Index

_

__call__() (nanoCAT.bde.dissociate_xyn.MolDissociater method) __getitem__() (dataCAT.PDBContainer method) __init__() (dataCAT.PDBContainer method) __len__() (dataCAT.PDBContainer method)

_at_pairs (CAT.attachment.mol_split_cm.SplitMol attribute) _bonds (CAT.attachment.remove_atoms_cm.RemoveAtoms attribute) _tmp_mol_list (CAT.attachment.mol_split_cm.SplitMol attribute) _vars_backup (CAT.attachment.mol_split_cm.SplitMol attribute) _xyz (CAT.attachment.as_array.AsArray attribute)

A

activation_strain (optional.qd attribute) add_ligands() (in module CAT.dye.addlig) allignment (optional.core attribute) anchor (optional.core attribute) (optional.ligand attribute) (optional.qd.multi_ligand attribute) angle_offset (optional.ligand.anchor attribute)

AsArray (class in CAT.attachment.as_array) assign_topology() (nanoCAT.bde.dissociate_xyn.MolDissociater method) atom_count (dataCAT.PDBContainer property) ATOM_COUNT_DTYPE (in module dataCAT.dtype) atoms (CAT.attachment.remove_atoms_cm.RemoveAtoms attribute) (dataCAT.PDBContainer property) ATOMS_DTYPE (in module dataCAT.dtype)

B

BACKUP_IDX_DTYPE (in module dataCAT.dtype) bond_count (dataCAT.PDBContainer property) BOND_COUNT_DTYPE (in module dataCAT.dtype) bonds (CAT.attachment.mol_split_cm.SplitMol attribute) (dataCAT.PDBContainer property)

BONDS_DTYPE (in module dataCAT.dtype) branch_distance (optional.ligand attribute) brute_uniform_idx() (in module CAT.attachment.distribution_brute) bulk_workflow() (in module nanoCAT.recipes) bulkiness (optional.qd attribute)

C

canonicalize ( attribute) cap_type (CAT.attachment.mol_split_cm.SplitMol attribute) CAT.attachment.distribution_brute module CAT.distribution module CAT.dye.addlig module cdft (in module nanoCAT.recipes) (optional.ligand attribute) cluster_size (optional.core.subset attribute) column ( attribute) combinations() (nanoCAT.bde.dissociate_xyn.MolDissociater method) concatenate() (dataCAT.PDBContainer method)

cone_angle (optional.ligand attribute) construct_qd (optional.qd attribute) coordination_outer() (in module nanoCAT.recipes) core (optional attribute) core_atom (optional.qd.dissociate attribute) core_core_dist (optional.qd.dissociate attribute) core_idx (nanoCAT.bde.dissociate_xyn.MolDissociater attribute) core_index (optional.qd.dissociate attribute) create_hdf5_group() (dataCAT.PDBContainer class method) create_hdf5_log() (in module dataCAT) create_prop_dset() (in module dataCAT) create_prop_group() (in module dataCAT) csv_lig (dataCAT.Database property) csv_qd (dataCAT.Database property)

D

d (optional.qd.bulkiness attribute) Database (class in dataCAT) database (optional attribute) dataCAT.dtype module dataCAT.hdf5_log module dataCAT.pdb_array module dataCAT.property_dset module DFProxy (class in dataCAT) difference() (dataCAT.PDBContainer method) dihedral (optional.ligand.anchor attribute)

dirname (dataCAT.Database property) (optional.core attribute) (optional.database attribute) (optional.ligand attribute) (optional.qd attribute) dissociate (optional.qd attribute) dissociate_bulk() (in module nanoCAT.recipes) dissociate_ligand() (in module nanoCAT.bde.dissociate_xyn) dissociate_surface() (in module nanoCAT.recipes) distance (optional.ligand.cone_angle attribute) distance_upper_bound (optional.qd.activation_strain attribute) distribute_idx() (in module CAT.distribution) DT_DTYPE (in module dataCAT.dtype) dump_csv (optional.qd.activation_strain attribute)

