Ligands with identical name collapse in single entity

[jaimergp]

Describe the bug

In multimeric complexes, some structures might have (incorrectly?) annotated copies of the same ligand with the same name, residue id and chain id. The computed ligand instances collapse in a single combined one as a result, but they might be indeed in different subunits of the protein, which should be reported as different.

To Reproduce Steps to reproduce the behavior:

1. Get attached PDB file: Mpro-x3113_0A_bound.zip

2. Run

from plip.structure.preparation import PDBComplex
path = "path/to/downloaded/attachment.pdb"
pdbcomplex = PDBComplex()
pdbcomplex.load_pdb(path)
print(*[lig.longname for lig in pdbcomplex.ligands])
# This should print two LIG instances, not one, plus the DMS artifacts

Expected behavior

I would like to see at least a warning that two instances of the same ligand were considered the same one. Ideally, PLIP could detect that although the name is identical, they are different instances given their positions in the complex, and as a result return the interaction profile for both pockets.

Screenshots

See how there are two ligands in two different pockes:

Desktop (please complete the following information):

• OS: Ubuntu 18 WSL2 on Windows 10
• Browser: Chrome
• Version: 88

Additional context

conda list

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1.14.4 py37hc58025e_1 conda-forge cftime 1.3.0 py37ha21ca33_0 conda-forge chardet 3.0.4 py37he5f6b98_1008 conda-forge click 7.1.2 pyh9f0ad1d_0 conda-forge coverage 5.3 py37h8f50634_1 conda-forge cryptography 3.2.1 py37hc72a4ac_0 conda-forge curl 7.71.1 he644dc0_8 conda-forge cycler 0.10.0 py_2 conda-forge dataclasses 0.7 py37_0 conda-forge decorator 4.4.2 py_0 conda-forge defusedxml 0.6.0 py_0 conda-forge entrypoints 0.3 py37hc8dfbb8_1002 conda-forge fontconfig 2.13.1 h1056068_1002 conda-forge freetype 2.10.4 he06d7ca_0 conda-forge gettext 0.19.8.1 h0b5b191_1005 conda-forge griddataformats 0.5.0 py_0 conda-forge gsd 2.4.0 py37ha21ca33_0 conda-forge hdf4 4.2.13 h10796ff_1004 conda-forge hdf5 1.10.6 nompi_h7c3c948_1111 conda-forge icu 67.1 he1b5a44_0 conda-forge idna 2.10 pyh9f0ad1d_0 conda-forge importlib-metadata 3.1.0 pyhd8ed1ab_0 conda-forge importlib_metadata 3.1.0 hd8ed1ab_0 conda-forge iniconfig 1.1.1 pyh9f0ad1d_0 conda-forge ipykernel 5.3.4 py37hc6149b9_1 conda-forge ipython 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hffdb5ce_3_cpython conda-forge python-dateutil 2.8.1 py_0 conda-forge python_abi 3.7 1_cp37m conda-forge pytz 2020.4 pyhd8ed1ab_0 conda-forge pyyaml 5.3.1 py37hb5d75c8_1 conda-forge pyzmq 20.0.0 py37h5a562af_1 conda-forge rdkit 2020.09.2 py37h713bca6_0 conda-forge readline 8.0 he28a2e2_2 conda-forge regex 2020.11.13 py37h4abf009_0 conda-forge reportlab 3.5.55 py37hd704e64_0 conda-forge requests 2.25.0 pyhd3deb0d_0 conda-forge retrying 1.3.3 py_2 conda-forge scikit-learn 0.23.2 py37hddcf8d6_3 conda-forge scipy 1.5.3 py37h8911b10_0 conda-forge seaborn 0.11.0 ha770c72_1 conda-forge seaborn-base 0.11.0 pyhd8ed1ab_1 conda-forge send2trash 1.5.0 py_0 conda-forge setuptools 49.6.0 py37he5f6b98_2 conda-forge simplejson 3.17.2 py37h8f50634_1 conda-forge six 1.15.0 pyh9f0ad1d_0 conda-forge sqlalchemy 1.3.20 py37h8f50634_0 conda-forge sqlite 3.33.0 h4cf870e_1 conda-forge statsmodels 0.12.1 py37ha21ca33_1 conda-forge swagger-spec-validator 2.7.3 pyh9f0ad1d_0 conda-forge terminado 0.9.1 py37hc8dfbb8_1 conda-forge testpath 0.4.4 py_0 conda-forge threadpoolctl 2.1.0 pyh5ca1d4c_0 conda-forge tk 8.6.10 hed695b0_1 conda-forge toml 0.10.2 pyhd8ed1ab_0 conda-forge tornado 6.1 py37h4abf009_0 conda-forge tqdm 4.54.0 pyhd8ed1ab_0 conda-forge traitlets 5.0.5 py_0 conda-forge typed-ast 1.4.1 py37h4abf009_1 conda-forge typing-extensions 3.7.4.3 0 conda-forge typing_extensions 3.7.4.3 py_0 conda-forge urllib3 1.25.11 py_0 conda-forge wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge webencodings 0.5.1 py_1 conda-forge wheel 0.35.1 pyh9f0ad1d_0 conda-forge widgetsnbextension 3.5.1 py37hc8dfbb8_4 conda-forge xlrd 1.2.0 py37_0 xorg-kbproto 1.0.7 h14c3975_1002 conda-forge xorg-libice 1.0.10 h516909a_0 conda-forge xorg-libsm 1.2.3 h84519dc_1000 conda-forge xorg-libx11 1.6.12 h516909a_0 conda-forge xorg-libxau 1.0.9 h14c3975_0 conda-forge xorg-libxdmcp 1.1.3 h516909a_0 conda-forge xorg-libxext 1.3.4 h516909a_0 conda-forge xorg-libxrender 0.9.10 h516909a_1002 conda-forge xorg-renderproto 0.11.1 h14c3975_1002 conda-forge xorg-xextproto 7.3.0 h14c3975_1002 conda-forge xorg-xproto 7.0.31 h14c3975_1007 conda-forge xz 5.2.5 h516909a_1 conda-forge yaml 0.2.5 h516909a_0 conda-forge zeromq 4.3.3 h58526e2_3 conda-forge zipp 3.4.0 py_0 conda-forge zlib 1.2.11 h516909a_1010 conda-forge zstd 1.4.5 h6597ccf_2 conda-forge ```

[jaimergp]

Sorry for the noise, it's not Plipify. It turns out that NGLView will show the biological units if available, by default, hence the duplicated ligands in the picture.

import nglview as nv
with open("Mpro-x3113_0A_bound.pdb") as f:
    v = nv.show_file(f, ext="pdb", default_representation=False)
    v.add_cartoon()
    v.add_ball_and_stick("LIG")
display(v)

[fkaiserbio]

Still good to know, thank you.