def __init__(self, full=0, mode='w', verbose=1, **kw ):
"""
@param mode: open file with this mode, w=override, a=append
@type mode: str
@param full: dispaly pymol structures in fill screen mode::
0 - normal mode
1 - full screen mode
2 - full screen and no menues
@type full: 0|1|2
"""
self.verbose = verbose
# name of .pml file
self.foutName = tempfile.mktemp() + '.pml'
# open for <appending|writing|reading>
self.fgenerate = open(self.foutName, mode)
# will contain PymolModels or lists of PymolModels
self.dic = {}
## add startup commands
self.initPymol()
## set arguments for display options (normal, full, all)
arg = '-q %s'%self.foutName
if full == 1:
arg = '-qe %s'%self.foutName
if full == 2:
arg = '-qei %s'%self.foutName
Executor.__init__( self, 'pymol', args=arg,
catch_err=1, catch_out=1, **kw )
def __init__(self, target, hmmdb=settings.hmm_db, noSearch=None, **kw):
"""
@param target: fasta sequence, fasta file, or PDBModel
@type target: PDBModel or str (fasta file) or [ str ] (fasta lines)
@param hmmdb: Pfam hmm database
@type hmmdb: str
@param noSearch: don't perform a seach
@type noSearch: 1 OR None
"""
self.hmmdb = hmmdb
Executor.__init__(self,
'hmmpfam',
f_in=tempfile.mktemp('.fasta'),
catch_out=1,
**kw)
self.target = target
self.fastaID = ''
if noSearch:
if self.verbose:
self.log.writeln(
'Profiles provided - No search will be performed.')
def __init__(self, ref_model, models, **kw):
"""
@param ref_model: reference
@type ref_model: PDBModel
@param models: structures to be compared with reference
@type models: [PDBModel]
@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)
"""
Executor.__init__(self, 'icmbrowser', template=self.inp_head, **kw)
self.f_ref = tempfile.mktemp('_icmcad_ref.pdb')
self.f_pdb = tempfile.mktemp('_icmcad_%i.pdb')
self.ref_model = ref_model
self.models = models
if not isinstance(self.models, list):
self.models = [self.models]
def __init__(self, model, **kw ):
"""
@param model: reference PDBModel
@type model: PDBModel
@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.temp_pdb = tempfile.mktemp('_foldx_.pdb')
self.temp_command = tempfile.mktemp('_foldx_.command')
self.temp_option = tempfile.mktemp('_foldx_.option')
self.temp_result = tempfile.mktemp('_foldx_.result')
self.temp_runlog = tempfile.mktemp('_foldx_.log')
self.temp_errlog = tempfile.mktemp('_foldx_.err')
Executor.__init__( self, 'fold_X', args='-manual %s %s %s'\
%(self.temp_pdb, self.temp_option,
self.temp_command), **kw )
self.model = model.clone()
## fold-X-allowed atoms for each res in standard order
self.aminoAcidDict = molUtils.aaAtoms
for k in self.aminoAcidDict:
if 'HN' not in self.aminoAcidDict[ k ]:
self.aminoAcidDict[ k ] += ['HN']
def __init__( self, model, **kw ):
"""
@param model: PDBModel
@type model:
@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.f_xyzrn = tempfile.mktemp('_msms.xyzrn')
## output file from MSMS, will add .area exiension to file
self.f_surf = tempfile.mktemp( )
arg =' -surface ases -if %s -af %s'%( self.f_xyzrn, self.f_surf )
Executor.__init__( self, 'msms', args=arg, **kw )
self.model = model.clone()
def __init__( self, model, **kw ):
"""
@param model: PDBModel
@type model:
@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.f_xyzrn = tempfile.mktemp('_msms.xyzrn')
## output file from MSMS, will add .area exiension to file
self.f_surf = tempfile.mktemp( )
arg =' -surface ases -if %s -af %s'%( self.f_xyzrn, self.f_surf )
