def test_delphiCharges2( self ):
"""
PDB2DelphiCharges test
"""
if self.local:
T.errWrite( 'loading PDB...' )
self.m1 = self.MODEL or PDBModel( T.testRoot( 'lig/1A19_dry.model' ) )
Test.MODEL = self.m1
if self.local:
T.errWriteln( 'Done.' )
if self.local:
T.errWrite( 'Adding hydrogens to model (reduce)...' )
self.rmodel = Reduce( self.m1, verbose=self.local ).run()
self.rmodel.xplor2amber()
if self.local:
T.errWriteln( 'Done.' )
ac = AtomCharger()
ac.charge(self.rmodel)
self.rmodel.addChainFromSegid()
self.dc = PDB2DelphiCharges( self.rmodel )
self.dc.prepare()
self.assertEqual( len(self.dc.resmap['LYS']), 2 ) # normal and N'
self.assertEqual( len(self.dc.resmap['SER']), 2 ) # normal and C'
if self.local:
T.errWriteln( 'writing delphi charge file to %s' % self.fcrg )
self.dc.tofile( self.fcrg )
self.assertTrue( os.path.exists( self.fcrg ) )
def test_delphiCharges2(self):
"""
PDB2DelphiCharges test
"""
if self.local:
T.errWrite('loading PDB...')
self.m1 = self.MODEL or PDBModel(T.testRoot('lig/1A19_dry.model'))
Test.MODEL = self.m1
if self.local:
T.errWriteln('Done.')
if self.local:
T.errWrite('Adding hydrogens to model (reduce)...')
self.rmodel = Reduce(self.m1, verbose=self.local).run()
self.rmodel.xplor2amber()
if self.local:
T.errWriteln('Done.')
ac = AtomCharger()
ac.charge(self.rmodel)
self.rmodel.addChainFromSegid()
self.dc = PDB2DelphiCharges(self.rmodel)
self.dc.prepare()
self.assertEqual(len(self.dc.resmap['LYS']), 2) # normal and N'
self.assertEqual(len(self.dc.resmap['SER']), 2) # normal and C'
if self.local:
T.errWriteln('writing delphi charge file to %s' % self.fcrg)
self.dc.tofile(self.fcrg)
self.assertTrue(os.path.exists(self.fcrg))
def isFailed( self ):
"""
Overrides Executor method
"""
if not os.path.exists(self.f_out_name):
T.errWrite( '\nSurfaceRacer result file %s does not exist. You have probably encountered a very rare SurfaceRacer round off error that have caused the program to terminate. Will now try to recalculate the surface with a slightly increased surface probe radii: increasing radii from %.3f to %.3f.\n'%(self.f_out_name, self.probe,self.probe+0.001))
return 1
return self.error is None
def isFailed(self):
"""
Overrides Executor method
"""
if not os.path.exists(self.f_out_name):
T.errWrite(
'\nSurfaceRacer result file %s does not exist. You have probably encountered a very rare SurfaceRacer round off error that have caused the program to terminate. Will now try to recalculate the surface with a slightly increased surface probe radii: increasing radii from %.3f to %.3f.\n'
% (self.f_out_name, self.probe, self.probe + 0.001))
return 1
return self.error is None
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 != list(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 N0.all( atomCast == list(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 N0.array(frameList).astype(N0.Float32)
def go(self, errorthreshold, n_iterations=1e10, nstep=10, verbose=1):
"""
Start the cluestering. Run until the error is below the error
treshold or the max number of iterations have been run.
@param errorthreshold: treshold value for error
@type errorthreshold: float
@param n_iterations: treshold value for number of iterations
(default: 1e10)
@type n_iterations: int
@param nstep: print information for every n'th step in the iteration
@type nstep: int
@return: array with cluster centers
@rtype: array('f')
"""
iteration = 0
rel_err = 1e10
error = 1.e10
msm = self.create_membership_matrix()
centers = self.calc_cluster_center(msm)
while rel_err > errorthreshold and iteration < n_iterations:
d2, msm, centers = self.iterate(centers)
old_error = error
error = self.error(msm, d2)
rel_err = abs(1. - error / old_error)
iteration = iteration + 1
if not iteration % nstep and verbose:
tools.errWrite("%i %f\n" % (iteration, error))
self.centers = centers
self.msm = msm
self.d2 = d2
return centers
def go(self, errorthreshold, n_iterations=1e10, nstep=10, verbose=1):
"""
Start the cluestering. Run until the error is below the error
treshold or the max number of iterations have been run.
