- make_bioassembly() (in module molsysmt.build)
- make_numba_signature() (in module molsysmt.lib.make_numba_signature)
- make_sequence() (molsysmt.thirds.tleap.tleap.TLeap method)
- make_water_box() (in module molsysmt.build)
- MasterRecord (class in molsysmt.native.pdb_atomic_coordinate_entry)
- matmul() (in module molsysmt.lib.math)
- MdltypRecord (class in molsysmt.native.pdb_atomic_coordinate_entry)
- merge() (in module molsysmt.basic)
- MiscellaneousFeaturesSection (class in molsysmt.native.pdb_atomic_coordinate_entry)
- MMTFTrajectoryFile (class in molsysmt.form.file_mmtf.to_mdtraj)
- Model (class in molsysmt.native.pdb_atomic_coordinate_entry)
- ModresRecord (class in molsysmt.native.pdb_atomic_coordinate_entry)
-
module
- molsysmt
- molsysmt.attribute
- molsysmt.attribute.attributes
- molsysmt.attribute.bonds_are_required_to_get_attribute
- molsysmt.attribute.is_attribute
- molsysmt.attribute.is_mechanical_attribute
- molsysmt.attribute.is_structural_attribute
- molsysmt.attribute.is_topological_attribute
- molsysmt.basic
- molsysmt.basic.add
- molsysmt.basic.append_structures
- molsysmt.basic.are_multiple_molecular_systems
- molsysmt.basic.compare
- molsysmt.basic.concatenate_structures
- molsysmt.basic.contains
- molsysmt.basic.convert
- molsysmt.basic.copy
- molsysmt.basic.extract
- molsysmt.basic.get
- molsysmt.basic.get_attributes
- molsysmt.basic.get_form
- molsysmt.basic.get_label
- molsysmt.basic.has_attribute
- molsysmt.basic.info
- molsysmt.basic.is_a_molecular_system
- molsysmt.basic.is_composed_of
- molsysmt.basic.iterator, [1]
- molsysmt.basic.merge
- molsysmt.basic.remove
- molsysmt.basic.select
- molsysmt.basic.selector
- molsysmt.basic.selector.amber
- molsysmt.basic.selector.mdanalysis
- molsysmt.basic.selector.mdtraj
- molsysmt.basic.selector.molsysmt
- molsysmt.basic.selector.molsysmt_old
- molsysmt.basic.selector.nglview
- molsysmt.basic.selector.parmed
- molsysmt.basic.set
- molsysmt.basic.view
- molsysmt.basic.where_is_attribute
- molsysmt.build
- molsysmt.build.add_bonds
- molsysmt.build.add_missing_bonds
- molsysmt.build.add_missing_heavy_atoms
- molsysmt.build.add_missing_hydrogens
- molsysmt.build.add_missing_terminal_cappings
- molsysmt.build.build_peptide
- molsysmt.build.define_new_chain
- molsysmt.build.get_disulfide_bonds
- molsysmt.build.get_missing_bonds
- molsysmt.build.get_missing_heavy_atoms
- molsysmt.build.get_missing_residues
- molsysmt.build.get_missing_terminal_cappings
- molsysmt.build.get_non_standard_residues
- molsysmt.build.has_hydrogens
- molsysmt.build.is_solvated
- molsysmt.build.make_bioassembly
- molsysmt.build.make_water_box
- molsysmt.build.mutate
- molsysmt.build.remove_bonds
- molsysmt.build.remove_overlapping_molecules
- molsysmt.build.solvate
- molsysmt.build.solve_atoms_with_alternate_location
- molsysmt.config
- molsysmt.config.logging_setup
- molsysmt.dependencies
- molsysmt.element
- molsysmt.element.atom
- molsysmt.element.atom.acceptors
- molsysmt.element.atom.charges
- molsysmt.element.atom.donors
- molsysmt.element.atom.get_atom_type_from_atom_name
- molsysmt.element.atom.names
- molsysmt.element.atom.names_cg
- molsysmt.element.bond
- molsysmt.element.bond.max_expected_bond_length
- molsysmt.element.chain
- molsysmt.element.chain.chain_names
- molsysmt.element.chain.get_chain_id
- molsysmt.element.chain.get_chain_index
- molsysmt.element.chain.get_chain_name
- molsysmt.element.chain.get_chain_type
- molsysmt.element.component
- molsysmt.element.component.get_component_id
- molsysmt.element.component.get_component_index
- molsysmt.element.component.get_component_name
- molsysmt.element.component.get_component_type
- molsysmt.element.component.get_n_components
- molsysmt.element.component.is_component_type
- molsysmt.element.entity
- molsysmt.element.entity.disaccharide
- molsysmt.element.entity.get_entity_id
- molsysmt.element.entity.get_entity_index
- molsysmt.element.entity.get_entity_name
- molsysmt.element.entity.get_entity_type
- molsysmt.element.entity.get_n_entities
- molsysmt.element.entity.monosaccharide
- molsysmt.element.group
- molsysmt.element.group.amino_acid
- molsysmt.element.group.amino_acid.get_1_letter_code_from_name
- molsysmt.element.group.amino_acid.get_bonded_atom_pairs
- molsysmt.element.group.amino_acid.get_group_db
- molsysmt.element.group.amino_acid.group_names
- molsysmt.element.group.amino_acid.group_types
- molsysmt.element.group.amino_acid.is_amino_acid
- molsysmt.element.group.get_bonded_atom_pairs
- molsysmt.element.group.get_group_type
- molsysmt.element.group.ion
- molsysmt.element.group.ion.get_bonded_atom_pairs
- molsysmt.element.group.ion.get_group_db
- molsysmt.element.group.ion.group_names
- molsysmt.element.group.ion.is_ion
- molsysmt.element.group.is_group_type
- molsysmt.element.group.lipid
- molsysmt.element.group.lipid.is_lipid
- molsysmt.element.group.lipid.lipid_names
- molsysmt.element.group.nucleotide
- molsysmt.element.group.nucleotide.is_nucleotide
- molsysmt.element.group.nucleotide.nucleotide_names
- molsysmt.element.group.saccharide
- molsysmt.element.group.saccharide.get_bonded_atom_pairs
- molsysmt.element.group.saccharide.get_group_db
- molsysmt.element.group.saccharide.group_names
- molsysmt.element.group.saccharide.is_saccharide
- molsysmt.element.group.small_molecule
- molsysmt.element.group.small_molecule.get_bonded_atom_pairs
- molsysmt.element.group.small_molecule.get_group_db
- molsysmt.element.group.small_molecule.group_names
- molsysmt.element.group.small_molecule.is_small_molecule
- molsysmt.element.group.small_molecule.small_molecule_is_amino_acid
- molsysmt.element.group.terminal_capping
- molsysmt.element.group.terminal_capping.get_bonded_atom_pairs
- molsysmt.element.group.terminal_capping.get_group_db
- molsysmt.element.group.terminal_capping.group_names
- molsysmt.element.group.terminal_capping.is_c_terminal_capping
- molsysmt.element.group.terminal_capping.is_n_terminal_capping
- molsysmt.element.group.terminal_capping.is_terminal_capping
- molsysmt.element.group.water
- molsysmt.element.group.water.get_bonded_atom_pairs
- molsysmt.element.group.water.is_water
- molsysmt.element.group.water.water_names
- molsysmt.element.is_composed_of
- molsysmt.element.is_element
- molsysmt.element.molecule
- molsysmt.element.molecule.disaccharide
- molsysmt.element.molecule.dna
- molsysmt.element.molecule.dna.names
- molsysmt.element.molecule.get_molecule_id
- molsysmt.element.molecule.get_molecule_index
- molsysmt.element.molecule.get_molecule_name
- molsysmt.element.molecule.get_molecule_type
- molsysmt.element.molecule.get_n_molecules
- molsysmt.element.molecule.ion
- molsysmt.element.molecule.is_molecule_type
- molsysmt.element.molecule.lipid
- molsysmt.element.molecule.monosaccharide
- molsysmt.element.molecule.peptide
- molsysmt.element.molecule.polysaccharide
- molsysmt.element.molecule.protein
- molsysmt.element.molecule.rna
- molsysmt.element.molecule.rna.names
- molsysmt.element.molecule.small_molecule
- molsysmt.element.molecule.water
- molsysmt.file
- molsysmt.file.close
- molsysmt.file.file_handler
- molsysmt.file.get_mode
- molsysmt.file.handlers
- molsysmt.file.handlers.mdtraj_HDF5TrajectoryFile
- molsysmt.file.handlers.mdtraj_HDF5TrajectoryFile.close_file
- molsysmt.file.handlers.mdtraj_HDF5TrajectoryFile.open_file
- molsysmt.file.is_closed
- molsysmt.file.is_file
- molsysmt.file.is_opened
- molsysmt.file.open
- molsysmt.form
- molsysmt.form.bcifreader_PdbxContainers_DataContainer
- molsysmt.form.bcifreader_PdbxContainers_DataContainer.add
- molsysmt.form.bcifreader_PdbxContainers_DataContainer.append_structures
- molsysmt.form.bcifreader_PdbxContainers_DataContainer.attributes
- molsysmt.form.bcifreader_PdbxContainers_DataContainer.copy
- molsysmt.form.bcifreader_PdbxContainers_DataContainer.extract
- molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_structural_attributes
- molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes
- molsysmt.form.bcifreader_PdbxContainers_DataContainer.has_attribute
- molsysmt.form.bcifreader_PdbxContainers_DataContainer.is_form
- molsysmt.form.bcifreader_PdbxContainers_DataContainer.iterators
- molsysmt.form.bcifreader_PdbxContainers_DataContainer.merge
- molsysmt.form.bcifreader_PdbxContainers_DataContainer.set
- molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_bcifreader_PdbxContainers_DataContainer
- molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_file_pdb
- molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_mdtraj_Trajectory
- molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_molsysmt_MolecularMechanics
- molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_molsysmt_MolSys
- molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_molsysmt_MolSys_bck
- molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_molsysmt_MolSys_bueno
- molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_molsysmt_Structures
- molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_molsysmt_Topology
- molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_openmm_Topology
- molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_string_amino_acids_1
- molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_string_amino_acids_3
- molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_string_pdb_id
- molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_string_pdb_text
- molsysmt.form.biopython_Seq
- molsysmt.form.biopython_Seq.add
- molsysmt.form.biopython_Seq.attributes
- molsysmt.form.biopython_Seq.copy
- molsysmt.form.biopython_Seq.extract
- molsysmt.form.biopython_Seq.get, [1]
- molsysmt.form.biopython_Seq.has_attribute
- molsysmt.form.biopython_Seq.is_form
- molsysmt.form.biopython_Seq.iterators
- molsysmt.form.biopython_Seq.merge
- molsysmt.form.biopython_Seq.set, [1]
- molsysmt.form.biopython_Seq.to_biopython_Seq
- molsysmt.form.biopython_Seq.to_biopython_SeqRecord
- molsysmt.form.biopython_SeqRecord
- molsysmt.form.biopython_SeqRecord.add
- molsysmt.form.biopython_SeqRecord.attributes
- molsysmt.form.biopython_SeqRecord.extract
- molsysmt.form.biopython_SeqRecord.get, [1]
- molsysmt.form.biopython_SeqRecord.has_attribute
- molsysmt.form.biopython_SeqRecord.is_form
- molsysmt.form.biopython_SeqRecord.iterators
- molsysmt.form.biopython_SeqRecord.merge
- molsysmt.form.biopython_SeqRecord.set, [1]
- molsysmt.form.biopython_SeqRecord.to_biopython_SeqRecord
- molsysmt.form.file_bcif
- molsysmt.form.file_bcif.add
- molsysmt.form.file_bcif.append_structures
- molsysmt.form.file_bcif.attributes
- molsysmt.form.file_bcif.copy
- molsysmt.form.file_bcif.download
- molsysmt.form.file_bcif.extract
- molsysmt.form.file_bcif.get, [1]
- molsysmt.form.file_bcif.has_attribute
- molsysmt.form.file_bcif.is_form
- molsysmt.form.file_bcif.iterators
- molsysmt.form.file_bcif.merge
- molsysmt.form.file_bcif.set, [1]
- molsysmt.form.file_bcif.to_bcifreader_PdbxContainers_DataContainer
- molsysmt.form.file_bcif.to_file_bcif
- molsysmt.form.file_bcif.to_file_h5msm
- molsysmt.form.file_bcif.to_mmcif_PdbxContainers_DataContainer
- molsysmt.form.file_bcif.to_molsysmt_MolSys
- molsysmt.form.file_bcif.to_molsysmt_Structures
- molsysmt.form.file_bcif.to_molsysmt_Topology
- molsysmt.form.file_bcif_gz
- molsysmt.form.file_bcif_gz.add
- molsysmt.form.file_bcif_gz.append_structures
- molsysmt.form.file_bcif_gz.attributes
- molsysmt.form.file_bcif_gz.copy
- molsysmt.form.file_bcif_gz.download
- molsysmt.form.file_bcif_gz.extract
- molsysmt.form.file_bcif_gz.get, [1]
- molsysmt.form.file_bcif_gz.has_attribute
- molsysmt.form.file_bcif_gz.is_form
- molsysmt.form.file_bcif_gz.iterators
- molsysmt.form.file_bcif_gz.merge
- molsysmt.form.file_bcif_gz.set, [1]
- molsysmt.form.file_bcif_gz.to_bcifreader_PdbxContainers_DataContainer
- molsysmt.form.file_bcif_gz.to_file_bcif_gz
- molsysmt.form.file_bcif_gz.to_file_h5msm
- molsysmt.form.file_bcif_gz.to_mmcif_PdbxContainers_DataContainer
- molsysmt.form.file_bcif_gz.to_molsysmt_MolSys
- molsysmt.form.file_bcif_gz.to_molsysmt_Structures
- molsysmt.form.file_bcif_gz.to_molsysmt_Topology
- molsysmt.form.file_cif
- molsysmt.form.file_cif.add
- molsysmt.form.file_cif.append_structures
- molsysmt.form.file_cif.attributes
- molsysmt.form.file_cif.copy
- molsysmt.form.file_cif.extract
- molsysmt.form.file_cif.get, [1]
- molsysmt.form.file_cif.has_attribute
- molsysmt.form.file_cif.is_form
- molsysmt.form.file_cif.iterators
- molsysmt.form.file_cif.merge
- molsysmt.form.file_cif.set, [1]
- molsysmt.form.file_cif.to_file_cif
- molsysmt.form.file_cif.to_molsysmt_CIFFileHandler
- molsysmt.form.file_crd
- molsysmt.form.file_crd.add
- molsysmt.form.file_crd.append_structures
- molsysmt.form.file_crd.attributes
- molsysmt.form.file_crd.copy
- molsysmt.form.file_crd.extract
- molsysmt.form.file_crd.get, [1]
- molsysmt.form.file_crd.has_attribute
- molsysmt.form.file_crd.is_form
- molsysmt.form.file_crd.iterators
- molsysmt.form.file_crd.merge
- molsysmt.form.file_crd.set, [1]
- molsysmt.form.file_crd.to_file_crd
- 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
- molsysmt.form.file_dcd.add
- molsysmt.form.file_dcd.append_structures
- molsysmt.form.file_dcd.attributes
- molsysmt.form.file_dcd.copy
- molsysmt.form.file_dcd.extract
- molsysmt.form.file_dcd.get, [1]
- molsysmt.form.file_dcd.has_attribute
- molsysmt.form.file_dcd.is_form
- molsysmt.form.file_dcd.iterators
- molsysmt.form.file_dcd.merge
- molsysmt.form.file_dcd.set, [1]
- molsysmt.form.file_dcd.to_file_dcd
- 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
- molsysmt.form.file_gro.add
- molsysmt.form.file_gro.append_structures
- molsysmt.form.file_gro.attributes
- molsysmt.form.file_gro.copy
- molsysmt.form.file_gro.extract
- molsysmt.form.file_gro.get, [1]
- molsysmt.form.file_gro.has_attribute
- molsysmt.form.file_gro.is_form
- molsysmt.form.file_gro.iterators
- molsysmt.form.file_gro.merge
- molsysmt.form.file_gro.set, [1]
- molsysmt.form.file_gro.to_file_gro
- 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
- molsysmt.form.file_h5.add
- molsysmt.form.file_h5.append_structures
- molsysmt.form.file_h5.attributes
- molsysmt.form.file_h5.copy
- molsysmt.form.file_h5.extract
- molsysmt.form.file_h5.get, [1]
- molsysmt.form.file_h5.has_attribute
- molsysmt.form.file_h5.is_form
- molsysmt.form.file_h5.iterators
- molsysmt.form.file_h5.merge
- molsysmt.form.file_h5.set, [1]
- molsysmt.form.file_h5.to_file_h5
- 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
- molsysmt.form.file_h5msm.add
- molsysmt.form.file_h5msm.append_structures
- molsysmt.form.file_h5msm.attributes
- molsysmt.form.file_h5msm.copy
