def tst_parsing_phil_single_sheet():
phil_hbond_portion = """\
hbond {
donor = chain A and resid 29 and name O
acceptor = chain A and resid 13 and name N
}
hbond {
donor = chain A and resid 13 and name O
acceptor = chain A and resid 29 and name N
}
hbond {
donor = chain A and resid 53 and name O
acceptor = chain A and resid 159 and name N
}
hbond {
donor = chain A and resid 157 and name O
acceptor = chain A and resid 53 and name N
}
hbond {
donor = chain A and resid 51 and name O
acceptor = chain A and resid 157 and name N
}
hbond {
donor = chain A and resid 76 and name O
acceptor = chain A and resid 54 and name N
}
hbond {
donor = chain A and resid 52 and name O
acceptor = chain A and resid 76 and name N
}
hbond {
donor = chain A and resid 74 and name O
acceptor = chain A and resid 52 and name N
}
"""
phil_str_1 = """\
secondary_structure.protein.sheet {
first_strand = chain A and resseq 13:14
sheet_id = A
strand {
selection = chain A and resseq 27:30
sense = antiparallel
bond_start_current = chain A and resseq 29 and name O
bond_start_previous = chain A and resseq 13 and name N
}
strand {
selection = chain A and resseq 156:159
sense = parallel
bond_start_current = chain A and resseq 156 and name O
bond_start_previous = chain A and resseq 28 and name N
}
strand {
selection = chain A and resseq 51:54
sense = parallel
bond_start_current = chain A and resseq 51 and name O
bond_start_previous = chain A and resseq 157 and name N
}
strand {
selection = chain A and resseq 74:77
sense = parallel
bond_start_current = chain A and resseq 74 and name O
bond_start_previous = chain A and resseq 52 and name N
}
%s
}
""" % phil_hbond_portion
phil_str_1_1 = """\
secondary_structure.protein.sheet {
first_strand = chain A and resseq 13:14
sheet_id = AA
strand {
selection = chain A and resseq 27:30
sense = antiparallel
bond_start_current = chain A and resseq 29 and name O
bond_start_previous = chain A and resseq 13 and name N
}
strand {
selection = chain A and resseq 156:159
sense = parallel
bond_start_current = chain A and resseq 156 and name O
bond_start_previous = chain A and resseq 28 and name N
}
strand {
selection = chain A and resseq 51:54
sense = parallel
bond_start_current = chain A and resseq 51 and name O
bond_start_previous = chain A and resseq 157 and name N
}
strand {
selection = chain A and resseq 74:77
sense = parallel
bond_start_current = chain A and resseq 74 and name O
bond_start_previous = chain A and resseq 52 and name N
}
}
"""
result1 = """
protein.sheet {
sheet_id = " A"
first_strand = chain 'A' and resid 13 through 14
strand {
selection = chain 'A' and resid 27 through 30
sense = antiparallel
bond_start_current = chain 'A' and resid 29 and name O
bond_start_previous = chain 'A' and resid 13 and name N
}
strand {
selection = chain 'A' and resid 156 through 159
sense = parallel
bond_start_current = chain 'A' and resid 156 and name O
bond_start_previous = chain 'A' and resid 28 and name N
}
strand {
selection = chain 'A' and resid 51 through 54
sense = parallel
bond_start_current = chain 'A' and resid 51 and name O
bond_start_previous = chain 'A' and resid 157 and name N
}
strand {
selection = chain 'A' and resid 74 through 77
sense = parallel
bond_start_current = chain 'A' and resid 74 and name O
bond_start_previous = chain 'A' and resid 52 and name N
}
hbond {
donor = chain A and resid 29 and name O
acceptor = chain A and resid 13 and name N
}
hbond {
donor = chain A and resid 13 and name O
acceptor = chain A and resid 29 and name N
}
hbond {
donor = chain A and resid 53 and name O
acceptor = chain A and resid 159 and name N
}
hbond {
donor = chain A and resid 157 and name O
acceptor = chain A and resid 53 and name N
}
hbond {
donor = chain A and resid 51 and name O
acceptor = chain A and resid 157 and name N
