Re: Consistency testsRe: Consistency tests|
Hi, Here is the patch for the file 'specific_fns/consistency_tests.py'. Ciao ! Sébastien Sebastien Morin wrote: Hi --
______________________________________
_______________________________________________
| |
|| Sebastien Morin ||
||| Etudiant au PhD en biochimie |||
|||| Laboratoire de resonance magnetique nucleaire ||||
||||| Dr Stephane Gagne |||||
|||| CREFSIP (Universite Laval, Quebec, CANADA) ||||
||| 1-418-656-2131 #4530 |||
|| ||
|_______________________________________________|
______________________________________
|
Index: specific_fns/consistency_tests.py
===================================================================
--- specific_fns/consistency_tests.py (revision 3324)
+++ specific_fns/consistency_tests.py (working copy)
@@ -1,6 +1,7 @@
###############################################################################
#
#
# Copyright (C) 2004-2006 Edward d'Auvergne
#
+# Copyright (C) 2007 Sebastien Morin <sebastien.morin.1 at ulaval.ca>
#
#
#
# This file is part of the program relax.
#
#
#
@@ -24,24 +25,24 @@
from string import replace
from base_class import Common_functions
-from maths_fns.jw_mapping import Mapping
+from maths_fns.consistency_tests import Consistency
-class Jw_mapping(Common_functions):
+class Consistency_tests(Common_functions):
def __init__(self, relax):
- """Class containing functions specific to reduced spectral density
mapping."""
+ """Class containing functions specific to consistency testing."""
self.relax = relax
def calculate(self, run=None, print_flag=1, sim_index=None):
- """Calculation of the spectral density values."""
+ """Calculation of the consistency functions."""
# Run argument.
self.run = run
# Test if the frequency has been set.
- if not hasattr(self.relax.data, 'jw_frq') or not
self.relax.data.jw_frq.has_key(self.run) or
type(self.relax.data.jw_frq[self.run]) != float:
+ if not hasattr(self.relax.data, 'ct_frq') or not
self.relax.data.ct_frq.has_key(self.run) or
type(self.relax.data.ct_frq[self.run]) != float:
raise RelaxError, "The frequency for the run " + `self.run` + "
has not been set up."
# Test if the nucleus type has been set.
@@ -52,7 +53,7 @@
if not self.relax.data.res.has_key(self.run):
raise RelaxNoSequenceError, self.run
- # Test if the CSA and bond length values have been set.
+ # Test if the CSA, bond length, angle Theta and correlation time
values have been set.
for i in xrange(len(self.relax.data.res[self.run])):
# Skip unselected residues.
if not self.relax.data.res[self.run][i].select:
@@ -66,11 +67,19 @@
if not hasattr(self.relax.data.res[self.run][i], 'r') or
self.relax.data.res[self.run][i].r == None:
raise RelaxNoValueError, "bond length"
+ # Angle Theta
+ if not hasattr(self.relax.data.res[self.run][i], 'orientation')
or self.relax.data.res[self.run][i].orientation == None:
+ raise RelaxNoValueError, "angle Theta"
+
+ # Correlation time
+ if not hasattr(self.relax.data.res[self.run][i], 'tc') or
self.relax.data.res[self.run][i].tc == None:
+ raise RelaxNoValueError, "correlation time"
+
# Frequency index.
- if self.relax.data.jw_frq[self.run] not in
self.relax.data.frq[self.run]:
- raise RelaxError, "No relaxation data corresponding to the
frequency " + `self.relax.data.jw_frq[self.run]` + " has been loaded."
+ if self.relax.data.ct_frq[self.run] not in
self.relax.data.frq[self.run]:
+ raise RelaxError, "No relaxation data corresponding to the
frequency " + `self.relax.data.ct_frq[self.run]` + " has been loaded."
- # Reduced spectral density mapping.
