def charge(self, model):
"""
Assign atom charges to given model
@param model: input structure
@type model: PDBModel
"""
q = N.array([], float)
for j, res in enumerate(model.resModels()):
refres = self.lookupResidue(res)
if refres is None:
if self.verbose:
self.log.add('Warning: no residue type for '+\
self.__resinfo(res,j) +\
'\nWhole residue will be set to charge 0.')
refres = res
refres['partial_charge'] = N.zeros(len(refres))
iref, i = refres.compareAtoms(res)
qres = N.take(refres['partial_charge'], iref)
if len(iref) < len(refres):
if self.verbose:
self.log.add('Warning: %i atoms missing from residue %s:'%\
(len(refres)-len(iref), self.__resinfo(res,j)) )
missing = MA.difference(range(len(refres)), iref)
self.log.add('\t' + str(N.take(refres['name'], missing)))
self.log.add(
'\tIgnored. Residue will have incomplete charge.')
if len(i) < len(res):
if self.verbose:
self.log.add('Warning: %i unknown atoms in residue %s:' %\
(len(res)-len(i), self.__resinfo(res,j)) )
missing = MA.difference(range(len(res)), i)
self.log.add('\t' + str(N.take(res['name'], missing)))
self.log.add(
'\tGiving up. Whole residue will be set to charge 0.')
qres = N.zeros(len(res))
## assert len(qres) == len(res), 'missmatch of atom number'
q = N.concatenate((q, qres))
assert len(q) == len(model), 'AtomCharger: missing charge records'
model['partial_charge'] = q
def charge(self, model):
"""
Assign atom charges to given model
@param model: input structure
@type model: PDBModel
"""
q = N.array( [], float )
for j,res in enumerate(model.resModels()):
refres = self.lookupResidue( res )
if refres is None:
if self.verbose:
self.log.add('Warning: no residue type for '+\
self.__resinfo(res,j) +\
'\nWhole residue will be set to charge 0.')
refres = res
refres['partial_charge'] = N.zeros( len(refres) )
iref, i = refres.compareAtoms( res )
qres = N.take( refres['partial_charge'], iref )
if len(iref) < len(refres):
if self.verbose:
self.log.add('Warning: %i atoms missing from residue %s:'%\
(len(refres)-len(iref), self.__resinfo(res,j)) )
missing = MA.difference( range(len(refres)), iref )
self.log.add('\t'+str(N.take( refres['name'], missing )) )
self.log.add(
'\tIgnored. Residue will have incomplete charge.')
if len(i) < len( res ):
if self.verbose:
self.log.add('Warning: %i unknown atoms in residue %s:' %\
(len(res)-len(i), self.__resinfo(res,j)) )
missing = MA.difference( range(len(res)), i )
self.log.add('\t'+str(N.take( res['name'], missing )) )
self.log.add('\tGiving up. Whole residue will be set to charge 0.')
qres = N.zeros( len(res) )
## assert len(qres) == len(res), 'missmatch of atom number'
q = N.concatenate( (q, qres ) )
assert len(q) == len(model), 'AtomCharger: missing charge records'
model['partial_charge'] = q
def processTrajs( self ):
"""
Extract reference model and member trajectories from rec, lig, and
com trajectories. Identify outlier member trajectories, if requested.
