def test_ResidueRelatrix_1LRP():
# This case has no Rosetta residues as only CA atoms exist in the PDB and the features database script would crashes. This is a test that the case is handled gracefully.
rr = ResidueRelatrix('1LRP', rosetta_scripts_path, rosetta_database_path, min_clustal_cut_off = 80, cache_dir = '/home/oconchus/temp')
atom_id_1 = 'C 89 '
chain_id = atom_id_1[0]
# Single jumps forward
seqres_id_1 = rr.convert(chain_id, atom_id_1, 'atom', 'seqres')
uniparc_id_1 = rr.convert(chain_id, seqres_id_1, 'seqres', 'uniparc')
# Double jumps forward
uniparc_id_2 = rr.convert(chain_id, atom_id_1, 'atom', 'uniparc')
# Single jumps backward
seqres_id_2 = rr.convert(chain_id, uniparc_id_1, 'uniparc', 'seqres')
atom_id_2 = rr.convert(chain_id, seqres_id_1, 'seqres', 'atom')
# Double/triple jumps backward
atom_id_3 = rr.convert(chain_id, uniparc_id_1, 'uniparc', 'atom')
assert(atom_id_1 == atom_id_2 and atom_id_2 == atom_id_3)
assert(seqres_id_1 == seqres_id_2)
assert(uniparc_id_1 == uniparc_id_2)
def test_ResidueRelatrix_1A2P():
rr = ResidueRelatrix('1A2P', rosetta_scripts_path, rosetta_database_path, min_clustal_cut_off = 80, cache_dir = '/home/oconchus/temp')
rosetta_id_1 = 79
# Single jumps forward
assert(rosetta_id_1 == 79)
atom_id_1 = rr.convert('A', rosetta_id_1, 'rosetta', 'atom')
assert(atom_id_1 == 'A 81 ')
seqres_id_1 = rr.convert('A', atom_id_1, 'atom', 'seqres')
assert(seqres_id_1 == 81)
uniparc_id_1 = rr.convert('A', seqres_id_1, 'seqres', 'uniparc')
assert(uniparc_id_1 == (u'UPI000013432A', 128))
# Double/triple jumps forward
seqres_id_2 = rr.convert('A', rosetta_id_1, 'rosetta', 'seqres')
assert(seqres_id_2 == 81)
uniparc_id_2 = rr.convert('A', rosetta_id_1, 'rosetta', 'uniparc')
assert(uniparc_id_2 == (u'UPI000013432A', 128))
# Double jumps forward
uniparc_id_3 = rr.convert('A', atom_id_1, 'atom', 'uniparc')
assert(uniparc_id_3 == (u'UPI000013432A', 128))
# Single jumps backward
seqres_id_3 = rr.convert('A', uniparc_id_1, 'uniparc', 'seqres')
assert(seqres_id_3 == 81)
atom_id_2 = rr.convert('A', seqres_id_3, 'seqres', 'atom')
assert(atom_id_2 == 'A 81 ')
rosetta_id_2 = rr.convert('A', atom_id_2, 'atom', 'rosetta')
assert(rosetta_id_2 == 79)
# Double/triple jumps backward
atom_id_3 = rr.convert('A', uniparc_id_1, 'uniparc', 'atom')
assert(atom_id_3 == 'A 81 ')
rosetta_id_3 = rr.convert('A', uniparc_id_1, 'uniparc', 'rosetta')
assert(rosetta_id_3 == 79)
rosetta_id_4 = rr.convert('A', seqres_id_3, 'seqres', 'rosetta')
assert(rosetta_id_4 == 79)
assert(rosetta_id_1 == rosetta_id_2 and rosetta_id_2 == rosetta_id_3 and rosetta_id_3 == rosetta_id_4)
assert(atom_id_1 == atom_id_2 and atom_id_2 == atom_id_3)
assert(seqres_id_1 == seqres_id_2 and seqres_id_2 == seqres_id_3)
assert(uniparc_id_1 == uniparc_id_2 and uniparc_id_2 == uniparc_id_3)
# Rosetta residue 3 maps to 'A 5 '
#print(rr.rosetta_to_atom_sequence_maps)
assert(rr.convert_from_rosetta(3, 'atom') == 'A 5 ')
assert(rr.convert_from_rosetta(3, 'seqres') == 5)
assert(rr.convert_from_rosetta(3, 'uniparc') == (u'UPI000013432A', 52))
def test_ResidueRelatrix_1A2C():
