pyqmmm.md¶

Components and utilities for managing MD workflows.

Modules

`pyqmmm.md.amber_toolkit`	A library of CPPTraj scripts and built-in generator functions.
`pyqmmm.md.bfactor_adder`
`pyqmmm.md.cc_coupling`
`pyqmmm.md.cluster_frame_indexer`	This script will find all frames in the main cluster and condense them.
`pyqmmm.md.compare_distances`
`pyqmmm.md.dccm_plot_formator`	Reads in DCCM data and formats it into the Kulik Lab standard format.
`pyqmmm.md.dssp_plotter`	Generate a DSSP plot from CPPTraj analysis
`pyqmmm.md.edia_chain_calculator`	This script takes EDIA output and cacluates the average chain EDIA scores.
`pyqmmm.md.gbsa_analyzer`	Process and analyze output from AMBER GBSA calculation
`pyqmmm.md.hbond_analyzer`	Analyze data from hydrogen bonding analysis based on hbond.gnu file.
`pyqmmm.md.hbond_compare`	Analyze data from hydrogen bonding analysis based on hbond.gnu file.
`pyqmmm.md.md_vitals_plotter`	Generates plots for energy, water density, RMSD, and RoG.
`pyqmmm.md.pdb_ensemble_generator`	Combines separate PDBs into a single ensemble.
`pyqmmm.md.ppm2png_converter`	Takes the PPM image output from VMD and converts them to PNGs.
`pyqmmm.md.quickcsa`	Performs charge shift analysis (CSA) form TeraChem output.
`pyqmmm.md.residue_lister`	Get a list of all residues in a PDB for the supplemental information.
`pyqmmm.md.restraint_plotter`	Creates a series of KDE plots based on HYSCORE-guided simulations
`pyqmmm.md.rmsd_clusters_colorcoder`	Plots a clustered trajectory by RMSD and identifies the centroid
`pyqmmm.md.rmsd_plotter`	Plot the RMSD analysis from CPPTraj