Index

_

__init__() (fragmenstein.igor.Igor method) (fragmenstein.m_rmsd.mRMSD method) (fragmenstein.Monster method) (fragmenstein.monster.ExtendedFMCSMode method) (fragmenstein.monster.GPM method) (fragmenstein.monster.IndexMap method) (fragmenstein.monster.SpecialCompareAtoms method) (fragmenstein.monster.Unmerge method) (fragmenstein.MProVictor method) (fragmenstein.MultiVictorPlacement method) (fragmenstein.Victor method) (fragmenstein.victor.MinimalPDBParser method) (fragmenstein.Victor.Monster method) (fragmenstein.walton.Walton method)

A

add_constraint_file() (fragmenstein.igor.Igor class method) add_constraint_to_warhead() (fragmenstein.Victor class method) add_extra_constraint() (fragmenstein.Victor method) analyse_postera() (fragmenstein.MProVictor class method) angle_constraint (fragmenstein.igor.Igor attribute) append() (fragmenstein.victor.MinimalPDBParser method)

atom_on_axis() (fragmenstein.walton.Walton method) atom_on_plane() (fragmenstein.walton.Walton method) atom_pair_constraint (fragmenstein.igor.Igor attribute) atom_to_origin() (fragmenstein.walton.Walton method) atomCompare (fragmenstein.monster.ExtendedFMCSMode attribute) atoms_in_bridge_cutoff (fragmenstein.Monster attribute) (fragmenstein.Victor.Monster attribute)

B

bond() (fragmenstein.monster.Unmerge method) bondCompare (fragmenstein.monster.ExtendedFMCSMode attribute)

BondProvenance (class in fragmenstein.monster) by_expansion() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method)

C

calculate() (fragmenstein.monster.Unmerge method) calculate_msd() (fragmenstein.m_rmsd.mRMSD method) calculate_rmsd() (fragmenstein.m_rmsd.mRMSD method) calculate_score() (fragmenstein.Victor method) capture_logs() (fragmenstein.Victor class method) capture_rdkit_log() (fragmenstein.Victor class method) capture_rosetta_log() (fragmenstein.Victor class method) check_possible_distances() (fragmenstein.monster.Unmerge method) CheckAtomCharge() (fragmenstein.monster.SpecialCompareAtoms method) CheckAtomChirality() (fragmenstein.monster.SpecialCompareAtoms method) CheckAtomRingMatch() (fragmenstein.monster.SpecialCompareAtoms method) checkpoint() (fragmenstein.Victor method) clear() (fragmenstein.monster.ExtendedFMCSMode method) closeness_weights (fragmenstein.Monster attribute) (fragmenstein.Victor.Monster attribute) closest_hit() (fragmenstein.Victor class method) collapse_mols() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) collapse_ring() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) color_in() (fragmenstein.walton.Walton method) (in module fragmenstein.display) color_scales (fragmenstein.walton.Walton attribute)

combine() (fragmenstein.Monster method) (fragmenstein.Victor method) (fragmenstein.Victor.Monster method) completeRingsOnly (fragmenstein.monster.ExtendedFMCSMode attribute) constrained_atoms (fragmenstein.Victor property) constraint_file (fragmenstein.igor.Igor attribute) constraint_function_type (fragmenstein.MProVictor attribute) (fragmenstein.Victor attribute) convert_origins_to_custom_map() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) coordinate_constraint (fragmenstein.igor.Igor attribute) copy() (fragmenstein.monster.ExtendedFMCSMode method) copy_all_possible_origins() (fragmenstein.m_rmsd.mRMSD class method) copy_bond() (fragmenstein.monster.BondProvenance class method) copy_names() (fragmenstein.Victor class method) copy_origins() (fragmenstein.m_rmsd.mRMSD class method) covalent_definitions (fragmenstein.Victor attribute) create_polygon() (fragmenstein.walton.Walton static method) custom_map (fragmenstein.Victor.Monster attribute) cutoff (fragmenstein.Monster attribute) (fragmenstein.monster.GPM attribute) (fragmenstein.monster.Unmerge attribute) (fragmenstein.Victor.Monster attribute)

