def test_SystemPDB(self):
pdb = T.testRoot('pep','pep.pdb')
self.f_out = T.tempDir()+os.sep+'SystemPDB'
if not os.path.exists(self.f_out): os.mkdir(self.f_out)
T.BROWSER.chdir(self.f_out)
self.r1 = System(amberPDB=pdb)
solvatedsys = self.r1.solvate('WAT', tmp=self.f_out)
def test_TrajCluster(self):
"""TrajCluster test"""
from Biskit.EnsembleTraj import traj2ensemble
traj = T.load( T.testRoot()+'/lig_pcr_00/traj.dat')
traj = traj2ensemble( traj )
aMask = traj.ref.mask( lambda a: a['name'] in ['CA','CB','CG'] )
traj = traj.thin( 1 )
traj.fit( aMask, verbose=self.local )
self.tc = TrajCluster( traj, verbose=self.local )
## check how many clusters that are needed with the given criteria
n_clusters = self.tc.calcClusterNumber( min_clst=3, max_clst=15,
rmsLimit=0.7, aMask=aMask )
## cluster
self.tc.cluster( n_clusters, aMask=aMask )
if self.local:
member_frames = self.tc.memberFrames()
print 'There are %i clusters where the members are:'%n_clusters
for i in range(n_clusters):
print 'Cluster %i (%i members): %s'%( i+1,
len(member_frames[i]),
member_frames[i] )
def test_autoprepare_2(self):
"""Test main AutoPrepare class. Prepare PDBID 1a0o chains A, B == [0,1]"""
f_check = T.testRoot('autoprepare', '1yer_h.pdb')
self.prepare = AutoPrepare(pdbid='1yer', chains=[0,1])
self.checkpdb = bi.PDBModel(f_check)
# self.savePdb(osp.join(T.testRoot(),'1a0o_prepared.pdb'))
self.comparePDB(self.prepare.getPdb(), self.checkpdb)
def test_molUtils( self ):
"""molUtils test"""
from Biskit import PDBModel
S = self
## load a structure
S.m = PDBModel( t.testRoot()+'/lig/1A19.pdb' )
S.model_1 = S.m.compress( S.m.maskProtein() )
## now sort in standard order
S.model_2 = sortAtomsOfModel( S.model_1)
## compare the atom order
cmp = []
for a in S.model_1.atomRange():
cmp += [ cmpAtoms( S.model_1.atoms[a], S.model_2.atoms[a] )]
self.assertEqual( N.sum(cmp), 159 )
## get the primaty sequence as a string
S.seq = S.model_1.sequence()
## convert it to a list of three letter code
S.seq=single2longAA(S.seq)
## convert it to a list in one letter code
S.seq=singleAA(S.seq)
self.assertEqual( ''.join(S.seq), S.model_1.sequence() )
def test_TrajCluster(self):
"""TrajCluster test"""
from Biskit.EnsembleTraj import traj2ensemble
traj = T.load(T.testRoot() + '/lig_pcr_00/traj.dat')
traj = traj2ensemble(traj)
aMask = traj.ref.mask(lambda a: a['name'] in ['CA', 'CB', 'CG'])
traj = traj.thin(1)
traj.fit(aMask, verbose=self.local)
self.tc = TrajCluster(traj, verbose=self.local)
## check how many clusters that are needed with the given criteria
n_clusters = self.tc.calcClusterNumber(min_clst=3,
max_clst=15,
rmsLimit=0.7,
aMask=aMask)
## cluster
self.tc.cluster(n_clusters, aMask=aMask)
if self.local:
member_frames = self.tc.memberFrames()
print 'There are %i clusters where the members are:' % n_clusters
for i in range(n_clusters):
print 'Cluster %i (%i members): %s' % (
i + 1, len(member_frames[i]), member_frames[i])
def test_molUtils(self):
"""molUtils test"""
from Biskit import PDBModel
S = self
## load a structure
S.m = PDBModel(t.testRoot() + '/lig/1A19.pdb')
S.model_1 = S.m.compress(S.m.maskProtein())
## now sort in standard order
S.model_2 = sortAtomsOfModel(S.model_1)
## compare the atom order
cmp = []
for a in S.model_1.atomRange():
cmp += [cmpAtoms(S.model_1.atoms[a], S.model_2.atoms[a])]
self.assertEqual(N0.sum(cmp), 159)
## get the primaty sequence as a string
S.seq = S.model_1.sequence()
## convert it to a list of three letter code
S.seq = single2longAA(S.seq)
## convert it to a list in one letter code
S.seq = singleAA(S.seq)
self.assertEqual(''.join(S.seq), S.model_1.sequence())
def test_SystemOFF(self):
"""Create System from OFF"""
off = T.testRoot('pep', 'pep.off')
self.f_out = T.tempDir() + os.sep + 'SystemOFF'
if not os.path.exists(self.f_out): os.mkdir(self.f_out)
T.BROWSER.chdir(self.f_out)
self.r1 = System(amberOFF=off)
solvatedsys = self.r1.solvate('WAT', tmp=self.f_out)
def test_SolventCreation(self):
"""SolventManager Solvent creation test"""
f_in = osp.join(T.testRoot(), 'solvents', 'solvent_template.cfg')
self.f_out = osp.join(T.tempDir(), 'solvent.db')
self.m = SolventManager()
solv = self.m.createSolvent(f_in)
# print solv.getProbeByName('CT').mask
self.m.saveSolvent(solv, db=self.f_out)
self.assertEqual(str(solv), str(self.m.getSolvent('ETA', self.f_out)))
def test_PCRModel(self):
"""PCRModel test"""