@param errorthreshold: treshold value for error
@type errorthreshold: float
@param n_iterations: treshold value for number of iterations
(default: 1e10)
@type n_iterations: int
@param nstep: print information for every n'th step in the iteration
@type nstep: int
@return: array with cluster centers
@rtype: array('f')
"""
iteration = 0
rel_err = 1e10
error = 1.e10
msm = self.create_membership_matrix()
centers = self.calc_cluster_center(msm)
while rel_err > errorthreshold and iteration < n_iterations:
d2, msm, centers = self.iterate(centers)
old_error = error
error = self.error(msm, d2)
rel_err = abs(1. - error/old_error)
iteration = iteration+1
if not iteration % nstep and verbose:
tools.errWrite( "%i %f\n" % (iteration, error) )
self.centers = centers
self.msm = msm
self.d2 = d2
return centers
def fit( self, mask=None, ref=None, n_it=1,
prof='rms', verbose=1, fit=1, **profInfos ):
"""
Superimpose all coordinate frames on reference coordinates. Put rms
values in a profile. If n_it > 1, the fraction of atoms considered
for the fit is put into a profile called |prof|_considered
(i.e. by default 'rms_considered').
:param mask: atom mask, atoms to consider default: [all]
:type mask: [1|0]
:param ref: use as reference, default: None, average Structure
:type ref: PDBModel
:param n_it: number of fit iterations, kicking out outliers on the way
1 -> classic single fit, 0 -> until convergence
(default: 1)
:type n_it: int
:param prof: save rms per frame in profile of this name, ['rms']
:type prof: str
:param verbose: print progress info to STDERR (default: 1)
:type verbose: 1|0
:param fit: transform frames after match, otherwise just calc rms
(default: 1)
:type fit: 1|0
:param profInfos: additional key=value pairs for rms profile info []
:type profInfos: key=value
"""
if ref is None:
refxyz = N0.average( self.frames, 0 )
else:
refxyz = ref.getXyz()
if mask is None:
mask = N0.ones( len( refxyz ), N0.Int32 )
refxyz = N0.compress( mask, refxyz, 0 )
if verbose: T.errWrite( "rmsd fitting..." )
rms = [] ## rms value of each frame
non_outliers = [] ## fraction of atoms considered for rms and fit
iterations = [] ## number of iterations performed on each frame
for i in range(0, len( self.frames) ):
xyz = self.frames[i]
if n_it != 1:
(r, t), rmsdList = rmsFit.match( refxyz,
N0.compress( mask, xyz, 0), n_it)
iterations.append( len( rmsdList ) )
non_outliers.append( rmsdList[-1][0] )
xyz_transformed = N0.dot( xyz, N0.transpose(r)) + t
rms += [ rmsdList[-1][1] ]
else:
r, t = rmsFit.findTransformation( refxyz,
N0.compress( mask, xyz, 0))
xyz_transformed = N0.dot( xyz, N0.transpose(r)) + t
d = N0.sqrt(N0.sum(N0.power( N0.compress(mask, xyz_transformed,0)\
- refxyz, 2), 1))
rms += [ N0.sqrt( N0.average(d**2) ) ]
if fit:
self.frames[i] = xyz_transformed.astype(N0.Float32)
if verbose and i%100 == 0:
T.errWrite( '#' )
self.setProfile( prof, rms, n_iterations=n_it, **profInfos )
if non_outliers:
self.setProfile( prof+'_considered', non_outliers,
n_iterations=n_it,
comment='fraction of atoms considered for iterative fit' )
if verbose: T.errWrite( 'done\n' )
def getFluct_local( self, mask=None, border_res=1,
left_atoms=['C'], right_atoms=['N'], verbose=1 ):
"""
Get mean displacement of each atom from it's average position after
fitting of each residue to the reference backbone coordinates of itself
and selected atoms of neighboring residues to the right and left.