+ # Consistency testing.
for i in xrange(len(self.relax.data.res[self.run])):
# Reassign data structure.
data = self.relax.data.res[self.run][i]
@@ -82,7 +91,7 @@
# Residue specific frequency index.
frq_index = None
for j in xrange(data.num_frq):
- if data.frq[j] == self.relax.data.jw_frq[self.run]:
+ if data.frq[j] == self.relax.data.ct_frq[self.run]:
frq_index = j
if frq_index == None:
continue
@@ -120,30 +129,30 @@
continue
# Initialise the function to calculate.
- self.jw = Mapping(frq=self.relax.data.jw_frq[self.run],
gx=self.relax.data.gx, gh=self.relax.data.gh, mu0=self.relax.data.mu0,
h_bar=self.relax.data.h_bar)
+ self.ct = Consistency(frq=self.relax.data.ct_frq[self.run],
gx=self.relax.data.gx, gh=self.relax.data.gh, mu0=self.relax.data.mu0,
h_bar=self.relax.data.h_bar)
- # Calculate the spectral density values.
- j0, jwx, jwh = self.jw.func(r=data.r, csa=data.csa, r1=r1,
r2=r2, noe=noe)
+ # Calculate the consistency functions.
+ j0, f_eta, f_r2 = self.ct.func(orientation=data.orientation,
tc=data.tc, r=data.r, csa=data.csa, r1=r1, r2=r2, noe=noe)
- # Reduced spectral density values.
+ # Consistency testing values.
if sim_index == None:
data.j0 = j0
- data.jwx = jwx
- data.jwh = jwh
+ data.f_eta = f_eta
+ data.f_r2 = f_r2
- # Monte Carlo simulated reduced spectral density values.
+ # Monte Carlo simulated consistency testing values.
else:
# Initialise the simulation data structures.
self.data_init(data, sim=1)
if data.j0_sim == None:
data.j0_sim = []
- data.jwx_sim = []
- data.jwh_sim = []
+ data.f_eta_sim = []
+ data.f_r2_sim = []
# Reduced spectral density values.
data.j0_sim.append(j0)
- data.jwx_sim.append(jwx)
- data.jwh_sim.append(jwh)
+ data.f_eta_sim.append(f_eta)
+ data.f_r2_sim.append(f_r2)
def data_init(self, data, sim=0):
@@ -175,11 +184,16 @@
csa: CSA value.
+ orientation: Angle between the 15N-1H vector and the principal axis
of the 15N chemical
+ shift tensor.
+
+ tc: Correlation time.
+
j0: Spectral density value at 0 MHz.
- jwx: Spectral density value at the frequency of the heteronucleus.
+ f_eta: Eta test.
- jwh: Spectral density value at the frequency of the heteronucleus.
+ f_r2: R2 test.
"""
# Initialise.
@@ -188,11 +202,13 @@
# Values.
names.append('r')
names.append('csa')
+ names.append('orientation')
+ names.append('tc')
- # Spectral density values.
+ # Consistency functions values.
names.append('j0')
- names.append('jwx')
- names.append('jwh')
+ names.append('f_eta')
+ names.append('f_r2')
return names
@@ -203,14 +219,18 @@
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
_______________________________________________________________________________________
- | | |
|
- | Data type | Object name | Value
|
-
|_______________________________________|______________|______________________________|
- | | |
|
- | Bond length | 'r' | 1.02 *
1e-10 |
- | | |
|
- | CSA | 'csa' | -170 * 1e-6
|
-
|_______________________________________|______________|______________________________|
+ | | |
|
+ | Data type | Object name | Value
|
+
|_______________________________________|_______________|_____________________________|
+ | | |
|
+ | Bond length | 'r' | 1.02 *
1e-10 |
+ | | |
|
+ | CSA | 'csa' | -170 *
1e-6 |
+ | | |
|
+ | Angle Theta | 'orientation' | 15.7
|
+ | | |
|
+ | Correlation time | 'tc' | 13 * 1e-9
|
+
|_______________________________________|_______________|_____________________________|
"""
@@ -222,7 +242,15 @@
if param == 'CSA':
return -170 * 1e-6
+ # Angle Theta
+ if param == 'orientation':
+ return 15.7
+ # Correlation time
+ if param == 'tc':
+ return 13 * 1e-9
+
+
def num_instances(self, run=None):
"""Function for returning the number of instances."""
