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[biopolymer] iCodes not being handled properly
See original GitHub issueDescribe the bug
Passing a PDB with residues with insertion codes such as what is demonstrated below leads to a squashed residue rather than two individual ones:
ATOM 2601 N ASN A 162 40.670 10.730 37.730 1.00 0.00 N
ATOM 2602 H ASN A 162 39.900 11.120 37.210 1.00 0.00 H
ATOM 2603 CA ASN A 162 41.770 10.100 37.120 1.00 0.00 C
ATOM 2604 HA ASN A 162 42.370 9.560 37.850 1.00 0.00 H
ATOM 2605 CB ASN A 162 41.320 9.150 36.020 1.00 0.00 C
ATOM 2606 HB2 ASN A 162 40.530 9.640 35.460 1.00 0.00 H
ATOM 2607 HB3 ASN A 162 42.210 8.900 35.450 1.00 0.00 H
ATOM 2608 CG ASN A 162 40.690 7.870 36.740 1.00 0.00 C
ATOM 2609 OD1 ASN A 162 39.540 7.890 37.200 1.00 0.00 O
ATOM 2610 ND2 ASN A 162 41.480 6.830 37.000 1.00 0.00 N
ATOM 2611 HD21 ASN A 162 41.080 6.200 37.690 1.00 0.00 H
ATOM 2612 HD22 ASN A 162 42.470 6.870 36.820 1.00 0.00 H
ATOM 2613 C ASN A 162 42.670 11.260 36.640 1.00 0.00 C
ATOM 2614 O ASN A 162 42.910 11.420 35.410 1.00 0.00 O
ATOM 2615 N ASN A 162B 41.670 10.730 37.730 1.00 0.00 N
ATOM 2616 H ASN A 162B 40.900 11.120 37.210 1.00 0.00 H
ATOM 2617 CA ASN A 162B 42.770 10.100 37.120 1.00 0.00 C
ATOM 2618 HA ASN A 162B 43.370 9.560 37.850 1.00 0.00 H
ATOM 2619 CB ASN A 162B 42.320 9.150 36.020 1.00 0.00 C
ATOM 2620 HB2 ASN A 162B 41.530 9.640 35.460 1.00 0.00 H
ATOM 2621 HB3 ASN A 162B 43.210 8.900 35.450 1.00 0.00 H
ATOM 2622 CG ASN A 162B 41.690 7.870 36.740 1.00 0.00 C
ATOM 2623 OD1 ASN A 162B 40.540 7.890 37.200 1.00 0.00 O
ATOM 2624 ND2 ASN A 162B 42.480 6.830 37.000 1.00 0.00 N
ATOM 2625 HD21 ASN A 162B 42.080 6.200 37.690 1.00 0.00 H
ATOM 2626 HD22 ASN A 162B 43.470 6.870 36.820 1.00 0.00 H
ATOM 2627 C ASN A 162B 43.670 11.260 36.640 1.00 0.00 C
ATOM 2628 O ASN A 162B 43.910 11.420 35.410 1.00 0.00 O
What hasn’t been tested:
- Insertion codes but with different residues (i.e. if you had
ASN 162andALA 162B)
To Reproduce
Loading the following PDB file on the biopolymer branch (tested on a clone made on the 21st June 2022) and looking at residue 162. T4-protein-icode.pdb.zip
from openff.toolkit import Molecule, Topology
protein = Molecule.from_polymer_pdb('T4-protein-icode.pdb')
protein.residues[-2].to_dict()
Output
We get twice the number of ASN atoms (i.e. the two ASN residues squashed together):
{'identifier': ('A', '162', 'ASN'),
'atom_indices': [2600,
2601,
2602,
2603,
2604,
2605,
2606,
2607,
2608,
2609,
2610,
2611,
2612,
2613,
2614,
2615,
2616,
2617,
2618,
2619,
2620,
2621,
2622,
2623,
2624,
2625,
2626,
2627]}
Computing environment (please complete the following information):
- Operating system: ubuntu 20.04 LTS
- Output of running
conda list
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
amberlite 22.0 pypi_0 pypi
ambertools 22.0 py38h6177452_1 conda-forge
amberutils 21.0 pypi_0 pypi
arpack 3.7.0 hdefa2d7_2 conda-forge
asttokens 2.0.5 pyhd8ed1ab_0 conda-forge
astunparse 1.6.3 pyhd8ed1ab_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
blosc 1.21.1 h83bc5f7_3 conda-forge
boost 1.74.0 py38h2b96118_5 conda-forge
boost-cpp 1.74.0 h75c5d50_8 conda-forge
brotli 1.0.9 h166bdaf_7 conda-forge