Executor.__init__( self, 'msms', args=arg, **kw )
self.model = model.clone()
def __init__(self, model, **kw):
"""
@param model: model analyze
@type model: PDBModel
@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.model = model
# self.model = model.clone( deepcopy=1 )
## temporary pdb-file
self.f_pdb = tempfile.mktemp('_dssp.pdb')
self.f_out = tempfile.mktemp('_dssp.out')
Executor.__init__(self,
'dsspcmbi',
args='-i %s' % self.f_pdb,
catch_err=1,
**kw)
def __init__(self, model, **kw):
"""
@param model: PDBModel
@type model:
@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)
"""
Executor.__init__(self,
'whatif',
template=self.whatif_script,
f_out='/dev/null',
**kw)
self.f_pdb = tempfile.mktemp('_whatif.pdb')
self.f_relativeASA = tempfile.mktemp('_whatif_relative.log')
self.f_residueASA = tempfile.mktemp('_whatif_residue.log')
self.model = model.clone()
def __init__( self, ref_model, models, **kw ):
"""
@param ref_model: reference
@type ref_model: PDBModel
@param models: structures to be compared with reference
@type models: [PDBModel]
@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)
"""
Executor.__init__( self, 'icmbrowser', template=self.inp_head, **kw )
self.f_ref = tempfile.mktemp('_icmcad_ref.pdb')
self.f_pdb = tempfile.mktemp('_icmcad_%i.pdb')
self.ref_model = ref_model
self.models = models
if not isinstance( self.models, list ):
self.models = [ self.models ]
def __init__( self, model, refmodel, **kw ):
"""
@param model: structure to be aligned to reference
@type model: PDBModel
@param refmodel: reference structure
@type refmodel: PDBModel
@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.f_pdbin = tempfile.mktemp( '_tmalign_in.pdb' )
self.f_pdbref= tempfile.mktemp( '_tmalign_ref.pdb' )
self.f_matrix= tempfile.mktemp( '_tmalign_matrix.out' )
Executor.__init__( self, 'tmalign',
args= '%s %s -m %s' % (self.f_pdbin, self.f_pdbref, self.f_matrix),
**kw )
self.refmodel = refmodel
self.model = model
def __init__( self, model, **kw ):
"""
@param model: model analyze
@type model: PDBModel
@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.model = model
# self.model = model.clone( deepcopy=1 )
## temporary pdb-file
self.f_pdb = tempfile.mktemp( '_dssp.pdb')
self.f_out = tempfile.mktemp( '_dssp.out')
Executor.__init__( self, 'dsspcmbi',
args='-na %s'%self.f_pdb,
catch_err=1, **kw )
def __init__(self, model, refmodel, **kw):
"""
@param model: structure to be aligned to reference
@type model: PDBModel
@param refmodel: reference structure
@type refmodel: PDBModel
@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.f_pdbin = tempfile.mktemp('_tmalign_in.pdb')
self.f_pdbref = tempfile.mktemp('_tmalign_ref.pdb')
self.f_matrix = tempfile.mktemp('_tmalign_matrix.out')
Executor.__init__(self,
'tmalign',
args='%s %s -m %s' %
(self.f_pdbin, self.f_pdbref, self.f_matrix),
**kw)
self.refmodel = refmodel
self.model = model
def __init__(self,
model,
tempdir=None,
args='',
autocap=False,
capN=[],
capC=[],
**kw):
"""
@param model: structure to be aligned to reference
@type model: PDBModel
@param tempdir: create dedicated temporary folder (default: None)
see Executor
@param tempdir: str | 0|1
@param args: additional command line arguments for reduce (default:'')
example: '-OLDpdb'
@type args: str
@param autocap: add capping NME and ACE residues to any (auto-detected)
false N- or C-terminal (default: False)
@type autocap: bool
