def test_sequenceRepeats(self):
"""match2seq sequence repeat test"""
seq1 = 'ABCDEFG~~~~~~~~~~~~~~~'
seq2 = '~~~~~'
mask1, mask2 = compareSequences( seq1, seq2 )
self.assert_( N.all( mask1 == N.zeros( len(seq1 ) )) )
self.assert_( N.all( mask2 == N.zeros( len(seq2 ) )) )
def test_sequenceRepeats(self):
"""match2seq sequence repeat test"""
seq1 = 'ABCDEFG~~~~~~~~~~~~~~~'
seq2 = '~~~~~'
mask1, mask2 = compareSequences(seq1, seq2)
self.assert_(N.all(mask1 == N.zeros(len(seq1))))
self.assert_(N.all(mask2 == N.zeros(len(seq2))))
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 permutInverse(n):
"""Returns inverse permutation given integers in range(len(n)),
such that permitInverse(permutInverse(range(4)))==range(4).
"""
n = Numeric.asarray(n)
pInv = Numeric.argsort(n)
assert Numeric.all(Numeric.equal(n, Numeric.argsort(pInv))), "Inverse not successful; input should be permutation of range(len(input))."
return pInv
def __collectFrames( self, pdbs, castAll=0 ):
"""
Read coordinates from list of pdb files.
@param pdbs: list of file names
@type pdbs: [str]
@param castAll: analyze atom content of each frame for casting
(default: 0)
@type castAll: 0|1
@return: frames x (N x 3) Numpy array (of float)
@rtype: array
"""
frameList = []
i = 0
atomCast = None
if self.verbose: T.errWrite('reading %i pdbs...' % len(pdbs) )
refNames = self.ref.atomNames() ## cache for atom checking
for f in pdbs:
## Load
m = PDBModel(f)
## compare atom order & content of first frame to reference pdb
if castAll or i==0:
atomCast, castRef = m.compareAtoms( self.ref )
if castRef != range( len( self.ref ) ):
## we can take away atoms from each frame but not from ref
raise TrajError("Reference PDB doesn't match %s."
%m.fileName)
if N.all( atomCast == range( len( m ) ) ):
atomCast = None ## no casting necessary
else:
if self.verbose: T.errWrite(' casting ')
## assert that frame fits reference
if atomCast:
m = m.take( atomCast )
## additional check on each 100st frame
if i%100 == 0 and m.atomNames() <> refNames:
raise TrajError("%s doesn't match reference pdb."%m.fileName )
frameList.append( m.xyz )
i += 1
if i%10 == 0 and self.verbose:
T.errWrite('#')
if self.verbose: T.errWrite( 'done\n' )
## convert to 3-D Numpy Array
return N.array(frameList).astype(N.Float32)
def __collectFrames(self, pdbs, castAll=0):
"""
Read coordinates from list of pdb files.
@param pdbs: list of file names
@type pdbs: [str]
@param castAll: analyze atom content of each frame for casting
(default: 0)
@type castAll: 0|1
@return: frames x (N x 3) Numpy array (of float)
@rtype: array
"""
frameList = []
i = 0
atomCast = None
if self.verbose: T.errWrite('reading %i pdbs...' % len(pdbs))
refNames = self.ref.atomNames() ## cache for atom checking
for f in pdbs:
## Load
m = PDBModel(f)
## compare atom order & content of first frame to reference pdb
if castAll or i == 0:
atomCast, castRef = m.compareAtoms(self.ref)
if castRef != range(len(self.ref)):
## we can take away atoms from each frame but not from ref
raise TrajError("Reference PDB doesn't match %s." %
m.fileName)
if N.all(atomCast == range(len(m))):
atomCast = None ## no casting necessary
else:
if self.verbose: T.errWrite(' casting ')
## assert that frame fits reference
if atomCast:
m = m.take(atomCast)
## additional check on each 100st frame
if i % 100 == 0 and m.atomNames() <> refNames:
raise TrajError("%s doesn't match reference pdb." % m.fileName)
frameList.append(m.xyz)
i += 1
if i % 10 == 0 and self.verbose:
T.errWrite('#')
if self.verbose: T.errWrite('done\n')
## convert to 3-D Numpy Array
return N.array(frameList).astype(N.Float32)
def test_match2seq(self):
"""match2seq test"""
## Reading pdb files
lig_traj = T.load(T.testRoot() + '/lig_pcr_00/traj.dat')[:2]
m = [m.compress(m.maskProtein()) for m in lig_traj]
## make the models different
m[1].removeRes(['ALA'])
mask1, mask2 = compareModels(m[0], m[1])
if self.local:
print 'Reading and comparing two models'
print '\nResidue masks to make the two maodels equal'
print 'mask1\n', mask1
print 'mask2\n', mask2
globals().update(locals())
self.assert_(N.all(mask1 == self.EXPECT[0]))
self.assert_(N.all(mask2 == self.EXPECT[1]))
def test_match2seq(self):
"""match2seq test"""
## Reading pdb files
lig_traj = T.load( T.testRoot() + '/lig_pcr_00/traj.dat' )[:2]
m = [ m.compress( m.maskProtein() ) for m in lig_traj ]
## make the models different
m[1].removeRes(['ALA'])
mask1, mask2 = compareModels( m[0], m[1] )
if self.local:
print 'Reading and comparing two models'
print '\nResidue masks to make the two maodels equal'
print 'mask1\n', mask1
print 'mask2\n', mask2
globals().update( locals() )
self.assert_( N.all(mask1 == self.EXPECT[0] ) )
self.assert_( N.all(mask2 == self.EXPECT[1] ) )
def changeModel( inFile, prefix, sourceModel ):
print '\nget ' + os.path.basename( inFile ) + '..',
model = PDBModel( inFile )
model.update()
model = model.sort()
eq = model.equals( sourceModel )
if not eq[0] and eq[1]:
raise ConvertError('source and other models are not equal: ' + str(eq))
# model.validSource()
model.setSource( sourceModel.validSource() )
#model.atomsChanged = 0
for k in model.atoms:
model.atoms[k,'changed'] = N.all( model[k] == sourceModel[k] )
model.xyzChanged = ( 0 != N.sum( N.ravel( model.xyz - sourceModel.xyz)) )
model.update( updateMissing=1 )
if model.xyzChanged:
doper = PDBDope( model )
if 'MS' in sourceModel.atoms.keys():
doper.addSurfaceRacer( probe=1.4 )
if 'density' in sourceModel.atoms.keys():
doper.addDensity()
if 'foldX' in sourceModel.info.keys():
doper.addFoldX()
if 'delphi' in sourceModel.info.keys():
doper.addDelphi()
outFile = os.path.dirname( inFile ) + '/' + prefix +\
T.stripFilename( inFile ) + '.model'
T.dump( model, outFile )
print '-> ' + os.path.basename( outFile )
def test_Whatif(self):
"""Whatif test"""
