Implicit H-bond interaction and Protein Helper function

[yuyuan871111]

A new method for detecting hydrogen-bond (H-bond) interactions in ProLIF. Before this, calculating H-bond interactions with ProLIF required a complete topology, including both heavy atoms and explicit hydrogens (explicit H-bond method).

This new implicit H-bond method can help users more easily calculate the H-bond interactions for experimental and computational structures without additional protonation steps.

[github-actions]

Type-checking report

Difference in type-hints coverage:

15a16,21
> │   ├── io
> │   │   ├── [x] __init__.py
> │   │   ├── [x] cif.py
> │   │   ├── [x] constants.py
> │   │   ├── [x] protein_helper.py
> │   │   └── [x] xml.py
43a50
>     ├── [x] test_constants.py
46a54
>     ├── [x] test_io.py
52c60
< Summary: 42/42 files have complete type hints (100.0%)
---
> Summary: 49/49 files have complete type hints (100.0%)

Overview

.
├── prolif
│   ├── [x] __init__.py
│   ├── [x] _version.py
│   ├── [x] datafiles.py
│   ├── [x] exceptions.py
│   ├── [x] fingerprint.py
│   ├── [x] ifp.py
│   ├── interactions
│   │   ├── [x] __init__.py
│   │   ├── [x] base.py
│   │   ├── [x] constants.py
│   │   ├── [x] interactions.py
│   │   ├── [x] utils.py
│   │   └── [x] water_bridge.py
│   ├── io
│   │   ├── [x] __init__.py
│   │   ├── [x] cif.py
│   │   ├── [x] constants.py
│   │   ├── [x] protein_helper.py
│   │   └── [x] xml.py
│   ├── [x] molecule.py
│   ├── [x] parallel.py
│   ├── [x] pickling.py
│   ├── plotting
│   │   ├── [x] __init__.py
│   │   ├── [x] barcode.py
│   │   ├── [x] complex3d.py
│   │   ├── network
│   │   │   ├── [x] __init__.py
│   │   │   └── [x] lignetwork.py
│   │   ├── [x] residues.py
│   │   └── [x] utils.py
│   ├── [x] rdkitmol.py
│   ├── [x] residue.py
│   ├── [x] typeshed.py
│   └── [x] utils.py
├── scripts
│   ├── [x] check_types.py
│   └── [x] test_build.py
└── tests
    ├── [x] __init__.py
    ├── [x] conftest.py
    ├── plotting
    │   ├── [x] __init__.py
    │   ├── [x] test_barcode.py
    │   ├── [x] test_complex3d.py
    │   ├── [x] test_network.py
    │   └── [x] test_residues.py
    ├── [x] test_constants.py
    ├── [x] test_fingerprint.py
    ├── [x] test_ifp.py
    ├── [x] test_interactions.py
    ├── [x] test_io.py
    ├── [x] test_molecule.py
    ├── [x] test_pickling.py
    ├── [x] test_residues.py
    └── [x] test_utils.py

Summary: 49/49 files have complete type hints (100.0%)

Remaining errors

Poe => mypy .
Success: no issues found in 50 source files

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 95.97%. Comparing base (185460c) to head (028ce6f).

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #302      +/-   ##
==========================================
+ Coverage   95.10%   95.97%   +0.87%     
==========================================
  Files          23       27       +4     
  Lines        1878     2287     +409     
==========================================
+ Hits         1786     2195     +409     
  Misses         92       92              

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