bond-summary¶

Detect and report covalent bond changes between consecutive molecular structures.

Synopsis¶

mlmm bond-summary -i R.xyz -i P.xyz
mlmm bond-summary -i R.xyz -i TS.xyz -i P.xyz
mlmm bond-summary -i R.pdb -i IM1.pdb -i IM2.pdb -i P.pdb

Description¶

bond-summary compares consecutive pairs of input structures and reports bonds that are formed or broken. For N input files it produces N − 1 comparison blocks (A→B, B→C, …).

Bond perception uses element-specific covalent radii with configurable tolerances. Distances are reported in Ångström.

Supported formats: XYZ, PDB, GJF (auto-detected by extension).

Options¶

Option	Description	Default
`-i, --input FILE`	Input structure file (repeat for each file, ≥ 2 required)	—
`--device TEXT`	Compute device (`cpu`, `cuda`)	`cpu`
`--bond-factor FLOAT`	Scaling factor for covalent radii sum	`1.20`
`--one-based / --zero-based`	Atom index convention in output	`--one-based`

Examples¶

Two-structure comparison¶

mlmm bond-summary -i 1.R.xyz -i 3.P.xyz

Output:

============================================================
  1.R.xyz  →  3.P.xyz
============================================================
Bond formed (2):
  - O14-H106 : 1.502 Å --> 1.011 Å
  - P95-O107 : 3.477 Å --> 1.523 Å
Bond broken (2):
  - P95-O97 : 1.585 Å --> 3.270 Å
  - H106-O107 : 1.034 Å --> 1.673 Å

Multi-structure (reaction pathway)¶

mlmm bond-summary -i 1.R.xyz -i 3.IM1.xyz -i 5.IM2.xyz -i 7.P.xyz

Produces three comparison blocks: R→IM1, IM1→IM2, IM2→P.

Notes¶

All input structures must have identical atom counts and element ordering.
Bond detection uses the same algorithm as the internal bond_changes module used by the all workflow for IRC endpoint validation.
To adjust sensitivity to borderline bonds (e.g., metal coordination at 2.0–2.4 Å), increase --bond-factor (e.g., 1.30).