Hydride - Adding hydrogen atoms to molecular models
Many tasks in structural biology ranging from simulations and hydrogen bond detection to mere visual analysis, require complete molecular models. However, most experimentally determined structures do not include the position of hydrogen atoms, due to their small size and electron density.
Hydride is an easy-to-use program and library written in Python that adds missing hydrogen atoms to molecular models based on known bond lengths and angles. Since it does not require force-field parameters for the specific molecule(s), it can be used for adding hydrogen atoms to almost any organic molecule - from small ligands to large protein complexes.
Installation
In order to use Hydride you need to have Python (at least 3.7) installed.
You can install Hydride via
$ pip install hydrideUsage
In its basic invocation Hydride reads an input structure file, adds hydrogen atoms to the molecular model and writes the resulting model into an output structure file.
$ hydride -i input_structure.pdb -o output_structure.pdbPython API
Hydride also provides a Python API to add hydrogen atoms to AtomArray objects from Biotite.
atom_array, _ = hydride.add_hydrogen(atom_array)
atom_array.coord = hydride.relax_hydrogen(atom_array)2 maintainers
Metadata
2 maintainers
Release files for hydride 1.2.3
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| hydride-1.2.3.tar.gz | 293.4 kB | Details |
Built distributions (wheels)
Total release size: 7.8 MB
Release files / hydride-1.2.3.tar.gz
| Download URL | hydride-1.2.3.tar.gz |
|---|---|
| Size | 293.4 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
d1d06dcfb4c4957f109bd2445a115021cf69ff7c1639cb3f96961c58b38c6453
|
|
BLAKE2b-256 checksum How to use checksums |
63a2d600d62ea1f551002503066576cd45a7bc478da1acdc44c8796d5b05dc19
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.1 CPython/3.11.10
|
Release files / hydride-1.2.3-cp312-cp312-win_amd64.whl
| Download URL | hydride-1.2.3-cp312-cp312-win_amd64.whl |
|---|---|
| Size | 422.0 kB |
| Tags | CPython 3.12 Windows x86-64 |
|
SHA-256 checksum How to use checksums |
051de12202d675e551b741e9f1734f375b504bd63486c5aa8b565f89d20c444d
|
|
BLAKE2b-256 checksum How to use checksums |
a42e9095f2ba3da50db53e21db7d93a85e8f96c0ebb7eb43f375e81596f46e32
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.1 CPython/3.11.10
|
Release files / hydride-1.2.3-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | hydride-1.2.3-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 1.2 MB |
| Tags | CPython 3.12 Linux glibc 2.17+ x86-64 |
|
SHA-256 checksum How to use checksums |
76ecdf1cebe6042549fa4580ee829670c472563a8b66b25cb74c48d4e0f1e2d2
|
|
BLAKE2b-256 checksum How to use checksums |
73d47ca768b20e6d62ee0c967c3e770ca9bf720b396f03111ccaf230e94a023c
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.1 CPython/3.11.10
|
Release files / hydride-1.2.3-cp312-cp312-macosx_11_0_arm64.whl
| Download URL | hydride-1.2.3-cp312-cp312-macosx_11_0_arm64.whl |
|---|---|
| Size | 440.3 kB |
| Tags | CPython 3.12 macOS 11.0+ ARM64 |
|
SHA-256 checksum How to use checksums |
2b7221eceb732539e42419c6612e5f9c6a33074ad0547e5048d0d5c38a23734c
|
|
BLAKE2b-256 checksum How to use checksums |
8723409e5c2b1cfaf918c4d9c84d7a3a9f930e293e05affc6b5d020d08b0a9de
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.1 CPython/3.11.10
|
Release files / hydride-1.2.3-cp312-cp312-macosx_10_9_x86_64.whl
| Download URL | hydride-1.2.3-cp312-cp312-macosx_10_9_x86_64.whl |
|---|---|
| Size | 451.2 kB |
| Tags | CPython 3.12 macOS 10.9+ x86-64 |
|
SHA-256 checksum How to use checksums |
3884f4969f2df7237e5bc8c82e47026b6c4ba91de3bbc546b5ac938b4365bac5
|
|
BLAKE2b-256 checksum How to use checksums |
0dfb6163b0f4f6b89daa9045bf15fd2546ce43e717614116a477c7a40b7d73b7
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.1 CPython/3.11.10
|
Release files / hydride-1.2.3-cp311-cp311-win_amd64.whl
