Index

_

__init__() (parmed.amber.AmberAsciiRestart method) (parmed.amber.AmberFormat method) (parmed.amber.AmberMask method) (parmed.amber.AmberMdcrd method) (parmed.amber.AmberParm method) (parmed.amber.AmoebaParm method) (parmed.amber.ChamberParm method) (parmed.amber.NetCDFRestart method) (parmed.amber.NetCDFTraj method) (parmed.amber.Rst7 method) (parmed.charmm.CharmmCrdFile method) (parmed.charmm.CharmmParameterSet method) (parmed.charmm.CharmmPsfFile method) (parmed.charmm.CharmmRstFile method) (parmed.gromacs.GromacsGroFile method), [1] (parmed.gromacs.GromacsTopologyFile method), [1] (parmed.openmm.MdcrdReporter method) (parmed.openmm.NetCDFReporter method) (parmed.openmm.ProgressReporter method) (parmed.openmm.RestartReporter method) (parmed.openmm.StateDataReporter method) (parmed.openmm.XmlFile method) (parmed.structure.Structure method) (parmed.topologyobjects.Angle method) (parmed.topologyobjects.AngleType method) (parmed.topologyobjects.Atom method) (parmed.topologyobjects.AtomList method) (parmed.topologyobjects.AtomType method) (parmed.topologyobjects.Bond method) (parmed.topologyobjects.BondType method) (parmed.topologyobjects.ChiralFrame method) (parmed.topologyobjects.Cmap method) (parmed.topologyobjects.Dihedral method) (parmed.topologyobjects.DihedralType method) (parmed.topologyobjects.DihedralTypeList method) (parmed.topologyobjects.Improper method) (parmed.topologyobjects.ImproperType method) (parmed.topologyobjects.MultipoleFrame method) (parmed.topologyobjects.NonbondedException method) (parmed.topologyobjects.NonbondedExceptionType method) (parmed.topologyobjects.OutOfPlaneBend method) (parmed.topologyobjects.OutOfPlaneBendType method) (parmed.topologyobjects.PiTorsion method) (parmed.topologyobjects.Residue method) (parmed.topologyobjects.ResidueList method) (parmed.topologyobjects.StretchBend method) (parmed.topologyobjects.StretchBendType method) (parmed.topologyobjects.TorsionTorsion method) (parmed.topologyobjects.TorsionTorsionType method) (parmed.topologyobjects.TrigonalAngle method) (parmed.topologyobjects.UreyBradley method) (parmed.unit.BaseUnit method) (parmed.unit.Quantity method) (parmed.unit.Unit method) (parmed.unit.UnitSystem method)