D

detailed_scores() (fragmenstein.igor.Igor class method) display_energy() (fragmenstein.igor.Igor method) display_mols() (in module fragmenstein.display) distance_cutoff (fragmenstein.monster.Unmerge attribute) distance_hits() (fragmenstein.Victor class method) dock() (fragmenstein.igor.Igor method) (fragmenstein.Victor method) download_map() (fragmenstein.igor.Igor class method)

draw_nicely() (fragmenstein.Monster method) (fragmenstein.Victor method) (fragmenstein.Victor.Monster method) dummy (fragmenstein.Monster attribute) (fragmenstein.Victor.Monster attribute) dummy_symbol (fragmenstein.Monster attribute) (fragmenstein.Victor.Monster attribute) duplicate() (fragmenstein.walton.Walton method)

E

enable_logfile() (fragmenstein.Victor class method) enable_stdout() (fragmenstein.Victor class method) error_to_catch (fragmenstein.Victor attribute) expand_custom_map() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) expand_ring() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method)

experimental_rotate() (fragmenstein.walton.Walton method) ExtendedFMCSMode (class in fragmenstein.monster) extract_atoms() (fragmenstein.Monster class method) (fragmenstein.Victor.Monster class method) extract_from_neighborhood() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) extract_mol() (fragmenstein.Victor class method) extract_mols() (fragmenstein.Victor class method)

F

fa_intra_rep (fragmenstein.igor.Igor attribute) fetch_postera() (fragmenstein.MProVictor class method) (in module fragmenstein.mpro.dataframe) find_closest_to_ligand() (fragmenstein.Victor class method) fix_custom_map() (fragmenstein.Monster method) (fragmenstein.monster.SpecialCompareAtoms method) (fragmenstein.Victor.Monster method) fix_hits() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) fix_scorefxn_weights() (fragmenstein.igor.Igor class method) flatten_trio() (fragmenstein.walton.Walton method) fragmenstein module fragmenstein.branding module fragmenstein.cli module fragmenstein.display module

fragmenstein.igor.pyrosetta_import module fragmenstein.m_rmsd module from_annotated_mols() (fragmenstein.m_rmsd.mRMSD class method) from_files() (fragmenstein.Victor class method) from_hit_codes() (fragmenstein.MProVictor class method) from_internal_xyz() (fragmenstein.m_rmsd.mRMSD class method) from_other_annotated_mols() (fragmenstein.m_rmsd.mRMSD class method) from_pdbblock() (fragmenstein.igor.Igor class method) from_pdbfile() (fragmenstein.igor.Igor class method) from_postera_row() (fragmenstein.MProVictor class method) from_smiles() (fragmenstein.walton.Walton class method) from_unannotated_mols() (fragmenstein.m_rmsd.mRMSD class method) from_unannotated_same_mols() (fragmenstein.m_rmsd.mRMSD class method) fromkeys() (fragmenstein.monster.ExtendedFMCSMode class method) full_blending() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method)

G

generate_overlap_mapping() (fragmenstein.m_rmsd.mRMSD static method) get() (fragmenstein.monster.ExtendedFMCSMode method) get_atom_map_fromProp() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) get_atomname() (fragmenstein.victor.MinimalPDBParser method) get_best_scoring() (fragmenstein.Monster class method) (fragmenstein.Victor.Monster class method) get_bond() (fragmenstein.monster.BondProvenance class method) get_bonds() (fragmenstein.monster.BondProvenance class method) get_centroid_of_atoms() (fragmenstein.walton.Walton method) get_centroid_of_ring() (fragmenstein.walton.Walton method) get_chain() (fragmenstein.victor.MinimalPDBParser method) get_close_indices() (fragmenstein.Monster class method) (fragmenstein.Victor.Monster class method) get_color_origins() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) get_combined_rmsd() (fragmenstein.Monster class method) (fragmenstein.Victor.Monster class method) get_custom() (fragmenstein.monster.SpecialCompareAtoms method) get_hit_by_name() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) get_inter_distance() (fragmenstein.monster.Unmerge method) get_isomers() (fragmenstein.Victor class method) get_isomers_smiles() (fragmenstein.Victor class method) get_key() (fragmenstein.monster.Unmerge method) get_largest_fragment() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) get_legend() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) get_max_serial() (fragmenstein.victor.MinimalPDBParser method)

