def finish(self):
"""
Overrides Executor method
"""
Executor.finish(self)
self.result = self.parse_result()
## if probe radius other than 1.4 A the relative surface exposure
## cannot be calculated, but allow this check to be a little flexible
## if we ate forced to slightly increase the radii to excape round off
## SurfaceRacer errors
try:
if round(self.probe, 1) == 1.4 and self.vdw_set == 1:
self.__relExposure('MS')
self.__relExposure('AS')
else:
EHandler.warning("No relative accessabilities calculated "+\
"when using a prob radius other than 1.4 A"+\
" or not using the Richards vdw radii set.")
except KeyError as what:
EHandler.warning("Missing standard accessibilities for some "+\
"atoms. No relative accesibilities calculated.")
if 'relMS' in self.result: del self.result['relMS']
if 'relAS' in self.result: del self.result['relAS']
def single2longAA( seq ):
"""
Convert string of 1-letter AA code into list of 3-letter AA codes.
:param seq: amino acid sequence in 1-letter code
:type seq: str
:return: list with the amino acids in 3-letter code
:rtype: [str]
"""
## invert AA dict
invTab = {}
for key in aaDicStandard:
invTab[ aaDicStandard[key] ] = key
result = []
for aa in seq:
try:
aa = aa.upper()
result += [ invTab[aa].upper() ]
except:
EHandler.warning("unknown residue: " + str(aa))
result += ['Xaa']
return result
def loadResContacts( self ):
"""
Uncompress residue contact matrix if necessary.
@return: dict with contact matrix and parameters OR None
@rtype: dict OR None
"""
## Backwards compatibility
if self.contacts is not None and type( self.contacts ) == str:
self.contacts = t.load( self.contacts )
EHandler.warning("loading old-style pickled contacts.")
return self.contacts
## New, uncompression from list of indices into raveled array
if self.contacts is not None and \
len( N0.shape( self.contacts['result'])) == 1:
try:
lenRec, lenLig = self.contacts['shape']
except:
EHandler.warning("uncompressing contacts without shape")
lenRec = self.rec().lenResidues()
lenLig = self.lig().lenResidues()
m = N0.zeros( lenRec * lenLig )
N0.put( m, self.contacts['result'], 1 )
self.contacts['result'] = N0.reshape( m, (lenRec, lenLig) )
return self.contacts
def loadResContacts(self):
"""
Uncompress residue contact matrix if necessary.
@return: dict with contact matrix and parameters OR None
@rtype: dict OR None
"""
## Backwards compatibility
if self.contacts is not None and type(self.contacts) == str:
self.contacts = t.load(self.contacts)
EHandler.warning("loading old-style pickled contacts.")
return self.contacts
## New, uncompression from list of indices into raveled array
if self.contacts is not None and \
len( N0.shape( self.contacts['result'])) == 1:
try:
lenRec, lenLig = self.contacts['shape']
except:
EHandler.warning("uncompressing contacts without shape")
lenRec = self.rec().lenResidues()
lenLig = self.lig().lenResidues()
m = N0.zeros(lenRec * lenLig)
N0.put(m, self.contacts['result'], 1)
self.contacts['result'] = N0.reshape(m, (lenRec, lenLig))
return self.contacts
def finish( self ):
"""
Overrides Executor method
"""
Executor.finish( self )
self.result = self.parse_result()
## if probe radius other than 1.4 A the relative surface exposure
## cannot be calculated, but allow this check to be a little flexible
## if we ate forced to slightly increase the radii to excape round off
## SurfaceRacer errors
try:
if round(self.probe, 1) == 1.4 and self.vdw_set == 1:
self.__relExposure('MS')
self.__relExposure('AS')
else:
EHandler.warning("No relative accessabilities calculated "+\
"when using a prob radius other than 1.4 A"+\
" or not using the Richards vdw radii set.")
except KeyError as what:
EHandler.warning("Missing standard accessibilities for some "+\
"atoms. No relative accesibilities calculated.")
if 'relMS' in self.result: del self.result['relMS']
if 'relAS' in self.result: del self.result['relAS']
def __defaults(self):
self.models = getattr(self, 'models', ComplexModelRegistry())
if getattr(self, 'rec_models', 0) != 0:
EHandler.warning(
're-creating model registry..re-pickle this list!')
for c in self.toList():
self.models.addComplex(c)
del self.rec_models
del self.lig_models
def __defaults( self ):
self.models = getattr( self, 'models', ComplexModelRegistry() )
if getattr( self, 'rec_models', 0) != 0:
EHandler.warning(
're-creating model registry..re-pickle this list!')
for c in self.toList():
self.models.addComplex( c )
del self.rec_models
del self.lig_models
def __getstate__(self):
"""
Called before pickling the object.
