Index

_

__init__() (molsysmt.form.biopython_Seq.TopologyIterator method) (molsysmt.form.biopython_SeqRecord.TopologyIterator method) (molsysmt.form.file_bcif.StructuresIterator method) (molsysmt.form.file_bcif.TopologyIterator method) (molsysmt.form.file_bcif_gz.StructuresIterator method) (molsysmt.form.file_bcif_gz.TopologyIterator method) (molsysmt.form.file_cif.StructuresIterator method) (molsysmt.form.file_cif.TopologyIterator method) (molsysmt.form.file_crd.StructuresIterator method) (molsysmt.form.file_crd.TopologyIterator method) (molsysmt.form.file_dcd.StructuresIterator method) (molsysmt.form.file_gro.StructuresIterator method) (molsysmt.form.file_gro.TopologyIterator method) (molsysmt.form.file_h5.StructuresIterator method) (molsysmt.form.file_h5.TopologyIterator method) (molsysmt.form.file_h5msm.StructuresIterator method) (molsysmt.form.file_h5msm.TopologyIterator method) (molsysmt.form.file_inpcrd.StructuresIterator method) (molsysmt.form.file_mol2.StructuresIterator method) (molsysmt.form.file_mol2.TopologyIterator method) (molsysmt.form.file_pdb.StructuresIterator method) (molsysmt.form.file_pdb.TopologyIterator method) (molsysmt.form.file_prmtop.StructuresIterator method) (molsysmt.form.file_prmtop.TopologyIterator method) (molsysmt.form.file_psf.TopologyIterator method) (molsysmt.form.file_trjpk.StructuresIterator method) (molsysmt.form.file_xtc.StructuresIterator method) (molsysmt.form.file_xyznpy.StructuresIterator method) (molsysmt.form.MDAnalysis_Topology.TopologyIterator method) (molsysmt.form.MDAnalysis_Universe.StructuresIterator method) (molsysmt.form.MDAnalysis_Universe.TopologyIterator method) (molsysmt.form.mdtraj_DCDTrajectoryFile.StructuresIterator method) (molsysmt.form.mdtraj_HDF5TrajectoryFile.StructuresIterator method) (molsysmt.form.mdtraj_HDF5TrajectoryFile.TopologyIterator method) (molsysmt.form.mdtraj_Topology.TopologyIterator method) (molsysmt.form.mdtraj_Trajectory.StructuresIterator method) (molsysmt.form.mdtraj_Trajectory.TopologyIterator method) (molsysmt.form.mdtraj_XTCTrajectoryFile.StructuresIterator method) (molsysmt.form.mmcif_PdbxContainers_DataContainer.StructuresIterator method) (molsysmt.form.mmcif_PdbxContainers_DataContainer.TopologyIterator method) (molsysmt.form.molsysmt_CIFFileHandler.StructuresIterator method) (molsysmt.form.molsysmt_CIFFileHandler.TopologyIterator method) (molsysmt.form.molsysmt_GROFileHandler.StructuresIterator method) (molsysmt.form.molsysmt_GROFileHandler.TopologyIterator method) (molsysmt.form.molsysmt_H5MSMFileHandler.StructuresIterator method) (molsysmt.form.molsysmt_MolSys.StructuresIterator method) (molsysmt.form.molsysmt_MolSys.TopologyIterator method) (molsysmt.form.molsysmt_Structures.StructuresIterator method) (molsysmt.form.molsysmt_StructuresDict.StructuresIterator method) (molsysmt.form.molsysmt_Topology.TopologyIterator method) (molsysmt.form.networkx_Graph.TopologyIterator method) (molsysmt.form.nglview_NGLWidget.StructuresIterator method) (molsysmt.form.nglview_NGLWidget.TopologyIterator method) (molsysmt.form.openmm_AmberInpcrdFile.StructuresIterator method) (molsysmt.form.openmm_AmberPrmtopFile.TopologyIterator method) (molsysmt.form.openmm_CharmmCrdFile.StructuresIterator method) (molsysmt.form.openmm_CharmmCrdFile.TopologyIterator method) (molsysmt.form.openmm_CharmmPsfFile.StructuresIterator method) (molsysmt.form.openmm_CharmmPsfFile.TopologyIterator method) (molsysmt.form.openmm_Context.StructuresIterator method) (molsysmt.form.openmm_Context.TopologyIterator method) (molsysmt.form.openmm_GromacsGroFile.StructuresIterator method) (molsysmt.form.openmm_GromacsGroFile.TopologyIterator method) (molsysmt.form.openmm_GromacsTopFile.TopologyIterator method) (molsysmt.form.openmm_Modeller.StructuresIterator method) (molsysmt.form.openmm_Modeller.TopologyIterator method) (molsysmt.form.openmm_PDBFile.StructuresIterator method) (molsysmt.form.openmm_PDBFile.TopologyIterator method) (molsysmt.form.openmm_Simulation.StructuresIterator method) (molsysmt.form.openmm_Simulation.TopologyIterator method) (molsysmt.form.openmm_State.StructuresIterator method) (molsysmt.form.openmm_State.TopologyIterator method) (molsysmt.form.openmm_System.StructuresIterator method) (molsysmt.form.openmm_System.TopologyIterator method) (molsysmt.form.openmm_Topology.TopologyIterator method) (molsysmt.form.parmed_Structure.StructuresIterator method) (molsysmt.form.parmed_Structure.TopologyIterator method) (molsysmt.form.pdbfixer_PDBFixer.StructuresIterator method) (molsysmt.form.pdbfixer_PDBFixer.TopologyIterator method) (molsysmt.form.pytraj_Topology.StructuresIterator method) (molsysmt.form.pytraj_Topology.TopologyIterator method) (molsysmt.form.pytraj_Trajectory.StructuresIterator method) (molsysmt.form.pytraj_Trajectory.TopologyIterator method) (molsysmt.form.string_alphafold_id.StructuresIterator method) (molsysmt.form.string_alphafold_id.TopologyIterator method) (molsysmt.form.string_amino_acids_1.TopologyIterator method) (molsysmt.form.string_amino_acids_3.TopologyIterator method) (molsysmt.form.string_pdb_id.StructuresIterator method) (molsysmt.form.string_pdb_id.TopologyIterator method) (molsysmt.form.string_pdb_text.StructuresIterator method) (molsysmt.form.string_pdb_text.TopologyIterator method) (molsysmt.form.XYZ.StructuresIterator method) (molsysmt.form.XYZ.TopologyIterator method) (molsysmt.third_party.openmm.reporters.H5MSMReporter method) (molsysmt.third_party.openmm.reporters.StructuresDictReporter method) (molsysmt.third_party.openmm.reporters.TQDMReporter method)

A

add() (in module molsysmt.basic) (in module molsysmt.form.biopython_Seq) (in module molsysmt.form.biopython_SeqRecord) (in module molsysmt.form.file_bcif) (in module molsysmt.form.file_bcif_gz) (in module molsysmt.form.file_cif) (in module molsysmt.form.file_crd) (in module molsysmt.form.file_dcd) (in module molsysmt.form.file_gro) (in module molsysmt.form.file_h5) (in module molsysmt.form.file_h5msm) (in module molsysmt.form.file_inpcrd) (in module molsysmt.form.file_mol2) (in module molsysmt.form.file_pdb) (in module molsysmt.form.file_prmtop) (in module molsysmt.form.file_psf) (in module molsysmt.form.file_trjpk) (in module molsysmt.form.file_xtc) (in module molsysmt.form.file_xyznpy) (in module molsysmt.form.MDAnalysis_Topology) (in module molsysmt.form.MDAnalysis_Universe) (in module molsysmt.form.mdtraj_DCDTrajectoryFile) (in module molsysmt.form.mdtraj_HDF5TrajectoryFile) (in module molsysmt.form.mdtraj_Topology) (in module molsysmt.form.mdtraj_Trajectory) (in module molsysmt.form.mdtraj_XTCTrajectoryFile) (in module molsysmt.form.mmcif_PdbxContainers_DataContainer) (in module molsysmt.form.molsysmt_CIFFileHandler) (in module molsysmt.form.molsysmt_GROFileHandler) (in module molsysmt.form.molsysmt_H5MSMFileHandler) (in module molsysmt.form.molsysmt_MolecularMechanics) (in module molsysmt.form.molsysmt_MolecularMechanicsDict) (in module molsysmt.form.molsysmt_MolSys) (in module molsysmt.form.molsysmt_PDBFileHandler) (in module molsysmt.form.molsysmt_Structures) (in module molsysmt.form.molsysmt_StructuresDict) (in module molsysmt.form.molsysmt_Topology) (in module molsysmt.form.networkx_Graph) (in module molsysmt.form.nglview_NGLWidget) (in module molsysmt.form.openmm_AmberInpcrdFile) (in module molsysmt.form.openmm_AmberPrmtopFile) (in module molsysmt.form.openmm_CharmmCrdFile) (in module molsysmt.form.openmm_CharmmPsfFile) (in module molsysmt.form.openmm_Context) (in module molsysmt.form.openmm_GromacsGroFile) (in module molsysmt.form.openmm_GromacsTopFile) (in module molsysmt.form.openmm_Modeller) (in module molsysmt.form.openmm_PDBFile) (in module molsysmt.form.openmm_Simulation) (in module molsysmt.form.openmm_State) (in module molsysmt.form.openmm_System) (in module molsysmt.form.openmm_Topology) (in module molsysmt.form.parmed_Structure) (in module molsysmt.form.pdbfixer_PDBFixer) (in module molsysmt.form.pytraj_Topology) (in module molsysmt.form.pytraj_Trajectory) (in module molsysmt.form.string_alphafold_id) (in module molsysmt.form.string_amino_acids_1) (in module molsysmt.form.string_amino_acids_3) (in module molsysmt.form.string_pdb_id) (in module molsysmt.form.string_pdb_text) (in module molsysmt.form.XYZ) add_allowed_plane_region() (in module molsysmt.third_party.openmm.forces) add_allowed_z_region() (in module molsysmt.third_party.openmm.forces) add_arrows() (in module molsysmt.third_party.nglview) add_bonds() (in module molsysmt.form.molsysmt_MolSys) add_constant_force() (in module molsysmt.third_party.openmm.forces) add_contacts() (in module molsysmt.third_party.nglview) add_cylinders() (in module molsysmt.third_party.nglview) add_forbidden_plane_region() (in module molsysmt.third_party.openmm.forces) add_forbidden_z_region() (in module molsysmt.third_party.openmm.forces)

add_harmonic_bond_force() (in module molsysmt.third_party.openmm.forces) add_hbonds() (in module molsysmt.third_party.nglview) add_missing_bonds() (in module molsysmt.build) add_missing_heavy_atoms() (in module molsysmt.build) add_missing_hydrogens() (in module molsysmt.build) add_missing_terminal_cappings() (in module molsysmt.build) add_plane_harmonic_restraint() (in module molsysmt.third_party.openmm.forces) add_point_harmonic_restraint() (in module molsysmt.third_party.openmm.forces) align_principal_axes() (in module molsysmt.structure) append_structures() (in module molsysmt.basic) (in module molsysmt.form.file_bcif) (in module molsysmt.form.file_bcif_gz) (in module molsysmt.form.file_cif) (in module molsysmt.form.file_crd) (in module molsysmt.form.file_dcd) (in module molsysmt.form.file_gro) (in module molsysmt.form.file_h5) (in module molsysmt.form.file_h5msm) (in module molsysmt.form.file_inpcrd) (in module molsysmt.form.file_mol2) (in module molsysmt.form.file_pdb) (in module molsysmt.form.file_prmtop) (in module molsysmt.form.file_psf) (in module molsysmt.form.file_trjpk) (in module molsysmt.form.file_xtc) (in module molsysmt.form.file_xyznpy) (in module molsysmt.form.MDAnalysis_Topology) (in module molsysmt.form.MDAnalysis_Universe) (in module molsysmt.form.mdtraj_DCDTrajectoryFile) (in module molsysmt.form.mdtraj_HDF5TrajectoryFile) (in module molsysmt.form.mdtraj_Topology) (in module molsysmt.form.mdtraj_Trajectory) (in module molsysmt.form.mdtraj_XTCTrajectoryFile) (in module molsysmt.form.mmcif_PdbxContainers_DataContainer) (in module molsysmt.form.molsysmt_CIFFileHandler) (in module molsysmt.form.molsysmt_GROFileHandler) (in module molsysmt.form.molsysmt_H5MSMFileHandler) (in module molsysmt.form.molsysmt_MolecularMechanics) (in module molsysmt.form.molsysmt_MolecularMechanicsDict) (in module molsysmt.form.molsysmt_MolSys) (in module molsysmt.form.molsysmt_PDBFileHandler) (in module molsysmt.form.molsysmt_Structures) (in module molsysmt.form.molsysmt_StructuresDict) (in module molsysmt.form.molsysmt_Topology) (in module molsysmt.form.networkx_Graph) (in module molsysmt.form.nglview_NGLWidget) (in module molsysmt.form.openmm_AmberInpcrdFile) (in module molsysmt.form.openmm_AmberPrmtopFile) (in module molsysmt.form.openmm_CharmmCrdFile) (in module molsysmt.form.openmm_CharmmPsfFile) (in module molsysmt.form.openmm_Context) (in module molsysmt.form.openmm_GromacsGroFile) (in module molsysmt.form.openmm_GromacsTopFile) (in module molsysmt.form.openmm_Modeller) (in module molsysmt.form.openmm_PDBFile) (in module molsysmt.form.openmm_Simulation) (in module molsysmt.form.openmm_State) (in module molsysmt.form.openmm_System) (in module molsysmt.form.openmm_Topology) (in module molsysmt.form.parmed_Structure) (in module molsysmt.form.pdbfixer_PDBFixer) (in module molsysmt.form.pytraj_Topology) (in module molsysmt.form.pytraj_Trajectory) (in module molsysmt.form.string_alphafold_id) (in module molsysmt.form.string_amino_acids_1) (in module molsysmt.form.string_amino_acids_3) (in module molsysmt.form.string_pdb_id) (in module molsysmt.form.string_pdb_text) (in module molsysmt.form.XYZ) are_multiple_molecular_systems() (in module molsysmt.basic) available_platforms() (in module molsysmt.third_party.openmm.platforms)

