def lowess2(x, y, xest, f=2./3., iter=3):
"""Returns estimated values of y in data points xest (or None if estimation fails).
Lowess smoother: Robust locally weighted regression.
The lowess function fits a nonparametric regression curve to a scatterplot.
The arrays x and y contain an equal number of elements; each pair
(x[i], y[i]) defines a data point in the scatterplot. The function returns
the estimated (smooth) values of y.
The smoothing span is given by f. A larger value for f will result in a
smoother curve. The number of robustifying iterations is given by iter. The
function will run faster with a smaller number of iterations."""
x = Numeric.asarray(x, 'd')
y = Numeric.asarray(y, 'd')
xest = Numeric.asarray(xest, 'd')
n = len(x)
nest = len(xest)
r = min(int(Numeric.ceil(f*n)),n-1) # radius: num. of points to take into LR
h = [Numeric.sort(abs(x-x[i]))[r] for i in range(n)] # distance of the r-th point from x[i]
w = Numeric.clip(abs(([x]-Numeric.transpose([x]))/h),0.0,1.0)
w = 1-w*w*w
w = w*w*w
hest = [Numeric.sort(abs(x-xest[i]))[r] for i in range(nest)] # r-th min. distance from xest[i] to x
west = Numeric.clip(abs(([xest]-Numeric.transpose([x]))/hest),0.0,1.0) # shape: (len(x), len(xest)
west = 1-west*west*west
west = west*west*west
yest = Numeric.zeros(n,'d')
yest2 = Numeric.zeros(nest,'d')
delta = Numeric.ones(n,'d')
try:
for iteration in range(iter):
# fit xest
for i in range(nest):
weights = delta * west[:,i]
b = Numeric.array([sum(weights*y), sum(weights*y*x)])
A = Numeric.array([[sum(weights), sum(weights*x)], [sum(weights*x), sum(weights*x*x)]])
beta = LinearAlgebra.solve_linear_equations(A,b)
yest2[i] = beta[0] + beta[1]*xest[i]
# fit x (to calculate residuals and delta)
for i in range(n):
weights = delta * w[:,i]
b = Numeric.array([sum(weights*y), sum(weights*y*x)])
A = Numeric.array([[sum(weights), sum(weights*x)], [sum(weights*x), sum(weights*x*x)]])
beta = LinearAlgebra.solve_linear_equations(A,b)
yest[i] = beta[0] + beta[1]*x[i]
residuals = y-yest
s = MLab.median(abs(residuals))
delta = Numeric.clip(residuals/(6*s),-1,1)
delta = 1-delta*delta
delta = delta*delta
except LinearAlgebra.LinAlgError:
print "Warning: NumExtn.lowess2: LinearAlgebra.solve_linear_equations: Singular matrix"
yest2 = None
return yest2
def logConfidence(x, R, clip=0):
"""
Estimate the probability of x NOT beeing a random observation from a
lognormal distribution that is described by a set of random values.
@param x: observed value
@type x: float
@param R: sample of random values
@type R: [float]
@param clip: clip zeros at this value 0->don't clip (default: 0)
@type clip: float
@return: confidence that x is not random, median of random distr.
@rtype: (float, float)
"""
if clip and 0 in R:
R = N.clip(R, clip, max(R))
if clip and x == 0:
x = clip
## remove 0 instead of clipping
R = N.compress(R, R)
if x == 0:
return 0, 0
## get mean and stdv of log-transformed random sample
alpha = N.average(N.log(R))
n = len(R)
beta = N.sqrt(N.sum(N.power(N.log(R) - alpha, 2)) / (n - 1.))
return logArea(x, alpha, beta), logMedian(alpha)
def logConfidence( x, R, clip=0 ):
"""
Estimate the probability of x NOT beeing a random observation from a
lognormal distribution that is described by a set of random values.
@param x: observed value
@type x: float
@param R: sample of random values
@type R: [float]
@param clip: clip zeros at this value 0->don't clip (default: 0)
@type clip: float
@return: confidence that x is not random, median of random distr.
@rtype: (float, float)
"""
if clip and 0 in R:
R = N.clip( R, clip, max( R ) )
if clip and x == 0:
x = clip
## remove 0 instead of clipping
R = N.compress( R, R )
if x == 0:
return 0, 0
## get mean and stdv of log-transformed random sample
alpha = N.average( N.log( R ) )
n = len( R )
beta = N.sqrt(N.sum(N.power(N.log( R ) - alpha, 2)) / (n - 1.))
return logArea( x, alpha, beta ), logMedian( alpha )
def test_model(self):
"""PDBDope test final model"""
from Biskit import PDBModel
if self.local:
print '\nData added to info record of model (key -- value):'
for k in self.d.m.info.keys():
print '%s -- %s'%(k, self.d.m.info[k])
print '\nAdded atom profiles:'
print self.M.atoms
print '\nAdded residue profiles:'
print self.M.residues
## check that nothing has changed
print '\nChecking that models are unchanged by doping ...'
