for v in values:
r+= T.clipStr( '\n - %s' % str(v), 75)
return r
#############
## TESTING
#############
import biskit.test as BT
class Test(BT.BiskitTest):
"""Test"""
def test_SettingsParser(self):
"""SettingsManager test"""
p = SettingsParser( T.dataRoot() + '/defaults/settings.cfg')
p.parse()
t = p.result.get('testparam', Setting())
self.assertEqual( (t.name, t.value), ('testparam', 42) )
return t.name, t.value
if __name__ == '__main__':
BT.localTest()
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 )
if __name__ == '__main__':
BT.localTest() ## pushes test PDBDope instance as 'd' into namespace
class Test(BT.BiskitTest):
"""Test case"""
def test_hexParser(self):
"""Dock.hexParser test"""
rec_dic = t.load(t.testRoot() + "/dock/rec/1A2P_model.dic")
lig_dic = t.load(t.testRoot() + "/dock/lig/1A19_model.dic")
self.h = HexParser(t.testRoot() + "/dock/hex/1A2P-1A19_hex8.out",
rec_dic, lig_dic)
c_lst = self.h.parseHex()
if self.local:
print(c_lst[1].info)
globals().update(locals())
self.assertSetEqual(
set(c_lst[1].info.keys()),
set([
'soln', 'rms', 'hex_clst', 'hex_eshape', 'model2', 'model1',
'hex_etotal', 'hex_eair', 'date'
]))
if __name__ == '__main__':
BT.localTest()
self.assertEqual(self.d.hexFailed, 0, 'Hex exited with error')
self.assertTrue(len(self.d.result) > 1, 'no results collected')
## dock receptor 1 vs. ligand one on remote host
# fmac2, fout2= d.createHexInp( 1, 1 )
# d.runHex( fmac2, log=0, ncpu=2, host='remote_host_name' )
class TestLong(TestCore):
"""Test case running a complete hex docking (ca. 30 min/CPU)"""
TAGS = [ BT.EXE, BT.LONG ]
def test_DockerLong(self):
"""Dock.Docker real test (20-30min/CPU)"""
self.dry_or_wet_run( run=True )
class TestShort(TestCore):
TAGS = [ BT.EXE ]
def test_DockerShort(self):
"""Dock.Docker dry run test"""
self.dry_or_wet_run( run=False )
if __name__ == '__main__':
BT.localTest(debug=False)
self.assertEqual(self.d.hexFailed, 0, 'Hex exited with error')
self.assertTrue(len(self.d.result) > 1, 'no results collected')
## dock receptor 1 vs. ligand one on remote host
# fmac2, fout2= d.createHexInp( 1, 1 )
# d.runHex( fmac2, log=0, ncpu=2, host='remote_host_name' )
class TestLong(TestCore):
"""Test case running a complete hex docking (ca. 30 min/CPU)"""
TAGS = [BT.EXE, BT.LONG]
def test_DockerLong(self):
"""Dock.Docker real test (20-30min/CPU)"""
self.dry_or_wet_run(run=True)
class TestShort(TestCore):
TAGS = [BT.EXE]
def test_DockerShort(self):
"""Dock.Docker dry run test"""
self.dry_or_wet_run(run=False)
if __name__ == '__main__':
BT.localTest(debug=False)
self.assertEqual( self.ref.lenChains(), self.m3.lenChains() )
self.assertEqual( refprot.atomNames(), m3prot.atomNames() )
class TestNoLeap( BT.BiskitTest ):
"""Test AmberParmBuilder (no dependency on tleap)"""
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,
verbose=self.local)
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' )
if __name__ == '__main__':
BT.localTest(debug=True)
class Test(BT.BiskitTest):
"""ErrorHandler test"""
def prepare(self):
import tempfile
self.f_out = tempfile.mktemp( '_test_ErrorHandler' )
def cleanUp(self):
T.tryRemove( self.f_out )
def test_ErrorHandler( self ):
"""ErrorHandler test"""
from biskit import LogFile
self.err_log = LogFile( self.f_out )
self.e = ErrorHandler( log=self.err_log )
self.e.warning( 'A warning' )
if self.local:
print('An error log file was written to %s'%self.f_out)
lines = open(self.err_log.fname).readlines()
self.assertEqual(lines[-1],'Warning (ignored): A warning\n')
if __name__ == '__main__':
BT.localTest(debug=0)
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)
if __name__ == '__main__':
BT.localTest() ## pushes test PDBDope instance as 'd' into namespace
