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src/b/i/biskit-2.4/Biskit/AmberEntropyMaster.py   biskit(Download)
 
        ## complex
        fname = T.stripSuffix( T.absfile( self.com, resolveLinks=0 ) )
        self.ref_com = fname + '_ref.complex'
        self.ref_blig= fname + '_blig.model'
    def nameRef( self, fname ):
        fname = T.stripSuffix( T.absfile( fname, resolveLinks=0 ) )
        return fname + '_ref.model'
 
 
    def nameRefCom( self, fname ):
        fname = T.stripSuffix( T.absfile( fname, resolveLinks=0 ) )
        @rtype: [str]
        """
        fname = T.stripSuffix( T.absfile( fname, resolveLinks=0 ) )
        members = range( traj.n_members )
 
    def saveProtocols( self ):
        """
        Save protocol to file.
        """
        f_prot = T.stripSuffix( T.absfile(self.fout) ) + '_protocols.dat'

src/b/i/biskit-2.4/scripts/Biskit/amber_pdb2parm.py   biskit(Download)
 
    if 'norun' in options:
        fbase = t.stripSuffix( t.absfile( options['i'] ) )
        options['leap_in'] = options.get('leap_in', fbase+'_leap.in')
        options['leap_pdb']= options.get('leap_pdb',fbase+'_forleap.pdb')

src/b/i/biskit-2.4/Biskit/AmberParmBuilder.py   biskit(Download)
        """
        f_out = t.absfile( f_out )
        f_out_crd = t.absfile( f_out_crd ) or t.stripSuffix( f_out ) + '.crd'
        f_out_pdb = t.absfile( f_out_pdb ) or t.stripSuffix( f_out ) +\
                    '_leap.pdb'
        """
        f_out = t.absfile( f_out )
        f_out_crd = t.absfile( f_out_crd ) or t.stripSuffix( f_out ) + '.crd'
 
        ## if there are hydrogens, recast them to standard amber names