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.assert_( 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.assert_(os.path.exists(self.fcrg))
def __init__(self,
data={},
chunk_size=5,
hosts=[],
niceness={'default': 20},
slave_script='',
verbose=1,
show_output=0,
add_hosts=1,
redistribute=1):
"""
@param data: dict of items to be processed
@type data: {str_id:any}
@param chunk_size: number of items that are processed per job
@type chunk_size: int
@param hosts: list of host-names
@type hosts: [str]
@param niceness: host niceness dictionary {str_host-name: int_niceness}
@type niceness: {str:int}
@param slave_script: absolute path to slave-script
@type slave_script: str
@param verbose: verbosity level (default: 1)
@type verbose: 1|0
@param show_output: display one xterm per slave (default: 0)
@type show_output: 1|0
@param add_hosts: add hosts to PVM before starting (default: 1)
@type add_hosts: 1|0
@param redistribute: at the end, send same job out several times
(default: 1)
@type redistribute: 1|0
"""
if add_hosts:
if verbose: T.errWrite('adding %i hosts to pvm...' % len(hosts))
pvm.addHosts(hosts=hosts)
if verbose: T.errWriteln('done')
JobMaster.__init__(self,
data,
chunk_size,
hosts,
niceness,
slave_script,
show_output=show_output,
redistribute=redistribute,
verbose=verbose)
self.progress = {}
self.disabled_hosts = []
self.slow_hosts = {}
self.verbose = verbose
## end of calculation is signalled on lockMsg
self.lock = RLock()
self.lockMsg = Condition(self.lock)
## this method is called when everything is calculated
self.call_done = 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 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 __init__(self, data={}, chunk_size=5,
hosts=[], niceness={'default':20},
slave_script='', verbose=1,
show_output=0, add_hosts=1, redistribute=1 ):
"""
@param data: dict of items to be processed
@type data: {str_id:any}
@param chunk_size: number of items that are processed per job
@type chunk_size: int
@param hosts: list of host-names
@type hosts: [str]
@param niceness: host niceness dictionary {str_host-name: int_niceness}
@type niceness: {str:int}
@param slave_script: absolute path to slave-script
@type slave_script: str
@param verbose: verbosity level (default: 1)
@type verbose: 1|0
@param show_output: display one xterm per slave (default: 0)
@type show_output: 1|0
@param add_hosts: add hosts to PVM before starting (default: 1)
@type add_hosts: 1|0
@param redistribute: at the end, send same job out several times
(default: 1)
@type redistribute: 1|0
"""
if add_hosts:
if verbose: T.errWrite('adding %i hosts to pvm...' % len(hosts) )
pvm.addHosts( hosts=hosts )
if verbose: T.errWriteln('done')
JobMaster.__init__( self, data, chunk_size, hosts, niceness,
slave_script, show_output=show_output,
redistribute=redistribute, verbose=verbose )
self.progress = {}
self.disabled_hosts = []
self.slow_hosts = {}
self.verbose = verbose
## end of calculation is signalled on lockMsg
self.lock = RLock()
self.lockMsg = Condition( self.lock )
## this method is called when everything is calculated
self.call_done = None