B

build_peptide() (in module molsysmt.build)

C

center() (in module molsysmt.structure) clear() (in module molsysmt.third_party.nglview) compare() (in module molsysmt.basic) concatenate_structures() (in module molsysmt.basic) contains() (in module molsysmt.basic) convert() (in module molsysmt.basic) copy() (in module molsysmt.basic) (in module molsysmt.form.biopython_Seq) (in module molsysmt.form.file_bcif) (in module molsysmt.form.file_bcif_gz) (in module molsysmt.form.file_cif) (in module molsysmt.form.file_crd) (in module molsysmt.form.file_dcd) (in module molsysmt.form.file_gro) (in module molsysmt.form.file_h5) (in module molsysmt.form.file_h5msm) (in module molsysmt.form.file_inpcrd) (in module molsysmt.form.file_mol2) (in module molsysmt.form.file_pdb) (in module molsysmt.form.file_prmtop) (in module molsysmt.form.file_psf) (in module molsysmt.form.file_trjpk) (in module molsysmt.form.file_xtc) (in module molsysmt.form.file_xyznpy) (in module molsysmt.form.MDAnalysis_Topology) (in module molsysmt.form.MDAnalysis_Universe) (in module molsysmt.form.mdtraj_DCDTrajectoryFile) (in module molsysmt.form.mdtraj_HDF5TrajectoryFile) (in module molsysmt.form.mdtraj_Topology) (in module molsysmt.form.mdtraj_Trajectory) (in module molsysmt.form.mdtraj_XTCTrajectoryFile) (in module molsysmt.form.mmcif_PdbxContainers_DataContainer) (in module molsysmt.form.molsysmt_CIFFileHandler) (in module molsysmt.form.molsysmt_GROFileHandler) (in module molsysmt.form.molsysmt_H5MSMFileHandler) (in module molsysmt.form.molsysmt_MolecularMechanics) (in module molsysmt.form.molsysmt_MolecularMechanicsDict) (in module molsysmt.form.molsysmt_MolSys) (in module molsysmt.form.molsysmt_PDBFileHandler) (in module molsysmt.form.molsysmt_Structures) (in module molsysmt.form.molsysmt_StructuresDict) (in module molsysmt.form.molsysmt_Topology) (in module molsysmt.form.networkx_Graph) (in module molsysmt.form.nglview_NGLWidget) (in module molsysmt.form.openmm_AmberInpcrdFile) (in module molsysmt.form.openmm_AmberPrmtopFile) (in module molsysmt.form.openmm_CharmmCrdFile) (in module molsysmt.form.openmm_CharmmPsfFile) (in module molsysmt.form.openmm_Context) (in module molsysmt.form.openmm_GromacsGroFile) (in module molsysmt.form.openmm_GromacsTopFile) (in module molsysmt.form.openmm_Modeller) (in module molsysmt.form.openmm_PDBFile) (in module molsysmt.form.openmm_Simulation) (in module molsysmt.form.openmm_State) (in module molsysmt.form.openmm_System) (in module molsysmt.form.openmm_Topology) (in module molsysmt.form.parmed_Structure) (in module molsysmt.form.pdbfixer_PDBFixer) (in module molsysmt.form.pytraj_Topology) (in module molsysmt.form.pytraj_Trajectory) (in module molsysmt.form.string_alphafold_id) (in module molsysmt.form.string_amino_acids_1) (in module molsysmt.form.string_amino_acids_3) (in module molsysmt.form.string_pdb_id) (in module molsysmt.form.string_pdb_text) (in module molsysmt.form.XYZ)

D

download() (in module molsysmt.form.file_bcif) (in module molsysmt.form.file_bcif_gz) (in module molsysmt.form.file_pdb)

E

extract() (in module molsysmt.basic) (in module molsysmt.form.biopython_Seq) (in module molsysmt.form.biopython_SeqRecord) (in module molsysmt.form.file_bcif) (in module molsysmt.form.file_bcif_gz) (in module molsysmt.form.file_cif) (in module molsysmt.form.file_crd) (in module molsysmt.form.file_dcd) (in module molsysmt.form.file_gro) (in module molsysmt.form.file_h5) (in module molsysmt.form.file_h5msm) (in module molsysmt.form.file_inpcrd) (in module molsysmt.form.file_mol2) (in module molsysmt.form.file_pdb) (in module molsysmt.form.file_prmtop) (in module molsysmt.form.file_psf) (in module molsysmt.form.file_trjpk) (in module molsysmt.form.file_xtc) (in module molsysmt.form.file_xyznpy) (in module molsysmt.form.MDAnalysis_Topology) (in module molsysmt.form.MDAnalysis_Universe) (in module molsysmt.form.mdtraj_DCDTrajectoryFile) (in module molsysmt.form.mdtraj_HDF5TrajectoryFile) (in module molsysmt.form.mdtraj_Topology) (in module molsysmt.form.mdtraj_Trajectory) (in module molsysmt.form.mdtraj_XTCTrajectoryFile) (in module molsysmt.form.mmcif_PdbxContainers_DataContainer) (in module molsysmt.form.molsysmt_CIFFileHandler) (in module molsysmt.form.molsysmt_GROFileHandler) (in module molsysmt.form.molsysmt_H5MSMFileHandler) (in module molsysmt.form.molsysmt_MolecularMechanics) (in module molsysmt.form.molsysmt_MolecularMechanicsDict) (in module molsysmt.form.molsysmt_MolSys) (in module molsysmt.form.molsysmt_PDBFileHandler) (in module molsysmt.form.molsysmt_Structures) (in module molsysmt.form.molsysmt_StructuresDict) (in module molsysmt.form.molsysmt_Topology) (in module molsysmt.form.networkx_Graph) (in module molsysmt.form.nglview_NGLWidget) (in module molsysmt.form.openmm_AmberInpcrdFile) (in module molsysmt.form.openmm_AmberPrmtopFile) (in module molsysmt.form.openmm_CharmmCrdFile) (in module molsysmt.form.openmm_CharmmPsfFile) (in module molsysmt.form.openmm_Context) (in module molsysmt.form.openmm_GromacsGroFile) (in module molsysmt.form.openmm_GromacsTopFile) (in module molsysmt.form.openmm_Modeller) (in module molsysmt.form.openmm_PDBFile) (in module molsysmt.form.openmm_Simulation) (in module molsysmt.form.openmm_State) (in module molsysmt.form.openmm_System) (in module molsysmt.form.openmm_Topology) (in module molsysmt.form.parmed_Structure) (in module molsysmt.form.pdbfixer_PDBFixer) (in module molsysmt.form.pytraj_Topology) (in module molsysmt.form.pytraj_Trajectory) (in module molsysmt.form.string_alphafold_id) (in module molsysmt.form.string_amino_acids_1) (in module molsysmt.form.string_amino_acids_3) (in module molsysmt.form.string_pdb_id) (in module molsysmt.form.string_pdb_text) (in module molsysmt.form.XYZ)

F

flip() (in module molsysmt.structure)

G

get() (in module molsysmt.basic) (in module molsysmt.form.molsysmt_PDBFileHandler) get_1_letter_code_from_name() (in module molsysmt.element.group.amino_acid) get_acceptor_atoms() (in module molsysmt.hbonds) get_angles() (in module molsysmt.structure) get_angles_from_box() (in module molsysmt.pbc) get_area_buried() (in module molsysmt.physchem) get_atom_type_from_atom_name() (in module molsysmt.element.atom) get_atomic_radius() (in module molsysmt.physchem) get_attributes() (in module molsysmt.basic) (in module molsysmt.form) get_bondgraph() (in module molsysmt.topology) get_box_from_lengths_and_angles() (in module molsysmt.pbc) get_box_with_shape() (in module molsysmt.pbc) get_buch_hbonds() (in module molsysmt.hbonds) get_buried_fraction() (in module molsysmt.physchem) get_center() (in module molsysmt.structure) get_charge() (in module molsysmt.physchem) get_contacts() (in module molsysmt.structure) get_covalent_blocks() (in module molsysmt.topology) get_dihedral_angles() (in module molsysmt.structure) get_dihedral_quartets() (in module molsysmt.topology) get_distances() (in module molsysmt.structure) get_disulfide_bonds() (in module molsysmt.build) get_donor_atoms() (in module molsysmt.hbonds) get_engine_forcefield() (in module molsysmt.molecular_mechanics) get_forces() (in module molsysmt.molecular_mechanics) get_form() (in module molsysmt.basic) get_group_type_from_group_name() (in module molsysmt.element.group) get_hydrophobicity() (in module molsysmt.physchem)

get_label() (in module molsysmt.basic) get_least_rmsd() (in module molsysmt.structure) get_lengths_and_angles_from_box() (in module molsysmt.pbc) get_lengths_from_box() (in module molsysmt.pbc) get_luzard_chandler_hbonds() (in module molsysmt.hbonds) get_mass() (in module molsysmt.physchem) get_maximum_distances() (in module molsysmt.structure) get_minimum_distances() (in module molsysmt.structure) get_missing_bonds() (in module molsysmt.build) get_missing_heavy_atoms() (in module molsysmt.build) get_missing_residues() (in module molsysmt.build) get_missing_terminal_cappings() (in module molsysmt.build) get_neighbors() (in module molsysmt.structure) get_non_bonded_potential_energy() (in module molsysmt.molecular_mechanics) get_non_standard_residues() (in module molsysmt.build) get_polarity() (in module molsysmt.physchem) get_potential_energy() (in module molsysmt.molecular_mechanics) get_principal_axes() (in module molsysmt.structure) get_radius_of_gyration() (in module molsysmt.structure) get_rmsd() (in module molsysmt.structure) get_sasa() (in module molsysmt.physchem) get_sequence_alignment() (in module molsysmt.topology) get_sequence_identity() (in module molsysmt.topology) get_shape_from_angles() (in module molsysmt.pbc) get_shape_from_box() (in module molsysmt.pbc) get_surface_area() (in module molsysmt.physchem) get_transmembrane_tendency() (in module molsysmt.physchem) get_volume() (in module molsysmt.physchem) get_volume_from_box() (in module molsysmt.pbc) get_volume_from_lengths_and_angles() (in module molsysmt.pbc)