- molsysmt.form.file_h5msm.extract
- molsysmt.form.file_h5msm.get_structural_attributes, [1]
- molsysmt.form.file_h5msm.get_topological_attributes, [1]
- molsysmt.form.file_h5msm.has_attribute
- molsysmt.form.file_h5msm.is_form
- molsysmt.form.file_h5msm.iterators
- molsysmt.form.file_h5msm.merge
- molsysmt.form.file_h5msm.set, [1]
- molsysmt.form.file_h5msm.to_file_h5msm
- 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
- molsysmt.form.file_inpcrd.add
- molsysmt.form.file_inpcrd.append_structures
- molsysmt.form.file_inpcrd.attributes
- molsysmt.form.file_inpcrd.copy
- molsysmt.form.file_inpcrd.extract
- molsysmt.form.file_inpcrd.get, [1]
- molsysmt.form.file_inpcrd.has_attribute
- molsysmt.form.file_inpcrd.is_form
- molsysmt.form.file_inpcrd.iterators
- molsysmt.form.file_inpcrd.merge
- molsysmt.form.file_inpcrd.set, [1]
- molsysmt.form.file_inpcrd.to_file_inpcrd
- molsysmt.form.file_inpcrd.to_molsysmt_Structures
- molsysmt.form.file_inpcrd.to_openmm_AmberInpcrdFile
- molsysmt.form.file_mmtf
- molsysmt.form.file_mmtf.add
- molsysmt.form.file_mmtf.append_structures
- molsysmt.form.file_mmtf.attributes
- molsysmt.form.file_mmtf.copy
- molsysmt.form.file_mmtf.download, [1]
- molsysmt.form.file_mmtf.extract
- molsysmt.form.file_mmtf.get, [1]
- molsysmt.form.file_mmtf.has_attribute
- molsysmt.form.file_mmtf.is_form
- molsysmt.form.file_mmtf.iterators
- molsysmt.form.file_mmtf.merge
- molsysmt.form.file_mmtf.set, [1]
- molsysmt.form.file_mmtf.to_file_mmtf
- molsysmt.form.file_mmtf.to_file_pdb
- molsysmt.form.file_mmtf.to_MDAnalysis_Universe
- molsysmt.form.file_mmtf.to_mdtraj, [1]
- molsysmt.form.file_mmtf.to_mmtf_MMTFDecoder
- molsysmt.form.file_mmtf.to_molsysmt_MolSys
- molsysmt.form.file_mmtf.to_molsysmt_Structures
- molsysmt.form.file_mmtf.to_molsysmt_Topology
- molsysmt.form.file_mmtf.to_openmm_Topology
- molsysmt.form.file_mmtf.to_string_amino_acids_1
- molsysmt.form.file_mmtf.to_string_amino_acids_3
- molsysmt.form.file_mmtf.to_string_pdb_text
- molsysmt.form.file_mol2
- molsysmt.form.file_mol2.add
- molsysmt.form.file_mol2.append_structures
- molsysmt.form.file_mol2.attributes
- molsysmt.form.file_mol2.copy
- molsysmt.form.file_mol2.extract
- molsysmt.form.file_mol2.get, [1]
- molsysmt.form.file_mol2.has_attribute
- molsysmt.form.file_mol2.is_form
- molsysmt.form.file_mol2.iterators
- molsysmt.form.file_mol2.merge
- molsysmt.form.file_mol2.set, [1]
- molsysmt.form.file_mol2.to_file_mol2
- 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_msmpk
- molsysmt.form.file_msmpk.add
- molsysmt.form.file_msmpk.append_structures
- molsysmt.form.file_msmpk.attributes
- molsysmt.form.file_msmpk.copy
- molsysmt.form.file_msmpk.extract
- molsysmt.form.file_msmpk.get, [1]
- molsysmt.form.file_msmpk.has_attribute
- molsysmt.form.file_msmpk.is_form
- molsysmt.form.file_msmpk.iterators
- molsysmt.form.file_msmpk.merge
- molsysmt.form.file_msmpk.set, [1]
- molsysmt.form.file_msmpk.to_file_msmpk
- molsysmt.form.file_msmpk.to_molsysmt_MolSys
- molsysmt.form.file_msmpk.to_molsysmt_Structures
- molsysmt.form.file_msmpk.to_molsysmt_Topology
- molsysmt.form.file_msmpk.to_nglview_NGLWidget
- molsysmt.form.file_msmpk.update_file
- molsysmt.form.file_pdb
- molsysmt.form.file_pdb.add
- molsysmt.form.file_pdb.append_structures
- molsysmt.form.file_pdb.attributes
- molsysmt.form.file_pdb.copy
- molsysmt.form.file_pdb.download
- molsysmt.form.file_pdb.extract
- molsysmt.form.file_pdb.get, [1]
- molsysmt.form.file_pdb.has_atoms_with_alternate_locations
- molsysmt.form.file_pdb.has_attribute
- molsysmt.form.file_pdb.is_form
- molsysmt.form.file_pdb.iterators
- molsysmt.form.file_pdb.merge
- molsysmt.form.file_pdb.replace_HETATM_by_ATOM_in_terminal_cappings
- molsysmt.form.file_pdb.set, [1]
- molsysmt.form.file_pdb.to_file_mol2
- molsysmt.form.file_pdb.to_file_pdb
- molsysmt.form.file_pdb.to_MDAnalysis_Topology
- molsysmt.form.file_pdb.to_MDAnalysis_topology_PDBParser, [1]
- 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
- molsysmt.form.file_prmtop.add
- molsysmt.form.file_prmtop.append_structures
- molsysmt.form.file_prmtop.attributes
- molsysmt.form.file_prmtop.copy
- molsysmt.form.file_prmtop.extract
- molsysmt.form.file_prmtop.get, [1]
- molsysmt.form.file_prmtop.has_attribute
- molsysmt.form.file_prmtop.is_form
- molsysmt.form.file_prmtop.iterators
- molsysmt.form.file_prmtop.merge
- molsysmt.form.file_prmtop.set, [1]
- molsysmt.form.file_prmtop.to_file_pdb
- molsysmt.form.file_prmtop.to_file_prmtop
- 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
- molsysmt.form.file_psf.add
- molsysmt.form.file_psf.append_structures
- molsysmt.form.file_psf.attributes
- molsysmt.form.file_psf.copy
- molsysmt.form.file_psf.extract
- molsysmt.form.file_psf.get, [1]
- molsysmt.form.file_psf.has_attribute
- molsysmt.form.file_psf.is_form
- molsysmt.form.file_psf.iterators
- molsysmt.form.file_psf.merge
- molsysmt.form.file_psf.set, [1]
- molsysmt.form.file_psf.to_file_psf
- molsysmt.form.file_psf.to_molsysmt_MolSys
- molsysmt.form.file_psf.to_molsysmt_MolSysOld
- 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
- molsysmt.form.file_trjpk.add
- molsysmt.form.file_trjpk.append_structures
- molsysmt.form.file_trjpk.attributes
- molsysmt.form.file_trjpk.copy
- molsysmt.form.file_trjpk.extract
- molsysmt.form.file_trjpk.get, [1]
- molsysmt.form.file_trjpk.has_attribute
- molsysmt.form.file_trjpk.is_form
- molsysmt.form.file_trjpk.iterators
- molsysmt.form.file_trjpk.merge
- molsysmt.form.file_trjpk.set, [1]
- molsysmt.form.file_trjpk.to_file_trjpk
- molsysmt.form.file_trjpk.to_molsysmt_StructuresDict
- molsysmt.form.file_xtc
- molsysmt.form.file_xtc.add
- molsysmt.form.file_xtc.append_structures
- molsysmt.form.file_xtc.attributes
- molsysmt.form.file_xtc.copy
- molsysmt.form.file_xtc.extract
- molsysmt.form.file_xtc.get, [1]
- molsysmt.form.file_xtc.has_attribute
- molsysmt.form.file_xtc.is_form
- molsysmt.form.file_xtc.iterators
- molsysmt.form.file_xtc.merge
- molsysmt.form.file_xtc.set, [1]
- molsysmt.form.file_xtc.to_file_xtc
- 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
- molsysmt.form.file_xyznpy.add
- molsysmt.form.file_xyznpy.append_structures
- molsysmt.form.file_xyznpy.attributes
- molsysmt.form.file_xyznpy.copy
- molsysmt.form.file_xyznpy.extract
- molsysmt.form.file_xyznpy.get, [1]
- molsysmt.form.file_xyznpy.has_attribute
- molsysmt.form.file_xyznpy.is_form
- molsysmt.form.file_xyznpy.iterators
- molsysmt.form.file_xyznpy.merge
- molsysmt.form.file_xyznpy.set, [1]
- molsysmt.form.file_xyznpy.to_file_xyznpy
- molsysmt.form.file_xyznpy.to_XYZ
- molsysmt.form.get_attributes
- molsysmt.form.has_attribute
- molsysmt.form.is_file
- molsysmt.form.is_item
- molsysmt.form.is_string
- molsysmt.form.iterators
- molsysmt.form.MDAnalysis_Topology
- molsysmt.form.MDAnalysis_Topology.add
- molsysmt.form.MDAnalysis_Topology.append_structures
- molsysmt.form.MDAnalysis_Topology.attributes
- molsysmt.form.MDAnalysis_Topology.copy
- molsysmt.form.MDAnalysis_Topology.extract
- molsysmt.form.MDAnalysis_Topology.get, [1]
- molsysmt.form.MDAnalysis_Topology.has_attribute
- molsysmt.form.MDAnalysis_Topology.is_form
- molsysmt.form.MDAnalysis_Topology.iterators
- molsysmt.form.MDAnalysis_Topology.merge
- molsysmt.form.MDAnalysis_Topology.set, [1]
- molsysmt.form.MDAnalysis_Topology.to_MDAnalysis_Topology
- molsysmt.form.MDAnalysis_Universe
- molsysmt.form.MDAnalysis_Universe.add
- molsysmt.form.MDAnalysis_Universe.append_structures
- molsysmt.form.MDAnalysis_Universe.attributes
- molsysmt.form.MDAnalysis_Universe.copy
- molsysmt.form.MDAnalysis_Universe.extract
- molsysmt.form.MDAnalysis_Universe.get, [1]
- molsysmt.form.MDAnalysis_Universe.has_attribute
- molsysmt.form.MDAnalysis_Universe.is_form
- molsysmt.form.MDAnalysis_Universe.iterators
- molsysmt.form.MDAnalysis_Universe.merge
- molsysmt.form.MDAnalysis_Universe.set, [1]
- molsysmt.form.MDAnalysis_Universe.to_file_pdb
- molsysmt.form.MDAnalysis_Universe.to_MDAnalysis_Universe
- 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
- molsysmt.form.mdtraj_DCDTrajectoryFile.add
- molsysmt.form.mdtraj_DCDTrajectoryFile.append_structures
- molsysmt.form.mdtraj_DCDTrajectoryFile.attributes
- molsysmt.form.mdtraj_DCDTrajectoryFile.copy
- molsysmt.form.mdtraj_DCDTrajectoryFile.extract
- molsysmt.form.mdtraj_DCDTrajectoryFile.get, [1]
- molsysmt.form.mdtraj_DCDTrajectoryFile.has_attribute
- molsysmt.form.mdtraj_DCDTrajectoryFile.is_form
- molsysmt.form.mdtraj_DCDTrajectoryFile.iterators
- molsysmt.form.mdtraj_DCDTrajectoryFile.merge
- molsysmt.form.mdtraj_DCDTrajectoryFile.set, [1]
- molsysmt.form.mdtraj_DCDTrajectoryFile.to_mdtraj_DCDTrajectoryFile
- molsysmt.form.mdtraj_DCDTrajectoryFile.to_molsysmt_MolSys
- molsysmt.form.mdtraj_DCDTrajectoryFile.to_molsysmt_Structures
- molsysmt.form.mdtraj_HDF5TrajectoryFile
- molsysmt.form.mdtraj_HDF5TrajectoryFile.add
- molsysmt.form.mdtraj_HDF5TrajectoryFile.append_structures
- molsysmt.form.mdtraj_HDF5TrajectoryFile.attributes
- molsysmt.form.mdtraj_HDF5TrajectoryFile.copy
- molsysmt.form.mdtraj_HDF5TrajectoryFile.extract
- molsysmt.form.mdtraj_HDF5TrajectoryFile.get, [1]
- molsysmt.form.mdtraj_HDF5TrajectoryFile.has_attribute
- molsysmt.form.mdtraj_HDF5TrajectoryFile.is_form
- molsysmt.form.mdtraj_HDF5TrajectoryFile.iterators
- molsysmt.form.mdtraj_HDF5TrajectoryFile.merge
- molsysmt.form.mdtraj_HDF5TrajectoryFile.set, [1]
- molsysmt.form.mdtraj_HDF5TrajectoryFile.to_mdtraj_HDF5TrajectoryFile
- 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
- molsysmt.form.mdtraj_Topology.add
- molsysmt.form.mdtraj_Topology.append_structures
- molsysmt.form.mdtraj_Topology.attributes
- molsysmt.form.mdtraj_Topology.copy
- molsysmt.form.mdtraj_Topology.extract
- molsysmt.form.mdtraj_Topology.get
- molsysmt.form.mdtraj_Topology.get_structural_attributes, [1]
- molsysmt.form.mdtraj_Topology.get_topological_attributes, [1]
- molsysmt.form.mdtraj_Topology.has_attribute
- molsysmt.form.mdtraj_Topology.is_form
- molsysmt.form.mdtraj_Topology.iterators
- molsysmt.form.mdtraj_Topology.merge
- molsysmt.form.mdtraj_Topology.set, [1]
- molsysmt.form.mdtraj_Topology.to_file_top
- molsysmt.form.mdtraj_Topology.to_mdtraj_Topology
- 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
- molsysmt.form.mdtraj_Trajectory.add
- molsysmt.form.mdtraj_Trajectory.append_structures
- molsysmt.form.mdtraj_Trajectory.attributes
- molsysmt.form.mdtraj_Trajectory.copy
- molsysmt.form.mdtraj_Trajectory.extract
- molsysmt.form.mdtraj_Trajectory.get, [1]
- molsysmt.form.mdtraj_Trajectory.has_attribute
- molsysmt.form.mdtraj_Trajectory.is_form
- molsysmt.form.mdtraj_Trajectory.iterators
- molsysmt.form.mdtraj_Trajectory.merge
- molsysmt.form.mdtraj_Trajectory.set, [1]
- 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_mdtraj_Trajectory
- 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
- molsysmt.form.mdtraj_XTCTrajectoryFile.add
- molsysmt.form.mdtraj_XTCTrajectoryFile.append_structures
- molsysmt.form.mdtraj_XTCTrajectoryFile.attributes
- molsysmt.form.mdtraj_XTCTrajectoryFile.copy
- molsysmt.form.mdtraj_XTCTrajectoryFile.extract
- molsysmt.form.mdtraj_XTCTrajectoryFile.get, [1]
- molsysmt.form.mdtraj_XTCTrajectoryFile.has_attribute
- molsysmt.form.mdtraj_XTCTrajectoryFile.is_form
- molsysmt.form.mdtraj_XTCTrajectoryFile.iterators
- molsysmt.form.mdtraj_XTCTrajectoryFile.merge
- molsysmt.form.mdtraj_XTCTrajectoryFile.set, [1]
- molsysmt.form.mdtraj_XTCTrajectoryFile.to_mdtraj_XTCTrajectoryFile
- molsysmt.form.mdtraj_XTCTrajectoryFile.to_molsysmt_Structures
- molsysmt.form.mmcif_PdbxContainers_DataContainer
- molsysmt.form.mmcif_PdbxContainers_DataContainer.add
- molsysmt.form.mmcif_PdbxContainers_DataContainer.append_structures
- molsysmt.form.mmcif_PdbxContainers_DataContainer.attributes
- molsysmt.form.mmcif_PdbxContainers_DataContainer.copy
- molsysmt.form.mmcif_PdbxContainers_DataContainer.extract
- molsysmt.form.mmcif_PdbxContainers_DataContainer.get_structural_attributes, [1]
- molsysmt.form.mmcif_PdbxContainers_DataContainer.get_topological_attributes, [1]
- molsysmt.form.mmcif_PdbxContainers_DataContainer.has_attribute
- molsysmt.form.mmcif_PdbxContainers_DataContainer.is_form
- molsysmt.form.mmcif_PdbxContainers_DataContainer.iterators
- molsysmt.form.mmcif_PdbxContainers_DataContainer.merge
- molsysmt.form.mmcif_PdbxContainers_DataContainer.set, [1]
- molsysmt.form.mmcif_PdbxContainers_DataContainer.to_file_pdb
- molsysmt.form.mmcif_PdbxContainers_DataContainer.to_mdtraj_Trajectory
- molsysmt.form.mmcif_PdbxContainers_DataContainer.to_mmcif_PdbxContainers_DataContainer
- 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.mmtf_MMTFDecoder
- molsysmt.form.mmtf_MMTFDecoder.add
- molsysmt.form.mmtf_MMTFDecoder.append_structures
- molsysmt.form.mmtf_MMTFDecoder.attributes
- molsysmt.form.mmtf_MMTFDecoder.copy
- molsysmt.form.mmtf_MMTFDecoder.extract
- molsysmt.form.mmtf_MMTFDecoder.get_structural_attributes, [1]
- molsysmt.form.mmtf_MMTFDecoder.get_topological_attributes, [1]
- molsysmt.form.mmtf_MMTFDecoder.has_attribute
- molsysmt.form.mmtf_MMTFDecoder.is_form
- molsysmt.form.mmtf_MMTFDecoder.iterators
- molsysmt.form.mmtf_MMTFDecoder.merge
- molsysmt.form.mmtf_MMTFDecoder.set, [1]
- molsysmt.form.mmtf_MMTFDecoder.to_file_mmtf
- molsysmt.form.mmtf_MMTFDecoder.to_file_pdb
- molsysmt.form.mmtf_MMTFDecoder.to_mdtraj_Trajectory
- molsysmt.form.mmtf_MMTFDecoder.to_mmtf_MMTFDecoder
- molsysmt.form.mmtf_MMTFDecoder.to_molsysmt_MolecularMechanics
- molsysmt.form.mmtf_MMTFDecoder.to_molsysmt_MolSys
- molsysmt.form.mmtf_MMTFDecoder.to_molsysmt_Structures
- molsysmt.form.mmtf_MMTFDecoder.to_molsysmt_Topology
- molsysmt.form.mmtf_MMTFDecoder.to_openmm_Topology
- molsysmt.form.mmtf_MMTFDecoder.to_string_amino_acids_1
- molsysmt.form.mmtf_MMTFDecoder.to_string_amino_acids_3
- molsysmt.form.mmtf_MMTFDecoder.to_string_pdb_text
- molsysmt.form.molsysmt_CIFFileHandler
- molsysmt.form.molsysmt_CIFFileHandler.add
- molsysmt.form.molsysmt_CIFFileHandler.append_structures
- molsysmt.form.molsysmt_CIFFileHandler.attributes
- molsysmt.form.molsysmt_CIFFileHandler.copy
- molsysmt.form.molsysmt_CIFFileHandler.extract
- molsysmt.form.molsysmt_CIFFileHandler.get, [1]
- molsysmt.form.molsysmt_CIFFileHandler.has_attribute
- molsysmt.form.molsysmt_CIFFileHandler.is_form
- molsysmt.form.molsysmt_CIFFileHandler.iterators
- molsysmt.form.molsysmt_CIFFileHandler.merge
- molsysmt.form.molsysmt_CIFFileHandler.set, [1]
- molsysmt.form.molsysmt_CIFFileHandler.to_molsysmt_CIFFileHandler
- molsysmt.form.molsysmt_GROFileHandler
- molsysmt.form.molsysmt_GROFileHandler.add
- molsysmt.form.molsysmt_GROFileHandler.append_structures
