xpid 2.1.1

Detector for XH-pi interactions in protein structures.

Xpid

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

Installation

Requires Python 3.9+.

git clone https://github.com/SeanWang5868/xpid
cd xpid
pip install .

Configuration

The detection of XH-π interactions depends on the position of H atoms. In order to add H to the structure before detecting, the path to the monomer library (e.g. CCP4 monomer library) needs to be specified.

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: $C_\pi$ (Ring Centroid), $\vec{n}$ (Ring Normal), $X$ (Donor Heavy Atom), $Xp$ (The projection of X onto the π plane), $H$ (Hydrogen).

Hudson System

$d_{X \text{--} C_\pi}$: $\le 4.5$ Å, $\angle X\text{--}H \text{--} \vec{n}$): $\le 40^\circ$. $d_{Xp \text{--} C_\pi}$: $\le 1.6$ Å $\text{for His, Trp-A}$, $\le 2.0$ Å $\text{for Phe, Trp-B, Tyr}$.

Plevin System

$d_{X \text{--} C_\pi}$: $< 4.3$ Å, $\angle X\text{--}H \text{--} C_\pi$: $> 120^\circ$, $\angle X \text{--} C_\pi \text{--} \vec{n}$): $< 25^\circ$.

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.
--jobs N	Number of CPU cores to use (Default: 1).
--h-mode N	Hydrogen handling mode (0=NoChange, 4=ReAddButWater).
--model ID	Model index to analyze (Default: 0; use all for NMR).
--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

xpid2