def randomSurfaces( base_folder, label, mask ):
"""
calculate surfaces for all peptides and return the
average and SD
"""
## container for results and standard deviations
MS, AS = {}, {}
MS_sd, AS_sd = {}, {}
## loop over peptide directories
for k in MOU.aaAtoms.keys():
dir = base_folder + 'GLY-%s-GLY_pcr/pcr_00'%(k)
fLst = glob.glob( dir + '/*.pdb')
msLst = []
asLst = []
## loop over pdb files for each peptide
T.flushPrint( '\nNow collecting data in %s'%dir )
for f in fLst:
## load peptide and remove waters and hydrogens
m = PDBModel( f )
m = m.compress( m.maskProtein() * m.maskHeavy() )
T.flushPrint( '.')
## add surface data
try:
d = PDBDope( m )
d.addSurfaceRacer( probe=1.4 )
## remove tailing GLY
m = m.compress( m.res2atomMask(mask) )
## collect surface data for each peptide
msLst += [ m.profile('MS') ]
asLst += [ m.profile('AS') ]
except:
print 'Failed calculating exposure for GLY-%s-GLY'%(k)
print '\t and file %s'%f
## get result dictionary for peptide
T.flushPrint('\nCollecting data ...\n')
msDic = {}
asDic = {}
msDic_sd = {}
asDic_sd = {}
j = 0
#atoms = [ a['name'] for a in m.atoms ]
for n in m['name']:
msDic[n] = N0.average(msLst)[j]
asDic[n] = N0.average(asLst)[j]
msDic_sd[n] = MAU.SD( msLst )[j]
asDic_sd[n] = MAU.SD( asLst )[j]
j += 1
MS[ k ] = msDic
AS[ k ] = asDic
MS_sd[ k ] = msDic_sd
AS_sd[ k ] = asDic_sd
return MS, AS, MS_sd, AS_sd
def randomSurfaces( base_folder, label, mask ):
"""
calculate surfaces for all peptides and return the
average and SD
"""
## container for results and standard deviations
MS, AS = {}, {}
MS_sd, AS_sd = {}, {}
## loop over peptide directories
for k in MOU.aaAtoms.keys():
dir = base_folder + 'GLY-%s-GLY_pcr/pcr_00'%(k)
fLst = glob.glob( dir + '/*.pdb')
msLst = []
asLst = []
## loop over pdb files for each peptide
T.flushPrint( '\nNow collecting data in %s'%dir )
for f in fLst:
## load peptide and remove waters and hydrogens
m = PDBModel( f )
m = m.compress( m.maskProtein() * m.maskHeavy() )
T.flushPrint( '.')
## add surface data
try:
d = PDBDope( m )
d.addSurfaceRacer( probe=1.4 )
## remove tailing GLY
m = m.compress( m.res2atomMask(mask) )
## collect surface data for each peptide
msLst += [ m.profile('MS') ]
asLst += [ m.profile('AS') ]
except:
print 'Failed calculating exposure for GLY-%s-GLY'%(k)
print '\t and file %s'%f
## get result dictionary for peptide
T.flushPrint('\nCollecting data ...\n')
msDic = {}
asDic = {}
msDic_sd = {}
asDic_sd = {}
j = 0
#atoms = [ a['name'] for a in m.atoms ]
for n in m['name']:
msDic[n] = N.average(msLst)[j]
asDic[n] = N.average(asLst)[j]
msDic_sd[n] = MAU.SD( msLst )[j]
asDic_sd[n] = MAU.SD( asLst )[j]
j += 1
MS[ k ] = msDic
AS[ k ] = asDic
MS_sd[ k ] = msDic_sd
AS_sd[ k ] = asDic_sd
return MS, AS, MS_sd, AS_sd
class Test(BT.BiskitTest):
"""Test AmberParmBuilder"""
TAGS = [BT.EXE]
def prepare(self):
root = T.testRoot() + '/amber/'
self.ref = PDBModel(T.testRoot() + '/amber/1HPT_0.pdb')
self.refdry = root + '1HPT_0dry.pdb'
self.dryparm = tempfile.mktemp('.parm', 'dry_')
self.drycrd = tempfile.mktemp('.crd', 'dry_')
self.drypdb = tempfile.mktemp('.pdb', 'dry_')
self.wetparm = tempfile.mktemp('.parm', 'wet_')
self.wetcrd = tempfile.mktemp('.crd', 'wet_')
