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)
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 )
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)
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()
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()
