Index

A

AbstractIO (class in pharmaforge.interfaces.abstractio) add_configurations_count() (in module pharmaforge.dbutils.mongo_utils) add_data() (pharmaforge.database.DataBase method) add_field() (pharmaforge.recipes.GeneralDatabase.GeneralRecipe method) add_field_from_kwargs() (pharmaforge.recipes.GeneralDatabase.GeneralRecipe method) add_field_to_all_documents() (in module pharmaforge.dbutils.mongo_utils) add_initial_coordinates() (pharmaforge.interfaces.scanning.Scan method) add_theory_to_collection() (in module pharmaforge.dbutils.create_mongodb_collections)

allow_parallel (pharmaforge.interfaces.deepmdio.DeepMDInterface attribute) (pharmaforge.interfaces.dftbio.DFTBInterface attribute) (pharmaforge.interfaces.gaussianio.GaussianInterface attribute) (pharmaforge.interfaces.psi4io.Psi4Interface attribute) (pharmaforge.interfaces.xtbio.XTBInterface attribute) apply() (pharmaforge.queries.query.Query method) assign_smiles() (in module pharmaforge.io.hdf5_utils) (in module pharmaforge.labeling.smiles) atom_types (pharmaforge.interfaces.scanning.Scan attribute)

C

calculate() (pharmaforge.interfaces.abstractio.AbstractIO method) (pharmaforge.stats.comparator.Comparator method) calculator (pharmaforge.interfaces.deepmdio.DeepMDInterface attribute) (pharmaforge.interfaces.dftbio.DFTBInterface attribute) (pharmaforge.interfaces.gaussianio.GaussianInterface attribute) (pharmaforge.interfaces.psi4io.Psi4Interface attribute) (pharmaforge.interfaces.scanning.Scan attribute) (pharmaforge.interfaces.xtbio.XTBInterface attribute) check_collections() (pharmaforge.recipes.GeneralDatabase.GeneralRecipe method) check_shared_molecules() (in module pharmaforge.io.hdf5_utils) chunk_calc() (pharmaforge.labeling.relabeler.Relabeler static method) clear_db() (pharmaforge.recipes.GeneralDatabase.GeneralRecipe method)

client (pharmaforge.database.Loader attribute) (pharmaforge.stats.comparator.Comparator attribute) clientloader() (in module pharmaforge.dbutils.mongo_utils) collection (pharmaforge.database.Loader attribute) combine_subdivided() (pharmaforge.labeling.relabeler.Relabeler method) Comparator (class in pharmaforge.stats.comparator) confirm_collections() (pharmaforge.recipes.QDPi1.QDPi1Recipe method) (pharmaforge.recipes.QDPi2.QDPi2Recipe method) coordinates (pharmaforge.interfaces.scanning.Scan attribute) count_docs_without_smiles_for_all_collections() (in module pharmaforge.dbutils.mongo_utils) count_molecules() (in module pharmaforge.labeling.smiles) count_water_molecules() (in module pharmaforge.labeling.smiles) create_collection() (in module pharmaforge.dbutils.create_mongodb_collections)

D

DataBase (class in pharmaforge.database) db (pharmaforge.database.Loader attribute) DeepMDData (class in pharmaforge.interfaces.deepmdio) DeepMDInterface (class in pharmaforge.interfaces.deepmdio)

DFTBInterface (class in pharmaforge.interfaces.dftbio) dihedrals (pharmaforge.interfaces.scanning.Scan attribute) display_query() (pharmaforge.queries.query.Query method) DPDataInterface (class in pharmaforge.interfaces.deepio)

E

e (pharmaforge.interfaces.deepmdio.DeepMDData attribute)

energies (pharmaforge.interfaces.scanning.Scan attribute)

F

f (pharmaforge.interfaces.deepmdio.DeepMDData attribute) find_all_unique() (pharmaforge.database.DataBase method) find_clusters() (pharmaforge.interfaces.abstractio.AbstractIO static method) find_empty_molecules() (pharmaforge.database.DataBase method)

find_molecule() (pharmaforge.database.DataBase method) find_shared_molecules() (pharmaforge.database.DataBase method) find_unique() (pharmaforge.database.DataBase method) forces (pharmaforge.interfaces.scanning.Scan attribute)

G

gauss_options (pharmaforge.interfaces.gaussianio.GaussianInterface attribute) GaussianInterface (class in pharmaforge.interfaces.gaussianio)

GeneralRecipe (class in pharmaforge.recipes.GeneralDatabase) get_forces() (pharmaforge.interfaces.deepmdio.DeepMDData method) get_potential_energy() (pharmaforge.interfaces.deepmdio.DeepMDData method)

H

hdf5_filename (pharmaforge.queries.query.Query attribute)

I

initial_structure (pharmaforge.interfaces.scanning.Scan attribute)

L

level_of_theory (pharmaforge.interfaces.dftbio.DFTBInterface attribute) (pharmaforge.interfaces.gaussianio.GaussianInterface attribute) (pharmaforge.interfaces.psi4io.Psi4Interface attribute) (pharmaforge.interfaces.xtbio.XTBInterface attribute)

list_collection_entry() (pharmaforge.database.Loader method) list_collections() (pharmaforge.database.Loader method) list_db_names() (pharmaforge.database.Loader method) Loader (class in pharmaforge.database)

