pyqmmm.qm¶

Components and utilities for managing QM workflows.

Modules

`pyqmmm.qm.bond_valence`	Calculates the bond valence for coordinating atoms across a reaction
`pyqmmm.qm.charge_spin_extractor`	Extract charge and spin data for a given subset of atoms for graphing.
`pyqmmm.qm.eda_analyze`
`pyqmmm.qm.energy_plotly`	Creates an energy profile for a TeraChem constrained geometry scan.
`pyqmmm.qm.energy_plotter`	Generalizable script for plotting the PES of an xyz trajectory.
`pyqmmm.qm.hydrogen_atom_optimizer`	Creates a list with the indices of all heavy atoms in an xyz.
`pyqmmm.qm.mechanism_plotter`
`pyqmmm.qm.missing_frame_checkup`	This script checks to see if any frames were not written to the mdcrd.
`pyqmmm.qm.orca_neb_restart`	Prepares a killed ORCA NEB job for a restart by moving and renaming files.
`pyqmmm.qm.orca_scan_plotter`	Plots the results of an ORCA scan.
`pyqmmm.qm.pdb_residue_extractor`	Extract specific residues from a PDB file and save them as a new file.
`pyqmmm.qm.pes_organizer`	This script will return the the charge and spin into a more readable format.
`pyqmmm.qm.qtaim_analyzer`	Creates paired bar plot for halogenase vs hydroxylase project.
`pyqmmm.qm.reaction_coordinate_collector`	Extract RC against energy and generate CSV.
`pyqmmm.qm.res_name_format_extractor`	Extract specific residues from a PDB file and save them as a new file.
`pyqmmm.qm.residue_decomposition`	Extract and compare energies from a residue decomposition analysis
`pyqmmm.qm.residue_numerator`	Allows you to change the starting residue of a PDB file.
`pyqmmm.qm.single-eda-analyze`
`pyqmmm.qm.traj_atom_filter`	Generate a new trajectory with only selected atoms.
`pyqmmm.qm.traj_atom_swapper`	Swap any two atoms in an xyz.
`pyqmmm.qm.traj_merger`	Combine frames into a single file.
`pyqmmm.qm.traj_movie_generator`	Breaks up TeraChem optimization XYZ file into individual frames.
`pyqmmm.qm.xyz_flipper`	Reverses an xyz trajectory, for example if it was run backwards for better convergence.