E

el_scale14 (optional.qd.activation_strain attribute)

export_dyes() (in module CAT.dye.addlig)

F

f (optional.core.subset attribute) fast_bulk_workflow() (in module nanoCAT.recipes) filename (dataCAT.OpenLig property) (dataCAT.OpenQD property) filter_data() (in module nanoCAT.recipes) filter_mol() (in module nanoCAT.recipes)

follow_edge (optional.core.subset attribute) FORMULA_DTYPE (in module dataCAT.dtype) from_csv() (dataCAT.Database method) from_hdf5() (dataCAT.Database method) (dataCAT.PDBContainer class method) from_molecules() (dataCAT.PDBContainer class method)

G

get_compkf() (in module nanoCAT.recipes) get_coordination_number() (in module nanoCAT.recipes) get_entropy() (in module nanoCAT.recipes) get_global_descriptors() (in module nanoCAT.recipes) get_lig_charge() (in module nanoCAT.recipes) get_mol_length() (in module nanoCAT.recipes)

get_pairs_closest() (nanoCAT.bde.dissociate_xyn.MolDissociater method) get_pairs_distance() (nanoCAT.bde.dissociate_xyn.MolDissociater method) group (optional.ligand.anchor attribute) group_format (optional.ligand.anchor attribute) group_idx (optional.ligand.anchor attribute) guess_bonds ( attribute) guess_core_core_dist() (in module nanoCAT.bde.guess_core_dist)

H

h_lim (optional.qd.bulkiness attribute)

hdf5 (dataCAT.Database property) hdf5_availability() (dataCAT.Database method)

I

identify_surface() (in module nanoCAT.bde.identify_surface) identify_surface_ch() (in module nanoCAT.bde.identify_surface) INDEX_DTYPE (in module dataCAT.dtype) index_to_pandas() (in module dataCAT) indices ( attribute)

input_cores input_ligands intersection() (dataCAT.PDBContainer method) items() (dataCAT.PDBContainer method) iter_start (optional.qd.activation_strain attribute)

J

job1 (optional.qd.activation_strain attribute) (optional.qd.dissociate attribute)

job2 (optional.qd.dissociate attribute)

K

k (optional.qd.activation_strain attribute) keep_files (optional.qd.dissociate attribute)

keys() (dataCAT.PDBContainer class method) kind (optional.ligand.anchor attribute)

L

lig_core_dist (optional.qd.dissociate attribute) lig_count (optional.qd.dissociate attribute) LIG_COUNT_DTYPE (in module dataCAT.dtype) LIG_IDX_DTYPE (in module dataCAT.dtype) lig_pairs (optional.qd.dissociate attribute) ligand (optional attribute)

ligand_anchor ligand_count (nanoCAT.bde.dissociate_xyn.MolDissociater attribute) ligand_smiles ligands (optional.qd.multi_ligand attribute) lj_scale14 (optional.qd.activation_strain attribute) log_to_dataframe() (in module dataCAT)

M

max_dist (nanoCAT.bde.dissociate_xyn.MolDissociater attribute) md (optional.qd.activation_strain attribute) mode (optional.core.subset attribute) module CAT.attachment.distribution_brute CAT.distribution CAT.dye.addlig dataCAT.dtype dataCAT.hdf5_log dataCAT.pdb_array dataCAT.property_dset nanoCAT.bde.guess_core_dist nanoCAT.bde.identify_surface nanoCAT.recipes.bulk nanoCAT.recipes.cdft_utils nanoCAT.recipes.charges nanoCAT.recipes.coordination_number nanoCAT.recipes.dissociation nanoCAT.recipes.entropy nanoCAT.recipes.fast_sigma nanoCAT.recipes.mark_surface nanoCAT.recipes.mol_filter nanoCAT.recipes.multi_ligand_job