m_ref = PDBModel( self.f )
m_ref = m_ref.compress( m_ref.maskProtein() )
for k in m_ref.atoms.keys():
#ref = [ m_ref.atoms[i][k] for i in m_ref.atomRange() ]
#mod = [ self.M.atoms[i][k] for i in self.M.atomRange() ]
self.assert_( N.all( m_ref[k] == self.M[k]) )
## display in Pymol
if self.local:
print "Starting PyMol..."
from Biskit.Pymoler import Pymoler
pm = Pymoler()
pm.addPdb( self.M, 'm' )
pm.colorAtoms( 'm', N.clip(self.M.profile('relAS'), 0.0, 100.0) )
pm.show()
def linearMap(self, data, data_min, data_max, val_min, val_max,
arr_min, arr_max, datatype):
k2,c2 = self.ScaleMap((val_min, val_max), (data_min, data_max))
if k2 == 1 and c2 == 0:
return data
new_arr = Numeric.clip(k2*data+c2, k2*data_min+c2, k2*data_max+c2)
#return new_arr.astype(data.dtype.char)
return new_arr.astype(datatype)
def UpdateX(x, deltaX, lowBound=None, highBound=None):
x = x + deltaX
if lowBound != None and highBound != None:
x = clip(x, lowBound, highBound)
elif lowBound != None:
x = Numeric.maximum(x, lowBound)
elif highBound != None:
x = Numeric.minimum(x, highBound)
return x
def fractionNativeSurface(self, cont, contRef ):
"""
fraction of atoms/residues that are involved in B{any} contacts
in both complexes.
@param cont: contact matrix
@type cont: matrix
@param contRef: reference contact matrix
@type contRef: matrix
@return: (fractRec, fractLig), fraction of atoms/residues that
are involved in any contacts in both complexes
@rtype: (float, float)
"""
lig, ligRef = N.clip( N.sum(cont),0,1), N.clip( N.sum(contRef), 0,1)
rec = N.clip( N.sum(cont, 1),0,1)
recRef = N.clip( N.sum(contRef, 1), 0,1)
fLig = N.sum( N.logical_and( lig, ligRef )) *1./ N.sum( ligRef )
fRec = N.sum( N.logical_and( rec, recRef )) *1./ N.sum( recRef )
return (fRec, fLig)
def test_conservation(self):
"""PDBDope.addConservation (Hmmer) test"""
if self.local: print "Adding conservation data...",
self.d.addConservation()
if self.local: print 'Done.'
## display in Pymol
if self.local:
print "Starting PyMol..."
from Biskit.Pymoler import Pymoler
pm = Pymoler()
pm.addPdb( self.M, 'm' )
pm.colorAtoms( 'm', N.clip(self.M.profile('cons_ent'), 0.0, 100.0) )
pm.show()
def relExposure( model, absSurf, key='AS', clip=1 ):
"""
Calculate how exposed an atom is relative to the same
atom in a GLY-XXX-GLY tripeptide, an approximation of
the unfolded state.
@param absSurf: Absolute MS OR AS values
@type absSurf: [float]
@param key: MS or AS
@type key: MS|AS
@param clip: clip values above 100% (default: 1)
@type clip: 1|0
@return: rel - list of relative accessible surfaces
@rtype: [float]
"""
if not key=='MS' and not key=='AS':
raise Exception,\
'Incorrect key for relative exposiure: %s '%key
rel = []
i=0
## loop over chains
for j in range( model.lenChains()):
c = model.takeChains([j])
k=0
cIdx = c.resIndex()
## and loop over atoms in chain
for a in c.atoms.iterDicts():
## N-terminal residue
if k < cIdx[1]:
rel = __Nter( a, rel, absSurf, key, i )
## C-terminal residue
if k >= cIdx[-1]:
rel = __Cter( a, rel, absSurf, key, i )
## everything but N- and C termini
if not k < cIdx[1] and not k >= cIdx[-1]:
rel = __bulk( a, rel, absSurf, key, i )
i+=1
k+=1
if clip:
return Numeric.clip( Numeric.array(rel), 0.0, 100.0 )
else:
return Numeric.array(rel)
def relExposure(model, absSurf, key='AS', clip=1):
"""
Calculate how exposed an atom is relative to the same
atom in a GLY-XXX-GLY tripeptide, an approximation of
the unfolded state.