@param capN: cap N-terminal of these chains (indices) with ACE ([])
@type capN: [ int ]
@param capC: cap C-terminal of these chains (indices) with NME ([])
@type capN: [ int ]
@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)
"""
tempdir = self.newtempfolder(tempdir)
self.f_pdbin = tempfile.mktemp('_in.pdb', 'reduce_', dir=tempdir)
f_out = tempfile.mktemp('_out.pdb', 'reduce_', dir=tempdir)
self.f_db = T.dataRoot() + '/reduce/reduce_wwPDB_het_dict.txt'
self.autocap = autocap
self.capN = capN
self.capC = capC
lenchains = model.lenChains()
Executor.__init__( self, 'reduce',
args= '%s -BUILD -Nterm%i -DB %s %s' %\
(args, lenchains, self.f_db, self.f_pdbin),
f_out=f_out, catch_err=True,
tempdir=tempdir,
**kw )
self.model = model
def __init__( self, model, tempdir=None, args='',
autocap=False, capN=[], capC=[],
**kw ):
"""
@param model: structure to be aligned to reference
@type model: PDBModel
@param tempdir: create dedicated temporary folder (default: None)
see Executor
@param tempdir: str | 0|1
@param args: additional command line arguments for reduce (default:'')
example: '-OLDpdb'
@type args: str
@param autocap: add capping NME and ACE residues to any (auto-detected)
false N- or C-terminal (default: False)
@type autocap: bool
@param capN: cap N-terminal of these chains (indices) with ACE ([])
@type capN: [ int ]
@param capC: cap C-terminal of these chains (indices) with NME ([])
@type capN: [ int ]
@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)
"""
tempdir = self.newtempfolder( tempdir )
self.f_pdbin = tempfile.mktemp( '_in.pdb', 'reduce_', dir=tempdir )
f_out= tempfile.mktemp( '_out.pdb', 'reduce_', dir=tempdir)
self.f_db = T.dataRoot() + '/reduce/reduce_wwPDB_het_dict.txt'
self.autocap = autocap
self.capN = capN
self.capC = capC
lenchains = model.lenChains()
Executor.__init__( self, 'reduce',
args= '%s -BUILD -Nterm%i -DB %s %s' %\
(args, lenchains, self.f_db, self.f_pdbin),
f_out=f_out, catch_err=True,
tempdir=tempdir,
**kw )
self.model = model
def __init__( self, hmmFile, fastaFile, fastaID, **kw ):
"""
@param hmmFile: path to hmm file (profile)
@type hmmFile: str
@param fastaFile: path to fasta search sequence
@type fastaFile: str
@param fastaID: fasta id of search sequence
@type fastaID: str
"""
self.fastaID = fastaID
Executor.__init__( self, 'hmmalign',
args=' -q %s %s'%(hmmFile, fastaFile), **kw )
def __init__( self, hmmName, hmmdb, **kw ):
"""
@param hmmName: hmm profile name
@type hmmName: str
@param hmmdb: Pfam hmm database
@type hmmdb: str
"""
self.hmmName = hmmName
Executor.__init__( self, 'hmmfetch',
args=' %s %s'%(hmmdb, hmmName), **kw )
self.f_out = tempfile.mktemp('.hmm')
def __init__( self, hmmdb, **kw ):
"""
@param hmmdb: Pfam hmm database
@type hmmdb: str
"""
Executor.__init__( self, 'hmmindex', args='%s'%hmmdb, **kw )
if not os.path.exists(hmmdb+'.ssi'):
if self.verbose:
self.log.writeln(
'HMMINDEX: Indexing hmm database. This will take a while')
self.run()
def __init__(self, hmmdb, **kw):
"""
@param hmmdb: Pfam hmm database
@type hmmdb: str
"""
Executor.__init__(self, 'hmmindex', args='%s' % hmmdb, **kw)
if not os.path.exists(hmmdb + '.ssi'):
if self.verbose:
self.log.writeln(
'HMMINDEX: Indexing hmm database. This will take a while')
self.run()
def __init__(self,
model,
cr=[0],
cl=None,
mode=2,
breaks=0,
catch_err=1,
**kw):
"""
Create a new Intervor instance for a given protein-protein complex.