get_mcs_mapping() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) get_mcs_mappings() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) get_MinMover() (fragmenstein.igor.Igor method) get_mod_FastRelax() (fragmenstein.igor.Igor method) get_mol() (fragmenstein.walton.Walton method) get_neighborhood() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) get_old_FastRelax() (fragmenstein.igor.Igor method) get_pair_rmsd() (fragmenstein.Monster class method) (fragmenstein.Victor.Monster class method) get_PertMinMover() (fragmenstein.igor.Igor method) get_plip_interactions() (fragmenstein.Victor method) get_point() (fragmenstein.walton.Walton method) get_positional_mapping() (fragmenstein.Monster class method) (fragmenstein.monster.GPM class method) (fragmenstein.monster.Unmerge class method) (fragmenstein.Victor.Monster class method) get_possible_map() (fragmenstein.monster.Unmerge method) get_residue_index() (fragmenstein.victor.MinimalPDBParser method) get_residue_name() (fragmenstein.victor.MinimalPDBParser method) get_ring_radius() (fragmenstein.walton.Walton method) get_serial() (fragmenstein.victor.MinimalPDBParser method) get_valid_matches() (fragmenstein.monster.SpecialCompareAtoms method) get_warhead_definition() (fragmenstein.Victor class method) goodness_sorter_factory() (fragmenstein.monster.Unmerge method) GPM (class in fragmenstein.monster) guess_origins() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) guess_warhead() (fragmenstein.Victor class method)

H

harmonize_warheads() (fragmenstein.Victor method) has_bond() (fragmenstein.monster.BondProvenance class method)

has_residue_index() (fragmenstein.victor.MinimalPDBParser method) has_residue_name() (fragmenstein.victor.MinimalPDBParser method) HIT_BASED (fragmenstein.m_rmsd.mRMSD attribute)

I

IDENTITY_BASED (fragmenstein.m_rmsd.mRMSD attribute) Igor (class in fragmenstein.igor) IndexMap (class in fragmenstein.monster) init_pyrosetta() (fragmenstein.igor.Igor static method) inspect_amide_torsions() (fragmenstein.Monster static method) (fragmenstein.Victor.Monster static method)

inventorize_warheads() (fragmenstein.Victor class method) is_origin_annotated() (fragmenstein.m_rmsd.mRMSD class method) is_xyz_annotated() (fragmenstein.m_rmsd.mRMSD class method) items() (fragmenstein.monster.ExtendedFMCSMode method)

J

join_neighboring_mols() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) journal (fragmenstein.Monster attribute) (fragmenstein.Victor attribute) (fragmenstein.Victor.Monster attribute)

judge_n_move_on() (fragmenstein.monster.Unmerge method)

K

keep_copies() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method)

keep_copy() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) keys() (fragmenstein.monster.ExtendedFMCSMode method)

L

Laboratory (class in fragmenstein.laboratory) ligand_score() (fragmenstein.igor.Igor method) LINKER (fragmenstein.monster.BondProvenance attribute)

linker_atom_zahl (fragmenstein.Monster property) (fragmenstein.Victor.Monster property) linker_element (fragmenstein.Monster attribute) (fragmenstein.Victor.Monster attribute)

M

main() (in module fragmenstein.cli) MAIN_NOVEL (fragmenstein.monster.BondProvenance attribute) make_all_warhead_combinations() (fragmenstein.Victor class method) make_chimera() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) make_coordinate_constraints_for_combination() (fragmenstein.Victor method) make_coordinate_constraints_for_placement() (fragmenstein.Victor method) make_covalent() (fragmenstein.Victor class method) make_ideal_mol() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) make_ligand_only_pose() (fragmenstein.igor.Igor method) make_maps() (fragmenstein.monster.Unmerge class method) make_output_folder() (fragmenstein.Victor method) make_pse() (fragmenstein.Monster method) (fragmenstein.Victor method) (fragmenstein.Victor.Monster method) make_steps_pse() (fragmenstein.Victor method) matchChiralTag (fragmenstein.monster.ExtendedFMCSMode attribute) matched (fragmenstein.Monster property) (fragmenstein.Victor.Monster property) matchFormalCharge (fragmenstein.monster.ExtendedFMCSMode attribute) matching_modes (fragmenstein.Monster attribute) (fragmenstein.Victor.Monster attribute) matchStereo (fragmenstein.monster.ExtendedFMCSMode attribute) matchValences (fragmenstein.monster.ExtendedFMCSMode attribute) max_from_mol() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) max_strikes (fragmenstein.monster.Unmerge attribute) maxDistance (fragmenstein.monster.ExtendedFMCSMode attribute) maximizeBonds (fragmenstein.monster.ExtendedFMCSMode attribute)