- molsysmt.form.molsysmt_GROFileHandler.attributes
- molsysmt.form.molsysmt_GROFileHandler.copy
- molsysmt.form.molsysmt_GROFileHandler.extract
- molsysmt.form.molsysmt_GROFileHandler.get, [1]
- molsysmt.form.molsysmt_GROFileHandler.has_attribute
- molsysmt.form.molsysmt_GROFileHandler.is_form
- molsysmt.form.molsysmt_GROFileHandler.iterators
- molsysmt.form.molsysmt_GROFileHandler.merge
- molsysmt.form.molsysmt_GROFileHandler.set, [1]
- molsysmt.form.molsysmt_GROFileHandler.to_molsysmt_GROFileHandler
- 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
- molsysmt.form.molsysmt_H5MSMFileHandler.add
- molsysmt.form.molsysmt_H5MSMFileHandler.append_structures
- molsysmt.form.molsysmt_H5MSMFileHandler.attributes
- molsysmt.form.molsysmt_H5MSMFileHandler.copy
- molsysmt.form.molsysmt_H5MSMFileHandler.extract
- molsysmt.form.molsysmt_H5MSMFileHandler.get_structural_attributes, [1]
- molsysmt.form.molsysmt_H5MSMFileHandler.get_topological_attributes, [1]
- molsysmt.form.molsysmt_H5MSMFileHandler.has_attribute
- molsysmt.form.molsysmt_H5MSMFileHandler.is_form
- molsysmt.form.molsysmt_H5MSMFileHandler.iterators
- molsysmt.form.molsysmt_H5MSMFileHandler.merge
- molsysmt.form.molsysmt_H5MSMFileHandler.set, [1]
- molsysmt.form.molsysmt_H5MSMFileHandler.to_molsysmt_H5MSMFileHandler
- 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
- molsysmt.form.molsysmt_MolecularMechanics.add
- molsysmt.form.molsysmt_MolecularMechanics.append_structures
- molsysmt.form.molsysmt_MolecularMechanics.attributes
- molsysmt.form.molsysmt_MolecularMechanics.copy
- molsysmt.form.molsysmt_MolecularMechanics.extract
- molsysmt.form.molsysmt_MolecularMechanics.get, [1]
- molsysmt.form.molsysmt_MolecularMechanics.has_attribute
- molsysmt.form.molsysmt_MolecularMechanics.is_form
- molsysmt.form.molsysmt_MolecularMechanics.iterators
- molsysmt.form.molsysmt_MolecularMechanics.merge
- molsysmt.form.molsysmt_MolecularMechanics.set, [1]
- molsysmt.form.molsysmt_MolecularMechanics.to_molsysmt_MolecularMechanics
- molsysmt.form.molsysmt_MolecularMechanics.to_molsysmt_MolecularMechanicsDict
- molsysmt.form.molsysmt_MolecularMechanicsDict
- molsysmt.form.molsysmt_MolecularMechanicsDict.add
- molsysmt.form.molsysmt_MolecularMechanicsDict.append_structures
- molsysmt.form.molsysmt_MolecularMechanicsDict.attributes
- molsysmt.form.molsysmt_MolecularMechanicsDict.copy
- molsysmt.form.molsysmt_MolecularMechanicsDict.extract
- molsysmt.form.molsysmt_MolecularMechanicsDict.get, [1]
- molsysmt.form.molsysmt_MolecularMechanicsDict.has_attribute
- molsysmt.form.molsysmt_MolecularMechanicsDict.is_form
- molsysmt.form.molsysmt_MolecularMechanicsDict.iterators
- molsysmt.form.molsysmt_MolecularMechanicsDict.merge
- molsysmt.form.molsysmt_MolecularMechanicsDict.set, [1]
- molsysmt.form.molsysmt_MolecularMechanicsDict.to_molsysmt_MolecularMechanics
- molsysmt.form.molsysmt_MolecularMechanicsDict.to_molsysmt_MolecularMechanicsDict
- molsysmt.form.molsysmt_MolSys
- molsysmt.form.molsysmt_MolSys.add
- molsysmt.form.molsysmt_MolSys.add_bonds
- molsysmt.form.molsysmt_MolSys.append_structures
- molsysmt.form.molsysmt_MolSys.attributes
- molsysmt.form.molsysmt_MolSys.copy
- molsysmt.form.molsysmt_MolSys.extract
- molsysmt.form.molsysmt_MolSys.get_mechanical_attributes, [1]
- molsysmt.form.molsysmt_MolSys.get_structural_attributes, [1]
- molsysmt.form.molsysmt_MolSys.get_topological_attributes, [1]
- molsysmt.form.molsysmt_MolSys.has_attribute
- molsysmt.form.molsysmt_MolSys.is_form
- molsysmt.form.molsysmt_MolSys.iterators
- molsysmt.form.molsysmt_MolSys.merge
- molsysmt.form.molsysmt_MolSys.old_get
- molsysmt.form.molsysmt_MolSys.remove_bonds
- molsysmt.form.molsysmt_MolSys.set, [1]
- 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_msmpk
- 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_MolSys
- 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_parmed_Structure
- 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
- molsysmt.form.molsysmt_PDBFileHandler.add
- molsysmt.form.molsysmt_PDBFileHandler.append_structures
- molsysmt.form.molsysmt_PDBFileHandler.attributes
- molsysmt.form.molsysmt_PDBFileHandler.copy
- molsysmt.form.molsysmt_PDBFileHandler.extract
- molsysmt.form.molsysmt_PDBFileHandler.get, [1]
- molsysmt.form.molsysmt_PDBFileHandler.has_attribute
- molsysmt.form.molsysmt_PDBFileHandler.is_form
- molsysmt.form.molsysmt_PDBFileHandler.iterators
- molsysmt.form.molsysmt_PDBFileHandler.merge
- molsysmt.form.molsysmt_PDBFileHandler.set, [1]
- molsysmt.form.molsysmt_PDBFileHandler.to_molsysmt_MolSys
- molsysmt.form.molsysmt_PDBFileHandler.to_molsysmt_PDBFileHandler
- 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
- molsysmt.form.molsysmt_Structures.add
- molsysmt.form.molsysmt_Structures.append_structures
- molsysmt.form.molsysmt_Structures.attributes
- molsysmt.form.molsysmt_Structures.copy
- molsysmt.form.molsysmt_Structures.extract
- molsysmt.form.molsysmt_Structures.get_structural_attributes, [1]
- molsysmt.form.molsysmt_Structures.has_attribute
- molsysmt.form.molsysmt_Structures.is_form
- molsysmt.form.molsysmt_Structures.iterators
- molsysmt.form.molsysmt_Structures.merge
- molsysmt.form.molsysmt_Structures.set, [1]
- molsysmt.form.molsysmt_Structures.to_file_h5msm
- molsysmt.form.molsysmt_Structures.to_molsysmt_Structures
- molsysmt.form.molsysmt_Structures.to_molsysmt_StructuresDict
- molsysmt.form.molsysmt_Structures.to_XYZ
- molsysmt.form.molsysmt_StructuresDict
- molsysmt.form.molsysmt_StructuresDict.add
- molsysmt.form.molsysmt_StructuresDict.append_structures
- molsysmt.form.molsysmt_StructuresDict.attributes
- molsysmt.form.molsysmt_StructuresDict.copy
- molsysmt.form.molsysmt_StructuresDict.extract
- molsysmt.form.molsysmt_StructuresDict.get, [1]
- molsysmt.form.molsysmt_StructuresDict.has_attribute
- molsysmt.form.molsysmt_StructuresDict.is_form
- molsysmt.form.molsysmt_StructuresDict.iterators
- molsysmt.form.molsysmt_StructuresDict.merge
- molsysmt.form.molsysmt_StructuresDict.set, [1]
- 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_StructuresDict
- molsysmt.form.molsysmt_StructuresDict.to_molsysmt_Topology
- molsysmt.form.molsysmt_Topology
- molsysmt.form.molsysmt_Topology.add
- molsysmt.form.molsysmt_Topology.add_bonds
- molsysmt.form.molsysmt_Topology.append_structures
- molsysmt.form.molsysmt_Topology.attributes
- molsysmt.form.molsysmt_Topology.copy
- molsysmt.form.molsysmt_Topology.extract
- molsysmt.form.molsysmt_Topology.get_topological_attributes, [1]
- molsysmt.form.molsysmt_Topology.has_attribute
- molsysmt.form.molsysmt_Topology.is_form
- molsysmt.form.molsysmt_Topology.iterators
- molsysmt.form.molsysmt_Topology.merge
- molsysmt.form.molsysmt_Topology.remove_bonds
- molsysmt.form.molsysmt_Topology.set, [1]
- 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_molsysmt_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
- molsysmt.form.networkx_Graph.add
- molsysmt.form.networkx_Graph.append_structures
- molsysmt.form.networkx_Graph.attributes
- molsysmt.form.networkx_Graph.copy
- molsysmt.form.networkx_Graph.extract
- molsysmt.form.networkx_Graph.get, [1]
- molsysmt.form.networkx_Graph.has_attribute
- molsysmt.form.networkx_Graph.is_form
- molsysmt.form.networkx_Graph.iterators
- molsysmt.form.networkx_Graph.merge
- molsysmt.form.networkx_Graph.set, [1]
- molsysmt.form.networkx_Graph.to_networkx_Graph
- molsysmt.form.nglview_NGLWidget
- molsysmt.form.nglview_NGLWidget.add
- molsysmt.form.nglview_NGLWidget.append_structures
- molsysmt.form.nglview_NGLWidget.attributes
- molsysmt.form.nglview_NGLWidget.copy
- molsysmt.form.nglview_NGLWidget.extract
- molsysmt.form.nglview_NGLWidget.get_structural_attributes, [1]
- molsysmt.form.nglview_NGLWidget.get_topological_attributes, [1]
- molsysmt.form.nglview_NGLWidget.has_attribute
- molsysmt.form.nglview_NGLWidget.is_form
- molsysmt.form.nglview_NGLWidget.iterators
- molsysmt.form.nglview_NGLWidget.merge
- molsysmt.form.nglview_NGLWidget.set, [1]
- 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_nglview_NGLWidget
- 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
- molsysmt.form.openmm_AmberInpcrdFile.add
- molsysmt.form.openmm_AmberInpcrdFile.append_structures
- molsysmt.form.openmm_AmberInpcrdFile.attributes
- molsysmt.form.openmm_AmberInpcrdFile.copy
- molsysmt.form.openmm_AmberInpcrdFile.extract
- molsysmt.form.openmm_AmberInpcrdFile.get, [1]
- molsysmt.form.openmm_AmberInpcrdFile.has_attribute
- molsysmt.form.openmm_AmberInpcrdFile.is_form
- molsysmt.form.openmm_AmberInpcrdFile.iterators
- molsysmt.form.openmm_AmberInpcrdFile.merge
- molsysmt.form.openmm_AmberInpcrdFile.set, [1]
- molsysmt.form.openmm_AmberInpcrdFile.to_molsysmt_Structures
- molsysmt.form.openmm_AmberInpcrdFile.to_openmm_AmberInpcrdFile
- molsysmt.form.openmm_AmberPrmtopFile
- molsysmt.form.openmm_AmberPrmtopFile.add
- molsysmt.form.openmm_AmberPrmtopFile.append_structures
- molsysmt.form.openmm_AmberPrmtopFile.attributes
- molsysmt.form.openmm_AmberPrmtopFile.copy
- molsysmt.form.openmm_AmberPrmtopFile.extract
- molsysmt.form.openmm_AmberPrmtopFile.get, [1]
- molsysmt.form.openmm_AmberPrmtopFile.has_attribute
- molsysmt.form.openmm_AmberPrmtopFile.is_form
- molsysmt.form.openmm_AmberPrmtopFile.iterators
- molsysmt.form.openmm_AmberPrmtopFile.merge
- molsysmt.form.openmm_AmberPrmtopFile.set, [1]
- molsysmt.form.openmm_AmberPrmtopFile.to_molsysmt_Topology
- molsysmt.form.openmm_AmberPrmtopFile.to_openmm_AmberPrmtopFile
- molsysmt.form.openmm_AmberPrmtopFile.to_openmm_System
- molsysmt.form.openmm_AmberPrmtopFile.to_openmm_Topology
- molsysmt.form.openmm_CharmmCrdFile
- molsysmt.form.openmm_CharmmCrdFile.add
- molsysmt.form.openmm_CharmmCrdFile.append_structures
- molsysmt.form.openmm_CharmmCrdFile.attributes
- molsysmt.form.openmm_CharmmCrdFile.copy
- molsysmt.form.openmm_CharmmCrdFile.extract
- molsysmt.form.openmm_CharmmCrdFile.get, [1]
- molsysmt.form.openmm_CharmmCrdFile.has_attribute
- molsysmt.form.openmm_CharmmCrdFile.is_form
- molsysmt.form.openmm_CharmmCrdFile.iterators
- molsysmt.form.openmm_CharmmCrdFile.merge
- molsysmt.form.openmm_CharmmCrdFile.set, [1]
- molsysmt.form.openmm_CharmmCrdFile.to_openmm_CharmmCrdFile
- molsysmt.form.openmm_CharmmPsfFile
- molsysmt.form.openmm_CharmmPsfFile.add
- molsysmt.form.openmm_CharmmPsfFile.append_structures
- molsysmt.form.openmm_CharmmPsfFile.attributes
- molsysmt.form.openmm_CharmmPsfFile.copy
- molsysmt.form.openmm_CharmmPsfFile.extract
- molsysmt.form.openmm_CharmmPsfFile.get, [1]
- molsysmt.form.openmm_CharmmPsfFile.has_attribute
- molsysmt.form.openmm_CharmmPsfFile.is_form
- molsysmt.form.openmm_CharmmPsfFile.iterators
- molsysmt.form.openmm_CharmmPsfFile.merge
- molsysmt.form.openmm_CharmmPsfFile.set, [1]
- molsysmt.form.openmm_CharmmPsfFile.to_molsysmt_Topology
- molsysmt.form.openmm_CharmmPsfFile.to_openmm_CharmmPsfFile
- molsysmt.form.openmm_CharmmPsfFile.to_openmm_Topology
- molsysmt.form.openmm_Context
- molsysmt.form.openmm_Context.add
- molsysmt.form.openmm_Context.append_structures
- molsysmt.form.openmm_Context.attributes
- molsysmt.form.openmm_Context.copy
- molsysmt.form.openmm_Context.extract
- molsysmt.form.openmm_Context.get_structural_attributes, [1]
- molsysmt.form.openmm_Context.get_topological_attributes, [1]
- molsysmt.form.openmm_Context.has_attribute
- molsysmt.form.openmm_Context.is_form
- molsysmt.form.openmm_Context.iterators
- molsysmt.form.openmm_Context.merge
- molsysmt.form.openmm_Context.set, [1]
- molsysmt.form.openmm_Context.to_molsysmt_Structures
- molsysmt.form.openmm_Context.to_openmm_Context
- molsysmt.form.openmm_Context.to_openmm_System
- molsysmt.form.openmm_GromacsGroFile
- molsysmt.form.openmm_GromacsGroFile.add
- molsysmt.form.openmm_GromacsGroFile.append_structures
- molsysmt.form.openmm_GromacsGroFile.attributes
- molsysmt.form.openmm_GromacsGroFile.copy
- molsysmt.form.openmm_GromacsGroFile.extract
- molsysmt.form.openmm_GromacsGroFile.get, [1]
- molsysmt.form.openmm_GromacsGroFile.has_attribute
- molsysmt.form.openmm_GromacsGroFile.is_form
- molsysmt.form.openmm_GromacsGroFile.iterators
- molsysmt.form.openmm_GromacsGroFile.merge
- molsysmt.form.openmm_GromacsGroFile.set, [1]
- 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_GromacsGroFile
- molsysmt.form.openmm_GromacsGroFile.to_openmm_Modeller
- molsysmt.form.openmm_GromacsGroFile.to_openmm_Topology
- molsysmt.form.openmm_GromacsTopFile
- molsysmt.form.openmm_GromacsTopFile.add
- molsysmt.form.openmm_GromacsTopFile.append_structures
- molsysmt.form.openmm_GromacsTopFile.attributes
- molsysmt.form.openmm_GromacsTopFile.copy
- molsysmt.form.openmm_GromacsTopFile.extract
- molsysmt.form.openmm_GromacsTopFile.get, [1]
- molsysmt.form.openmm_GromacsTopFile.has_attribute
- molsysmt.form.openmm_GromacsTopFile.is_form
- molsysmt.form.openmm_GromacsTopFile.iterators
- molsysmt.form.openmm_GromacsTopFile.merge
- molsysmt.form.openmm_GromacsTopFile.set, [1]
- molsysmt.form.openmm_GromacsTopFile.to_molsysmt_Topology
- molsysmt.form.openmm_GromacsTopFile.to_openmm_GromacsTopFile
- molsysmt.form.openmm_GromacsTopFile.to_openmm_Topology
- molsysmt.form.openmm_Modeller
- molsysmt.form.openmm_Modeller.add
- molsysmt.form.openmm_Modeller.append_structures
- molsysmt.form.openmm_Modeller.attributes
- molsysmt.form.openmm_Modeller.copy
- molsysmt.form.openmm_Modeller.extract
- molsysmt.form.openmm_Modeller.get_structural_attributes, [1]
- molsysmt.form.openmm_Modeller.get_topological_attributes, [1]
- molsysmt.form.openmm_Modeller.has_attribute
- molsysmt.form.openmm_Modeller.is_form
- molsysmt.form.openmm_Modeller.iterators
- molsysmt.form.openmm_Modeller.merge
- molsysmt.form.openmm_Modeller.set, [1]
- 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_Modeller
- 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
- molsysmt.form.openmm_PDBFile.add
- molsysmt.form.openmm_PDBFile.append_structures
- molsysmt.form.openmm_PDBFile.attributes
- molsysmt.form.openmm_PDBFile.copy
- molsysmt.form.openmm_PDBFile.extract
- molsysmt.form.openmm_PDBFile.get, [1]
- molsysmt.form.openmm_PDBFile.has_attribute
- molsysmt.form.openmm_PDBFile.is_form
- molsysmt.form.openmm_PDBFile.iterators
- molsysmt.form.openmm_PDBFile.merge
- molsysmt.form.openmm_PDBFile.set, [1]
- 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_PDBFile
- molsysmt.form.openmm_PDBFile.to_openmm_Topology
- molsysmt.form.openmm_Simulation
- molsysmt.form.openmm_Simulation.add
- molsysmt.form.openmm_Simulation.append_structures
- molsysmt.form.openmm_Simulation.attributes
- molsysmt.form.openmm_Simulation.copy
- molsysmt.form.openmm_Simulation.extract
