def prepare(self):
"""
Overrides Executor method.
"""
Executor.prepare(self)
## if setGrid hasn't been called yet, create automatic grid
if not self.gsize:
self.setGrid()
if self.protonate:
reducer = Reduce(self.model,
verbose=self.verbose,
autocap=self.autocap,
tempdir=self.tempdir,
cwd=self.cwd,
log=self.log,
debug=self.debug)
if self.verbose:
self.log.add('adding hydrogen atoms to input structure\n')
self.delphimodel = reducer.run()
else:
self.delphimodel = self.model.clone()
self.delphimodel.xplor2amber()
if not os.path.exists(self.f_radii):
self.__prepareRadii()
if not os.path.exists(self.f_charges):
self.__prepareCharges(self.f_charges)
self.delphimodel.writePdb(self.f_pdb)
def prepare( self ):
"""
Overrides Executor method.
"""
Executor.prepare( self )
## self.__prepareFolder()
## if setGrid hasn't been called yet, create automatic grid
if not self.gsize:
self.setGrid()
if self.protonate:
reducer = Reduce( self.model, verbose=self.verbose,
autocap=self.autocap,
tempdir=self.tempdir, cwd=self.cwd,
log=self.log, debug=self.debug )
if self.verbose:
self.log.add('adding hydrogen atoms to input structure\n')
self.delphimodel = reducer.run()
else:
self.delphimodel = self.model.clone()
self.delphimodel.xplor2amber()
if not os.path.exists( self.f_charges ):
self.__prepareCharges( self.f_charges )
self.delphimodel.writePdb( self.f_pdb )
def cleanup(self):
"""
Tidy up the mess you created.
"""
if not self.debug:
T.tryRemove(self.f_pdb)
if not self.keep_map:
T.tryRemove(self.f_map)
Executor.cleanup(self)
def cleanup( self ):
"""
Tidy up the mess you created.
"""
if not self.debug:
T.tryRemove( self.f_pdb )
if not self.keep_map:
T.tryRemove( self.f_map )
Executor.cleanup( self )
def finish(self):
"""
Overrides Executor method
"""
Executor.finish(self)
self.result = self.parseOutput()
def __init__(self,
model,
template=None,
topologies=None,
f_charges=None,
f_radii=None,
f_map=None,
addcharge=True,
protonate=True,
autocap=False,
indi=4.0,
exdi=80.0,
salt=0.15,
ionrad=2,
prbrad=1.4,
bndcon=4,
scale=2.3,
perfil=60,
**kw):
"""
@param model: structure for which potential should be calculated
@type model: PDBModel
@param template: delphi command file template [None=use default]
@type template: str
@param f_radii: alternative delphi atom radii file [None=use default]
@type f_radii: str
@param topologies: alternative list of residue charge/topology files
[default: amber/residues/all*]
@type topologies: [ str ]
@param f_charges: alternative delphi charge file
[default: create custom]
@type f_charges: str
@param f_map : output file name for potential map [None= discard]
@type f_map : str
@param addcharge: build atomic partial charges with AtomCharger
[default: True]
@type addcharge: bool
@param protonate: (re-)build hydrogen atoms with reduce program (True)
see L{Biskit.Reduce}
@type protonate: bool
@param autocap: add capping NME and ACE residues to any (auto-detected)
false N- or C-terminal and chain breaks (default: False)
see L{Biskit.Reduce} and L{Biskit.PDBCleaner}
@type autocap: bool
@param indi: interior dilectric (4.0)
@param exdi: exterior dielectric (80.0)
@param salt: salt conc. in M (0.15)
@param ionrad: ion radius (2)
@param prbrad: probe radius (1.4)
@param bndcon: boundary condition (4, delphi default is 2)
@param scale: grid spacing (2.3)
@param perfil: grid fill factor in % (for automatic grid, 60)
@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)
"""
template = template or os.path.join(T.dataRoot(), 'delphi',
self.F_PARAMS)
tempdir = self.newtempfolder(tempdir=True) ## create new temp folder
f_in = tempfile.mktemp('.inp', 'delphi_', dir=tempdir)
self.f_pdb = tempfile.mktemp('.pdb', 'delphi_', dir=tempdir)
self.keep_map = f_map is not None
self.f_map = f_map or \
tempfile.mktemp( '_mapout.phi', 'delphi_', dir=tempdir )
## self.f_map = None
self.f_radiisrc = os.path.join(T.dataRoot(), 'delphi', self.F_RADII)
self.f_radii = f_radii or os.path.join(tempdir, 'radii.siz')
self.topologies = topologies or self.F_RESTYPES