:param mask: N_atoms x 1 array of 0||1, atoms for which fluctuation
should be calculated
:type mask: array
:param border_res: number of neighboring residues to use for fitting
:type border_res: int
:param left_atoms: atoms (names) to use from these neighbore residues
:type left_atoms: [str]
:param right_atoms: atoms (names) to use from these neighbore residues
:type right_atoms: [str]
:return: Numpy array ( N_unmasked x 1 ) of float
:rtype: array
"""
if mask is None:
mask = N0.ones( len( self.frames[0] ), N0.Int32 )
if verbose: T.errWrite( "rmsd fitting per residue..." )
residues = N0.nonzero( self.ref.atom2resMask( mask ) )
## backbone atoms used for fit
fit_atoms_right = N0.nonzero( self.ref.mask( right_atoms ) )
fit_atoms_left = N0.nonzero( self.ref.mask( left_atoms ) )
## chain index of each residue
rchainMap = N0.take( self.ref.chainMap(), self.ref.resIndex() )
result = []
for res in residues:
i_res, i_border = self.__resWindow(res, border_res, rchainMap,
fit_atoms_left, fit_atoms_right)
try:
if not len( i_res ): raise PDBError('empty residue')
t_res = self.takeAtoms( i_res + i_border )
i_center = range( len( i_res ) )
mask_BB = t_res.ref.maskBB() * t_res.ref.maskHeavy()
## fit with border atoms ..
t_res.fit( ref=t_res.ref, mask=mask_BB, verbose=0 )
## .. but calculate only with center residue atoms
frames = N0.take( t_res.frames, i_center, 1 )
avg = N0.average( frames )
rmsd = N0.average(N0.sqrt(N0.sum(N0.power(frames - avg, 2), 2) ))
result.extend( rmsd )
if verbose: T.errWrite('#')
except ZeroDivisionError:
result.extend( N0.zeros( len(i_res), N0.Float32 ) )
T.errWrite('?' + str( res ))
if verbose: T.errWriteln( "done" )
return result
def parse2new(self, source, ref=None, traj=None):
"""
Create / Replace Trajectory from the source list of PDBModels or PDBs.
Args:
source (str): list of file names or PDBModel instances
ref (str or PDBModel): reference structure instance or file
traj (Biskit.md.Trajectory): existing instance to be updated
Returns:
Biskit.Trajectory: new Trajectory instance
"""
r = traj
if traj is None:
import biskit.md
r = biskit.md.Trajectory()
r.setRef(B.PDBModel(ref or source[0]))
n_frames = len(source)
if self.rmwat:
r.ref = r.ref.compress(N.logical_not(r.ref.maskSolvent()))
r.resIndex = r.ref.resMap()
refNames = r.ref.atomNames() ## cache for atom checking
if self.verbose: T.errWrite('reading %i pdbs...' % n_frames)
r.frames = N.zeros(
(n_frames, r.ref.lenAtoms(), 3)) ## target coordinate array
r.frameNames = ['#%i07' % i for i in range(n_frames)]
atomCast = None
reportIntervall = 1 if n_frames < 100 else round(n_frames / 100)
for i, f in enumerate(source):
m = B.PDBModel(f)
## compare atom order & content of first frame to reference pdb
if self.analyzeEach or i == 0:
atomCast, castRef = m.compareAtoms(r.ref)
if castRef != list(range(r.ref.lenAtoms())):
## we can remove/reorder atoms from each frame but not from ref
raise P.TrajParserError("Reference PDB doesn't match %s." %
m.fileName)
if N.all(atomCast == list(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 % reportIntervall == 0 and m.atomNames() != refNames:
raise P.TrajParserError("%s doesn't match reference pdb." %
m.fileName)
r.frames[i] = m.xyz
if type(f) is str: ## save original file name
r.frameNames[i] = T.stripFilename(f)
if i % reportIntervall == 0 and self.verbose:
T.errWrite('#')
if self.verbose: T.errWrite('done\n')
return r