@param absSurf: Absolute MS OR AS values
@type absSurf: [float]
@param key: MS or AS
@type key: MS|AS
@param clip: clip values above 100% (default: 1)
@type clip: 1|0
@return: rel - list of relative accessible surfaces
@rtype: [float]
"""
if not key == 'MS' and not key == 'AS':
raise Exception,\
'Incorrect key for relative exposiure: %s '%key
rel = []
i = 0
## loop over chains
for j in range(model.lenChains()):
c = model.takeChains([j])
k = 0
cIdx = c.resIndex()
## and loop over atoms in chain
for a in c.atoms.iterDicts():
## N-terminal residue
if k < cIdx[1]:
rel = __Nter(a, rel, absSurf, key, i)
## C-terminal residue
if k >= cIdx[-1]:
rel = __Cter(a, rel, absSurf, key, i)
## everything but N- and C termini
if not k < cIdx[1] and not k >= cIdx[-1]:
rel = __bulk(a, rel, absSurf, key, i)
i += 1
k += 1
if clip:
return Numeric.clip(Numeric.array(rel), 0.0, 100.0)
else:
return Numeric.array(rel)
def entropy( self, emmProb, nullProb ):
"""
calculate entropy for normalized probabilities scaled by aa freq.
emmProb & nullProb is shape 1,len(alphabet)
@param emmProb: emmission probabilities
@type emmProb: array
@param nullProb: null probabilities
@type nullProb: array
@return: entropy value
@rtype: float
"""
## remove zeros to avoid log error
emmProb = N.clip(emmProb, 1.e-10, 1.)
return N.sum( emmProb * N.log(emmProb/nullProb) )
def logConfidence( x, R, clip=1e-32 ):
"""
Estimate the probability of x NOT beeing a random observation from a
lognormal distribution that is described by a set of random values.
The exact solution to this problem is in L{Biskit.Statistics.lognormal}.
@param x: observed value
@type x: float
@param R: sample of random values; 0 -> don't clip (default: 1e-32)
@type R: [float]
@param clip: clip zeros at this value
@type clip: float
@return: confidence that x is not random, mean of random distrib.
@rtype: (float, float)
"""
if clip and 0 in R:
R = N.clip( R, clip, max( R ) )
## get mean and stdv of log-transformed random sample
mean = N.average( N.log( R ) )
n = len( R )
stdv = N.sqrt(N.sum(N.power(N.log( R ) - mean, 2)) / (n - 1.))
## create dense lognormal distribution representing the random sample
stop = max( R ) * 50.0
step = stop / 100000
start = step / 10.0
X = [(v, p_lognormal(v, mean, stdv) ) for v in N.arange(start, stop, step)]
## analyse distribution
d = Density( X )
return d.findConfidenceInterval( x * 1.0 )[0], d.average()
def logConfidence(x, R, clip=1e-32):
"""
Estimate the probability of x NOT beeing a random observation from a
lognormal distribution that is described by a set of random values.
The exact solution to this problem is in L{Biskit.Statistics.lognormal}.
@param x: observed value
@type x: float
@param R: sample of random values; 0 -> don't clip (default: 1e-32)
@type R: [float]
@param clip: clip zeros at this value
@type clip: float
@return: confidence that x is not random, mean of random distrib.
@rtype: (float, float)
"""
if clip and 0 in R:
R = N.clip(R, clip, max(R))
## get mean and stdv of log-transformed random sample
mean = N.average(N.log(R))
n = len(R)
stdv = N.sqrt(N.sum(N.power(N.log(R) - mean, 2)) / (n - 1.))
## create dense lognormal distribution representing the random sample
stop = max(R) * 50.0
step = stop / 100000
start = step / 10.0
X = [(v, p_lognormal(v, mean, stdv)) for v in N.arange(start, stop, step)]
## analyse distribution
d = Density(X)
return d.findConfidenceInterval(x * 1.0)[0], d.average()
pardict["Zeropoint"] = str(zpoint)
pardict["Zeropoint_Error"] = zpoint_err
self.logfile.write("Photometric ZeroPoint of " +
os.path.basename(fitsfile) + ": " + str(zpoint))
#---------------- Temporary zero point correction --------------------#
## Commented 24-Sep-2002 as per Bugzilla bug #1800
##
## zpointCor=fUtil.zeroPointCorrection(imfilter)
## zpoint+= zpointCor
## self.logfile.write("ZeroPoint %s corrected by %.2f mag" % (imfilter,zpointCor))
## print "ZeroPoint %s corrected by %.2f mag" % (imfilter,zpointCor)
##
#---------------- End temporary zero point correction ----------------#
flux[i, :] = Numeric.clip(flux[i, :], 1e-100, 1e100)
m[i, :] = Numeric.where(
detected, -2.5 * Numeric.log10(abs(flux[i, :])) + zpoint,
m[i, :])
m[i, :] = Numeric.where(nondetected, 99.0, m[i, :])
m[i, :] = Numeric.where(nonobserved, -99.0, m[i, :])
# the filter specific extinction correction is applied.
m_corr[i, :] = Numeric.where(nondetected, 99.0,
m[i, :] - filterXCorr)
m_corr[i, :] = Numeric.where(nonobserved, -99, m_corr[i, :])
m_bpz[i, :] = Numeric.where(nondetected, 99.0,
m_corr[i, :] + ap_corr[i, :])
m_bpz[i, :] = Numeric.where(nonobserved, -99, m_bpz[i, :])
# clip values from being too small or large, i.e. 0 or inf.
def lowessW(x, y, xest, f=2./3., iter=3, dWeights=None, callback=None):
"""Returns estimated values of y in data points xest (or None if estimation fails).