H

H5MSMReporter (class in molsysmt.third_party.openmm.reporters) has_atoms_with_alternate_locations() (in module molsysmt.form.file_pdb) has_attribute() (in module molsysmt.basic) (in module molsysmt.form) (in module molsysmt.form.biopython_Seq) (in module molsysmt.form.biopython_SeqRecord) (in module molsysmt.form.file_bcif) (in module molsysmt.form.file_bcif_gz) (in module molsysmt.form.file_cif) (in module molsysmt.form.file_crd) (in module molsysmt.form.file_dcd) (in module molsysmt.form.file_gro) (in module molsysmt.form.file_h5) (in module molsysmt.form.file_h5msm) (in module molsysmt.form.file_inpcrd) (in module molsysmt.form.file_mol2) (in module molsysmt.form.file_pdb) (in module molsysmt.form.file_prmtop) (in module molsysmt.form.file_psf) (in module molsysmt.form.file_trjpk) (in module molsysmt.form.file_xtc) (in module molsysmt.form.file_xyznpy) (in module molsysmt.form.MDAnalysis_Topology) (in module molsysmt.form.MDAnalysis_Universe) (in module molsysmt.form.mdtraj_DCDTrajectoryFile) (in module molsysmt.form.mdtraj_HDF5TrajectoryFile) (in module molsysmt.form.mdtraj_Topology) (in module molsysmt.form.mdtraj_Trajectory) (in module molsysmt.form.mdtraj_XTCTrajectoryFile) (in module molsysmt.form.mmcif_PdbxContainers_DataContainer) (in module molsysmt.form.molsysmt_CIFFileHandler) (in module molsysmt.form.molsysmt_GROFileHandler) (in module molsysmt.form.molsysmt_H5MSMFileHandler) (in module molsysmt.form.molsysmt_MolecularMechanics) (in module molsysmt.form.molsysmt_MolecularMechanicsDict) (in module molsysmt.form.molsysmt_MolSys) (in module molsysmt.form.molsysmt_PDBFileHandler) (in module molsysmt.form.molsysmt_Structures) (in module molsysmt.form.molsysmt_StructuresDict) (in module molsysmt.form.molsysmt_Topology) (in module molsysmt.form.networkx_Graph) (in module molsysmt.form.nglview_NGLWidget) (in module molsysmt.form.openmm_AmberInpcrdFile) (in module molsysmt.form.openmm_AmberPrmtopFile) (in module molsysmt.form.openmm_CharmmCrdFile) (in module molsysmt.form.openmm_CharmmPsfFile) (in module molsysmt.form.openmm_Context) (in module molsysmt.form.openmm_GromacsGroFile) (in module molsysmt.form.openmm_GromacsTopFile) (in module molsysmt.form.openmm_Modeller) (in module molsysmt.form.openmm_PDBFile) (in module molsysmt.form.openmm_Simulation) (in module molsysmt.form.openmm_State) (in module molsysmt.form.openmm_System) (in module molsysmt.form.openmm_Topology) (in module molsysmt.form.parmed_Structure) (in module molsysmt.form.pdbfixer_PDBFixer) (in module molsysmt.form.pytraj_Topology) (in module molsysmt.form.pytraj_Trajectory) (in module molsysmt.form.string_alphafold_id) (in module molsysmt.form.string_amino_acids_1) (in module molsysmt.form.string_amino_acids_3) (in module molsysmt.form.string_pdb_id) (in module molsysmt.form.string_pdb_text) (in module molsysmt.form.XYZ)

has_hydrogens() (in module molsysmt.build) has_pbc() (in module molsysmt.pbc)

I

info() (in module molsysmt.basic) is_a_molecular_system() (in module molsysmt.basic) is_amino_acid() (in module molsysmt.element.group.amino_acid) is_composed_of() (in module molsysmt.basic) is_form() (in module molsysmt.form.biopython_Seq) (in module molsysmt.form.biopython_SeqRecord) (in module molsysmt.form.file_bcif) (in module molsysmt.form.file_bcif_gz) (in module molsysmt.form.file_cif) (in module molsysmt.form.file_crd) (in module molsysmt.form.file_dcd) (in module molsysmt.form.file_gro) (in module molsysmt.form.file_h5) (in module molsysmt.form.file_h5msm) (in module molsysmt.form.file_inpcrd) (in module molsysmt.form.file_mol2) (in module molsysmt.form.file_pdb) (in module molsysmt.form.file_prmtop) (in module molsysmt.form.file_psf) (in module molsysmt.form.file_trjpk) (in module molsysmt.form.file_xtc) (in module molsysmt.form.file_xyznpy) (in module molsysmt.form.MDAnalysis_Topology) (in module molsysmt.form.MDAnalysis_Universe) (in module molsysmt.form.mdtraj_DCDTrajectoryFile) (in module molsysmt.form.mdtraj_HDF5TrajectoryFile) (in module molsysmt.form.mdtraj_Topology) (in module molsysmt.form.mdtraj_Trajectory) (in module molsysmt.form.mdtraj_XTCTrajectoryFile) (in module molsysmt.form.mmcif_PdbxContainers_DataContainer) (in module molsysmt.form.molsysmt_CIFFileHandler) (in module molsysmt.form.molsysmt_GROFileHandler) (in module molsysmt.form.molsysmt_H5MSMFileHandler) (in module molsysmt.form.molsysmt_MolecularMechanics) (in module molsysmt.form.molsysmt_MolecularMechanicsDict) (in module molsysmt.form.molsysmt_MolSys) (in module molsysmt.form.molsysmt_PDBFileHandler) (in module molsysmt.form.molsysmt_Structures) (in module molsysmt.form.molsysmt_StructuresDict) (in module molsysmt.form.molsysmt_Topology) (in module molsysmt.form.networkx_Graph) (in module molsysmt.form.nglview_NGLWidget) (in module molsysmt.form.openmm_AmberInpcrdFile) (in module molsysmt.form.openmm_AmberPrmtopFile) (in module molsysmt.form.openmm_CharmmCrdFile) (in module molsysmt.form.openmm_CharmmPsfFile) (in module molsysmt.form.openmm_Context) (in module molsysmt.form.openmm_GromacsGroFile) (in module molsysmt.form.openmm_GromacsTopFile) (in module molsysmt.form.openmm_Modeller) (in module molsysmt.form.openmm_PDBFile) (in module molsysmt.form.openmm_Simulation) (in module molsysmt.form.openmm_State) (in module molsysmt.form.openmm_System) (in module molsysmt.form.openmm_Topology) (in module molsysmt.form.parmed_Structure) (in module molsysmt.form.pdbfixer_PDBFixer) (in module molsysmt.form.pytraj_Topology) (in module molsysmt.form.pytraj_Trajectory) (in module molsysmt.form.string_alphafold_id) (in module molsysmt.form.string_amino_acids_1) (in module molsysmt.form.string_amino_acids_3) (in module molsysmt.form.string_pdb_id) (in module molsysmt.form.string_pdb_text) (in module molsysmt.form.XYZ)

is_ion() (in module molsysmt.element.group.ion) is_lipid() (in module molsysmt.element.group.lipid) is_nucleotide() (in module molsysmt.element.group.nucleotide) is_saccharide() (in module molsysmt.element.group.saccharide) is_small_molecule() (in module molsysmt.element.group.small_molecule) is_solvated() (in module molsysmt.build) is_terminal_capping() (in module molsysmt.element.group.terminal_capping) is_water() (in module molsysmt.element.group.water)

L

least_rmsd_align() (in module molsysmt.structure)

least_rmsd_fit() (in module molsysmt.structure) loading_failures() (in module molsysmt.third_party.openmm.platforms)

