20:22:12 2009
@@ -1,1 +1,1 @@
-/1.3:1-9792
+/1.3:1-9811
Modified: branches/bmrb/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/structure/main.py?rev=9812&r1=9811&r2=9812&view=diff
==============================================================================
--- branches/bmrb/generic_fns/structure/main.py (original)
+++ branches/bmrb/generic_fns/structure/main.py Tue Oct 27 20:22:12 2009
@@ -31,7 +31,7 @@
# 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, return_molecule, return_residue, return_spin, spin_loop
+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 import pipes
from generic_fns.structure.internal import Internal
from generic_fns.structure.scientific import Scientific_data
@@ -59,7 +59,89 @@
if hasattr(spin, 'xh_vect'):
del spin.xh_vect
-
+
+def get_pos(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.
+ @type str_id: int or str
+ @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
+ """
+
+ # Test if the current data pipe exists.
+ pipes.test()
+
+ # Test if the structure exists.
+ if not hasattr(cdp, 'structure') or not cdp.structure.num_models() or
not cdp.structure.num_molecules():
+ raise RelaxNoPdbError
+
+ # 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:
+ model_index = model_index + 1
+ last_model = model_num
+
+ # Remove the '+' regular expression character from the mol, res, and
spin names!
+ if mol_name and search('\+', mol_name):
+ mol_name = replace(mol_name, '+', '')
+ if res_name and search('\+', res_name):
+ res_name = replace(res_name, '+', '')
+ if atom_name and search('\+', atom_name):
+ atom_name = replace(atom_name, '+', '')
+
+ # The spin identification string. The residue name and spin num is
not included to allow molecules with point mutations to be used as different
models.
+ id = generate_spin_id(mol_name=mol_name, res_num=res_num,
res_name=None, spin_name=atom_name)
+
+ # Get the spin container.
+ spin_cont = return_spin(id)
+
+ # Skip the spin if it doesn't exist.
+ if spin_cont == None:
+ continue
+
+ # Add the position vector to the spin container.
+ if ave_pos:
+ spin_cont.pos = pos
+ else:
+ if not hasattr(spin_cont, 'pos'):
+ spin_cont.pos = []
+ spin_cont.pos.append(pos)
+
+ # Update pseudo-atoms.
+ for spin in spin_loop():
+ if hasattr(spin, 'members'):
+ # Get the spin positions.
+ positions = []
+ for atom in spin.members:
+ # Get the spin container.
+ subspin = return_spin(atom)
+
+ # Test that the spin exists.
+ if subspin == None:
+ raise RelaxNoSpinError(atom)
+
+ # Test the position.
+ if not hasattr(subspin, 'pos') or not subspin.pos:
+ raise RelaxError("Positional information is not
available for the atom '%s'." % atom)
+
+ # Store the position.
+ positions.append([])
+ for i in range(len(subspin.pos)):
+ positions[-1].append(subspin.pos[i].tolist())
+
+ # The averaging.
+ if spin.averaging == 'linear':
+ spin.pos = linear_ave(positions)
+
+
def load_spins(spin_id=None, str_id=None, combine_models=True,
ave_pos=False):
"""Load the spins from the structural object into the relax data store.
@@ -200,7 +282,7 @@
=======
A number of parsers are available for reading PDB files. These include:
-
+
- 'scientific', the Scientific Python PDB parser.
- 'internal', a low quality yet fast PDB parser built into relax.
Modified: branches/bmrb/prompt/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/prompt/structure.py?rev=9812&r1=9811&r2=9812&view=diff
==============================================================================
--- branches/bmrb/prompt/structure.py (original)
+++ branches/bmrb/prompt/structure.py Tue Oct 27 20:22:12 2009
@@ -204,6 +204,55 @@
generic_fns.structure.geometric.create_vector_dist(length=length,
symmetry=symmetry, file=file, dir=dir, force=force)
+ def get_pos(self, spin_id=None, ave_pos=True):
+ """Extract the atomic positions from the loaded structures for the
given spins.
+
+ Keyword Arguments
+ ~~~~~~~~~~~~~~~~~
+
+ spin_id: The spin identification string.
+
+ ave_pos: A flag specifying if the position of the atom is to be
averaged across models.
+
+
+ Description
+ ~~~~~~~~~~~
+
+ This function allows the atomic positions of the spins to be
extracted from the loaded
+ structures. This is automatically performed by the
structure.load_spins() user function,
+ but if the sequence information is generated in other ways, this
user function allows the
+ structural information to be obtained.
+
+ 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.