}
hbond {
donor = chain A and resid 76 and name O
acceptor = chain A and resid 54 and name N
}
hbond {
donor = chain A and resid 52 and name O
acceptor = chain A and resid 76 and name N
}
hbond {
donor = chain A and resid 74 and name O
acceptor = chain A and resid 52 and name N
}
}"""
result1_1 = """
protein.sheet {
sheet_id = " A"
first_strand = chain 'A' and resid 13 through 14
strand {
selection = chain 'A' and resid 27 through 30
sense = antiparallel
bond_start_current = chain 'A' and resid 29 and name O
bond_start_previous = chain 'A' and resid 13 and name N
}
strand {
selection = chain 'A' and resid 156 through 159
sense = parallel
bond_start_current = chain 'A' and resid 156 and name O
bond_start_previous = chain 'A' and resid 28 and name N
}
strand {
selection = chain 'A' and resid 51 through 54
sense = parallel
bond_start_current = chain 'A' and resid 51 and name O
bond_start_previous = chain 'A' and resid 157 and name N
}
strand {
selection = chain 'A' and resid 74 through 77
sense = parallel
bond_start_current = chain 'A' and resid 74 and name O
bond_start_previous = chain 'A' and resid 52 and name N
}
}"""
annot, ss_from_file = get_annotation(
phil_lines=phil_str_1,
pdb_lines=pdb_1ywf_sample_strings)
assert annot.get_n_helices() == 0
assert annot.get_n_sheets() == 1
sh = annot.sheets[0]
assert sh.get_n_defined_hbonds() == 8
assert annot.get_n_defined_hbonds() == 8
res = sh.as_restraint_group(show_hbonds=True)
assert not test_utils.show_diff(res, result1,
strip_trailing_whitespace=True)
res = sh.as_restraint_group(show_hbonds=False)
assert not test_utils.show_diff(res, result1_1,
strip_trailing_whitespace=True)
print("OK")
def tst_parsing_phil_single_helix():
phil_hbond_portion = """\
hbond {
donor = chain A and resid 37 and name O
acceptor = chain A and resid 41 and name N
}
hbond {
donor = chain A and resid 38 and name O
acceptor = chain A and resid 42 and name N
}
hbond {
donor = chain A and resid 39 and name O
acceptor = chain A and resid 43 and name N
}
hbond {
donor = chain A and resid 40 and name O
acceptor = chain A and resid 44 and name N
}
hbond {
donor = chain A and resid 41 and name O
acceptor = chain A and resid 45 and name N
}
hbond {
donor = chain A and resid 42 and name O
acceptor = chain A and resid 46 and name N
}
hbond {
donor = chain A and resid 43 and name O
acceptor = chain A and resid 47 and name N
}
hbond {
donor = chain A and resid 44 and name O
acceptor = chain A and resid 48 and name N
}
"""
phil_str1 = """\
secondary_structure.protein.helix {
selection = chain A and resseq 37:48
helix_type = *alpha pi 3_10 unknown
%s
}
""" % phil_hbond_portion
phil_str2 = """\
secondary_structure.protein.helix {
selection = chain A and resseq 37:48
helix_type = alpha *pi 3_10 unknown
}
"""
phil_str3 = """\
secondary_structure.protein.helix {
selection = chain A and resseq 37:48
helix_type = alpha pi *3_10 unknown
}
"""
phil_str4 = """\
secondary_structure.protein.helix {
selection = chain A and resseq 37:48
helix_type = alpha pi 3_10 *unknown
}
"""
phil_str5 = """\
secondary_structure.protein.helix {
serial_number = 1
selection = chain A and resseq 37:48
helix_type = *alpha pi 3_10 unknown
}
"""
phil_str6 = """\
secondary_structure.protein.helix {
serial_number = 2
helix_identifier = A
selection = chain A and resseq 37:48
helix_type = *alpha pi 3_10 unknown
}
"""
phil_str7 = """\
secondary_structure.protein.helix {
serial_number = 3
helix_identifier = BB
selection = chain A and resseq 37:48
helix_type = *alpha pi 3_10 unknown
}
"""
phil_str8 = """\
secondary_structure.protein.helix {
serial_number = 1
helix_identifier = C12
selection = chain A and resseq 37:48
helix_type = *alpha pi 3_10 unknown
}
"""
phil_str9 = """\
secondary_structure.protein.helix {
serial_number = 1