self.f_charges = f_charges or tempfile.mktemp(
'.crg', 'delphi_', dir=tempdir)
self.protonate = protonate
self.autocap = autocap
self.addcharge = addcharge
## DELPHI run parameters
self.indi = indi # interior dilectric(4.0)
self.exdi = exdi # exterior dielectric(80.0)
self.salt = salt # salt conc. in M (0.15)
self.ionrad = ionrad # ion radius (2)
self.prbrad = prbrad # probe radius (1.4)
self.bndcon = bndcon # boundary condition (4, delphi default is 2)
## DELPHI parameters for custom grid
self.scale = scale # grid spacing (2.3)
self.perfil = perfil # grid fill factor in % (for automatic grid, 60)
self.gsize = None
self.acenter = None
self.strcenter = '(0.0,0.0,0.0)'
kw['tempdir'] = tempdir
kw['cwd'] = tempdir
Executor.__init__(self,
'delphi',
template=template,
f_in=f_in,
args=f_in,
catch_err=True,
**kw)
self.model = model
self.delphimodel = None
def finish( self ):
"""
Overrides Executor method
"""
Executor.finish( self )
self.result = self.parseOutput()
def __init__( self,
model,
template=None,
topologies=None,
f_charges=None,
f_radii=None,
f_map=None,
addcharge=True,
protonate=True,
autocap=False,
indi=4.0, exdi=80.0, salt=0.15, ionrad=2, prbrad=1.4,
bndcon=4, scale=2.3, perfil=60,
**kw ):
"""
@param model: structure for which potential should be calculated
@type model: PDBModel
@param template: delphi command file template [None=use default]
@type template: str
@param f_radii: alternative delphi atom radii file [None=use default]
@type f_radii: str
@param topologies: alternative list of residue charge/topology files
[default: amber/residues/all*]
@type topologies: [ str ]
@param f_charges: alternative delphi charge file
[default: create custom]
@type f_charges: str
@param f_map : output file name for potential map [None= discard]
@type f_map : str
@param addcharge: build atomic partial charges with AtomCharger
[default: True]
@type addcharge: bool
@param protonate: (re-)build hydrogen atoms with reduce program (True)
see L{Biskit.Reduce}
@type protonate: bool
@param autocap: add capping NME and ACE residues to any (auto-detected)
false N- or C-terminal and chain breaks (default: False)
see L{Biskit.Reduce} and L{Biskit.PDBCleaner}
@type autocap: bool
@param indi: interior dilectric (4.0)
@param exdi: exterior dielectric (80.0)
@param salt: salt conc. in M (0.15)
@param ionrad: ion radius (2)
@param prbrad: probe radius (1.4)
@param bndcon: boundary condition (4, delphi default is 2)
@param scale: grid spacing (2.3)
@param perfil: grid fill factor in % (for automatic grid, 60)
@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)
"""
template = template or os.path.join(T.dataRoot(),'delphi',self.F_PARAMS)
tempdir = self.newtempfolder( tempdir=True ) ## create new temp folder
f_in = tempfile.mktemp( '.inp', 'delphi_', dir=tempdir )
self.f_pdb = tempfile.mktemp( '.pdb', 'delphi_', dir=tempdir)
self.keep_map = f_map is not None
self.f_map = f_map or \
tempfile.mktemp( '_mapout.phi', 'delphi_', dir=tempdir )
## self.f_map = None
self.f_radii = f_radii or os.path.join(
T.dataRoot(),'delphi',self.F_RADII)
self.topologies = topologies or self.F_RESTYPES
self.f_charges = f_charges or tempfile.mktemp( '.crg', 'delphi_',
dir=tempdir )
self.protonate = protonate
self.autocap = autocap
self.addcharge = addcharge
## DELPHI run parameters
self.indi=indi # interior dilectric(4.0)
self.exdi=exdi # exterior dielectric(80.0)
self.salt=salt # salt conc. in M (0.15)
self.ionrad=ionrad # ion radius (2)
self.prbrad=prbrad # probe radius (1.4)
self.bndcon=bndcon # boundary condition (4, delphi default is 2)
## DELPHI parameters for custom grid
self.scale=scale # grid spacing (2.3)
self.perfil=perfil # grid fill factor in % (for automatic grid, 60)
self.gsize = None
self.acenter = None
self.strcenter = '(0.0,0.0,0.0)'
kw['tempdir'] = tempdir
kw['cwd'] = tempdir
Executor.__init__( self, 'delphi',
template=template,
f_in=f_in,
args=f_in,
catch_err=True,
**kw )
self.model = model
self.delphimodel = None