Index

A

add_prefix_suffix() (in module aqme.utils) add_stable_conformers() (in module aqme.filter) adjust_cluster_threshold() (in module aqme.filter) analyze_abnormal() (qcorr method) analyze_isom() (qcorr method) analyze_normal() (qcorr method) ani_optimize() (cmin method) apply_energy_window_filter() (in module aqme.filter) apply_pre_energy_filter() (in module aqme.filter) apply_rmsd_and_energy_filter() (in module aqme.filter) aqme module aqme.cmin module aqme.csearch.base module

aqme.filter module aqme.qcorr module aqme.qcorr_utils module aqme.qdescp module aqme.qprep module aqme.utils module assign_atomic_properties() (qdescp method) auto_sampling() (csearch method)

B

blocking_wrapper() (in module aqme.utils)

C

cclib_atoms_coords() (in module aqme.utils) cclib_gen() (qcorr method) cclib_init() (qcorr method) charge_mult_cmin() (cmin method) check_crest() (in module aqme.utils) check_dependencies() (in module aqme.utils) check_files() (in module aqme.utils) check_geometric_match() (in module aqme.filter) check_isomerization() (in module aqme.qcorr_utils) check_level_of_theory() (qprep method) check_run() (in module aqme.utils)

check_version() (in module aqme.utils) check_xtb() (in module aqme.utils) cleanup() (qdescp method) cluster_conformers() (in module aqme.filter) cmin (class in aqme.cmin) command_line_args() (in module aqme.utils) compute_cmin() (cmin method) compute_confs() (csearch method) compute_pairwise_rms_distances() (in module aqme.filter) conformer_filters() (in module aqme.filter) conformer_generation() (csearch method) csearch (class in aqme.csearch)

D

detect_linear() (in module aqme.qcorr_utils)

determine_cluster_points() (in module aqme.filter)

E

embed_conf() (csearch method)

extract_cluster_centroids() (in module aqme.filter)

F

filters() (in module aqme.filter) finalize() (Logger method) find_metal_atom() (csearch method)

fix_imag_freqs() (qcorr method) format_lists() (in module aqme.utils) full_check() (in module aqme.qcorr_utils)

G

gather_files_and_run() (qdescp method) gen_connectivity() (in module aqme.qcorr_utils) genConformer_r() (csearch method) geom_filter() (in module aqme.filter) get_boltz_n_save_csv() (qdescp method) get_boltz_props() (qdescp method) get_cclib_params() (in module aqme.qcorr_utils) get_cmin_model() (cmin method)

get_conf_RMS() (in module aqme.utils) get_files() (in module aqme.utils) get_header() (qprep method) get_info_input() (in module aqme.utils) get_ir_squareplanar_geometry() (in module aqme.filter) get_json_data() (in module aqme.qcorr_utils) get_tail() (qprep method) get_unique_files() (qdescp method)

I

initial_csearch_run() (qdescp method)

initial_xtb_check() (qdescp method)

L

load_from_yaml() (in module aqme.utils) load_jobs() (cmin method) (csearch method)

load_sdf() (in module aqme.utils) load_variables() (in module aqme.utils) Logger (class in aqme.utils)

M

min_after_embed() (csearch method) min_and_E_calc() (csearch method) module aqme aqme.cmin aqme.csearch.base aqme.filter aqme.qcorr aqme.qcorr_utils aqme.qdescp aqme.qprep aqme.utils

mol_from_sdf_or_mol_or_mol2() (in module aqme.utils) morfeus_properties() (qdescp method) move_file() (in module aqme.utils)

O

organize_outputs() (qcorr method)

P

periodic_table() (in module aqme.utils)

process_aqme_csv() (qdescp method)

Q

qcorr (class in aqme.qcorr) qcorr_fixing() (qcorr method) qcorr_processing() (qcorr method) qdescp (class in aqme.qdescp)

qdescp_nmr_workflow() (qdescp method) qdescp_set_up() (qdescp method) qdescp_xtb_workflow() (qdescp method) qprep (class in aqme.qprep) qprep_coords() (qprep method)

R

rdkit_search() (csearch method) rdkit_to_sdf() (csearch method) read_file() (in module aqme.utils)

read_xyz_charge_mult() (in module aqme.utils) run_command() (in module aqme.utils) run_csearch() (csearch method) run_opt_xtb() (qdescp method)

S

sdf_2_com() (qprep method)

set_destination() (in module aqme.utils)

W

write() (Logger method) (qprep method) write_clustered_sdf() (in module aqme.filter)

write_confs() (cmin method) write_csv_boltz_data() (qdescp method) write_qcorr_csv() (qcorr method)