helix_identifier = D123
selection = chain A and resseq 37:48
helix_type = *alpha pi 3_10 unknown
}
"""
result1 = """\
protein.helix {
helix_identifier = 0
selection = chain 'A' and resid 37 through 48
helix_type = alpha
hbond {
donor = chain A and resid 37 and name O
acceptor = chain A and resid 41 and name N
}
hbond {
donor = chain A and resid 38 and name O
acceptor = chain A and resid 42 and name N
}
hbond {
donor = chain A and resid 39 and name O
acceptor = chain A and resid 43 and name N
}
hbond {
donor = chain A and resid 40 and name O
acceptor = chain A and resid 44 and name N
}
hbond {
donor = chain A and resid 41 and name O
acceptor = chain A and resid 45 and name N
}
hbond {
donor = chain A and resid 42 and name O
acceptor = chain A and resid 46 and name N
}
hbond {
donor = chain A and resid 43 and name O
acceptor = chain A and resid 47 and name N
}
hbond {
donor = chain A and resid 44 and name O
acceptor = chain A and resid 48 and name N
}
}"""
result1_1 = """\
protein.helix {
helix_identifier = 0
selection = chain 'A' and resid 37 through 48
helix_type = alpha
}"""
result2_9 = """\
==================================================
protein.helix {
helix_identifier = 0
selection = chain 'A' and resid 37 through 48
helix_type = pi
}
HELIX 0 0 ASP A 37 GLY A 48 3 12
==================================================
protein.helix {
helix_identifier = 0
selection = chain 'A' and resid 37 through 48
helix_type = 3_10
}
HELIX 0 0 ASP A 37 GLY A 48 5 12
==================================================
protein.helix {
helix_identifier = 0
selection = chain 'A' and resid 37 through 48
helix_type = unknown
}
HELIX 0 0 ASP A 37 GLY A 48 1 12
==================================================
protein.helix {
serial_number = 1
helix_identifier = 1
selection = chain 'A' and resid 37 through 48
helix_type = alpha
}
HELIX 1 1 ASP A 37 GLY A 48 1 12
==================================================
protein.helix {
serial_number = 2
helix_identifier = A
selection = chain 'A' and resid 37 through 48
helix_type = alpha
}
HELIX 2 A ASP A 37 GLY A 48 1 12
==================================================
protein.helix {
serial_number = 3
helix_identifier = BB
selection = chain 'A' and resid 37 through 48
helix_type = alpha
}
HELIX 3 BB ASP A 37 GLY A 48 1 12
==================================================
protein.helix {
serial_number = 1
helix_identifier = C12
selection = chain 'A' and resid 37 through 48
helix_type = alpha
}
HELIX 1 C12 ASP A 37 GLY A 48 1 12
==================================================
protein.helix {
serial_number = 1
helix_identifier = D123
selection = chain 'A' and resid 37 through 48
helix_type = alpha
}
HELIX 1 D12 ASP A 37 GLY A 48 1 12
"""
annot, ss_from_file = get_annotation(
phil_lines=phil_str1,
pdb_lines=pdb_1ywf_sample_strings)
assert annot.get_n_helices() == 1
assert annot.get_n_sheets() == 0
h = annot.helices[0]
assert h.get_n_defined_hbonds() == 8
assert annot.get_n_defined_hbonds() == 8
res = h.as_restraint_group(show_hbonds=True)
assert not test_utils.show_diff(res, result1,
strip_trailing_whitespace=True)
res = h.as_restraint_group(show_hbonds=False)
assert not test_utils.show_diff(res, result1_1,
strip_trailing_whitespace=True)
out = StringIO()
for ph_str in [phil_str2, phil_str3, phil_str4, phil_str5, phil_str6,
phil_str7, phil_str8, phil_str9]:
print >> out, "="*50
annot, ss_from_file = get_annotation(
phil_lines=ph_str,
pdb_lines=pdb_1ywf_sample_strings)
assert annot.get_n_defined_hbonds() == 0
assert annot.get_n_helices() == 1
assert annot.get_n_sheets() == 0
h = annot.helices[0]
print >> out, h.as_restraint_group()
print >> out, h.as_pdb_str()
assert not test_utils.show_diff(out.getvalue(), result2_9,
strip_trailing_whitespace=True)
print "OK"