brotli-bin 1.0.9 h166bdaf_7 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
ca-certificates 2022.6.15 ha878542_0 conda-forge
cachetools 5.2.0 pypi_0 pypi
cairo 1.16.0 ha61ee94_1011 conda-forge
certifi 2022.6.15 py38h578d9bd_0 conda-forge
cudatoolkit 11.7.0 hd8887f6_10 conda-forge
curl 7.83.1 h7bff187_0 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
cython 0.29.30 py38hfa26641_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
executing 0.8.3 pyhd8ed1ab_0 conda-forge
expat 2.4.8 h27087fc_0 conda-forge
fftw 3.3.10 nompi_h77c792f_102 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 hab24e00_0 conda-forge
fontconfig 2.14.0 h8e229c2_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.33.3 py38h0a891b7_0 conda-forge
freetype 2.10.4 h0708190_1 conda-forge
gettext 0.19.8.1 h73d1719_1008 conda-forge
giflib 5.2.1 h36c2ea0_2 conda-forge
greenlet 1.1.2 py38hfa26641_2 conda-forge
hdf4 4.2.15 h10796ff_3 conda-forge
hdf5 1.12.1 nompi_h2386368_104 conda-forge
icu 70.1 h27087fc_0 conda-forge
importlib-metadata 4.11.4 py38h578d9bd_0 conda-forge
importlib_resources 5.8.0 pyhd8ed1ab_0 conda-forge
ipython 8.4.0 py38h578d9bd_0 conda-forge
jedi 0.18.1 py38h578d9bd_1 conda-forge
jpeg 9e h166bdaf_1 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.3 py38h43d8883_0 conda-forge
krb5 1.19.3 h3790be6_0 conda-forge
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
lerc 3.0 h9c3ff4c_0 conda-forge
libblas 3.9.0 15_linux64_openblas conda-forge
libbrotlicommon 1.0.9 h166bdaf_7 conda-forge
libbrotlidec 1.0.9 h166bdaf_7 conda-forge
libbrotlienc 1.0.9 h166bdaf_7 conda-forge
libcblas 3.9.0 15_linux64_openblas conda-forge
libcurl 7.83.1 h7bff187_0 conda-forge
libdeflate 1.12 h166bdaf_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 12.1.0 h8d9b700_16 conda-forge
libgfortran-ng 12.1.0 h69a702a_16 conda-forge
libgfortran5 12.1.0 hdcd56e2_16 conda-forge
libglib 2.70.2 h174f98d_4 conda-forge
libgomp 12.1.0 h8d9b700_16 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.9.0 15_linux64_openblas conda-forge
libnetcdf 4.8.1 nompi_h329d8a1_102 conda-forge
libnghttp2 1.47.0 h727a467_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libopenblas 0.3.20 pthreads_h78a6416_0 conda-forge
libpng 1.6.37 h21135ba_2 conda-forge
libssh2 1.10.0 ha56f1ee_2 conda-forge
libstdcxx-ng 12.1.0 ha89aaad_16 conda-forge
libtiff 4.4.0 hc85c160_1 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libwebp 1.2.2 h3452ae3_0 conda-forge
libwebp-base 1.2.2 h7f98852_1 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libzip 1.8.0 h4de3113_1 conda-forge
libzlib 1.2.12 h166bdaf_1 conda-forge
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
lzo 2.10 h516909a_1000 conda-forge
matplotlib-base 3.5.2 py38h826bfd8_0 conda-forge
matplotlib-inline 0.1.3 pyhd8ed1ab_0 conda-forge
mdtraj 1.9.7 py38h0f83e44_1 conda-forge
mmpbsa-py 16.0 pypi_0 pypi
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
ncurses 6.3 h27087fc_1 conda-forge
netcdf-fortran 4.5.4 nompi_h2b6e579_100 conda-forge
networkx 2.8.4 pyhd8ed1ab_0 conda-forge
nomkl 1.0 h5ca1d4c_0 conda-forge
numexpr 2.8.0 py38h97b1c41_102 conda-forge
numpy 1.22.4 py38h99721a1_0 conda-forge
ocl-icd 2.3.1 h7f98852_0 conda-forge
ocl-icd-system 1.0.0 1 conda-forge