"""
try:
if type( self.frames ) == list or self.frames.dtype.char == 'd':
EHandler.warning("Converting coordinates to float array.")
self.frames = N0.array( self.frames ).astype(N0.Float32)
except:
EHandler.warning('Could not convert frames to float array.', 1)
return self.__dict__
def writePdb( self, index, fname):
"""
Write (possibly transformed) coordinates back to pdb.
:param index: frame index in trajectory
:type index: int
:param fname: name of new file
:type fname: str
"""
try:
self.getPDBModel( index ).writePdb( fname )
except:
EHandler.error('Error writing %s.' % fname)
def __substitute( self, fragments, name, value ):
"""
Look in all not yet substituted fragments for parts that can be
substituted by value and, if successful, create a new fragment
:param fragments: fragment tuples
:type fragments: [ (str, str) ]
:param name: substitution variable name
:type name: str
:param value: susbtitution value in current environment
:type value: str
:return: fragment tuples
:rtype: [ (str, str) ]
"""
result = []
try:
for abs, subst in fragments:
if not subst: ## unsubstituted fragment
## pos = abs.find( value )
pos = self.__find_subpath( abs, value )
if pos != -1:
end = pos + len( value )
f1, f2, f3 = abs[0:pos], abs[pos:end], abs[end:]
if f1:
result += [ (f1, None) ] ## unsubstituted head
result += [ (f2, name) ] ## new substitution
if f3:
result += [ (f3, None) ] ## unsubstituted tail
else:
result += [ (abs, subst) ]
else:
result += [ (abs, subst ) ]
except OSError as why:
EHandler.fatal("Substituting path fragments: \n" +
str( fragments ) + '\nname: ' + str( name ) +
'\nvalue:' + str( value ) )
return result
def __substitute(self, fragments, name, value):
"""
Look in all not yet substituted fragments for parts that can be
substituted by value and, if successful, create a new fragment
:param fragments: fragment tuples
:type fragments: [ (str, str) ]
:param name: substitution variable name
:type name: str
:param value: susbtitution value in current environment
:type value: str
:return: fragment tuples
:rtype: [ (str, str) ]
"""
result = []
try:
for abs, subst in fragments:
if not subst: ## unsubstituted fragment
## pos = abs.find( value )
pos = self.__find_subpath(abs, value)
if pos != -1:
end = pos + len(value)
f1, f2, f3 = abs[0:pos], abs[pos:end], abs[end:]
if f1:
result += [(f1, None)] ## unsubstituted head
result += [(f2, name)] ## new substitution
if f3:
result += [(f3, None)] ## unsubstituted tail
else:
result += [(abs, subst)]
else:
result += [(abs, subst)]
except OSError as why:
EHandler.fatal("Substituting path fragments: \n" + str(fragments) +
'\nname: ' + str(name) + '\nvalue:' + str(value))
return result
def __syncModel( self, new_model, old_model ):
"""
Connect new rec or lig model to old one, to minimize storage.
@param new_model: PDBModel / XplorModel
@type new_model: PDBModel
@param old_model: PDBModel / XplorModel
@type old_model: PDBModel
@return: PDBModel / XplorModel, new model that only keeps
changes relative to old, the old model becomes the
source of the new, if possible
@rtype: PDBModel
"""
## try to fix atom order of new_model so that it is identical to old
if old_model.equals( new_model ) != [1,1]:
i_new, i_old = new_model.compareAtoms( old_model )
if len( i_new ) == len( new_model ):
new_model.keep( i_new )
## create result model that only keeps difference of new and old
if old_model.equals( new_model ) == [1,1]:
## stays compatible with XplorModel.__init__ and PDBModel.__init
r = old_model.__class__( source=old_model )
r.setXyz( new_model.getXyz() )
## check for profiles identical to source and adapt 'changed'
r.update()
if not MU.arrayEqual( r.xyz, old_model.xyz ):
r.removeProfile( 'relASA', 'ASA_sc', 'ASA_total', 'ASA_bb' )
return r
EHandler.warning(
'ComplexVC: Cannot connect new to old PDBModel.')
new_model.disconnect()
return new_model
def __syncModel(self, new_model, old_model):
"""
Connect new rec or lig model to old one, to minimize storage.