@@ -246,7 +274,7 @@
# Loop over residue data:
for residue in self.relax.data.res[run]:
-
+
# Check for sufficient data
if not hasattr(residue, 'relax_data'):
residue.select = 0
@@ -266,24 +294,28 @@
def return_data_name(self, name):
"""
- Reduced spectral density mapping data type string matching patterns
+ Consistency testing data type string matching patterns
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
____________________________________________________________________________________________
- | | |
|
- | Data type | Object name | Patterns
|
-
|________________________|______________|__________________________________________________|
- | | |
|
- | J(0) | 'j0' | '^[Jj]0$' or '[Jj]\(0\)'
|
- | | |
|
- | J(wX) | 'jwx' | '^[Jj]w[Xx]$' or
'[Jj]\(w[Xx]\)' |
- | | |
|
- | J(wH) | 'jwh' | '^[Jj]w[Hh]$' or
'[Jj]\(w[Hh]\)' |
- | | |
|
- | Bond length | 'r' | '^r$' or '[Bb]ond[
-_][Ll]ength' |
- | | |
|
- | CSA | 'csa' | '^[Cc][Ss][Aa]$'
|
-
|________________________|______________|__________________________________________________|
+ | | |
|
+ | Data type | Object name | Patterns
|
+
|_______________________|_______________|__________________________________________________|
+ | | |
|
+ | J(0) | 'j0' | '^[Jj]0$' or '[Jj]\(0\)'
|
+ | | |
|
+ | F_eta | 'f_eta' | '^[Ff]_[Ee][Tt][Aa]$'
|
+ | | |
|
+ | F_R2 | 'f_r2' | '^[Ff]_[Rr]2$'
|
+ | | |
|
+ | Bond length | 'r' | '^r$' or '[Bb]ond[
-_][Ll]ength' |
+ | | |
|
+ | CSA | 'csa' | '^[Cc][Ss][Aa]$'
|
+ | | |
|
+ | Angle Theta | 'orientation' |
'^[Oo][Rr][Ii][Ee][Nn][Tt][Aa][Tt][Ii][Oo][Nn]$' |
+ | | |
|
+ | Correlation time | 'tc' | '^[Tt]c$'
|
+
|_______________________|_______________|__________________________________________________|
"""
@@ -292,12 +324,12 @@
return 'j0'
# J(wX).
- if search('^[Jj]w[Xx]$', name) or search('[Jj]\(w[Xx]\)', name):
- return 'jwx'
+ if search('^[Ff]_[Ee][Tt][Aa]$', name):
+ return 'f_eta'
# J(wH).
- if search('^[Jj]w[Hh]$', name) or search('[Jj]\(w[Hh]\)', name):
- return 'jwh'
+ if search('^^[Ff]_[Rr]2$', name):
+ return 'f_r2'
# Bond length.
if search('^r$', name) or search('[Bb]ond[ -_][Ll]ength', name):
@@ -307,7 +339,15 @@
if search('^[Cc][Ss][Aa]$', name):
return 'csa'
+ # Angle Theta
+ if search('^[Oo][Rr][Ii][Ee][Nn][Tt][Aa][Tt][Ii][Oo][Nn]$', name):
+ return 'orientation'
+ # Correlation time
+ if search('^[Tt]c$', name):
+ return 'tc'
+
+
def return_grace_string(self, data_type):
"""Function for returning the Grace string representing the data
type for axis labelling."""
@@ -319,12 +359,12 @@
return '\\qJ(0)\\Q'
# J(wX).
- elif object_name == 'jwx':
- return '\\qJ(\\xw\\f{}\\sX\\N)\\Q'
+ elif object_name == 'f_eta':
+ return '\\qF\\s\\xh\\Q'
# J(wH).
- elif object_name == 'jwh':
- return '\\qJ(\\xw\\f{}\\sH\\N)\\Q'
+ elif object_name == 'f_r2':
+ return '\\qF\\sR2\\Q'
# Bond length.
elif object_name == 'r':
@@ -334,7 +374,15 @@
elif object_name == 'csa':
return '\\qCSA\\Q'
+ # Angle Theta
+ elif object_name == 'orientation':
+ return '\\q\\xq\\Q'
+ # Correlation time
+ elif object_name == 'tc':
+ return '\\q\\xt\\f{}c\\Q'
+
+
def return_units(self, data_type):
"""Function for returning a string representing the parameters units.
