GROFileHandler

molsysmt.native.GROFileHandler is the native low-level file handler class in MolSysMT for reading and writing Gromacs GRO (.gro) coordinate files.

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Overview and Handler Role

GROFileHandler manages file stream reading and line parsing for Gromacs .gro files. It handles fixed-column coordinate fields, residue numbering, atom labels, velocity vectors, and triclinic box vectors in nanometers.

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Class Attributes and Parsed Records

Inside GROFileHandler, parsed lines are exposed as structured field dictionaries:

Attribute / Property	Data Type	Description
file	io.StringIO or File Handle	Active stream handle pointing to string memory buffer or disk file.
title	String	Header title line read from the first line of the GRO file.
n_atoms	Integer	Total number of atoms declared on line 2 of the GRO file.
content	Dictionary	Structured dictionary holding parsed atom names, residue IDs, coordinates (nm), and velocities.

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Practical Usage and Streaming Workflow

import molsysmt as msm
from molsysmt.native import GROFileHandler

# 1. Instantiate GROFileHandler
handler = GROFileHandler("system.gro", io_mode="r")

# 2. Access parsed title and atom counts
print(handler.title, handler.n_atoms)

# 3. Close handle
handler.close()

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Performance and I/O Invariants

• Nanometer Unit Invariant: Automatically parses coordinates directly in nanometers (nm) and velocities in nm/ps.

• Fixed-Column Line Parser: High-speed fixed-width string slicer for fast GRO file loading.