A

AbstractBasicAuthHandler (parmed.utils.six.Module_six_moves_urllib_request attribute) AbstractDigestAuthHandler (parmed.utils.six.Module_six_moves_urllib_request attribute) accelerations() (parmed.amber.BeemanRestart property) AcceptorDonor (class in parmed) (class in parmed.topologyobjects) acos() (in module parmed.unit.unit_math) acosh() (in module parmed.unit.unit_math) Action (class in parmed.tools.actions) ActionButton (class in parmed.tools.gui.guitools) add12_6_4 (class in parmed.tools.actions) add_atom() (parmed.modeller.residue.ResidueTemplate method) (parmed.modeller.ResidueTemplate method) (parmed.Residue method) (parmed.ResidueList method) (parmed.Structure method) (parmed.structure.Structure method) (parmed.topologyobjects.Residue method) (parmed.topologyobjects.ResidueList method) add_atom_to_residue() (parmed.Structure method) (parmed.structure.Structure method) add_bond() (parmed.modeller.residue.ResidueTemplate method) (parmed.modeller.ResidueTemplate method) add_box() (parmed.amber.AmberMdcrd method) (parmed.amber.asciicrd.AmberMdcrd method) (parmed.amber.netcdffiles.NetCDFTraj method) (parmed.amber.NetCDFTraj method) add_cell_lengths_angles() (parmed.amber.netcdffiles.NetCDFTraj method) (parmed.amber.NetCDFTraj method) add_coordinates() (parmed.amber.AmberMdcrd method) (parmed.amber.asciicrd.AmberMdcrd method) (parmed.amber.netcdffiles.NetCDFTraj method) (parmed.amber.NetCDFTraj method) add_flag() (parmed.amber.AmberFormat method) (parmed.amber.amberformat.AmberFormat method) (parmed.amber.readparm.AmberFormat method) add_forces() (parmed.amber.netcdffiles.NetCDFTraj method) (parmed.amber.NetCDFTraj method) add_metaclass() (in module parmed.utils.six) add_move() (in module parmed.utils.six) add_nbfix() (parmed.AtomType method) (parmed.topologyobjects.AtomType method) add_parm() (parmed.tools.ParmList method) (parmed.tools.parmlist.ParmList method) add_remd_indices() (parmed.amber.netcdffiles.NetCDFTraj method) (parmed.amber.NetCDFTraj method) add_residue() (parmed.amber.titratable_residues.TitratableResidueList method) add_state() (parmed.amber.titratable_residues.TitratableResidue method) add_states() (parmed.amber.titratable_residues.TitratableResidue method) add_temp0() (parmed.amber.netcdffiles.NetCDFTraj method) (parmed.amber.NetCDFTraj method) add_time() (parmed.amber.netcdffiles.NetCDFTraj method) (parmed.amber.NetCDFTraj method) add_timer() (parmed.utils.timer.Timer method) add_vdw() (parmed.tinker.topologyobjects.Atom method) add_velocities() (parmed.amber.netcdffiles.NetCDFTraj method) (parmed.amber.NetCDFTraj method) addAtomicNumber (class in parmed.tools.actions) addbase (parmed.utils.six.Module_six_moves_urllib_response attribute) AddCard() (parmed.amber.mdin.Mdin method) (parmed.amber.mdin.mdin.Mdin method) addclosehook (parmed.utils.six.Module_six_moves_urllib_response attribute) addCoarseGrain() (in module parmed.tools.coarsegrain) addDihedral (class in parmed.tools.actions) addExclusions (class in parmed.tools.actions) addinfo (parmed.utils.six.Module_six_moves_urllib_response attribute) addinfourl (parmed.utils.six.Module_six_moves_urllib_response attribute) addLJType (class in parmed.tools.actions) AddLJType() (in module parmed.tools.addljtype) addOn() (in module parmed.amber.mdin.mdin) addPDB (class in parmed.tools.actions) AddPDBError AddPDBWarning all_residues (parmed.residue.AminoAcidResidue attribute) (parmed.residue.DNAResidue attribute) (parmed.residue.RNAResidue attribute) alternate_location() (parmed.formats.pdb.PDBFile.AtomLookupKey property) (parmed.formats.PDBFile.AtomLookupKey property) amber6() (in module parmed.tools.changeradii) AmberAsciiRestart (class in parmed.amber), [1] (class in parmed.amber.asciicrd) AmberError AmberFormat (class in parmed.amber), [1] (class in parmed.amber.amberformat) (class in parmed.amber.readparm) AmberIncompatibleWarning AmberMask (class in parmed.amber), [1] (class in parmed.amber.mask)

