xpid 0.0.2

XH-/PI interaction detection

Xpid

Xpid is a Gemmi-based tool designed to detect XH-π interactions in PDB/mmCIF files.

Installation

Requires Python 3.9+.

pip install xpid

Configuration

The detection of XH–π interactions depends on the positions of hydrogen atoms. To add hydrogens to the structure before detection, the path to a monomer library must be specified (e.g., the CCP4 Monomer Library).

xpid --set-mon-lib /Users/abc123/monomers

Quick Start

Scans a directory or PDB/mmCIF file and save results into a JSON file.

xpid ./data

Output: ./data/xpid_output/xpid_results.json

Geometric Criteria

Definitions: * C_π: Ring Centroid

• n: Ring Normal Vector
• X: Donor Heavy Atom
• X_proj: The projection of X onto the π plane
• H: Hydrogen

Hudson System

• Distance (X - C_π): ≤ 4.5 Å
• Angle (X - H, n): ≤ 40°
• Distance (X_proj - C_π):
  • ≤ 1.6 Å (for His, Trp-A)
  • ≤ 2.0 Å (for Phe, Trp-B, Tyr)

Plevin System

• Distance (X - C_π): < 4.3 Å
• Angle (X - H - C_π): > 120°
• Angle (X - C_π, n): < 25°

Command Options

Argument	Description
inputs	Input file (.cif, .pdb) or directory path.
--out-dir	Specify custom output directory.
--separate	Save results as separate files per PDB (Default: Merge).
--file-type	Output format: json (default) or csv.
-v, --verbose	Output detailed metrics (angles, coords, B-factors).
--log	Enable log file saving.
--h-mode N	Hydrogen handling mode (0=NoChange, 4=ReAddButWater).
--jobs N	Number of CPU cores to use (Default: 1).
--model ID	Model index to analyze (Default: 0; use all for NMR).
--mon-lib	Custom Monomer Library path ("/Users/abc123/monomers").
--set-mon-lib	Set default Monomer Library ("/Users/abc123/monomers").
--show-mon-lib-config	Show current Monomer Library status.
--pi-res	Limit acceptor residues (e.g., TRP,TYR).
--donor-res	Limit donor residues (e.g., HIS,ARG).
--donor-atom	Limit donor element types (e.g., N,O).

Output Data

Simple Mode (Default)

• PDB ID, Resolution
• Chain, Name, ID for X-donor and $\pi$ Residues.
• Distance ($d_{X \text{--} C_\pi}$)

Detailed Mode (-v)

• Includes all Simple fields plus:
• Secondary structure: Type (H/G/I/E/C) and Region IDs.
• Coordinates: Flattened x, y, z for $\pi$-center and X-atom.
• Geometric parameters: $\angle X\text{--}H \text{--} \vec{n}$, $\angle X\text{--}H \text{--} C_\pi$, $\angle X \text{--} C_\pi \text{--} \vec{n}$, $d_{Xp \text{--} C_\pi}$
• B-factors: Average B-factor for ring atoms and X-atom.

Dependencies

• gemmi
• numpy

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Contact

Sean Wang ([e-mail])

York Structural Biology Laboratory (YSBL), University of York