@param new_model: PDBModel / XplorModel
@type new_model: PDBModel
@param old_model: PDBModel / XplorModel
@type old_model: PDBModel
@return: PDBModel / XplorModel, new model that only keeps
changes relative to old, the old model becomes the
source of the new, if possible
@rtype: PDBModel
"""
## try to fix atom order of new_model so that it is identical to old
if old_model.equals(new_model) != [1, 1]:
i_new, i_old = new_model.compareAtoms(old_model)
if len(i_new) == len(new_model):
new_model.keep(i_new)
## create result model that only keeps difference of new and old
if old_model.equals(new_model) == [1, 1]:
## stays compatible with XplorModel.__init__ and PDBModel.__init
r = old_model.__class__(source=old_model)
r.setXyz(new_model.getXyz())
## check for profiles identical to source and adapt 'changed'
r.update()
if not MU.arrayEqual(r.xyz, old_model.xyz):
r.removeProfile('relASA', 'ASA_sc', 'ASA_total', 'ASA_bb')
return r
EHandler.warning('ComplexVC: Cannot connect new to old PDBModel.')
new_model.disconnect()
return new_model
def validate( self ):
"""
Validate the path to the binary.
:raise ExeConfigError: if environment is not fit for running
the program
"""
try:
self.bin = T.absbinary( self.bin ) ## raises IOError if not found
missing = self.update_environment()
report = '%s is missing environment variables: %r'\
% (self.name, missing )
if missing and self.strict:
raise ExeConfigError(report)
if missing:
EHandler.warning( report )
except IOError as e:
## re-raise but silence reporting of IOError in stack trace
raise ExeConfigError(str(e) + ' Check %s!' % self.dat) from None
def concat( self, *traj ):
"""
Concatenate this with other trajectories. The ref model of the
new Trajectory is a 'semi-deep' copy of this trajectorie's model.
(see :class:`PDBModel.take()` )::
concat( traj [, traj2, traj3, ..] ) -> Trajectory
:param traj: one or more Trajectory with identical atoms as this one
:type traj: Trajectories
:return: concatenated trajecties
:rtype: Trajectory
"""
if len( traj ) == 0:
return self
r = self.__class__()
r.frames = N0.concatenate( (self.frames, traj[0].frames), 0 )
r.setRef( self.ref.clone())
if self.frameNames and traj[0].frameNames:
r.frameNames = self.frameNames + traj[0].frameNames
try:
if self.pc is not None and traj[0].pc is not None:
r.pc['p'] = N0.concatenate( (self.pc['p'], traj[0].pc['p']),0)
r.pc['u'] = N0.concatenate( (self.pc['u'], traj[0].pc['u']),0)
except TypeError as why:
EHandler.error('cannot concat PC '+str(why) )
r.profiles = self.profiles.concat( traj[0].profiles )
## recursively add other trajectories
return r.concat( *traj[1:] )
def _cease( self, ref ):
try:
self.alive = False
except:
EHandler.warning('error in CrossView._cease')
pass
def concat(self, *profiles):
"""
Concatenate all profiles in this with corresponding profiles in the
given ProfileCollection(s). Profiles that are not found in all
ProfileCollections are skipped::
p0.concat( p1 [, p2, ..]) -> single ProfileCollection with the
same number of profiles as p0 but with the length of p0+p1+p2..
:param profiles: profile(s) to concatenate
:type profiles: ProfileCollection(s)
:return: concatenated profile(s)
:rtype: ProfileCollection / subclass
"""
## end recursion (no more arguments)
if len(profiles) == 0:
return self
next = profiles[0]
r = self.__class__()
