Index

_

__init__() (ties.Config method) (ties.Ligand method) (ties.Pair method) (ties.Protein method)

A

align_molecules_using_mcs (ties.Config property) allow_disjoint_components (ties.Config property) ambertools_antechamber (ties.Config property) ambertools_home (ties.Config property) ambertools_parmchk2 (ties.Config property)

ambertools_tleap (ties.Config property) antechamber_dr (ties.Config property) antechamber_prepare_mol2() (ties.Ligand method) are_atom_names_correct() (ties.Ligand method) atom_pair_q_atol (ties.Config property)

C

check_json_file() (ties.Pair method) complex_tleap_in (ties.Config property) Config (class in ties), [1]

convert_acprep_to_mol2() (ties.Ligand method) coordinates_file (ties.Config property) correct_atom_names() (ties.Ligand method)

G

generate_frcmod() (ties.Ligand method) get_element_map() (ties.Config static method)

get_path() (ties.Protein method) get_serializable() (ties.Config method)

I

ignore_charges_completely (ties.Config property)

L

lig_acprep_dir (ties.Config property) lig_dir (ties.Config property) lig_frcmod_dir (ties.Config property) lig_unique_atom_names_dir (ties.Config property) Ligand (class in ties), [1]

ligand_ff (ties.Config property) ligand_ff_name (ties.Config property) ligand_files (ties.Config property) ligand_net_charge (ties.Config property) ligand_tleap_in (ties.Config property) ligands_contain_q (ties.Config property)

M

make_atom_names_unique() (ties.Pair method) manually_matched_atom_pairs (ties.Config property) manually_mismatched_pairs (ties.Config property) md_engine (ties.Config property)

merge_frcmod_files() (ties.Pair method) module ties.generator ties.helpers ties.topology_superimposer

N

net_charge_threshold (ties.Config property)

O

overlap_fractions() (ties.Pair method)

overwrite_coordinates_with() (ties.Ligand method)

P

Pair (class in ties), [1] pair_morphfrcmods_dir (ties.Config property) pair_morphfrmocs_tests_dir (ties.Config property) pair_unique_atom_names_dir (ties.Config property)

prep_dir (ties.Config property) Protein (class in ties), [1] protein (ties.Config property) protein_ff (ties.Config property)

R

redistribute_q_over_unmatched (ties.Config property)

removeDU_atoms() (ties.Ligand method) renaming_map (ties.Ligand property)

S

set_suptop() (ties.Pair method)

superimpose() (ties.Pair method) superimposition_starting_pair (ties.Config property)

T

ties.generator module ties.helpers module

ties.topology_superimposer module

U

use_element_in_superimposition (ties.Config property)

use_hybrid_single_dual_top (ties.Config property) use_original_coor (ties.Config property)

W

workdir (ties.Config property)