## Loading PDB...
self.m_com = PCRModel(t.testRoot() + "/com/1BGS.psf",
t.testRoot() + "/com/1BGS.pdb")
self.m_rec = PCRModel(t.testRoot() + "/rec/1A2P.psf",
t.testRoot() + "/rec/1A2P.pdb")
## remove waters
self.m_com = self.m_com.compress(self.m_com.maskProtein())
self.m_rec = self.m_rec.compress(self.m_rec.maskProtein())
## fit the complex structure to the free receptor
m_com_fit = self.m_com.magicFit(self.m_rec)
## calculate the rmsd between the original complex and the
## one fitted to the free receptor
rms = m_com_fit.rms(self.m_com, fit=0)
if self.local:
print 'Rmsd between the two complex structures: %.2f Angstrom' % rms
self.assertAlmostEqual(rms, 58.7844130314, 4)
def test_PCRModel( self ):
"""PCRModel test"""
## Loading PDB...
self.m_com = PCRModel( t.testRoot() + "/com/1BGS.psf",
t.testRoot() + "/com/1BGS.pdb" )
self.m_rec = PCRModel( t.testRoot() + "/rec/1A2P.psf",
t.testRoot() + "/rec/1A2P.pdb" )
## remove waters
self.m_com = self.m_com.compress( self.m_com.maskProtein() )
self.m_rec = self.m_rec.compress( self.m_rec.maskProtein() )
## fit the complex structure to the free receptor
m_com_fit = self.m_com.magicFit( self.m_rec )
## calculate the rmsd between the original complex and the
## one fitted to the free receptor
rms = m_com_fit.rms(self.m_com, fit=0)
if self.local:
print 'Rmsd between the two complex structures: %.2f Angstrom'%rms
self.assertAlmostEqual(rms, 58.7844130314, 4)
def test_OFFManager(self):
"""OFFManager test"""
f_in = T.testRoot('solvents','ETAWAT20.off')
self.m = OFFManager(offFile=f_in)
self.assertEqual(self.m.getUnits(), ['ETA','ETAWAT20','WAT'])
self.assertEqual(self.m.getResidueList('ETAWAT20',unique=True), ['WAT','ETA'])
self.assertAlmostEqual(self.m.getVolume('ETAWAT20'), 7988.43038, 4)
self.assertFalse(self.m.getVolume('ETA'))
self.assertFalse(self.m.isParameter('ETA'))
res = self.m.getResidue('ETA')
self.assertEqual(res.charge, 0)
self.assertEqual(res.connectivity[0], (1,2))
def test_QualSlave(self):
"""QualSlave test"""
import os
jobs = {0: T.testRoot() + '/lig_pcr_00/traj.dat'}
self.feps = '%s/rms_traj.eps' % os.path.dirname(jobs[0])
slave = QualSlave()
slave.initialize({'verbose': 0})
r = slave.go(jobs)
if self.VERBOSITY > 2:
self.log.write('eps written to ' + self.feps)
self.assert_(os.path.exists(self.feps))
def test_QualSlave(self):
"""QualSlave test"""
import os
jobs = {0: T.testRoot() + '/lig_pcr_00/traj.dat'}
self.feps = '%s/rms_traj.eps' % os.path.dirname( jobs[0] )
slave = QualSlave()
slave.initialize( {'verbose':0} )
r = slave.go( jobs )
if self.VERBOSITY > 2:
self.log.write('eps written to ' + self.feps )
self.assert_( os.path.exists( self.feps ) )
def test_ReduceCoordinates(self):
"""ReduceCoordinates test"""
self.m = PDBModel(T.testRoot() + '/com/1BGS.pdb')
self.m = self.m.compress(N.logical_not(self.m.maskH2O()))
self.m.atoms.set('test', range(len(self.m)))
self.red = ReduceCoordinates(self.m, 4)
self.mred = self.red.reduceToModel()
if self.local:
print '\nAtoms before reduction %i' % self.m.lenAtoms()
print 'Atoms After reduction %i' % self.mred.lenAtoms()
self.assertEqual(self.mred.lenAtoms(), 445)
def test_ReduceCoordinates(self):
"""ReduceCoordinates test"""
self.m = PDBModel( T.testRoot()+'/com/1BGS.pdb' )