"""
## free rec
self.ref_frec = self.nameRef( self.rec )
t, self.ex_frec, self.members_frec = self.loadTraj(
self.rec, self.ex_frec, self.ref_frec )
n_rec_members = t.n_members
self.cr = self.cr or range( t.ref.lenChains( breaks=0 ) )
del t
## free lig
self.ref_flig = self.nameRef( self.lig )
t, self.ex_flig, self.members_flig = self.loadTraj(
self.lig, self.ex_flig, self.ref_flig )
n_lig_members = t.n_members
del t
## complex
fname = T.stripSuffix( T.absfile( self.com, resolveLinks=0 ) )
self.ref_com = fname + '_ref.complex'
self.ref_blig= fname + '_blig.model'
self.ref_brec= fname + '_brec.model'
t, self.ex_com, self.members_com = self.loadTraj(
self.com, self.ex_com )
n_com_members = t.n_members
self.cl = self.cl or MU.difference( range(t.ref.lenChains()), self.cr)
rec = t.ref.takeChains( self.cr, breaks=0 )
lig = t.ref.takeChains( self.cl, breaks=0 )
del t
self.dumpMissing( Complex( rec, lig ), self.ref_com )
self.dumpMissing( rec, self.ref_brec )
self.dumpMissing( lig, self.ref_blig )
self.equalizeMemberCount( n_rec_members, n_lig_members, n_com_members )
if self.jack: self.prepareJackknife()
def processTrajs( self ):
"""
Extract reference model and member trajectories from rec, lig, and
com trajectories. Identify outlier member trajectories, if requested.
"""
## free rec
self.ref_frec = self.nameRef( self.rec )
t, self.ex_frec, self.members_frec = self.loadTraj(
self.rec, self.ex_frec, self.ref_frec )
n_rec_members = t.n_members
self.cr = self.cr or range( t.ref.lenChains( breaks=0 ) )
del t
## free lig
self.ref_flig = self.nameRef( self.lig )
t, self.ex_flig, self.members_flig = self.loadTraj(
self.lig, self.ex_flig, self.ref_flig )
n_lig_members = t.n_members
del t
## complex
fname = T.stripSuffix( T.absfile( self.com, resolveLinks=0 ) )
self.ref_com = fname + '_ref.complex'
self.ref_blig= fname + '_blig.model'
self.ref_brec= fname + '_brec.model'
t, self.ex_com, self.members_com = self.loadTraj(
self.com, self.ex_com )
n_com_members = t.n_members
self.cl = self.cl or MU.difference( range(t.ref.lenChains()), self.cr)
rec = t.ref.takeChains( self.cr, breaks=0 )
lig = t.ref.takeChains( self.cl, breaks=0 )
del t
self.dumpMissing( Complex( rec, lig ), self.ref_com )
self.dumpMissing( rec, self.ref_brec )
self.dumpMissing( lig, self.ref_blig )
self.equalizeMemberCount( n_rec_members, n_lig_members, n_com_members )
if self.jack: self.prepareJackknife()
def __add1(self, n_members, excluded, index):
"""
Add one number from range( n_members ) to list of excluded indices
@param n_members: number of member trajectories
@type n_members: int
@param excluded: excluded member trajectories
@type excluded: [ int ]
@param index:
@type index: int
@return: the indices of all excluded member trajectories
@rtype: [ int ]
"""
remaining = MU.difference(range(n_members), excluded)
new_i = remaining[index]
return excluded + [new_i]
def __add1( self, n_members, excluded, index ):
"""
Add one number from range( n_members ) to list of excluded indices
@param n_members: number of member trajectories
@type n_members: int
@param excluded: excluded member trajectories
@type excluded: [ int ]
@param index:
@type index: int
@return: the indices of all excluded member trajectories
@rtype: [ int ]
"""
remaining = MU.difference( range( n_members ), excluded )
new_i = remaining[index]
return excluded + [ new_i ]
def __exclude(self, traj, exclude):
"""
Exclude members from a (set of) Trajectory.
@param traj: input trajectory
@type traj: EnsembleTraj
@param exclude: set of indices to be excluded
@type exclude: [ int ]
@return:
@rtype: EnsembleTraj
"""
if exclude == None or len(exclude) == 0:
return traj
members = range(traj.n_members)
if self.verbose:
self.log.add("excluding members: " + str(exclude))
return traj.takeMembers(MU.difference(members, exclude))
def __add3(self, n_members, excluded, trippleIndex):
"""
Add a tripple of numbers from range( n_members ) to be
excluded for error estimation. Tripples are chosen to have
minimal overlap. For 10 trajectories (*n_members*=10), the
first 3 tripples will be (1,2,3), (4,5,6), (7,8,9).
