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 dump(self, o):
"""
Try to pickle an object to the currently valid path.
@return: the absolute path to which o was pickled
@rtype: str
"""
try:
f = self.local()
T.dump(f, o)
return f
except:
T.errWriteln("Couldn't dump to %s (constructed from %s)" %\
self.formatted(), self.local() )
raise
def dump( self, o ):
"""
Try to pickle an object to the currently valid path.
@return: the absolute path to which o was pickled
@rtype: str
"""
try:
f = self.local()
T.dump( f, o )
return f
except:
T.errWriteln("Couldn't dump to %s (constructed from %s)" %\
self.formatted(), self.local() )
raise
def _assign_seg_ids(self):
"""
Assign new segment id to each chain.
"""
counter = self.chainIdOffset
for chain in self.chains:
## Assemble segid from pdb code + one letter out of A to Z
chain.segment_id = self.pdbname()[:3] + string.uppercase[counter]
counter = counter + 1
try: # report changed segement ids
chain_id = chain.chain_id
self.log.add("changed segment ID of chain "+chain_id+\
" to "+chain.segment_id)
except:
T.errWriteln("_assign_seg_ids(): logerror")
def _assign_seg_ids(self):
"""
Assign new segment id to each chain.
"""
counter = self.chainIdOffset
for chain in self.chains:
## Assemble segid from pdb code + one letter out of A to Z
chain.segment_id = self.pdbname()[:3] + string.uppercase[counter]
counter = counter + 1
try: # report changed segement ids
chain_id = chain.chain_id
self.log.add("changed segment ID of chain "+chain_id+\
" to "+chain.segment_id)
except:
T.errWriteln("_assign_seg_ids(): logerror")
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 extractWaters(self):
"""
Write waters into separate pdb file, called |pdbCode|_waters.pdb.
"""
try:
fTarget = self.outPath + '/' +\
self.pdbname()[:4] + '_waters.pdb'
pdb = PDBFile( fTarget, mode='w' )
waters = []
for key in ['HOH', 'DOD']:
if self.pdb.molecules.has_key( key ):
waters += self.pdb.molecules[ key ]
pdb.nextChain(chain_id='', segment_id='1XWW')
for w in waters:
pdb.nextResidue('TIP3')
## XPLOR wants "ATOM" not "HETATM":
pdb.het_flag = 0
pdb.writeAtom('OH2', w.atoms['O'].position)
## keep TIP3 waters as well
if len(waters) == 0:
try:
TIP3_waters = self.pdb.molecules[ 'TIP3' ]
except:
TIP3_waters = []
for w in TIP3_waters:
pdb.nextResidue('TIP3')
## XPLOR wants "ATOM" not "HETATM":
pdb.het_flag = 0
pdb.writeAtom('OH2', w.atoms['OH2'].position)
pdb.writeAtom('H1', w.atoms['H1'].position)
pdb.writeAtom('H2', w.atoms['H2'].position)
pdb.close()
except:
T.errWriteln("Error writing waters to %s: " % fTarget )
T.errWriteln( T.lastError() )
def extractWaters(self):
"""
Write waters into separate pdb file, called |pdbCode|_waters.pdb.
"""
try:
fTarget = self.outPath + '/' +\
self.pdbname()[:4] + '_waters.pdb'
pdb = PDBFile(fTarget, mode='w')
waters = []
for key in ['HOH', 'DOD']:
if self.pdb.molecules.has_key(key):
waters += self.pdb.molecules[key]
pdb.nextChain(chain_id='', segment_id='1XWW')
for w in waters:
pdb.nextResidue('TIP3')
## XPLOR wants "ATOM" not "HETATM":
pdb.het_flag = 0
pdb.writeAtom('OH2', w.atoms['O'].position)
## keep TIP3 waters as well
if len(waters) == 0:
try:
TIP3_waters = self.pdb.molecules['TIP3']
except:
TIP3_waters = []
for w in TIP3_waters:
pdb.nextResidue('TIP3')
## XPLOR wants "ATOM" not "HETATM":
pdb.het_flag = 0
pdb.writeAtom('OH2', w.atoms['OH2'].position)
pdb.writeAtom('H1', w.atoms['H1'].position)
pdb.writeAtom('H2', w.atoms['H2'].position)
pdb.close()
except:
T.errWriteln("Error writing waters to %s: " % fTarget)
T.errWriteln(T.lastError())
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 reportClustering(self, raw=None):
"""
Report the clustering result.