M

make_bioassembly() (in module molsysmt.build) make_water_box() (in module molsysmt.build) merge() (in module molsysmt.basic) (in module molsysmt.form.biopython_Seq) (in module molsysmt.form.biopython_SeqRecord) (in module molsysmt.form.file_bcif) (in module molsysmt.form.file_bcif_gz) (in module molsysmt.form.file_cif) (in module molsysmt.form.file_crd) (in module molsysmt.form.file_dcd) (in module molsysmt.form.file_gro) (in module molsysmt.form.file_h5) (in module molsysmt.form.file_h5msm) (in module molsysmt.form.file_inpcrd) (in module molsysmt.form.file_mol2) (in module molsysmt.form.file_pdb) (in module molsysmt.form.file_prmtop) (in module molsysmt.form.file_psf) (in module molsysmt.form.file_trjpk) (in module molsysmt.form.file_xtc) (in module molsysmt.form.file_xyznpy) (in module molsysmt.form.MDAnalysis_Topology) (in module molsysmt.form.MDAnalysis_Universe) (in module molsysmt.form.mdtraj_DCDTrajectoryFile) (in module molsysmt.form.mdtraj_HDF5TrajectoryFile) (in module molsysmt.form.mdtraj_Topology) (in module molsysmt.form.mdtraj_Trajectory) (in module molsysmt.form.mdtraj_XTCTrajectoryFile) (in module molsysmt.form.mmcif_PdbxContainers_DataContainer) (in module molsysmt.form.molsysmt_CIFFileHandler) (in module molsysmt.form.molsysmt_GROFileHandler) (in module molsysmt.form.molsysmt_H5MSMFileHandler) (in module molsysmt.form.molsysmt_MolecularMechanics) (in module molsysmt.form.molsysmt_MolecularMechanicsDict) (in module molsysmt.form.molsysmt_MolSys) (in module molsysmt.form.molsysmt_PDBFileHandler) (in module molsysmt.form.molsysmt_Structures) (in module molsysmt.form.molsysmt_StructuresDict) (in module molsysmt.form.molsysmt_Topology) (in module molsysmt.form.networkx_Graph) (in module molsysmt.form.nglview_NGLWidget) (in module molsysmt.form.openmm_AmberInpcrdFile) (in module molsysmt.form.openmm_AmberPrmtopFile) (in module molsysmt.form.openmm_CharmmCrdFile) (in module molsysmt.form.openmm_CharmmPsfFile) (in module molsysmt.form.openmm_Context) (in module molsysmt.form.openmm_GromacsGroFile) (in module molsysmt.form.openmm_GromacsTopFile) (in module molsysmt.form.openmm_Modeller) (in module molsysmt.form.openmm_PDBFile) (in module molsysmt.form.openmm_Simulation) (in module molsysmt.form.openmm_State) (in module molsysmt.form.openmm_System) (in module molsysmt.form.openmm_Topology) (in module molsysmt.form.parmed_Structure) (in module molsysmt.form.pdbfixer_PDBFixer) (in module molsysmt.form.pytraj_Topology) (in module molsysmt.form.pytraj_Trajectory) (in module molsysmt.form.string_alphafold_id) (in module molsysmt.form.string_amino_acids_1) (in module molsysmt.form.string_amino_acids_3) (in module molsysmt.form.string_pdb_id) (in module molsysmt.form.string_pdb_text) (in module molsysmt.form.XYZ) module molsysmt.basic.iterator molsysmt.form.biopython_Seq.set molsysmt.form.biopython_Seq.to_biopython_SeqRecord molsysmt.form.biopython_SeqRecord.set molsysmt.form.file_bcif.set molsysmt.form.file_bcif.to_mmcif_PdbxContainers_DataContainer molsysmt.form.file_bcif.to_molsysmt_MolSys molsysmt.form.file_bcif_gz.set molsysmt.form.file_bcif_gz.to_mmcif_PdbxContainers_DataContainer molsysmt.form.file_bcif_gz.to_molsysmt_MolSys molsysmt.form.file_cif.set molsysmt.form.file_crd.set molsysmt.form.file_crd.to_molsysmt_MolSys molsysmt.form.file_crd.to_molsysmt_Structures molsysmt.form.file_crd.to_molsysmt_Topology molsysmt.form.file_crd.to_openmm_CharmmCrdFile molsysmt.form.file_dcd.set molsysmt.form.file_dcd.to_mdtraj_DCDTrajectoryFile molsysmt.form.file_dcd.to_molsysmt_MolSys molsysmt.form.file_dcd.to_molsysmt_Structures molsysmt.form.file_gro.set molsysmt.form.file_gro.to_mdtraj_GroTrajectoryFile molsysmt.form.file_gro.to_mdtraj_Topology molsysmt.form.file_gro.to_mdtraj_Trajectory molsysmt.form.file_gro.to_molsysmt_GROFileHandler molsysmt.form.file_gro.to_molsysmt_MolSys molsysmt.form.file_gro.to_molsysmt_Structures molsysmt.form.file_gro.to_molsysmt_Topology molsysmt.form.file_gro.to_nglview_NGLWidget molsysmt.form.file_gro.to_openmm_GromacsGroFile molsysmt.form.file_gro.to_openmm_Modeller molsysmt.form.file_gro.to_openmm_Topology molsysmt.form.file_h5.set molsysmt.form.file_h5.to_file_pdb molsysmt.form.file_h5.to_mdtraj_HDF5TrajectoryFile molsysmt.form.file_h5.to_mdtraj_Topology molsysmt.form.file_h5.to_mdtraj_Trajectory molsysmt.form.file_h5.to_molsysmt_MolSys molsysmt.form.file_h5.to_molsysmt_Structures molsysmt.form.file_h5.to_molsysmt_Topology molsysmt.form.file_h5.to_nglview_NGLWidget molsysmt.form.file_h5.to_openmm_Topology molsysmt.form.file_h5msm.get_structural_attributes molsysmt.form.file_h5msm.get_topological_attributes molsysmt.form.file_h5msm.set molsysmt.form.file_h5msm.to_molsysmt_H5MSMFileHandler molsysmt.form.file_h5msm.to_molsysmt_MolSys molsysmt.form.file_h5msm.to_molsysmt_Structures molsysmt.form.file_h5msm.to_molsysmt_Topology molsysmt.form.file_h5msm.to_nglview_NGLWidget molsysmt.form.file_h5msm.to_string_amino_acids_1 molsysmt.form.file_h5msm.to_string_amino_acids_3 molsysmt.form.file_inpcrd.set molsysmt.form.file_inpcrd.to_molsysmt_Structures molsysmt.form.file_inpcrd.to_openmm_AmberInpcrdFile molsysmt.form.file_mol2.set molsysmt.form.file_mol2.to_file_pdb molsysmt.form.file_mol2.to_mdtraj_Topology molsysmt.form.file_mol2.to_mdtraj_Trajectory molsysmt.form.file_mol2.to_molsysmt_MolSys molsysmt.form.file_mol2.to_molsysmt_Structures molsysmt.form.file_mol2.to_molsysmt_Topology molsysmt.form.file_mol2.to_nglview_NGLWidget molsysmt.form.file_mol2.to_openmm_Modeller molsysmt.form.file_mol2.to_openmm_Topology molsysmt.form.file_mol2.to_parmed_Structure molsysmt.form.file_pdb.set molsysmt.form.file_pdb.to_file_mol2 molsysmt.form.file_pdb.to_MDAnalysis_Topology molsysmt.form.file_pdb.to_MDAnalysis_topology_PDBParser molsysmt.form.file_pdb.to_MDAnalysis_Universe molsysmt.form.file_pdb.to_mdtraj_PDBTrajectoryFile molsysmt.form.file_pdb.to_mdtraj_Topology molsysmt.form.file_pdb.to_mdtraj_Trajectory molsysmt.form.file_pdb.to_molsysmt_MolSys molsysmt.form.file_pdb.to_molsysmt_PDBFileHandler molsysmt.form.file_pdb.to_molsysmt_Structures molsysmt.form.file_pdb.to_molsysmt_Topology molsysmt.form.file_pdb.to_nglview_NGLWidget molsysmt.form.file_pdb.to_openmm_Modeller molsysmt.form.file_pdb.to_openmm_PDBFile molsysmt.form.file_pdb.to_openmm_Simulation molsysmt.form.file_pdb.to_openmm_System molsysmt.form.file_pdb.to_openmm_Topology molsysmt.form.file_pdb.to_parmed_Structure molsysmt.form.file_pdb.to_pdbfixer_PDBFixer molsysmt.form.file_pdb.to_pytraj_Topology molsysmt.form.file_pdb.to_pytraj_Trajectory molsysmt.form.file_pdb.to_string_pdb_text molsysmt.form.file_prmtop.set molsysmt.form.file_prmtop.to_file_pdb molsysmt.form.file_prmtop.to_mdtraj_Topology molsysmt.form.file_prmtop.to_molsysmt_MolSys molsysmt.form.file_prmtop.to_molsysmt_Topology molsysmt.form.file_prmtop.to_nglview_NGLWidget molsysmt.form.file_prmtop.to_openmm_AmberPrmtopFile molsysmt.form.file_prmtop.to_openmm_Modeller molsysmt.form.file_prmtop.to_openmm_Topology molsysmt.form.file_psf.set molsysmt.form.file_psf.to_molsysmt_MolSys molsysmt.form.file_psf.to_molsysmt_Topology molsysmt.form.file_psf.to_openmm_CharmmPsfFile molsysmt.form.file_psf.to_openmm_Topology molsysmt.form.file_trjpk.set molsysmt.form.file_trjpk.to_molsysmt_StructuresDict molsysmt.form.file_xtc.set molsysmt.form.file_xtc.to_mdtraj_Trajectory molsysmt.form.file_xtc.to_mdtraj_XTCTrajectoryFile molsysmt.form.file_xtc.to_molsysmt_Structures molsysmt.form.file_xyznpy.set molsysmt.form.file_xyznpy.to_XYZ molsysmt.form.MDAnalysis_Topology.set molsysmt.form.MDAnalysis_Universe.set molsysmt.form.MDAnalysis_Universe.to_file_pdb molsysmt.form.MDAnalysis_Universe.to_mdtraj_Trajectory molsysmt.form.MDAnalysis_Universe.to_molsysmt_MolSys molsysmt.form.MDAnalysis_Universe.to_molsysmt_Structures molsysmt.form.MDAnalysis_Universe.to_molsysmt_Topology molsysmt.form.MDAnalysis_Universe.to_nglview_NGLWidget molsysmt.form.mdtraj_DCDTrajectoryFile.set molsysmt.form.mdtraj_DCDTrajectoryFile.to_molsysmt_MolSys molsysmt.form.mdtraj_DCDTrajectoryFile.to_molsysmt_Structures molsysmt.form.mdtraj_HDF5TrajectoryFile.set molsysmt.form.mdtraj_HDF5TrajectoryFile.to_mdtraj_Topology molsysmt.form.mdtraj_HDF5TrajectoryFile.to_molsysmt_MolSys molsysmt.form.mdtraj_HDF5TrajectoryFile.to_molsysmt_Structures molsysmt.form.mdtraj_HDF5TrajectoryFile.to_molsysmt_Topology molsysmt.form.mdtraj_HDF5TrajectoryFile.to_openmm_Topology molsysmt.form.mdtraj_Topology.get_structural_attributes molsysmt.form.mdtraj_Topology.get_topological_attributes molsysmt.form.mdtraj_Topology.set molsysmt.form.mdtraj_Topology.to_file_top molsysmt.form.mdtraj_Topology.to_mdtraj_Trajectory molsysmt.form.mdtraj_Topology.to_molsysmt_Topology molsysmt.form.mdtraj_Topology.to_openmm_Topology molsysmt.form.mdtraj_Topology.to_parmed_GromacsTopologyFile molsysmt.form.mdtraj_Topology.to_parmed_Structure molsysmt.form.mdtraj_Topology.to_string_amino_acids_1 molsysmt.form.mdtraj_Topology.to_string_amino_acids_3 molsysmt.form.mdtraj_Trajectory.set molsysmt.form.mdtraj_Trajectory.to_biopython_Seq molsysmt.form.mdtraj_Trajectory.to_biopython_SeqRecord molsysmt.form.mdtraj_Trajectory.to_file_pdb molsysmt.form.mdtraj_Trajectory.to_file_xtc molsysmt.form.mdtraj_Trajectory.to_mdtraj_Topology molsysmt.form.mdtraj_Trajectory.to_molsysmt_MolSys molsysmt.form.mdtraj_Trajectory.to_molsysmt_Structures molsysmt.form.mdtraj_Trajectory.to_molsysmt_Topology molsysmt.form.mdtraj_Trajectory.to_nglview_NGLWidget molsysmt.form.mdtraj_Trajectory.to_openmm_Modeller molsysmt.form.mdtraj_Trajectory.to_openmm_Topology molsysmt.form.mdtraj_Trajectory.to_parmed_Structure molsysmt.form.mdtraj_Trajectory.to_pdbfixer_PDBFixer molsysmt.form.mdtraj_Trajectory.to_pytraj_Topology molsysmt.form.mdtraj_Trajectory.to_pytraj_Trajectory molsysmt.form.mdtraj_Trajectory.to_string_amino_acids_1 molsysmt.form.mdtraj_Trajectory.to_string_amino_acids_3 molsysmt.form.mdtraj_XTCTrajectoryFile.set molsysmt.form.mdtraj_XTCTrajectoryFile.to_molsysmt_Structures