measure_map() (fragmenstein.monster.Unmerge method) merge_pair() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) merge_pairing_lists() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) migrate_origin() (fragmenstein.m_rmsd.mRMSD class method) migrate_sw_origins() (fragmenstein.Victor method) MinimalPDBParser (class in fragmenstein.victor) minimize() (fragmenstein.igor.Igor method) mmff_minimize() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) MMFF_score() (fragmenstein.igor.Igor method) (fragmenstein.Monster method) (fragmenstein.Victor method) (fragmenstein.Victor.Monster method) mock() (fragmenstein.m_rmsd.mRMSD class method) module fragmenstein fragmenstein.branding fragmenstein.cli fragmenstein.display fragmenstein.igor.pyrosetta_import fragmenstein.m_rmsd mol_from_pose() (fragmenstein.igor.Igor method) Monster (class in fragmenstein) monster_average_position (fragmenstein.Victor attribute) monster_mmff_minisation (fragmenstein.Victor attribute) monster_throw_on_discard (fragmenstein.Victor attribute) MProVictor (class in fragmenstein) mRMSD (class in fragmenstein.m_rmsd) MultiVictorPlacement (class in fragmenstein)

N

no_blending() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method)

num_common (fragmenstein.Monster property) (fragmenstein.Victor.Monster property)

O

offness() (fragmenstein.monster.Unmerge method) offset() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) offset_connections() (fragmenstein.victor.MinimalPDBParser method) offset_serials() (fragmenstein.victor.MinimalPDBParser method)

origin_from_mol() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) ORIGINAL (fragmenstein.monster.BondProvenance attribute) OTHER_NOVEL (fragmenstein.monster.BondProvenance attribute) overannotate() (fragmenstein.m_rmsd.mRMSD class method)

P

parse() (fragmenstein.victor.MinimalPDBParser method) partial_blending() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) partially_blend_hits() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) per_atom_scores() (fragmenstein.igor.Igor method) percent_common (fragmenstein.Monster property) (fragmenstein.Victor.Monster property) pick (fragmenstein.monster.Unmerge attribute) pick_best() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) place() (fragmenstein.Monster method) (fragmenstein.MProVictor method) (fragmenstein.MultiVictorPlacement method) (fragmenstein.Victor method) (fragmenstein.Victor.Monster method) place_from_map() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) place_smiles() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) poised_pose_fx() (fragmenstein.MProVictor static method)

pop() (fragmenstein.monster.ExtendedFMCSMode method) popitem() (fragmenstein.monster.ExtendedFMCSMode method) pose (fragmenstein.igor.Igor attribute) pose2str() (fragmenstein.igor.Igor method) pose_fx() (fragmenstein.MProVictor static method) pose_mod_step() (fragmenstein.Victor method) possible_definitions (fragmenstein.Victor attribute) post_ff_addition_step() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) post_igor_step() (fragmenstein.Victor method) post_monster_step() (fragmenstein.Victor method) post_params_step() (fragmenstein.Victor method) posthoc_refine() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) pre_igor_step() (fragmenstein.Victor method) preminimized_mol (fragmenstein.Victor property) preminimized_undummied_mol (fragmenstein.Victor property) pretweak() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) print_coords() (fragmenstein.walton.Walton method) propagate_alternatives() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method)

Q

quick_reanimate() (fragmenstein.Victor method)

quick_reanimation (fragmenstein.Victor attribute)