mol (CAT.attachment.as_array.AsArray attribute) (CAT.attachment.mol_split_cm.SplitMol attribute) (CAT.attachment.remove_atoms_cm.RemoveAtoms attribute) (nanoCAT.bde.dissociate_xyn.MolDissociater attribute) mol_format (optional.database attribute) MolDissociater (class in nanoCAT.bde.dissociate_xyn) mongodb (dataCAT.Database property) (optional.database attribute) MSG_DTYPE (in module dataCAT.dtype) multi_anchor_filter (optional.ligand.anchor attribute) multi_ligand (optional.qd attribute)

N

nanoCAT.bde.guess_core_dist module nanoCAT.bde.identify_surface module nanoCAT.recipes.bulk module nanoCAT.recipes.cdft_utils module nanoCAT.recipes.charges module nanoCAT.recipes.coordination_number module

nanoCAT.recipes.dissociation module nanoCAT.recipes.entropy module nanoCAT.recipes.fast_sigma module nanoCAT.recipes.mark_surface module nanoCAT.recipes.mol_filter module nanoCAT.recipes.multi_ligand_job module ndframe (dataCAT.DFProxy attribute)

O

OpenLig (class in dataCAT) OpenQD (class in dataCAT)

optimize (optional.ligand attribute) (optional.qd attribute) overwrite (optional.database attribute)

P

path	PDBContainer (class in dataCAT) prop_to_dataframe() (in module dataCAT)

Q

qd (optional attribute)

QD_IDX_DTYPE (in module dataCAT.dtype) qd_opt (optional.qd.dissociate attribute)

R

randomness (optional.core.subset attribute) read (optional.database attribute) read_csv() (in module nanoCAT.recipes) remove (optional.ligand.anchor attribute) remove_bulk() (nanoCAT.bde.dissociate_xyn.MolDissociater method) RemoveAtoms (class in CAT.attachment.remove_atoms_cm)

replace_surface() (in module nanoCAT.recipes) reset_hdf5_log() (in module dataCAT) row ( attribute) row_accumulator() (in module nanoCAT.recipes) run_fast_sigma() (in module nanoCAT.recipes) run_jobs() (in module nanoCAT.recipes)

S

s1 (optional.qd.activation_strain attribute) (optional.qd.dissociate attribute) s2 (optional.qd.dissociate attribute) sa_scores() (in module CAT.dye.addlig) sanitize_smiles_df() (in module nanoCAT.recipes)

scale (dataCAT.PDBContainer property) shift_cutoff (optional.qd.activation_strain attribute) split (optional.ligand attribute) SplitMol (class in CAT.attachment.mol_split_cm) subset (optional.core attribute) symmetric_difference() (dataCAT.PDBContainer method)

T

thread_safe (optional.database attribute) to_hdf5() (dataCAT.PDBContainer method) to_molecules() (dataCAT.PDBContainer method)

to_rdkit() (dataCAT.PDBContainer method) topology (nanoCAT.bde.dissociate_xyn.MolDissociater attribute) (optional.qd.dissociate attribute)

U

uniform_idx() (in module CAT.distribution) union() (dataCAT.PDBContainer method) update_csv() (dataCAT.Database method) update_hdf5() (dataCAT.Database method)

update_hdf5_log() (in module dataCAT) update_mongodb() (dataCAT.Database method) update_prop_dset() (in module dataCAT) use_ff (optional.qd.activation_strain attribute)

V

validate_hdf5() (dataCAT.PDBContainer class method) validate_prop_group() (in module dataCAT)

values() (dataCAT.PDBContainer method) VERSION_DTYPE (in module dataCAT.dtype)

W

weight (optional.core.subset attribute) write (dataCAT.OpenLig property) (dataCAT.OpenQD property) (optional.database attribute)

X

xyn_pre_opt (optional.qd.dissociate attribute)