self.wetpdb = tempfile.mktemp('.pdb', 'wet_')
self.leapout = tempfile.mktemp('.out', 'leap_')
def cleanUp(self):
if not self.DEBUG:
T.tryRemove(self.dryparm)
T.tryRemove(self.drycrd)
T.tryRemove(self.drypdb)
T.tryRemove(self.wetparm)
T.tryRemove(self.wetcrd)
T.tryRemove(self.wetpdb)
T.tryRemove(self.leapout)
def test_AmberParmMirror(self):
"""AmberParmBuilder.parmMirror test"""
ref = self.ref
mask = N.logical_not(ref.maskH2O()) ## keep protein and Na+ ion
self.mdry = ref.compress(mask)
self.a = AmberParmBuilder(self.mdry,
verbose=self.local,
leap_out=self.leapout,
debug=self.DEBUG)
self.a.parmMirror(f_out=self.dryparm, f_out_crd=self.drycrd)
self.a.parm2pdb(self.dryparm, self.drycrd, self.drypdb)
self.m1 = PDBModel(self.drypdb)
self.m2 = PDBModel(self.refdry)
eq = N.array(self.m1.xyz == self.m2.xyz)
self.assert_(eq.all())
def test_AmberParmSolvated(self):
"""AmberParmBuilder.parmSolvated test"""
## remove waters and hydrogens
self.mdry = self.ref.compress(self.ref.maskProtein())
self.mdry = self.mdry.compress(self.mdry.maskHeavy())
self.a = AmberParmBuilder(self.mdry,
leap_out=self.leapout,
verbose=self.local,
debug=self.DEBUG)
self.a.parmSolvated(self.wetparm,
f_out_crd=self.wetcrd,
f_out_pdb=self.wetpdb,
box=2.5)
self.m3 = PDBModel(self.wetpdb)
m3prot = self.m3.compress(self.m3.maskProtein())
refprot = self.ref.compress(self.ref.maskProtein())
refprot.xplor2amber()
self.assertEqual(self.ref.lenChains(), self.m3.lenChains())
self.assertEqual(refprot.atomNames(), m3prot.atomNames())
def test_capIrregular(self):
"""AmberParmBuilder.capNME & capACE test"""
gfp = PDBModel('1GFL')
normal = gfp.takeResidues([10, 11])
chromo = gfp.takeResidues([64, 65])
self.a = AmberParmBuilder(normal)
self.m4 = self.a.capACE(normal, 0)
self.assertEqual(len(self.m4), 17)
## del chromo.residues['biomol']
self.m5 = self.a.capACE(chromo, 0)
self.m5 = self.a.capNME(self.m5, 0)
self.assertEqual(self.m5.sequence(), 'XSYX')
class Test( BT.BiskitTest ):
"""Test AmberParmBuilder"""
TAGS = [ BT.EXE ]
def prepare(self):
root = T.testRoot() + '/amber/'
self.ref = PDBModel( T.testRoot() + '/amber/1HPT_0.pdb')
self.refdry = root + '1HPT_0dry.pdb'
self.dryparm = tempfile.mktemp('.parm', 'dry_')
self.drycrd = tempfile.mktemp('.crd', 'dry_')
self.drypdb = tempfile.mktemp('.pdb', 'dry_')
self.wetparm = tempfile.mktemp('.parm', 'wet_')
self.wetcrd = tempfile.mktemp('.crd', 'wet_')
self.wetpdb = tempfile.mktemp('.pdb', 'wet_')
self.leapout = tempfile.mktemp('.out', 'leap_')
def cleanUp(self):
if not self.DEBUG:
T.tryRemove( self.dryparm )
T.tryRemove( self.drycrd )
T.tryRemove( self.drypdb )
T.tryRemove( self.wetparm )
T.tryRemove( self.wetcrd )
T.tryRemove( self.wetpdb )
T.tryRemove( self.leapout )
def test_AmberParmMirror(self):
"""AmberParmBuilder.parmMirror test"""
ref = self.ref
mask = N.logical_not( ref.maskH2O() ) ## keep protein and Na+ ion
self.mdry = ref.compress( mask )
self.a = AmberParmBuilder( self.mdry, verbose=self.local,
leap_out=self.leapout,
debug=self.DEBUG )
self.a.parmMirror(f_out=self.dryparm,
f_out_crd=self.drycrd )
self.a.parm2pdb( self.dryparm, self.drycrd, self.drypdb )
self.m1 = PDBModel(self.drypdb)
