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src/b/i/biskit-2.4/Biskit/Dock/XRefineComplex.py   biskit(Download)
 
        ## location of additional XPlor scripts, required by refine.inp
        self.path = t.dataRoot() + '/xplor/inpRefine/'
 
        if len( self.path ) > 80-16:
        try:
            t.tryRemove( self.path, tree=True )
            shutil.copytree( t.dataRoot() + '/xplor/inpRefine',
                             self.path )
        except OSError, why:
    x = XRefineComplex(c, ##"~/data/tmp",
                       inp=\
                       t.dataRoot() + '/xplor/inpRefine/refine.inp',
##                        xout = 'test_xplor.log',
                       debug=1,

src/b/i/biskit-2.4/Biskit/AmberLeap.py   biskit(Download)
        self.fparm = tempfile.mktemp('.parm', 'top_')
        self.flog  = tempfile.mktemp('.log', 'leap_')
        self.template = T.dataRoot() + '/amber/leap/solvate_box.leap'
 
    def cleanUp(self):

src/b/i/biskit-2.4/Biskit/AmberParmBuilder.py   biskit(Download)
 
    ## leap script for solvated topology
    F_leap_in = t.dataRoot() + '/amber/leap/solvate_box.leap'
    ## PDB with ACE capping residue
    F_ace_cap = t.dataRoot() + '/amber/leap/ace_cap.pdb'
    ## PDB with NME capping residue
    F_nme_cap = t.dataRoot() + '/amber/leap/nme_cap.pdb'

src/b/i/biskit-2.4/Biskit/SettingsManager.py   biskit(Download)
    def test_SettingsManager(self):
        """SettingsManager test"""
 
        f_in = T.dataRoot() + '/defaults/settings.cfg'
        self.f_out =  T.tempDir() + '/settings.cfg'

src/b/i/biskit-2.4/Biskit/SurfaceRacer.py   biskit(Download)
                os.symlink( self.exe.bin, binlnk )
 
            radii_txt = T.dataRoot() + '/surface_racer_3/radii.txt'
 
            target = os.path.join(folder, 'radii.txt')

src/b/i/biskit-2.4/Biskit/Dock/ComplexRandomizer.py   biskit(Download)
        self.rec_out = tempfile.mktemp( "rec_out.pdb" )
 
        self.inp_template = t.dataRoot() +\
            '/xplor/rb_minimize_complex.inp'
 
        self.param19 = t.dataRoot() + \

src/b/i/biskit-2.4/Biskit/Xplorer.py   biskit(Download)
    def test_Xplorer( self ):
        """Xplorer test"""
 
        ## input template variables
        param = T.dataRoot() + '/xplor/toppar/param19.pro'

src/b/i/biskit-2.4/Biskit/settings.py   biskit(Download)
import user, sys
 
__CFG_DEFAULT = T.dataRoot() + '/defaults/settings.cfg'
__CFG_USER    = user.home + '/.biskit/settings.cfg'
 
projectRoot= T.projectRoot()
 
pymol_scripts = T.dataRoot() + '/pymol/'
 
 

src/b/i/biskit-2.4/Biskit/SettingsParser.py   biskit(Download)
    def test_SettingsParser(self):
        """SettingsManager test"""
        p = SettingsParser( T.dataRoot() + '/defaults/settings.cfg')
 
        p.parse()

src/b/i/biskit-2.4/Biskit/PDBCleaner.py   biskit(Download)
 
    ## PDB with ACE capping residue
    F_ace_cap = t.dataRoot() + '/amber/leap/ace_cap.pdb'
    ## PDB with NME capping residue
    F_nme_cap = t.dataRoot() + '/amber/leap/nme_cap.pdb'

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