def newtempfolder( self, tempdir=None ):
"""
Create a new unique file name for a temporary folder or return the
system-wide existing tempfolder.
@param tempdir: folder for temporary files, will be created if not
existing (default: None ... use system default)
if set to True: create a new tempdir within default
@type tempdir: str | True
"""
if tempdir is True:
return tempfile.mktemp( '',
self.__class__.__name__.lower() + '_',
t.tempDir() )
else:
return tempdir or t.tempDir()
def newtempfolder(self, tempdir=None):
"""
Create a new unique file name for a temporary folder or return the
system-wide existing tempfolder.
@param tempdir: folder for temporary files, will be created if not
existing (default: None ... use system default)
if set to True: create a new tempdir within default
@type tempdir: str | True
"""
if tempdir is True:
return tempfile.mktemp('',
self.__class__.__name__.lower() + '_',
t.tempDir())
else:
return tempdir or t.tempDir()
def __prepareFolder( self ):
"""
The surfrace binary, radii files and the PDB have to be in the
current working directory. Otherwise we get a pretty silent
segmentation fault.
@return temp folder
@rtype str
"""
try:
folder = T.tempDir()
binlnk = os.path.join( folder, self.exe.name )
if not os.path.exists( binlnk ):
os.symlink( self.exe.bin, binlnk )
radii_txt = T.dataRoot() + '/surface_racer_3/radii.txt'
target = os.path.join(folder, 'radii.txt')
if not os.path.exists( target ):
os.symlink( radii_txt, target )
self.exe.bin = binlnk
return folder + '/'
except OSError, error:
raise SurfaceRacer_Error, \
'Error preparing temporary folder for SurfaceRacer\n'+\
'Error: %r\n' % error +\
'folder: %r\n' % folder +\
'binary: %r\n' % self.exe.bin +\
'binary link: %r' % binlnk
def __prepareFolder( self ):
"""
The surfrace binary, radii files and the PDB have to be in the
current working directory. Otherwise we get a pretty silent
segmentation fault.
@return temp folder
@rtype str
"""
try:
folder = T.tempDir()
binlnk = os.path.join( folder, self.exe.name )
if not os.path.exists( binlnk ):
os.symlink( self.exe.bin, binlnk )
radii_txt = T.dataRoot() + '/surface_racer_3/radii.txt'
target = os.path.join(folder, 'radii.txt')
if not os.path.exists( target ):
os.symlink( radii_txt, target )
self.exe.bin = binlnk
return folder + '/'
except OSError, error:
raise SurfaceRacer_Error, \
'Error preparing temporary folder for SurfaceRacer\n'+\
'Error: %r\n' % error +\
'folder: %r\n' % folder +\
'binary: %r\n' % self.exe.bin +\
'binary link: %r' % binlnk
def __minimize_complex( self, com ):
"""
Use Xplor to rigid body minimize the random complex.
@param com: random complex
@type com: Complex
"""
xp = ComplexMinimizer( com, t.tempDir(), log=self.xp_log )
xp.run()
def __minimize_complex(self, com):
"""
Use Xplor to rigid body minimize the random complex.
@param com: random complex
@type com: Complex
"""
xp = ComplexMinimizer(com, t.tempDir(), log=self.xp_log)
xp.run()
def __init__(self, models, **kw):
"""
@param models: if more than one model is given they are
concatenated and the energy is calculated
for the two together.
@type models: PDBModels
@param kw: additional key=value parameters for Executor:
@type kw: key=value pairs
::
debug - 0|1, keep all temporary files (default: 0)
verbose - 0|1, print progress messages to log (log != STDOUT)
node - str, host for calculation (None->local) NOT TESTED
(default: None)
nice - int, nice level (default: 0)
log - Biskit.LogFile, program log (None->STOUT) (default: None)
"""
self.models = models
## Potentials to use, pII3.0 is the default setting
self.pairPot = 'prosa2003.pair-cb' # default: pII3.0.pair-cb
self.surfPot = 'prosa2003.surf-cb' # default: pII3.0.surf-cb
## temp files for prosa pdb file and prosa output file
self.prosaPdbFile = tempfile.mktemp('_prosa2003.pdb')
self.prosaOutput = tempfile.mktemp('_prosa2003.out')
self.temp_dir = T.tempDir()
prosaInput = tempfile.mktemp('_prosa2003.inp')
## set default values
self.objectName = 'obj1'
self.lower_k = 1
self.upper_k = 600
self.pot_lb = 0.
self.pot_ub = 15.
Executor.__init__(self,
'prosa2003',
template=self.inp,
f_in=prosaInput,
**kw)
## check the path to the potential files
self.checkPotentials()
def __init__(self, models, **kw ):
"""
@param models: if more than one model is given they are
concatenated and the energy is calculated
for the two together.
@type models: PDBModels
@param kw: additional key=value parameters for Executor:
@type kw: key=value pairs
::
debug - 0|1, keep all temporary files (default: 0)
verbose - 0|1, print progress messages to log (log != STDOUT)
node - str, host for calculation (None->local) NOT TESTED
(default: None)
nice - int, nice level (default: 0)
log - Biskit.LogFile, program log (None->STOUT) (default: None)
"""
self.models = models
## Potentials to use, pII3.0 is the default setting
self.pairPot = 'prosa2003.pair-cb' # default: pII3.0.pair-cb
self.surfPot = 'prosa2003.surf-cb' # default: pII3.0.surf-cb
## temp files for prosa pdb file and prosa output file
self.prosaPdbFile = tempfile.mktemp('_prosa2003.pdb')
self.prosaOutput = tempfile.mktemp('_prosa2003.out')
self.temp_dir = T.tempDir()
prosaInput = tempfile.mktemp('_prosa2003.inp')
## set default values
self.objectName = 'obj1'
self.lower_k = 1
self.upper_k = 600
self.pot_lb = 0.
self.pot_ub = 15.
Executor.__init__( self, 'prosa2003', template=self.inp,
f_in=prosaInput, **kw )
## check the path to the potential files
self.checkPotentials()
def test_SettingsManager(self):
"""SettingsManager test"""
f_in = T.dataRoot() + '/defaults/settings.cfg'
self.f_out = T.tempDir() + '/settings.cfg'
self.m = SettingsManager( f_in, self.f_out,
createmissing=True,
verbose=self.local )
ns = locals() ## fetch local namespace
self.m.updateNamespace( ns ) ## parse and insert options into namespace
if self.local:
globals().update( locals() ) ## publish namespace for debugging
r = self.m.settings2dict()['testparam']
self.assertEqual( r, 42) ## from 'int-testparam = 42' in settings.cfg
def test_SettingsManager(self):
"""SettingsManager test"""
f_in = T.dataRoot() + '/defaults/settings.cfg'
self.f_out = T.tempDir() + '/settings.cfg'
self.m = SettingsManager(f_in,
self.f_out,
createmissing=True,
verbose=self.local)
ns = locals() ## fetch local namespace
self.m.updateNamespace(ns) ## parse and insert options into namespace
if self.local:
globals().update(locals()) ## publish namespace for debugging
r = self.m.settings2dict()['testparam']
self.assertEqual(r, 42) ## from 'int-testparam = 42' in settings.cfg
def prepare(self):
self.fname = T.testRoot() + '/com/1BGS_original.pdb'
self.outPath = T.tempDir()
def prepare(self):
self.fname = T.testRoot() + '/com/1BGS_original.pdb'
self.outPath = T.tempDir()