@param model: Structure of receptor, ligand and water
@type model: Biskit.PDBModel
@param cr: receptor chains (default: [0] = first chain)
@type cr: [ int ]
@param cl: ligand chains (default: None = all remaining protein chains)
@type cl: [ int ]
@param breaks: consider chain breaks (backbone gaps) (default: 0)
@type breaks: bool or 1|0
@param mode: what to calculate (default 2, = all with shelling order)
@type mode: int
@param catch_err: deviate STDERR to temporary file (default 1)
@type catch_err: bool or 0|1
@param **kw: any other keyword=value pair recognized by Executor
"""
Executor.__init__(self, 'intervor', catch_err=catch_err, **kw)
assert isinstance( model, B.PDBModel ), \
'requires PDBModel instance'
assert model is not None, 'requires PDBModel instance'
self.model = model
self.breaks = breaks
self.chains_rec = cr
self.chains_lig = cl or self.__getLigandChains(model, cr)
self.local_model = None #: will hold modified copy of model
self.mode = mode
## intervor puts several output files into current working directory
## but respect cwd from Executor.__init__ or ExeConfig/exe_intervor.dat
self.cwd = self.cwd or tempfile.gettempdir()
#: will be used by intervor for different output files
self.f_prefix = tempfile.mktemp(dir=self.exe.cwd)
self.f_pdb = self.f_prefix + '_intervor.pdb'
self.result = {}
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,
template,
leaprc=None,
**kw ):
"""
@param template: template for leap input file (file or string)
@type template: str
@param leaprc: forcefield code (leaprc file ending, e.g. 'ff99')
OR leaprc file name (e.g, 'leaprc.f99')
OR leaprc path witin $AMBERHOME
OR leaprc path
default: take value from exe_tleap.dat
@type leaprc: str
@param f_in: complete leap input file -- existing or not, to be kept
(default: create from template and then discard)
@type f_in: str
@param f_out: file for leap log output (default: discard)
@type f_out: str
@param out_parm: parm output file name (default: 'top.parm')
@type out_parm: str
@param out_crd : coordinate output file name (default '0.crd' )
@type out_crd : str
@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)
"""
# override some Executor defaults unless they are freshly given
kw['catchout'] = kw.get('catchout',0)
Executor.__init__( self, 'tleap', template=template, **kw )
self.args = '-f %s' % self.f_in
self.leaprc = self.findLeaprc( leaprc or self.exe.leaprc )
## set some defaults that may or may not have been specified
self.out_parm = kw.get('out_parm', 'top.parm' )
self.out_crd = kw.get('out_crd', '0.crd')
def __init__( self, hmmName, hmmdb=settings.hmm_db, **kw ):
"""
@param hmmName: hmm profile name
@type hmmName: str
@param hmmdb: Pfam hmm database
@type hmmdb: str
**kw - all Executor parameters, in particular:
@param f_out: target file name for profile.hmm, prevents its deletion
@type f_out: str
@param debug:
@param log:
@param ...
"""
self.hmmName = hmmName
Executor.__init__( self, 'hmmfetch',
args=' %s %s'%(hmmdb, hmmName), **kw )
def __init__( self, hmmFile, fastaFile, fastaID, **kw ):
"""
@param hmmFile: path to hmm file (profile)
@type hmmFile: str
@param fastaFile: path to fasta search sequence
@type fastaFile: str
@param fastaID: fasta id of search sequence
@type fastaID: str
"""
self.fastaID = fastaID
self.hmmFile = hmmFile
self.fastaFile = fastaFile
assert T.fileLength( self.hmmFile ) > 10, \
'input HMM file missing or empty'
Executor.__init__( self, 'hmmalign',
args=' -q %s %s'%(hmmFile, fastaFile), **kw )
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, template, leaprc=None, **kw):
"""
@param template: template for leap input file (file or string)
@type template: str
@param leaprc: forcefield code (leaprc file ending, e.g. 'ff99')
OR leaprc file name (e.g, 'leaprc.f99')
OR leaprc path witin $AMBERHOME
OR leaprc path
default: take value from exe_tleap.dat
@type leaprc: str
@param f_in: complete leap input file -- existing or not, to be kept
(default: create from template and then discard)
@type f_in: str
@param f_out: file for leap log output (default: discard)
@type f_out: str
@param out_parm: parm output file name (default: 'top.parm')
@type out_parm: str
@param out_crd : coordinate output file name (default '0.crd' )
@type out_crd : str
@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)
"""
# override some Executor defaults unless they are freshly given
kw['catchout'] = kw.get('catchout', 0)
Executor.__init__(self, 'tleap', template=template, **kw)
self.args = '-f %s' % self.f_in
self.leaprc = self.findLeaprc(leaprc or self.exe.leaprc)
## set some defaults that may or may not have been specified
self.out_parm = kw.get('out_parm', 'top.parm')
self.out_crd = kw.get('out_crd', '0.crd')
def __init__( self, model, cr=[0], cl=None, mode=2, breaks=0,
catch_err=1, **kw ):
"""
Create a new Intervor instance for a given protein-protein complex.
