Cookbook

Welcome to the MolSysMT Cookbook. Here, you will find self-contained recipes designed to solve structural biology tasks with elegance, speed, and reproducibility.

Each recipe combines multiple MolSysMT tools and demonstrates how to interface with external engines such as OpenMM, MDAnalysis, NetworkX, and NGLView.

Recipe	Objective
Assigning charges before a bounded export	Calculating ligand or conventional protein charges with explicit model and coverage.
Applying an explicit chemical template	Filling declared chemical assignments while preserving a ligand pose.
Building Complex Dimers	Harvesting, superimposing, and merging monomers from multi-chain PDBs into a complete complex.
Working with NGLView	Rendering molecular scenes with cartoon ribbons, pocket surfaces, and annotation vectors in NGLView.
Working with OpenMM	Setting up, solvating, and executing an OpenMM molecular dynamics simulation with in-memory frame streaming.
Big Data Trajectories	Streaming and slicing large trajectory datasets with constant memory using H5MSM.
From PDB to Solvated Box	Preparing, capping, and solvating experimental structures in a neutral periodic box.
Binding Pocket Isolation	Extracting active site residues and computing ligand contact distances using spatial selections.
Trajectory Analysis	Computing RMSD, per-residue RMSF, and radius of gyration time series across trajectory structures.
In Silico Mutagenesis	Introducing point mutations in memory, rebuilding side chains, and superimposing against the wild type.
Form Conversions	Converting molecular systems across OpenMM, MDAnalysis, NetworkX, MDTraj, and BioPython.
Reading and writing native SDF	Reading and writing a bounded native SDF subset without RDKit.
Reading and writing prepared PDBQT	Reading prepared AutoDock data and preserving declared torsion trees.
Auditing residue chemistry before repair	Distinguishing supported residue atom gaps from unassessed chemistry before repair.
Comparing sparse interactions across structures	Comparing synthetic interaction observations across selected structures and atom sets.
Migrating an H5MSM file	Translating a 0.4 molecular-system file into the modular H5MSM 0.5 schema.
Preparing aromatic participants	Preparing complete ring participants from declared aromatic chemistry.
Preparing charged participants	Recognizing local charged centers and selecting complete chemical participants.
Saving ionic analyses	Calculating, naming, saving, and querying an ionic-contact analysis.
Saving cation-pi analyses	Saving attributed cation–π observations and a separate geometric proposal.
Saving coordination and water paths	Saving metal candidates and one- or two-water paths with original provenance.
Saving hydrophobic analyses	Naming, saving and remapping a typed fragment-interface analysis.
Saving halogen-bond analyses	Naming, saving and remapping four-role halogen observations.
Saving hydrogen-bond analyses	Persisting named hydrogen-bond definitions and sparse coverage.
Saving aromatic interaction analyses	Calculating, naming, saving, and querying aromatic ring geometry.

Tip

Use these recipes as templates for your computational structural biology pipelines. For detailed function documentation and arguments, consult the Toolbox and API Reference.