Module atom 

Atom coordinate parsing.

This module provides functions to parse atom coordinates from various formats:

• String format: "H 0 0 0; O 0 0 1.2"
• List format: ["H 0 0 0", "O 0 0 1.2"]
• Z-matrix format: "O; H 1 0.94; H 1 0.94 2 104.5"

Supports ghost atoms (GHOST-X, X- prefix) and labeled atoms (H1, H2).

Structs

AtomInfo

Information about a parsed atom.

ZmatEntry

Z-matrix entry for a single atom.

Enums

Unit

Unit of length for coordinates.

Constants

ANG_TO_BOHR

Angstrom to Bohr conversion constant.

BOHR_TO_ANG

Bohr to Angstrom conversion constant.

Functions

cart2zmat

Convert Cartesian coordinates to z-matrix format.

charge_to_symbol 🔒

Convert atomic number to element symbol.

cross3 🔒

Compute cross product of two 3D vectors.

dot3 🔒

Compute dot product of two 3D vectors.

find_atom_index 🔒

Find atom index by name in z-matrix.

mat_vec_mul 🔒

Multiply 3x3 matrix by 3-vector.

norm3 🔒

Compute norm of 3D vector.

parse_atom_line 🔒

Parse a single atom line.

parse_atom_string

Parse atom coordinates from a string.

parse_atom_symbol

Parse atom symbol, extracting element symbol and ghost status.

parse_float 🔒

Parse a float value with error context.

parse_zmatrix

Parse z-matrix format coordinates.

parse_zmatrix_to_entries 🔒

Parse z-matrix string to ZmatEntry structs and atom labels.

rotation_mat 🔒

Rodrigues’ rotation formula: rotate by angle theta around axis vec. Returns 3x3 rotation matrix.

symbol_to_charge

Get atomic number from element symbol using bse lookup.

zmat2cart

Convert z-matrix entries back to Cartesian coordinates.

zmat_entries_to_cart 🔒

Convert ZmatEntry structs to Cartesian coordinates.

zmatrix_to_cartesian 🔒

Convert z-matrix parameters to Cartesian coordinates.