molsysmt.form.mmcif_PdbxContainers_DataContainer.get_structural_attributes molsysmt.form.mmcif_PdbxContainers_DataContainer.get_topological_attributes molsysmt.form.mmcif_PdbxContainers_DataContainer.set molsysmt.form.mmcif_PdbxContainers_DataContainer.to_file_pdb molsysmt.form.mmcif_PdbxContainers_DataContainer.to_mdtraj_Trajectory molsysmt.form.mmcif_PdbxContainers_DataContainer.to_molsysmt_MolecularMechanics molsysmt.form.mmcif_PdbxContainers_DataContainer.to_molsysmt_MolSys molsysmt.form.mmcif_PdbxContainers_DataContainer.to_molsysmt_Structures molsysmt.form.mmcif_PdbxContainers_DataContainer.to_molsysmt_Topology molsysmt.form.mmcif_PdbxContainers_DataContainer.to_openmm_Topology molsysmt.form.mmcif_PdbxContainers_DataContainer.to_string_amino_acids_1 molsysmt.form.mmcif_PdbxContainers_DataContainer.to_string_amino_acids_3 molsysmt.form.mmcif_PdbxContainers_DataContainer.to_string_pdb_id molsysmt.form.mmcif_PdbxContainers_DataContainer.to_string_pdb_text molsysmt.form.molsysmt_CIFFileHandler.set molsysmt.form.molsysmt_GROFileHandler.set molsysmt.form.molsysmt_GROFileHandler.to_molsysmt_MolSys molsysmt.form.molsysmt_GROFileHandler.to_molsysmt_Structures molsysmt.form.molsysmt_GROFileHandler.to_molsysmt_Topology molsysmt.form.molsysmt_GROFileHandler.to_nglview_NGLWidget molsysmt.form.molsysmt_H5MSMFileHandler.get_structural_attributes molsysmt.form.molsysmt_H5MSMFileHandler.get_topological_attributes molsysmt.form.molsysmt_H5MSMFileHandler.to_molsysmt_MolSys molsysmt.form.molsysmt_H5MSMFileHandler.to_molsysmt_Structures molsysmt.form.molsysmt_H5MSMFileHandler.to_molsysmt_Topology molsysmt.form.molsysmt_H5MSMFileHandler.to_nglview_NGLWidget molsysmt.form.molsysmt_MolecularMechanics.set molsysmt.form.molsysmt_MolecularMechanics.to_molsysmt_MolecularMechanicsDict molsysmt.form.molsysmt_MolecularMechanicsDict.set molsysmt.form.molsysmt_MolecularMechanicsDict.to_molsysmt_MolecularMechanics molsysmt.form.molsysmt_MolSys.get_mechanical_attributes molsysmt.form.molsysmt_MolSys.get_structural_attributes molsysmt.form.molsysmt_MolSys.get_topological_attributes molsysmt.form.molsysmt_MolSys.set molsysmt.form.molsysmt_MolSys.to_biopython_Seq molsysmt.form.molsysmt_MolSys.to_biopython_SeqRecord molsysmt.form.molsysmt_MolSys.to_file_h5msm molsysmt.form.molsysmt_MolSys.to_file_pdb molsysmt.form.molsysmt_MolSys.to_file_psf molsysmt.form.molsysmt_MolSys.to_mdtraj_Topology molsysmt.form.molsysmt_MolSys.to_mdtraj_Trajectory molsysmt.form.molsysmt_MolSys.to_molsysmt_MolecularMechanics molsysmt.form.molsysmt_MolSys.to_molsysmt_MolecularMechanicsDict molsysmt.form.molsysmt_MolSys.to_molsysmt_Structures molsysmt.form.molsysmt_MolSys.to_molsysmt_Topology molsysmt.form.molsysmt_MolSys.to_networkx_Graph molsysmt.form.molsysmt_MolSys.to_nglview_NGLWidget molsysmt.form.molsysmt_MolSys.to_openmm_Context molsysmt.form.molsysmt_MolSys.to_openmm_Modeller molsysmt.form.molsysmt_MolSys.to_openmm_Simulation molsysmt.form.molsysmt_MolSys.to_openmm_System molsysmt.form.molsysmt_MolSys.to_openmm_Topology molsysmt.form.molsysmt_MolSys.to_pdbfixer_PDBFixer molsysmt.form.molsysmt_MolSys.to_pytraj_Topology molsysmt.form.molsysmt_MolSys.to_pytraj_Trajectory molsysmt.form.molsysmt_MolSys.to_string_amino_acids_1 molsysmt.form.molsysmt_MolSys.to_string_amino_acids_3 molsysmt.form.molsysmt_MolSys.to_string_pdb_text molsysmt.form.molsysmt_MolSys.to_XYZ molsysmt.form.molsysmt_PDBFileHandler.to_molsysmt_MolSys molsysmt.form.molsysmt_PDBFileHandler.to_molsysmt_Structures molsysmt.form.molsysmt_PDBFileHandler.to_molsysmt_Topology molsysmt.form.molsysmt_PDBFileHandler.to_nglview_NGLWidget molsysmt.form.molsysmt_Structures.get_structural_attributes molsysmt.form.molsysmt_Structures.set molsysmt.form.molsysmt_Structures.to_file_h5msm molsysmt.form.molsysmt_Structures.to_molsysmt_StructuresDict molsysmt.form.molsysmt_Structures.to_XYZ molsysmt.form.molsysmt_StructuresDict.set molsysmt.form.molsysmt_StructuresDict.to_file_trjpk molsysmt.form.molsysmt_StructuresDict.to_molsysmt_MolecularMechanics molsysmt.form.molsysmt_StructuresDict.to_molsysmt_MolSys molsysmt.form.molsysmt_StructuresDict.to_molsysmt_Structures molsysmt.form.molsysmt_StructuresDict.to_molsysmt_Topology molsysmt.form.molsysmt_Topology.get_topological_attributes molsysmt.form.molsysmt_Topology.set molsysmt.form.molsysmt_Topology.to_file_h5msm molsysmt.form.molsysmt_Topology.to_file_pdb molsysmt.form.molsysmt_Topology.to_file_psf molsysmt.form.molsysmt_Topology.to_mdtraj_Topology molsysmt.form.molsysmt_Topology.to_networkx_Graph molsysmt.form.molsysmt_Topology.to_nglview_NGLWidget molsysmt.form.molsysmt_Topology.to_openmm_Topology molsysmt.form.molsysmt_Topology.to_parmed_Structure molsysmt.form.molsysmt_Topology.to_pytraj_Topology molsysmt.form.molsysmt_Topology.to_string_amino_acids_1 molsysmt.form.molsysmt_Topology.to_string_amino_acids_3 molsysmt.form.molsysmt_Topology.to_string_pdb_text molsysmt.form.networkx_Graph.set molsysmt.form.nglview_NGLWidget.get_structural_attributes molsysmt.form.nglview_NGLWidget.get_topological_attributes molsysmt.form.nglview_NGLWidget.to_molsysmt_MolSys molsysmt.form.nglview_NGLWidget.to_molsysmt_Structures molsysmt.form.nglview_NGLWidget.to_molsysmt_Topology molsysmt.form.nglview_NGLWidget.to_openmm_Topology molsysmt.form.nglview_NGLWidget.to_string_amino_acids_1 molsysmt.form.nglview_NGLWidget.to_string_amino_acids_3 molsysmt.form.nglview_NGLWidget.to_string_pdb_text molsysmt.form.openmm_AmberInpcrdFile.set molsysmt.form.openmm_AmberInpcrdFile.to_molsysmt_Structures molsysmt.form.openmm_AmberPrmtopFile.set molsysmt.form.openmm_AmberPrmtopFile.to_molsysmt_Topology molsysmt.form.openmm_AmberPrmtopFile.to_openmm_System molsysmt.form.openmm_AmberPrmtopFile.to_openmm_Topology molsysmt.form.openmm_CharmmCrdFile.set molsysmt.form.openmm_CharmmPsfFile.set molsysmt.form.openmm_CharmmPsfFile.to_molsysmt_Topology molsysmt.form.openmm_CharmmPsfFile.to_openmm_Topology molsysmt.form.openmm_Context.get_structural_attributes molsysmt.form.openmm_Context.get_topological_attributes molsysmt.form.openmm_Context.set molsysmt.form.openmm_Context.to_molsysmt_Structures molsysmt.form.openmm_Context.to_openmm_System molsysmt.form.openmm_GromacsGroFile.set molsysmt.form.openmm_GromacsGroFile.to_molsysmt_MolSys molsysmt.form.openmm_GromacsGroFile.to_molsysmt_Structures molsysmt.form.openmm_GromacsGroFile.to_molsysmt_Topology molsysmt.form.openmm_GromacsGroFile.to_openmm_Modeller molsysmt.form.openmm_GromacsGroFile.to_openmm_Topology molsysmt.form.openmm_GromacsTopFile.set molsysmt.form.openmm_GromacsTopFile.to_molsysmt_Topology molsysmt.form.openmm_GromacsTopFile.to_openmm_Topology molsysmt.form.openmm_Modeller.get_structural_attributes molsysmt.form.openmm_Modeller.get_topological_attributes molsysmt.form.openmm_Modeller.set molsysmt.form.openmm_Modeller.to_file_pdb molsysmt.form.openmm_Modeller.to_mdtraj_Topology molsysmt.form.openmm_Modeller.to_mdtraj_Trajectory molsysmt.form.openmm_Modeller.to_molsysmt_MolSys molsysmt.form.openmm_Modeller.to_molsysmt_Structures molsysmt.form.openmm_Modeller.to_molsysmt_Topology molsysmt.form.openmm_Modeller.to_nglview_NGLWidget molsysmt.form.openmm_Modeller.to_openmm_Simulation molsysmt.form.openmm_Modeller.to_openmm_System molsysmt.form.openmm_Modeller.to_openmm_Topology molsysmt.form.openmm_Modeller.to_pdbfixer_PDBFixer molsysmt.form.openmm_PDBFile.set molsysmt.form.openmm_PDBFile.to_mdtraj_Topology molsysmt.form.openmm_PDBFile.to_mdtraj_Trajectory molsysmt.form.openmm_PDBFile.to_molsysmt_MolSys molsysmt.form.openmm_PDBFile.to_molsysmt_Structures molsysmt.form.openmm_PDBFile.to_molsysmt_Topology molsysmt.form.openmm_PDBFile.to_nglview_NGLWidget molsysmt.form.openmm_PDBFile.to_openmm_Topology molsysmt.form.openmm_Simulation.get_structural_attributes molsysmt.form.openmm_Simulation.get_topological_attributes molsysmt.form.openmm_Simulation.set molsysmt.form.openmm_Simulation.to_file_pdb molsysmt.form.openmm_Simulation.to_molsysmt_MolSys molsysmt.form.openmm_Simulation.to_molsysmt_Structures molsysmt.form.openmm_Simulation.to_molsysmt_Topology molsysmt.form.openmm_Simulation.to_openmm_Context molsysmt.form.openmm_Simulation.to_openmm_Modeller molsysmt.form.openmm_Simulation.to_openmm_Topology molsysmt.form.openmm_Simulation.to_pdbfixer_PDBFixer molsysmt.form.openmm_State.set molsysmt.form.openmm_State.to_molsysmt_Structures molsysmt.form.openmm_State.to_XYZ molsysmt.form.openmm_System.get_structural_attributes molsysmt.form.openmm_System.get_topological_attributes molsysmt.form.openmm_System.set molsysmt.form.openmm_System.to_openmm_Context molsysmt.form.openmm_Topology.get_structural_attributes molsysmt.form.openmm_Topology.get_topological_attributes molsysmt.form.openmm_Topology.set molsysmt.form.openmm_Topology.to_file_pdb molsysmt.form.openmm_Topology.to_file_psf molsysmt.form.openmm_Topology.to_mdtraj_Topology molsysmt.form.openmm_Topology.to_molsysmt_MolSys molsysmt.form.openmm_Topology.to_molsysmt_Topology molsysmt.form.openmm_Topology.to_networkx_Graph molsysmt.form.openmm_Topology.to_nglview_NGLWidget molsysmt.form.openmm_Topology.to_openmm_Context molsysmt.form.openmm_Topology.to_openmm_Modeller molsysmt.form.openmm_Topology.to_openmm_PDBFile molsysmt.form.openmm_Topology.to_openmm_Simulation molsysmt.form.openmm_Topology.to_openmm_System molsysmt.form.openmm_Topology.to_parmed_Structure molsysmt.form.openmm_Topology.to_pdbfixer_PDBFixer molsysmt.form.openmm_Topology.to_string_amino_acids_1 molsysmt.form.openmm_Topology.to_string_amino_acids_3 molsysmt.form.openmm_Topology.to_string_pdb_text molsysmt.form.parmed_Structure.set molsysmt.form.parmed_Structure.to_file_cif molsysmt.form.parmed_Structure.to_file_mol2 molsysmt.form.parmed_Structure.to_file_pdb molsysmt.form.parmed_Structure.to_file_psf molsysmt.form.parmed_Structure.to_mdtraj_Topology molsysmt.form.parmed_Structure.to_mdtraj_Trajectory molsysmt.form.parmed_Structure.to_molsysmt_MolSys molsysmt.form.parmed_Structure.to_molsysmt_Structures molsysmt.form.parmed_Structure.to_molsysmt_Topology