PDB Beta Factor Helper

GitHub Link to Code.

PDB beta factor helper for structure visualization.

This module provides utilities for extracting trajectory frames and creating PDB files with custom beta factors for visualization purposes.

class mdxplain.structure_visualization.helper.pdb_beta_factor_helper.PdbBetaFactorHelper

Helper for creating PDB files with custom beta factors.

Provides methods for extracting frames from trajectories and saving them as PDB files with custom beta factors for visualization in PyMOL.

Examples

>>> # Extract frame as PDB with beta factors
>>> beta_factors = np.array([0.0, 50.0, 100.0, ...])  # Per-atom
>>> pdb_path = PdbBetaFactorHelper.create_pdb_with_beta_factors(
...     pipeline_data, traj_idx=0, frame_idx=100,
...     beta_factors=beta_factors, output_path="output.pdb"
... )

static create_pdb_with_beta_factors(pipeline_data: PipelineData, traj_idx: int, frame_idx: int, beta_factors: np.ndarray, output_path: str) → str

Create PDB with custom beta factors.

Extracts a frame and saves it with custom beta factors for each atom. Beta factors are used for coloring in PyMOL.

Parameters

pipeline_dataPipelineData

Pipeline data object

traj_idxint

Trajectory index

frame_idxint

Frame index within trajectory

beta_factorsnp.ndarray

Beta factors for all atoms, shape (n_atoms,)

output_pathstr

Path where to save the PDB file

Returns

str

Path to created PDB file

Raises

ValueError

If beta_factors shape doesn’t match number of atoms

Examples

>>> # Create PDB with importance-based beta factors
>>> topology = pipeline.data.trajectory_data.trajectories[0].topology
>>> beta_factors = np.zeros(topology.n_atoms)
>>> # Set beta factors based on residue importance...
>>> pdb_path = PdbBetaFactorHelper.create_pdb_with_beta_factors(
...     pipeline_data, 0, 100, beta_factors, "output.pdb"
... )

Notes

• Beta factors should be in range 0-100 for optimal PyMOL visualization

• All atoms in the frame receive the provided beta factors

• Memmap-safe: only loads one frame

static get_topology(pipeline_data: PipelineData, traj_idx: int = 0) → md.Topology

Get topology from a trajectory.

Convenience method to access topology for residue information.

Parameters

pipeline_dataPipelineData

Pipeline data object

traj_idxint, default=0

Trajectory index to get topology from

Returns

mdtraj.Topology

Topology object

Examples

>>> topology = PdbBetaFactorHelper.get_topology(pipeline_data, 0)
>>> print(f"Number of residues: {topology.n_residues}")