+
+
+ Example
+ ~~~~~~~
+
+ For a model-free backbone amide nitrogen analysis whereby the N
spins have already been
+ created, to obtain the backbone N positions from the file '1F3Y.pdb'
(which is a single
+ protein), type the following two user functions:
+
+ relax> structure.read_pdb('1F3Y.pdb')
+ relax> structure.get_pos(spin_id='@N')
+ """
+
+ # Function intro text.
+ if self.__relax__.interpreter.intro:
+ text = sys.ps3 + "structure.get_pos("
+ text = text + "spin_id=" + repr(spin_id)
+ text = text + ", ave_pos=" + repr(ave_pos) + ")"
+ print(text)
+
+ # The argument checks.
+ check.is_str(spin_id, 'spin identification string', can_be_none=True)
+ check.is_bool(ave_pos, 'average position flag')
+
+ # Execute the functional code.
+ generic_fns.structure.main.get_pos(spin_id=spin_id, ave_pos=ave_pos)
+
+
def delete(self):
"""Delete all structural information from the current data pipe.
@@ -241,7 +290,7 @@
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.
+ ave_pos: A flag specifying if the position of the atom is to be
averaged across models.
Description
@@ -256,15 +305,15 @@
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 structures
will be loaded into the spin
- container. If False, then the positions from all structures will be
loaded.
+ 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.
Example
~~~~~~~
For a model-free backbone amide nitrogen analysis, to load just the
backbone N sequence from
- the file '1F3Y.pdb' (which is a single protein), type the follow two
user functions:
+ the file '1F3Y.pdb' (which is a single protein), type the following
two user functions:
relax> structure.read_pdb('1F3Y.pdb')
relax> structure.load_spins(spin_id='@N')
@@ -278,7 +327,6 @@
relax> structure.load_spins(spin_id=':G@C8&@N1')
relax> structure.load_spins(spin_id=':C@C5&@C6')
relax> structure.load_spins(spin_id=':U@N3&@C5&@C6')
-
"""
# Function intro text.
Modified: branches/bmrb/sample_scripts/full_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/sample_scripts/full_analysis.py?rev=9812&r1=9811&r2=9812&view=diff
==============================================================================
--- branches/bmrb/sample_scripts/full_analysis.py (original)
+++ branches/bmrb/sample_scripts/full_analysis.py Tue Oct 27 20:22:12 2009
@@ -211,6 +211,9 @@
# Setup.
self.relax = relax
+ # User variable checks.
+ self.check_vars()
+
# MI - Local tm.
################
@@ -387,6 +390,94 @@
raise RelaxError("Unknown diffusion model, change the value of
'DIFF_MODEL'")
+ def check_vars(self):
+ """Check that the user has set the variables correctly."""
+
+ # The diff model.
+ valid_models = ['local_tm', 'sphere', 'oblate', 'prolate',
'ellipsoid', 'final']
+ if DIFF_MODEL not in valid_models:
+ raise RelaxError("The DIFF_MODEL user variable '%s' is
incorrectly set. It must be one of %s." % (DIFF_MODEL, valid_models))
+
+ # Model-free models.
+ mf_models = ['m0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8',
'm9']
+ local_tm_models = ['tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6',
'tm7', 'tm8', 'tm9']
+ if not isinstance(MF_MODELS, list):
+ raise RelaxError("The MF_MODELS user variable must be a list.")
+ if not isinstance(LOCAL_TM_MODELS, list):
+ raise RelaxError("The LOCAL_TM_MODELS user variable must be a
list.")
+ for i in range(len(MF_MODELS)):
+ if MF_MODELS[i] not in mf_models:
+ raise RelaxError("The MF_MODELS user variable '%s' is
incorrectly set. It must be one of %s." % (MF_MODELS, mf_models))
+ for i in range(len(LOCAL_TM_MODELS)):
+ if LOCAL_TM_MODELS[i] not in local_tm_models:
+ raise RelaxError("The LOCAL_TM_MODELS user variable '%s' is
incorrectly set. It must be one of %s." % (LOCAL_TM_MODELS, local_tm_models))
+
+ # PDB file.
+ if PDB_FILE and not isinstance(PDB_FILE, str):
+ raise RelaxError("The PDB_FILE user variable '%s' is incorrectly
set. It should either be a string or None." % PDB_FILE)
+
+ # Sequence data.
+ if not isinstance(SEQ_ARGS, list):
+ raise RelaxError("The SEQ_ARGS user variable '%s' must be a
list." % SEQ_ARGS)
+ if len(SEQ_ARGS) != 8:
+ raise RelaxError("The SEQ_ARGS user variable '%s' must be a list
with eight elements." % SEQ_ARGS)
+ if not isinstance(SEQ_ARGS[0], str):
+ raise RelaxError("The file name component of the SEQ_ARGS user
variable '%s' must be a string." % SEQ_ARGS)
+ for i in range(1, 8):
+ if SEQ_ARGS[i] != None and not isinstance(SEQ_ARGS[i], int):
+ raise RelaxError("The column components of the SEQ_ARGS user
variable '%s' must be either None or integers." % SEQ_ARGS)
+
+ # Atom name.