def tst_parsing_phil_single_helix():
phil_hbond_portion = """\
hbond {
donor = chain A and resid 37 and name O
acceptor = chain A and resid 41 and name N
}
hbond {
donor = chain A and resid 38 and name O
acceptor = chain A and resid 42 and name N
}
hbond {
donor = chain A and resid 39 and name O
acceptor = chain A and resid 43 and name N
}
hbond {
donor = chain A and resid 40 and name O
acceptor = chain A and resid 44 and name N
}
hbond {
donor = chain A and resid 41 and name O
acceptor = chain A and resid 45 and name N
}
hbond {
donor = chain A and resid 42 and name O
acceptor = chain A and resid 46 and name N
}
hbond {
donor = chain A and resid 43 and name O
acceptor = chain A and resid 47 and name N
}
hbond {
donor = chain A and resid 44 and name O
acceptor = chain A and resid 48 and name N
}
"""
phil_str1 = """\
secondary_structure.protein.helix {
selection = chain A and resseq 37:48
helix_type = *alpha pi 3_10 unknown
%s
}
""" % phil_hbond_portion
phil_str2 = """\
secondary_structure.protein.helix {
selection = chain A and resseq 37:48
helix_type = alpha *pi 3_10 unknown
}
"""
phil_str3 = """\
secondary_structure.protein.helix {
selection = chain A and resseq 37:48
helix_type = alpha pi *3_10 unknown
}
"""
phil_str4 = """\
secondary_structure.protein.helix {
selection = chain A and resseq 37:48
helix_type = alpha pi 3_10 *unknown
}
"""
phil_str5 = """\
secondary_structure.protein.helix {
serial_number = 1
selection = chain A and resseq 37:48
helix_type = *alpha pi 3_10 unknown
}
"""
phil_str6 = """\
secondary_structure.protein.helix {
serial_number = 2
helix_identifier = A
selection = chain A and resseq 37:48
helix_type = *alpha pi 3_10 unknown
}
"""
phil_str7 = """\
secondary_structure.protein.helix {
serial_number = 3
helix_identifier = BB
selection = chain A and resseq 37:48
helix_type = *alpha pi 3_10 unknown
}
"""
phil_str8 = """\
secondary_structure.protein.helix {
serial_number = 1
helix_identifier = C12
selection = chain A and resseq 37:48
helix_type = *alpha pi 3_10 unknown
}
"""
phil_str9 = """\
secondary_structure.protein.helix {
serial_number = 1
helix_identifier = D123
selection = chain A and resseq 37:48
helix_type = *alpha pi 3_10 unknown
}
"""
result1 = """\
protein.helix {
helix_identifier = 0
selection = chain 'A' and resid 37 through 48
helix_type = alpha
hbond {
donor = chain A and resid 37 and name O
acceptor = chain A and resid 41 and name N
}
hbond {
donor = chain A and resid 38 and name O
acceptor = chain A and resid 42 and name N
}
hbond {
donor = chain A and resid 39 and name O
acceptor = chain A and resid 43 and name N
}
hbond {
donor = chain A and resid 40 and name O
acceptor = chain A and resid 44 and name N
}
hbond {
donor = chain A and resid 41 and name O
acceptor = chain A and resid 45 and name N
}
hbond {
donor = chain A and resid 42 and name O
acceptor = chain A and resid 46 and name N
}
hbond {
donor = chain A and resid 43 and name O
acceptor = chain A and resid 47 and name N
}
hbond {
donor = chain A and resid 44 and name O
acceptor = chain A and resid 48 and name N
}
}"""
result1_1 = """\
protein.helix {
helix_identifier = 0
selection = chain 'A' and resid 37 through 48
helix_type = alpha
}"""
result2_9 = """\
==================================================
protein.helix {
helix_identifier = 0
selection = chain 'A' and resid 37 through 48
helix_type = pi
}
HELIX 0 0 ASP A 37 GLY A 48 3 12
==================================================
protein.helix {
helix_identifier = 0
selection = chain 'A' and resid 37 through 48
helix_type = 3_10
}
HELIX 0 0 ASP A 37 GLY A 48 5 12
==================================================
protein.helix {
helix_identifier = 0
selection = chain 'A' and resid 37 through 48
helix_type = unknown
}
HELIX 0 0 ASP A 37 GLY A 48 1 12