Writes:
- clustering results to L{F_CLUSTER_LOG}
- blast records to L{F_BLAST_OUT}
- blast records of centers to L{F_CLUSTER_BLAST_OUT}
- raw clustering results to L{F_CLUSTER_RAW} if raw not None
@param raw: write raw clustering result to disk (default: None)
@type raw: 1|0
"""
try:
if self.verbose:
f = open(self.outFolder + self.F_CLUSTER_LOG, 'w', 1)
for cluster in self.clusters:
f.write("%i\t" % (len(cluster)))
for id in cluster:
f.write("%s:%.2f " %
(id, self.record_dic[id].resolution))
f.write("\n")
f.close()
## write blast records of centers to disc
centers = [c[0] for c in self.clusters]
self.writeClusteredBlastResult( \
self.outFolder + self.F_BLAST_OUT,
self.outFolder + self.F_CLUSTER_BLAST_OUT, centers )
self.copyClusterOut(raw=raw)
except IOError, why:
T.errWriteln("Can't write cluster report." + str(why))
def reportClustering( self, raw=None ):
"""
Report the clustering result.
Writes:
- clustering results to L{F_CLUSTER_LOG}
- blast records to L{F_BLAST_OUT}
- blast records of centers to L{F_CLUSTER_BLAST_OUT}
- raw clustering results to L{F_CLUSTER_RAW} if raw not None
@param raw: write raw clustering result to disk (default: None)
@type raw: 1|0
"""
try:
if self.verbose:
f = open( self.outFolder +self.F_CLUSTER_LOG, 'w', 1)
for cluster in self.clusters:
f.write( "%i\t" % ( len( cluster )))
for id in cluster:
f.write("%s:%.2f "%(id,self.record_dic[id].resolution))
f.write( "\n")
f.close()
## write blast records of centers to disc
centers = [ c[0] for c in self.clusters ]
self.writeClusteredBlastResult( \
self.outFolder + self.F_BLAST_OUT,
self.outFolder + self.F_CLUSTER_BLAST_OUT, centers )
self.copyClusterOut( raw=raw )
except IOError, why:
T.errWriteln( "Can't write cluster report." + str(why) )
os.unlink(f)
t.dump(complex_lst, options['o'])
else:
subLst = checkListStatus(complex_lst, update, force, version)
if subLst:
## initialize nodes, and start distributed calculation
master = ContactMaster(complex_lst,
int(options['c']),
cpus_all[:host_number],
refComplex=refComplex,
updateOnly=update,
force=force,
niceness=nice_dic,
outFile=options['o'],
com_version=version,
show_output=show_x,
add_hosts=add_hosts)
master.start()
else:
t.flushPrint("\n #### Nothing to update! #### ")
except IOError, why:
t.errWriteln("IOError while working on %s:" % t.absfile(options['i']) \
+ str(why) )
t.errWriteln(t.lastErrorTrace())
for fname in srcfiles:
fname = t.absfile( fname )
shutil.copy( fname, fname + '_' )
methods = re_lst( module, exclude )
fold = open( fname + '_' )
fnew = open( fname, 'w' )
i = 0
for l in fold:
i += 1
l = replace_import_statement( l, module, importas )
l, occurrences = replace_line( l, methods, importas + '.' )
if occurrences > 0:
t.errWriteln( '%s %5i %2i matches:\n\t%s' %
(t.stripFilename(fname), i, occurrences, l) )
fnew.write( l )
fnew.close()
fold.close()
except:
syntax()
for fname in srcfiles:
fname = t.absfile(fname)
shutil.copy(fname, fname + '_')
methods = re_lst(module, exclude)
fold = open(fname + '_')
fnew = open(fname, 'w')
i = 0
for l in fold:
i += 1
l = replace_import_statement(l, module, importas)
l, occurrences = replace_line(l, methods, importas + '.')
if occurrences > 0:
t.errWriteln('%s %5i %2i matches:\n\t%s' %
(t.stripFilename(fname), i, occurrences, l))
fnew.write(l)
fnew.close()
fold.close()
except:
syntax()
complex_lst += sub
os.unlink( f )
t.dump( complex_lst, options['o'] )
else:
subLst = checkListStatus(complex_lst, update, force, version )
if subLst:
## initialize nodes, and start distributed calculation
master = ContactMaster(complex_lst, int( options['c'] ),
cpus_all[:host_number],
refComplex = refComplex,
updateOnly = update,
force = force,
niceness = nice_dic,
outFile = options['o'],
com_version = version,
show_output = show_x,
add_hosts = add_hosts)
master.start()
else:
t.flushPrint( "\n #### Nothing to update! #### " )
except IOError, why:
t.errWriteln("IOError while working on %s:" % t.absfile(options['i']) \
+ str(why) )
t.errWriteln( t.lastErrorTrace() )
