ml.process

Process ab-initio molecular dynamics simulations.

Functions

add_esp_charges(charges_df, esp_scheme, ...)	Add the "upper" and "lower" columns from a CSV file to a DataFrame by removing and re-adding the "replicates" column.
calculate_esp(component_atoms, scheme)	Calculate the electrostatic potential (ESP) of a molecular component.
check_file_exists(filename)	Check if a file with the given name exists.
collect_esp_components(first_job, last_job, step)	Loops over replicates and single points and collects metal-centered ESPs.
combine_qm_charges(first_job, last_job, step)	Combines the charge_mull.xls files generate by TeraChem single points.
combine_qm_replicates()	Combine the all_charges.xls files for replicates into a master charge file.
combine_replicates([all_charges, all_coors])	Collects charges or coordinates into a xls and xyz file across replicates.
combine_sp_xyz()	Combines single point xyz's for all replicates.
final_charge_dataset(charge_file, template, ...)	Create final charge data set.
get_residue_identifiers(template[, by_atom])	Gets the residue identifiers such as Ala1 or Cys24.
pairwise_charge_features(structure, charge_data)	Generate pairwise charge features for a given metalloenzyme structure.
pairwise_distances_csv(pdb_traj_path, ...[, ...])	Calculate pairwise distances between residue centers of mass and save the result to a CSV file.
summed_residue_charge(charge_data, template)	Sums the charges for all atoms by residue.
xyz2pdb_traj()	Converts an xyz trajectory file into a pdb trajectory file.