##!!! BIG FAT WARNING: empty profilecollection does not imply empty model
## an empty PC w/o any profiles currently doesn't know which length
## is is supposed to have. If profLength == 0 for real, then
## the next PC's profiles don't need to be skipped
## Otherwise,
## this creates too-short profiles if the PC parent model has
## non-zero length and simply doesn't have any profiles registered.
## ## special case 1: concat something to empty profile collection
## if not self.keys():
## return next.clone().concat( *profiles[1:] )
##
## ## special case 2: concat empty profile collection to this one
## if not next.keys():
## return self.clone().concat( *profiles[1:] )
##
allkeys = M.union(list(self.profiles.keys()), list(next.keys()))
## for k, p in self.profiles.items():
for k in allkeys:
p = self.profiles.get(k, None)
pnext = next.profiles.get(k, None)
infos = {}
if p is None:
default = next[k, 'default']
p = self.__clonedefault(pnext, self.profLength(), default)
infos = next.infos[k]
if pnext is None:
default = self[k, 'default']
pnext = self.__clonedefault(p, next.profLength(), default)
infos = self.infos[k]
try:
if isinstance(p, N.ndarray):
if len(pnext) == 0:
pnext = pnext.astype(p.dtype)
r.set(k, N.concatenate((p, pnext)), **infos)
else:
r.set(k, p + pnext, **infos)
except:
EHandler.warning("Profile %s skipped during concat." % k,
error=1)
r.remove(k)
return r.concat(*profiles[1:])
def _cease(self, ref):
try:
self.alive = False
except:
EHandler.warning('error in CrossView._cease')
pass
def concat( self, *profiles ):
"""
Concatenate all profiles in this with corresponding profiles in the
given ProfileCollection(s). Profiles that are not found in all
ProfileCollections are skipped::
p0.concat( p1 [, p2, ..]) -> single ProfileCollection with the
same number of profiles as p0 but with the length of p0+p1+p2..
:param profiles: profile(s) to concatenate
:type profiles: ProfileCollection(s)
:return: concatenated profile(s)
:rtype: ProfileCollection / subclass
"""
## end recursion (no more arguments)
if len( profiles ) == 0:
return self
next = profiles[0]
r = self.__class__()
##!!! BIG FAT WARNING: empty profilecollection does not imply empty model
## an empty PC w/o any profiles currently doesn't know which length
## is is supposed to have. If profLength == 0 for real, then
## the next PC's profiles don't need to be skipped
## Otherwise,
## this creates too-short profiles if the PC parent model has
## non-zero length and simply doesn't have any profiles registered.
## ## special case 1: concat something to empty profile collection
## if not self.keys():
## return next.clone().concat( *profiles[1:] )
##
## ## special case 2: concat empty profile collection to this one
## if not next.keys():
## return self.clone().concat( *profiles[1:] )
##
allkeys = M.union( list(self.profiles.keys()), list(next.keys()) )
## for k, p in self.profiles.items():
for k in allkeys:
p = self.profiles.get(k, None)
pnext = next.profiles.get(k, None)
infos = {}
if p is None:
default = next[k,'default']
p = self.__clonedefault(pnext, self.profLength(), default)
infos = next.infos[k]
if pnext is None:
default = self[k,'default']
pnext = self.__clonedefault(p, next.profLength(), default)
infos = self.infos[k]
try:
if isinstance( p, N.ndarray ):
if len(pnext) == 0:
pnext = pnext.astype(p.dtype)
r.set( k, N.concatenate( (p, pnext) ), **infos )
else:
r.set( k, p + pnext, **infos )
except:
EHandler.warning("Profile %s skipped during concat." % k,
error=1)
r.remove( k )
return r.concat( *profiles[1:] )
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
## General Public License for more details.
##
## You find a copy of the GNU General Public License in the file
## license.txt along with this program; if not, write to the Free
## Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
"""
Protein-protein docking related modules
"""
from biskit import EHandler
try:
from .complex import Complex, ComplexError
from .complexList import ComplexList, ComplexListError
from .complexModelRegistry import ComplexModelRegistry, RegistryError
from .complexvc import ComplexVC
from .complexvcList import ComplexVCList
from .complextraj import ComplexTraj, ComplexTrajError
from .complexrandomizer import ComplexRandomizer, ComplexMinimizer
from .docker import Docker, DockerError
## from FixedList import FixedList
## from HexParser import HexParser
from .delphiBindingEnergy import DelphiBindingEnergy
## from Intervor import Intervor
## from PatchGenerator import PatchGenerator
## from PatchGeneratorFromOrbit import PatchGeneratorFromOrbit
except IOError as why:
EHandler.warning("Couldn't import all biskit.dock modules.\n" + str(why))
def concatEnsembles( self, *traj ):
"""
Concatenate this with other trajectories in a zig zac manner,
resulting in an ensembleTraj with additional members.