==================================================
protein.helix {
serial_number = 1
helix_identifier = 1
selection = chain 'A' and resid 37 through 48
helix_type = alpha
}
HELIX 1 1 ASP A 37 GLY A 48 1 12
==================================================
protein.helix {
serial_number = 2
helix_identifier = A
selection = chain 'A' and resid 37 through 48
helix_type = alpha
}
HELIX 2 A ASP A 37 GLY A 48 1 12
==================================================
protein.helix {
serial_number = 3
helix_identifier = BB
selection = chain 'A' and resid 37 through 48
helix_type = alpha
}
HELIX 3 BB ASP A 37 GLY A 48 1 12
==================================================
protein.helix {
serial_number = 1
helix_identifier = C12
selection = chain 'A' and resid 37 through 48
helix_type = alpha
}
HELIX 1 C12 ASP A 37 GLY A 48 1 12
==================================================
protein.helix {
serial_number = 1
helix_identifier = D123
selection = chain 'A' and resid 37 through 48
helix_type = alpha
}
HELIX 1 D12 ASP A 37 GLY A 48 1 12
"""
annot, ss_from_file = get_annotation(
phil_lines=phil_str1,
pdb_lines=pdb_1ywf_sample_strings)
assert annot.get_n_helices() == 1
assert annot.get_n_sheets() == 0
h = annot.helices[0]
assert h.get_n_defined_hbonds() == 8
assert annot.get_n_defined_hbonds() == 8
res = h.as_restraint_group(show_hbonds=True)
assert not test_utils.show_diff(res, result1,
strip_trailing_whitespace=True)
res = h.as_restraint_group(show_hbonds=False)
assert not test_utils.show_diff(res, result1_1,
strip_trailing_whitespace=True)
out = StringIO()
for ph_str in [phil_str2, phil_str3, phil_str4, phil_str5, phil_str6,
phil_str7, phil_str8, phil_str9]:
print("="*50, file=out)
annot, ss_from_file = get_annotation(
phil_lines=ph_str,
pdb_lines=pdb_1ywf_sample_strings)
assert annot.get_n_defined_hbonds() == 0
assert annot.get_n_helices() == 1
assert annot.get_n_sheets() == 0
h = annot.helices[0]
print(h.as_restraint_group(), file=out)
print(h.as_pdb_str(), file=out)
assert not test_utils.show_diff(out.getvalue(), result2_9,
strip_trailing_whitespace=True)
print("OK")
def tst_parsing_phil_single_sheet():
phil_hbond_portion = """\
hbond {
donor = chain A and resid 29 and name O
acceptor = chain A and resid 13 and name N
}
hbond {
donor = chain A and resid 13 and name O
acceptor = chain A and resid 29 and name N
}
hbond {
donor = chain A and resid 53 and name O
acceptor = chain A and resid 159 and name N
}
hbond {
donor = chain A and resid 157 and name O
acceptor = chain A and resid 53 and name N
}
hbond {
donor = chain A and resid 51 and name O
acceptor = chain A and resid 157 and name N
}
hbond {
donor = chain A and resid 76 and name O
acceptor = chain A and resid 54 and name N
}
hbond {
donor = chain A and resid 52 and name O
acceptor = chain A and resid 76 and name N
}
hbond {
donor = chain A and resid 74 and name O
acceptor = chain A and resid 52 and name N
}
"""
phil_str_1 = """\
secondary_structure.protein.sheet {
first_strand = chain A and resseq 13:14
sheet_id = A
strand {
selection = chain A and resseq 27:30
sense = antiparallel
bond_start_current = chain A and resseq 29 and name O
bond_start_previous = chain A and resseq 13 and name N
}
strand {
selection = chain A and resseq 156:159
sense = parallel
bond_start_current = chain A and resseq 156 and name O
bond_start_previous = chain A and resseq 28 and name N
}
strand {
selection = chain A and resseq 51:54
sense = parallel
bond_start_current = chain A and resseq 51 and name O
bond_start_previous = chain A and resseq 157 and name N
}
strand {
selection = chain A and resseq 74:77
sense = parallel
bond_start_current = chain A and resseq 74 and name O
bond_start_previous = chain A and resseq 52 and name N
}
%s
}
""" % phil_hbond_portion
phil_str_1_1 = """\
