fragmenstein package

Subpackages

• fragmenstein.monster package
  • Monster
    • Monster.MMFF_score()
    • Monster.__init__()
    • Monster.atoms_in_bridge_cutoff
    • Monster.by_expansion()
    • Monster.closeness_weights
    • Monster.collapse_mols()
    • Monster.collapse_ring()
    • Monster.combine()
    • Monster.convert_origins_to_custom_map()
    • Monster.cutoff
    • Monster.draw_nicely()
    • Monster.dummy
    • Monster.dummy_symbol
    • Monster.expand_custom_map()
    • Monster.expand_ring()
    • Monster.extract_atoms()
    • Monster.extract_from_neighborhood()
    • Monster.fix_custom_map()
    • Monster.fix_hits()
    • Monster.full_blending()
    • Monster.get_atom_map_fromProp()
    • Monster.get_best_scoring()
    • Monster.get_close_indices()
    • Monster.get_color_origins()
    • Monster.get_combined_rmsd()
    • Monster.get_hit_by_name()
    • Monster.get_largest_fragment()
    • Monster.get_legend()
    • Monster.get_mcs_mapping()
    • Monster.get_mcs_mappings()
    • Monster.get_neighborhood()
    • Monster.get_pair_rmsd()
    • Monster.get_positional_mapping()
    • Monster.guess_origins()
    • Monster.inspect_amide_torsions()
    • Monster.join_neighboring_mols()
    • Monster.journal
    • Monster.keep_copies()
    • Monster.keep_copy()
    • Monster.linker_atom_zahl
    • Monster.linker_element
    • Monster.make_chimera()
    • Monster.make_ideal_mol()
    • Monster.make_pse()
    • Monster.matched
    • Monster.matching_modes
    • Monster.max_from_mol()
    • Monster.merge_pair()
    • Monster.merge_pairing_lists()
    • Monster.mmff_minimize()
    • Monster.no_blending()
    • Monster.num_common
    • Monster.offset()
    • Monster.origin_from_mol()
    • Monster.partial_blending()
    • Monster.partially_blend_hits()
    • Monster.percent_common
    • Monster.pick_best()
    • Monster.place()
    • Monster.place_from_map()
    • Monster.place_smiles()
    • Monster.post_ff_addition_step()
    • Monster.posthoc_refine()
    • Monster.pretweak()
    • Monster.propagate_alternatives()
    • Monster.rectify()
    • Monster.renumber_followup_custom_map()
    • Monster.sample_new_conformation()
    • Monster.save_commonality()
    • Monster.save_temp()
    • Monster.score_mol()
    • Monster.show()
    • Monster.show_comparison()
    • Monster.simply_merge_hits()
    • Monster.stdev_from_mol()
    • Monster.store_origin_colors_atomically()
    • Monster.store_positions()
    • Monster.strict_matching_mode
    • Monster.throw_on_discard
    • Monster.to_3Dmol()
    • Monster.to_nglview()
    • Monster.transfer_ring_data()
  • fragmenstein.monster.bond_provenance module
    • BondProvenance
      • BondProvenance.LINKER
      • BondProvenance.MAIN_NOVEL
      • BondProvenance.ORIGINAL
      • BondProvenance.OTHER_NOVEL
      • BondProvenance.UNASSIGNED
      • BondProvenance.copy_bond()
      • BondProvenance.get_bond()
      • BondProvenance.get_bonds()
      • BondProvenance.has_bond()
      • BondProvenance.set_all_bonds()
      • BondProvenance.set_bond()
      • BondProvenance.set_bonds()
  • fragmenstein.monster.positional_mapping module
    • GPM
      • GPM.__init__()
      • GPM.cutoff
      • GPM.get_positional_mapping()
  • fragmenstein.monster.unmerge_mapper module
    • Unmerge
      • Unmerge.__init__()
      • Unmerge.bond()
      • Unmerge.calculate()
      • Unmerge.check_possible_distances()
      • Unmerge.cutoff
      • Unmerge.distance_cutoff
      • Unmerge.get_inter_distance()
      • Unmerge.get_key()
      • Unmerge.get_positional_mapping()
      • Unmerge.get_possible_map()
      • Unmerge.goodness_sorter_factory()
      • Unmerge.judge_n_move_on()
      • Unmerge.make_maps()
      • Unmerge.max_strikes
