Author: bugman
Date: Wed Jul 28 11:38:32 2010
New Revision: 11382
URL: http://svn.gna.org/viewcvs/relax?rev=11382&view=rev
Log:
The attached proton PDB name is no longer hardcoded to 'H' in the
dauvergne_protocol auto analysis.
Modified:
1.3/auto_analyses/dauvergne_protocol.py
1.3/sample_scripts/full_analysis.py
Modified: 1.3/auto_analyses/dauvergne_protocol.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/auto_analyses/dauvergne_protocol.py?rev=11382&r1=11381&r2=11382&view=diff
==============================================================================
--- 1.3/auto_analyses/dauvergne_protocol.py (original)
+++ 1.3/auto_analyses/dauvergne_protocol.py Wed Jul 28 11:38:32 2010
@@ -155,7 +155,7 @@
class dAuvergne_protocol:
- def __init__(self, diff_model=None, 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'], pdb_file=None,
seq_args=None, het_name=None, relax_data=None, unres=None, exclude=None,
bond_length=None, csa=None, hetnuc=None, proton='1H', grid_inc=11,
min_algor='newton', mc_num=500, max_iter=None, user_fns=None, conv_loop=True):
+ def __init__(self, diff_model=None, 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'], pdb_file=None,
seq_args=None, het_name=None, attached_name='H', relax_data=None, unres=None,
exclude=None, bond_length=None, csa=None, hetnuc=None, proton='1H',
grid_inc=11, min_algor='newton', mc_num=500, max_iter=None, user_fns=None,
conv_loop=True):
"""Perform the full model-free analysis protocol of d'Auvergne and
Gooley, 2008b.
@keyword diff_model: The global diffusion model to optimise.
This can be one of 'local_tm', 'sphere', 'oblate', 'prolate', 'ellipsoid', or
'final'.
@@ -170,6 +170,8 @@
@type seq_args: list of lists of [str, None or str, None
or int, None or int, None or int, None or int, None or int, None or int, None
or int, None or str]
@keyword het_name: The heteronucleus atom name
corresponding to that of the PDB file (used if the spin name is not in the
sequence data).
@type het_name: None or str
+ @keyword attached_name: The name of the proton attached to the
heteronucleus.
+ @type attached_name: str
@keyword relax_data: The relaxation data (data type,
frequency label, frequency, file name, dir, mol_name_col, res_num_col,
res_name_col, spin_num_col, spin_name_col, data_col, error_col, sep). These
are the arguments to the relax_data.read() user function, please see the
documentation for that function for more information.
@type relax_data: list of lists of [str, str, float, str,
None or str, None or int, None or int, None or int, None or int, None or int,
None or int, None or int, None or str]
@keyword unres: The file containing the list of
unresolved spins to exclude from the analysis (set this to None if no spin is
to be excluded).
@@ -205,6 +207,7 @@
self.pdb_file = pdb_file
self.seq_args = seq_args
self.het_name = het_name
+ self.attached_name = attached_name
self.relax_data = relax_data
self.unres = unres
self.exclude = exclude
@@ -309,7 +312,7 @@
# Load the PDB file and calculate the unit vectors
parallel to the XH bond.
if self.pdb_file:
self.interpreter.structure.read_pdb(self.pdb_file)
- self.interpreter.structure.vectors(attached='H')
+
self.interpreter.structure.vectors(attached=self.attached_name)
# Add an arbitrary diffusion tensor which will be
optimised.
if self.diff_model == 'sphere':
@@ -484,6 +487,8 @@
# Atom name.
if not isinstance(self.het_name, str):
raise RelaxError("The het_name heteronucleus atom name user
variable '%s' must be a string." % self.het_name)
+ if not isinstance(self.attached_name, str):
+ raise RelaxError("The attached_name proton atom name user
variable '%s' must be a string." % self.attached_name)
# Relaxation data.
if not isinstance(self.relax_data, list):
@@ -793,7 +798,7 @@
# Load the PDB file and calculate the unit vectors parallel to
the XH bond.
if not local_tm and self.pdb_file:
self.interpreter.structure.read_pdb(self.pdb_file)
- self.interpreter.structure.vectors(attached='H')
+
self.interpreter.structure.vectors(attached=self.attached_name)
# Load the relaxation data.
for data in self.relax_data:
Modified: 1.3/sample_scripts/full_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/full_analysis.py?rev=11382&r1=11381&r2=11382&view=diff
==============================================================================
--- 1.3/sample_scripts/full_analysis.py (original)
+++ 1.3/sample_scripts/full_analysis.py Wed Jul 28 11:38:32 2010
@@ -156,8 +156,9 @@
# The sequence data (file name, dir, mol_name_col, res_num_col,
res_name_col, spin_num_col, spin_name_col, sep). These are the arguments to
the sequence.read() user function, for more information please see the
documentation for that function.
SEQ_ARGS = ['noe.600.out', None, None, 1, 2, None, None, None]
-# The heteronucleus atom name corresponding to that of the PDB file (used if
the spin name is not in the sequence data).
+# The heteronucleus and attached proton names corresponding to those in the
PDB file (used if the spin name is not in the sequence data).
HET_NAME = 'N'
+ATTACHED_NAME = 'H'
# The relaxation data (data type, frequency label, frequency, file name,
dir, mol_name_col, res_num_col, res_name_col, spin_num_col, spin_name_col,
data_col, error_col, sep). These are the arguments to the relax_data.read()
user function, please see the documentation for that function for more
information.
RELAX_DATA = [['R1', '600', 599.719 * 1e6, 'r1.600.out', None, None, 1, 2,
None, None, 3, 4, None],
@@ -194,4 +195,4 @@
# Execution (do not change!).
-dAuvergne_protocol(diff_model=DIFF_MODEL, mf_models=MF_MODELS,
local_tm_models=LOCAL_TM_MODELS, pdb_file=PDB_FILE, seq_args=SEQ_ARGS,
het_name=HET_NAME, relax_data=RELAX_DATA, unres=UNRES, exclude=EXCLUDE,
bond_length=BOND_LENGTH, csa=CSA, hetnuc=HETNUC, proton=PROTON,
grid_inc=GRID_INC, min_algor=MIN_ALGOR, mc_num=MC_NUM, conv_loop=CONV_LOOP)
+dAuvergne_protocol(diff_model=DIFF_MODEL, mf_models=MF_MODELS,
local_tm_models=LOCAL_TM_MODELS, pdb_file=PDB_FILE, seq_args=SEQ_ARGS,
het_name=HET_NAME,attached_name=ATTACHED_NAME, relax_data=RELAX_DATA,
unres=UNRES, exclude=EXCLUDE, bond_length=BOND_LENGTH, csa=CSA,
hetnuc=HETNUC, proton=PROTON, grid_inc=GRID_INC, min_algor=MIN_ALGOR,
mc_num=MC_NUM, conv_loop=CONV_LOOP)
r11382 - in /1.3: auto_analyses/dauvergne_protocol.py sample_scripts/full_analysis.py