Python PDBModel.profile方法代码示例

# 需要导入模块: from Biskit import PDBModel [as 别名]
# 或者: from Biskit.PDBModel import profile [as 别名]
class LongTest( BT.BiskitTest ):

    TAGS = [ BT.EXE, BT.LONG ]


    def prepare(self):
        from Biskit import PDBModel
        self.f = T.testRoot() + '/com/1BGS.pdb'

        self.M = PDBModel( self.f )
        self.M = self.M.compress( self.M.maskProtein() )

        self.d = PDBDope( self.M )

    def test_conservation(self):
        """PDBDope.addConservation (Hmmer) test"""
        if self.local: print "Adding conservation data...",
        self.d.addConservation()
        if self.local: print 'Done.'

        ## display in Pymol
        if self.local:
            print "Starting PyMol..."
            from Biskit.Pymoler import Pymoler

            pm = Pymoler()
            pm.addPdb( self.M, 'm' )
            pm.colorAtoms( 'm', N.clip(self.M.profile('cons_ent'), 0.0, 100.0) )
            pm.show()

    def test_delphi(self):
        """PDBDope.addDelphi test"""
        if self.local:
            self.log.add( 'Calculating Delphi electrostatic potential' )
            self.log.add( '' )

        self.d.addDelphi( scale=1.2 )
        
        self.assertAlmostEqual( self.M['delphi']['scharge'], 0.95, 1 )

# 需要导入模块: from Biskit import PDBModel [as 别名]
# 或者: from Biskit.PDBModel import profile [as 别名]
def main(options):

    ##################
    ## files and names
    receptorName = absfile(options['r'])
    receptorCode = stripFilename(receptorName)[0:4]
    ligandName = absfile(options['l'])          
    ligandCode = stripFilename(ligandName)[0:4]  
    complexName = absfile(options['c'])
    rm = options['rm']
    lm = options['lm']
    
    if rm or lm:
        rn = rm or '1'
        ln = lm or '1'
        baseName = receptorCode + '_' + rn + '-' + ligandCode + '_' + ln
    else:
        baseName = receptorCode + '-' + ligandCode

    ## hex macro name
    macName = baseName + '_hex.mac'

    ## hex rotation matrix output name
    outName_all = baseName + '_hex.out' 
    outName_clust = baseName + '_hex_cluster.out'


    ## load model dictionaries, if they exist in the same directory
    ## as the corresponding pdb-file and start with the same pdb-code
    ## and ends with '_model.dic'
    try:
        rec_dic = stripFilename(options['r'])[:4] + '_model.dic'
        rec_path = options['r'][:options['r'].rfind('/')]

        lig_dic = stripFilename(options['l'])[:4] + '_model.dic'
        lig_path = options['l'][:options['l'].rfind('/')]

        rec = load( absfile(rec_path + '/' + rec_dic) )
        lig = load( absfile(lig_path + '/' + lig_dic) )
        
        print 'Loading dictionaries'
        
        if type(rec) is dict:
            rec = rec[1]
            
        if type(lig) is dict:
            lig = lig[1]
        
    ## could not load dictionaty, will load pdb-file insted
    except:
        print 'Loading pdb files'
        rec = PDBModel(receptorName)
        lig = PDBModel(ligandName)

    #############################
    ## get structural information


    ## add surface profiles if not there
    if not rec.atoms.has_key('relASA'):
        flushPrint('\nCalculating receptor surface profile')
        rec_asa = PDBDope( rec )
        rec_asa.addASA()
    if not lig.atoms.has_key('relASA'):
        flushPrint('\nCalculating ligand surface profile')
        lig_asa = PDBDope( lig )
        lig_asa.addASA()

    ## surface masks, > 95% exposed
    rec_surf_mask = greater( rec.profile('relASA'), 95 )
    lig_surf_mask = greater( lig.profile('relASA'), 95 )

    ## maximun and medisn distance from centre of mass to any surface atom
    recMax, recMin = centerSurfDist( rec, rec_surf_mask )
    ligMax, ligMin = centerSurfDist( lig, lig_surf_mask )

    ## approxinate max and min center to centre distance
    maxDist = recMax + ligMax 
    minDist = recMin + ligMin
    print '\n\nReceptor and ligand max radius are %i and %i A, respectively.'\
          %( recMax, ligMax )
    print 'Receptor and ligand min radius are %i and %i A, respectively.'\
          %( recMin, ligMin )

    ## molecular separation and search range to be used in the docking
    molSep = ( maxDist + minDist ) / 2
    molRange = 2 * ( maxDist - molSep )
    print 'A molecular separation of %i A and a search range of +-%i will be used.'\
          %( molSep, molRange )

    ## determine docking mode to use
    macroDocking = 0
    if recMax > 30 and ligMax > 30:
        print '\nWARNING! Both the receptor and ligand radius is greater than 30 A.\n'     
        
    if recMax > 30:
        print '\nReceptor has a radius that exceeds 30 A -> Macro docking will be used'
        macroDocking = 1


#.........这里部分代码省略.........