secondary_structure.protein.sheet {
first_strand = chain A and resseq 13:14
sheet_id = AA
strand {
selection = chain A and resseq 27:30
sense = antiparallel
bond_start_current = chain A and resseq 29 and name O
bond_start_previous = chain A and resseq 13 and name N
}
strand {
selection = chain A and resseq 156:159
sense = parallel
bond_start_current = chain A and resseq 156 and name O
bond_start_previous = chain A and resseq 28 and name N
}
strand {
selection = chain A and resseq 51:54
sense = parallel
bond_start_current = chain A and resseq 51 and name O
bond_start_previous = chain A and resseq 157 and name N
}
strand {
selection = chain A and resseq 74:77
sense = parallel
bond_start_current = chain A and resseq 74 and name O
bond_start_previous = chain A and resseq 52 and name N
}
}
"""
result1 = """
protein.sheet {
sheet_id = " A"
first_strand = chain 'A' and resid 13 through 14
strand {
selection = chain 'A' and resid 27 through 30
sense = antiparallel
bond_start_current = chain 'A' and resid 29 and name O
bond_start_previous = chain 'A' and resid 13 and name N
}
strand {
selection = chain 'A' and resid 156 through 159
sense = parallel
bond_start_current = chain 'A' and resid 156 and name O
bond_start_previous = chain 'A' and resid 28 and name N
}
strand {
selection = chain 'A' and resid 51 through 54
sense = parallel
bond_start_current = chain 'A' and resid 51 and name O
bond_start_previous = chain 'A' and resid 157 and name N
}
strand {
selection = chain 'A' and resid 74 through 77
sense = parallel
bond_start_current = chain 'A' and resid 74 and name O
bond_start_previous = chain 'A' and resid 52 and name N
}
hbond {
donor = chain A and resid 29 and name O
acceptor = chain A and resid 13 and name N
}
hbond {
donor = chain A and resid 13 and name O
acceptor = chain A and resid 29 and name N
}
hbond {
donor = chain A and resid 53 and name O
acceptor = chain A and resid 159 and name N
}
hbond {
donor = chain A and resid 157 and name O
acceptor = chain A and resid 53 and name N
}
hbond {
donor = chain A and resid 51 and name O
acceptor = chain A and resid 157 and name N
}
hbond {
donor = chain A and resid 76 and name O
acceptor = chain A and resid 54 and name N
}
hbond {
donor = chain A and resid 52 and name O
acceptor = chain A and resid 76 and name N
}
hbond {
donor = chain A and resid 74 and name O
acceptor = chain A and resid 52 and name N
}
}"""
result1_1 = """
protein.sheet {
sheet_id = " A"
first_strand = chain 'A' and resid 13 through 14
strand {
selection = chain 'A' and resid 27 through 30
sense = antiparallel
bond_start_current = chain 'A' and resid 29 and name O
bond_start_previous = chain 'A' and resid 13 and name N
}
strand {
selection = chain 'A' and resid 156 through 159
sense = parallel
bond_start_current = chain 'A' and resid 156 and name O
bond_start_previous = chain 'A' and resid 28 and name N
}
strand {
selection = chain 'A' and resid 51 through 54
sense = parallel
bond_start_current = chain 'A' and resid 51 and name O
bond_start_previous = chain 'A' and resid 157 and name N
}
strand {
selection = chain 'A' and resid 74 through 77
sense = parallel
bond_start_current = chain 'A' and resid 74 and name O
bond_start_previous = chain 'A' and resid 52 and name N
}
}"""
annot, ss_from_file = get_annotation(
phil_lines=phil_str_1,
pdb_lines=pdb_1ywf_sample_strings)
assert annot.get_n_helices() == 0
assert annot.get_n_sheets() == 1
sh = annot.sheets[0]
assert sh.get_n_defined_hbonds() == 8
assert annot.get_n_defined_hbonds() == 8
res = sh.as_restraint_group(show_hbonds=True)
assert not test_utils.show_diff(res, result1,
strip_trailing_whitespace=True)
res = sh.as_restraint_group(show_hbonds=False)
assert not test_utils.show_diff(res, result1_1,
strip_trailing_whitespace=True)
print "OK"