API Documentation

autosolvate.autosolvate.startboxgen(argumentList)	Wrap function that parses command line options for autosolvate boxgen, adds solvent box to a given solute, and generates related force field parameters.
autosolvate.autosolvate.solventBoxBuilder(xyzfile)	Solvated molecule in specified solvent.
autosolvate.autosolvate.solventBoxBuilder.build()	Build the solvated system
autosolvate.autosolvate.AmberParamsBuilder(xyzfile)	This class handles the Amber parameter creation for one single molecule.
autosolvate.multicomponent.startmulticomponent(args)	Wrap function that parses command line options for autosolvate multicomponent module, generate solvent box and related force field parameters.
autosolvate.multicomponent.startmulticomponent_fromfile(file)	Start the multicomponent solvation process from a json file.
autosolvate.multicomponent.MulticomponentParamsBuilder(xyzfile)	Create amber parameter files for a single xyz or pdb file with multiple separate fragments.
autosolvate.multicomponent.MulticomponentSolventBoxBuilder(xyzfile)	Build a solvent box for a single molecule complex as the solute and single solvent
autosolvate.multicomponent.MixtureBuilder([...])	Create amber parameter files for a single solute with mixed solvents
autosolvate.multicomponent.MixtureBuilder.add_solute(xyzfile)	add a solute molecule
autosolvate.multicomponent.MixtureBuilder.add_solvent([...])	add a type of solvent
autosolvate.multicomponent.MixtureBuilder.build()	Start to build the mixed solvent box.
autosolvate.startboxgen(argumentList)	Wrap function that parses command line options for autosolvate boxgen, adds solvent box to a given solute, and generates related force field parameters.
autosolvate.generatetrajs.startmd(argumentList)	Wrap function that parses command line options for autosolvate clustergen, generates inputfiles for Amber and TeraChem, runs MM and QMMM stages.
autosolvate.generatetrajs.writeMMminInput([...])	Write Amber MM minimization input file
autosolvate.generatetrajs.writeMMheatInput([...])	Write Amber MM heating input file
autosolvate.generatetrajs.writeMMNVEInput([...])	Write Amber MM NVE input file
autosolvate.generatetrajs.writeMMNPTInput([...])	Write Amber MM NPT input file
autosolvate.generatetrajs.runMM([filename, ...])	Equilibrate with MM
autosolvate.generatetrajs.writeQMMMTemplate([...])	Write Terachem file-based interface to Amber
autosolvate.generatetrajs.writeQMMMMinInput([...])	Write QMMM min input file
autosolvate.generatetrajs.writeQMMMInput([...])	Write QMMM heating or NPT trajectory input file
autosolvate.generatetrajs.runQMMM([...])	Run QMMM minimization, heating and NVT trajectory run
autosolvate.clustergen.clustergen([...])	Extract microsolvated cluster around center solute
autosolvate.clustergen.startclustergen(...)	Wrap function that parses command line options for autosolvate clustergen, extracts microsolvated clusters from trajectory,