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src/b/i/biskit-2.4/Biskit/AmberParmBuilder.py   biskit(Download)
from Biskit.PDBCleaner import PDBCleaner
from Biskit.AmberLeap import AmberLeap
from Biskit import Executor
 
class AmberError( BiskitError ):
        args = '-p %s %s' % (f_parm, '-aatm'*aatm )
 
        x = Executor('ambpdb', args, f_in=f_crd, f_out=f_out,
                     log=self.log, verbose=1, catch_err=1)
 

src/b/i/biskit-2.4/Biskit/Hmmer.py   biskit(Download)
import Biskit.molTools as MT
import Biskit.molUtils as MU
from Biskit import Executor, TemplateError, PDBModel, StdLog, EHandler
 
 
class HmmerdbIndex( Executor ):
    """
    Checks if the hmm database has been indexed or not,
    if not indexing will be done.
    """
class HmmerSearch( Executor ):
    """
    Search hmm database (using the hmmpfam program) with a sequence
    in fasta format.
    If the profile names have been provided - skip the search and
class HmmerProfile( Executor ):
    """
    Get the hmm profile with name hmmName from hmm databse
    (using the program hmmfetch) and calculate 3 different conservation
    scores.
class HmmerAlign( Executor ):
    """
    Align fasta formated sequence to hmm profile (using hmmalign).
    """
 

src/b/i/biskit-2.4/scripts/Biskit/pdb2xplor.py   biskit(Download)
from Biskit.Errors import XplorInputError
 
from Biskit import Executor
from Biskit import settings
from Biskit import Pymoler

src/b/i/biskit-2.4/Biskit/SurfaceRacer.py   biskit(Download)
import numpy.oldnumeric as N
 
from Biskit import Executor, TemplateError, EHandler
import Biskit.settings as S
import Biskit.tools as T
class SurfaceRacer( Executor ):
    """
    Run SurfaceRacer
    ================
 

src/b/i/biskit-2.4/Biskit/msms.py   biskit(Download)
## import Mslib
 
from Biskit import Executor, TemplateError, ExeConfigCache, ExeConfigError
## import Biskit.settings as S
 
 
class Pdb2xyzrnError( Exception ):
    pass
 
class Pdb2xyzrn( Executor ):
class MSMS( Executor ):
    """
    MSMS
    ====
 

src/b/i/biskit-2.4/Biskit/Fold_X.py   biskit(Download)
"""
 
from Biskit import Executor, TemplateError
from Biskit import BiskitError
 
class Fold_X( Executor ):
    """
    Run fold_X with given PDBModel
    ==============================
      Returns a dictionary with energy terms.

src/b/i/biskit-2.4/Biskit/DSSP.py   biskit(Download)
import tempfile
import numpy.oldnumeric as N
from Biskit import Executor, TemplateError
import Biskit.tools as T
import Biskit.molUtils as MU
class Dssp( Executor ):
    """
    Run Dssp
    ========
    The DSSP program will define the secondary structure of a given

src/b/i/biskit-2.4/Biskit/Dock/Intervor.py   biskit(Download)
import Biskit as B
import Biskit.tools as T
from Biskit import Executor, TemplateError
 
 
class IntervorError( Exception ):
    pass
 
class Intervor( Executor ):

src/b/i/biskit-2.4/Biskit/reduce.py   biskit(Download)
import numpy as N
 
from Biskit import Executor, PDBModel, PDBCleaner
import Biskit.tools as T
 
class ReduceError( Exception ):
    pass
 
class Reduce( Executor ):

src/b/i/biskit-2.4/Biskit/Mod/Aligner.py   biskit(Download)
from Biskit.Errors import *
 
from Biskit import Executor, TemplateError
 
 
class AlignerError( BiskitError ):
    pass
 
 
class TCoffee( Executor ):

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