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 list(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 list(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.assertTrue(N.all(m_ref[k] == self.M[k]))
## display in Pymol
if self.local:
print("Starting PyMol...")
from biskit.exe.pymoler import Pymoler
pm = Pymoler()
pm.addPdb(self.M, 'm')
pm.colorAtoms('m', N0.clip(self.M.profile('relAS'), 0.0, 100.0))
pm.show()
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 list(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 list(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.assertTrue( N.all( m_ref[k] == self.M[k]) )
## display in Pymol
if self.local:
print("Starting PyMol...")
from biskit.exe.pymoler import Pymoler
pm = Pymoler()
pm.addPdb( self.M, 'm' )
pm.colorAtoms( 'm', N0.clip(self.M.profile('relAS'), 0.0, 100.0) )
pm.show()
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 = N0.clip( N0.sum(cont),0,1), N0.clip( N0.sum(contRef), 0,1)
rec = N0.clip( N0.sum(cont, 1),0,1)
recRef = N0.clip( N0.sum(contRef, 1), 0,1)
fLig = N0.sum( N0.logical_and( lig, ligRef )) *1./ N0.sum( ligRef )
fRec = N0.sum( N0.logical_and( rec, recRef )) *1./ N0.sum( recRef )
return (fRec, fLig)
def __test_conservation(self):
"""PDBDope.addConservation (Hmmer) test"""
if self.local: print("Adding conservation data...", end=' ')
self.d.addConservation()
if self.local: print('Done.')
## display in Pymol
if self.local:
print("Starting PyMol...")
from biskit.exe.pymoler import Pymoler
pm = Pymoler()
pm.addPdb( self.M, 'm' )
pm.colorAtoms( 'm', N0.clip(self.M.profile('cons_ent'), 0.0, 100.0) )
pm.show()
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 = N0.clip(N0.sum(cont), 0,
1), N0.clip(N0.sum(contRef), 0, 1)
rec = N0.clip(N0.sum(cont, 1), 0, 1)
recRef = N0.clip(N0.sum(contRef, 1), 0, 1)
fLig = N0.sum(N0.logical_and(lig, ligRef)) * 1. / N0.sum(ligRef)
fRec = N0.sum(N0.logical_and(rec, recRef)) * 1. / N0.sum(recRef)
return (fRec, fLig)
def __test_conservation(self):
"""PDBDope.addConservation (Hmmer) test"""
if self.local: print("Adding conservation data...", end=' ')
self.d.addConservation()
if self.local: print('Done.')
## display in Pymol
if self.local:
print("Starting PyMol...")
from biskit.exe.pymoler import Pymoler
pm = Pymoler()
pm.addPdb(self.M, 'm')
pm.colorAtoms('m', N0.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 N0.clip( N0.array(rel), 0.0, 100.0 )
else:
return N0.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 N0.clip(N0.array(rel), 0.0, 100.0)
else:
return N0.array(rel)
def calc_membership_matrix(self, d2):
## remove 0s (if a cluster center is exactly on one item)
d2 = N0.clip(d2, N0.power(1e200, 1 - self.w), 1e300)
q = N0.power(d2, 1. / (1. - self.w))
return q / N0.sum(q)
def calc_membership_matrix(self, d2):
## remove 0s (if a cluster center is exactly on one item)
d2 = N0.clip( d2, N0.power(1e200, 1-self.w), 1e300 )
q = N0.power(d2, 1. / (1. - self.w))
return q / N0.sum(q)