Author: macraild
Date: Thu Mar 16 18:10:55 2006
New Revision: 2396
URL: http://svn.gna.org/viewcvs/relax?rev=2396&view=rev
Log:
Some further fixes to the auto_select fuctionallity. Adds support for
other run types and fixes problem loading relax_fit data
Modified:
branches/auto_select/data.py
branches/auto_select/generic_fns/intensity.py
branches/auto_select/generic_fns/selection.py
branches/auto_select/generic_fns/sequence.py
branches/auto_select/specific_fns/relax_data.py
branches/auto_select/specific_fns/relax_fit.py
Modified: branches/auto_select/data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/auto_select/data.py?rev=2396&r1=2395&r2=2396&view=diff
==============================================================================
--- branches/auto_select/data.py (original)
+++ branches/auto_select/data.py Thu Mar 16 18:10:55 2006
@@ -46,7 +46,7 @@
self.diff = SpecificData()
# The residue specific data.
- self.res = Residue()
+ self.res = Residue(self)
# The name of the runs.
self.run_names = []
@@ -138,8 +138,11 @@
########################
class Residue(DictType):
- def __init__(self):
+ def __init__(self, global_data):
"""Class containing all the residue specific data."""
+
+ # Store the global data
+ self.__global_data__ = global_data
def __repr__(self):
@@ -162,12 +165,18 @@
def add_list(self, key):
"""Function for adding an empty container to the dictionary."""
- self[key] = ResidueList()
+ self[key] = ResidueList(key, self.__global_data__)
class ResidueList(ListType):
- def __init__(self):
+ def __init__(self, key, global_data):
"""Empty data container for residue specific data."""
+
+ # Store the key
+ self.__key__ = key
+
+ # Store the global data
+ self.__global_data__ = global_data
def __repr__(self):
@@ -182,35 +191,72 @@
def add_item(self):
"""Function for appending an empty container to the list."""
- self.append(ResidueElement())
+ self.append(ResidueElement(self.__key__, self.__global_data__))
class ResidueElement(object):
- def __init__(self):
+ def __init__(self, key, global_data):
"""Empty container for residue specific data for a single residue."""
- self.userSelect = 1
-
-
- def autoSelect(self):
- """Function to automatically deselect residues lacking relax_data"""
-
- if not hasattr(self, 'relax_data'):
- return 0
-
- if hasattr(self, 'params'):
- if len(self.params) < len(self.relax_data):
- return 0
-
- return 1
+ # Store the key
+ self.__key__ = key
+
+ # Store the global data
+ self.__global_data__ = global_data
+
+ self.user_select = 1
+
+
+ def auto_select(self):
+ """Function to automatically deselect residues lacking sufficient
data"""
+
+ # Get the run type
+ run_type_list = self.__global_data__.run_types
+ run_names = self.__global_data__.run_names
+ run_type = run_type_list[run_names.index(self.__key__)]
+
+ # Check for sufficient data for mf or jw run type
+ if run_type == 'mf' or run_type == 'jw':
+ if not hasattr(self, 'relax_data'):
+ return 0
+
+ # Require 3 or more data points
+ if len(self.relax_data) < 3:
+ return 0
+
+ # and require at least as many data points as params to prevent
+ # under-fitting
+ if hasattr(self, 'params'):
+ if len(self.params) < len(self.relax_data):
+ return 0
+
+ return 1
+
+ # Check for sufficient data for relax_fit run_type
+ elif run_type == 'relax_fit':
+ if not hasattr(self, 'intensities'):
+ return 0
+
+ # Require 3 or more data points
+ if len(self.intensities) < 3:
+ return 0
+ return 1
+
+ # Check for sufficient data for noe run_type
+ elif run_type == 'noe':
+ if not ( hasattr(self, 'ref') and hasattr(self, 'sat') ):
+ return 0
+
+ # All other run types
+ else:
+ return 1
def __getattr__(self, name):
"""Force on-the-fly evaluation of select every time it is
referenced"""
- # The list of data maps.
if name == 'select':
- return (self.autoSelect() and self.userSelect)
+ return (self.auto_select() and self.user_select)
raise AttributeError, name
@@ -222,7 +268,7 @@
for name in dir(self):
if match("^__", name):
continue
- if name == 'autoSelect' or name == 'userSelect':
+ if name == 'auto_select' or name == 'user_select':
continue
text = text + "%-25s%-100s\n" % (name, `getattr(self, name)`)
@@ -236,7 +282,7 @@
"""Prevent accidental rebinding of select."""
# The list of prescribed attributes.
- dontRebind = ['select', 'autoSelect']
+ dontRebind = ['select', 'auto_select']
if name in dontRebind:
# Allow initial binding of the attribute.
@@ -245,7 +291,7 @@
# But prevent rebinding.
else:
- raise AttributeError, """Can't rebind automated residue
selection. Use userSelect instead (do select.res())"""
+ raise AttributeError, """Can't rebind automated residue
selection. Use user_select instead (do select.res())"""
# Normal behaviour for attributes not in list.
self.__dict__[name] = value
Modified: branches/auto_select/generic_fns/intensity.py
URL:
http://svn.gna.org/viewcvs/relax/branches/auto_select/generic_fns/intensity.py?rev=2396&r1=2395&r2=2396&view=diff
==============================================================================
--- branches/auto_select/generic_fns/intensity.py (original)
+++ branches/auto_select/generic_fns/intensity.py Thu Mar 16 18:10:55 2006
@@ -152,8 +152,8 @@
data = self.relax.data.res[self.run][index]
