A high performance drop-in replacement for Biotite’s PDBFile written in Rust.
Installation
fastpdb can be installed via
$ pip install fastpdbUsage
You can simply replace biotite.structure.io.pdb.PDBFile by fastpdb.PDBFile. The methods and their parameters are the same.
import fastpdb
in_file = fastpdb.PDBFile.read("path/to/file.pdb")
atom_array = in_file.get_structure(model=1)
out_file = fastpdb.PDBFile()
out_file.set_structure(atom_array)
out_file.write("path/to/another_file.pdb")Note that fastpdb does not yet support the hybrid-36 PDB format.
Performance
fastpdb is multiple times faster than biotite.
2 maintainers
Metadata
2 maintainers
Release files for fastpdb 1.3.3
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| fastpdb-1.3.3.tar.gz | 2.9 MB | Details |
Built distributions (wheels)
Total release size: 6.7 MB
Release files / fastpdb-1.3.3.tar.gz
| Download URL | fastpdb-1.3.3.tar.gz |
|---|---|
| Size | 2.9 MB |
| Tags | Source |
|
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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Release files / fastpdb-1.3.3-cp313-cp313-win_amd64.whl
| Download URL | fastpdb-1.3.3-cp313-cp313-win_amd64.whl |
|---|---|
| Size | 229.0 kB |
| Tags | CPython 3.13 Windows x86-64 |
|
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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Release files / fastpdb-1.3.3-cp313-cp313-manylinux_2_34_x86_64.whl
| Download URL | fastpdb-1.3.3-cp313-cp313-manylinux_2_34_x86_64.whl |
|---|---|
| Size | 372.3 kB |
| Tags | CPython 3.13 Linux glibc 2.34+ x86-64 |
|
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Release files / fastpdb-1.3.3-cp313-cp313-macosx_11_0_arm64.whl
| Download URL | fastpdb-1.3.3-cp313-cp313-macosx_11_0_arm64.whl |
|---|---|
| Size | 333.1 kB |
| Tags | CPython 3.13 macOS 11.0+ ARM64 |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Release files / fastpdb-1.3.3-cp312-cp312-win_amd64.whl
| Download URL | fastpdb-1.3.3-cp312-cp312-win_amd64.whl |
|---|---|
| Size | 229.3 kB |
| Tags | CPython 3.12 Windows x86-64 |
|
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No |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Release files / fastpdb-1.3.3-cp312-cp312-manylinux_2_34_x86_64.whl
| Download URL | fastpdb-1.3.3-cp312-cp312-manylinux_2_34_x86_64.whl |
|---|---|
| Size | 373.0 kB |
| Tags | CPython 3.12 Linux glibc 2.34+ x86-64 |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Release files / fastpdb-1.3.3-cp312-cp312-macosx_11_0_arm64.whl
| Download URL | fastpdb-1.3.3-cp312-cp312-macosx_11_0_arm64.whl |
|---|---|
| Size | 333.7 kB |
| Tags | CPython 3.12 macOS 11.0+ ARM64 |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Release files / fastpdb-1.3.3-cp311-cp311-win_amd64.whl
| Download URL | fastpdb-1.3.3-cp311-cp311-win_amd64.whl |
|---|---|
| Size | 229.5 kB |
| Tags | CPython 3.11 Windows x86-64 |
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No |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Release files / fastpdb-1.3.3-cp311-cp311-manylinux_2_34_x86_64.whl
| Download URL | fastpdb-1.3.3-cp311-cp311-manylinux_2_34_x86_64.whl |
|---|---|
| Size | 373.4 kB |
| Tags | CPython 3.11 Linux glibc 2.34+ x86-64 |
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No |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Release files / fastpdb-1.3.3-cp311-cp311-macosx_11_0_arm64.whl
| Download URL | fastpdb-1.3.3-cp311-cp311-macosx_11_0_arm64.whl |
|---|---|
| Size | 337.9 kB |
| Tags | CPython 3.11 macOS 11.0+ ARM64 |
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No |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Release files / fastpdb-1.3.3-cp310-cp310-win_amd64.whl
| Download URL | fastpdb-1.3.3-cp310-cp310-win_amd64.whl |
|---|---|
| Size | 229.4 kB |
| Tags | CPython 3.10 Windows x86-64 |
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| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Release files / fastpdb-1.3.3-cp310-cp310-manylinux_2_34_x86_64.whl
| Download URL | fastpdb-1.3.3-cp310-cp310-manylinux_2_34_x86_64.whl |
|---|---|
| Size | 373.3 kB |
| Tags | CPython 3.10 Linux glibc 2.34+ x86-64 |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Release files / fastpdb-1.3.3-cp310-cp310-macosx_11_0_arm64.whl
| Download URL | fastpdb-1.3.3-cp310-cp310-macosx_11_0_arm64.whl |
|---|---|
| Size | 337.7 kB |
| Tags | CPython 3.10 macOS 11.0+ ARM64 |
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| Uploaded via |
twine/6.1.0 CPython/3.12.9
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