from Biskit import PDBModel
## Loading PDB...
f = T.testRoot()+"/com/1BGS.pdb"
m = PDBModel(f)
m = m.compress( m.maskProtein() )
m = m.compress( m.maskHeavy() )
## Starting WhatIf
x = WhatIf( m, debug=0, verbose=0 )
## Running
atomAcc, resAcc, resMask = x.run()
if self.local:
## check that model hasn't changed
m_ref = PDBModel(f)
m_ref = m.compress( m.maskProtein() )
for k in m_ref.atoms.keys():
if not N.all(m_ref[k] == m[k]):
print 'Not equal ', k
else:
print 'Equal ', k
## display exposed residues in PyMol
from Pymoler import Pymoler
pm = Pymoler()
model = pm.addPdb( m, '1' )
pm.colorRes( '1', resAcc[:,0] )
pm.show()
print "\nResult for first 10 atoms/residues: "
print '\nAccessability (A^2):\n', atomAcc[:10]
print '\nResidue accessability (A^2)'
print '[total, backbone, sidechain]:\n', resAcc[:10]
print '\nExposed residue mask:\n',resMask[:10]
print '\nTotal atom accessability (A^2): %.2f'%sum(atomAcc)
print ' residue accessability (A^2): %.2f'%sum(resAcc)[0]
self.assertAlmostEqual( N.sum(resAcc[:,0]), 2814.6903, 7 )
def test_Whatif(self):
"""Whatif test"""
from Biskit import PDBModel
## Loading PDB...
f = T.testRoot() + "/com/1BGS.pdb"
m = PDBModel(f)
m = m.compress(m.maskProtein())
m = m.compress(m.maskHeavy())
## Starting WhatIf
x = WhatIf(m, debug=0, verbose=0)
## Running
atomAcc, resAcc, resMask = x.run()
if self.local:
## check that model hasn't changed
m_ref = PDBModel(f)
m_ref = m.compress(m.maskProtein())
for k in m_ref.atoms.keys():
if not N.all(m_ref[k] == m[k]):
print 'Not equal ', k
else:
print 'Equal ', k
## display exposed residues in PyMol
from Pymoler import Pymoler
pm = Pymoler()
model = pm.addPdb(m, '1')
pm.colorRes('1', resAcc[:, 0])
pm.show()
print "\nResult for first 10 atoms/residues: "
print '\nAccessability (A^2):\n', atomAcc[:10]
print '\nResidue accessability (A^2)'
print '[total, backbone, sidechain]:\n', resAcc[:10]
print '\nExposed residue mask:\n', resMask[:10]
print '\nTotal atom accessability (A^2): %.2f' % sum(atomAcc)
print ' residue accessability (A^2): %.2f' % sum(resAcc)[0]
self.assertAlmostEqual(N.sum(resAcc[:, 0]), 2814.6903, 7)
def test_SparseArray(self):
"""SparseArray test"""
a = N.zeros((6, ), N.Float32)
self.sa = SparseArray(a.shape)
self.sa[3] = 1.
self.sa[5] = 2.
b = N.zeros((5, 6), N.Float32)
b[0, 1] = 3.
b[0, 2] = 4
b[4, 2] = 5
b[3, 0] = 6
self.sb = SparseArray(b)
self.sb.append(self.sa)
if self.local:
print self.sa.toarray()
self.assert_(N.all(self.sb.toarray() == self.EXPECTED))
def test_SparseArray(self):
"""SparseArray test"""
a = N.zeros( (6,), N.Float32 )
self.sa = SparseArray( a.shape )
self.sa[3] = 1.
self.sa[5] = 2.
b = N.zeros( (5, 6), N.Float32 )
b[0,1] = 3.
b[0,2] = 4
b[4,2] = 5
b[3,0] = 6
self.sb = SparseArray( b )
self.sb.append( self.sa )
if self.local:
print self.sa.toarray()
self.assert_( N.all( self.sb.toarray() == self.EXPECTED) )
def test_hist( self ):
"""hist test"""
self.x = Numeric.arange( 4, 12, 1.2 )
self.data = density( self.x, 3, hist=1 )
self.assert_( Numeric.all( self.data == self.EXPECT) )
def test_hist(self):
"""hist test"""
self.x = Numeric.arange(4, 12, 1.2)
self.data = density(self.x, 3, hist=1)
self.assert_(Numeric.all(self.data == self.EXPECT))