Overview of Tools#

As a Multi-Toolkit, MolSysMT organizes its functional API into specialized tool compartments (namespaces). Each compartment is dedicated to a specific domain of molecular operations — from system preparation and coordinate geometry to topological connectivity, periodic boundary conditions, physical-chemical properties, and third-party interoperability.

This modular architecture provides clean, purpose-built function names without cluttering your global scope, maintaining a uniform vocabulary across all 89 supported forms.

Basic#

The Basic module (molsysmt.basic) provides core, form-agnostic operations used across almost every workflow.

  • Key Operations: get, set, select, convert, build, view, compare, add, contains, copy, remove, append_structures.

  • Philosophy: Universal interaction layer operating identically on any molecular representation — whether a disk file (PDB, mmCIF, GRO), an in-memory object (OpenMM Topology, MDAnalysis Universe), or a native MolSys.

Form#

The Form module (molsysmt.form) manages form discovery, support tier inspection, form-specific conversions, and attribute capability reporting.

  • Key Operations: get_form, is_form, show_forms, get_attributes.

  • Philosophy: Dynamic introspection layer that determines how attributes and structural features are extracted or converted across supported data forms.

Element#

The Element module (molsysmt.element) provides targeted access and manipulation across biological structural tiers.

  • Sub-namespaces: atom, group (amino acids, nucleotides, ions), component, molecule, entity, chain.

  • Philosophy: Hierarchical queries allowing operations tailored to specific structural scales (e.g., querying alpha-carbon atoms of a chain or retrieving residue sequences for specific protein entities).

Build#

The Build module (molsysmt.build) provides native structure preparation, capping, hydrogen placement, solvation, and molecular repair capabilities.

  • Key Operations: get_missing_heavy_atoms, add_missing_heavy_atoms, get_missing_terminal_cappings, add_missing_terminal_cappings, add_missing_hydrogens, solvate, add_counterions, mutate.

  • Philosophy: Complete, simulation-ready system preparation executed natively in Python without requiring external software installations like PDBFixer or OpenMM.

Structure#

The Structure module (molsysmt.structure) handles coordinate geometry, spatial measurements, structural analysis, and 3D transformations.

  • Key Operations: get_distances, get_contacts, get_sasa, get_rmsd, get_rmsf, fit, align, get_radius_of_gyration, get_principal_axes, get_dihedral_angles, center, translate, rotate.

  • Philosophy: High-performance analytical operations executed on precompiled Rust kernels. Coordinates follow strict geometric contracts: nanometer units, NumPy array shape (n_structures, n_atoms, 3), right-handed 3×3 rotation matrices, and deterministic fitting requiring at least three non-collinear atoms.

Topology#

The Topology module (molsysmt.topology) governs chemical connectivity, bond matrices, sequence extraction, and secondary structure assignment.

  • Key Operations: get_bond_graph, get_covalent_blocks, get_covalent_chains, get_covalent_paths, get_sequence, get_secondary_structure.

  • Philosophy: Fast topological inventory management preserving stable element identifiers rather than renumbering them, maintaining chemical integrity across form conversions.

PBC#

The PBC module (molsysmt.pbc) manages periodic boundary conditions, unit cell box vectors, and boundary unwrapping.

  • Key Operations: get_box, set_box, unwrap, wrap, get_box_volume, get_box_angles.

  • Philosophy: Automatic handling of periodic boundary conditions across simulations, ensuring correct distance and contact calculations under minimum image conventions.

Physchem#

The Physchem module (molsysmt.physchem) computes physical and chemical properties of molecular systems.

  • Key Operations: get_charge, get_mass, get_degrees_of_freedom, get_molecular_weight.

  • Philosophy: Automated calculation of physical-chemical descriptors carrying explicit physical units (pyunitwizard).

Molecular Mechanics#

The Molecular Mechanics module (molsysmt.molecular_mechanics) handles forcefield definitions, atom types, and mechanics parameters.

  • Key Operations: get_forcefield, get_atom_type, get_partial_charge.

  • Philosophy: Inspection and management of molecular mechanics forcefield assignments and parameter sets.

Hbonds#

The Hbonds module (molsysmt.hbonds) detects and analyzes hydrogen-bonding networks across structures and trajectories.

  • Key Operations: get_hbonds, get_hbond_acceptors, get_hbond_donors.

  • Philosophy: Geometric and distance-angle based detection of hydrogen bonds for structural stability analysis.

Third Party#

The Third Party module (molsysmt.third_party) hosts specialized bridges to external software packages in the computational biology ecosystem.

  • Supported Integrations: OpenMM, MDAnalysis, MDTraj, ParmEd, PyTraj, RDKit, Biopython, NGLView, MolSysViewer.

  • Philosophy: Zero-friction handshakes allowing MolSysMT to delegate specialized computation or visualization to external engines without writing custom file conversion scripts.

How to Explore the Tools

  • Step-by-Step Tutorials: To learn how to use each tool with interactive code examples, explore the Tools User Guide.

  • Technical Specifications: To consult exact function signatures, argument types, docstrings, and developer API details, visit the Technical API Documentation.