+ if not isinstance(HET_NAME, str):
+ raise RelaxError("The HET_NAME heteronucleus atom name user
variable '%s' must be a string." % HET_NAME)
+
+ # Relaxation data.
+ if not isinstance(RELAX_DATA, list):
+ raise RelaxError("The RELAX_DATA user variable '%s' must be a
list." % RELAX_DATA)
+ for i in range(len(RELAX_DATA)):
+ if len(RELAX_DATA[i]) != 13:
+ raise RelaxError("The RELAX_DATA user variable component
'%s' must be a list of 13 elements." % RELAX_DATA[i])
+ if not isinstance(RELAX_DATA[i][0], str):
+ raise RelaxError("The data type component '%s' of the
RELAX_DATA user variable must be a string." % RELAX_DATA[i][0])
+ if not isinstance(RELAX_DATA[i][1], str):
+ raise RelaxError("The frequency label component '%s' of the
RELAX_DATA user variable must be a string." % RELAX_DATA[i][1])
+ if not isinstance(RELAX_DATA[i][2], float):
+ raise RelaxError("The frequency component '%s' of the
RELAX_DATA user variable must be a floating point number." % RELAX_DATA[i][2])
+ if not isinstance(RELAX_DATA[i][3], str):
+ raise RelaxError("The file name component '%s' of the
RELAX_DATA user variable must be a string." % RELAX_DATA[i][3])
+ for j in range(4, 13):
+ if RELAX_DATA[i][j] != None and not
isinstance(RELAX_DATA[i][j], int):
+ raise RelaxError("The column components of the
RELAX_DATA user variable '%s' must be either None or integers." %
RELAX_DATA[i])
+
+ # Unresolved and exclude files.
+ if UNRES and not isinstance(UNRES, str):
+ raise RelaxError("The UNRES user variable '%s' is incorrectly
set. It should either be a string or None." % UNRES)
+ if EXCLUDE and not isinstance(EXCLUDE, str):
+ raise RelaxError("The EXCLUDE user variable '%s' is incorrectly
set. It should either be a string or None." % EXCLUDE)
+
+ # Spin vars.
+ if not isinstance(BOND_LENGTH, float):
+ raise RelaxError("The BOND_LENGTH user variable '%s' is
incorrectly set. It should be a floating point number." % BOND_LENGTH)
+ if not isinstance(CSA, float):
+ raise RelaxError("The CSA user variable '%s' is incorrectly set.
It should be a floating point number." % CSA)
+ if not isinstance(HETNUC, str):
+ raise RelaxError("The HETNUC user variable '%s' is incorrectly
set. It should be a string." % HETNUC)
+ if not isinstance(PROTON, str):
+ raise RelaxError("The PROTON user variable '%s' is incorrectly
set. It should be a string." % PROTON)
+
+ # Min vars.
+ if not isinstance(GRID_INC, int):
+ raise RelaxError("The GRID_INC user variable '%s' is incorrectly
set. It should be an integer." % GRID_INC)
+ if not isinstance(MIN_ALGOR, str):
+ raise RelaxError("The MIN_ALGOR user variable '%s' is
incorrectly set. It should be a string." % MIN_ALGOR)
+ if not isinstance(MC_NUM, int):
+ raise RelaxError("The MC_NUM user variable '%s' is incorrectly
set. It should be an integer." % MC_NUM)
+
+ # Looping.
+ if not isinstance(CONV_LOOP, bool):
+ raise RelaxError("The CONV_LOOP user variable '%s' is
incorrectly set. It should be one of the booleans True or False." %
CONV_LOOP)
+
+
def convergence(self):
"""Test for the convergence of the global model."""
Modified: branches/bmrb/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/specific_fns/frame_order.py?rev=9812&r1=9811&r2=9812&view=diff
==============================================================================
--- branches/bmrb/specific_fns/frame_order.py (original)
+++ branches/bmrb/specific_fns/frame_order.py Tue Oct 27 20:22:12 2009
@@ -730,7 +730,7 @@
# Set the default bounds.
if default_bounds:
lower.append(0.0)
- upper.append(pi * (1.0 - 1.0/incs[i]))
+ upper.append(pi)
# Get the grid row.
if not row:
r9812 - in /branches/bmrb: ./ generic_fns/structure/ prompt/ sample_scripts/ specific_fns/