@param model: Structure of receptor, ligand and water
@type model: Biskit.PDBModel
@param cr: receptor chains (default: [0] = first chain)
@type cr: [ int ]
@param cl: ligand chains (default: None = all remaining protein chains)
@type cl: [ int ]
@param breaks: consider chain breaks (backbone gaps) (default: 0)
@type breaks: bool or 1|0
@param mode: what to calculate (default 2, = all with shelling order)
@type mode: int
@param catch_err: deviate STDERR to temporary file (default 1)
@type catch_err: bool or 0|1
@param **kw: any other keyword=value pair recognized by Executor
"""
Executor.__init__( self, 'intervor', catch_err=catch_err, **kw )
assert isinstance( model, B.PDBModel ), \
'requires PDBModel instance'
assert model is not None, 'requires PDBModel instance'
self.model = model
self.breaks= breaks
self.chains_rec = cr
self.chains_lig = cl or self.__getLigandChains( model, cr )
self.local_model = None #: will hold modified copy of model
self.mode = mode
## intervor puts several output files into current working directory
## but respect cwd from Executor.__init__ or ExeConfig/exe_intervor.dat
self.cwd = self.cwd or tempfile.gettempdir()
#: will be used by intervor for different output files
self.f_prefix = tempfile.mktemp( dir=self.exe.cwd )
self.f_pdb = self.f_prefix + '_intervor.pdb'
self.result = {}
def __init__(self, hmmName, hmmdb=settings.hmm_db, **kw):
"""
@param hmmName: hmm profile name
@type hmmName: str
@param hmmdb: Pfam hmm database
@type hmmdb: str
**kw - all Executor parameters, in particular:
@param f_out: target file name for profile.hmm, prevents its deletion
@type f_out: str
@param debug:
@param log:
@param ...
"""
self.hmmName = hmmName
Executor.__init__(self,
'hmmfetch',
args=' %s %s' % (hmmdb, hmmName),
**kw)
def __init__(self, hmmFile, fastaFile, fastaID, **kw):
"""
@param hmmFile: path to hmm file (profile)
@type hmmFile: str
@param fastaFile: path to fasta search sequence
@type fastaFile: str
@param fastaID: fasta id of search sequence
@type fastaID: str
"""
self.fastaID = fastaID
self.hmmFile = hmmFile
self.fastaFile = fastaFile
assert T.fileLength( self.hmmFile ) > 10, \
'input HMM file missing or empty'
Executor.__init__(self,
'hmmalign',
args=' -q %s %s' % (hmmFile, fastaFile),
**kw)
def __init__(self, seq1, seq2, **kw ):
"""
@param seq1: sequence string
@type seq1: str
@param seq2: sequence string
@type seq2: str
"""
self.seq1 = seq1
self.seq2 = seq2
self.inp1 = tempfile.mktemp('_seq1.fasta')
self.inp2 = tempfile.mktemp('_seq2.fasta')
# Blast Identities and Expext value
self.ex_identity = re.compile('.+ Identities = (\d+)/(\d+) ')
self.ex_expect = re.compile('.+ Expect = ([\d\-e\.]+)')
blastcmd = '-i %s -j %s -M BLOSUM62 -p blastp -F F'\
%(self.inp1, self.inp2)
Executor.__init__( self, 'bl2seq', blastcmd, catch_out=1, **kw )
def __init__(self, seq1, seq2, **kw):
"""
@param seq1: sequence string
@type seq1: str
@param seq2: sequence string
@type seq2: str
"""
self.seq1 = seq1
self.seq2 = seq2
self.inp1 = tempfile.mktemp('_seq1.fasta')
self.inp2 = tempfile.mktemp('_seq2.fasta')
# Blast Identities and Expext value
self.ex_identity = re.compile('.+ Identities = (\d+)/(\d+) ')
self.ex_expect = re.compile('.+ Expect = ([\d\-e\.]+)')
blastcmd = '-i %s -j %s -M BLOSUM62 -p blastp -F F'\
%(self.inp1, self.inp2)
Executor.__init__(self, 'bl2seq', blastcmd, catch_out=1, **kw)
def __init__( self, target, hmmdb=settings.hmm_db, noSearch=None, **kw ):
"""
@param target: fasta sequence, fasta file, or PDBModel
@type target: PDBModel or str (fasta file) or [ str ] (fasta lines)
@param hmmdb: Pfam hmm database
@type hmmdb: str
@param noSearch: don't perform a seach
@type noSearch: 1 OR None
"""
self.hmmdb = hmmdb
Executor.__init__( self, 'hmmpfam', f_in= tempfile.mktemp('.fasta'),
catch_out=1, **kw )
self.target = target
self.fastaID = ''
if noSearch:
if self.verbose:
self.log.writeln(
'Profiles provided - No search will be performed.')