@@ -354,14 +402,23 @@
elif object_name == 'csa':
return 'ppm'
+ # Angle Theta
+ elif object_name == 'orientation':
+ return 'degrees'
+ # Correlation time
+ elif object_name == 'tc':
+ return 'ns'
+
+
def set(self, run=None, value=None, error=None, param=None, index=None):
"""
- Reduced spectral density mapping set details
+ Consistency testing set details
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- In reduced spectral density mapping, only two values can be set, the
bond length and CSA
- value. These must be set prior to the calculation of spectral
density values.
+ In consistency testing, only four values can be set, the bond
length, CSA, angle
+ Theta and correlation time values. These must be set prior to the
calculation
+ of consistency functions.
"""
@@ -374,26 +431,30 @@
if param == None:
# The values are supplied by the user:
if value:
- # Test if the length of the value array is equal to 2.
- if len(value) != 2:
- raise RelaxError, "The length of " + `len(value)` + " of
the value array must be equal to two."
+ # Test if the length of the value array is equal to 4.
+ if len(value) != 4:
+ raise RelaxError, "The length of " + `len(value)` + " of
the value array must be equal to four."
# Default values.
else:
# Set 'value' to an empty array.
value = []
- # CSA and Bond length.
+ # CSA, Bond length Angle Theta and Correlation time.
value.append(self.default_value('csa'))
value.append(self.default_value('r'))
+ value.append(self.default_value('orientation'))
+ value.append(self.default_value('tc'))
# Initilise data.
if not hasattr(self.relax.data.res[self.run][index], 'csa') or
not hasattr(self.relax.data.res[self.run][index], 'csa'):
self.data_init(self.relax.data.res[self.run][index])
- # CSA and Bond length.
+ # CSA, bond length, angle Theta and correlation time.
setattr(self.relax.data.res[self.run][index], 'csa',
float(value[0]))
setattr(self.relax.data.res[self.run][index], 'r',
float(value[1]))
+ setattr(self.relax.data.res[self.run][index], 'orientation',
float(value[2]))
+ setattr(self.relax.data.res[self.run][index], 'tc',
float(value[3]))
# Individual data type.
@@ -403,7 +464,7 @@
# Get the object.
object_name = self.return_data_name(param)
if not object_name:
- raise RelaxError, "The reduced spectral density mapping data
type " + `param` + " does not exist."
+ raise RelaxError, "The consistency tests data type " +
`param` + " does not exist."
# Initialise all data if it doesn't exist.
if not hasattr(self.relax.data.res[self.run][index],
object_name):
@@ -422,7 +483,7 @@
def set_frq(self, run=None, frq=None):
- """Function for selecting which relaxation data to use in the J(w)
mapping."""
+ """Function for selecting which relaxation data to use in the
consistency tests."""
# Run argument.
self.run = run
@@ -431,21 +492,21 @@
if not self.run in self.relax.data.run_names:
raise RelaxNoRunError, self.run
- # Test if the run type is set to 'jw'.
+ # Test if the run type is set to 'ct'.
function_type =
self.relax.data.run_types[self.relax.data.run_names.index(self.run)]
- if function_type != 'jw':
+ if function_type != 'ct':
raise RelaxFuncSetupError,
self.relax.specific_setup.get_string(function_type)
# Test if the frequency has been set.
- if hasattr(self.relax.data, 'jw_frq') and
self.relax.data.jw_frq.has_key(self.run):
+ if hasattr(self.relax.data, 'ct_frq') and
self.relax.data.ct_frq.has_key(self.run):
raise RelaxError, "The frequency for the run " + `self.run` + "
has already been set."
# Create the data structure if it doesn't exist.
- if not hasattr(self.relax.data, 'jw_frq'):
- self.relax.data.jw_frq = {}
+ if not hasattr(self.relax.data, 'ct_frq'):
+ self.relax.data.ct_frq = {}
# Set the frequency.
- self.relax.data.jw_frq[self.run] = frq
+ self.relax.data.ct_frq[self.run] = frq
def set_error(self, run, instance, index, error):
@@ -458,13 +519,13 @@
if index == 0:
self.relax.data.res[self.run][instance].j0_err = error
- # Return J(wX) sim data.