self.m2 = PDBModel(self.refdry)
eq = N.array( self.m1.xyz == self.m2.xyz )
self.assert_( eq.all() )
def test_AmberParmSolvated( self ):
"""AmberParmBuilder.parmSolvated test"""
## remove waters and hydrogens
self.mdry = self.ref.compress( self.ref.maskProtein() )
self.mdry = self.mdry.compress( self.mdry.maskHeavy() )
self.a = AmberParmBuilder( self.mdry,
leap_out=self.leapout,
verbose=self.local, debug=self.DEBUG)
self.a.parmSolvated( self.wetparm, f_out_crd=self.wetcrd,
f_out_pdb=self.wetpdb,
box=2.5 )
self.m3 = PDBModel( self.wetpdb )
m3prot = self.m3.compress( self.m3.maskProtein() )
refprot= self.ref.compress( self.ref.maskProtein() )
refprot.xplor2amber()
self.assertEqual( self.ref.lenChains(), self.m3.lenChains() )
self.assertEqual( refprot.atomNames(), m3prot.atomNames() )
def test_capIrregular( self ):
"""AmberParmBuilder.capNME & capACE test"""
gfp = PDBModel('1GFL')
normal = gfp.takeResidues([10,11])
chromo = gfp.takeResidues([64,65])
self.a = AmberParmBuilder( normal )
self.m4 = self.a.capACE( normal, 0 )
self.assertEqual( len(self.m4), 17 )
## del chromo.residues['biomol']
self.m5 = self.a.capACE( chromo, 0 )
self.m5 = self.a.capNME( self.m5, 0 )
self.assertEqual( self.m5.sequence(), 'XSYX' )
class Test(BT.BiskitTest):
"""Test AmberParmBuilder"""
TAGS = [BT.EXE]
def prepare(self):
root = T.testRoot() + '/amber/'
self.ref = PDBModel(T.testRoot() + '/amber/1HPT_0.pdb')
self.refdry = root + '1HPT_0dry.pdb'
self.dryparm = tempfile.mktemp('.parm', 'dry_')
self.drycrd = tempfile.mktemp('.crd', 'dry_')
self.drypdb = tempfile.mktemp('.pdb', 'dry_')
self.wetparm = tempfile.mktemp('.parm', 'wet_')
self.wetcrd = tempfile.mktemp('.crd', 'wet_')
self.wetpdb = tempfile.mktemp('.pdb', 'wet_')
self.leapout = tempfile.mktemp('.out', 'leap_')
def cleanUp(self):
if not self.DEBUG:
T.tryRemove(self.dryparm)
T.tryRemove(self.drycrd)
T.tryRemove(self.drypdb)
T.tryRemove(self.wetparm)
T.tryRemove(self.wetcrd)
T.tryRemove(self.wetpdb)
T.tryRemove(self.leapout)
def test_AmberParmMirror(self):
"""AmberParmBuilder.parmMirror test"""
ref = self.ref
mask = N0.logical_not(ref.maskH2O()) ## keep protein and Na+ ion
self.mdry = ref.compress(mask)
self.a = AmberParmBuilder(self.mdry,
verbose=self.local,
leap_out=self.leapout,
debug=self.DEBUG)
self.a.parmMirror(f_out=self.dryparm, f_out_crd=self.drycrd)
self.a.parm2pdb(self.dryparm, self.drycrd, self.drypdb)
self.m1 = PDBModel(self.drypdb)
self.m2 = PDBModel(self.refdry)
eq = N0.array(self.m1.xyz == self.m2.xyz)
self.assert_(eq.all())
def test_AmberParmSolvated(self):
"""AmberParmBuilder.parmSolvated test"""
## remove waters and hydrogens
self.mdry = self.ref.compress(self.ref.maskProtein())
self.mdry = self.mdry.compress(self.mdry.maskHeavy())
self.a = AmberParmBuilder(self.mdry,
leap_out=self.leapout,
verbose=self.local,
debug=self.DEBUG)
self.a.parmSolvated(self.wetparm,
f_out_crd=self.wetcrd,
f_out_pdb=self.wetpdb,
box=2.5)
self.m3 = PDBModel(self.wetpdb)
m3prot = self.m3.compress(self.m3.maskProtein())
refprot = self.ref.compress(self.ref.maskProtein())
refprot.xplor2amber()
self.assertEqual(self.ref.lenChains(), self.m3.lenChains())
self.assertEqual(refprot.atomNames(), m3prot.atomNames())