AmberMdcrd (class in parmed.amber), [1] (class in parmed.amber.asciicrd) AmberOFFLibrary (class in parmed.amber) (class in parmed.amber.offlib) (class in parmed.modeller) AmberParameterSet (class in parmed.amber) (class in parmed.amber.parameters) AmberParm (class in parmed.amber), [1] (class in parmed.amber.readparm) AmberWarning AmbiguousParmError AminoAcidResidue (class in parmed.residue) amoeba() (parmed.amber.AmberParm property) (parmed.amber.AmoebaParm property) (parmed.amber.ChamberParm property) (parmed.amber.readparm.AmberParm property) (parmed.amber.readparm.ChamberParm property) AmoebaNonbondedExceptionType (class in parmed) (class in parmed.topologyobjects) AmoebaParameterSet (class in parmed.tinker.parameterfile) AmoebaParm (class in parmed.amber), [1] Angle (class in parmed) (class in parmed.tools.coarsegrain) (class in parmed.topologyobjects), [1] angle() (in module parmed.geometry) ANGLE_FORCE_GROUP (parmed.Structure attribute) (parmed.structure.Structure attribute) angle_partners() (parmed.Atom property) (parmed.ExtraPoint property) (parmed.topologyobjects.Atom property) (parmed.topologyobjects.ExtraPoint property) angle_to() (parmed.Atom method) (parmed.topologyobjects.Atom method) AngleBend (class in parmed.tinker.topologyobjects) AngleList (class in parmed.tinker.topologyobjects) anglere (parmed.tinker.parameterfile.AmoebaParameterSet attribute) angles_inc_h() (parmed.amber.AmberParm property) (parmed.amber.readparm.AmberParm property) angles_without_h() (parmed.amber.AmberParm property) (parmed.amber.readparm.AmberParm property) AngleType (class in parmed) (class in parmed.topologyobjects), [1] append() (parmed.AtomList method) (parmed.DihedralTypeList method) (parmed.formats.pdbx.PdbxContainers.ContainerBase method) (parmed.formats.pdbx.PdbxContainers.DataCategory method) (parmed.tools.exceptions.WarningList method) (parmed.topologyobjects.AtomList method) (parmed.topologyobjects.DihedralTypeList method) (parmed.topologyobjects.TrackedList method) (parmed.TrackedList method) (parmed.unit.quantity.Quantity method) appendAttribute() (parmed.formats.pdbx.PdbxContainers.DataCategory method) appendAttributeExtendRows() (parmed.formats.pdbx.PdbxContainers.DataCategory method) apply_patch() (parmed.modeller.residue.ResidueTemplate method) (parmed.modeller.ResidueTemplate method) Argument (class in parmed.tools.argumentlist) ArgumentError ArgumentList (class in parmed.tools.argumentlist) asin() (in module parmed.unit.unit_math) asinh() (in module parmed.unit.unit_math) assertCountEqual() (in module parmed.utils.six) assertRaisesRegex() (in module parmed.utils.six) assertRegex() (in module parmed.utils.six) assign_bonds() (parmed.Structure method) (parmed.structure.Structure method) assign_nbidx_from_types() (parmed.AtomList method) (parmed.topologyobjects.AtomList method) assignValue() (parmed.utils.netcdf.netcdf_variable method) atan() (in module parmed.unit.unit_math) atan2() (in module parmed.unit.unit_math) atanh() (in module parmed.unit.unit_math) Atom (class in parmed) (class in parmed.tinker.topologyobjects) (class in parmed.topologyobjects), [1] atom_inter_flags (parmed.tinker.system.TinkerAnalout attribute) AtomicMultipole (class in parmed.tinker.topologyobjects) AtomicMultipoleList (class in parmed.tinker.topologyobjects) AtomList (class in parmed) (class in parmed.tinker.topologyobjects) (class in parmed.topologyobjects), [1] atomre (parmed.tinker.parameterfile.AmoebaParameterSet attribute) AtomType (class in parmed) (class in parmed.topologyobjects), [1] attributePart() (parmed.formats.pdbx.PdbxContainers.CifName static method)

B

b() (in module parmed.utils.six) BadParmWarning BaseDimension (class in parmed.unit.basedimension) BaseHandler (parmed.utils.six.Module_six_moves_urllib_request attribute) BaseUnit (class in parmed.unit) (class in parmed.unit.baseunit) BeemanRestart (class in parmed.amber) Bond (class in parmed) (class in parmed.topologyobjects), [1] BOND_FORCE_GROUP (parmed.Structure attribute) (parmed.structure.Structure attribute) BOND_ORDER_MAP (parmed.formats.mol2.Mol2File attribute) (parmed.formats.Mol2File attribute) bond_partners() (parmed.Atom property) (parmed.ExtraPoint property) (parmed.topologyobjects.Atom property) (parmed.topologyobjects.ExtraPoint property) bond_to() (parmed.Atom method) (parmed.topologyobjects.Atom method) bond_type() (parmed.AtomType property) (parmed.topologyobjects.AtomType property) bondi() (in module parmed.tools.changeradii) BondList (class in parmed.tinker.topologyobjects) bonds_inc_h() (parmed.amber.AmberParm property) (parmed.amber.readparm.AmberParm property) bonds_without_h() (parmed.amber.AmberParm property) (parmed.amber.readparm.AmberParm property) BondStretch (class in parmed.tinker.topologyobjects)

