コード例 #1
0
ファイル: PDBDope.py プロジェクト: daojiaoxiehui/biskit
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', N0.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)

    ## EXPECT_1RQ4 = '.EEEEE.SSHHHHHHHHHHHHHHHEEEEEEEE.SS.EEEEE..SS...EEEEEEE.SSTTT.....EEEEEESSS..EEEEEETTTTEEEE.GGGTT...TT.EEEE.SS.SSHHHHHHHHTS.STT.EE.HHHHHHHHHHHHT..SS...HHHHHHHHHHHHHTHHHHH.HHHHHHHHGGGT.TT...EE..HHHHHHHTTHHHHHHHGGG.SS.SEEEETTEEESSHHHHHTT..EE.......SS.SSSS..EEEETTEEEEHHHHHHH.....EEEEE.SSHHHHHHHHHHHHHHHEEEEEEEEETTEEEEEE...S...EEEEEEE.SSSSS.....EEEEEETTT..EEEEEETTTTEEEE.GGGTT...TT.EEEE.SS..SHHHHHHHS...TTT.EE.TTHHHHHHHHHHT..SS...HHHHHHHHHHHHHHHHHHH.HHHHHHHGGGSS.TT...EE..HHHHHHHHTHHHHHHHGGG.SS.SEEEETTEEE.SHHHHHTT..EE........S.STTSS.EEESSSEEEEHHHHHHH.......EEEEE.EEEEEE.TTS.EEEEESS.EEEE..HHHHHHHHHHHHHT..EEEE.S..STT.B..EEEE...EEEEE...EEEE.TTS.EEEEETTEEEEE..TTHHHHHHHHHHTT..EEEE.S..STT.B..EEEE...EEEEEEEEEEEE.TTS.EEEEETTEEEEE..TTHHHHHHHHHHHT.EEEEE.S..STT.B..EEEE...EEEEEEEEEEEE.TTS.EEEEETTEEEEE..TTHHHHHHHHHHTT.EEEEE.S..STT.B..EEEE...EEEEE.EEEEEE.SSS.EEEEETTEEEEE..HHHHHHHHHHHHHT..EEEE.S..STT.B..EEEE...EEEEEEEEEEEE.TTS.EEEEETTEEEEE..HHHHHHHHHHHHTT.EEEEE.S..STT.B..EEEE...EEEEEEEEEEEE.TTS.EEEEETTEEEEE..TTHHHHHHHHHHTT.EEEEE.S..STT.B..EEEE...EEEEE.EEEEEE.TTS.EEEEETTB..EE..TTHHHHHHHHHHHT..EEEE.SS.STT.B..EEEE.....EEE.EEEEEE.TTS.EEEEETTEEEEE..THHHHHHHHHHHHT..EEEE.S..STT.B..EEEE...EEEEE.EEEEEE.SSS.EEEEETTEEEEE..TTHHHHHHHHHTTT..EEEE.S..STT.B..EEEE.'
    EXPECT_1RQ4 = '.EEEEE.SSHHHHHHHHHHHHHHHEEEEEEEE.SS.EEEEE..SS...EEEEEEE.SSTTT.....EEEEEESSS..EEEEEETTTTEEEE.GGGTT...TT.EEEE.SS.SSHHHHHHHHTS.STT.EE.HHHHHHHHHHHHT..SS...HHHHHHHHHHHIIIIIHHH.HHHHHHHHGGGT.TT...EE..HHHHHHHTTHHHHHHHGGG.SS.SEEEETTEEESSHHHHHTT..EE.......SS.SSSS..EEEETTEEEEHHHHHHH.....EEEEE.SSHHHHHHHHHHHHHHHEEEEEEEEETTEEEEEE...S...EEEEEEE.SSSSS.....EEEEEETTT..EEEEEETTTTEEEE.GGGTT...TT.EEEE.SS..SHHHHHHHS...TTT.EE.TTHHHHHHHHHHT..SS...HHHHHHHHHHHIIIIIHHH.HHHHHHHGGGSS.TT...EE..HHHHHHHHTHHHHHHHGGG.SS.SEEEETTEEE.SHHHHHTT..EE........S.STTSS.EEESSSEEEEHHHHHHH.......EEEEE.EEEEEE.TTS.EEEEESS.EEEE..HHHHHHHHHHHHHT..EEEE.S..STT.B..EEEE...EEEEE...EEEE.TTS.EEEEETTEEEEE..TTHHHHHHHHHHTT..EEEE.S..STT.B..EEEE...EEEEEEEEEEEE.TTS.EEEEETTEEEEE..TTHHHHHHHHHHHT.EEEEE.S..STT.B..EEEE...EEEEEEEEEEEE.TTS.EEEEETTEEEEE..TTHHHHHHHHHHTT.EEEEE.S..STT.B..EEEE...EEEEE.EEEEEE.SSS.EEEEETTEEEEE..HHHHHHHHHHHHHT..EEEE.S..STT.B..EEEE...EEEEEEEEEEEE.TTS.EEEEETTEEEEE..HHHHHHHHHHHHTT.EEEEE.S..STT.B..EEEE...EEEEEEEEEEEE.TTS.EEEEETTEEEEE..TTHHHHHHHHHHTT.EEEEE.S..STT.B..EEEE...EEEEE.EEEEEE.TTS.EEEEETTB..EE..TTHHHHHHHHHHHT..EEEE.SS.STT.B..EEEE.....EEE.EEEEEE.TTS.EEEEETTEEEEE..THHHHHHHHHHHHT..EEEE.S..STT.B..EEEE...EEEEE.EEEEEE.SSS.EEEEETTEEEEE..TTHHHHHHHHHTTT..EEEE.S..STT.B..EEEE.'

