Index

C

calculate_charge_schemes() (in module qa.analyze) calculate_esp() (in module qa.analyze) centroid_distance() (in module qa.analyze) charge_matrix() (in module qa.analyze) charge_matrix_analysis() (in module qa.analyze) check_esp_failed() (in module qa.manage) check_file() (in module qa.manage) check_file_exists() (in module qa.manage) check_folder() (in module qa.manage) check_valid_resname() (in module qa.process) clean_incomplete_xyz() (in module qa.process) clean_qm_jobs() (in module qa.process) cli() (in module qa.cli)

collect_esp_components() (in module qa.manage) combine_qm_charges() (in module qa.process) combine_qm_charges_replicates() (in module qa.analyze) combine_qm_replicates() (in module qa.process) combine_replicates() (in module qa.process) combine_restarts_new() (in module qa.process) combine_restarts_old() (in module qa.process) combine_sp_xyz() (in module qa.process) combine_xyzs() (in module qa.process) compute_rmsd() (in module qa.analyze) copy_script() (in module qa.manage) cpptraj_covars() (in module qa.analyze) cpus (in module multiwfn_submit_creator) create_combined_csv() (in module qa.predict)

D

data_processing() (in module qa.predict)

divide (in module multiwfn_submit_creator)

E

esp_combined_barchart() (in module qa.plot) esp_dist_plot() (in module qa.plot)

esp_kde_dist_plot() (in module qa.plot) esp_separate_barchart() (in module qa.plot)

F

final_value (in module multiwfn_submit_creator) find_stalled() (in module qa.manage)

first (in module multiwfn_submit_creator) first_last_tuples (in module multiwfn_submit_creator) format_plot() (in module qa.plot)

G

get_aa_identifiers() (in module qa.reference) get_atom_count() (in module qa.process) get_charge_distributions() (in module qa.plot) get_charge_file() (in module qa.process) get_joint_qres() (in module qa.analyze) get_parity_plot() (in module qa.plot)

get_pdb() (in module qa.process) get_protein_sequence() (in module qa.process) get_res_atom_indices() (in module qa.process) get_residue_identifiers() (in module qa.process) get_rmsd() (in module qa.analyze) get_xyz() (in module qa.process)

H

heatmap() (in module qa.plot)

J

job_dirs (in module multiwfn_submit_creator)

M

mc6 (in module qa.cli) mc6s (in module qa.cli) mc6sa (in module qa.cli) mc7 (in module qa.cli) module multiwfn_submit_creator qa qa.analyze qa.cli qa.manage qa.plot qa.predict qa.process qa.reference, [1]

multiwfn_submit_creator module mutations (in module qa.predict)

N

nodes (in module multiwfn_submit_creator)

P

pairwise_distances_csv() (in module qa.analyze) parse_components() (in module qa.analyze)

plot_feature_importance() (in module qa.plot) plot_rmsd() (in module qa.plot)

Q

qa module qa.analyze module qa.cli module qa.manage module

qa.plot module qa.predict module qa.process module qa.reference module, [1]

R

replicate_interval_submit() (in module qa.manage) replicates (in module multiwfn_submit_creator)

run_all_replicates() (in module qa.manage), [1] run_ml() (in module qa.predict)

S

sequence() (in module qa.reference) shuffle_data() (in module qa.predict) simple_xyz_combine() (in module qa.process)

sliced (in module multiwfn_submit_creator) step (in module multiwfn_submit_creator) string_to_list() (in module qa.process) summed_residue_charge() (in module qa.process)

T

task (in module multiwfn_submit_creator)

td_coupling() (in module qa.analyze) time_coupling_plot() (in module qa.plot)

W

welcome() (in module qa.cli)

X

xyz2pdb() (in module qa.process)

xyz2pdb_ensemble() (in module qa.process) xyz2pdb_traj() (in module qa.process)