BondType (class in parmed) (class in parmed.topologyobjects), [1] BookmarkedFile (class in parmed.tinker.parameterfile) box() (parmed.amber.AmberAsciiRestart property) (parmed.amber.AmberMdcrd property) (parmed.amber.AmberParm property) (parmed.amber.asciicrd.AmberAsciiRestart property) (parmed.amber.asciicrd.AmberMdcrd property) (parmed.amber.BeemanRestart property) (parmed.amber.netcdffiles.NetCDFRestart property) (parmed.amber.netcdffiles.NetCDFTraj property) (parmed.amber.NetCDFRestart property) (parmed.amber.NetCDFTraj property) (parmed.amber.readparm.AmberParm property) (parmed.amber.readparm.Rst7 property) (parmed.amber.Rst7 property) (parmed.charmm.CharmmCrdFile property) (parmed.charmm.charmmcrds.CharmmCrdFile property) (parmed.charmm.charmmcrds.CharmmRstFile property) (parmed.charmm.CharmmRstFile property) (parmed.Structure property) (parmed.structure.Structure property) box_lengths_and_angles_to_vectors() (in module parmed.geometry) box_vectors() (parmed.amber.readparm.Rst7 property) (parmed.amber.Rst7 property) (parmed.Structure property) (parmed.structure.Structure property) box_vectors_to_lengths_and_angles() (in module parmed.geometry) build_opener (parmed.utils.six.Module_six_moves_urllib_request attribute)

C

CacheFTPHandler (parmed.utils.six.Module_six_moves_urllib_request attribute) canonical_improper_order() (in module parmed.utils) categoryPart() (parmed.formats.pdbx.PdbxContainers.CifName static method) cd (class in parmed.tools.actions) cell_angles() (parmed.amber.AmberAsciiRestart property) (parmed.amber.asciicrd.AmberAsciiRestart property) (parmed.amber.netcdffiles.NetCDFRestart property) (parmed.amber.NetCDFRestart property) cell_lengths() (parmed.amber.AmberAsciiRestart property) (parmed.amber.asciicrd.AmberAsciiRestart property) (parmed.amber.netcdffiles.NetCDFRestart property) (parmed.amber.NetCDFRestart property) cell_lengths_angles() (parmed.amber.netcdffiles.NetCDFTraj property) (parmed.amber.NetCDFTraj property) center_of_mass() (in module parmed.geometry) chain() (parmed.formats.pdb.PDBFile.AtomLookupKey property) (parmed.formats.PDBFile.AtomLookupKey property) chamber (class in parmed.tools.actions) chamber() (parmed.amber.AmberParm property) (parmed.amber.AmoebaParm property) (parmed.amber.ChamberParm property) (parmed.amber.readparm.AmberParm property) (parmed.amber.readparm.ChamberParm property) ChamberError ChamberParm (class in parmed.amber), [1] (class in parmed.amber.readparm) change (class in parmed.tools.actions) change() (parmed.amber.mdin.Mdin method) (parmed.amber.mdin.mdin.Mdin method) changeLJ14Pair (class in parmed.tools.actions) changeLJPair (class in parmed.tools.actions) ChangeLJPairError changeLJSingleType (class in parmed.tools.actions) changeProtState (class in parmed.tools.actions) changeRadii (class in parmed.tools.actions) ChangeRadiiError changeRedoxState (class in parmed.tools.actions) ChangeStateError charge() (parmed.Atom property) (parmed.topologyobjects.Atom property) CharmmCrdFile (class in parmed.charmm), [1] (class in parmed.charmm.charmmcrds) CharmmError CharmmImproperMatchingMixin (class in parmed.charmm.parameters) CharmmParameterSet (class in parmed.charmm), [1] (class in parmed.charmm.parameters) CharmmPsfEOF CharmmPsfFile (class in parmed.charmm), [1] (class in parmed.charmm.psf) CharmmRstFile (class in parmed.charmm), [1] (class in parmed.charmm.charmmcrds) CharmmWarning check() (parmed.amber.mdin.Mdin method) (parmed.amber.mdin.mdin.Mdin method) (parmed.amber.titratable_residues.TitratableResidue method) check_validity() (in module parmed.tools.checkvalidity) checkValidity (class in parmed.tools.actions) ChiralFrame (class in parmed) (class in parmed.topologyobjects), [1] ChRad() (in module parmed.tools.changeradii) CIFFile (class in parmed.formats) (class in parmed.formats.pdb) CifName (class in parmed.formats.pdbx.PdbxContainers) claim() (parmed.topologyobjects.TrackedList method) (parmed.TrackedList method) clapp() (in module parmed.scripts) clear_cmap() (parmed.charmm.CharmmPsfFile method) (parmed.charmm.psf.CharmmPsfFile method) close() (parmed.amber.netcdffiles.NetCDFRestart method) (parmed.amber.netcdffiles.NetCDFTraj method) (parmed.amber.NetCDFRestart method) (parmed.amber.NetCDFTraj method) (parmed.utils.netcdf.netcdf_file method) Cmap (class in parmed) (class in parmed.topologyobjects), [1]