The ref model of the new Trajectory is a 'semi-deep' copy of this
trajectorie's model.(see :class:`PDBModel.take()` )::
concat( traj [, traj2, traj3, ..] ) -> Trajectory
:param traj: with identical atoms as this one
:type traj: one or more EnsembleTrajectory
@todo: fix so that pc, and profiles are not lost
"""
if len( traj ) == 0:
return self
r = self.__class__( n_members = self.n_members + traj[0].n_members )
min_members = min( self.n_members, traj[0].n_members )
min_frames = min( self.lenFrames(), traj[0].lenFrames() )
steps = self.lenFrames()//self.n_members + \
traj[0].lenFrames()//traj[0].n_members
def __everyOther( traj_0, traj_1, list_0, list_1, minMembers,
minFrames, loops ):
result = []
for j in range( 0, minMembers/2 ):
for i in range( j*loops , j*loops + minFrames*2/minMembers ):
result += [ list_0[i] ]
result += [ list_1[i] ]
while i < j*traj_0.n_members:
result += [ list_0[i] ]
while i < j*traj_1.n_members:
result += [ list_1[i] ]
return result
frames = __everyOther( self, traj[0], self.frames,
traj[0].frames, min_members,
min_frames, steps )
r.frames = N0.array(frames)
r.setRef( self.ref.clone())
if self.frameNames and traj[0].frameNames:
r.frameNames = __everyOther( self, traj[0], self.frameNames,
traj[0].frameNames, min_members,
min_frames, steps )
try:
# NOT TESTED!!
if self.pc and traj[0].pc:
r.pc['p'] = __everyOther( self, traj[0], self.pc['p'],
traj[0].pc['p'], min_members, steps )
r.pc['u'] = __everyOther( self, traj[0], self.pc['u'],
traj[0].pc['u'], min_members, steps )
# r.pc['p'] = N0.concatenate( (self.pc['p'], traj[0].pc['p']),0)
# r.pc['u'] = N0.concatenate( (self.pc['u'], traj[0].pc['u']),0)
except TypeError as why:
EHandler.error('cannot concat PC '+str(why) )
# r.profiles = self.profiles.concat( traj[0].profiles )
## recursively add other trajectories
return r.concat( *traj[1:] )
def concatEnsembles( self, *traj ):
"""
Concatenate this with other trajectories in a zig zac manner,
resulting in an ensembleTraj with additional members.
The ref model of the new Trajectory is a 'semi-deep' copy of this
trajectorie's model.(see :class:`PDBModel.take()` )::
concat( traj [, traj2, traj3, ..] ) -> Trajectory
:param traj: with identical atoms as this one
:type traj: one or more EnsembleTrajectory
@todo: fix so that pc, and profiles are not lost
"""
if len( traj ) == 0:
return self
r = self.__class__( n_members = self.n_members + traj[0].n_members )
min_members = min( self.n_members, traj[0].n_members )
min_frames = min( self.lenFrames(), traj[0].lenFrames() )
steps = self.lenFrames()//self.n_members + \
traj[0].lenFrames()//traj[0].n_members
def __everyOther( traj_0, traj_1, list_0, list_1, minMembers,
minFrames, loops ):
result = []
for j in range( 0, minMembers/2 ):
for i in range( j*loops , j*loops + minFrames*2/minMembers ):
result += [ list_0[i] ]
result += [ list_1[i] ]
while i < j*traj_0.n_members:
result += [ list_0[i] ]
while i < j*traj_1.n_members:
result += [ list_1[i] ]
return result
frames = __everyOther( self, traj[0], self.frames,
traj[0].frames, min_members,
min_frames, steps )
r.frames = N0.array(frames)
r.setRef( self.ref.clone())
if self.frameNames and traj[0].frameNames:
r.frameNames = __everyOther( self, traj[0], self.frameNames,
traj[0].frameNames, min_members,
min_frames, steps )
try:
# NOT TESTED!!
if self.pc and traj[0].pc:
r.pc['p'] = __everyOther( self, traj[0], self.pc['p'],
traj[0].pc['p'], min_members, steps )
r.pc['u'] = __everyOther( self, traj[0], self.pc['u'],
traj[0].pc['u'], min_members, steps )
# r.pc['p'] = N0.concatenate( (self.pc['p'], traj[0].pc['p']),0)
# r.pc['u'] = N0.concatenate( (self.pc['u'], traj[0].pc['u']),0)
except TypeError as why:
EHandler.error('cannot concat PC '+str(why) )
# r.profiles = self.profiles.concat( traj[0].profiles )
## recursively add other trajectories
return r.concat( *traj[1:] )