+ # Return F_eta sim data.
if index == 1:
- self.relax.data.res[self.run][instance].jwx_err = error
+ self.relax.data.res[self.run][instance].f_eta_err = error
- # Return J(wH) sim data.
+ # Return F_R2 sim data.
if index == 2:
- self.relax.data.res[self.run][instance].jwh_err = error
+ self.relax.data.res[self.run][instance].f_r2_err = error
def sim_return_param(self, run, instance, index):
@@ -481,13 +542,13 @@
if index == 0:
return self.relax.data.res[self.run][instance].j0_sim
- # Return J(wX) sim data.
+ # Return F_eta sim data.
if index == 1:
- return self.relax.data.res[self.run][instance].jwx_sim
+ return self.relax.data.res[self.run][instance].f_eta_sim
- # Return J(wH) sim data.
+ # Return F_R2 sim data.
if index == 2:
- return self.relax.data.res[self.run][instance].jwh_sim
+ return self.relax.data.res[self.run][instance].f_r2_sim
def sim_return_selected(self, run, instance):
@@ -521,7 +582,7 @@
self.relax.data.res[run][i].relax_sim_data = sim_data
- def write_columnar_line(self, file=None, num=None, name=None,
select=None, data_set=None, nucleus=None, wH=None, j0=None, jwx=None,
jwh=None, r=None, csa=None, ri_labels=None, remap_table=None,
frq_labels=None, frq=None, ri=None, ri_error=None):
+ def write_columnar_line(self, file=None, num=None, name=None,
select=None, data_set=None, nucleus=None, wH=None, j0=None, f_eta=None,
f_r2=None, r=None, csa=None, ri_labels=None, remap_table=None,
frq_labels=None, frq=None, ri=None, ri_error=None):
"""Function for printing a single line of the columnar formatted
results."""
# Residue number and name.
@@ -538,8 +599,8 @@
# Parameters.
file.write("%-25s " % j0)
- file.write("%-25s " % jwx)
- file.write("%-25s " % jwh)
+ file.write("%-25s " % f_eta)
+ file.write("%-25s " % f_r2)
file.write("%-25s " % r)
file.write("%-25s " % csa)
@@ -597,7 +658,7 @@
ri_error.append('Ri_error_(' +
self.relax.data.ri_labels[self.run][i] + "_" +
self.relax.data.frq_labels[self.run][self.relax.data.remap_table[self.run][i]]
+ ")")
# Write the header line.
- self.write_columnar_line(file=file, num='Num', name='Name',
select='Selected', data_set='Data_set', nucleus='Nucleus',
wH='Proton_frq_(MHz)', j0='J(0)', jwx='J(wX)', jwh='J(wH)',
r='Bond_length_(A)', csa='CSA_(ppm)', ri_labels='Ri_labels',
remap_table='Remap_table', frq_labels='Frq_labels', frq='Frequencies', ri=ri,
ri_error=ri_error)
+ self.write_columnar_line(file=file, num='Num', name='Name',
select='Selected', data_set='Data_set', nucleus='Nucleus',
wH='Proton_frq_(MHz)', j0='J(0)', f_eta='F_eta', f_r2='F_R2',
r='Bond_length_(A)', csa='CSA_(ppm)', ri_labels='Ri_labels',
remap_table='Remap_table', frq_labels='Frq_labels', frq='Frequencies', ri=ri,
ri_error=ri_error)
# Values.
@@ -607,7 +668,7 @@
nucleus = self.relax.generic.nuclei.find_nucleus()
# The proton frequency in MHz.
- wH = self.relax.data.jw_frq[self.run] / 1e6
+ wH = self.relax.data.ct_frq[self.run] / 1e6
# Relaxation data setup.
try:
@@ -631,15 +692,15 @@
if hasattr(data, 'j0'):
j0 = data.j0
- # J(wX).
- jwx = None
- if hasattr(data, 'jwx'):
- jwx = data.jwx
+ # F_eta.
+ f_eta = None
+ if hasattr(data, 'f_eta'):
+ f_eta = data.f_eta
- # J(wH).
- jwh = None
- if hasattr(data, 'jwh'):
- jwh = data.jwh
+ # F_R2.