- molsysmt.form.openmm_Simulation.get_structural_attributes, [1]
- molsysmt.form.openmm_Simulation.get_topological_attributes, [1]
- molsysmt.form.openmm_Simulation.has_attribute
- molsysmt.form.openmm_Simulation.is_form
- molsysmt.form.openmm_Simulation.iterators
- molsysmt.form.openmm_Simulation.merge
- molsysmt.form.openmm_Simulation.set, [1]
- molsysmt.form.openmm_Simulation.to_file_msmpk
- 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_Simulation
- molsysmt.form.openmm_Simulation.to_openmm_Topology
- molsysmt.form.openmm_Simulation.to_pdbfixer_PDBFixer
- molsysmt.form.openmm_State
- molsysmt.form.openmm_State.add
- molsysmt.form.openmm_State.append_structures
- molsysmt.form.openmm_State.attributes
- molsysmt.form.openmm_State.copy
- molsysmt.form.openmm_State.extract
- molsysmt.form.openmm_State.get, [1]
- molsysmt.form.openmm_State.has_attribute
- molsysmt.form.openmm_State.is_form
- molsysmt.form.openmm_State.iterators
- molsysmt.form.openmm_State.merge
- molsysmt.form.openmm_State.set, [1]
- molsysmt.form.openmm_State.to_molsysmt_Structures
- molsysmt.form.openmm_State.to_openmm_State
- molsysmt.form.openmm_State.to_XYZ
- molsysmt.form.openmm_System
- molsysmt.form.openmm_System.add
- molsysmt.form.openmm_System.append_structures
- molsysmt.form.openmm_System.attributes
- molsysmt.form.openmm_System.copy
- molsysmt.form.openmm_System.extract
- molsysmt.form.openmm_System.get_structural_attributes, [1]
- molsysmt.form.openmm_System.get_topological_attributes, [1]
- molsysmt.form.openmm_System.has_attribute
- molsysmt.form.openmm_System.is_form
- molsysmt.form.openmm_System.iterators
- molsysmt.form.openmm_System.merge
- molsysmt.form.openmm_System.set, [1]
- molsysmt.form.openmm_System.to_openmm_Context
- molsysmt.form.openmm_System.to_openmm_Simulation
- molsysmt.form.openmm_System.to_openmm_System
- molsysmt.form.openmm_Topology
- molsysmt.form.openmm_Topology.add
- molsysmt.form.openmm_Topology.append_structures
- molsysmt.form.openmm_Topology.attributes
- molsysmt.form.openmm_Topology.copy
- molsysmt.form.openmm_Topology.extract
- molsysmt.form.openmm_Topology.get_structural_attributes, [1]
- molsysmt.form.openmm_Topology.get_topological_attributes, [1]
- molsysmt.form.openmm_Topology.has_attribute
- molsysmt.form.openmm_Topology.is_form
- molsysmt.form.openmm_Topology.iterators
- molsysmt.form.openmm_Topology.merge
- molsysmt.form.openmm_Topology.set, [1]
- 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_openmm_Topology
- 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.openmm_Topology.write_topology_in_h5msm
- molsysmt.form.parmed_Structure
- molsysmt.form.parmed_Structure.add
- molsysmt.form.parmed_Structure.append_structures
- molsysmt.form.parmed_Structure.attributes
- molsysmt.form.parmed_Structure.copy
- molsysmt.form.parmed_Structure.extract
- molsysmt.form.parmed_Structure.get, [1]
- molsysmt.form.parmed_Structure.has_attribute
- molsysmt.form.parmed_Structure.is_form
- molsysmt.form.parmed_Structure.iterators
- molsysmt.form.parmed_Structure.merge
- molsysmt.form.parmed_Structure.set, [1]
- 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, [1]
- molsysmt.form.parmed_Structure.to_parmed_Structure
- molsysmt.form.pdbfixer_PDBFixer
- molsysmt.form.pdbfixer_PDBFixer.add
- molsysmt.form.pdbfixer_PDBFixer.append_structures
- molsysmt.form.pdbfixer_PDBFixer.attributes
- molsysmt.form.pdbfixer_PDBFixer.copy
- molsysmt.form.pdbfixer_PDBFixer.extract
- molsysmt.form.pdbfixer_PDBFixer.get_structural_attributes, [1]
- molsysmt.form.pdbfixer_PDBFixer.get_topological_attributes, [1]
- molsysmt.form.pdbfixer_PDBFixer.has_attribute
- molsysmt.form.pdbfixer_PDBFixer.is_form
- molsysmt.form.pdbfixer_PDBFixer.iterators
- molsysmt.form.pdbfixer_PDBFixer.merge
- molsysmt.form.pdbfixer_PDBFixer.set, [1]
- 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_pdbfixer_PDBFixer
- molsysmt.form.pdbfixer_PDBFixer.to_string_amino_acids_1
- molsysmt.form.pdbfixer_PDBFixer.to_string_amino_acids_3
- molsysmt.form.pytraj_Topology
- molsysmt.form.pytraj_Topology.add
- molsysmt.form.pytraj_Topology.append_structures
- molsysmt.form.pytraj_Topology.attributes
- molsysmt.form.pytraj_Topology.copy
- molsysmt.form.pytraj_Topology.extract
- molsysmt.form.pytraj_Topology.get, [1]
- molsysmt.form.pytraj_Topology.has_attribute
- molsysmt.form.pytraj_Topology.is_form
- molsysmt.form.pytraj_Topology.iterators
- molsysmt.form.pytraj_Topology.merge
- molsysmt.form.pytraj_Topology.set, [1]
- molsysmt.form.pytraj_Topology.to_molsysmt_Topology
- molsysmt.form.pytraj_Topology.to_pytraj_Topology
- molsysmt.form.pytraj_Topology.to_pytraj_Trajectory
- molsysmt.form.pytraj_Trajectory
- molsysmt.form.pytraj_Trajectory.add
- molsysmt.form.pytraj_Trajectory.append_structures
- molsysmt.form.pytraj_Trajectory.attributes
- molsysmt.form.pytraj_Trajectory.copy
- molsysmt.form.pytraj_Trajectory.extract
- molsysmt.form.pytraj_Trajectory.get, [1]
- molsysmt.form.pytraj_Trajectory.has_attribute
- molsysmt.form.pytraj_Trajectory.is_form
- molsysmt.form.pytraj_Trajectory.iterators
- molsysmt.form.pytraj_Trajectory.merge
- molsysmt.form.pytraj_Trajectory.set, [1]
- 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.pytraj_Trajectory.to_pytraj_Trajectory
- molsysmt.form.string_alphafold_id
- molsysmt.form.string_alphafold_id.add
- molsysmt.form.string_alphafold_id.append_structures
- molsysmt.form.string_alphafold_id.attributes
- molsysmt.form.string_alphafold_id.copy
- molsysmt.form.string_alphafold_id.extract
- molsysmt.form.string_alphafold_id.get_structural_attributes, [1]
- molsysmt.form.string_alphafold_id.get_topological_attributes, [1]
- molsysmt.form.string_alphafold_id.has_attribute
- molsysmt.form.string_alphafold_id.is_form
- molsysmt.form.string_alphafold_id.iterators
- molsysmt.form.string_alphafold_id.merge
- molsysmt.form.string_alphafold_id.set, [1]
- 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_alphafold_id
- 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
- molsysmt.form.string_amino_acids_1.add
- molsysmt.form.string_amino_acids_1.append_structures
- molsysmt.form.string_amino_acids_1.attributes
- molsysmt.form.string_amino_acids_1.copy
- molsysmt.form.string_amino_acids_1.extract
- molsysmt.form.string_amino_acids_1.get, [1]
- molsysmt.form.string_amino_acids_1.has_attribute
- molsysmt.form.string_amino_acids_1.is_form
- molsysmt.form.string_amino_acids_1.iterators
- molsysmt.form.string_amino_acids_1.merge
- molsysmt.form.string_amino_acids_1.set, [1]
- 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_1
- molsysmt.form.string_amino_acids_1.to_string_amino_acids_3
- molsysmt.form.string_amino_acids_3
- molsysmt.form.string_amino_acids_3.add
- molsysmt.form.string_amino_acids_3.append_structures
- molsysmt.form.string_amino_acids_3.attributes
- molsysmt.form.string_amino_acids_3.copy
- molsysmt.form.string_amino_acids_3.extract
- molsysmt.form.string_amino_acids_3.get, [1]
- molsysmt.form.string_amino_acids_3.has_attribute
- molsysmt.form.string_amino_acids_3.is_form
- molsysmt.form.string_amino_acids_3.iterators
- molsysmt.form.string_amino_acids_3.merge
- molsysmt.form.string_amino_acids_3.set, [1]
- 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_amino_acids_3.to_string_amino_acids_3
- molsysmt.form.string_pdb_id
- molsysmt.form.string_pdb_id.add
- molsysmt.form.string_pdb_id.append_structures
- molsysmt.form.string_pdb_id.attributes
- molsysmt.form.string_pdb_id.copy
- molsysmt.form.string_pdb_id.extract
- molsysmt.form.string_pdb_id.get_structural_attributes, [1]
- molsysmt.form.string_pdb_id.get_topological_attributes, [1]
- molsysmt.form.string_pdb_id.has_attribute
- molsysmt.form.string_pdb_id.is_form
- molsysmt.form.string_pdb_id.iterators
- molsysmt.form.string_pdb_id.merge
- molsysmt.form.string_pdb_id.set, [1]
- molsysmt.form.string_pdb_id.to_bcifreader_PdbxContainers_DataContainer
- 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_mmtf
- molsysmt.form.string_pdb_id.to_file_msmpk
- 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_mmtf_MMTFDecoder
- 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_id
- molsysmt.form.string_pdb_id.to_string_pdb_text
- molsysmt.form.string_pdb_text
- molsysmt.form.string_pdb_text.add
- molsysmt.form.string_pdb_text.append_structures
- molsysmt.form.string_pdb_text.attributes
- molsysmt.form.string_pdb_text.copy
- molsysmt.form.string_pdb_text.extract
- molsysmt.form.string_pdb_text.get_structural_attributes, [1]
- molsysmt.form.string_pdb_text.get_topological_attributes, [1]
- molsysmt.form.string_pdb_text.has_attribute
- molsysmt.form.string_pdb_text.is_form
- molsysmt.form.string_pdb_text.iterators
- molsysmt.form.string_pdb_text.merge
- molsysmt.form.string_pdb_text.set, [1]
- 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.string_pdb_text.to_string_pdb_text
- molsysmt.form.XYZ
- molsysmt.form.XYZ.add
- molsysmt.form.XYZ.append_structures
- molsysmt.form.XYZ.attributes
- molsysmt.form.XYZ.copy
- molsysmt.form.XYZ.extract
- molsysmt.form.XYZ.get_rank_3_XYZ
- molsysmt.form.XYZ.get_structural_attributes, [1]
- molsysmt.form.XYZ.get_topological_attributes, [1]
- molsysmt.form.XYZ.has_attribute
- molsysmt.form.XYZ.is_form
- molsysmt.form.XYZ.iterators
- molsysmt.form.XYZ.merge
- molsysmt.form.XYZ.set, [1]
- 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.form.XYZ.to_XYZ
- molsysmt.hbonds
- molsysmt.hbonds.get_acceptor_atoms
- molsysmt.hbonds.get_buch_hbonds
- molsysmt.hbonds.get_donor_atoms
- molsysmt.hbonds.get_luzard_chandler_hbonds
- molsysmt.lib
- molsysmt.lib.make_numba_signature
- molsysmt.lib.math
- molsysmt.lib.pbc
- molsysmt.lib.pbc.box_is_orthogonal
- molsysmt.lib.pbc.get_angles_from_box
- molsysmt.lib.pbc.get_box_from_lengths_and_angles
- molsysmt.lib.pbc.get_lengths_and_angles_from_box
- molsysmt.lib.pbc.get_lengths_from_box
- molsysmt.lib.pbc.unwrap
- molsysmt.lib.pbc.wrap_to_mic
- molsysmt.lib.pbc.wrap_to_pbc
- molsysmt.lib.series
- molsysmt.lib.structure
- molsysmt.lib.structure.flip
- molsysmt.lib.structure.get_angles
- molsysmt.lib.structure.get_center
- molsysmt.lib.structure.get_dihedral_angles
- molsysmt.lib.structure.get_distances
- molsysmt.lib.structure.get_least_rmsd
- molsysmt.lib.structure.get_least_rmsd_rotation_and_translation
- molsysmt.lib.structure.get_mic_angles
- molsysmt.lib.structure.get_mic_dihedral_angles
- molsysmt.lib.structure.get_mic_distances
- molsysmt.lib.structure.get_principal_geometric_axes
- molsysmt.lib.structure.get_principal_inertia_axes
- molsysmt.lib.structure.get_rmsd
- molsysmt.lib.structure.principal_component_analysis
- molsysmt.lib.structure.set_dihedral_angles
- molsysmt.lib.structure.set_mic_dihedral_angles
- molsysmt.lib.structure.shift_dihedral_angles
- molsysmt.lib.structure.shift_mic_dihedral_angles
- molsysmt.molecular_dynamics
- molsysmt.molecular_dynamics.run_NPT_equilibration
- molsysmt.molecular_dynamics.run_NVT_equilibration
- molsysmt.molecular_mechanics
- molsysmt.molecular_mechanics.forcefields
- molsysmt.molecular_mechanics.get_engine_forcefield
- molsysmt.molecular_mechanics.get_forces
- molsysmt.molecular_mechanics.get_non_bonded_potential_energy
- molsysmt.molecular_mechanics.get_num_degrees_of_freedom
- molsysmt.molecular_mechanics.get_potential_energy
- molsysmt.molecular_mechanics.potential_energy_minimization
- molsysmt.native
- molsysmt.native.cif_file_handler
- molsysmt.native.file_tng
- molsysmt.native.file_xtc
- molsysmt.native.gro_file_handler
- molsysmt.native.h5msm_file_handler
- molsysmt.native.molecular_mechanics
- molsysmt.native.molecular_mechanics_dict
- molsysmt.native.molsys
- molsysmt.native.pdb_atomic_coordinate_entry
- molsysmt.native.pdb_file_handler
- molsysmt.native.simulation
- molsysmt.native.simulation_dict
- molsysmt.native.structures
- molsysmt.native.structures_dict
- molsysmt.native.topology
- molsysmt.native.trajectory_file
- molsysmt.pbc
- molsysmt.pbc.get_angles_from_box
- molsysmt.pbc.get_box_from_lengths_and_angles
- molsysmt.pbc.get_box_with_shape
- molsysmt.pbc.get_lengths_and_angles_from_box
- molsysmt.pbc.get_lengths_from_box
- molsysmt.pbc.get_shape_from_angles
- molsysmt.pbc.get_shape_from_box
- molsysmt.pbc.get_volume_from_box
- molsysmt.pbc.get_volume_from_lengths_and_angles
- molsysmt.pbc.has_pbc
- molsysmt.pbc.unwrap
- molsysmt.pbc.wrap_to_mic
- molsysmt.pbc.wrap_to_pbc
- molsysmt.physchem
- molsysmt.physchem.get_area_buried
- molsysmt.physchem.get_atomic_radius
- molsysmt.physchem.get_buried_fraction
- molsysmt.physchem.get_charge
- molsysmt.physchem.get_hydrophobicity
- molsysmt.physchem.get_mass
- molsysmt.physchem.get_polarity
- molsysmt.physchem.get_sasa
- molsysmt.physchem.get_surface_area
- molsysmt.physchem.get_transmembrane_tendency
- molsysmt.physchem.get_volume
- molsysmt.structure
- molsysmt.structure.align_principal_axes
- molsysmt.structure.center
- molsysmt.structure.flip
- molsysmt.structure.get_angles
- molsysmt.structure.get_center
- molsysmt.structure.get_contacts
- molsysmt.structure.get_dihedral_angles
- molsysmt.structure.get_distances
- molsysmt.structure.get_least_rmsd
- molsysmt.structure.get_maximum_distances
- molsysmt.structure.get_minimum_distances
- molsysmt.structure.get_neighbors
- molsysmt.structure.get_principal_axes
- molsysmt.structure.get_radius_of_gyration
- molsysmt.structure.get_rmsd
- molsysmt.structure.least_rmsd_align
- molsysmt.structure.least_rmsd_fit
- molsysmt.structure.move_away
- molsysmt.structure.principal_component_analysis
- molsysmt.structure.rotate
- molsysmt.structure.set_dihedral_angles
- molsysmt.structure.shift_dihedral_angles
- molsysmt.structure.show_contacts
- molsysmt.structure.translate
- molsysmt.supported
- molsysmt.supported.engines
- molsysmt.supported.supported
- molsysmt.supported.syntaxes
- molsysmt.supported.viewers
- molsysmt.systems
- molsysmt.thirds
- molsysmt.thirds.nglview
- molsysmt.thirds.nglview.add_arrows
- molsysmt.thirds.nglview.add_contacts
- molsysmt.thirds.nglview.add_cylinders
- molsysmt.thirds.nglview.add_hbonds
- molsysmt.thirds.nglview.clear
- molsysmt.thirds.nglview.load_html_in_jupyter_notebook
- molsysmt.thirds.nglview.patching_nglview
- molsysmt.thirds.nglview.set_color
- molsysmt.thirds.nglview.set_color_by_value
- molsysmt.thirds.nglview.show_as_balls_and_sticks
- molsysmt.thirds.nglview.show_as_cartoon
- molsysmt.thirds.nglview.show_as_licorice
- molsysmt.thirds.nglview.show_as_surface
- molsysmt.thirds.nglview.show_gui
- molsysmt.thirds.nglview.standardize_view
- molsysmt.thirds.nglview.write_html
- molsysmt.thirds.openmm
- molsysmt.thirds.openmm.forces
- molsysmt.thirds.openmm.forces.add_allowed_plane_region