R

read_postera() (in module fragmenstein.mpro.dataframe) reanimate() (fragmenstein.Victor method) reanimate_n_store() (fragmenstein.Victor method) rectify() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) refresh_nglview() (fragmenstein.walton.Walton method) relax_with_ED() (fragmenstein.igor.Igor class method) remove_other_hetatms (fragmenstein.Victor attribute) renumber_followup_custom_map() (fragmenstein.Monster static method) (fragmenstein.Victor.Monster static method)

repack_neighbors() (fragmenstein.igor.Igor method) residues_in_selector() (fragmenstein.igor.Igor method) residues_in_vector() (fragmenstein.igor.Igor method) retrieve_best_victor() (fragmenstein.MultiVictorPlacement method) retrieve_scores() (fragmenstein.MultiVictorPlacement method) ring_on_plane() (fragmenstein.walton.Walton method) ringCompare (fragmenstein.monster.ExtendedFMCSMode attribute) ringMatchesRingOnly (fragmenstein.monster.ExtendedFMCSMode attribute) rotate() (fragmenstein.walton.Walton method) rotational_approach (fragmenstein.monster.Unmerge attribute)

S

sample_new_conformation() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) save_commonality() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) save_temp() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) score_mol() (fragmenstein.Monster static method) (fragmenstein.Victor.Monster static method) score_split() (fragmenstein.igor.Igor method) seedSmarts (fragmenstein.monster.ExtendedFMCSMode attribute) set_all_bonds() (fragmenstein.monster.BondProvenance class method) set_bond() (fragmenstein.monster.BondProvenance class method) set_bonds() (fragmenstein.monster.BondProvenance class method) set_serial() (fragmenstein.victor.MinimalPDBParser method) setdefault() (fragmenstein.monster.ExtendedFMCSMode method) show() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) (fragmenstein.walton.Walton method) show3d() (fragmenstein.walton.Walton method)

show_comparison() (fragmenstein.Monster method) (fragmenstein.Victor method) (fragmenstein.Victor.Monster method) simply_merge_hits() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) slack_me() (fragmenstein.Victor class method) slugify() (fragmenstein.Victor class method) SpecialCompareAtoms (class in fragmenstein.monster) stdev_from_mol() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) store() (fragmenstein.monster.Unmerge method) store_origin_colors_atomically() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) store_positions() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) strict_matching_mode (fragmenstein.Monster attribute) (fragmenstein.Victor.Monster attribute) summarize() (fragmenstein.Victor method) superpose_by_map() (fragmenstein.walton.Walton method) superpose_by_mcs() (fragmenstein.walton.Walton method)

T

template_sorter_factory() (fragmenstein.monster.Unmerge method) tethered_relax() (fragmenstein.igor.Igor class method) threshold (fragmenstein.monster.ExtendedFMCSMode attribute) throw_on_discard (fragmenstein.Monster attribute) (fragmenstein.Victor.Monster attribute) timeout (fragmenstein.monster.ExtendedFMCSMode attribute) to_3Dmol() (fragmenstein.Monster method) (fragmenstein.Victor method) (fragmenstein.Victor.Monster method) to_nglview() (fragmenstein.Monster method) (fragmenstein.Victor method) (fragmenstein.Victor.Monster method) (fragmenstein.walton.Walton method)

to_simple_smiles() (fragmenstein.Victor static method) transfer_ring_data() (fragmenstein.Monster method) (fragmenstein.Victor.Monster method) transform() (fragmenstein.walton.Walton method) translate() (fragmenstein.walton.Walton method) translate_by_point() (fragmenstein.walton.Walton method) translate_parallel() (fragmenstein.walton.Walton method)

U

UNASSIGNED (fragmenstein.monster.BondProvenance attribute) unconstrained_heavy_atoms (fragmenstein.Victor property) Unmerge (class in fragmenstein.monster)

unmerge_inner() (fragmenstein.monster.Unmerge method) update() (fragmenstein.monster.ExtendedFMCSMode method) uses_pyrosetta (fragmenstein.Victor attribute)

V

validate() (fragmenstein.Victor method) values() (fragmenstein.monster.ExtendedFMCSMode method)

verbose (fragmenstein.monster.ExtendedFMCSMode attribute) Victor (class in fragmenstein) Victor.Monster (class in fragmenstein)

W

Walton (class in fragmenstein.walton)

warhead_definitions (fragmenstein.Victor attribute) work_path (fragmenstein.Victor attribute)

X

Xrepack_neighbors() (fragmenstein.igor.Igor method)

XYZ_BASED (fragmenstein.m_rmsd.mRMSD attribute)