fragmenstein package
Subpackages
- fragmenstein.monster package
MonsterMonster.MMFF_score()Monster.__init__()Monster.atoms_in_bridge_cutoffMonster.by_expansion()Monster.closeness_weightsMonster.collapse_mols()Monster.collapse_ring()Monster.combine()Monster.convert_origins_to_custom_map()Monster.cutoffMonster.draw_nicely()Monster.dummyMonster.dummy_symbolMonster.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.journalMonster.keep_copies()Monster.keep_copy()Monster.linker_atom_zahlMonster.linker_elementMonster.make_chimera()Monster.make_ideal_mol()Monster.make_pse()Monster.matchedMonster.matching_modesMonster.max_from_mol()Monster.merge_pair()Monster.merge_pairing_lists()Monster.mmff_minimize()Monster.no_blending()Monster.num_commonMonster.offset()Monster.origin_from_mol()Monster.partial_blending()Monster.partially_blend_hits()Monster.percent_commonMonster.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_modeMonster.throw_on_discardMonster.to_3Dmol()Monster.to_nglview()Monster.transfer_ring_data()
- fragmenstein.monster.bond_provenance module
BondProvenanceBondProvenance.LINKERBondProvenance.MAIN_NOVELBondProvenance.ORIGINALBondProvenance.OTHER_NOVELBondProvenance.UNASSIGNEDBondProvenance.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
- fragmenstein.monster.unmerge_mapper module
UnmergeUnmerge.__init__()Unmerge.bond()Unmerge.calculate()Unmerge.check_possible_distances()Unmerge.cutoffUnmerge.distance_cutoffUnmerge.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_strikesUnmerge.measure_map()Unmerge.offness()Unmerge.pickUnmerge.rotational_approachUnmerge.store()Unmerge.template_sorter_factory()Unmerge.unmerge_inner()
- fragmenstein.monster.mcs_mapping module
SpecialCompareAtomsIndexMapExtendedFMCSModeExtendedFMCSMode.__init__()ExtendedFMCSMode.atomCompareExtendedFMCSMode.bondCompareExtendedFMCSMode.clear()ExtendedFMCSMode.completeRingsOnlyExtendedFMCSMode.copy()ExtendedFMCSMode.fromkeys()ExtendedFMCSMode.get()ExtendedFMCSMode.items()ExtendedFMCSMode.keys()ExtendedFMCSMode.matchChiralTagExtendedFMCSMode.matchFormalChargeExtendedFMCSMode.matchStereoExtendedFMCSMode.matchValencesExtendedFMCSMode.maxDistanceExtendedFMCSMode.maximizeBondsExtendedFMCSMode.pop()ExtendedFMCSMode.popitem()ExtendedFMCSMode.ringCompareExtendedFMCSMode.ringMatchesRingOnlyExtendedFMCSMode.seedSmartsExtendedFMCSMode.setdefault()ExtendedFMCSMode.thresholdExtendedFMCSMode.timeoutExtendedFMCSMode.update()ExtendedFMCSMode.values()ExtendedFMCSMode.verbose
- fragmenstein.igor package
IgorIgor.MMFF_score()Igor.Xrepack_neighbors()Igor.__init__()Igor.add_constraint_file()Igor.angle_constraintIgor.atom_pair_constraintIgor.constraint_fileIgor.coordinate_constraintIgor.detailed_scores()Igor.display_energy()Igor.dock()Igor.download_map()Igor.fa_intra_repIgor.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.poseIgor.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
VictorVictor.MMFF_score()Victor.MonsterVictor.Monster.MMFF_score()Victor.Monster.__init__()Victor.Monster.atoms_in_bridge_cutoffVictor.Monster.by_expansion()Victor.Monster.closeness_weightsVictor.Monster.collapse_mols()Victor.Monster.collapse_ring()Victor.Monster.combine()Victor.Monster.convert_origins_to_custom_map()Victor.Monster.custom_mapVictor.Monster.cutoffVictor.Monster.draw_nicely()Victor.Monster.dummyVictor.Monster.dummy_symbolVictor.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.journalVictor.Monster.keep_copies()Victor.Monster.keep_copy()Victor.Monster.linker_atom_zahlVictor.Monster.linker_elementVictor.Monster.make_chimera()Victor.Monster.make_ideal_mol()Victor.Monster.make_pse()Victor.Monster.matchedVictor.Monster.matching_modesVictor.Monster.max_from_mol()Victor.Monster.merge_pair()Victor.Monster.merge_pairing_lists()Victor.Monster.mmff_minimize()Victor.Monster.no_blending()Victor.Monster.num_commonVictor.Monster.offset()Victor.Monster.origin_from_mol()Victor.Monster.partial_blending()Victor.Monster.partially_blend_hits()Victor.Monster.percent_commonVictor.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_modeVictor.Monster.throw_on_discardVictor.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_atomsVictor.constraint_function_typeVictor.copy_names()Victor.covalent_definitionsVictor.distance_hits()Victor.dock()Victor.draw_nicely()Victor.enable_logfile()Victor.enable_stdout()Victor.error_to_catchVictor.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.journalVictor.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_positionVictor.monster_mmff_minisationVictor.monster_throw_on_discardVictor.place()Victor.pose_mod_step()Victor.possible_definitionsVictor.post_igor_step()Victor.post_monster_step()Victor.post_params_step()Victor.pre_igor_step()Victor.preminimized_molVictor.preminimized_undummied_molVictor.quick_reanimate()Victor.quick_reanimationVictor.reanimate()Victor.reanimate_n_store()Victor.remove_other_hetatmsVictor.show_comparison()Victor.slack_me()Victor.slugify()Victor.summarize()Victor.to_3Dmol()Victor.to_nglview()Victor.to_simple_smiles()Victor.unconstrained_heavy_atomsVictor.uses_pyrosettaVictor.validate()Victor.warhead_definitionsVictor.work_path
MinimalPDBParserMinimalPDBParser.__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
WaltonWalton.__init__()Walton.atom_on_axis()Walton.atom_on_plane()Walton.atom_to_origin()Walton.color_in()Walton.color_scalesWalton.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
- fragmenstein.laboratory package
- fragmenstein.mpro package
- fragmenstein.cli package
- fragmenstein.branding submodule
- fragmenstein.m_rmsd submodule
- Module contents
mRMSDmRMSD.HIT_BASEDmRMSD.IDENTITY_BASEDmRMSD.XYZ_BASEDmRMSD.__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()
- Module contents
- fragmenstein.branding submodule
Module contents
See GitHub documentation