      • Unmerge.measure_map()
      • Unmerge.offness()
      • Unmerge.pick
      • Unmerge.rotational_approach
      • Unmerge.store()
      • Unmerge.template_sorter_factory()
      • Unmerge.unmerge_inner()
  • fragmenstein.monster.mcs_mapping module
    • SpecialCompareAtoms
      • SpecialCompareAtoms.CheckAtomCharge()
      • SpecialCompareAtoms.CheckAtomChirality()
      • SpecialCompareAtoms.CheckAtomRingMatch()
      • SpecialCompareAtoms.__init__()
      • SpecialCompareAtoms.fix_custom_map()
      • SpecialCompareAtoms.get_custom()
      • SpecialCompareAtoms.get_valid_matches()
    • IndexMap
      • IndexMap.__init__()
    • ExtendedFMCSMode
      • ExtendedFMCSMode.__init__()
      • ExtendedFMCSMode.atomCompare
      • ExtendedFMCSMode.bondCompare
      • ExtendedFMCSMode.clear()
      • ExtendedFMCSMode.completeRingsOnly
      • ExtendedFMCSMode.copy()
      • ExtendedFMCSMode.fromkeys()
      • ExtendedFMCSMode.get()
      • ExtendedFMCSMode.items()
      • ExtendedFMCSMode.keys()
      • ExtendedFMCSMode.matchChiralTag
      • ExtendedFMCSMode.matchFormalCharge
      • ExtendedFMCSMode.matchStereo
      • ExtendedFMCSMode.matchValences
      • ExtendedFMCSMode.maxDistance
      • ExtendedFMCSMode.maximizeBonds
      • ExtendedFMCSMode.pop()
      • ExtendedFMCSMode.popitem()
      • ExtendedFMCSMode.ringCompare
      • ExtendedFMCSMode.ringMatchesRingOnly
      • ExtendedFMCSMode.seedSmarts
      • ExtendedFMCSMode.setdefault()
      • ExtendedFMCSMode.threshold
      • ExtendedFMCSMode.timeout
      • ExtendedFMCSMode.update()
      • ExtendedFMCSMode.values()
      • ExtendedFMCSMode.verbose
• fragmenstein.igor package
  • Igor
    • Igor.MMFF_score()
    • Igor.Xrepack_neighbors()
    • Igor.__init__()
    • Igor.add_constraint_file()
    • Igor.angle_constraint
    • Igor.atom_pair_constraint
    • Igor.constraint_file
    • Igor.coordinate_constraint
    • Igor.detailed_scores()
    • Igor.display_energy()
    • Igor.dock()
    • Igor.download_map()
    • Igor.fa_intra_rep
    • Igor.fix_scorefxn_weights()
    • Igor.from_pdbblock()
    • Igor.from_pdbfile()
    • Igor.get_MinMover()
    • Igor.get_PertMinMover()
    • Igor.get_mod_FastRelax()
    • Igor.get_old_FastRelax()
    • Igor.init_pyrosetta()
    • Igor.ligand_score()
    • Igor.make_ligand_only_pose()
    • Igor.minimize()
    • Igor.mol_from_pose()
    • Igor.per_atom_scores()
    • Igor.pose
    • Igor.pose2str()
    • Igor.relax_with_ED()
    • Igor.repack_neighbors()
    • Igor.residues_in_selector()
    • Igor.residues_in_vector()
    • Igor.score_split()
    • Igor.tethered_relax()
  • fragmenstein.igor.pyrosetta_import submodule
• fragmenstein.victor package
  • Victor
    • Victor.MMFF_score()
    • Victor.Monster
      • Victor.Monster.MMFF_score()
      • Victor.Monster.__init__()
      • Victor.Monster.atoms_in_bridge_cutoff
      • Victor.Monster.by_expansion()
      • Victor.Monster.closeness_weights
      • Victor.Monster.collapse_mols()
      • Victor.Monster.collapse_ring()
      • Victor.Monster.combine()
      • Victor.Monster.convert_origins_to_custom_map()
      • Victor.Monster.custom_map
      • Victor.Monster.cutoff
      • Victor.Monster.draw_nicely()
      • Victor.Monster.dummy
      • Victor.Monster.dummy_symbol
      • Victor.Monster.expand_custom_map()
      • Victor.Monster.expand_ring()
      • Victor.Monster.extract_atoms()
      • Victor.Monster.extract_from_neighborhood()
      • Victor.Monster.fix_custom_map()
      • Victor.Monster.fix_hits()
      • Victor.Monster.full_blending()
      • Victor.Monster.get_atom_map_fromProp()
      • Victor.Monster.get_best_scoring()
      • Victor.Monster.get_close_indices()
      • Victor.Monster.get_color_origins()