molsysmt.form.parmed_Structure.to_nglview_NGLWidget molsysmt.form.parmed_Structure.to_openmm_Modeller molsysmt.form.parmed_Structure.to_openmm_Topology molsysmt.form.parmed_Structure.to_parmed_GromacsTopologyFile molsysmt.form.pdbfixer_PDBFixer.get_structural_attributes molsysmt.form.pdbfixer_PDBFixer.get_topological_attributes molsysmt.form.pdbfixer_PDBFixer.set molsysmt.form.pdbfixer_PDBFixer.to_biopython_Seq molsysmt.form.pdbfixer_PDBFixer.to_biopython_SeqRecord molsysmt.form.pdbfixer_PDBFixer.to_file_pdb molsysmt.form.pdbfixer_PDBFixer.to_mdtraj_Topology molsysmt.form.pdbfixer_PDBFixer.to_mdtraj_Trajectory molsysmt.form.pdbfixer_PDBFixer.to_molsysmt_MolSys molsysmt.form.pdbfixer_PDBFixer.to_molsysmt_Structures molsysmt.form.pdbfixer_PDBFixer.to_molsysmt_Topology molsysmt.form.pdbfixer_PDBFixer.to_nglview_NGLWidget molsysmt.form.pdbfixer_PDBFixer.to_openmm_Modeller molsysmt.form.pdbfixer_PDBFixer.to_openmm_Topology molsysmt.form.pdbfixer_PDBFixer.to_string_amino_acids_1 molsysmt.form.pdbfixer_PDBFixer.to_string_amino_acids_3 molsysmt.form.pytraj_Topology.set molsysmt.form.pytraj_Topology.to_molsysmt_Topology molsysmt.form.pytraj_Topology.to_pytraj_Trajectory molsysmt.form.pytraj_Trajectory.set molsysmt.form.pytraj_Trajectory.to_molsysmt_MolSys molsysmt.form.pytraj_Trajectory.to_molsysmt_Structures molsysmt.form.pytraj_Trajectory.to_molsysmt_Topology molsysmt.form.pytraj_Trajectory.to_nglview_NGLWidget molsysmt.form.pytraj_Trajectory.to_pytraj_Topology molsysmt.form.string_alphafold_id.get_structural_attributes molsysmt.form.string_alphafold_id.get_topological_attributes molsysmt.form.string_alphafold_id.set molsysmt.form.string_alphafold_id.to_file_bcif molsysmt.form.string_alphafold_id.to_file_fasta molsysmt.form.string_alphafold_id.to_file_h5msm molsysmt.form.string_alphafold_id.to_file_pdb molsysmt.form.string_alphafold_id.to_mdtraj_Topology molsysmt.form.string_alphafold_id.to_mdtraj_Trajectory molsysmt.form.string_alphafold_id.to_mmcif_PdbxContainers_DataContainer molsysmt.form.string_alphafold_id.to_molsysmt_MolSys molsysmt.form.string_alphafold_id.to_molsysmt_Structures molsysmt.form.string_alphafold_id.to_molsysmt_Topology molsysmt.form.string_alphafold_id.to_nglview_NGLWidget molsysmt.form.string_alphafold_id.to_openmm_Modeller molsysmt.form.string_alphafold_id.to_openmm_PDBFile molsysmt.form.string_alphafold_id.to_openmm_Topology molsysmt.form.string_alphafold_id.to_string_amino_acids_1 molsysmt.form.string_alphafold_id.to_string_pdb_text molsysmt.form.string_amino_acids_1.set molsysmt.form.string_amino_acids_1.to_biopython_Seq molsysmt.form.string_amino_acids_1.to_biopython_SeqRecord molsysmt.form.string_amino_acids_1.to_string_amino_acids_3 molsysmt.form.string_amino_acids_3.set molsysmt.form.string_amino_acids_3.to_biopython_Seq molsysmt.form.string_amino_acids_3.to_biopython_SeqRecord molsysmt.form.string_amino_acids_3.to_string_amino_acids_1 molsysmt.form.string_pdb_id.get_structural_attributes molsysmt.form.string_pdb_id.get_topological_attributes molsysmt.form.string_pdb_id.set molsysmt.form.string_pdb_id.to_file_bcif molsysmt.form.string_pdb_id.to_file_bcif_gz molsysmt.form.string_pdb_id.to_file_fasta molsysmt.form.string_pdb_id.to_file_h5msm molsysmt.form.string_pdb_id.to_file_pdb molsysmt.form.string_pdb_id.to_mdtraj_Topology molsysmt.form.string_pdb_id.to_mdtraj_Trajectory molsysmt.form.string_pdb_id.to_mmcif_PdbxContainers_DataContainer molsysmt.form.string_pdb_id.to_molsysmt_MolSys molsysmt.form.string_pdb_id.to_molsysmt_Structures molsysmt.form.string_pdb_id.to_molsysmt_Topology molsysmt.form.string_pdb_id.to_nglview_NGLWidget molsysmt.form.string_pdb_id.to_openmm_Modeller molsysmt.form.string_pdb_id.to_openmm_PDBFile molsysmt.form.string_pdb_id.to_openmm_Topology molsysmt.form.string_pdb_id.to_pdbfixer_PDBFixer molsysmt.form.string_pdb_id.to_string_pdb_text molsysmt.form.string_pdb_text.get_structural_attributes molsysmt.form.string_pdb_text.get_topological_attributes molsysmt.form.string_pdb_text.set molsysmt.form.string_pdb_text.to_file_pdb molsysmt.form.string_pdb_text.to_mdtraj_Topology molsysmt.form.string_pdb_text.to_mdtraj_Trajectory molsysmt.form.string_pdb_text.to_molsysmt_MolSys molsysmt.form.string_pdb_text.to_molsysmt_PDBFileHandler molsysmt.form.string_pdb_text.to_molsysmt_Structures molsysmt.form.string_pdb_text.to_molsysmt_Topology molsysmt.form.string_pdb_text.to_nglview_NGLWidget molsysmt.form.string_pdb_text.to_openmm_Modeller molsysmt.form.string_pdb_text.to_openmm_PDBFile molsysmt.form.string_pdb_text.to_openmm_Simulation molsysmt.form.string_pdb_text.to_openmm_System molsysmt.form.string_pdb_text.to_openmm_Topology molsysmt.form.string_pdb_text.to_pdbfixer_PDBFixer molsysmt.form.XYZ.get_structural_attributes molsysmt.form.XYZ.get_topological_attributes molsysmt.form.XYZ.set molsysmt.form.XYZ.to_file_xyznpy molsysmt.form.XYZ.to_molsysmt_MolecularMechanics molsysmt.form.XYZ.to_molsysmt_MolSys molsysmt.form.XYZ.to_molsysmt_Structures molsysmt.form.XYZ.to_molsysmt_Topology molsysmt.third_party.nglview.load_html_in_jupyter_notebook molsysmt.basic.iterator module molsysmt.form.biopython_Seq.set module molsysmt.form.biopython_Seq.to_biopython_SeqRecord module molsysmt.form.biopython_SeqRecord.set module molsysmt.form.file_bcif.set module molsysmt.form.file_bcif.to_mmcif_PdbxContainers_DataContainer module molsysmt.form.file_bcif.to_molsysmt_MolSys module molsysmt.form.file_bcif_gz.set module molsysmt.form.file_bcif_gz.to_mmcif_PdbxContainers_DataContainer module molsysmt.form.file_bcif_gz.to_molsysmt_MolSys module molsysmt.form.file_cif.set module molsysmt.form.file_crd.set module molsysmt.form.file_crd.to_molsysmt_MolSys module molsysmt.form.file_crd.to_molsysmt_Structures module molsysmt.form.file_crd.to_molsysmt_Topology module molsysmt.form.file_crd.to_openmm_CharmmCrdFile module molsysmt.form.file_dcd.set module molsysmt.form.file_dcd.to_mdtraj_DCDTrajectoryFile module molsysmt.form.file_dcd.to_molsysmt_MolSys module molsysmt.form.file_dcd.to_molsysmt_Structures module molsysmt.form.file_gro.set module molsysmt.form.file_gro.to_mdtraj_GroTrajectoryFile module molsysmt.form.file_gro.to_mdtraj_Topology module molsysmt.form.file_gro.to_mdtraj_Trajectory module molsysmt.form.file_gro.to_molsysmt_GROFileHandler module molsysmt.form.file_gro.to_molsysmt_MolSys module molsysmt.form.file_gro.to_molsysmt_Structures module molsysmt.form.file_gro.to_molsysmt_Topology module molsysmt.form.file_gro.to_nglview_NGLWidget module molsysmt.form.file_gro.to_openmm_GromacsGroFile module molsysmt.form.file_gro.to_openmm_Modeller module molsysmt.form.file_gro.to_openmm_Topology module molsysmt.form.file_h5.set module molsysmt.form.file_h5.to_file_pdb module molsysmt.form.file_h5.to_mdtraj_HDF5TrajectoryFile module molsysmt.form.file_h5.to_mdtraj_Topology module molsysmt.form.file_h5.to_mdtraj_Trajectory module molsysmt.form.file_h5.to_molsysmt_MolSys module molsysmt.form.file_h5.to_molsysmt_Structures module molsysmt.form.file_h5.to_molsysmt_Topology module molsysmt.form.file_h5.to_nglview_NGLWidget module molsysmt.form.file_h5.to_openmm_Topology module molsysmt.form.file_h5msm.get_structural_attributes module molsysmt.form.file_h5msm.get_topological_attributes module molsysmt.form.file_h5msm.set module molsysmt.form.file_h5msm.to_molsysmt_H5MSMFileHandler module molsysmt.form.file_h5msm.to_molsysmt_MolSys module molsysmt.form.file_h5msm.to_molsysmt_Structures module molsysmt.form.file_h5msm.to_molsysmt_Topology module molsysmt.form.file_h5msm.to_nglview_NGLWidget module molsysmt.form.file_h5msm.to_string_amino_acids_1 module molsysmt.form.file_h5msm.to_string_amino_acids_3 module molsysmt.form.file_inpcrd.set module molsysmt.form.file_inpcrd.to_molsysmt_Structures module molsysmt.form.file_inpcrd.to_openmm_AmberInpcrdFile module molsysmt.form.file_mol2.set module molsysmt.form.file_mol2.to_file_pdb module molsysmt.form.file_mol2.to_mdtraj_Topology module molsysmt.form.file_mol2.to_mdtraj_Trajectory module molsysmt.form.file_mol2.to_molsysmt_MolSys module molsysmt.form.file_mol2.to_molsysmt_Structures module molsysmt.form.file_mol2.to_molsysmt_Topology module molsysmt.form.file_mol2.to_nglview_NGLWidget module molsysmt.form.file_mol2.to_openmm_Modeller module molsysmt.form.file_mol2.to_openmm_Topology module molsysmt.form.file_mol2.to_parmed_Structure module molsysmt.form.file_pdb.set module molsysmt.form.file_pdb.to_file_mol2 module molsysmt.form.file_pdb.to_MDAnalysis_Topology module molsysmt.form.file_pdb.to_MDAnalysis_topology_PDBParser module molsysmt.form.file_pdb.to_MDAnalysis_Universe module molsysmt.form.file_pdb.to_mdtraj_PDBTrajectoryFile module molsysmt.form.file_pdb.to_mdtraj_Topology module molsysmt.form.file_pdb.to_mdtraj_Trajectory module molsysmt.form.file_pdb.to_molsysmt_MolSys module molsysmt.form.file_pdb.to_molsysmt_PDBFileHandler module molsysmt.form.file_pdb.to_molsysmt_Structures module molsysmt.form.file_pdb.to_molsysmt_Topology module molsysmt.form.file_pdb.to_nglview_NGLWidget module molsysmt.form.file_pdb.to_openmm_Modeller module molsysmt.form.file_pdb.to_openmm_PDBFile module molsysmt.form.file_pdb.to_openmm_Simulation module molsysmt.form.file_pdb.to_openmm_System module molsysmt.form.file_pdb.to_openmm_Topology module molsysmt.form.file_pdb.to_parmed_Structure module molsysmt.form.file_pdb.to_pdbfixer_PDBFixer module molsysmt.form.file_pdb.to_pytraj_Topology module molsysmt.form.file_pdb.to_pytraj_Trajectory module molsysmt.form.file_pdb.to_string_pdb_text module molsysmt.form.file_prmtop.set module molsysmt.form.file_prmtop.to_file_pdb module molsysmt.form.file_prmtop.to_mdtraj_Topology module molsysmt.form.file_prmtop.to_molsysmt_MolSys module molsysmt.form.file_prmtop.to_molsysmt_Topology module molsysmt.form.file_prmtop.to_nglview_NGLWidget module molsysmt.form.file_prmtop.to_openmm_AmberPrmtopFile module molsysmt.form.file_prmtop.to_openmm_Modeller module molsysmt.form.file_prmtop.to_openmm_Topology module