- molsysmt.thirds.openmm.forces.add_allowed_z_region
- molsysmt.thirds.openmm.forces.add_constant_force
- molsysmt.thirds.openmm.forces.add_forbidden_plane_region
- molsysmt.thirds.openmm.forces.add_forbidden_z_region
- molsysmt.thirds.openmm.forces.add_harmonic_bond_force
- molsysmt.thirds.openmm.forces.add_plane_harmonic_restraint
- molsysmt.thirds.openmm.forces.add_point_harmonic_restraint
- molsysmt.thirds.openmm.forces.pin_atoms
- molsysmt.thirds.openmm.platforms
- molsysmt.thirds.openmm.platforms.platforms
- molsysmt.thirds.openmm.reporters
- molsysmt.thirds.openmm.reporters.h5msm
- molsysmt.thirds.openmm.reporters.MolSys
- molsysmt.thirds.openmm.reporters.StructuresDict
- molsysmt.thirds.openmm.reporters.tqdm
- molsysmt.thirds.tleap
- molsysmt.thirds.tleap.tleap
- molsysmt.topology
- molsysmt.topology.get_bondgraph
- molsysmt.topology.get_covalent_blocks
- molsysmt.topology.get_covalent_chains
- molsysmt.topology.get_dihedral_quartets
- molsysmt.topology.get_sequence_alignment
- molsysmt.topology.get_sequence_identity
- molecular_system (molsysmt.basic.iterator.Iterator attribute)
- MolecularMechanics (class in molsysmt.native.molecular_mechanics)
- Molecules_DataFrame (class in molsysmt.native.topology)
- MolSys (class in molsysmt.native.molsys)
-
molsysmt
-
molsysmt.attribute
-
molsysmt.attribute.attributes
-
molsysmt.attribute.bonds_are_required_to_get_attribute
-
molsysmt.attribute.is_attribute
-
molsysmt.attribute.is_mechanical_attribute
-
molsysmt.attribute.is_structural_attribute
-
molsysmt.attribute.is_topological_attribute
-
molsysmt.basic
-
molsysmt.basic.add
-
molsysmt.basic.append_structures
-
molsysmt.basic.are_multiple_molecular_systems
-
molsysmt.basic.compare
-
molsysmt.basic.concatenate_structures
-
molsysmt.basic.contains
-
molsysmt.basic.convert
-
molsysmt.basic.copy
-
molsysmt.basic.extract
-
molsysmt.basic.get
-
molsysmt.basic.get_attributes
-
molsysmt.basic.get_form
-
molsysmt.basic.get_label
-
molsysmt.basic.has_attribute
-
molsysmt.basic.info
-
molsysmt.basic.is_a_molecular_system
-
molsysmt.basic.is_composed_of
-
molsysmt.basic.iterator
-
molsysmt.basic.merge
-
molsysmt.basic.remove
-
molsysmt.basic.select
-
molsysmt.basic.selector
-
molsysmt.basic.selector.amber
-
molsysmt.basic.selector.mdanalysis
-
molsysmt.basic.selector.mdtraj
-
molsysmt.basic.selector.molsysmt
-
molsysmt.basic.selector.molsysmt_old
-
molsysmt.basic.selector.nglview
-
molsysmt.basic.selector.parmed
-
molsysmt.basic.set
-
molsysmt.basic.view
-
molsysmt.basic.where_is_attribute
-
molsysmt.build
-
molsysmt.build.add_bonds
-
molsysmt.build.add_missing_bonds
-
molsysmt.build.add_missing_heavy_atoms
-
molsysmt.build.add_missing_hydrogens
-
molsysmt.build.add_missing_terminal_cappings
-
molsysmt.build.build_peptide
-
molsysmt.build.define_new_chain
-
molsysmt.build.get_disulfide_bonds
-
molsysmt.build.get_missing_bonds
-
molsysmt.build.get_missing_heavy_atoms
-
molsysmt.build.get_missing_residues
-
molsysmt.build.get_missing_terminal_cappings
-
molsysmt.build.get_non_standard_residues
-
molsysmt.build.has_hydrogens
-
molsysmt.build.is_solvated
-
molsysmt.build.make_bioassembly
-
molsysmt.build.make_water_box
-
molsysmt.build.mutate
-
molsysmt.build.remove_bonds
-
molsysmt.build.remove_overlapping_molecules
-
molsysmt.build.solvate
-
molsysmt.build.solve_atoms_with_alternate_location
-
molsysmt.config
-
molsysmt.config.logging_setup
-
molsysmt.dependencies
-
molsysmt.element
-
molsysmt.element.atom
-
molsysmt.element.atom.acceptors
-
molsysmt.element.atom.charges
-
molsysmt.element.atom.donors
-
molsysmt.element.atom.get_atom_type_from_atom_name
-
molsysmt.element.atom.names
-
molsysmt.element.atom.names_cg
-
molsysmt.element.bond
-
molsysmt.element.bond.max_expected_bond_length
-
molsysmt.element.chain
-
molsysmt.element.chain.chain_names
-
molsysmt.element.chain.get_chain_id
-
molsysmt.element.chain.get_chain_index
-
molsysmt.element.chain.get_chain_name
-
molsysmt.element.chain.get_chain_type
-
molsysmt.element.component
-
molsysmt.element.component.get_component_id
-
molsysmt.element.component.get_component_index
-
molsysmt.element.component.get_component_name
-
molsysmt.element.component.get_component_type
-
molsysmt.element.component.get_n_components
-
molsysmt.element.component.is_component_type
-
molsysmt.element.entity
-
molsysmt.element.entity.disaccharide
-
molsysmt.element.entity.get_entity_id
-
molsysmt.element.entity.get_entity_index
-
molsysmt.element.entity.get_entity_name
-
molsysmt.element.entity.get_entity_type
-
molsysmt.element.entity.get_n_entities
-
molsysmt.element.entity.monosaccharide
-
molsysmt.element.group
-
molsysmt.element.group.amino_acid
-
molsysmt.element.group.amino_acid.get_1_letter_code_from_name
-
molsysmt.element.group.amino_acid.get_bonded_atom_pairs
-
molsysmt.element.group.amino_acid.get_group_db
-
molsysmt.element.group.amino_acid.group_names
-
molsysmt.element.group.amino_acid.group_types
-
molsysmt.element.group.amino_acid.is_amino_acid
-
molsysmt.element.group.get_bonded_atom_pairs
-
molsysmt.element.group.get_group_type
-
molsysmt.element.group.ion
-
molsysmt.element.group.ion.get_bonded_atom_pairs
-
molsysmt.element.group.ion.get_group_db
-
molsysmt.element.group.ion.group_names
-
molsysmt.element.group.ion.is_ion
-
molsysmt.element.group.is_group_type
-
molsysmt.element.group.lipid
-
molsysmt.element.group.lipid.is_lipid
-
molsysmt.element.group.lipid.lipid_names
-
molsysmt.element.group.nucleotide
-
molsysmt.element.group.nucleotide.is_nucleotide
-
molsysmt.element.group.nucleotide.nucleotide_names
-
molsysmt.element.group.saccharide
-
molsysmt.element.group.saccharide.get_bonded_atom_pairs
-
molsysmt.element.group.saccharide.get_group_db
-
molsysmt.element.group.saccharide.group_names
-
molsysmt.element.group.saccharide.is_saccharide
-
molsysmt.element.group.small_molecule
-
molsysmt.element.group.small_molecule.get_bonded_atom_pairs
-
molsysmt.element.group.small_molecule.get_group_db
-
molsysmt.element.group.small_molecule.group_names
-
molsysmt.element.group.small_molecule.is_small_molecule
-
molsysmt.element.group.small_molecule.small_molecule_is_amino_acid
-
molsysmt.element.group.terminal_capping
-
molsysmt.element.group.terminal_capping.get_bonded_atom_pairs
-
molsysmt.element.group.terminal_capping.get_group_db
-
molsysmt.element.group.terminal_capping.group_names
-
molsysmt.element.group.terminal_capping.is_c_terminal_capping
-
molsysmt.element.group.terminal_capping.is_n_terminal_capping
-
molsysmt.element.group.terminal_capping.is_terminal_capping
-
molsysmt.element.group.water
-
molsysmt.element.group.water.get_bonded_atom_pairs
-
molsysmt.element.group.water.is_water
-
molsysmt.element.group.water.water_names
-
molsysmt.element.is_composed_of
-
molsysmt.element.is_element
-
molsysmt.element.molecule
-
molsysmt.element.molecule.disaccharide
-
molsysmt.element.molecule.dna
-
molsysmt.element.molecule.dna.names
-
molsysmt.element.molecule.get_molecule_id
-
molsysmt.element.molecule.get_molecule_index
-
molsysmt.element.molecule.get_molecule_name
-
molsysmt.element.molecule.get_molecule_type
-
molsysmt.element.molecule.get_n_molecules
-
molsysmt.element.molecule.ion
-
molsysmt.element.molecule.is_molecule_type
-
molsysmt.element.molecule.lipid
-
molsysmt.element.molecule.monosaccharide
-
molsysmt.element.molecule.peptide
-
molsysmt.element.molecule.polysaccharide
-
molsysmt.element.molecule.protein
-
molsysmt.element.molecule.rna
-
molsysmt.element.molecule.rna.names
-
molsysmt.element.molecule.small_molecule
-
molsysmt.element.molecule.water
-
molsysmt.file
-
molsysmt.file.close
-
molsysmt.file.file_handler
-
molsysmt.file.get_mode
-
molsysmt.file.handlers
-
molsysmt.file.handlers.mdtraj_HDF5TrajectoryFile
-
molsysmt.file.handlers.mdtraj_HDF5TrajectoryFile.close_file
-
molsysmt.file.handlers.mdtraj_HDF5TrajectoryFile.open_file
-
molsysmt.file.is_closed
-
molsysmt.file.is_file
-
molsysmt.file.is_opened
-
molsysmt.file.open
-
molsysmt.form
-
molsysmt.form.bcifreader_PdbxContainers_DataContainer
-
molsysmt.form.bcifreader_PdbxContainers_DataContainer.add
-
molsysmt.form.bcifreader_PdbxContainers_DataContainer.append_structures
-
molsysmt.form.bcifreader_PdbxContainers_DataContainer.attributes
-
molsysmt.form.bcifreader_PdbxContainers_DataContainer.copy
-
molsysmt.form.bcifreader_PdbxContainers_DataContainer.extract
-
molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_structural_attributes
-
molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes
-
molsysmt.form.bcifreader_PdbxContainers_DataContainer.has_attribute
-
molsysmt.form.bcifreader_PdbxContainers_DataContainer.is_form
-
molsysmt.form.bcifreader_PdbxContainers_DataContainer.iterators
-
molsysmt.form.bcifreader_PdbxContainers_DataContainer.merge
-
molsysmt.form.bcifreader_PdbxContainers_DataContainer.set
-
molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_bcifreader_PdbxContainers_DataContainer
-
molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_file_pdb
-
molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_mdtraj_Trajectory
-
molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_molsysmt_MolecularMechanics
-
molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_molsysmt_MolSys
-
molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_molsysmt_MolSys_bck
-
molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_molsysmt_MolSys_bueno
-
molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_molsysmt_Structures
-
molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_molsysmt_Topology
-
molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_openmm_Topology
-
molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_string_amino_acids_1
-
molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_string_amino_acids_3
-
molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_string_pdb_id
-
molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_string_pdb_text
-
molsysmt.form.biopython_Seq
-
molsysmt.form.biopython_Seq.add
-
molsysmt.form.biopython_Seq.attributes
-
molsysmt.form.biopython_Seq.copy
-
molsysmt.form.biopython_Seq.extract
-
molsysmt.form.biopython_Seq.get
-
molsysmt.form.biopython_Seq.has_attribute
-
molsysmt.form.biopython_Seq.is_form
-
molsysmt.form.biopython_Seq.iterators
-
molsysmt.form.biopython_Seq.merge
-
molsysmt.form.biopython_Seq.set
-
molsysmt.form.biopython_Seq.to_biopython_Seq
-
molsysmt.form.biopython_Seq.to_biopython_SeqRecord
-
molsysmt.form.biopython_SeqRecord
-
molsysmt.form.biopython_SeqRecord.add
-
molsysmt.form.biopython_SeqRecord.attributes
-
molsysmt.form.biopython_SeqRecord.extract
-
molsysmt.form.biopython_SeqRecord.get
-
molsysmt.form.biopython_SeqRecord.has_attribute
-
molsysmt.form.biopython_SeqRecord.is_form
-
molsysmt.form.biopython_SeqRecord.iterators
-
molsysmt.form.biopython_SeqRecord.merge
-
molsysmt.form.biopython_SeqRecord.set
-
molsysmt.form.biopython_SeqRecord.to_biopython_SeqRecord
-
molsysmt.form.file_bcif
-
molsysmt.form.file_bcif.add
-
molsysmt.form.file_bcif.append_structures
-
molsysmt.form.file_bcif.attributes
-
molsysmt.form.file_bcif.copy
-
molsysmt.form.file_bcif.download
-
molsysmt.form.file_bcif.extract
-
molsysmt.form.file_bcif.get
-
molsysmt.form.file_bcif.has_attribute
-
molsysmt.form.file_bcif.is_form
-
molsysmt.form.file_bcif.iterators
-
molsysmt.form.file_bcif.merge
-
molsysmt.form.file_bcif.set
-
molsysmt.form.file_bcif.to_bcifreader_PdbxContainers_DataContainer
-
molsysmt.form.file_bcif.to_file_bcif
-
molsysmt.form.file_bcif.to_file_h5msm
-
molsysmt.form.file_bcif.to_mmcif_PdbxContainers_DataContainer
-
molsysmt.form.file_bcif.to_molsysmt_MolSys
-
molsysmt.form.file_bcif.to_molsysmt_Structures
-
molsysmt.form.file_bcif.to_molsysmt_Topology
-
molsysmt.form.file_bcif_gz
-
molsysmt.form.file_bcif_gz.add
-
molsysmt.form.file_bcif_gz.append_structures
-
molsysmt.form.file_bcif_gz.attributes
-
molsysmt.form.file_bcif_gz.copy
-
molsysmt.form.file_bcif_gz.download
-
molsysmt.form.file_bcif_gz.extract
-
molsysmt.form.file_bcif_gz.get
-
molsysmt.form.file_bcif_gz.has_attribute
-
molsysmt.form.file_bcif_gz.is_form
-
molsysmt.form.file_bcif_gz.iterators
-
molsysmt.form.file_bcif_gz.merge
-
molsysmt.form.file_bcif_gz.set
-
molsysmt.form.file_bcif_gz.to_bcifreader_PdbxContainers_DataContainer
-
molsysmt.form.file_bcif_gz.to_file_bcif_gz
-
molsysmt.form.file_bcif_gz.to_file_h5msm
-
molsysmt.form.file_bcif_gz.to_mmcif_PdbxContainers_DataContainer
-
molsysmt.form.file_bcif_gz.to_molsysmt_MolSys
-
molsysmt.form.file_bcif_gz.to_molsysmt_Structures
-
molsysmt.form.file_bcif_gz.to_molsysmt_Topology
-
molsysmt.form.file_cif
-
molsysmt.form.file_cif.add
-
molsysmt.form.file_cif.append_structures
-
molsysmt.form.file_cif.attributes
-
molsysmt.form.file_cif.copy
-
molsysmt.form.file_cif.extract
-
molsysmt.form.file_cif.get
-
molsysmt.form.file_cif.has_attribute
-
molsysmt.form.file_cif.is_form
-
molsysmt.form.file_cif.iterators
-
molsysmt.form.file_cif.merge
-
molsysmt.form.file_cif.set
-
molsysmt.form.file_cif.to_file_cif
-
molsysmt.form.file_cif.to_molsysmt_CIFFileHandler
-
molsysmt.form.file_crd
-
molsysmt.form.file_crd.add
-
molsysmt.form.file_crd.append_structures
-
molsysmt.form.file_crd.attributes
-
molsysmt.form.file_crd.copy
-
molsysmt.form.file_crd.extract
-
molsysmt.form.file_crd.get
-
molsysmt.form.file_crd.has_attribute
-
molsysmt.form.file_crd.is_form
-
molsysmt.form.file_crd.iterators
-
molsysmt.form.file_crd.merge
-
molsysmt.form.file_crd.set
-
molsysmt.form.file_crd.to_file_crd
-
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
-
molsysmt.form.file_dcd.add
-
molsysmt.form.file_dcd.append_structures
-
molsysmt.form.file_dcd.attributes
-
molsysmt.form.file_dcd.copy
-
molsysmt.form.file_dcd.extract
-
molsysmt.form.file_dcd.get
-
molsysmt.form.file_dcd.has_attribute
-
molsysmt.form.file_dcd.is_form
-
molsysmt.form.file_dcd.iterators
-
molsysmt.form.file_dcd.merge
-
molsysmt.form.file_dcd.set
-
molsysmt.form.file_dcd.to_file_dcd
-
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
-
molsysmt.form.file_gro.add
-
molsysmt.form.file_gro.append_structures
-
molsysmt.form.file_gro.attributes
-
molsysmt.form.file_gro.copy
-
molsysmt.form.file_gro.extract
-
molsysmt.form.file_gro.get
-
molsysmt.form.file_gro.has_attribute
-
molsysmt.form.file_gro.is_form
-
molsysmt.form.file_gro.iterators
-
molsysmt.form.file_gro.merge
-
molsysmt.form.file_gro.set
-
molsysmt.form.file_gro.to_file_gro
-
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
-
molsysmt.form.file_h5.add
-
molsysmt.form.file_h5.append_structures
-
molsysmt.form.file_h5.attributes
-
molsysmt.form.file_h5.copy
-
molsysmt.form.file_h5.extract