| Download URL | hydride-1.2.3-cp311-cp311-win_amd64.whl |
|---|---|
| Size | 425.5 kB |
| Tags | CPython 3.11 Windows x86-64 |
|
SHA-256 checksum How to use checksums |
6220f9159bcb1a5e985382dff5d25fcf0c848896190265d4d43a0252a039691e
|
|
BLAKE2b-256 checksum How to use checksums |
ff5a2c72655c2554840081d61b5680a067f4b8c1bc746032ab8f355846aeb750
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.1 CPython/3.11.10
|
Release files / hydride-1.2.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | hydride-1.2.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 1.2 MB |
| Tags | CPython 3.11 Linux glibc 2.17+ x86-64 |
|
SHA-256 checksum How to use checksums |
c196b287c7dd6ceb6e98d52aec1f8755f9bd641146b55a3236bae58c48ddf6be
|
|
BLAKE2b-256 checksum How to use checksums |
ed28c52153387c6efa7ac7d9c3c5df068aa686d8468c797f9a045d0993c77913
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.1 CPython/3.11.10
|
Release files / hydride-1.2.3-cp311-cp311-macosx_11_0_arm64.whl
| Download URL | hydride-1.2.3-cp311-cp311-macosx_11_0_arm64.whl |
|---|---|
| Size | 441.2 kB |
| Tags | CPython 3.11 macOS 11.0+ ARM64 |
|
SHA-256 checksum How to use checksums |
f6ef6875d6f720de694fe53254648e886c83681d05fe4988a823a2dbd06d38fb
|
|
BLAKE2b-256 checksum How to use checksums |
93ec0894ec1e38266e183db3e5ac148d7bddab4fda2f25447ec13716ec05d8fe
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.1 CPython/3.11.10
|
Release files / hydride-1.2.3-cp311-cp311-macosx_10_9_x86_64.whl
| Download URL | hydride-1.2.3-cp311-cp311-macosx_10_9_x86_64.whl |
|---|---|
| Size | 452.8 kB |
| Tags | CPython 3.11 macOS 10.9+ x86-64 |
|
SHA-256 checksum How to use checksums |
5b249a18109d60ce990c0a47d07620863dfe3f23495aa1e04ca15e9e086ffc9e
|
|
BLAKE2b-256 checksum How to use checksums |
755cad922192c64eada9bba98bd3a9255faf4faae78adfd4537d11eb2ed1b8e3
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.1 CPython/3.11.10
|
Release files / hydride-1.2.3-cp310-cp310-win_amd64.whl
| Download URL | hydride-1.2.3-cp310-cp310-win_amd64.whl |
|---|---|
| Size | 425.2 kB |
| Tags | CPython 3.10 Windows x86-64 |
|
SHA-256 checksum How to use checksums |
86fe627e9fd4cbc0ffcf0bfd753c9981efd9faacf012f78db3dcc696d27603eb
|
|
BLAKE2b-256 checksum How to use checksums |
c1c0daa5811a3966b0e799911a1dfcce285592c943bc738023cafe3232b8dbc9
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.1 CPython/3.11.10
|
Release files / hydride-1.2.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | hydride-1.2.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 1.1 MB |
| Tags | CPython 3.10 Linux glibc 2.17+ x86-64 |
|
SHA-256 checksum How to use checksums |
7e4cb5cf8e3d91e2c112cc5eb14a74128bd9cdc9c0ec459ebe97c7ecdf97688d
|
|
BLAKE2b-256 checksum How to use checksums |
75129f099405f6ca08ca5a7a9af0028dcb454e36b2d39f11e3c8b254e18ba7b8
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.1 CPython/3.11.10
|
Release files / hydride-1.2.3-cp310-cp310-macosx_11_0_arm64.whl
| Download URL | hydride-1.2.3-cp310-cp310-macosx_11_0_arm64.whl |
|---|---|
| Size | 441.3 kB |
| Tags | CPython 3.10 macOS 11.0+ ARM64 |
|
SHA-256 checksum How to use checksums |
8de87d9e874a68d2aec0f86bed83de9922904b4bbe917c057b8779c9e6f9cca3
|
|
BLAKE2b-256 checksum How to use checksums |
3ee2571dea528b7bdac95d817e16580bea37d8ac8fe64131c60101066fee3640
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.1 CPython/3.11.10
|
Release files / hydride-1.2.3-cp310-cp310-macosx_10_9_x86_64.whl
| Download URL | hydride-1.2.3-cp310-cp310-macosx_10_9_x86_64.whl |
|---|---|
| Size | 452.6 kB |
| Tags | CPython 3.10 macOS 10.9+ x86-64 |
|
SHA-256 checksum How to use checksums |
6c2bd5adfe7bcfb5c45de084fc2b77358c495364104820dd61cabf3b8a589e66
|
|
BLAKE2b-256 checksum How to use checksums |
fa47a5a3fba3da41a1b07e2230640d8ca28d07f49a0dc397d91aa851b621ebd5
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.1 CPython/3.11.10
|