# Rosetta residue 45 -> 'A 44A' is an insertion residue which does not appear in the UniParc sequence
rr = ResidueRelatrix('1A2C', rosetta_scripts_path, rosetta_database_path, min_clustal_cut_off = 80, cache_dir = '/home/oconchus/temp', starting_clustal_cut_off = 82)
rosetta_id_1 = 157
chain_id = rr.convert_from_rosetta(rosetta_id_1, 'atom')[0]
# Single jumps forward
atom_id_1 = rr.convert(chain_id, rosetta_id_1, 'rosetta', 'atom')
assert(atom_id_1 == 'H 124 ')
seqres_id_1 = rr.convert(chain_id, atom_id_1, 'atom', 'seqres')
assert(seqres_id_1== 121)
uniparc_id_1 = rr.convert(chain_id, seqres_id_1, 'seqres', 'uniparc')
assert(uniparc_id_1 == (u'UPI0000136ECD', 484))
# Double/triple jumps forward
seqres_id_2 = rr.convert(chain_id, rosetta_id_1, 'rosetta', 'seqres')
uniparc_id_2 = rr.convert(chain_id, rosetta_id_1, 'rosetta', 'uniparc')
# Double jumps forward
uniparc_id_3 = rr.convert(chain_id, atom_id_1, 'atom', 'uniparc')
# Single jumps backward
seqres_id_3 = rr.convert(chain_id, uniparc_id_1, 'uniparc', 'seqres')
atom_id_2 = rr.convert(chain_id, seqres_id_2, 'seqres', 'atom')
rosetta_id_2 = rr.convert(chain_id, atom_id_2, 'atom', 'rosetta')
# Double/triple jumps backward
atom_id_3 = rr.convert(chain_id, uniparc_id_1, 'uniparc', 'atom')
rosetta_id_3 = rr.convert(chain_id, uniparc_id_1, 'uniparc', 'rosetta')
rosetta_id_4 = rr.convert(chain_id, seqres_id_2, 'seqres', 'rosetta')
assert(rosetta_id_1 == rosetta_id_2 and rosetta_id_2 == rosetta_id_3 and rosetta_id_3 == rosetta_id_4)
assert(atom_id_1 == atom_id_2 and atom_id_2 == atom_id_3)
assert(seqres_id_1 == seqres_id_2 and seqres_id_2 == seqres_id_3)
assert(uniparc_id_1 == uniparc_id_2 and uniparc_id_2 == uniparc_id_3)
def test_ResidueRelatrix_104L():
# Rosetta residue 45 -> 'A 44A' is an insertion residue which does not appear in the UniParc sequence
rr = ResidueRelatrix('104L', rosetta_scripts_path, rosetta_database_path, min_clustal_cut_off = 80, cache_dir = '/home/oconchus/temp')
rosetta_id_1 = 45
# Single jumps forward
atom_id_1 = rr.convert('A', rosetta_id_1, 'rosetta', 'atom')
seqres_id_1 = rr.convert('A', atom_id_1, 'atom', 'seqres')
uniparc_id_1 = rr.convert('A', seqres_id_1, 'seqres', 'uniparc')
# Double/triple jumps forward
seqres_id_2 = rr.convert('A', rosetta_id_1, 'rosetta', 'seqres')
uniparc_id_2 = rr.convert('A', rosetta_id_1, 'rosetta', 'uniparc')
# Double jumps forward
uniparc_id_3 = rr.convert('A', atom_id_1, 'atom', 'uniparc')
# Single jumps backward
seqres_id_3 = rr.convert('A', uniparc_id_1, 'uniparc', 'seqres')
atom_id_2 = rr.convert('A', seqres_id_2, 'seqres', 'atom')
rosetta_id_2 = rr.convert('A', atom_id_2, 'atom', 'rosetta')
# Double/triple jumps backward
atom_id_3 = rr.convert('A', uniparc_id_1, 'uniparc', 'atom')
rosetta_id_3 = rr.convert('A', uniparc_id_1, 'uniparc', 'rosetta')
rosetta_id_4 = rr.convert('A', seqres_id_2, 'seqres', 'rosetta')
assert(rosetta_id_1 == rosetta_id_2 and rosetta_id_2 == rosetta_id_4)
assert(rosetta_id_3 == None)
assert(atom_id_1 == atom_id_2)
assert(atom_id_3 == None)
assert(seqres_id_1 == seqres_id_2)
assert(seqres_id_3 == None)
assert(uniparc_id_1 == uniparc_id_2 and uniparc_id_2 == uniparc_id_3)