Lowess smoother: Robust locally weighted regression.
The lowess function fits a nonparametric regression curve to a scatterplot.
The arrays x and y contain an equal number of elements; each pair
(x[i], y[i]) defines a data point in the scatterplot. The function returns
the estimated (smooth) values of y.
The smoothing span is given by f. A larger value for f will result in a
smoother curve. The number of robustifying iterations is given by iter. The
function will run faster with a smaller number of iterations.
Data points may be assigned weights; if None, all weights equal 1.
"""
x = Numeric.asarray(x, 'd')
y = Numeric.asarray(y, 'd')
xest = Numeric.asarray(xest, 'd')
n = len(x)
if n <> len(y):
raise AttributeError, "Error: lowessW(x,y,xest,f,iter,dWeights): len(x)=%i not equal to len(y)=%i" % (len(x), len(y))
nest = len(xest)
# weights of data points (optional)
if dWeights <> None:
dWeights = Numeric.asarray(dWeights, 'd')
if len(dWeights) <> n:
raise AttributeError, "Error: lowessW(x,y,xest,f,iter,dWeights): len(dWeights)=%i not equal to len(x)=%i" % (len(dWeights), len(x))
## dWeights = dWeights.reshape((n,1))
else:
## dWeights = Numeric.ones((n,1))
dWeights = Numeric.ones((n,))
r = min(int(Numeric.ceil(f*n)),n-1) # radius: num. of points to take into LR
h = [Numeric.sort(abs(x-x[i]))[r] for i in range(n)] # distance of the r-th point from x[i]
w = Numeric.clip(abs(([x]-Numeric.transpose([x]))/h),0.0,1.0)
w = 1-w*w*w
w = w*w*w
hest = [Numeric.sort(abs(x-xest[i]))[r] for i in range(nest)] # r-th min. distance from xest[i] to x
west = Numeric.clip(abs(([xest]-Numeric.transpose([x]))/hest),0.0,1.0) # shape: (len(x), len(xest))
west = 1-west*west*west
west = west*west*west
yest = Numeric.zeros(n,'d')
yest2 = Numeric.zeros(nest,'d')
delta = Numeric.ones(n,'d')
try:
for iteration in range(int(iter)):
# fit xest
for i in range(nest):
## print delta.shape, west[:,i].shape, dWeights.shape
weights = delta * west[:,i] * dWeights
b = Numeric.array([sum(weights*y), sum(weights*y*x)])
A = Numeric.array([[sum(weights), sum(weights*x)], [sum(weights*x), sum(weights*x*x)]])
beta = LinearAlgebra.solve_linear_equations(A,b)
yest2[i] = beta[0] + beta[1]*xest[i]
# fit x (to calculate residuals and delta)
for i in range(n):
weights = delta * w[:,i] * dWeights
b = Numeric.array([sum(weights*y), sum(weights*y*x)])
A = Numeric.array([[sum(weights), sum(weights*x)], [sum(weights*x), sum(weights*x*x)]])
beta = LinearAlgebra.solve_linear_equations(A,b)
yest[i] = beta[0] + beta[1]*x[i]
residuals = y-yest
s = MLab.median(abs(residuals))
delta = Numeric.clip(residuals/(6*s),-1,1)
delta = 1-delta*delta
delta = delta*delta
if callback: callback()
except LinearAlgebra.LinAlgError:
print "Warning: NumExtn.lowessW: LinearAlgebra.solve_linear_equations: Singular matrix"
yest2 = None
return yest2
def calc_membership_matrix(self, d2):
## remove 0s (if a cluster center is exactly on one item)
d2 = N.clip( d2, N.power(1e200, 1-self.w), 1e300 )
q = N.power(d2, 1. / (1. - self.w))
return q / N.sum(q)
def clipped_exp(x):
return Numeric.exp(Numeric.clip(x,-709., 709))
def calc_membership_matrix(self, d2):
## remove 0s (if a cluster center is exactly on one item)
d2 = N.clip(d2, N.power(1e200, 1 - self.w), 1e300)
q = N.power(d2, 1. / (1. - self.w))
return q / N.sum(q)
