Index A | B | C | D | E | F | G | I | L | M | N | P | R | S | T A align_modeller() (in module prepmd.align_together) align_together() (in module prepmd.align_together) B best_fit_transform() (in module prepmd.lib.icp) C check_platforms() (in module prepmd.run) create_ligand_system() (in module prepmd.ligand) D describeNextReport() (prepmd.metadynamics.RMSDReporter method) dist() (in module prepmd.analysis) E entry_point() (in module prepmd.add_modeller_license) (in module prepmd.align_together) (in module prepmd.prep) (in module prepmd.run) F fasta() (in module prepmd.model) fix() (in module prepmd.fix) fix_missing_residues() (in module prepmd.model) fix_nonstandard_cif() (in module prepmd.fix) G get_alignment_info() (in module prepmd.model) get_best_pdb() (in module prepmd.model) get_em_map() (in module prepmd.download) get_ends_deletion() (in module prepmd.align_together) get_fullseq_pdb() (in module prepmd.get_residues) get_gaps() (in module prepmd.align_together) get_ligand_centroid_traj() (in module prepmd.analysis) get_objective_functions() (in module prepmd.model) get_representative_rmsd_frames() (in module prepmd.metadynamics) get_residues_pdb() (in module prepmd.get_residues) get_selection_traj() (in module prepmd.analysis) get_structure() (in module prepmd.download) get_uniprot_sequence() (in module prepmd.download) I icp() (in module prepmd.lib.icp) id_generator() (in module prepmd.prep) is_residue() (in module prepmd.util) is_residue_sequence() (in module prepmd.util) L load_universe() (in module prepmd.ligand) M make_forcefield() (in module prepmd.run) mark_innermost_gap() (in module prepmd.align_together) mark_missing_ends() (in module prepmd.align_together) module prepmd prepmd.add_modeller_license prepmd.align_together prepmd.analysis prepmd.download prepmd.fix prepmd.get_residues prepmd.lib prepmd.lib.icp prepmd.lib.mdaCIF prepmd.ligand prepmd.metadynamics prepmd.model prepmd.pdb2pqr prepmd.point_cloud prepmd.prep prepmd.run prepmd.util N nearest_neighbor() (in module prepmd.lib.icp) P pdb_back_to_mmcif() (in module prepmd.ligand) prep() (in module prepmd.prep) prepmd module prepmd.add_modeller_license module prepmd.align_together module prepmd.analysis module prepmd.download module prepmd.fix module prepmd.get_residues module prepmd.lib module prepmd.lib.icp module prepmd.lib.mdaCIF module prepmd.ligand module prepmd.metadynamics module prepmd.model module prepmd.pdb2pqr module prepmd.point_cloud module prepmd.prep module prepmd.run module prepmd.util module print_mask() (in module prepmd.align_together) R remove_from_model() (in module prepmd.align_together) remove_hetatms_unk() (in module prepmd.fix) report() (prepmd.metadynamics.RMSDReporter method) restore_metadata_pdb() (in module prepmd.fix) retitle_alignment() (in module prepmd.model) RMSDIncrease RMSDReporter (class in prepmd.metadynamics) run() (in module prepmd.run) run_pdb2pqr() (in module prepmd.pdb2pqr) S score_pdb_map() (in module prepmd.point_cloud) setup_license() (in module prepmd.add_modeller_license) solvate_openff() (in module prepmd.ligand) split_pdb_ligand() (in module prepmd.ligand) StopSimulation T test_sim() (in module prepmd.run) three_to_one() (in module prepmd.util) three_to_one_sequence() (in module prepmd.util) to_point_cloud() (in module prepmd.point_cloud)