-
molsysmt.form.file_h5.get
-
molsysmt.form.file_h5.has_attribute
-
molsysmt.form.file_h5.is_form
-
molsysmt.form.file_h5.iterators
-
molsysmt.form.file_h5.merge
-
molsysmt.form.file_h5.set
-
molsysmt.form.file_h5.to_file_h5
-
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
-
molsysmt.form.file_h5msm.add
-
molsysmt.form.file_h5msm.append_structures
-
molsysmt.form.file_h5msm.attributes
-
molsysmt.form.file_h5msm.copy
-
molsysmt.form.file_h5msm.extract
-
molsysmt.form.file_h5msm.get_structural_attributes
-
molsysmt.form.file_h5msm.get_topological_attributes
-
molsysmt.form.file_h5msm.has_attribute
-
molsysmt.form.file_h5msm.is_form
-
molsysmt.form.file_h5msm.iterators
-
molsysmt.form.file_h5msm.merge
-
molsysmt.form.file_h5msm.set
-
molsysmt.form.file_h5msm.to_file_h5msm
|
-
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
-
molsysmt.form.file_inpcrd.add
-
molsysmt.form.file_inpcrd.append_structures
-
molsysmt.form.file_inpcrd.attributes
-
molsysmt.form.file_inpcrd.copy
-
molsysmt.form.file_inpcrd.extract
-
molsysmt.form.file_inpcrd.get
-
molsysmt.form.file_inpcrd.has_attribute
-
molsysmt.form.file_inpcrd.is_form
-
molsysmt.form.file_inpcrd.iterators
-
molsysmt.form.file_inpcrd.merge
-
molsysmt.form.file_inpcrd.set
-
molsysmt.form.file_inpcrd.to_file_inpcrd
-
molsysmt.form.file_inpcrd.to_molsysmt_Structures
-
molsysmt.form.file_inpcrd.to_openmm_AmberInpcrdFile
-
molsysmt.form.file_mmtf
-
molsysmt.form.file_mmtf.add
-
molsysmt.form.file_mmtf.append_structures
-
molsysmt.form.file_mmtf.attributes
-
molsysmt.form.file_mmtf.copy
-
molsysmt.form.file_mmtf.download
-
molsysmt.form.file_mmtf.extract
-
molsysmt.form.file_mmtf.get
-
molsysmt.form.file_mmtf.has_attribute
-
molsysmt.form.file_mmtf.is_form
-
molsysmt.form.file_mmtf.iterators
-
molsysmt.form.file_mmtf.merge
-
molsysmt.form.file_mmtf.set
-
molsysmt.form.file_mmtf.to_file_mmtf
-
molsysmt.form.file_mmtf.to_file_pdb
-
molsysmt.form.file_mmtf.to_MDAnalysis_Universe
-
molsysmt.form.file_mmtf.to_mdtraj
-
molsysmt.form.file_mmtf.to_mmtf_MMTFDecoder
-
molsysmt.form.file_mmtf.to_molsysmt_MolSys
-
molsysmt.form.file_mmtf.to_molsysmt_Structures
-
molsysmt.form.file_mmtf.to_molsysmt_Topology
-
molsysmt.form.file_mmtf.to_openmm_Topology
-
molsysmt.form.file_mmtf.to_string_amino_acids_1
-
molsysmt.form.file_mmtf.to_string_amino_acids_3
-
molsysmt.form.file_mmtf.to_string_pdb_text
-
molsysmt.form.file_mol2
-
molsysmt.form.file_mol2.add
-
molsysmt.form.file_mol2.append_structures
-
molsysmt.form.file_mol2.attributes
-
molsysmt.form.file_mol2.copy
-
molsysmt.form.file_mol2.extract
-
molsysmt.form.file_mol2.get
-
molsysmt.form.file_mol2.has_attribute
-
molsysmt.form.file_mol2.is_form
-
molsysmt.form.file_mol2.iterators
-
molsysmt.form.file_mol2.merge
-
molsysmt.form.file_mol2.set
-
molsysmt.form.file_mol2.to_file_mol2
-
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_msmpk
-
molsysmt.form.file_msmpk.add
-
molsysmt.form.file_msmpk.append_structures
-
molsysmt.form.file_msmpk.attributes
-
molsysmt.form.file_msmpk.copy
-
molsysmt.form.file_msmpk.extract
-
molsysmt.form.file_msmpk.get
-
molsysmt.form.file_msmpk.has_attribute
-
molsysmt.form.file_msmpk.is_form
-
molsysmt.form.file_msmpk.iterators
-
molsysmt.form.file_msmpk.merge
-
molsysmt.form.file_msmpk.set
-
molsysmt.form.file_msmpk.to_file_msmpk
-
molsysmt.form.file_msmpk.to_molsysmt_MolSys
-
molsysmt.form.file_msmpk.to_molsysmt_Structures
-
molsysmt.form.file_msmpk.to_molsysmt_Topology
-
molsysmt.form.file_msmpk.to_nglview_NGLWidget
-
molsysmt.form.file_msmpk.update_file
-
molsysmt.form.file_pdb
-
molsysmt.form.file_pdb.add
-
molsysmt.form.file_pdb.append_structures
-
molsysmt.form.file_pdb.attributes
-
molsysmt.form.file_pdb.copy
-
molsysmt.form.file_pdb.download
-
molsysmt.form.file_pdb.extract
-
molsysmt.form.file_pdb.get
-
molsysmt.form.file_pdb.has_atoms_with_alternate_locations
-
molsysmt.form.file_pdb.has_attribute
-
molsysmt.form.file_pdb.is_form
-
molsysmt.form.file_pdb.iterators
-
molsysmt.form.file_pdb.merge
-
molsysmt.form.file_pdb.replace_HETATM_by_ATOM_in_terminal_cappings
-
molsysmt.form.file_pdb.set
-
molsysmt.form.file_pdb.to_file_mol2
-
molsysmt.form.file_pdb.to_file_pdb
-
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
-
molsysmt.form.file_prmtop.add
-
molsysmt.form.file_prmtop.append_structures
-
molsysmt.form.file_prmtop.attributes
-
molsysmt.form.file_prmtop.copy
-
molsysmt.form.file_prmtop.extract
-
molsysmt.form.file_prmtop.get
-
molsysmt.form.file_prmtop.has_attribute
-
molsysmt.form.file_prmtop.is_form
-
molsysmt.form.file_prmtop.iterators
-
molsysmt.form.file_prmtop.merge
-
molsysmt.form.file_prmtop.set
-
molsysmt.form.file_prmtop.to_file_pdb
-
molsysmt.form.file_prmtop.to_file_prmtop
-
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
-
molsysmt.form.file_psf.add
-
molsysmt.form.file_psf.append_structures
-
molsysmt.form.file_psf.attributes
-
molsysmt.form.file_psf.copy
-
molsysmt.form.file_psf.extract
-
molsysmt.form.file_psf.get
-
molsysmt.form.file_psf.has_attribute
-
molsysmt.form.file_psf.is_form
-
molsysmt.form.file_psf.iterators
-
molsysmt.form.file_psf.merge
-
molsysmt.form.file_psf.set
-
molsysmt.form.file_psf.to_file_psf
-
molsysmt.form.file_psf.to_molsysmt_MolSys
-
molsysmt.form.file_psf.to_molsysmt_MolSysOld
-
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
-
molsysmt.form.file_trjpk.add
-
molsysmt.form.file_trjpk.append_structures
-
molsysmt.form.file_trjpk.attributes
-
molsysmt.form.file_trjpk.copy
-
molsysmt.form.file_trjpk.extract
-
molsysmt.form.file_trjpk.get
-
molsysmt.form.file_trjpk.has_attribute
-
molsysmt.form.file_trjpk.is_form
-
molsysmt.form.file_trjpk.iterators
-
molsysmt.form.file_trjpk.merge
-
molsysmt.form.file_trjpk.set
-
molsysmt.form.file_trjpk.to_file_trjpk
-
molsysmt.form.file_trjpk.to_molsysmt_StructuresDict
-
molsysmt.form.file_xtc
-
molsysmt.form.file_xtc.add
-
molsysmt.form.file_xtc.append_structures
-
molsysmt.form.file_xtc.attributes
-
molsysmt.form.file_xtc.copy
-
molsysmt.form.file_xtc.extract
-
molsysmt.form.file_xtc.get
-
molsysmt.form.file_xtc.has_attribute
-
molsysmt.form.file_xtc.is_form
-
molsysmt.form.file_xtc.iterators
-
molsysmt.form.file_xtc.merge
-
molsysmt.form.file_xtc.set
-
molsysmt.form.file_xtc.to_file_xtc
-
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
-
molsysmt.form.file_xyznpy.add
-
molsysmt.form.file_xyznpy.append_structures
-
molsysmt.form.file_xyznpy.attributes
-
molsysmt.form.file_xyznpy.copy
-
molsysmt.form.file_xyznpy.extract
-
molsysmt.form.file_xyznpy.get
-
molsysmt.form.file_xyznpy.has_attribute
-
molsysmt.form.file_xyznpy.is_form
-
molsysmt.form.file_xyznpy.iterators
-
molsysmt.form.file_xyznpy.merge
-
molsysmt.form.file_xyznpy.set
-
molsysmt.form.file_xyznpy.to_file_xyznpy
-
molsysmt.form.file_xyznpy.to_XYZ
-
molsysmt.form.get_attributes
-
molsysmt.form.has_attribute
-
molsysmt.form.is_file
-
molsysmt.form.is_item
-
molsysmt.form.is_string
-
molsysmt.form.iterators
-
molsysmt.form.MDAnalysis_Topology
-
molsysmt.form.MDAnalysis_Topology.add
-
molsysmt.form.MDAnalysis_Topology.append_structures
-
molsysmt.form.MDAnalysis_Topology.attributes
-
molsysmt.form.MDAnalysis_Topology.copy
-
molsysmt.form.MDAnalysis_Topology.extract
-
molsysmt.form.MDAnalysis_Topology.get
-
molsysmt.form.MDAnalysis_Topology.has_attribute
-
molsysmt.form.MDAnalysis_Topology.is_form
-
molsysmt.form.MDAnalysis_Topology.iterators
-
molsysmt.form.MDAnalysis_Topology.merge
-
molsysmt.form.MDAnalysis_Topology.set
-
molsysmt.form.MDAnalysis_Topology.to_MDAnalysis_Topology
-
molsysmt.form.MDAnalysis_Universe
-
molsysmt.form.MDAnalysis_Universe.add
-
molsysmt.form.MDAnalysis_Universe.append_structures
-
molsysmt.form.MDAnalysis_Universe.attributes
-
molsysmt.form.MDAnalysis_Universe.copy
-
molsysmt.form.MDAnalysis_Universe.extract
-
molsysmt.form.MDAnalysis_Universe.get
-
molsysmt.form.MDAnalysis_Universe.has_attribute
-
molsysmt.form.MDAnalysis_Universe.is_form
-
molsysmt.form.MDAnalysis_Universe.iterators
-
molsysmt.form.MDAnalysis_Universe.merge
-
molsysmt.form.MDAnalysis_Universe.set
-
molsysmt.form.MDAnalysis_Universe.to_file_pdb
-
molsysmt.form.MDAnalysis_Universe.to_MDAnalysis_Universe
-
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
-
molsysmt.form.mdtraj_DCDTrajectoryFile.add
-
molsysmt.form.mdtraj_DCDTrajectoryFile.append_structures
-
molsysmt.form.mdtraj_DCDTrajectoryFile.attributes
-
molsysmt.form.mdtraj_DCDTrajectoryFile.copy
-
molsysmt.form.mdtraj_DCDTrajectoryFile.extract
-
molsysmt.form.mdtraj_DCDTrajectoryFile.get
-
molsysmt.form.mdtraj_DCDTrajectoryFile.has_attribute
-
molsysmt.form.mdtraj_DCDTrajectoryFile.is_form
-
molsysmt.form.mdtraj_DCDTrajectoryFile.iterators
-
molsysmt.form.mdtraj_DCDTrajectoryFile.merge
-
molsysmt.form.mdtraj_DCDTrajectoryFile.set
-
molsysmt.form.mdtraj_DCDTrajectoryFile.to_mdtraj_DCDTrajectoryFile
-
molsysmt.form.mdtraj_DCDTrajectoryFile.to_molsysmt_MolSys
-
molsysmt.form.mdtraj_DCDTrajectoryFile.to_molsysmt_Structures
-
molsysmt.form.mdtraj_HDF5TrajectoryFile
-
molsysmt.form.mdtraj_HDF5TrajectoryFile.add
-
molsysmt.form.mdtraj_HDF5TrajectoryFile.append_structures
-
molsysmt.form.mdtraj_HDF5TrajectoryFile.attributes
-
molsysmt.form.mdtraj_HDF5TrajectoryFile.copy
-
molsysmt.form.mdtraj_HDF5TrajectoryFile.extract
-
molsysmt.form.mdtraj_HDF5TrajectoryFile.get
-
molsysmt.form.mdtraj_HDF5TrajectoryFile.has_attribute
-
molsysmt.form.mdtraj_HDF5TrajectoryFile.is_form
-
molsysmt.form.mdtraj_HDF5TrajectoryFile.iterators
-
molsysmt.form.mdtraj_HDF5TrajectoryFile.merge
-
molsysmt.form.mdtraj_HDF5TrajectoryFile.set
-
molsysmt.form.mdtraj_HDF5TrajectoryFile.to_mdtraj_HDF5TrajectoryFile
-
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
-
molsysmt.form.mdtraj_Topology.add
-
molsysmt.form.mdtraj_Topology.append_structures
-
molsysmt.form.mdtraj_Topology.attributes
-
molsysmt.form.mdtraj_Topology.copy
-
molsysmt.form.mdtraj_Topology.extract
-
molsysmt.form.mdtraj_Topology.get
-
molsysmt.form.mdtraj_Topology.get_structural_attributes
-
molsysmt.form.mdtraj_Topology.get_topological_attributes
-
molsysmt.form.mdtraj_Topology.has_attribute
-
molsysmt.form.mdtraj_Topology.is_form
-
molsysmt.form.mdtraj_Topology.iterators
-
molsysmt.form.mdtraj_Topology.merge
-
molsysmt.form.mdtraj_Topology.set
-
molsysmt.form.mdtraj_Topology.to_file_top
-
molsysmt.form.mdtraj_Topology.to_mdtraj_Topology
-
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
-
molsysmt.form.mdtraj_Trajectory.add
-
molsysmt.form.mdtraj_Trajectory.append_structures
-
molsysmt.form.mdtraj_Trajectory.attributes
-
molsysmt.form.mdtraj_Trajectory.copy
-
molsysmt.form.mdtraj_Trajectory.extract
-
molsysmt.form.mdtraj_Trajectory.get
-
molsysmt.form.mdtraj_Trajectory.has_attribute
-
molsysmt.form.mdtraj_Trajectory.is_form
-
molsysmt.form.mdtraj_Trajectory.iterators
-
molsysmt.form.mdtraj_Trajectory.merge
-
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_mdtraj_Trajectory
-
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
-
molsysmt.form.mdtraj_XTCTrajectoryFile.add
-
molsysmt.form.mdtraj_XTCTrajectoryFile.append_structures
-
molsysmt.form.mdtraj_XTCTrajectoryFile.attributes
-
molsysmt.form.mdtraj_XTCTrajectoryFile.copy
-
molsysmt.form.mdtraj_XTCTrajectoryFile.extract
-
molsysmt.form.mdtraj_XTCTrajectoryFile.get
-
molsysmt.form.mdtraj_XTCTrajectoryFile.has_attribute
-
molsysmt.form.mdtraj_XTCTrajectoryFile.is_form
-
molsysmt.form.mdtraj_XTCTrajectoryFile.iterators
-
molsysmt.form.mdtraj_XTCTrajectoryFile.merge
-
molsysmt.form.mdtraj_XTCTrajectoryFile.set
-
molsysmt.form.mdtraj_XTCTrajectoryFile.to_mdtraj_XTCTrajectoryFile
-
molsysmt.form.mdtraj_XTCTrajectoryFile.to_molsysmt_Structures
-
molsysmt.form.mmcif_PdbxContainers_DataContainer
-
molsysmt.form.mmcif_PdbxContainers_DataContainer.add
-
molsysmt.form.mmcif_PdbxContainers_DataContainer.append_structures
-
molsysmt.form.mmcif_PdbxContainers_DataContainer.attributes
-
molsysmt.form.mmcif_PdbxContainers_DataContainer.copy
-
molsysmt.form.mmcif_PdbxContainers_DataContainer.extract
-
molsysmt.form.mmcif_PdbxContainers_DataContainer.get_structural_attributes
-
molsysmt.form.mmcif_PdbxContainers_DataContainer.get_topological_attributes
-
molsysmt.form.mmcif_PdbxContainers_DataContainer.has_attribute
-
molsysmt.form.mmcif_PdbxContainers_DataContainer.is_form
-
molsysmt.form.mmcif_PdbxContainers_DataContainer.iterators
-
molsysmt.form.mmcif_PdbxContainers_DataContainer.merge
-
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_mmcif_PdbxContainers_DataContainer
-
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.mmtf_MMTFDecoder
-
molsysmt.form.mmtf_MMTFDecoder.add
-
molsysmt.form.mmtf_MMTFDecoder.append_structures
-
molsysmt.form.mmtf_MMTFDecoder.attributes
-
molsysmt.form.mmtf_MMTFDecoder.copy
-
molsysmt.form.mmtf_MMTFDecoder.extract
-
molsysmt.form.mmtf_MMTFDecoder.get_structural_attributes
-
molsysmt.form.mmtf_MMTFDecoder.get_topological_attributes
-
molsysmt.form.mmtf_MMTFDecoder.has_attribute
-
molsysmt.form.mmtf_MMTFDecoder.is_form
-
molsysmt.form.mmtf_MMTFDecoder.iterators
-
molsysmt.form.mmtf_MMTFDecoder.merge
-
molsysmt.form.mmtf_MMTFDecoder.set
-
molsysmt.form.mmtf_MMTFDecoder.to_file_mmtf
-
molsysmt.form.mmtf_MMTFDecoder.to_file_pdb
-
molsysmt.form.mmtf_MMTFDecoder.to_mdtraj_Trajectory
-
molsysmt.form.mmtf_MMTFDecoder.to_mmtf_MMTFDecoder
-
molsysmt.form.mmtf_MMTFDecoder.to_molsysmt_MolecularMechanics
-
molsysmt.form.mmtf_MMTFDecoder.to_molsysmt_MolSys
-
molsysmt.form.mmtf_MMTFDecoder.to_molsysmt_Structures
-
molsysmt.form.mmtf_MMTFDecoder.to_molsysmt_Topology
-
molsysmt.form.mmtf_MMTFDecoder.to_openmm_Topology
-
molsysmt.form.mmtf_MMTFDecoder.to_string_amino_acids_1
-
molsysmt.form.mmtf_MMTFDecoder.to_string_amino_acids_3
-
molsysmt.form.mmtf_MMTFDecoder.to_string_pdb_text
-
molsysmt.form.molsysmt_CIFFileHandler
-
molsysmt.form.molsysmt_CIFFileHandler.add
-
molsysmt.form.molsysmt_CIFFileHandler.append_structures
-
molsysmt.form.molsysmt_CIFFileHandler.attributes
-
molsysmt.form.molsysmt_CIFFileHandler.copy
-
molsysmt.form.molsysmt_CIFFileHandler.extract
-
molsysmt.form.molsysmt_CIFFileHandler.get
-
molsysmt.form.molsysmt_CIFFileHandler.has_attribute
-
molsysmt.form.molsysmt_CIFFileHandler.is_form
-
molsysmt.form.molsysmt_CIFFileHandler.iterators
-
molsysmt.form.molsysmt_CIFFileHandler.merge
-
molsysmt.form.molsysmt_CIFFileHandler.set
-
molsysmt.form.molsysmt_CIFFileHandler.to_molsysmt_CIFFileHandler
-
molsysmt.form.molsysmt_GROFileHandler
-
molsysmt.form.molsysmt_GROFileHandler.add
-
molsysmt.form.molsysmt_GROFileHandler.append_structures
-
molsysmt.form.molsysmt_GROFileHandler.attributes
-
molsysmt.form.molsysmt_GROFileHandler.copy
-