molsysmt.form.file_psf.set module molsysmt.form.file_psf.to_molsysmt_MolSys module molsysmt.form.file_psf.to_molsysmt_Topology module molsysmt.form.file_psf.to_openmm_CharmmPsfFile module molsysmt.form.file_psf.to_openmm_Topology module molsysmt.form.file_trjpk.set module molsysmt.form.file_trjpk.to_molsysmt_StructuresDict module molsysmt.form.file_xtc.set module molsysmt.form.file_xtc.to_mdtraj_Trajectory module molsysmt.form.file_xtc.to_mdtraj_XTCTrajectoryFile module molsysmt.form.file_xtc.to_molsysmt_Structures module molsysmt.form.file_xyznpy.set module molsysmt.form.file_xyznpy.to_XYZ module molsysmt.form.MDAnalysis_Topology.set module molsysmt.form.MDAnalysis_Universe.set module molsysmt.form.MDAnalysis_Universe.to_file_pdb module molsysmt.form.MDAnalysis_Universe.to_mdtraj_Trajectory module molsysmt.form.MDAnalysis_Universe.to_molsysmt_MolSys module molsysmt.form.MDAnalysis_Universe.to_molsysmt_Structures module molsysmt.form.MDAnalysis_Universe.to_molsysmt_Topology module molsysmt.form.MDAnalysis_Universe.to_nglview_NGLWidget module molsysmt.form.mdtraj_DCDTrajectoryFile.set module molsysmt.form.mdtraj_DCDTrajectoryFile.to_molsysmt_MolSys module molsysmt.form.mdtraj_DCDTrajectoryFile.to_molsysmt_Structures module molsysmt.form.mdtraj_HDF5TrajectoryFile.set module molsysmt.form.mdtraj_HDF5TrajectoryFile.to_mdtraj_Topology module molsysmt.form.mdtraj_HDF5TrajectoryFile.to_molsysmt_MolSys module molsysmt.form.mdtraj_HDF5TrajectoryFile.to_molsysmt_Structures module molsysmt.form.mdtraj_HDF5TrajectoryFile.to_molsysmt_Topology module molsysmt.form.mdtraj_HDF5TrajectoryFile.to_openmm_Topology module molsysmt.form.mdtraj_Topology.get_structural_attributes module molsysmt.form.mdtraj_Topology.get_topological_attributes module molsysmt.form.mdtraj_Topology.set module molsysmt.form.mdtraj_Topology.to_file_top module molsysmt.form.mdtraj_Topology.to_mdtraj_Trajectory module molsysmt.form.mdtraj_Topology.to_molsysmt_Topology module molsysmt.form.mdtraj_Topology.to_openmm_Topology module molsysmt.form.mdtraj_Topology.to_parmed_GromacsTopologyFile module molsysmt.form.mdtraj_Topology.to_parmed_Structure module molsysmt.form.mdtraj_Topology.to_string_amino_acids_1 module molsysmt.form.mdtraj_Topology.to_string_amino_acids_3 module molsysmt.form.mdtraj_Trajectory.set module molsysmt.form.mdtraj_Trajectory.to_biopython_Seq module molsysmt.form.mdtraj_Trajectory.to_biopython_SeqRecord module molsysmt.form.mdtraj_Trajectory.to_file_pdb module molsysmt.form.mdtraj_Trajectory.to_file_xtc module molsysmt.form.mdtraj_Trajectory.to_mdtraj_Topology module molsysmt.form.mdtraj_Trajectory.to_molsysmt_MolSys module molsysmt.form.mdtraj_Trajectory.to_molsysmt_Structures module molsysmt.form.mdtraj_Trajectory.to_molsysmt_Topology module molsysmt.form.mdtraj_Trajectory.to_nglview_NGLWidget module molsysmt.form.mdtraj_Trajectory.to_openmm_Modeller module molsysmt.form.mdtraj_Trajectory.to_openmm_Topology module molsysmt.form.mdtraj_Trajectory.to_parmed_Structure module molsysmt.form.mdtraj_Trajectory.to_pdbfixer_PDBFixer module molsysmt.form.mdtraj_Trajectory.to_pytraj_Topology module molsysmt.form.mdtraj_Trajectory.to_pytraj_Trajectory module molsysmt.form.mdtraj_Trajectory.to_string_amino_acids_1 module molsysmt.form.mdtraj_Trajectory.to_string_amino_acids_3 module molsysmt.form.mdtraj_XTCTrajectoryFile.set module molsysmt.form.mdtraj_XTCTrajectoryFile.to_molsysmt_Structures module molsysmt.form.mmcif_PdbxContainers_DataContainer.get_structural_attributes module molsysmt.form.mmcif_PdbxContainers_DataContainer.get_topological_attributes module molsysmt.form.mmcif_PdbxContainers_DataContainer.set module molsysmt.form.mmcif_PdbxContainers_DataContainer.to_file_pdb module molsysmt.form.mmcif_PdbxContainers_DataContainer.to_mdtraj_Trajectory module molsysmt.form.mmcif_PdbxContainers_DataContainer.to_molsysmt_MolecularMechanics module molsysmt.form.mmcif_PdbxContainers_DataContainer.to_molsysmt_MolSys module molsysmt.form.mmcif_PdbxContainers_DataContainer.to_molsysmt_Structures module molsysmt.form.mmcif_PdbxContainers_DataContainer.to_molsysmt_Topology module molsysmt.form.mmcif_PdbxContainers_DataContainer.to_openmm_Topology module molsysmt.form.mmcif_PdbxContainers_DataContainer.to_string_amino_acids_1 module molsysmt.form.mmcif_PdbxContainers_DataContainer.to_string_amino_acids_3 module molsysmt.form.mmcif_PdbxContainers_DataContainer.to_string_pdb_id module molsysmt.form.mmcif_PdbxContainers_DataContainer.to_string_pdb_text module molsysmt.form.molsysmt_CIFFileHandler.set module molsysmt.form.molsysmt_GROFileHandler.set module molsysmt.form.molsysmt_GROFileHandler.to_molsysmt_MolSys module molsysmt.form.molsysmt_GROFileHandler.to_molsysmt_Structures module molsysmt.form.molsysmt_GROFileHandler.to_molsysmt_Topology module molsysmt.form.molsysmt_GROFileHandler.to_nglview_NGLWidget module molsysmt.form.molsysmt_H5MSMFileHandler.get_structural_attributes module molsysmt.form.molsysmt_H5MSMFileHandler.get_topological_attributes module molsysmt.form.molsysmt_H5MSMFileHandler.to_molsysmt_MolSys module molsysmt.form.molsysmt_H5MSMFileHandler.to_molsysmt_Structures module molsysmt.form.molsysmt_H5MSMFileHandler.to_molsysmt_Topology module molsysmt.form.molsysmt_H5MSMFileHandler.to_nglview_NGLWidget module molsysmt.form.molsysmt_MolecularMechanics.set module molsysmt.form.molsysmt_MolecularMechanics.to_molsysmt_MolecularMechanicsDict module molsysmt.form.molsysmt_MolecularMechanicsDict.set module molsysmt.form.molsysmt_MolecularMechanicsDict.to_molsysmt_MolecularMechanics module molsysmt.form.molsysmt_MolSys.get_mechanical_attributes module molsysmt.form.molsysmt_MolSys.get_structural_attributes module molsysmt.form.molsysmt_MolSys.get_topological_attributes module molsysmt.form.molsysmt_MolSys.set module molsysmt.form.molsysmt_MolSys.to_biopython_Seq module molsysmt.form.molsysmt_MolSys.to_biopython_SeqRecord module molsysmt.form.molsysmt_MolSys.to_file_h5msm module molsysmt.form.molsysmt_MolSys.to_file_pdb module molsysmt.form.molsysmt_MolSys.to_file_psf module molsysmt.form.molsysmt_MolSys.to_mdtraj_Topology module molsysmt.form.molsysmt_MolSys.to_mdtraj_Trajectory module molsysmt.form.molsysmt_MolSys.to_molsysmt_MolecularMechanics module molsysmt.form.molsysmt_MolSys.to_molsysmt_MolecularMechanicsDict module molsysmt.form.molsysmt_MolSys.to_molsysmt_Structures module molsysmt.form.molsysmt_MolSys.to_molsysmt_Topology module molsysmt.form.molsysmt_MolSys.to_networkx_Graph module molsysmt.form.molsysmt_MolSys.to_nglview_NGLWidget module molsysmt.form.molsysmt_MolSys.to_openmm_Context module molsysmt.form.molsysmt_MolSys.to_openmm_Modeller module molsysmt.form.molsysmt_MolSys.to_openmm_Simulation module molsysmt.form.molsysmt_MolSys.to_openmm_System module molsysmt.form.molsysmt_MolSys.to_openmm_Topology module molsysmt.form.molsysmt_MolSys.to_pdbfixer_PDBFixer module molsysmt.form.molsysmt_MolSys.to_pytraj_Topology module molsysmt.form.molsysmt_MolSys.to_pytraj_Trajectory module molsysmt.form.molsysmt_MolSys.to_string_amino_acids_1 module molsysmt.form.molsysmt_MolSys.to_string_amino_acids_3 module molsysmt.form.molsysmt_MolSys.to_string_pdb_text module molsysmt.form.molsysmt_MolSys.to_XYZ module molsysmt.form.molsysmt_PDBFileHandler.to_molsysmt_MolSys module molsysmt.form.molsysmt_PDBFileHandler.to_molsysmt_Structures module molsysmt.form.molsysmt_PDBFileHandler.to_molsysmt_Topology module molsysmt.form.molsysmt_PDBFileHandler.to_nglview_NGLWidget module molsysmt.form.molsysmt_Structures.get_structural_attributes module molsysmt.form.molsysmt_Structures.set module molsysmt.form.molsysmt_Structures.to_file_h5msm module molsysmt.form.molsysmt_Structures.to_molsysmt_StructuresDict module molsysmt.form.molsysmt_Structures.to_XYZ module molsysmt.form.molsysmt_StructuresDict.set module molsysmt.form.molsysmt_StructuresDict.to_file_trjpk module molsysmt.form.molsysmt_StructuresDict.to_molsysmt_MolecularMechanics module molsysmt.form.molsysmt_StructuresDict.to_molsysmt_MolSys module molsysmt.form.molsysmt_StructuresDict.to_molsysmt_Structures module molsysmt.form.molsysmt_StructuresDict.to_molsysmt_Topology module molsysmt.form.molsysmt_Topology.get_topological_attributes module molsysmt.form.molsysmt_Topology.set module molsysmt.form.molsysmt_Topology.to_file_h5msm module molsysmt.form.molsysmt_Topology.to_file_pdb module molsysmt.form.molsysmt_Topology.to_file_psf module molsysmt.form.molsysmt_Topology.to_mdtraj_Topology module molsysmt.form.molsysmt_Topology.to_networkx_Graph module molsysmt.form.molsysmt_Topology.to_nglview_NGLWidget module molsysmt.form.molsysmt_Topology.to_openmm_Topology module molsysmt.form.molsysmt_Topology.to_parmed_Structure module molsysmt.form.molsysmt_Topology.to_pytraj_Topology module molsysmt.form.molsysmt_Topology.to_string_amino_acids_1 module molsysmt.form.molsysmt_Topology.to_string_amino_acids_3 module molsysmt.form.molsysmt_Topology.to_string_pdb_text module molsysmt.form.networkx_Graph.set module molsysmt.form.nglview_NGLWidget.get_structural_attributes module molsysmt.form.nglview_NGLWidget.get_topological_attributes module molsysmt.form.nglview_NGLWidget.to_molsysmt_MolSys module molsysmt.form.nglview_NGLWidget.to_molsysmt_Structures module molsysmt.form.nglview_NGLWidget.to_molsysmt_Topology module molsysmt.form.nglview_NGLWidget.to_openmm_Topology module molsysmt.form.nglview_NGLWidget.to_string_amino_acids_1 module molsysmt.form.nglview_NGLWidget.to_string_amino_acids_3 module molsysmt.form.nglview_NGLWidget.to_string_pdb_text module molsysmt.form.openmm_AmberInpcrdFile.set module molsysmt.form.openmm_AmberInpcrdFile.to_molsysmt_Structures module molsysmt.form.openmm_AmberPrmtopFile.set module molsysmt.form.openmm_AmberPrmtopFile.to_molsysmt_Topology module molsysmt.form.openmm_AmberPrmtopFile.to_openmm_System module molsysmt.form.openmm_AmberPrmtopFile.to_openmm_Topology module molsysmt.form.openmm_CharmmCrdFile.set module molsysmt.form.openmm_CharmmPsfFile.set module molsysmt.form.openmm_CharmmPsfFile.to_molsysmt_Topology module molsysmt.form.openmm_CharmmPsfFile.to_openmm_Topology module molsysmt.form.openmm_Context.get_structural_attributes module molsysmt.form.openmm_Context.get_topological_attributes module molsysmt.form.openmm_Context.set module molsysmt.form.openmm_Context.to_molsysmt_Structures module molsysmt.form.openmm_Context.to_openmm_System module molsysmt.form.openmm_GromacsGroFile.set module molsysmt.form.openmm_GromacsGroFile.to_molsysmt_MolSys module molsysmt.form.openmm_GromacsGroFile.to_molsysmt_Structures module molsysmt.form.openmm_GromacsGroFile.to_molsysmt_Topology module molsysmt.form.openmm_GromacsGroFile.to_openmm_Modeller module molsysmt.form.openmm_GromacsGroFile.to_openmm_Topology module molsysmt.form.openmm_GromacsTopFile.set module molsysmt.form.openmm_GromacsTopFile.to_molsysmt_Topology module molsysmt.form.openmm_GromacsTopFile.to_openmm_Topology module molsysmt.form.openmm_Modeller.get_structural_attributes module molsysmt.form.openmm_Modeller.get_topological_attributes module molsysmt.form.openmm_Modeller.set module molsysmt.form.openmm_Modeller.to_file_pdb module molsysmt.form.openmm_Modeller.to_mdtraj_Topology module molsysmt.form.openmm_Modeller.to_mdtraj_Trajectory module molsysmt.form.openmm_Modeller.to_molsysmt_MolSys module molsysmt.form.openmm_Modeller.to_molsysmt_Structures module molsysmt.form.openmm_Modeller.to_molsysmt_Topology module molsysmt.form.openmm_Modeller.to_nglview_NGLWidget module molsysmt.form.openmm_Modeller.to_openmm_Simulation module molsysmt.form.openmm_Modeller.to_openmm_System module molsysmt.form.openmm_Modeller.to_openmm_Topology module molsysmt.form.openmm_Modeller.to_pdbfixer_PDBFixer module molsysmt.form.openmm_PDBFile.set module molsysmt.form.openmm_PDBFile.to_mdtraj_Topology module molsysmt.form.openmm_PDBFile.to_mdtraj_Trajectory module molsysmt.form.openmm_PDBFile.to_molsysmt_MolSys module molsysmt.form.openmm_PDBFile.to_molsysmt_Structures module molsysmt.form.openmm_PDBFile.to_molsysmt_Topology module molsysmt.form.openmm_PDBFile.to_nglview_NGLWidget module molsysmt.form.openmm_PDBFile.to_openmm_Topology module molsysmt.form.openmm_Simulation.get_structural_attributes module molsysmt.form.openmm_Simulation.get_topological_attributes module molsysmt.form.openmm_Simulation.set module molsysmt.form.openmm_Simulation.to_file_pdb module molsysmt.form.openmm_Simulation.to_molsysmt_MolSys module molsysmt.form.openmm_Simulation.to_molsysmt_Structures module molsysmt.form.openmm_Simulation.to_molsysmt_Topology module molsysmt.form.openmm_Simulation.to_openmm_Context module molsysmt.form.openmm_Simulation.to_openmm_Modeller module molsysmt.form.openmm_Simulation.to_openmm_Topology module molsysmt.form.openmm_Simulation.to_pdbfixer_PDBFixer module molsysmt.form.openmm_State.set module molsysmt.form.openmm_State.to_molsysmt_Structures module molsysmt.form.openmm_State.to_XYZ module molsysmt.form.openmm_System.get_structural_attributes module molsysmt.form.openmm_System.get_topological_attributes module molsysmt.form.openmm_System.set module molsysmt.form.openmm_System.to_openmm_Context module molsysmt.form.openmm_Topology.get_structural_attributes module molsysmt.form.openmm_Topology.get_topological_attributes module molsysmt.form.openmm_Topology.set module molsysmt.form.openmm_Topology.to_file_pdb module molsysmt.form.openmm_Topology.to_file_psf module molsysmt.form.openmm_Topology.to_mdtraj_Topology module molsysmt.form.openmm_Topology.to_molsysmt_MolSys module molsysmt.form.openmm_Topology.to_molsysmt_Topology module molsysmt.form.openmm_Topology.to_networkx_Graph module molsysmt.form.openmm_Topology.to_nglview_NGLWidget module molsysmt.form.openmm_Topology.to_openmm_Context module molsysmt.form.openmm_Topology.to_openmm_Modeller module molsysmt.form.openmm_Topology.to_openmm_PDBFile module molsysmt.form.openmm_Topology.to_openmm_Simulation module molsysmt.form.openmm_Topology.to_openmm_System module molsysmt.form.openmm_Topology.to_parmed_Structure module molsysmt.form.openmm_Topology.to_pdbfixer_PDBFixer module molsysmt.form.openmm_Topology.to_string_amino_acids_1 module molsysmt.form.openmm_Topology.to_string_amino_acids_3 module molsysmt.form.openmm_Topology.to_string_pdb_text module molsysmt.form.parmed_Structure.set module molsysmt.form.parmed_Structure.to_file_cif module molsysmt.form.parmed_Structure.to_file_mol2 module molsysmt.form.parmed_Structure.to_file_pdb module molsysmt.form.parmed_Structure.to_file_psf module molsysmt.form.parmed_Structure.to_mdtraj_Topology module molsysmt.form.parmed_Structure.to_mdtraj_Trajectory module molsysmt.form.parmed_Structure.to_molsysmt_MolSys module molsysmt.form.parmed_Structure.to_molsysmt_Structures module molsysmt.form.parmed_Structure.to_molsysmt_Topology module molsysmt.form.parmed_Structure.to_nglview_NGLWidget module molsysmt.form.parmed_Structure.to_openmm_Modeller module molsysmt.form.parmed_Structure.to_openmm_Topology module molsysmt.form.parmed_Structure.to_parmed_GromacsTopologyFile module molsysmt.form.pdbfixer_PDBFixer.get_structural_attributes module molsysmt.form.pdbfixer_PDBFixer.get_topological_attributes module molsysmt.form.pdbfixer_PDBFixer.set module molsysmt.form.pdbfixer_PDBFixer.to_biopython_Seq module molsysmt.form.pdbfixer_PDBFixer.to_biopython_SeqRecord module molsysmt.form.pdbfixer_PDBFixer.to_file_pdb module molsysmt.form.pdbfixer_PDBFixer.to_mdtraj_Topology module molsysmt.form.pdbfixer_PDBFixer.to_mdtraj_Trajectory module molsysmt.form.pdbfixer_PDBFixer.to_molsysmt_MolSys module molsysmt.form.pdbfixer_PDBFixer.to_molsysmt_Structures module molsysmt.form.pdbfixer_PDBFixer.to_molsysmt_Topology module molsysmt.form.pdbfixer_PDBFixer.to_nglview_NGLWidget module molsysmt.form.pdbfixer_PDBFixer.to_openmm_Modeller module molsysmt.form.pdbfixer_PDBFixer.to_openmm_Topology module molsysmt.form.pdbfixer_PDBFixer.to_string_amino_acids_1 module molsysmt.form.pdbfixer_PDBFixer.to_string_amino_acids_3 module molsysmt.form.pytraj_Topology.set module molsysmt.form.pytraj_Topology.to_molsysmt_Topology module molsysmt.form.pytraj_Topology.to_pytraj_Trajectory module molsysmt.form.pytraj_Trajectory.set module molsysmt.form.pytraj_Trajectory.to_molsysmt_MolSys module molsysmt.form.pytraj_Trajectory.to_molsysmt_Structures module molsysmt.form.pytraj_Trajectory.to_molsysmt_Topology module molsysmt.form.pytraj_Trajectory.to_nglview_NGLWidget module molsysmt.form.pytraj_Trajectory.to_pytraj_Topology module molsysmt.form.string_alphafold_id.get_structural_attributes module molsysmt.form.string_alphafold_id.get_topological_attributes module molsysmt.form.string_alphafold_id.set module molsysmt.form.string_alphafold_id.to_file_bcif module molsysmt.form.string_alphafold_id.to_file_fasta module molsysmt.form.string_alphafold_id.to_file_h5msm module molsysmt.form.string_alphafold_id.to_file_pdb module molsysmt.form.string_alphafold_id.to_mdtraj_Topology module molsysmt.form.string_alphafold_id.to_mdtraj_Trajectory module molsysmt.form.string_alphafold_id.to_mmcif_PdbxContainers_DataContainer module molsysmt.form.string_alphafold_id.to_molsysmt_MolSys module molsysmt.form.string_alphafold_id.to_molsysmt_Structures module molsysmt.form.string_alphafold_id.to_molsysmt_Topology module molsysmt.form.string_alphafold_id.to_nglview_NGLWidget module molsysmt.form.string_alphafold_id.to_openmm_Modeller module molsysmt.form.string_alphafold_id.to_openmm_PDBFile module molsysmt.form.string_alphafold_id.to_openmm_Topology module molsysmt.form.string_alphafold_id.to_string_amino_acids_1 module molsysmt.form.string_alphafold_id.to_string_pdb_text module molsysmt.form.string_amino_acids_1.set module molsysmt.form.string_amino_acids_1.to_biopython_Seq module molsysmt.form.string_amino_acids_1.to_biopython_SeqRecord module molsysmt.form.string_amino_acids_1.to_string_amino_acids_3 module molsysmt.form.string_amino_acids_3.set module molsysmt.form.string_amino_acids_3.to_biopython_Seq module molsysmt.form.string_amino_acids_3.to_biopython_SeqRecord module molsysmt.form.string_amino_acids_3.to_string_amino_acids_1 module molsysmt.form.string_pdb_id.get_structural_attributes module molsysmt.form.string_pdb_id.get_topological_attributes module molsysmt.form.string_pdb_id.set module molsysmt.form.string_pdb_id.to_file_bcif module molsysmt.form.string_pdb_id.to_file_bcif_gz module molsysmt.form.string_pdb_id.to_file_fasta module molsysmt.form.string_pdb_id.to_file_h5msm module molsysmt.form.string_pdb_id.to_file_pdb module molsysmt.form.string_pdb_id.to_mdtraj_Topology module molsysmt.form.string_pdb_id.to_mdtraj_Trajectory module molsysmt.form.string_pdb_id.to_mmcif_PdbxContainers_DataContainer module molsysmt.form.string_pdb_id.to_molsysmt_MolSys module molsysmt.form.string_pdb_id.to_molsysmt_Structures module molsysmt.form.string_pdb_id.to_molsysmt_Topology module molsysmt.form.string_pdb_id.to_nglview_NGLWidget module molsysmt.form.string_pdb_id.to_openmm_Modeller module molsysmt.form.string_pdb_id.to_openmm_PDBFile module molsysmt.form.string_pdb_id.to_openmm_Topology module molsysmt.form.string_pdb_id.to_pdbfixer_PDBFixer module molsysmt.form.string_pdb_id.to_string_pdb_text module molsysmt.form.string_pdb_text.get_structural_attributes module molsysmt.form.string_pdb_text.get_topological_attributes module molsysmt.form.string_pdb_text.set module molsysmt.form.string_pdb_text.to_file_pdb module molsysmt.form.string_pdb_text.to_mdtraj_Topology module molsysmt.form.string_pdb_text.to_mdtraj_Trajectory module molsysmt.form.string_pdb_text.to_molsysmt_MolSys module molsysmt.form.string_pdb_text.to_molsysmt_PDBFileHandler module molsysmt.form.string_pdb_text.to_molsysmt_Structures module molsysmt.form.string_pdb_text.to_molsysmt_Topology module molsysmt.form.string_pdb_text.to_nglview_NGLWidget module molsysmt.form.string_pdb_text.to_openmm_Modeller module molsysmt.form.string_pdb_text.to_openmm_PDBFile module molsysmt.form.string_pdb_text.to_openmm_Simulation module molsysmt.form.string_pdb_text.to_openmm_System module molsysmt.form.string_pdb_text.to_openmm_Topology module molsysmt.form.string_pdb_text.to_pdbfixer_PDBFixer module molsysmt.form.XYZ.get_structural_attributes module molsysmt.form.XYZ.get_topological_attributes module molsysmt.form.XYZ.set module molsysmt.form.XYZ.to_file_xyznpy module molsysmt.form.XYZ.to_molsysmt_MolecularMechanics module molsysmt.form.XYZ.to_molsysmt_MolSys module molsysmt.form.XYZ.to_molsysmt_Structures module molsysmt.form.XYZ.to_molsysmt_Topology module molsysmt.third_party.nglview.load_html_in_jupyter_notebook module move_away() (in module molsysmt.structure) mutate() (in module molsysmt.build)

