Index

_

__init__() (QMzyme.SelectionSchemes.ChargeShiftAnalysis method) (QMzyme.SelectionSchemes.DistanceCutoff method) (QMzyme.SelectionSchemes.SelectionScheme method)

A

add_atom() (QMzyme.QMzymeRegion.QMzymeRegion method) add_region() (QMzyme.QMzymeModel.QMzymeModel method) align_to() (QMzyme.QMzymeRegion.QMzymeRegion method) AlphaCarbon (class in QMzyme.TruncationSchemes)

assign_to_region() (QMzyme.CalculateModel.CalculationBase method) (QMzyme.CalculateModel.MultiscaleCalculationBase method) atom_group (QMzyme.QMzymeRegion.QMzymeRegion property) atomic_number (QMzyme.QMzymeAtom.QMzymeAtom property)

B

backbone_atoms (in module QMzyme.configuration.__init__)

balance_charge() (in module QMzyme.truncation_utils) BetaCarbon (class in QMzyme.TruncationSchemes)

C

CalculateModel (class in QMzyme.CalculateModel) CalculationBase (class in QMzyme.CalculateModel) CalculationFactory (class in QMzyme.CalculateModel) cap_H() (in module QMzyme.truncation_utils) ChargeShiftAnalysis (class in QMzyme.SelectionSchemes) check_filename() (in module QMzyme.utils)

check_missing_attr() (QMzyme.QMzymeRegion.QMzymeRegion method) combine() (QMzyme.QMzymeRegion.QMzymeRegion method) combine_regions_and_methods() (QMzyme.CalculateModel.CalculateModel method) compute_translation_and_rotation() (in module QMzyme.utils) create_apo_holo_regions() (QMzyme.SelectionSchemes.ChargeShiftAnalysis method) create_new_atom() (in module QMzyme.truncation_utils) creation_attr (QMzyme.QMzymeRegion.QMzymeRegion property)

D

DistanceCutoff (class in QMzyme.SelectionSchemes)

E

element_name_to_atomic_number (in module QMzyme.configuration.__init__)

F

find_nearby_residues() (QMzyme.QMzymeRegion.QMzymeRegion method)

G

GenerateModel (class in QMzyme.GenerateModel) get_atom() (QMzyme.QMzymeRegion.QMzymeRegion method) (QMzyme.QMzymeRegion.QMzymeResidue method) get_atom_properties() (QMzyme.RegionBuilder.RegionBuilder method) get_atoms() (QMzyme.QMzymeRegion.QMzymeRegion method) get_backbone_atoms() (QMzyme.QMzymeRegion.QMzymeResidue method) get_chain() (QMzyme.QMzymeAtom.QMzymeAtom method) get_following_Natom() (in module QMzyme.truncation_utils) get_ids() (QMzyme.QMzymeRegion.QMzymeRegion method) get_indices() (QMzyme.QMzymeRegion.QMzymeRegion method)

get_ix_array_from_ids() (QMzyme.QMzymeRegion.QMzymeRegion method) get_neighbors() (in module QMzyme.MDAnalysisWrapper) get_overlapping_atoms() (QMzyme.QMzymeRegion.QMzymeRegion method) get_preceding_Catom() (in module QMzyme.truncation_utils) get_region() (QMzyme.QMzymeModel.QMzymeModel method) (QMzyme.RegionBuilder.RegionBuilder method) get_region_names() (QMzyme.QMzymeModel.QMzymeModel method) get_residue() (QMzyme.QMzymeRegion.QMzymeRegion method) guess_charge() (QMzyme.QMzymeRegion.QMzymeRegion method) (QMzyme.QMzymeRegion.QMzymeResidue method)

H

has_atom() (QMzyme.QMzymeRegion.QMzymeRegion method) has_Cterm_neighbor() (in module QMzyme.truncation_utils)

has_Nterm_neighbor() (in module QMzyme.truncation_utils) has_region() (QMzyme.QMzymeModel.QMzymeModel method) has_residue() (QMzyme.QMzymeRegion.QMzymeRegion method)

I

ids (QMzyme.QMzymeRegion.QMzymeRegion property) import_region() (QMzyme.QMzymeModel.QMzymeModel method) init_atom() (QMzyme.RegionBuilder.RegionBuilder method)

init_atom_group() (QMzyme.RegionBuilder.RegionBuilder method) init_universe() (in module QMzyme.MDAnalysisWrapper) is_within() (QMzyme.QMzymeAtom.QMzymeAtom method) ix_array (QMzyme.QMzymeRegion.QMzymeRegion property)

K

kabsch_transform() (in module QMzyme.utils)

M

make_selection() (in module QMzyme.utils) make_writer() (QMzyme.Writers.WriterFactory static method) MDA_AtomGroup_selection() (in module QMzyme.utils) MDA_str_selection() (in module QMzyme.utils) method_name() (QMzyme.SelectionSchemes.SelectionScheme method), [1] module QMzyme.aqme.qprep QMzyme.CalculateModel QMzyme.configuration.__init__ QMzyme.GenerateModel QMzyme.MDAnalysisWrapper QMzyme.SelectionSchemes QMzyme.truncation_utils QMzyme.TruncationSchemes QMzyme.utils

MultiscaleCalculationBase (class in QMzyme.CalculateModel)

N

n_atoms (QMzyme.QMzymeRegion.QMzymeRegion property) (QMzyme.RegionBuilder.RegionBuilder property)

n_regions (QMzyme.QMzymeModel.QMzymeModel property) n_residues (QMzyme.QMzymeRegion.QMzymeRegion property) (QMzyme.RegionBuilder.RegionBuilder property)