molsysmt.form.molsysmt_GROFileHandler.extract
-
molsysmt.form.molsysmt_GROFileHandler.get
-
molsysmt.form.molsysmt_GROFileHandler.has_attribute
-
molsysmt.form.molsysmt_GROFileHandler.is_form
-
molsysmt.form.molsysmt_GROFileHandler.iterators
-
molsysmt.form.molsysmt_GROFileHandler.merge
-
molsysmt.form.molsysmt_GROFileHandler.set
-
molsysmt.form.molsysmt_GROFileHandler.to_molsysmt_GROFileHandler
-
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
-
molsysmt.form.molsysmt_H5MSMFileHandler.add
-
molsysmt.form.molsysmt_H5MSMFileHandler.append_structures
-
molsysmt.form.molsysmt_H5MSMFileHandler.attributes
-
molsysmt.form.molsysmt_H5MSMFileHandler.copy
-
molsysmt.form.molsysmt_H5MSMFileHandler.extract
-
molsysmt.form.molsysmt_H5MSMFileHandler.get_structural_attributes
-
molsysmt.form.molsysmt_H5MSMFileHandler.get_topological_attributes
-
molsysmt.form.molsysmt_H5MSMFileHandler.has_attribute
-
molsysmt.form.molsysmt_H5MSMFileHandler.is_form
-
molsysmt.form.molsysmt_H5MSMFileHandler.iterators
-
molsysmt.form.molsysmt_H5MSMFileHandler.merge
-
molsysmt.form.molsysmt_H5MSMFileHandler.set
-
molsysmt.form.molsysmt_H5MSMFileHandler.to_molsysmt_H5MSMFileHandler
-
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
-
molsysmt.form.molsysmt_MolecularMechanics.add
-
molsysmt.form.molsysmt_MolecularMechanics.append_structures
-
molsysmt.form.molsysmt_MolecularMechanics.attributes
-
molsysmt.form.molsysmt_MolecularMechanics.copy
-
molsysmt.form.molsysmt_MolecularMechanics.extract
-
molsysmt.form.molsysmt_MolecularMechanics.get
-
molsysmt.form.molsysmt_MolecularMechanics.has_attribute
-
molsysmt.form.molsysmt_MolecularMechanics.is_form
-
molsysmt.form.molsysmt_MolecularMechanics.iterators
-
molsysmt.form.molsysmt_MolecularMechanics.merge
-
molsysmt.form.molsysmt_MolecularMechanics.set
-
molsysmt.form.molsysmt_MolecularMechanics.to_molsysmt_MolecularMechanics
-
molsysmt.form.molsysmt_MolecularMechanics.to_molsysmt_MolecularMechanicsDict
-
molsysmt.form.molsysmt_MolecularMechanicsDict
-
molsysmt.form.molsysmt_MolecularMechanicsDict.add
-
molsysmt.form.molsysmt_MolecularMechanicsDict.append_structures
-
molsysmt.form.molsysmt_MolecularMechanicsDict.attributes
-
molsysmt.form.molsysmt_MolecularMechanicsDict.copy
-
molsysmt.form.molsysmt_MolecularMechanicsDict.extract
-
molsysmt.form.molsysmt_MolecularMechanicsDict.get
-
molsysmt.form.molsysmt_MolecularMechanicsDict.has_attribute
-
molsysmt.form.molsysmt_MolecularMechanicsDict.is_form
-
molsysmt.form.molsysmt_MolecularMechanicsDict.iterators
-
molsysmt.form.molsysmt_MolecularMechanicsDict.merge
-
molsysmt.form.molsysmt_MolecularMechanicsDict.set
-
molsysmt.form.molsysmt_MolecularMechanicsDict.to_molsysmt_MolecularMechanics
-
molsysmt.form.molsysmt_MolecularMechanicsDict.to_molsysmt_MolecularMechanicsDict
-
molsysmt.form.molsysmt_MolSys
-
molsysmt.form.molsysmt_MolSys.add
-
molsysmt.form.molsysmt_MolSys.add_bonds
-
molsysmt.form.molsysmt_MolSys.append_structures
-
molsysmt.form.molsysmt_MolSys.attributes
-
molsysmt.form.molsysmt_MolSys.copy
-
molsysmt.form.molsysmt_MolSys.extract
-
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.has_attribute
-
molsysmt.form.molsysmt_MolSys.is_form
-
molsysmt.form.molsysmt_MolSys.iterators
-
molsysmt.form.molsysmt_MolSys.merge
-
molsysmt.form.molsysmt_MolSys.old_get
-
molsysmt.form.molsysmt_MolSys.remove_bonds
-
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_msmpk
-
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_MolSys
-
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_parmed_Structure
-
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
-
molsysmt.form.molsysmt_PDBFileHandler.add
-
molsysmt.form.molsysmt_PDBFileHandler.append_structures
-
molsysmt.form.molsysmt_PDBFileHandler.attributes
-
molsysmt.form.molsysmt_PDBFileHandler.copy
-
molsysmt.form.molsysmt_PDBFileHandler.extract
-
molsysmt.form.molsysmt_PDBFileHandler.get
-
molsysmt.form.molsysmt_PDBFileHandler.has_attribute
-
molsysmt.form.molsysmt_PDBFileHandler.is_form
-
molsysmt.form.molsysmt_PDBFileHandler.iterators
-
molsysmt.form.molsysmt_PDBFileHandler.merge
-
molsysmt.form.molsysmt_PDBFileHandler.set
-
molsysmt.form.molsysmt_PDBFileHandler.to_molsysmt_MolSys
-
molsysmt.form.molsysmt_PDBFileHandler.to_molsysmt_PDBFileHandler
-
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
-
molsysmt.form.molsysmt_Structures.add
-
molsysmt.form.molsysmt_Structures.append_structures
-
molsysmt.form.molsysmt_Structures.attributes
-
molsysmt.form.molsysmt_Structures.copy
-
molsysmt.form.molsysmt_Structures.extract
-
molsysmt.form.molsysmt_Structures.get_structural_attributes
-
molsysmt.form.molsysmt_Structures.has_attribute
-
molsysmt.form.molsysmt_Structures.is_form
-
molsysmt.form.molsysmt_Structures.iterators
-
molsysmt.form.molsysmt_Structures.merge
-
molsysmt.form.molsysmt_Structures.set
-
molsysmt.form.molsysmt_Structures.to_file_h5msm
-
molsysmt.form.molsysmt_Structures.to_molsysmt_Structures
-
molsysmt.form.molsysmt_Structures.to_molsysmt_StructuresDict
-
molsysmt.form.molsysmt_Structures.to_XYZ
-
molsysmt.form.molsysmt_StructuresDict
-
molsysmt.form.molsysmt_StructuresDict.add
-
molsysmt.form.molsysmt_StructuresDict.append_structures
-
molsysmt.form.molsysmt_StructuresDict.attributes
-
molsysmt.form.molsysmt_StructuresDict.copy
-
molsysmt.form.molsysmt_StructuresDict.extract
-
molsysmt.form.molsysmt_StructuresDict.get
-
molsysmt.form.molsysmt_StructuresDict.has_attribute
-
molsysmt.form.molsysmt_StructuresDict.is_form
-
molsysmt.form.molsysmt_StructuresDict.iterators
-
molsysmt.form.molsysmt_StructuresDict.merge
-
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_StructuresDict
-
molsysmt.form.molsysmt_StructuresDict.to_molsysmt_Topology
-
molsysmt.form.molsysmt_Topology
-
molsysmt.form.molsysmt_Topology.add
-
molsysmt.form.molsysmt_Topology.add_bonds
-
molsysmt.form.molsysmt_Topology.append_structures
-
molsysmt.form.molsysmt_Topology.attributes
-
molsysmt.form.molsysmt_Topology.copy
-
molsysmt.form.molsysmt_Topology.extract
-
molsysmt.form.molsysmt_Topology.get_topological_attributes
-
molsysmt.form.molsysmt_Topology.has_attribute
-
molsysmt.form.molsysmt_Topology.is_form
-
molsysmt.form.molsysmt_Topology.iterators
-
molsysmt.form.molsysmt_Topology.merge
-
molsysmt.form.molsysmt_Topology.remove_bonds
-
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_molsysmt_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
-
molsysmt.form.networkx_Graph.add
-
molsysmt.form.networkx_Graph.append_structures
-
molsysmt.form.networkx_Graph.attributes
-
molsysmt.form.networkx_Graph.copy
-
molsysmt.form.networkx_Graph.extract
-
molsysmt.form.networkx_Graph.get
-
molsysmt.form.networkx_Graph.has_attribute
-
molsysmt.form.networkx_Graph.is_form
-
molsysmt.form.networkx_Graph.iterators
-
molsysmt.form.networkx_Graph.merge
-
molsysmt.form.networkx_Graph.set
-
molsysmt.form.networkx_Graph.to_networkx_Graph
-
molsysmt.form.nglview_NGLWidget
-
molsysmt.form.nglview_NGLWidget.add
-
molsysmt.form.nglview_NGLWidget.append_structures
-
molsysmt.form.nglview_NGLWidget.attributes
-
molsysmt.form.nglview_NGLWidget.copy
-
molsysmt.form.nglview_NGLWidget.extract
-
molsysmt.form.nglview_NGLWidget.get_structural_attributes
-
molsysmt.form.nglview_NGLWidget.get_topological_attributes
-
molsysmt.form.nglview_NGLWidget.has_attribute
-
molsysmt.form.nglview_NGLWidget.is_form
-
molsysmt.form.nglview_NGLWidget.iterators
-
molsysmt.form.nglview_NGLWidget.merge
-
molsysmt.form.nglview_NGLWidget.set
-
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_nglview_NGLWidget
-
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
-
molsysmt.form.openmm_AmberInpcrdFile.add
-
molsysmt.form.openmm_AmberInpcrdFile.append_structures
-
molsysmt.form.openmm_AmberInpcrdFile.attributes
-
molsysmt.form.openmm_AmberInpcrdFile.copy
-
molsysmt.form.openmm_AmberInpcrdFile.extract
-
molsysmt.form.openmm_AmberInpcrdFile.get
-
molsysmt.form.openmm_AmberInpcrdFile.has_attribute
-
molsysmt.form.openmm_AmberInpcrdFile.is_form
-
molsysmt.form.openmm_AmberInpcrdFile.iterators
-
molsysmt.form.openmm_AmberInpcrdFile.merge
-
molsysmt.form.openmm_AmberInpcrdFile.set
-
molsysmt.form.openmm_AmberInpcrdFile.to_molsysmt_Structures
-
molsysmt.form.openmm_AmberInpcrdFile.to_openmm_AmberInpcrdFile
-
molsysmt.form.openmm_AmberPrmtopFile
-
molsysmt.form.openmm_AmberPrmtopFile.add
-
molsysmt.form.openmm_AmberPrmtopFile.append_structures
-
molsysmt.form.openmm_AmberPrmtopFile.attributes
-
molsysmt.form.openmm_AmberPrmtopFile.copy
-
molsysmt.form.openmm_AmberPrmtopFile.extract
-
molsysmt.form.openmm_AmberPrmtopFile.get
-
molsysmt.form.openmm_AmberPrmtopFile.has_attribute
-
molsysmt.form.openmm_AmberPrmtopFile.is_form
-
molsysmt.form.openmm_AmberPrmtopFile.iterators
-
molsysmt.form.openmm_AmberPrmtopFile.merge
-
molsysmt.form.openmm_AmberPrmtopFile.set
-
molsysmt.form.openmm_AmberPrmtopFile.to_molsysmt_Topology
-
molsysmt.form.openmm_AmberPrmtopFile.to_openmm_AmberPrmtopFile
-
molsysmt.form.openmm_AmberPrmtopFile.to_openmm_System
-
molsysmt.form.openmm_AmberPrmtopFile.to_openmm_Topology
-
molsysmt.form.openmm_CharmmCrdFile
-
molsysmt.form.openmm_CharmmCrdFile.add
-
molsysmt.form.openmm_CharmmCrdFile.append_structures
-
molsysmt.form.openmm_CharmmCrdFile.attributes
-
molsysmt.form.openmm_CharmmCrdFile.copy
-
molsysmt.form.openmm_CharmmCrdFile.extract
-
molsysmt.form.openmm_CharmmCrdFile.get
-
molsysmt.form.openmm_CharmmCrdFile.has_attribute
-
molsysmt.form.openmm_CharmmCrdFile.is_form
-
molsysmt.form.openmm_CharmmCrdFile.iterators
-
molsysmt.form.openmm_CharmmCrdFile.merge
-
molsysmt.form.openmm_CharmmCrdFile.set
-
molsysmt.form.openmm_CharmmCrdFile.to_openmm_CharmmCrdFile
-
molsysmt.form.openmm_CharmmPsfFile
-
molsysmt.form.openmm_CharmmPsfFile.add
-
molsysmt.form.openmm_CharmmPsfFile.append_structures
-
molsysmt.form.openmm_CharmmPsfFile.attributes
-
molsysmt.form.openmm_CharmmPsfFile.copy
-
molsysmt.form.openmm_CharmmPsfFile.extract
-
molsysmt.form.openmm_CharmmPsfFile.get
-
molsysmt.form.openmm_CharmmPsfFile.has_attribute
-
molsysmt.form.openmm_CharmmPsfFile.is_form
-
molsysmt.form.openmm_CharmmPsfFile.iterators
-
molsysmt.form.openmm_CharmmPsfFile.merge
-
molsysmt.form.openmm_CharmmPsfFile.set
-
molsysmt.form.openmm_CharmmPsfFile.to_molsysmt_Topology
-
molsysmt.form.openmm_CharmmPsfFile.to_openmm_CharmmPsfFile
-
molsysmt.form.openmm_CharmmPsfFile.to_openmm_Topology
-
molsysmt.form.openmm_Context
-
molsysmt.form.openmm_Context.add
-
molsysmt.form.openmm_Context.append_structures
-
molsysmt.form.openmm_Context.attributes
-
molsysmt.form.openmm_Context.copy
-
molsysmt.form.openmm_Context.extract
-
molsysmt.form.openmm_Context.get_structural_attributes
-
molsysmt.form.openmm_Context.get_topological_attributes
-
molsysmt.form.openmm_Context.has_attribute
-
molsysmt.form.openmm_Context.is_form
-
molsysmt.form.openmm_Context.iterators
-
molsysmt.form.openmm_Context.merge
-
molsysmt.form.openmm_Context.set
-
molsysmt.form.openmm_Context.to_molsysmt_Structures
-
molsysmt.form.openmm_Context.to_openmm_Context
-
molsysmt.form.openmm_Context.to_openmm_System
-
molsysmt.form.openmm_GromacsGroFile
-
molsysmt.form.openmm_GromacsGroFile.add
-
molsysmt.form.openmm_GromacsGroFile.append_structures
-
molsysmt.form.openmm_GromacsGroFile.attributes
-
molsysmt.form.openmm_GromacsGroFile.copy
-
molsysmt.form.openmm_GromacsGroFile.extract
-
molsysmt.form.openmm_GromacsGroFile.get
-
molsysmt.form.openmm_GromacsGroFile.has_attribute
-
molsysmt.form.openmm_GromacsGroFile.is_form
-
molsysmt.form.openmm_GromacsGroFile.iterators
-
molsysmt.form.openmm_GromacsGroFile.merge
-
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_GromacsGroFile
-
molsysmt.form.openmm_GromacsGroFile.to_openmm_Modeller
-
molsysmt.form.openmm_GromacsGroFile.to_openmm_Topology
-
molsysmt.form.openmm_GromacsTopFile
-
molsysmt.form.openmm_GromacsTopFile.add
-
molsysmt.form.openmm_GromacsTopFile.append_structures
-
molsysmt.form.openmm_GromacsTopFile.attributes
-
molsysmt.form.openmm_GromacsTopFile.copy
-
molsysmt.form.openmm_GromacsTopFile.extract
-
molsysmt.form.openmm_GromacsTopFile.get
-
molsysmt.form.openmm_GromacsTopFile.has_attribute
-
molsysmt.form.openmm_GromacsTopFile.is_form
-
molsysmt.form.openmm_GromacsTopFile.iterators
-
molsysmt.form.openmm_GromacsTopFile.merge
-
molsysmt.form.openmm_GromacsTopFile.set
-
molsysmt.form.openmm_GromacsTopFile.to_molsysmt_Topology
-
molsysmt.form.openmm_GromacsTopFile.to_openmm_GromacsTopFile
-
molsysmt.form.openmm_GromacsTopFile.to_openmm_Topology
-
molsysmt.form.openmm_Modeller
-
molsysmt.form.openmm_Modeller.add
-
molsysmt.form.openmm_Modeller.append_structures
-
molsysmt.form.openmm_Modeller.attributes
-
molsysmt.form.openmm_Modeller.copy
-
molsysmt.form.openmm_Modeller.extract
-
molsysmt.form.openmm_Modeller.get_structural_attributes
-
molsysmt.form.openmm_Modeller.get_topological_attributes
-
molsysmt.form.openmm_Modeller.has_attribute
-
molsysmt.form.openmm_Modeller.is_form
-
molsysmt.form.openmm_Modeller.iterators
-
molsysmt.form.openmm_Modeller.merge
-
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_Modeller
-
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
-
molsysmt.form.openmm_PDBFile.add
-
molsysmt.form.openmm_PDBFile.append_structures
-
molsysmt.form.openmm_PDBFile.attributes
-
molsysmt.form.openmm_PDBFile.copy
-
molsysmt.form.openmm_PDBFile.extract
-
molsysmt.form.openmm_PDBFile.get
-
molsysmt.form.openmm_PDBFile.has_attribute
-
molsysmt.form.openmm_PDBFile.is_form
-
molsysmt.form.openmm_PDBFile.iterators
-
molsysmt.form.openmm_PDBFile.merge
-
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_PDBFile
-
molsysmt.form.openmm_PDBFile.to_openmm_Topology
-
molsysmt.form.openmm_Simulation
-
molsysmt.form.openmm_Simulation.add
-
molsysmt.form.openmm_Simulation.append_structures
-
molsysmt.form.openmm_Simulation.attributes
-
molsysmt.form.openmm_Simulation.copy
-
molsysmt.form.openmm_Simulation.extract
-
molsysmt.form.openmm_Simulation.get_structural_attributes
-
molsysmt.form.openmm_Simulation.get_topological_attributes
-
molsysmt.form.openmm_Simulation.has_attribute
-
molsysmt.form.openmm_Simulation.is_form
-
molsysmt.form.openmm_Simulation.iterators
-
molsysmt.form.openmm_Simulation.merge
-
molsysmt.form.openmm_Simulation.set
-
molsysmt.form.openmm_Simulation.to_file_msmpk
-
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_Simulation
-
molsysmt.form.openmm_Simulation.to_openmm_Topology
-
molsysmt.form.openmm_Simulation.to_pdbfixer_PDBFixer
-
molsysmt.form.openmm_State
-
molsysmt.form.openmm_State.add
-
molsysmt.form.openmm_State.append_structures
-
molsysmt.form.openmm_State.attributes
-
molsysmt.form.openmm_State.copy
-
