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Implicit H-bond interaction and Protein Helper function #302

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8977493
protein_helper function (#275)
yuyuan871111 Jul 17, 2025
b8f39fe
Merge remote-tracking branch 'origin' into gsoc_implicit_hbond
cbouy Jul 17, 2025
c36c0c3
Implicit hbond main function (#284)
yuyuan871111 Aug 26, 2025
ff71fe8
patch to cover all lines by tests
yuyuan871111 Aug 27, 2025
028ce6f
fix bugs: make it readable if cif template have single quote ' in nam…
yuyuan871111 Aug 27, 2025
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514 changes: 514 additions & 0 deletions docs/notebooks/implicit-hbond.ipynb
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9 changes: 8 additions & 1 deletion docs/source/modules/utils.rst
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Expand Up @@ -2,4 +2,11 @@ Helper functions
================

.. automodule:: prolif.utils
:members: get_residues_near_ligand, select_over_trajectory, pandas_series_to_bv, to_dataframe, to_bitvectors
:members: get_residues_near_ligand, select_over_trajectory, pandas_series_to_bv, to_dataframe, to_bitvectors

.. automodule:: prolif.io.protein_helper
:members: ProteinHelper, assign_bond_orders_from_smiles, strip_bonds, assign_intra_props

.. automodule:: prolif.io.cif
:members: cif_template_reader, cif_parser_lite

7 changes: 7 additions & 0 deletions docs/source/tutorials.rst
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Expand Up @@ -66,3 +66,10 @@ interactions, ignoring backbone interactions and such, you can have a look at th
tutorial:

:ref:`notebooks/advanced:Advanced usage`

**Implicit hydrogen methods**: If your topology does not contain hydrogen atoms, you can
still use the implicit hydrogen methods to generate interaction fingerprints. This method is
useful for quickly comparing your experimental structure with computational results.

- :ref:`notebooks/implicit-hbond:Implicit hydrogen bond interaction`

44 changes: 44 additions & 0 deletions prolif/data/implicitHbond/1.D.sdf
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1.D
RDKit 3D

18 20 0 0 1 0 0 0 0 0999 V2000
-1.3760 -10.2730 -22.0380 O 0 0 0 0 0 0 0 0 0 0 0 0
-2.0280 -9.0170 -22.2620 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.3380 -8.2530 -20.9460 C 0 0 1 0 0 0 0 0 0 0 0 0
-1.1470 -7.9570 -20.1840 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.7210 -6.6180 -20.5300 C 0 0 1 0 0 0 0 0 0 0 0 0
0.3710 -6.6620 -21.8290 N 0 0 0 0 0 0 0 0 0 0 0 0
0.7880 -5.6430 -22.6800 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.9940 -3.5860 -23.6340 C 0 0 0 0 0 0 0 0 0 0 0 0
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2.2550 -5.4100 -24.5670 C 0 0 0 0 0 0 0 0 0 0 0 0
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1.1210 -7.7990 -22.3520 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.9450 -5.8760 -21.0320 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.0060 -6.9150 -21.3020 C 0 0 2 0 0 0 0 0 0 0 0 0
-4.1460 -6.6070 -20.4800 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
3 2 1 6
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11 12 1 0
11 13 2 0
13 14 1 0
14 15 2 0
16 17 1 0
17 18 1 1
M END
$$$$
70 changes: 70 additions & 0 deletions prolif/data/implicitHbond/1.D_protonated.sdf
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1.D
PyMOL3.1 3D 0

31 33 0 0 1 0 0 0 0 0999 V2000
3.3265 -6.9320 -25.3719 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.3673 -6.9486 -22.3298 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.3824 -8.3951 -22.8820 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.9799 -9.2258 -22.7503 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.2929 -5.1710 -20.2770 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.2570 -6.1500 -19.6618 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.7152 -5.3091 -21.9342 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.2136 -10.7045 -22.8800 H 0 0 0 0 0 0 0 0 0 0 0 0
3.5233 -5.3771 -26.1489 H 0 0 0 0 0 0 0 0 0 0 0 0
-4.3452 -5.6702 -20.5462 H 0 0 0 0 0 0 0 0 0 0 0 0
1.0283 -8.7848 -21.8963 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.9832 -8.8914 -20.3424 H 0 0 0 0 0 0 0 0 0 0 0 0
0.7377 -2.5274 -23.6773 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.3760 -10.2730 -22.0380 O 0 0 0 0 0 0 0 0 0 0 0 0
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1.1210 -7.7990 -22.3520 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.9450 -5.8760 -21.0320 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.0060 -6.9150 -21.3020 C 0 0 2 0 0 0 0 0 0 0 0 0
-4.1460 -6.6070 -20.4800 O 0 0 0 0 0 0 0 0 0 0 0 0
8 14 1 0 0 0 0
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7 29 1 0 0 0 0
29 30 1 0 0 0 0
2 30 1 0 0 0 0
30 31 1 0 0 0 0
10 31 1 0 0 0 0
M END
$$$$
17 changes: 17 additions & 0 deletions prolif/data/implicitHbond/README.md
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The example is originally from PLINDER tutorial dataset `1s2g__1__1.A_2.C__1.D`.

Raw file from PLINDER:
* `ligand_files/1.D.sdf`
* `receptor.pdb`

A manually modified version of `receptor.pdb` by replacing resname `HIS` to `HSD` was tested for certain protonated state.
* `receptor_hsd.pdb`

Suggested by [our PDB tutorial](https://prolif.readthedocs.io/en/latest/notebooks/pdb.html#pdb):
The protonated protein was prepared with [PypKa](https://pypka.org/) and its default settings.
* `receptor_ph7_amber.pdb`
However, some atoms are too close to recognize bonds correctly. Need to fix manually.
* `receptor_ph7_amber2.pdb`

The protonated ligand was prepared by PyMOL3.
* `ligand_files/1.D_protonated.sdf`
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