openff-forcefields 2.0.0 pyh6c4a22f_0 conda-forge
openff-interchange 0.1.4 pyhd8ed1ab_0 conda-forge
openff-interchange-base 0.1.4 pyh6c4a22f_0 conda-forge
openff-toolkit 0.10.1+112.g349d3fa4 dev_0 <develop>
openff-units 0.1.6 pyh6c4a22f_0 conda-forge
openff-utilities 0.1.5 pyh6c4a22f_0 conda-forge
openjpeg 2.4.0 hb52868f_1 conda-forge
openmm 7.7.0 py38h4b4c9af_1 conda-forge
openssl 1.1.1o h166bdaf_0 conda-forge
packaging 21.3 pyhd8ed1ab_0 conda-forge
packmol 20.010 h86c2bf4_0 conda-forge
packmol-memgen 1.2.3rc0 pypi_0 pypi
pandas 1.4.2 py38h47df419_2 conda-forge
panedr 0.5.2 py_0 conda-forge
parmed 3.4.3 py38hfa26641_2 conda-forge
parso 0.8.3 pyhd8ed1ab_0 conda-forge
pbr 5.9.0 pyhd8ed1ab_0 conda-forge
pcre 8.45 h9c3ff4c_0 conda-forge
pdb4amber 22.0 pypi_0 pypi
perl 5.32.1 2_h7f98852_perl5 conda-forge
pexpect 4.8.0 pyh9f0ad1d_2 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 9.1.1 py38h0ee0e06_1 conda-forge
pint 0.19.2 pyhd8ed1ab_0 conda-forge
pip 22.1.2 pyhd8ed1ab_0 conda-forge
pixman 0.40.0 h36c2ea0_0 conda-forge
prompt-toolkit 3.0.29 pyha770c72_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
pycairo 1.21.0 py38h9c00e7a_1 conda-forge
pydantic 1.9.1 py38h0a891b7_0 conda-forge
pygments 2.12.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge
pytables 3.7.0 py38hdb04529_0 conda-forge
python 3.8.13 h582c2e5_0_cpython conda-forge
python-constraint 1.4.0 py_0 conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python_abi 3.8 2_cp38 conda-forge
pytraj 2.0.6 pypi_0 pypi
pytz 2022.1 pyhd8ed1ab_0 conda-forge
rdkit 2022.03.3 py38ha829ea6_0 conda-forge
readline 8.1.2 h0f457ee_0 conda-forge
reportlab 3.5.68 py38hadf75a6_1 conda-forge
sander 22.0 pypi_0 pypi
scipy 1.8.1 py38h1ee437e_0 conda-forge
setuptools 62.6.0 py38h578d9bd_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
smirnoff99frosst 1.1.0 pyh44b312d_0 conda-forge
snappy 1.1.9 hbd366e4_1 conda-forge
sqlalchemy 1.4.37 py38h0a891b7_0 conda-forge
sqlite 3.38.5 h4ff8645_0 conda-forge
stack_data 0.3.0 pyhd8ed1ab_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
traitlets 5.3.0 pyhd8ed1ab_0 conda-forge
typing-extensions 4.2.0 hd8ed1ab_1 conda-forge
typing_extensions 4.2.0 pyha770c72_1 conda-forge
unicodedata2 14.0.0 py38h0a891b7_1 conda-forge
wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
xmltodict 0.13.0 pyhd8ed1ab_0 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.0.10 h7f98852_0 conda-forge
xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
xorg-libx11 1.7.2 h7f98852_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h7f98852_1 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-libxt 1.2.1 h7f98852_2 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.5 h516909a_1 conda-forge
zipp 3.8.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.12 h166bdaf_1 conda-forge
zstd 1.5.2 h8a70e8d_1 conda-forge
Additional context
Issue Analytics
- State:
- Created a year ago
- Comments:10 (8 by maintainers)
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Just some background for people who don’t know what insertion codes are/their function: https://bioinformatics.stackexchange.com/questions/11587/what-is-the-aim-of-insertion-codes-in-the-pdb-file-format
I think this is completed after #1372