molsysmt.form.openmm_State.extract
-
molsysmt.form.openmm_State.get
-
molsysmt.form.openmm_State.has_attribute
-
molsysmt.form.openmm_State.is_form
-
molsysmt.form.openmm_State.iterators
-
molsysmt.form.openmm_State.merge
-
molsysmt.form.openmm_State.set
-
molsysmt.form.openmm_State.to_molsysmt_Structures
-
molsysmt.form.openmm_State.to_openmm_State
-
molsysmt.form.openmm_State.to_XYZ
-
molsysmt.form.openmm_System
-
molsysmt.form.openmm_System.add
-
molsysmt.form.openmm_System.append_structures
-
molsysmt.form.openmm_System.attributes
-
molsysmt.form.openmm_System.copy
-
molsysmt.form.openmm_System.extract
-
molsysmt.form.openmm_System.get_structural_attributes
-
molsysmt.form.openmm_System.get_topological_attributes
-
molsysmt.form.openmm_System.has_attribute
-
molsysmt.form.openmm_System.is_form
-
molsysmt.form.openmm_System.iterators
-
molsysmt.form.openmm_System.merge
-
molsysmt.form.openmm_System.set
-
molsysmt.form.openmm_System.to_openmm_Context
-
molsysmt.form.openmm_System.to_openmm_Simulation
-
molsysmt.form.openmm_System.to_openmm_System
-
molsysmt.form.openmm_Topology
-
molsysmt.form.openmm_Topology.add
-
molsysmt.form.openmm_Topology.append_structures
-
molsysmt.form.openmm_Topology.attributes
-
molsysmt.form.openmm_Topology.copy
-
molsysmt.form.openmm_Topology.extract
-
molsysmt.form.openmm_Topology.get_structural_attributes
-
molsysmt.form.openmm_Topology.get_topological_attributes
-
molsysmt.form.openmm_Topology.has_attribute
-
molsysmt.form.openmm_Topology.is_form
-
molsysmt.form.openmm_Topology.iterators
-
molsysmt.form.openmm_Topology.merge
-
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_openmm_Topology
-
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.openmm_Topology.write_topology_in_h5msm
-
molsysmt.form.parmed_Structure
-
molsysmt.form.parmed_Structure.add
-
molsysmt.form.parmed_Structure.append_structures
-
molsysmt.form.parmed_Structure.attributes
-
molsysmt.form.parmed_Structure.copy
-
molsysmt.form.parmed_Structure.extract
-
molsysmt.form.parmed_Structure.get
-
molsysmt.form.parmed_Structure.has_attribute
-
molsysmt.form.parmed_Structure.is_form
-
molsysmt.form.parmed_Structure.iterators
-
molsysmt.form.parmed_Structure.merge
-
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.parmed_Structure.to_parmed_Structure
-
molsysmt.form.pdbfixer_PDBFixer
-
molsysmt.form.pdbfixer_PDBFixer.add
-
molsysmt.form.pdbfixer_PDBFixer.append_structures
-
molsysmt.form.pdbfixer_PDBFixer.attributes
-
molsysmt.form.pdbfixer_PDBFixer.copy
-
molsysmt.form.pdbfixer_PDBFixer.extract
-
molsysmt.form.pdbfixer_PDBFixer.get_structural_attributes
-
molsysmt.form.pdbfixer_PDBFixer.get_topological_attributes
-
molsysmt.form.pdbfixer_PDBFixer.has_attribute
-
molsysmt.form.pdbfixer_PDBFixer.is_form
-
molsysmt.form.pdbfixer_PDBFixer.iterators
-
molsysmt.form.pdbfixer_PDBFixer.merge
-
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_pdbfixer_PDBFixer
-
molsysmt.form.pdbfixer_PDBFixer.to_string_amino_acids_1
-
molsysmt.form.pdbfixer_PDBFixer.to_string_amino_acids_3
-
molsysmt.form.pytraj_Topology
-
molsysmt.form.pytraj_Topology.add
-
molsysmt.form.pytraj_Topology.append_structures
-
molsysmt.form.pytraj_Topology.attributes
-
molsysmt.form.pytraj_Topology.copy
-
molsysmt.form.pytraj_Topology.extract
-
molsysmt.form.pytraj_Topology.get
-
molsysmt.form.pytraj_Topology.has_attribute
-
molsysmt.form.pytraj_Topology.is_form
-
molsysmt.form.pytraj_Topology.iterators
-
molsysmt.form.pytraj_Topology.merge
-
molsysmt.form.pytraj_Topology.set
-
molsysmt.form.pytraj_Topology.to_molsysmt_Topology
-
molsysmt.form.pytraj_Topology.to_pytraj_Topology
-
molsysmt.form.pytraj_Topology.to_pytraj_Trajectory
-
molsysmt.form.pytraj_Trajectory
-
molsysmt.form.pytraj_Trajectory.add
-
molsysmt.form.pytraj_Trajectory.append_structures
-
molsysmt.form.pytraj_Trajectory.attributes
-
molsysmt.form.pytraj_Trajectory.copy
-
molsysmt.form.pytraj_Trajectory.extract
-
molsysmt.form.pytraj_Trajectory.get
-
molsysmt.form.pytraj_Trajectory.has_attribute
-
molsysmt.form.pytraj_Trajectory.is_form
-
molsysmt.form.pytraj_Trajectory.iterators
-
molsysmt.form.pytraj_Trajectory.merge
-
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.pytraj_Trajectory.to_pytraj_Trajectory
-
molsysmt.form.string_alphafold_id
-
molsysmt.form.string_alphafold_id.add
-
molsysmt.form.string_alphafold_id.append_structures
-
molsysmt.form.string_alphafold_id.attributes
-
molsysmt.form.string_alphafold_id.copy
-
molsysmt.form.string_alphafold_id.extract
-
molsysmt.form.string_alphafold_id.get_structural_attributes
-
molsysmt.form.string_alphafold_id.get_topological_attributes
-
molsysmt.form.string_alphafold_id.has_attribute
-
molsysmt.form.string_alphafold_id.is_form
-
molsysmt.form.string_alphafold_id.iterators
-
molsysmt.form.string_alphafold_id.merge
-
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_alphafold_id
-
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
-
molsysmt.form.string_amino_acids_1.add
-
molsysmt.form.string_amino_acids_1.append_structures
-
molsysmt.form.string_amino_acids_1.attributes
-
molsysmt.form.string_amino_acids_1.copy
-
molsysmt.form.string_amino_acids_1.extract
-
molsysmt.form.string_amino_acids_1.get
-
molsysmt.form.string_amino_acids_1.has_attribute
-
molsysmt.form.string_amino_acids_1.is_form
-
molsysmt.form.string_amino_acids_1.iterators
-
molsysmt.form.string_amino_acids_1.merge
-
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_1
-
molsysmt.form.string_amino_acids_1.to_string_amino_acids_3
-
molsysmt.form.string_amino_acids_3
-
molsysmt.form.string_amino_acids_3.add
-
molsysmt.form.string_amino_acids_3.append_structures
-
molsysmt.form.string_amino_acids_3.attributes
-
molsysmt.form.string_amino_acids_3.copy
-
molsysmt.form.string_amino_acids_3.extract
-
molsysmt.form.string_amino_acids_3.get
-
molsysmt.form.string_amino_acids_3.has_attribute
-
molsysmt.form.string_amino_acids_3.is_form
-
molsysmt.form.string_amino_acids_3.iterators
-
molsysmt.form.string_amino_acids_3.merge
-
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_amino_acids_3.to_string_amino_acids_3
-
molsysmt.form.string_pdb_id
-
molsysmt.form.string_pdb_id.add
-
molsysmt.form.string_pdb_id.append_structures
-
molsysmt.form.string_pdb_id.attributes
-
molsysmt.form.string_pdb_id.copy
-
molsysmt.form.string_pdb_id.extract
-
molsysmt.form.string_pdb_id.get_structural_attributes
-
molsysmt.form.string_pdb_id.get_topological_attributes
-
molsysmt.form.string_pdb_id.has_attribute
-
molsysmt.form.string_pdb_id.is_form
-
molsysmt.form.string_pdb_id.iterators
-
molsysmt.form.string_pdb_id.merge
-
molsysmt.form.string_pdb_id.set
-
molsysmt.form.string_pdb_id.to_bcifreader_PdbxContainers_DataContainer
-
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_mmtf
-
molsysmt.form.string_pdb_id.to_file_msmpk
-
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_mmtf_MMTFDecoder
-
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_id
-
molsysmt.form.string_pdb_id.to_string_pdb_text
-
molsysmt.form.string_pdb_text
-
molsysmt.form.string_pdb_text.add
-
molsysmt.form.string_pdb_text.append_structures
-
molsysmt.form.string_pdb_text.attributes
-
molsysmt.form.string_pdb_text.copy
-
molsysmt.form.string_pdb_text.extract
-
molsysmt.form.string_pdb_text.get_structural_attributes
-
molsysmt.form.string_pdb_text.get_topological_attributes
-
molsysmt.form.string_pdb_text.has_attribute
-
molsysmt.form.string_pdb_text.is_form
-
molsysmt.form.string_pdb_text.iterators
-
molsysmt.form.string_pdb_text.merge
-
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.string_pdb_text.to_string_pdb_text
-
molsysmt.form.XYZ
-
molsysmt.form.XYZ.add
-
molsysmt.form.XYZ.append_structures
-
molsysmt.form.XYZ.attributes
-
molsysmt.form.XYZ.copy
-
molsysmt.form.XYZ.extract
-
molsysmt.form.XYZ.get_rank_3_XYZ
-
molsysmt.form.XYZ.get_structural_attributes
-
molsysmt.form.XYZ.get_topological_attributes
-
molsysmt.form.XYZ.has_attribute
-
molsysmt.form.XYZ.is_form
-
molsysmt.form.XYZ.iterators
-
molsysmt.form.XYZ.merge
-
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.form.XYZ.to_XYZ
-
molsysmt.hbonds
-
molsysmt.hbonds.get_acceptor_atoms
-
molsysmt.hbonds.get_buch_hbonds
-
molsysmt.hbonds.get_donor_atoms
-
molsysmt.hbonds.get_luzard_chandler_hbonds
-
molsysmt.lib
-
molsysmt.lib.make_numba_signature
-
molsysmt.lib.math
-
molsysmt.lib.pbc
-
molsysmt.lib.pbc.box_is_orthogonal
-
molsysmt.lib.pbc.get_angles_from_box
-
molsysmt.lib.pbc.get_box_from_lengths_and_angles
-
molsysmt.lib.pbc.get_lengths_and_angles_from_box
-
molsysmt.lib.pbc.get_lengths_from_box
-
molsysmt.lib.pbc.unwrap
-
molsysmt.lib.pbc.wrap_to_mic
-
molsysmt.lib.pbc.wrap_to_pbc
-
molsysmt.lib.series
-
molsysmt.lib.structure
-
molsysmt.lib.structure.flip
-
molsysmt.lib.structure.get_angles
-
molsysmt.lib.structure.get_center
-
molsysmt.lib.structure.get_dihedral_angles
-
molsysmt.lib.structure.get_distances
-
molsysmt.lib.structure.get_least_rmsd
-
molsysmt.lib.structure.get_least_rmsd_rotation_and_translation
-
molsysmt.lib.structure.get_mic_angles
-
molsysmt.lib.structure.get_mic_dihedral_angles
-
molsysmt.lib.structure.get_mic_distances
-
molsysmt.lib.structure.get_principal_geometric_axes
-
molsysmt.lib.structure.get_principal_inertia_axes
-
molsysmt.lib.structure.get_rmsd
-
molsysmt.lib.structure.principal_component_analysis
-
molsysmt.lib.structure.set_dihedral_angles
-
molsysmt.lib.structure.set_mic_dihedral_angles
-
molsysmt.lib.structure.shift_dihedral_angles
-
molsysmt.lib.structure.shift_mic_dihedral_angles
-
molsysmt.molecular_dynamics
-
molsysmt.molecular_dynamics.run_NPT_equilibration
-
molsysmt.molecular_dynamics.run_NVT_equilibration
-
molsysmt.molecular_mechanics
-
molsysmt.molecular_mechanics.forcefields
-
molsysmt.molecular_mechanics.get_engine_forcefield
-
molsysmt.molecular_mechanics.get_forces
-
molsysmt.molecular_mechanics.get_non_bonded_potential_energy
-
molsysmt.molecular_mechanics.get_num_degrees_of_freedom
-
molsysmt.molecular_mechanics.get_potential_energy
-
molsysmt.molecular_mechanics.potential_energy_minimization
-
molsysmt.native
-
molsysmt.native.cif_file_handler
-
molsysmt.native.file_tng
-
molsysmt.native.file_xtc
-
molsysmt.native.gro_file_handler
-
molsysmt.native.h5msm_file_handler
-
molsysmt.native.molecular_mechanics
-
molsysmt.native.molecular_mechanics_dict
-
molsysmt.native.molsys
-
molsysmt.native.pdb_atomic_coordinate_entry
-
molsysmt.native.pdb_file_handler
-
molsysmt.native.simulation
-
molsysmt.native.simulation_dict
-
molsysmt.native.structures
-
molsysmt.native.structures_dict
-
molsysmt.native.topology
-
molsysmt.native.trajectory_file
-
molsysmt.pbc
-
molsysmt.pbc.get_angles_from_box
-
molsysmt.pbc.get_box_from_lengths_and_angles
-
molsysmt.pbc.get_box_with_shape
-
molsysmt.pbc.get_lengths_and_angles_from_box
-
molsysmt.pbc.get_lengths_from_box
-
molsysmt.pbc.get_shape_from_angles
-
molsysmt.pbc.get_shape_from_box
-
molsysmt.pbc.get_volume_from_box
-
molsysmt.pbc.get_volume_from_lengths_and_angles
-
molsysmt.pbc.has_pbc
-
molsysmt.pbc.unwrap
-
molsysmt.pbc.wrap_to_mic
-
molsysmt.pbc.wrap_to_pbc
-
molsysmt.physchem
-
molsysmt.physchem.get_area_buried
-
molsysmt.physchem.get_atomic_radius
-
molsysmt.physchem.get_buried_fraction
-
molsysmt.physchem.get_charge
-
molsysmt.physchem.get_hydrophobicity
-
molsysmt.physchem.get_mass
-
molsysmt.physchem.get_polarity
-
molsysmt.physchem.get_sasa
-
molsysmt.physchem.get_surface_area
-
molsysmt.physchem.get_transmembrane_tendency
-
molsysmt.physchem.get_volume
-
molsysmt.structure
-
molsysmt.structure.align_principal_axes
-
molsysmt.structure.center
-
molsysmt.structure.flip
-
molsysmt.structure.get_angles
-
molsysmt.structure.get_center
-
molsysmt.structure.get_contacts
-
molsysmt.structure.get_dihedral_angles
-
molsysmt.structure.get_distances
-
molsysmt.structure.get_least_rmsd
-
molsysmt.structure.get_maximum_distances
-
molsysmt.structure.get_minimum_distances
-
molsysmt.structure.get_neighbors
-
molsysmt.structure.get_principal_axes
-
molsysmt.structure.get_radius_of_gyration
-
molsysmt.structure.get_rmsd
-
molsysmt.structure.least_rmsd_align
-
molsysmt.structure.least_rmsd_fit
-
molsysmt.structure.move_away
-
molsysmt.structure.principal_component_analysis
-
molsysmt.structure.rotate
-
molsysmt.structure.set_dihedral_angles
-
molsysmt.structure.shift_dihedral_angles
-
molsysmt.structure.show_contacts
-
molsysmt.structure.translate
-
molsysmt.supported
-
molsysmt.supported.engines
-
molsysmt.supported.supported
-
molsysmt.supported.syntaxes
-
molsysmt.supported.viewers
-
molsysmt.systems
-
molsysmt.thirds
-
molsysmt.thirds.nglview
-
molsysmt.thirds.nglview.add_arrows
-
molsysmt.thirds.nglview.add_contacts
-
molsysmt.thirds.nglview.add_cylinders
-
molsysmt.thirds.nglview.add_hbonds
-
molsysmt.thirds.nglview.clear
-
molsysmt.thirds.nglview.load_html_in_jupyter_notebook
-
molsysmt.thirds.nglview.patching_nglview
-
molsysmt.thirds.nglview.set_color
-
molsysmt.thirds.nglview.set_color_by_value
-
molsysmt.thirds.nglview.show_as_balls_and_sticks
-
molsysmt.thirds.nglview.show_as_cartoon
-
molsysmt.thirds.nglview.show_as_licorice
-
molsysmt.thirds.nglview.show_as_surface
-
molsysmt.thirds.nglview.show_gui
-
molsysmt.thirds.nglview.standardize_view
-
molsysmt.thirds.nglview.write_html
-
molsysmt.thirds.openmm
-
molsysmt.thirds.openmm.forces
-
molsysmt.thirds.openmm.forces.add_allowed_plane_region
-
molsysmt.thirds.openmm.forces.add_allowed_z_region
-
molsysmt.thirds.openmm.forces.add_constant_force
-
molsysmt.thirds.openmm.forces.add_forbidden_plane_region
-
molsysmt.thirds.openmm.forces.add_forbidden_z_region
-
molsysmt.thirds.openmm.forces.add_harmonic_bond_force
-
molsysmt.thirds.openmm.forces.add_plane_harmonic_restraint
-
molsysmt.thirds.openmm.forces.add_point_harmonic_restraint
-
molsysmt.thirds.openmm.forces.pin_atoms
-
molsysmt.thirds.openmm.platforms
-
molsysmt.thirds.openmm.platforms.platforms
-
molsysmt.thirds.openmm.reporters
-
molsysmt.thirds.openmm.reporters.h5msm
-
molsysmt.thirds.openmm.reporters.MolSys
-
molsysmt.thirds.openmm.reporters.StructuresDict
-
molsysmt.thirds.openmm.reporters.tqdm
-
molsysmt.thirds.tleap
-
molsysmt.thirds.tleap.tleap
-
molsysmt.topology
-
molsysmt.topology.get_bondgraph
-
molsysmt.topology.get_covalent_blocks
-
molsysmt.topology.get_covalent_chains
-
molsysmt.topology.get_dihedral_quartets
-
molsysmt.topology.get_sequence_alignment
-
molsysmt.topology.get_sequence_identity
- MolSysReporter (class in molsysmt.thirds.openmm.reporters.MolSys)
- move_away() (in module molsysmt.structure)
- MtrixRecord (class in molsysmt.native.pdb_atomic_coordinate_entry)
- mutate() (in module molsysmt.build)
|