+ f_r2 = None
+ if hasattr(data, 'f_r2'):
+ f_r2 = data.f_r2
# Bond length.
r = None
@@ -671,7 +732,7 @@
ri_error.append(None)
# Write the line.
- self.write_columnar_line(file=file, num=data.num,
name=data.name, select=data.select, data_set='value', nucleus=nucleus,
wH=`wH`, j0=`j0`, jwx=`jwx`, jwh=`jwh`, r=`r`, csa=`csa`,
ri_labels=ri_labels, remap_table=remap_table, frq_labels=frq_labels, frq=frq,
ri=ri, ri_error=ri_error)
+ self.write_columnar_line(file=file, num=data.num,
name=data.name, select=data.select, data_set='value', nucleus=nucleus,
wH=`wH`, j0=`j0`, f_eta=`f_eta`, f_r2=`f_r2`, r=`r`, csa=`csa`,
ri_labels=ri_labels, remap_table=remap_table, frq_labels=frq_labels, frq=frq,
ri=ri, ri_error=ri_error)
# Errors.
@@ -693,15 +754,15 @@
if hasattr(data, 'j0_err'):
j0 = data.j0_err
- # J(wX).
- jwx = None
- if hasattr(data, 'jwx_err'):
- jwx = data.jwx_err
+ # F_eta.
+ f_eta = None
+ if hasattr(data, 'f_eta_err'):
+ f_eta = data.f_eta_err
- # J(wH).
- jwh = None
- if hasattr(data, 'jwh_err'):
- jwh = data.jwh_err
+ # F_R2.
+ f_r2 = None
+ if hasattr(data, 'f_r2_err'):
+ f_r2 = data.f_r2_err
# Bond length.
r = None
@@ -721,7 +782,7 @@
ri_error.append(None)
# Write the line.
- self.write_columnar_line(file=file, num=data.num,
name=data.name, select=data.select, data_set='error', nucleus=nucleus,
wH=`wH`, j0=`j0`, jwx=`jwx`, jwh=`jwh`, r=`r`, csa=`csa`,
ri_labels=ri_labels, remap_table=remap_table, frq_labels=frq_labels, frq=frq,
ri=ri, ri_error=ri_error)
+ self.write_columnar_line(file=file, num=data.num,
name=data.name, select=data.select, data_set='error', nucleus=nucleus,
wH=`wH`, j0=`j0`, f_eta=`f_eta`, f_r2=`f_r2`, r=`r`, csa=`csa`,
ri_labels=ri_labels, remap_table=remap_table, frq_labels=frq_labels, frq=frq,
ri=ri, ri_error=ri_error)
# Simulation values.
@@ -739,15 +800,15 @@
if hasattr(data, 'j0_sim'):
j0 = data.j0_sim[i]
- # J(wX).
- jwx = None
- if hasattr(data, 'jwx_sim'):
- jwx = data.jwx_sim[i]
+ # F_eta.
+ f_eta = None
+ if hasattr(data, 'f_eta_sim'):
+ f_eta = data.f_eta_sim[i]
- # J(wH).
- jwh = None
- if hasattr(data, 'jwh_sim'):
- jwh = data.jwh_sim[i]
+ # F_R2.
+ f_r2 = None
+ if hasattr(data, 'f_r2_sim'):
+ f_r2 = data.f_r2_sim[i]
# Bond length.
r = None
@@ -778,4 +839,4 @@
ri_error.append(None)
# Write the line.
- self.write_columnar_line(file=file, num=data.num,
name=data.name, select=data.select, data_set='sim_'+`i`, nucleus=nucleus,
wH=`wH`, j0=`j0`, jwx=`jwx`, jwh=`jwh`, r=`r`, csa=`csa`,
ri_labels=ri_labels, remap_table=remap_table, frq_labels=frq_labels, frq=frq,
ri=ri, ri_error=ri_error)
+ self.write_columnar_line(file=file, num=data.num,
name=data.name, select=data.select, data_set='sim_'+`i`, nucleus=nucleus,
wH=`wH`, j0=`j0`, f_eta=`f_eta`, f_r2=`f_r2`, r=`r`, csa=`csa`,
ri_labels=ri_labels, remap_table=remap_table, frq_labels=frq_labels, frq=frq,
ri=ri, ri_error=ri_error)