self.m = self.m.compress( N.logical_not( self.m.maskH2O() ) )
self.m.atoms.set('test', range(len(self.m)))
self.red = ReduceCoordinates( self.m, 4 )
self.mred = self.red.reduceToModel()
if self.local:
print '\nAtoms before reduction %i'% self.m.lenAtoms()
print 'Atoms After reduction %i'% self.mred.lenAtoms()
self.assertEqual( self.mred.lenAtoms(), 445 )
def test_Pymoler(self):
"""Pymoler test"""
self.traj = T.load( T.testRoot() + '/lig_pcr_00/traj.dat' )
self.pm = Pymoler( full=0, verbose=self.local )
mname = self.pm.addMovie( [ self.traj[i] for i in range(0,100,20) ] )
sel = self.pm.makeSel({'residue':29})
## self.pm.add('show stick, %s' % sel)
self.pm.add('show surface, %s' % sel)
self.pm.add('mplay')
if not self.local:
self.pm.add('quit')
self.pm.run() ## old style call "pm.show()" also works
self.assert_( self.pm.pid is not None )
def test_Pymoler(self):
"""Pymoler test"""
self.traj = T.load(T.testRoot() + '/lig_pcr_00/traj.dat')
self.pm = Pymoler(full=0, verbose=self.local)
mname = self.pm.addMovie([self.traj[i] for i in range(0, 100, 20)])
sel = self.pm.makeSel({'residue': 29})
## self.pm.add('show stick, %s' % sel)
self.pm.add('show surface, %s' % sel)
self.pm.add('mplay')
if not self.local:
self.pm.add('quit')
self.pm.run() ## old style call "pm.show()" also works
self.assert_(self.pm.pid is not None)
def checkSite(self):
"Control wether the site has changed the form. If so, exit as everything will fail."
# Check that html website is similar to the content when this module was written
import difflib
checkhtml = open(T.testRoot('pdb2pqr_html.txt'),'r').read()
webhtml = self._html.read()
ratio = difflib.SequenceMatcher(lambda x: x == " ", checkhtml, webhtml).ratio()
if ratio < 0.9:
self.log.warn('Website seems different since this module was coded. Similarity: %3f'%ratio)
# Check form has mandatory controls
controls = set([c.name for c in self.br.form.controls])
if controls != PDB2PQRInterface.KNOWNCONTROLS:
# Something has changed!
# First check if all mandatory controls are there
self.log.warning("Changes in webserver form.")
if PDB2PQRInterface.MANDATORYCONTROLS < controls: return True
else:
raise FormChange, "Missing controls in form: ", PDB2PQRInterface.MANDATORYCONTROLS - controls
else:
return True
def test_Trajectory(self):
"""Trajectory test"""
## f = T.testRoot() + '/lig_pc2_00/pdb/'
## allfiles = os.listdir( f )
## pdbs = []
## for fn in allfiles:
## try:
## if (fn[-7:].upper() == '.PDB.GZ'):
## pdbs += [f + fn]
## except:
## pass
## ref = pdbs[0]
## traj = Trajectory( pdbs[:3], ref, rmwat=0 )
## Loading
self.traj = T.load(T.testRoot() + '/lig_pcr_00/traj.dat')
## sort frames after frameNames
self.traj.sortFrames()
## sort atoms
self.traj.sortAtoms()
## remove waters
self.traj = self.traj.compressAtoms(
N.logical_not(self.traj.ref.maskH2O()))
## get fluctuation on a residue level
r1 = self.traj.getFluct_local(verbose=self.local)
## fit backbone of frames to reference structure
self.traj.fit(ref=self.traj.ref,
mask=self.traj.ref.maskBB(),
verbose=self.local)
self.assertAlmostEqual(N.sum(self.traj.profile('rms')),
58.101235746353879, 2)
def setOFF(self, amberOFF, unitname=None):
"""
Save Amber Object file as :class:`OFFManager.OFFManager` object in :attr:`amberOFF`. :attr:`unitName` will be set.