# Skip unselected residues.
- if not data.select:
- continue
+ #if not data.select:
+ # continue
# Assign the data.
self.assign_func(run=self.run, i=index, intensity=intensity)
Modified: branches/auto_select/generic_fns/selection.py
URL:
http://svn.gna.org/viewcvs/relax/branches/auto_select/generic_fns/selection.py?rev=2396&r1=2395&r2=2396&view=diff
==============================================================================
--- branches/auto_select/generic_fns/selection.py (original)
+++ branches/auto_select/generic_fns/selection.py Thu Mar 16 18:10:55 2006
@@ -53,10 +53,10 @@
data = self.relax.data.res[self.run][i]
# Reverse the selection.
- if data.userSelect:
- data.userSelect = 0
+ if data.user_select:
+ data.user_select = 0
else:
- data.userSelect = 1
+ data.user_select = 1
def sel_all(self, run=None):
@@ -77,7 +77,7 @@
# Loop over the sequence and set the selection flag to 1.
for i in xrange(len(self.relax.data.res[self.run])):
- self.relax.data.res[self.run][i].userSelect = 1
+ self.relax.data.res[self.run][i].user_select = 1
def sel_read(self, run=None, file=None, dir=None, change_all=None):
@@ -118,11 +118,11 @@
# Unselect all residues.
if change_all:
- data.userSelect = 0
+ data.user_select = 0
# Select the residue if it is in the list select.
if data.num in select:
- data.userSelect = 1
+ data.user_select = 1
# Match flag.
no_match = 0
@@ -170,7 +170,7 @@
# Unselect all residues.
if change_all:
- data.userSelect = 0
+ data.user_select = 0
# Skip the residue if there is no match to 'num'.
if type(num) == int:
@@ -186,7 +186,7 @@
continue
# Select the residue.
- data.userSelect = 1
+ data.user_select = 1
# Match flag.
no_match = 0
@@ -214,7 +214,7 @@
# Loop over the sequence and set the selection flag to 0.
for i in xrange(len(self.relax.data.res[self.run])):
- self.relax.data.res[self.run][i].userSelect = 0
+ self.relax.data.res[self.run][i].user_select = 0
def unsel_read(self, run=None, file=None, dir=None, change_all=None):
@@ -255,11 +255,11 @@
# Select all residues.
if change_all:
- data.userSelect = 1
+ data.user_select = 1
# Unselect the residue if it is in the list unselect.
if data.num in unselect:
- data.userSelect = 0
+ data.user_select = 0
# Match flag.
no_match = 0
@@ -307,7 +307,7 @@
# Select all residues.
if change_all:
- data.userSelect = 1
+ data.user_select = 1
# Skip the residue if there is no match to 'num'.
if type(num) == int:
@@ -323,7 +323,7 @@
continue
# Unselect the residue.
- data.userSelect = 0
+ data.user_select = 0
# Match flag.
no_match = 0
Modified: branches/auto_select/generic_fns/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/branches/auto_select/generic_fns/sequence.py?rev=2396&r1=2395&r2=2396&view=diff
==============================================================================
--- branches/auto_select/generic_fns/sequence.py (original)
+++ branches/auto_select/generic_fns/sequence.py Thu Mar 16 18:10:55 2006
@@ -54,7 +54,7 @@
# Insert the data.
self.relax.data.res[run][index].num = res_num
self.relax.data.res[run][index].name = res_name
- self.relax.data.res[run][index].userSelect = select
+ self.relax.data.res[run][index].user_select = select
def copy(self, run1=None, run2=None):
@@ -87,7 +87,7 @@
# Insert the data.
self.relax.data.res[run2][i].num =
self.relax.data.res[run1][i].num
self.relax.data.res[run2][i].name =
self.relax.data.res[run1][i].name
- self.relax.data.res[run2][i].userSelect =
self.relax.data.res[run1][i].userSelect
+ self.relax.data.res[run2][i].user_select =
self.relax.data.res[run1][i].user_select
def data_names(self):
Modified: branches/auto_select/specific_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/auto_select/specific_fns/relax_data.py?rev=2396&r1=2395&r2=2396&view=diff
==============================================================================
--- branches/auto_select/specific_fns/relax_data.py (original)
+++ branches/auto_select/specific_fns/relax_data.py Thu Mar 16 18:10:55 2006
@@ -631,15 +631,15 @@
#################
# Loop over the sequence.
- for index in xrange(len(self.relax.data.res[self.run])):
+ #for index in xrange(len(self.relax.data.res[self.run])):
# Remap the data structure
'self.relax.data.res[self.run][index]'.
- data = self.relax.data.res[self.run][index]
+ # data = self.relax.data.res[self.run][index]
# No data loaded for this residue.
- if index not in index_list:
+ # if index not in index_list:
# If no relaxation data exists, unselect the residue.
- if not hasattr(data, 'relax_data'):
- data.select = 0
+ # if not hasattr(data, 'relax_data'):
+ # data.select = 0
def return_value(self, run, i, data_type):
Modified: branches/auto_select/specific_fns/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/auto_select/specific_fns/relax_fit.py?rev=2396&r1=2395&r2=2396&view=diff
==============================================================================
--- branches/auto_select/specific_fns/relax_fit.py (original)
+++ branches/auto_select/specific_fns/relax_fit.py Thu Mar 16 18:10:55 2006
@@ -223,8 +223,8 @@
data = self.relax.data.res[self.run][i]
# Skip unselected residues.
- if not data.select:
- continue
+ #if not data.select:
+ # continue
# Loop over the data structure names.
for name in data_names:
@@ -570,9 +570,9 @@
continue
# Skip and unselect residues which have no data.
- if not hasattr(data, 'intensities'):
- data.select = 0
- continue
+ #if not hasattr(data, 'intensities'):
+ # data.select = 0
+ # continue
# Initialise the average intensity and standard deviation
data structures.
if not hasattr(data, 'ave_intensities'):
r2396 - in /branches/auto_select: ./ generic_fns/ specific_fns/