      • Victor.Monster.get_combined_rmsd()
      • Victor.Monster.get_hit_by_name()
      • Victor.Monster.get_largest_fragment()
      • Victor.Monster.get_legend()
      • Victor.Monster.get_mcs_mapping()
      • Victor.Monster.get_mcs_mappings()
      • Victor.Monster.get_neighborhood()
      • Victor.Monster.get_pair_rmsd()
      • Victor.Monster.get_positional_mapping()
      • Victor.Monster.guess_origins()
      • Victor.Monster.inspect_amide_torsions()
      • Victor.Monster.join_neighboring_mols()
      • Victor.Monster.journal
      • Victor.Monster.keep_copies()
      • Victor.Monster.keep_copy()
      • Victor.Monster.linker_atom_zahl
      • Victor.Monster.linker_element
      • Victor.Monster.make_chimera()
      • Victor.Monster.make_ideal_mol()
      • Victor.Monster.make_pse()
      • Victor.Monster.matched
      • Victor.Monster.matching_modes
      • Victor.Monster.max_from_mol()
      • Victor.Monster.merge_pair()
      • Victor.Monster.merge_pairing_lists()
      • Victor.Monster.mmff_minimize()
      • Victor.Monster.no_blending()
      • Victor.Monster.num_common
      • Victor.Monster.offset()
      • Victor.Monster.origin_from_mol()
      • Victor.Monster.partial_blending()
      • Victor.Monster.partially_blend_hits()
      • Victor.Monster.percent_common
      • Victor.Monster.pick_best()
      • Victor.Monster.place()
      • Victor.Monster.place_from_map()
      • Victor.Monster.place_smiles()
      • Victor.Monster.post_ff_addition_step()
      • Victor.Monster.posthoc_refine()
      • Victor.Monster.pretweak()
      • Victor.Monster.propagate_alternatives()
      • Victor.Monster.rectify()
      • Victor.Monster.renumber_followup_custom_map()
      • Victor.Monster.sample_new_conformation()
      • Victor.Monster.save_commonality()
      • Victor.Monster.save_temp()
      • Victor.Monster.score_mol()
      • Victor.Monster.show()
      • Victor.Monster.show_comparison()
      • Victor.Monster.simply_merge_hits()
      • Victor.Monster.stdev_from_mol()
      • Victor.Monster.store_origin_colors_atomically()
      • Victor.Monster.store_positions()
      • Victor.Monster.strict_matching_mode
      • Victor.Monster.throw_on_discard
      • Victor.Monster.to_3Dmol()
      • Victor.Monster.to_nglview()
      • Victor.Monster.transfer_ring_data()
    • Victor.__init__()
    • Victor.add_constraint_to_warhead()
    • Victor.add_extra_constraint()
    • Victor.calculate_score()
    • Victor.capture_logs()
    • Victor.capture_rdkit_log()
    • Victor.capture_rosetta_log()
    • Victor.checkpoint()
    • Victor.closest_hit()
    • Victor.combine()
    • Victor.constrained_atoms
    • Victor.constraint_function_type
    • Victor.copy_names()
    • Victor.covalent_definitions
    • Victor.distance_hits()
    • Victor.dock()
    • Victor.draw_nicely()
    • Victor.enable_logfile()
    • Victor.enable_stdout()
    • Victor.error_to_catch
    • Victor.extract_mol()
    • Victor.extract_mols()
    • Victor.find_closest_to_ligand()
    • Victor.from_files()
    • Victor.get_isomers()
    • Victor.get_isomers_smiles()
    • Victor.get_plip_interactions()
    • Victor.get_warhead_definition()
    • Victor.guess_warhead()
    • Victor.harmonize_warheads()
    • Victor.inventorize_warheads()
    • Victor.journal
    • Victor.make_all_warhead_combinations()
    • Victor.make_coordinate_constraints_for_combination()
    • Victor.make_coordinate_constraints_for_placement()
    • Victor.make_covalent()
    • Victor.make_output_folder()
    • Victor.make_pse()
    • Victor.make_steps_pse()
    • Victor.migrate_sw_origins()
    • Victor.monster_average_position
    • Victor.monster_mmff_minisation
    • Victor.monster_throw_on_discard
