pdbfixer-neoralab 0.1.4

Fixes problems in PDB files

PDBFixer

PDBFixer is an easy to use Python API for fixing problems in Protein Data Bank files in preparation for simulating them. It can automatically fix the following problems:

• Add missing heavy atoms.
• Add missing hydrogen atoms.
• Build missing loops.
• Convert non-standard residues to their standard equivalents.
• Select a single position for atoms with multiple alternate positions listed.
• Delete unwanted chains from the model.
• Delete unwanted heterogens.
• Build a water box for explicit solvent simulations.

See our manual

Installation

PDBFixer can be installed from PyPI using pip or uv (requires Python 3.13 or newer):

pip install pdbfixer

uv pip install pdbfixer

Conda and mamba packages are also available:

conda install -c conda-forge pdbfixer

Alternatively you can install from source, as described in the manual.

Versioning

PDBFixer uses versioningit to derive its version from Git tags. Building from a source checkout therefore requires either a cloned repository with Git metadata or a source distribution that already includes the generated version. When no tag information is available, the default version reported is 0+unknown. To see the version that will be used for a build, run:

python -m versioningit

Usage

PDBFixer is now distributed purely as a Python API. The historical web and command-line interfaces have been removed in favour of direct use from Python code.

from pdbfixer import PDBFixer

fixer = PDBFixer(filename="input.pdb")
fixer.findMissingResidues()
fixer.findMissingAtoms()
fixer.addMissingAtoms()
fixer.addMissingHydrogens(pH=7.0)