def __init__( self, target, hmmdb, noSearch=None, **kw ):
"""
@param target: sequence
@type target: PDBModel or fasta file
@param hmmdb: Pfam hmm database
@type hmmdb: str
@param noSearch: don't perform a seach
@type noSearch: 1 OR None
"""
self.fName = tempfile.mktemp('.fasta')
self.hmmdb = hmmdb
Executor.__init__( self, 'hmmpfam', catch_out=1,
args=' %s %s'%(hmmdb, self.fName), **kw )
self.target = target
self.fastaID = ''
if noSearch:
if self.verbose:
self.log.writeln(
'Profiles provided - No search will be performed.')
def __init__( self, model, **kw ):
"""
@param model: PDBModel
@type model:
@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)
"""
Executor.__init__( self, 'whatif', template=self.whatif_script,
f_out='/dev/null', **kw )
self.f_pdb = tempfile.mktemp('_whatif.pdb')
self.f_relativeASA = tempfile.mktemp('_whatif_relative.log')
self.f_residueASA = tempfile.mktemp('_whatif_residue.log')
self.model = model.clone()
def __init__( self, model, **kw ):
"""
@param model: reference
@type model: PDBModel
@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.f_pdb = tempfile.mktemp('_pdb_to_xyzrn.pdb')
## gpdb_to_xyzrn have to be run i the local directory where
## it resides. Otherwise it will not find the data file
## called "atmtypenumbers".
if not os.path.exists( T.dataRoot() + '/msms/'):
raise Pdb2xyzrnError, 'Cannot find msms directory. This should reside in ~biskit/Biskit/data/msms'
fmsms = T.dataRoot() + '/msms/'
## use biskit-version of pdb_to_xyzrn by default
exe = ExeConfigCache.get('pdb2xyzrn', strict=1)
try:
exe.validate()
except ExeConfigError:
exe.bin = fmsms + '/gpdb_to_xyzrn'
Executor.__init__( self, 'pdb2xyzrn', f_in=self.f_pdb,
cwd=fmsms, **kw )
self.model = model
def __init__(self, full=0, mode='w', verbose=1, **kw):
"""
@param mode: open file with this mode, w=override, a=append
@type mode: str
@param full: dispaly pymol structures in fill screen mode::
0 - normal mode
1 - full screen mode
2 - full screen and no menues
@type full: 0|1|2
"""
self.verbose = verbose
# name of .pml file
self.foutName = tempfile.mktemp() + '.pml'
# open for <appending|writing|reading>
self.fgenerate = open(self.foutName, mode)
# will contain PymolModels or lists of PymolModels
self.dic = {}
## add startup commands
self.initPymol()
## set arguments for display options (normal, full, all)
arg = '-q %s' % self.foutName
if full == 1:
arg = '-qe %s' % self.foutName
if full == 2:
arg = '-qei %s' % self.foutName
Executor.__init__(self,
'pymol',
args=arg,
catch_err=1,
catch_out=1,
**kw)
def __init__( self, model, **kw ):
"""
@param model: reference
@type model: PDBModel
@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.f_pdb = tempfile.mktemp('_pdb_to_xyzrn.pdb')
## gpdb_to_xyzrn have to be run i the local directory where
## it resides. Otherwise it will not find the data file
## called "atmtypenumbers".
if not os.path.exists( T.dataRoot() + '/msms/'):
raise Pdb2xyzrnError, 'Cannot find msms directory. This should reside in ~biskit/Biskit/data/msms'
fmsms = T.dataRoot() + '/msms/'
## use biskit-version of pdb_to_xyzrn by default
exe = ExeConfigCache.get('pdb2xyzrn', strict=1)
try:
exe.validate()
except ExeConfigError:
exe.bin = fmsms + '/gpdb_to_xyzrn'
Executor.__init__( self, 'pdb2xyzrn', f_in=self.f_pdb,
cwd=fmsms, **kw )
self.model = model
def __init__( self, model, probe, vdw_set=1, mode=3, mask=None, **kw ):
"""
SurfaceRacer creates three output files::
result.txt - contains breakdown of surface areas and is writen
to the directory where the program resides. This
file is discarded here.
