def test_GetMolTypeCountList(self):
cing.verbosity = verbosityDebug
entryId = 'test'
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status='new')
mol = Molecule('test')
project.appendMolecule(mol)
c = mol.addChain('A')
c.addResidue('ALA', 1, Nterminal = True)
c.addResidue('VAL', 2)
c.addResidue('PHE', 3)
c.addResidue('ARG', 4)
c.addResidue('GLU', 5, Cterminal = True)
c = mol.addChain('B')
c.addResidue('DG', 1, Nterminal = True)
c.addResidue('DA', 2)
c.addResidue('DT', 3)
c.addResidue('DC', 4, Cterminal = True)
c = mol.addChain('C')
c.addResidue('RGUA', 1, convention=INTERNAL_0, Nterminal = True)
c.addResidue('RADE', 2, convention=INTERNAL_0, )
c.addResidue('URA', 3, convention=INTERNAL_0, ) # not RTHY normally of course.
c.addResidue('RTHY', 4, convention=INTERNAL_0, )
c.addResidue('RCYT', 5, convention=INTERNAL_0, Cterminal = True)
c = mol.addChain('D')
for i in range(1,11):
c.addResidue('HOH', i )
# end for
c = mol.addChain('E') # Unknown residue to CING
c.addResidue('ACE', 1 )
c = mol.addChain('F') # Ions are also other
c.addResidue('CA2P', 1 )
for residue in mol.allResidues():
residue.addAllAtoms()
# end for
mol.updateAll()
nTmessage( mol.format() )
for c in mol.allChains():
nTmessage( c.format() )
nTmessage( "idxMolType: %s" % (c.getIdxMolType()))
# end for
nTmessage("Count the molecule types")
molTypeCountList = mol.getMolTypeCountList()
p_protein_count = molTypeCountList[ mapMoltypeToInt[PROTEIN_STR] ]
p_dna_count = molTypeCountList[ mapMoltypeToInt[DNA_STR] ]
p_rna_count = molTypeCountList[ mapMoltypeToInt[RNA_STR] ]
p_water_count = molTypeCountList[ mapMoltypeToInt[WATER_STR] ]
p_other_count = molTypeCountList[ mapMoltypeToInt[OTHER_STR] ]
self.assertEqual(1, p_protein_count)
self.assertEqual(1, p_dna_count )
self.assertEqual(1, p_rna_count )
self.assertEqual(1, p_water_count)
self.assertEqual(2, p_other_count)
nTmessage("Count the residue types")
molTypeResidueCountList = mol.getMolTypeResidueCountList()
p_res_protein_count = molTypeResidueCountList[ mapMoltypeToInt[PROTEIN_STR] ]
p_res_dna_count = molTypeResidueCountList[ mapMoltypeToInt[DNA_STR] ]
p_res_rna_count = molTypeResidueCountList[ mapMoltypeToInt[RNA_STR] ]
p_res_water_count = molTypeResidueCountList[ mapMoltypeToInt[WATER_STR] ]
p_res_other_count = molTypeResidueCountList[ mapMoltypeToInt[OTHER_STR] ]
self.assertEqual(5, p_res_protein_count)
self.assertEqual(4, p_res_dna_count )
self.assertEqual(5, p_res_rna_count )
self.assertEqual(10, p_res_water_count)
self.assertEqual(2, p_res_other_count)
nTmessage("Select a list of residues.")
inputResList = (('A', 5),('B', 2),('A', 6),('X', 1)) # The last 2 are non-existing residues
# should give two warnings for a non-existing residue
resList = project.decodeResidueList( inputResList )
self.assertEqual(2, len(resList) )
def test_GetMolTypeCountList(self):
cing.verbosity = verbosityDebug
entryId = 'test'
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status='new')
mol = Molecule('test')
project.appendMolecule(mol)
c = mol.addChain('A')
c.addResidue('ALA', 1, Nterminal=True)
c.addResidue('VAL', 2)
c.addResidue('PHE', 3)
c.addResidue('ARG', 4)
c.addResidue('GLU', 5, Cterminal=True)
c = mol.addChain('B')
c.addResidue('DG', 1, Nterminal=True)
c.addResidue('DA', 2)
c.addResidue('DT', 3)
c.addResidue('DC', 4, Cterminal=True)
c = mol.addChain('C')
c.addResidue('RGUA', 1, convention=INTERNAL_0, Nterminal=True)
c.addResidue(
'RADE',
2,
convention=INTERNAL_0,
)
c.addResidue(
'URA',
3,
convention=INTERNAL_0,
) # not RTHY normally of course.
c.addResidue(
'RTHY',
4,
convention=INTERNAL_0,
)
c.addResidue('RCYT', 5, convention=INTERNAL_0, Cterminal=True)
c = mol.addChain('D')
for i in range(1, 11):
c.addResidue('HOH', i)
# end for
c = mol.addChain('E') # Unknown residue to CING
c.addResidue('ACE', 1)
c = mol.addChain('F') # Ions are also other
c.addResidue('CA2P', 1)
for residue in mol.allResidues():
residue.addAllAtoms()
# end for
mol.updateAll()
nTmessage(mol.format())
for c in mol.allChains():
nTmessage(c.format())
nTmessage("idxMolType: %s" % (c.getIdxMolType()))
# end for
nTmessage("Count the molecule types")
molTypeCountList = mol.getMolTypeCountList()
p_protein_count = molTypeCountList[mapMoltypeToInt[PROTEIN_STR]]
p_dna_count = molTypeCountList[mapMoltypeToInt[DNA_STR]]
p_rna_count = molTypeCountList[mapMoltypeToInt[RNA_STR]]
p_water_count = molTypeCountList[mapMoltypeToInt[WATER_STR]]
p_other_count = molTypeCountList[mapMoltypeToInt[OTHER_STR]]
self.assertEqual(1, p_protein_count)
self.assertEqual(1, p_dna_count)
self.assertEqual(1, p_rna_count)
self.assertEqual(1, p_water_count)
self.assertEqual(2, p_other_count)
nTmessage("Count the residue types")
molTypeResidueCountList = mol.getMolTypeResidueCountList()
p_res_protein_count = molTypeResidueCountList[
mapMoltypeToInt[PROTEIN_STR]]
p_res_dna_count = molTypeResidueCountList[mapMoltypeToInt[DNA_STR]]
p_res_rna_count = molTypeResidueCountList[mapMoltypeToInt[RNA_STR]]
p_res_water_count = molTypeResidueCountList[mapMoltypeToInt[WATER_STR]]
p_res_other_count = molTypeResidueCountList[mapMoltypeToInt[OTHER_STR]]
self.assertEqual(5, p_res_protein_count)
self.assertEqual(4, p_res_dna_count)
self.assertEqual(5, p_res_rna_count)
self.assertEqual(10, p_res_water_count)
self.assertEqual(2, p_res_other_count)
nTmessage("Select a list of residues.")
inputResList = (('A', 5), ('B', 2), ('A', 6), ('X', 1)
) # The last 2 are non-existing residues
# should give two warnings for a non-existing residue
resList = project.decodeResidueList(inputResList)
self.assertEqual(2, len(resList))