:arg str amberOFF: Path to amber object file.
:arg str unitname: Name of the unit we should use in the future. If not given, automatically take the first unit found in the file.
"""
from OFFManager import OFFManager
# Special case: test
# Grab off from testing directory
if amberOFF.lower() == 'test':
print "WORKING WITH A TEST SYSTEM!"
amberOFF = T.testRoot('pep', 'pep.off')
self.name = 'testsystem'
self.sysFilePath = self.name + '.msys'
self.amberOFF = OFFManager(amberOFF)
if not unitname:
units = self.amberOFF.getUnits()
unitname = units[0]
self.unitName = unitname
self.__createRef()
def test_Trajectory(self):
"""Trajectory test"""
## f = T.testRoot() + '/lig_pc2_00/pdb/'
## allfiles = os.listdir( f )
## pdbs = []
## for fn in allfiles:
## try:
## if (fn[-7:].upper() == '.PDB.GZ'):
## pdbs += [f + fn]
## except:
## pass
## ref = pdbs[0]
## traj = Trajectory( pdbs[:3], ref, rmwat=0 )
## Loading
self.traj = T.load(T.testRoot() + '/lig_pcr_00/traj.dat')
## sort frames after frameNames
self.traj.sortFrames()
## sort atoms
self.traj.sortAtoms()
## remove waters
self.traj = self.traj.compressAtoms(
N.logical_not( self.traj.ref.maskH2O()) )
## get fluctuation on a residue level
r1 = self.traj.getFluct_local( verbose=self.local )
## fit backbone of frames to reference structure
self.traj.fit( ref=self.traj.ref,
mask=self.traj.ref.maskBB(), verbose=self.local )
self.assertAlmostEqual( N.sum( self.traj.profile('rms') ),
58.101235746353879, 2 )
def prepare(self):
self.f = os.path.join(tools.testRoot(), 'eedensity/3tgi.ezd.gz')
self.p = None
def test_PDB2PQR_byID(self):
"""Test PDB2PQR interface. Protonate PDB selected by ID. """
pqr_check = PQRParseFile(T.testRoot('autoprepare', '1yer.pqr')).getModel()
self.b = PDB2PQRInterface()
pqr_out = self.b.protonatePDB(pdbid='1yer',twait=2)
self.comparePDB(pqr_out, pqr_check)
def prepare(self):
self.fname = T.testRoot() + '/rec/1A2P_rec_original.pdb'
self.outPath = T.tempDir()
def test_PepSettingsParser(self):
"""Parse settings config file"""
cfg = T.testRoot('pep', 'pep_amber_mdmix.cfg')
settings = MDSettingsConfigFileParser().parse(cfg)
assert len(settings) == 2
assert settings[0].trajfrequency == 2000
def test_PepSystemParser(self):
"""Parse system config file"""
cfg = T.testRoot('pep', 'pep_amber_mdmix.cfg')
system = SystemConfigFileParser().parse(cfg)
def test_PepReplica(self):
rfile = T.testRoot('pep', 'pep_mdmix', 'MD', '')
def prepare(self):
self.fname = T.testRoot() + '/rec/1A2P_rec_original.pdb'
self.outPath = T.tempDir()
def prepare(self):
self.f = T.testRoot() + '/amber/sim.rst'
self.fref = T.testRoot() + '/amber/1HPT_0.pdb'
self.p = AmberRstParser(self.f)
def prepare( self ):
self.f = os.path.join( tools.testRoot(), 'eedensity/3tgi.ezd.gz' )
self.p = None
def test_PepSettingsParserMulti(self):
"""Parse settings config file with multiple MDSETTINGS entries"""
cfg = T.testRoot('pep', 'multisettings.cfg')
settings = MDSettingsConfigFileParser().parse(cfg)
assert len(settings) == 5
assert settings[-1].trajfrequency == 500
def prepare(self):
root = T.testRoot() + '/amber/'
self.finp = root + 'sim.crd.gz'
self.fref = root + '1HPT_0.pdb'
self.fout = tempfile.mktemp('.dat', 'traj_')
def prepare(self):
self.f = T.testRoot()+'/amber/sim.rst'
self.fref = T.testRoot()+'/amber/1HPT_0.pdb'
self.p = AmberRstParser( self.f )
