def exercise_detect_link_problems():
open("tmp_mmtbx_utils_asn_nag.pdb", "w").write(
"""\
CRYST1 124.702 124.702 71.573 90.00 90.00 90.00 P 4 21 2
ATOM 3196 N ASN A 284 36.622 -19.654 35.782 1.00 19.63 N
ATOM 3197 CA ASN A 284 36.491 -18.279 35.327 1.00 19.79 C
ATOM 3198 C ASN A 284 35.037 -17.835 35.322 1.00 20.05 C
ATOM 3199 O ASN A 284 34.751 -16.634 35.341 1.00 28.11 O
ATOM 3200 CB ASN A 284 37.063 -18.130 33.915 1.00 21.07 C
ATOM 3201 CG ASN A 284 38.549 -17.829 33.904 1.00 20.78 C
ATOM 3202 OD1 ASN A 284 39.040 -17.053 34.702 1.00 19.74 O
ATOM 3203 ND2 ASN A 284 39.263 -18.449 32.968 1.00 21.82 N
ATOM 3204 H ASN A 284 36.875 -20.208 35.174 1.00 23.56 H
ATOM 3205 HD21 ASN A 284 38.893 -18.679 32.227 1.00 26.19 H
ATOM 3206 HA ASN A 284 36.987 -17.719 35.944 1.00 19.79 H
ATOM 3207 HB2 ASN A 284 36.900 -18.947 33.418 1.00 21.07 H
ATOM 3208 HB3 ASN A 284 36.591 -17.419 33.454 1.00 21.07 H
ATOM 3209 HD22 ASN A 284 38.878 -18.991 32.422 1.00 21.82 H
HETATM 5988 C1 NAG A 467 40.601 -17.959 32.799 1.00 27.22 C
HETATM 5989 C2 NAG A 467 41.289 -19.314 32.714 1.00 22.16 C
HETATM 5990 C3 NAG A 467 42.783 -19.123 32.507 1.00 54.68 C
HETATM 5991 C4 NAG A 467 43.034 -18.265 31.278 1.00 23.55 C
HETATM 5992 C5 NAG A 467 42.261 -16.957 31.391 1.00 33.78 C
HETATM 5993 C6 NAG A 467 42.388 -16.125 30.141 1.00 24.49 C
HETATM 5994 C7 NAG A 467 41.114 -21.444 33.906 1.00 21.47 C
HETATM 5995 C8 NAG A 467 40.844 -22.107 35.214 1.00 20.34 C
HETATM 5996 N2 NAG A 467 41.041 -20.110 33.902 1.00 24.73 N
HETATM 5997 O3 NAG A 467 43.399 -20.391 32.338 1.00 54.77 O
HETATM 5998 O4 NAG A 467 44.417 -17.960 31.155 1.00 53.51 O
HETATM 5999 O5 NAG A 467 40.861 -17.215 31.600 1.00 31.39 O
HETATM 6000 O6 NAG A 467 41.470 -15.043 30.154 1.00 46.51 O
HETATM 6001 O7 NAG A 467 41.392 -22.081 32.897 1.00 22.76 O
HETATM 6002 H1 NAG A 467 40.952 -17.467 33.566 1.00 32.66 H
HETATM 6003 H2 NAG A 467 40.934 -19.790 31.940 1.00 26.59 H
HETATM 6004 H3 NAG A 467 43.163 -18.682 33.290 1.00 65.62 H
HETATM 6005 H4 NAG A 467 42.738 -18.746 30.482 1.00 28.26 H
HETATM 6006 H5 NAG A 467 42.608 -16.449 32.148 1.00 40.54 H
HETATM 6007 H61 NAG A 467 42.210 -16.687 29.363 1.00 29.39 H
HETATM 6008 H62 NAG A 467 43.296 -15.773 30.082 1.00 29.39 H
HETATM 6009 H81 NAG A 467 40.882 -23.076 35.101 1.00 24.41 H
HETATM 6010 H82 NAG A 467 39.958 -21.851 35.532 1.00 24.41 H
HETATM 6011 H83 NAG A 467 41.516 -21.829 35.865 1.00 24.41 H
HETATM 6012 HN2 NAG A 467 40.836 -19.681 34.680 1.00 29.67 H
HETATM 6013 HO3 NAG A 467 42.779 -20.998 32.145 1.00 65.72 H
HETATM 6014 HO4 NAG A 467 44.884 -18.471 31.711 1.00 64.21 H
HETATM 6015 HO6 NAG A 467 40.829 -15.206 30.746 1.00 55.81 H
"""
)
result = utils.detect_hydrogen_nomenclature_problem(pdb_file="tmp_mmtbx_utils_asn_nag.pdb")
assert result.n_asn_hd22 == 0
