Martinize 2 workflow

Martinize 2 is the main command line interface entry point for vermouth. It does many interesting things which will be explained here later, and in the end you should end up with a topology for your system. Graph central in atom recognition/identification

Pipeline

Make bonds

MakeBonds

Repair graph

RepairGraph

CanonicalizeModifications

Resolution transformation

DoMapping

Post processing

ApplyRubberBand

Important command line options

Martinize2 CLI options