<file>.txt - contains the accessible, molecular surface areas
and average curvature information parsed here.
The filename is that of the input pdb file but
with a .txt extension.
<file>_residue.txt - new in version 5.0 and not used by this wrapper
stdout - some general information about the calculation.
Redirected to /dev/null
@param model: model analyze
@type model: PDBModel
@param probe: probe radii, Angstrom
@type probe: float
@param vdw_set: Van del Waals radii set (default: 1)::
1 - Richards (1977)
2 - Chothia (1976)
@type vdw_set: 1|2
@param mode: calculation mode (default: 3)::
1- Accessible surface area only
2- Accessible and molecular surface areas
3- Accessible, molecular surface areas and
average curvature
@type mode: 1|2|3
@param mask: optional atom mask to apply before calling surface racer
(default: heavy atoms AND NOT solvent)
@type mask: [ bool ]
@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)
"""
Executor.__init__( self, 'surfaceracer', template=self.inp,\
**kw )
self.model = model.clone()
self.mask = mask if mask is not None else \
model.maskHeavy() * N0.logical_not( model.maskSolvent())
self.model = self.model.compress( self.mask )
## will be filled in by self.prepare() after the temp folder is ready
self.f_pdb = None
self.f_pdb_name = None
self.f_out_name = None
## parameters that can be changed
self.probe = probe
self.vdw_set = vdw_set
self.mode = mode
## random data dictionaries
self.ranMS = SRT.ranMS
self.ranAS = SRT.ranAS
self.ranMS_Nter = SRT.ranMS_N
self.ranAS_Nter = SRT.ranAS_N
self.ranMS_Cter = SRT.ranMS_C
self.ranAS_Cter = SRT.ranAS_C
## count failures
self.i_failed = 0
def __init__(self,
model,
template=None,
topologies=None,
f_charges=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 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 != None
self.f_map = f_map or \
tempfile.mktemp( '_mapout.phi', 'delphi_', dir=tempdir )
## self.f_map = None
self.f_radii = None
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 __init__( self, model, template=None, topologies=None,
f_charges=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 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 != None
self.f_map = f_map or \
tempfile.mktemp( '_mapout.phi', 'delphi_', dir=tempdir )
## self.f_map = None
self.f_radii = None
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 __init__( self, model, probe, vdw_set=1, mode=3, mask=None, **kw ):
"""
SurfaceRacer creates three output files::
result.txt - contains breakdown of surface areas and is writen
to the directory where the program resides. This
file is discarded here.
<file>.txt - contains the accessible, molecular surface areas
and average curvature information parsed here.
The filename is that of the input pdb file but
with a .txt extension.
<file>_residue.txt - new in version 5.0 and not used by this wrapper
stdout - some general information about the calculation.
Redirected to /dev/null
@param model: model analyze
@type model: PDBModel
@param probe: probe radii, Angstrom
@type probe: float
@param vdw_set: Van del Waals radii set (default: 1)::
1 - Richards (1977)
2 - Chothia (1976)
@type vdw_set: 1|2
@param mode: calculation mode (default: 3)::
1- Accessible surface area only
2- Accessible and molecular surface areas
3- Accessible, molecular surface areas and
average curvature
@type mode: 1|2|3
@param mask: optional atom mask to apply before calling surface racer
(default: heavy atoms AND NOT solvent)
@type mask: [ bool ]
@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)
"""
Executor.__init__( self, 'surfaceracer', template=self.inp,\
**kw )
self.model = model.clone()
self.mask = mask if mask is not None else \
model.maskHeavy() * N.logical_not( model.maskSolvent())
self.model = self.model.compress( self.mask )
## will be filled in by self.prepare() after the temp folder is ready
self.f_pdb = None
self.f_pdb_name = None
self.f_out_name = None
## parameters that can be changed
self.probe = probe
self.vdw_set = vdw_set
self.mode = mode
## random data dictionaries
self.ranMS = SRT.ranMS
self.ranAS = SRT.ranAS
self.ranMS_Nter = SRT.ranMS_N
self.ranAS_Nter = SRT.ranAS_N
self.ranMS_Cter = SRT.ranMS_C
self.ranAS_Cter = SRT.ranAS_C
## count failures
self.i_failed = 0