    def test_addSecondaryNonFiltered(self):
        from Biskit import PDBModel
        m = PDBModel('1R4Q')
        d = PDBDope(m)
        d.addSecondaryStructure()

        r = m.compress(m.maskProtein())['secondary']
        self.assertEqual(''.join(r), self.EXPECT_1RQ4)
コード例 #2
0
ファイル: PDBDope.py プロジェクト: ostrokach/biskit
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 )
コード例 #3
0
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', N0.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)
コード例 #4
0
ファイル: hexInput.py プロジェクト: ostrokach/biskit
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


    #####################
    ## write macro file
              
    macOpen= open(macName, 'w')

    macOpen.write('# ------------------- ' + macName + ' -----------------------\n')
    macOpen.write(' \n')
    macOpen.write('open_receptor '+receptorName+'\n')
    macOpen.write('open_ligand '+ligandName+'\n')

    if complexName[-4:] == '.pdb':
        macOpen.write('open_complex '+complexName+'\n')

    macOpen.write('\n')


    head = """
# -------------- general settings ----------------
disc_cache 1                   # disc cache on (0 off)
docking_sort_mode 1            # Sort solutions by cluster (0 by energy)
docking_cluster_mode 1         # Display all clusters (0 display best)
docking_cluster_threshold 2.00
# docking_cluster_bumps  number

# ------------ molecule orientation --------------
molecule_separation %(separation)i
commit_view """%({'separation': round(molSep)} )


    macro ="""
# -------------- macro docking -------------------
macro_min_coverage 25
macro_sphere_radius 15
macro_docking_separation 25
activate_macro_model"""
    
    
    tail = """
# -------------- docking setup -------------------
docking_search_mode 0          # full rotational search

receptor_range_angle 180       # 0, 15, 30, 45, 60, 75, 90, 180
docking_receptor_samples 720   # 362, 492, 642, 720, 980, 1280

ligand_range_angle 180
docking_ligand_samples 720

twist_range_angle 360          # 0, 15, 30, 60, 90, 180, 360
docking_alpha_samples 128      # 64, 128, 256

r12_step 0.500000              # 0.1, 0.2, 0.25, 0.5, 0.75, 1, 1.5, 2
r12_range %(range)i

docking_radial_filter 0        # Radial Envelope Filter - None
# docking_radial_filter 0        # Radial Envelope Filter - Re-entrant
# docking_radial_filter 0        # Radial Envelope Filter - Starlike

grid_size 0.600                # 0.4, 0.5, 0.6, 0.75, 1.0
#  docking_electrostatics 0       # use only surface complimentarity
docking_electrostatics 1      # use electrostatic term for scoring clusters

docking_main_scan 16     # 
docking_main_search 26

max_docking_solutions %(nr_sol)i # number of solutions to save

# -------------- post-processing ----------------
docking_refine 0    # None
#  docking_refine 1    # Backbone Bumps and volumes
#  docking_refine 2    # MM energies
#  docking_refine 3    # MM minimization

# ---------------- run docking ------------------
activate_docking
save_docking %(output_clust)s
#  save_range 1 512 ./ dock .pdb