@param n_members: number of member trajectories
@type n_members: int
@param excluded: excluded member trajectories
@type excluded: [ int ]
@param trippleIndex:
@type trippleIndex: int
@return: the indices of all excluded member trajectories
@rtype: [ int ]
"""
remaining = MU.difference(range(n_members), excluded)
tripple = self.tripples(remaining, trippleIndex + 1)[-1]
return MU.union(excluded, list(tripple))
def __exclude( self, traj, exclude ):
"""
Exclude members from a (set of) Trajectory.
@param traj: input trajectory
@type traj: EnsembleTraj
@param exclude: set of indices to be excluded
@type exclude: [ int ]
@return:
@rtype: EnsembleTraj
"""
if exclude == None or len( exclude ) == 0:
return traj
members = range( traj.n_members )
if self.verbose:
self.log.add("excluding members: " + str(exclude))
return traj.takeMembers( MU.difference( members, exclude ) )
def __add3( self, n_members, excluded, trippleIndex ):
"""
Add a tripple of numbers from range( n_members ) to be
excluded for error estimation. Tripples are chosen to have
minimal overlap. For 10 trajectories (*n_members*=10), the
first 3 tripples will be (1,2,3), (4,5,6), (7,8,9).
@param n_members: number of member trajectories
@type n_members: int
@param excluded: excluded member trajectories
@type excluded: [ int ]
@param trippleIndex:
@type trippleIndex: int
@return: the indices of all excluded member trajectories
@rtype: [ int ]
"""
remaining = MU.difference( range( n_members ), excluded )
tripple = self.tripples( remaining, trippleIndex+1 )[-1]
return MU.union( excluded, list(tripple) )
print " -h |host1 host2 host3 ..| -e |host4 host5 ..|]"
print " -n ... search phrase"
print " -a ... kill all without asking"
print " -f ... don't ask anything at all"
print " -h ... only look on these hosts (default: all)"
print " -e ... exclude one or more hosts from killing"
sys.exit(0)
o = cmdDict({'h': nodes_all})
phrase = o['n']
hosts = toList(o['h'])
user = getpass.getuser()
ask = 'a' not in o
force = 'f' in o
if 'e' in o:
hosts = MU.difference(hosts, toList(o['e']))
msg = "KILL All jobs matching '%s' on all hosts?? Y/N " % phrase
if (not ask) and (force or string.upper(raw_input(msg)) != 'Y'):
print "Aborted."
sys.exit()
for h in hosts:
try:
kill(h, phrase, user, ask)
except KeyboardInterrupt:
print "\nAborted."
sys.exit()
except Exception, why:
print "Error killing %s: " % str(why), lastError()
print " -h |host1 host2 host3 ..| -e |host4 host5 ..|]"
print " -n ... search phrase"
print " -a ... kill all without asking"
print " -f ... don't ask anything at all"
print " -h ... only look on these hosts (default: all)"
print " -e ... exclude one or more hosts from killing"
sys.exit(0)
o = cmdDict( { 'h':nodes_all } )
phrase = o['n']
hosts = toList( o['h'] )
user = getpass.getuser()
ask = 'a' not in o
force= 'f' in o
if 'e' in o:
hosts = MU.difference( hosts, toList( o['e'] ) )
msg = "KILL All jobs matching '%s' on all hosts?? Y/N " % phrase
if (not ask) and (force or string.upper( raw_input( msg ) ) != 'Y'):
print "Aborted."
sys.exit()
for h in hosts:
try:
kill( h, phrase, user, ask )
except KeyboardInterrupt:
print "\nAborted."
sys.exit()
except Exception, why:
print "Error killing %s: " % str(why), lastError()