API Reference

This section documents the curated public API. Each entry below links to a generated page with method/function details.

Builder

mofbuilder.MetalOrganicFrameworkBuilder([...])	Orchestrates MOF building: load net and topology, place nodes and linkers, optimize, supercell, defects, write.
mofbuilder.core.Framework([comm, ostream])	Holds the built MOF: graph, cell, merged data, and options for writing, solvation, and MD.

Modelling and Simulation

mofbuilder.md.OpenmmSetup(gro_file, top_file)	Set up and execute GROMACS/OPENMM simulations for molecular dynamics.
mofbuilder.md.SolvationBuilder([comm, ostream])	Builder for the creation of solvated molecular structures in a periodic box.
mofbuilder.md.LinkerForceFieldGenerator([...])	Forcefield generation and mapping for linker molecules in MOFs.
mofbuilder.md.GromacsForcefieldMerger([...])	Main class responsible for assembling and merging GROMACS forcefield files for MOF simulations.
mofbuilder.md.ForceFieldMapper([comm, ostream])	Mapping utility for transferring GROMACS forcefield sections between isomorphic molecules.

Input and Output

mofbuilder.io.CifReader([comm, ostream, ...])	Class for reading CIF files, extracting symmetry and atomic site information, and providing atom coordinates in the primitive cell.
mofbuilder.io.CifWriter([comm, ostream, ...])	Writer for crystallographic CIF files (Crystallographic Information File, .cif).
mofbuilder.io.PdbReader([comm, ostream, ...])	Class for reading and processing atomic coordinates from PDB files.
mofbuilder.io.PdbWriter([comm, ostream, ...])	Writer for PDB format structure files.
mofbuilder.io.GroReader([comm, ostream, ...])	Reader for GROMACS .gro coordinate files.
mofbuilder.io.GroWriter([comm, ostream, ...])	Write atomic structure data to GROMACS .gro coordinate files.
mofbuilder.io.XyzReader([comm, ostream, ...])	Reader for XYZ molecular coordinate files.
mofbuilder.io.XyzWriter([comm, ostream, ...])	Writer for XYZ coordinate files.

Visualization

mofbuilder.visualization.Viewer([comm, ...])

Visualization interface using py3Dmol for MOFbuilder.

Note

The analysis module is currently under development and is not yet part of the public interface.