# ------------ also save all solutions ----------
docking_sort_mode 0            # Sort solutions by energy (1 by cluster)
save_docking %(output_all)s""" \
    %({'range':round(molRange), 'output_all':outName_all,
       'nr_sol':int(options['sol']), 'output_clust':outName_clust} )
    

    macOpen.writelines( head )

    ## select certain models
    if rm or lm:
        macOpen.write('\n')
        macOpen.write('\n# -------------- select models -------------------\n')
    if rm:
        select_rec_model = 'dock_receptor_model %s'%rm
        macOpen.write( select_rec_model + '\n')
    if lm:
        select_lig_model = 'dock_ligand_model %s'%lm
        macOpen.write( select_lig_model + '\n')
        
    ## macro docking will not work with multiple models, if both are added to
    ##  the hex macro file - macrodocking will be skipped during the docking run 
    if macroDocking:
        macOpen.writelines( macro )

    macOpen.writelines( tail )
    
    macOpen.close()
コード例 #5
0
ファイル: hexInput.py プロジェクト: ostrokach/biskit
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

    #####################
    ## write macro file

    macOpen = open(macName, 'w')

    macOpen.write('# ------------------- ' + macName +
                  ' -----------------------\n')
    macOpen.write(' \n')
    macOpen.write('open_receptor ' + receptorName + '\n')
    macOpen.write('open_ligand ' + ligandName + '\n')

    if complexName[-4:] == '.pdb':
        macOpen.write('open_complex ' + complexName + '\n')

    macOpen.write('\n')

    head = """
# -------------- general settings ----------------
disc_cache 1                   # disc cache on (0 off)
docking_sort_mode 1            # Sort solutions by cluster (0 by energy)
docking_cluster_mode 1         # Display all clusters (0 display best)
docking_cluster_threshold 2.00
# docking_cluster_bumps  number

# ------------ molecule orientation --------------
molecule_separation %(separation)i
commit_view """ % ({
        'separation': round(molSep)
    })

    macro = """
# -------------- macro docking -------------------
macro_min_coverage 25
macro_sphere_radius 15
macro_docking_separation 25
activate_macro_model"""


    tail = """
# -------------- docking setup -------------------
docking_search_mode 0          # full rotational search

receptor_range_angle 180       # 0, 15, 30, 45, 60, 75, 90, 180
docking_receptor_samples 720   # 362, 492, 642, 720, 980, 1280

ligand_range_angle 180
docking_ligand_samples 720

twist_range_angle 360          # 0, 15, 30, 60, 90, 180, 360
docking_alpha_samples 128      # 64, 128, 256

r12_step 0.500000              # 0.1, 0.2, 0.25, 0.5, 0.75, 1, 1.5, 2
r12_range %(range)i

docking_radial_filter 0        # Radial Envelope Filter - None
# docking_radial_filter 0        # Radial Envelope Filter - Re-entrant
# docking_radial_filter 0        # Radial Envelope Filter - Starlike

grid_size 0.600                # 0.4, 0.5, 0.6, 0.75, 1.0
#  docking_electrostatics 0       # use only surface complimentarity
docking_electrostatics 1      # use electrostatic term for scoring clusters

docking_main_scan 16     # 
docking_main_search 26

max_docking_solutions %(nr_sol)i # number of solutions to save

# -------------- post-processing ----------------
docking_refine 0    # None
#  docking_refine 1    # Backbone Bumps and volumes
#  docking_refine 2    # MM energies
#  docking_refine 3    # MM minimization

# ---------------- run docking ------------------
activate_docking
save_docking %(output_clust)s
#  save_range 1 512 ./ dock .pdb

# ------------ also save all solutions ----------
docking_sort_mode 0            # Sort solutions by energy (1 by cluster)
save_docking %(output_all)s""" \
    %({'range':round(molRange), 'output_all':outName_all,
       'nr_sol':int(options['sol']), 'output_clust':outName_clust} )

    macOpen.writelines(head)

    ## select certain models
    if rm or lm:
        macOpen.write('\n')
        macOpen.write('\n# -------------- select models -------------------\n')
    if rm:
        select_rec_model = 'dock_receptor_model %s' % rm
        macOpen.write(select_rec_model + '\n')
    if lm:
        select_lig_model = 'dock_ligand_model %s' % lm
        macOpen.write(select_lig_model + '\n')

    ## macro docking will not work with multiple models, if both are added to
    ##  the hex macro file - macrodocking will be skipped during the docking run
    if macroDocking:
        macOpen.writelines(macro)

    macOpen.writelines(tail)

    macOpen.close()