def exercise_detect_link_problems():
with open("tmp_mmtbx_utils_asn_nag.pdb", "w") as f:
f.write("""\
CRYST1 124.702 124.702 71.573 90.00 90.00 90.00 P 4 21 2
ATOM 3196 N ASN A 284 36.622 -19.654 35.782 1.00 19.63 N
ATOM 3197 CA ASN A 284 36.491 -18.279 35.327 1.00 19.79 C
ATOM 3198 C ASN A 284 35.037 -17.835 35.322 1.00 20.05 C
ATOM 3199 O ASN A 284 34.751 -16.634 35.341 1.00 28.11 O
ATOM 3200 CB ASN A 284 37.063 -18.130 33.915 1.00 21.07 C
ATOM 3201 CG ASN A 284 38.549 -17.829 33.904 1.00 20.78 C
ATOM 3202 OD1 ASN A 284 39.040 -17.053 34.702 1.00 19.74 O
ATOM 3203 ND2 ASN A 284 39.263 -18.449 32.968 1.00 21.82 N
ATOM 3204 H ASN A 284 36.875 -20.208 35.174 1.00 23.56 H
ATOM 3205 HD21 ASN A 284 38.893 -18.679 32.227 1.00 26.19 H
ATOM 3206 HA ASN A 284 36.987 -17.719 35.944 1.00 19.79 H
ATOM 3207 HB2 ASN A 284 36.900 -18.947 33.418 1.00 21.07 H
ATOM 3208 HB3 ASN A 284 36.591 -17.419 33.454 1.00 21.07 H
ATOM 3209 HD22 ASN A 284 38.878 -18.991 32.422 1.00 21.82 H
HETATM 5988 C1 NAG A 467 40.601 -17.959 32.799 1.00 27.22 C
HETATM 5989 C2 NAG A 467 41.289 -19.314 32.714 1.00 22.16 C
HETATM 5990 C3 NAG A 467 42.783 -19.123 32.507 1.00 54.68 C
HETATM 5991 C4 NAG A 467 43.034 -18.265 31.278 1.00 23.55 C
HETATM 5992 C5 NAG A 467 42.261 -16.957 31.391 1.00 33.78 C
HETATM 5993 C6 NAG A 467 42.388 -16.125 30.141 1.00 24.49 C
HETATM 5994 C7 NAG A 467 41.114 -21.444 33.906 1.00 21.47 C
HETATM 5995 C8 NAG A 467 40.844 -22.107 35.214 1.00 20.34 C
HETATM 5996 N2 NAG A 467 41.041 -20.110 33.902 1.00 24.73 N
HETATM 5997 O3 NAG A 467 43.399 -20.391 32.338 1.00 54.77 O
HETATM 5998 O4 NAG A 467 44.417 -17.960 31.155 1.00 53.51 O
HETATM 5999 O5 NAG A 467 40.861 -17.215 31.600 1.00 31.39 O
HETATM 6000 O6 NAG A 467 41.470 -15.043 30.154 1.00 46.51 O
HETATM 6001 O7 NAG A 467 41.392 -22.081 32.897 1.00 22.76 O
HETATM 6002 H1 NAG A 467 40.952 -17.467 33.566 1.00 32.66 H
HETATM 6003 H2 NAG A 467 40.934 -19.790 31.940 1.00 26.59 H
HETATM 6004 H3 NAG A 467 43.163 -18.682 33.290 1.00 65.62 H
HETATM 6005 H4 NAG A 467 42.738 -18.746 30.482 1.00 28.26 H
HETATM 6006 H5 NAG A 467 42.608 -16.449 32.148 1.00 40.54 H
HETATM 6007 H61 NAG A 467 42.210 -16.687 29.363 1.00 29.39 H
HETATM 6008 H62 NAG A 467 43.296 -15.773 30.082 1.00 29.39 H
HETATM 6009 H81 NAG A 467 40.882 -23.076 35.101 1.00 24.41 H
HETATM 6010 H82 NAG A 467 39.958 -21.851 35.532 1.00 24.41 H
HETATM 6011 H83 NAG A 467 41.516 -21.829 35.865 1.00 24.41 H
HETATM 6012 HN2 NAG A 467 40.836 -19.681 34.680 1.00 29.67 H
HETATM 6013 HO3 NAG A 467 42.779 -20.998 32.145 1.00 65.72 H
HETATM 6014 HO4 NAG A 467 44.884 -18.471 31.711 1.00 64.21 H
HETATM 6015 HO6 NAG A 467 40.829 -15.206 30.746 1.00 55.81 H
""")
result = utils.detect_hydrogen_nomenclature_problem(
pdb_file="tmp_mmtbx_utils_asn_nag.pdb")
assert (result.n_asn_hd22 == 0)