P

pin_atoms() (in module molsysmt.third_party.openmm.forces)

potential_energy_minimization() (in module molsysmt.molecular_mechanics) principal_component_analysis() (in module molsysmt.structure)

R

remove() (in module molsysmt.basic) remove_overlapping_molecules() (in module molsysmt.build)

replace_HETATM_by_ATOM_in_terminal_cappings() (in module molsysmt.form.file_pdb) rotate() (in module molsysmt.structure)

S

select() (in module molsysmt.basic) set() (in module molsysmt.basic) (in module molsysmt.form.molsysmt_H5MSMFileHandler) (in module molsysmt.form.molsysmt_PDBFileHandler) (in module molsysmt.form.nglview_NGLWidget) set_color() (in module molsysmt.third_party.nglview) set_color_by_value() (in module molsysmt.third_party.nglview) set_dihedral_angles() (in module molsysmt.structure) shift_dihedral_angles() (in module molsysmt.structure) show_as_balls_and_sticks() (in module molsysmt.third_party.nglview) show_as_cartoon() (in module molsysmt.third_party.nglview) show_as_licorice() (in module molsysmt.third_party.nglview) show_as_surface() (in module molsysmt.third_party.nglview) show_contacts() (in module molsysmt.structure) show_gui() (in module molsysmt.third_party.nglview) solvate() (in module molsysmt.build) solve_atoms_with_alternate_location() (in module molsysmt.build) standardize_view() (in module molsysmt.third_party.nglview) StructuresDictReporter (class in molsysmt.third_party.openmm.reporters) StructuresIterator (class in molsysmt.form.file_bcif) (class in molsysmt.form.file_bcif_gz) (class in molsysmt.form.file_cif) (class in molsysmt.form.file_crd) (class in molsysmt.form.file_dcd) (class in molsysmt.form.file_gro) (class in molsysmt.form.file_h5) (class in molsysmt.form.file_h5msm) (class in molsysmt.form.file_inpcrd) (class in molsysmt.form.file_mol2) (class in molsysmt.form.file_pdb) (class in molsysmt.form.file_prmtop) (class in molsysmt.form.file_trjpk) (class in molsysmt.form.file_xtc) (class in molsysmt.form.file_xyznpy) (class in molsysmt.form.MDAnalysis_Universe) (class in molsysmt.form.mdtraj_DCDTrajectoryFile) (class in molsysmt.form.mdtraj_HDF5TrajectoryFile) (class in molsysmt.form.mdtraj_Trajectory) (class in molsysmt.form.mdtraj_XTCTrajectoryFile) (class in molsysmt.form.mmcif_PdbxContainers_DataContainer) (class in molsysmt.form.molsysmt_CIFFileHandler) (class in molsysmt.form.molsysmt_GROFileHandler) (class in molsysmt.form.molsysmt_H5MSMFileHandler) (class in molsysmt.form.molsysmt_MolSys) (class in molsysmt.form.molsysmt_Structures) (class in molsysmt.form.molsysmt_StructuresDict) (class in molsysmt.form.nglview_NGLWidget) (class in molsysmt.form.openmm_AmberInpcrdFile) (class in molsysmt.form.openmm_CharmmCrdFile) (class in molsysmt.form.openmm_CharmmPsfFile) (class in molsysmt.form.openmm_Context) (class in molsysmt.form.openmm_GromacsGroFile) (class in molsysmt.form.openmm_Modeller) (class in molsysmt.form.openmm_PDBFile) (class in molsysmt.form.openmm_Simulation) (class in molsysmt.form.openmm_State) (class in molsysmt.form.openmm_System) (class in molsysmt.form.parmed_Structure) (class in molsysmt.form.pdbfixer_PDBFixer) (class in molsysmt.form.pytraj_Topology) (class in molsysmt.form.pytraj_Trajectory) (class in molsysmt.form.string_alphafold_id) (class in molsysmt.form.string_pdb_id) (class in molsysmt.form.string_pdb_text) (class in molsysmt.form.XYZ)

T

TopologyIterator (class in molsysmt.form.biopython_Seq) (class in molsysmt.form.biopython_SeqRecord) (class in molsysmt.form.file_bcif) (class in molsysmt.form.file_bcif_gz) (class in molsysmt.form.file_cif) (class in molsysmt.form.file_crd) (class in molsysmt.form.file_gro) (class in molsysmt.form.file_h5) (class in molsysmt.form.file_h5msm) (class in molsysmt.form.file_mol2) (class in molsysmt.form.file_pdb) (class in molsysmt.form.file_prmtop) (class in molsysmt.form.file_psf) (class in molsysmt.form.MDAnalysis_Topology) (class in molsysmt.form.MDAnalysis_Universe) (class in molsysmt.form.mdtraj_HDF5TrajectoryFile) (class in molsysmt.form.mdtraj_Topology) (class in molsysmt.form.mdtraj_Trajectory) (class in molsysmt.form.mmcif_PdbxContainers_DataContainer) (class in molsysmt.form.molsysmt_CIFFileHandler) (class in molsysmt.form.molsysmt_GROFileHandler) (class in molsysmt.form.molsysmt_MolSys) (class in molsysmt.form.molsysmt_Topology) (class in molsysmt.form.networkx_Graph) (class in molsysmt.form.nglview_NGLWidget) (class in molsysmt.form.openmm_AmberPrmtopFile) (class in molsysmt.form.openmm_CharmmCrdFile) (class in molsysmt.form.openmm_CharmmPsfFile) (class in molsysmt.form.openmm_Context) (class in molsysmt.form.openmm_GromacsGroFile) (class in molsysmt.form.openmm_GromacsTopFile) (class in molsysmt.form.openmm_Modeller) (class in molsysmt.form.openmm_PDBFile) (class in molsysmt.form.openmm_Simulation) (class in molsysmt.form.openmm_State) (class in molsysmt.form.openmm_System) (class in molsysmt.form.openmm_Topology) (class in molsysmt.form.parmed_Structure) (class in molsysmt.form.pdbfixer_PDBFixer) (class in molsysmt.form.pytraj_Topology) (class in molsysmt.form.pytraj_Trajectory) (class in molsysmt.form.string_alphafold_id) (class in molsysmt.form.string_amino_acids_1) (class in molsysmt.form.string_amino_acids_3) (class in molsysmt.form.string_pdb_id) (class in molsysmt.form.string_pdb_text) (class in molsysmt.form.XYZ)

TQDMReporter (class in molsysmt.third_party.openmm.reporters) translate() (in module molsysmt.structure)

U

unwrap() (in module molsysmt.pbc)

V

view() (in module molsysmt.basic)

W

where_is_attribute() (in module molsysmt.basic) wrap_to_mic() (in module molsysmt.pbc)

wrap_to_pbc() (in module molsysmt.pbc) write_html() (in module molsysmt.third_party.nglview) write_topology_in_h5msm() (in module molsysmt.form.openmm_Topology)