M

mask (pharmaforge.interfaces.scanning.Scan attribute) model (pharmaforge.interfaces.deepmdio.DeepMDInterface attribute) modify_field_by_query() (in module pharmaforge.dbutils.mongo_utils) modify_hdf5_file() (in module pharmaforge.io.hdf5_utils) modify_molecule_name() (in module pharmaforge.io.hdf5_utils) modify_single_field() (in module pharmaforge.dbutils.mongo_utils) module pharmaforge.database pharmaforge.dbutils.create_mongodb_collections pharmaforge.dbutils.mongo_utils pharmaforge.interfaces.abstractio pharmaforge.interfaces.deepio pharmaforge.interfaces.deepmdio pharmaforge.interfaces.dftbio pharmaforge.interfaces.gaussianio pharmaforge.interfaces.psi4io pharmaforge.interfaces.scanning pharmaforge.interfaces.xtbio pharmaforge.io.hdf5_utils pharmaforge.labeling.get_smiles pharmaforge.labeling.relabeler pharmaforge.labeling.smiles pharmaforge.queries.query pharmaforge.recipes.GeneralDatabase pharmaforge.recipes.QDPi1 pharmaforge.recipes.QDPi2 pharmaforge.stats.comparator

N

new_hdf5_file_with_smiles() (in module pharmaforge.io.hdf5_utils) (in module pharmaforge.labeling.smiles)

O

obtain_feature() (pharmaforge.database.DataBase method) ObtainDeepData() (pharmaforge.interfaces.abstractio.AbstractIO method) ObtainQueryData() (pharmaforge.interfaces.abstractio.AbstractIO method) open_client() (pharmaforge.recipes.GeneralDatabase.GeneralRecipe method)

options_dict (pharmaforge.interfaces.dftbio.DFTBInterface attribute) (pharmaforge.interfaces.gaussianio.GaussianInterface attribute) (pharmaforge.interfaces.psi4io.Psi4Interface attribute) (pharmaforge.interfaces.xtbio.XTBInterface attribute)

P

parse_query() (pharmaforge.queries.query.Query method) parsed_query (pharmaforge.queries.query.Query attribute) pharmaforge.database module pharmaforge.dbutils.create_mongodb_collections module pharmaforge.dbutils.mongo_utils module pharmaforge.interfaces.abstractio module pharmaforge.interfaces.deepio module pharmaforge.interfaces.deepmdio module pharmaforge.interfaces.dftbio module pharmaforge.interfaces.gaussianio module pharmaforge.interfaces.psi4io module pharmaforge.interfaces.scanning module pharmaforge.interfaces.xtbio module pharmaforge.io.hdf5_utils module pharmaforge.labeling.get_smiles module

pharmaforge.labeling.relabeler module pharmaforge.labeling.smiles module pharmaforge.queries.query module pharmaforge.recipes.GeneralDatabase module pharmaforge.recipes.QDPi1 module pharmaforge.recipes.QDPi2 module pharmaforge.stats.comparator module plot_molecule_frequency_histogram() (in module pharmaforge.dbutils.mongo_utils) plot_scan() (pharmaforge.interfaces.scanning.Scan method) pprint_one_entry() (pharmaforge.recipes.GeneralDatabase.GeneralRecipe method) process_angle_scan() (pharmaforge.interfaces.scanning.Scan static method) process_bond_scan() (pharmaforge.interfaces.scanning.Scan static method) process_files_with_smiles() (in module pharmaforge.labeling.get_smiles) process_hdf5() (pharmaforge.recipes.GeneralDatabase.GeneralRecipe method) process_hdf5_folder() (in module pharmaforge.dbutils.create_mongodb_collections) process_multiple_hdf5_files() (in module pharmaforge.io.hdf5_utils) process_structure() (pharmaforge.interfaces.abstractio.AbstractIO static method) (pharmaforge.interfaces.scanning.Scan static method) psi4_options (pharmaforge.interfaces.psi4io.Psi4Interface attribute) Psi4Interface (class in pharmaforge.interfaces.psi4io)

Q

QDPi1Recipe (class in pharmaforge.recipes.QDPi1) QDPi2Recipe (class in pharmaforge.recipes.QDPi2)

Query (class in pharmaforge.queries.query) querystring (pharmaforge.queries.query.Query attribute)

R

read() (pharmaforge.interfaces.deepio.DPDataInterface method) relabel() (pharmaforge.labeling.relabeler.Relabeler method) relabel_chunk() (pharmaforge.labeling.relabeler.Relabeler static method)

Relabeler (class in pharmaforge.labeling.relabeler) result_to_ase() (pharmaforge.queries.query.Query static method) results (pharmaforge.queries.query.Query attribute) results_to_deepmdkit() (pharmaforge.queries.query.Query method)

S

save_molecule_to_xyz() (in module pharmaforge.io.hdf5_utils) (in module pharmaforge.labeling.smiles) Scan (class in pharmaforge.interfaces.scanning) scan() (pharmaforge.interfaces.scanning.Scan method) select_collection() (pharmaforge.database.Loader method)

select_data() (pharmaforge.labeling.relabeler.Relabeler method) select_db() (pharmaforge.database.Loader method) set_environment() (pharmaforge.interfaces.dftbio.DFTBInterface method) single_point() (pharmaforge.interfaces.xtbio.XTBInterface method) subdivided_relabel() (pharmaforge.labeling.relabeler.Relabeler method)

T

theorylevels (pharmaforge.queries.query.Query attribute)

to_database() (pharmaforge.labeling.relabeler.Relabeler method) torsion_angles (pharmaforge.interfaces.scanning.Scan attribute)

U

unit (pharmaforge.interfaces.scanning.Scan attribute)

V

verify_all_shared_molecules() (in module pharmaforge.io.hdf5_utils)

W

write() (pharmaforge.interfaces.deepio.DPDataInterface method)

write_xyz() (pharmaforge.interfaces.scanning.Scan method)

X

xtb_options (pharmaforge.interfaces.xtbio.XTBInterface attribute)

XTBInterface (class in pharmaforge.interfaces.xtbio)