    • Victor.place()
    • Victor.pose_mod_step()
    • Victor.possible_definitions
    • Victor.post_igor_step()
    • Victor.post_monster_step()
    • Victor.post_params_step()
    • Victor.pre_igor_step()
    • Victor.preminimized_mol
    • Victor.preminimized_undummied_mol
    • Victor.quick_reanimate()
    • Victor.quick_reanimation
    • Victor.reanimate()
    • Victor.reanimate_n_store()
    • Victor.remove_other_hetatms
    • Victor.show_comparison()
    • Victor.slack_me()
    • Victor.slugify()
    • Victor.summarize()
    • Victor.to_3Dmol()
    • Victor.to_nglview()
    • Victor.to_simple_smiles()
    • Victor.unconstrained_heavy_atoms
    • Victor.uses_pyrosetta
    • Victor.validate()
    • Victor.warhead_definitions
    • Victor.work_path
  • MinimalPDBParser
    • MinimalPDBParser.__init__()
    • MinimalPDBParser.append()
    • MinimalPDBParser.get_atomname()
    • MinimalPDBParser.get_chain()
    • MinimalPDBParser.get_max_serial()
    • MinimalPDBParser.get_residue_index()
    • MinimalPDBParser.get_residue_name()
    • MinimalPDBParser.get_serial()
    • MinimalPDBParser.has_residue_index()
    • MinimalPDBParser.has_residue_name()
    • MinimalPDBParser.offset_connections()
    • MinimalPDBParser.offset_serials()
    • MinimalPDBParser.parse()
    • MinimalPDBParser.set_serial()
• fragmenstein.walton package
  • Walton
    • Walton.__init__()
    • Walton.atom_on_axis()
    • Walton.atom_on_plane()
    • Walton.atom_to_origin()
    • Walton.color_in()
    • Walton.color_scales
    • Walton.create_polygon()
    • Walton.duplicate()
    • Walton.experimental_rotate()
    • Walton.flatten_trio()
    • Walton.from_smiles()
    • Walton.get_centroid_of_atoms()
    • Walton.get_centroid_of_ring()
    • Walton.get_mol()
    • Walton.get_point()
    • Walton.get_ring_radius()
    • Walton.print_coords()
    • Walton.refresh_nglview()
    • Walton.ring_on_plane()
    • Walton.rotate()
    • Walton.show()
    • Walton.show3d()
    • Walton.superpose_by_map()
    • Walton.superpose_by_mcs()
    • Walton.to_nglview()
    • Walton.transform()
    • Walton.translate()
    • Walton.translate_by_point()
    • Walton.translate_parallel()
• MultiVictorPlacement class
  • MultiVictorPlacement
    • MultiVictorPlacement.__init__()
    • MultiVictorPlacement.place()
    • MultiVictorPlacement.retrieve_best_victor()
    • MultiVictorPlacement.retrieve_scores()
• fragmenstein.laboratory package
  • Laboratory
• fragmenstein.mpro package
  • MProVictor
    • MProVictor.__init__()
    • MProVictor.analyse_postera()
    • MProVictor.constraint_function_type
    • MProVictor.fetch_postera()
    • MProVictor.from_hit_codes()
    • MProVictor.from_postera_row()
    • MProVictor.place()
    • MProVictor.poised_pose_fx()
    • MProVictor.pose_fx()
  • fetch_postera()
  • read_postera()
• fragmenstein.cli package
  • main()
• fragmenstein.branding submodule
  • Module contents
• fragmenstein.m_rmsd submodule
  • Module contents
    • mRMSD
      • mRMSD.HIT_BASED
      • mRMSD.IDENTITY_BASED
      • mRMSD.XYZ_BASED
      • mRMSD.__init__()
      • mRMSD.calculate_msd()
      • mRMSD.calculate_rmsd()
      • mRMSD.copy_all_possible_origins()
      • mRMSD.copy_origins()
      • mRMSD.from_annotated_mols()
      • mRMSD.from_internal_xyz()
      • mRMSD.from_other_annotated_mols()
      • mRMSD.from_unannotated_mols()
      • mRMSD.from_unannotated_same_mols()
      • mRMSD.generate_overlap_mapping()
      • mRMSD.is_origin_annotated()
      • mRMSD.is_xyz_annotated()
      • mRMSD.migrate_origin()
      • mRMSD.mock()
      • mRMSD.overannotate()
• fragmenstein.branding submodule
  • Module contents
    • color_in()
    • display_mols()

Module contents

See GitHub documentation