P

positions (QMzyme.QMzymeRegion.QMzymeRegion property) print_overview() (QMzyme.QMzymeModel.QMzymeModel method)

protein_residues (in module QMzyme.configuration.__init__) pymol_visualize() (QMzyme.QMzymeModel.QMzymeModel method)

Q

QM_Method (class in QMzyme.CalculateModel) QMMMWriter (class in QMzyme.Writers) QMQM2Writer (class in QMzyme.Writers) QMWriter (class in QMzyme.Writers) QMXTBWriter (class in QMzyme.Writers) QMzyme.aqme.qprep module QMzyme.CalculateModel module QMzyme.configuration.__init__ module QMzyme.GenerateModel module

QMzyme.MDAnalysisWrapper module QMzyme.SelectionSchemes module QMzyme.truncation_utils module QMzyme.TruncationSchemes module QMzyme.utils module QMzymeAtom (class in QMzyme.QMzymeAtom) QMzymeModel (class in QMzyme.QMzymeModel) QMzymeRegion (class in QMzyme.QMzymeRegion) QMzymeResidue (class in QMzyme.QMzymeRegion)

R

read_charges() (QMzyme.QMzymeRegion.QMzymeRegion method) (QMzyme.QMzymeRegion.QMzymeResidue method) reference() (QMzyme.SelectionSchemes.ChargeShiftAnalysis method) (QMzyme.SelectionSchemes.DistanceCutoff method) (QMzyme.SelectionSchemes.SelectionScheme method), [1] (QMzyme.Writers.QMQM2Writer method) (QMzyme.Writers.QMWriter method) (QMzyme.Writers.QMXTBWriter method) (QMzyme.Writers.Writer method) region (QMzyme.QMzymeAtom.QMzymeAtom property) RegionBuilder (class in QMzyme.RegionBuilder) register_writer() (QMzyme.Writers.WriterFactory static method)

remove_atom() (QMzyme.QMzymeRegion.QMzymeRegion method) (QMzyme.QMzymeRegion.QMzymeResidue method) remove_region() (QMzyme.QMzymeModel.QMzymeModel method) removed_atoms (QMzyme.QMzymeRegion.QMzymeResidue property) rename() (QMzyme.QMzymeRegion.QMzymeRegion method) reset_creation_attr() (QMzyme.QMzymeRegion.QMzymeRegion method) resids (QMzyme.QMzymeRegion.QMzymeRegion property) residue_charges (in module QMzyme.configuration.__init__) residues (QMzyme.QMzymeRegion.QMzymeRegion property) return_region() (QMzyme.SelectionSchemes.SelectionScheme method), [1] (QMzyme.TruncationSchemes.TruncationScheme method) rmsd() (in module QMzyme.utils)

S

scheme_selection() (in module QMzyme.utils) segids (QMzyme.QMzymeRegion.QMzymeRegion property) select_atoms() (in module QMzyme.MDAnalysisWrapper) (QMzyme.SelectionSchemes.ChargeShiftAnalysis method) (QMzyme.SelectionSchemes.DistanceCutoff method) (QMzyme.SelectionSchemes.SelectionScheme method), [1] select_cat_residues() (QMzyme.SelectionSchemes.ChargeShiftAnalysis method) SelectionScheme (class in QMzyme.SelectionSchemes), [1] set_atom_segid() (QMzyme.QMzymeRegion.QMzymeRegion method) set_bond_length() (in module QMzyme.truncation_utils) set_catalytic_center() (QMzyme.GenerateModel.GenerateModel method) set_chain() (QMzyme.QMzymeRegion.QMzymeResidue method) set_charge() (QMzyme.QMzymeRegion.QMzymeRegion method)

set_constraints() (QMzyme.Writers.Writer method) set_creation_attr() (QMzyme.QMzymeRegion.QMzymeRegion method) set_fixed() (QMzyme.QMzymeAtom.QMzymeAtom method) set_fixed_atoms() (QMzyme.QMzymeRegion.QMzymeRegion method) set_method() (QMzyme.QMzymeRegion.QMzymeRegion method) set_neighbor() (QMzyme.QMzymeAtom.QMzymeAtom method) set_point_charge() (QMzyme.QMzymeAtom.QMzymeAtom method) set_region() (QMzyme.GenerateModel.GenerateModel method) sorted_atoms() (QMzyme.QMzymeRegion.QMzymeRegion method) store_calculation_results() (QMzyme.QMzymeRegion.QMzymeRegion method) store_pickle() (QMzyme.QMzymeModel.QMzymeModel method) subtract() (QMzyme.QMzymeRegion.QMzymeRegion method) summarize() (QMzyme.QMzymeRegion.QMzymeRegion method)

T

TerminalAlphaCarbon (class in QMzyme.TruncationSchemes) truncate() (QMzyme.GenerateModel.GenerateModel method) (QMzyme.TruncationSchemes.AlphaCarbon method) (QMzyme.TruncationSchemes.BetaCarbon method) (QMzyme.TruncationSchemes.TerminalAlphaCarbon method) (QMzyme.TruncationSchemes.TruncationScheme method)

TruncationScheme (class in QMzyme.TruncationSchemes)

U

uniquify_atom() (QMzyme.RegionBuilder.RegionBuilder method)

universe_selection() (in module QMzyme.MDAnalysisWrapper)

W

write() (QMzyme.QMzymeRegion.QMzymeRegion method) (QMzyme.Writers.QMQM2Writer method) (QMzyme.Writers.QMWriter method) (QMzyme.Writers.QMXTBWriter method) (QMzyme.Writers.Writer method)

write_input() (QMzyme.GenerateModel.GenerateModel method) Writer (class in QMzyme.Writers) WriterFactory (class in QMzyme.Writers) writers (QMzyme.Writers.WriterFactory attribute)

X

XTB_Method (class in QMzyme.CalculateModel)