def __ssBonds( self, model, cutoff=4. ):
"""
Identify disulfide bonds.
@param model: model
@type model: PDBModel
@param cutoff: distance cutoff for S-S distance (default: 4.0)
@type cutoff: float
@return: list with numbers of residue pairs forming S-S
@rtype: [(int, int)]
"""
m = model.compress( model.mask( ['SG'] ) )
if len( m ) < 2:
return []
pw = MU.pairwiseDistances( m.xyz, m.xyz )
pw = N.less( pw, cutoff )
r = []
for i in range( len( pw ) ):
for j in range( i+1, len(pw) ):
if pw[i,j]:
r += [ (m.atoms['residue_number'][i],
m.atoms['residue_number'][j]) ]
return r
def __ssBonds(self, model, cutoff=4.):
"""
Identify disulfide bonds.
@param model: model
@type model: PDBModel
@param cutoff: distance cutoff for S-S distance (default: 4.0)
@type cutoff: float
@return: list with numbers of residue pairs forming S-S
@rtype: [(int, int)]
"""
m = model.compress(model.mask(['SG']))
if len(m) < 2:
return []
pw = MU.pairwiseDistances(m.xyz, m.xyz)
pw = N.less(pw, cutoff)
r = []
for i in range(len(pw)):
for j in range(i + 1, len(pw)):
if pw[i, j]:
r += [(m.atoms['residue_number'][i],
m.atoms['residue_number'][j])]
return r
def getSS( model, cutoff=4.0 ):
cys_mask = model.mask( lambda a: a['residue_name'] in ['CYS', 'CYX']\
and a['name'] == 'SG')
model = model.compress( cys_mask )
diff = MU.pairwiseDistances( model.xyz, model.xyz )
count = N.sum( N.sum( N.less( diff, cutoff ) ) ) - model.lenAtoms()
return count / 2
def getSS(model, cutoff=4.0):
cys_mask = model.mask( lambda a: a['residue_name'] in ['CYS', 'CYX']\
and a['name'] == 'SG')
model = model.compress(cys_mask)
diff = MU.pairwiseDistances(model.xyz, model.xyz)
count = N.sum(N.sum(N.less(diff, cutoff))) - model.lenAtoms()
return count / 2
## extract single copy m0.report() m = m0.takeChains( [0, 2, 3 ] ) ## quick and dirty 2D-view # G.plot( zip( m.xyz[:,0], m.xyz[:,1] ) ) m.gnuplot() m0.report( plot=1 ) #------------------------------------- ## distance/contact matrix import Biskit.mathUtils as MU pw = MU.pairwiseDistances( m.xyz, m.xyz ) ## nicer graphics with Matrixplot p = MatrixPlot( pw, step=25 ) p.show() ## simple binary contact plot with gnuplot ## cont = pw * N.less( pw, 10 ) cont = N.less( pw, 10 ) G.scatter( zip( *N.nonzero( cont ) ) ) # ## inter-molecular contacts only #