CMAP_FORCE_GROUP (parmed.Structure attribute) (parmed.structure.Structure attribute) CmapType (class in parmed) (class in parmed.topologyobjects) cntrl (class in parmed.amber.mdin.cntrl) CoarseGrainError combining_rule() (parmed.parameters.ParameterSet property) (parmed.ParameterSet property) (parmed.Structure property) (parmed.structure.Structure property) completedefault() (parmed.tools.parmed_cmd.ParmedCmd method) condense() (parmed.parameters.ParameterSet method) (parmed.ParameterSet method) constpH() (parmed.amber.mdin.Mdin method) (parmed.amber.mdin.mdin.Mdin method) constPressure() (parmed.amber.mdin.Mdin method) (parmed.amber.mdin.mdin.Mdin method) constTemp() (parmed.amber.mdin.Mdin method) (parmed.amber.mdin.mdin.Mdin method) constVolume() (parmed.amber.mdin.Mdin method) (parmed.amber.mdin.mdin.Mdin method) ContainerBase (class in parmed.formats.pdbx.PdbxContainers) ContentTooShortError (parmed.utils.six.Module_six_moves_urllib_error attribute) conversion_factor_to() (parmed.unit.baseunit.BaseUnit method) (parmed.unit.unit.ScaledUnit method) (parmed.unit.unit.Unit method) ConvertFromPSF() (in module parmed.amber) coordinates() (parmed.amber.AmberAsciiRestart property) (parmed.amber.AmberMdcrd property) (parmed.amber.asciicrd.AmberAsciiRestart property) (parmed.amber.asciicrd.AmberMdcrd property) (parmed.amber.BeemanRestart property) (parmed.amber.netcdffiles.NetCDFRestart property) (parmed.amber.netcdffiles.NetCDFTraj property) (parmed.amber.NetCDFRestart property) (parmed.amber.NetCDFTraj property) (parmed.charmm.CharmmCrdFile property) (parmed.charmm.charmmcrds.CharmmCrdFile property) (parmed.charmm.charmmcrds.CharmmRstFile property) (parmed.charmm.CharmmRstFile property) (parmed.modeller.residue.ResidueTemplate property) (parmed.modeller.ResidueTemplate property) (parmed.namd.NamdBinCoor property) (parmed.namd.namdbinfiles.NamdBinCoor property) (parmed.Structure property) (parmed.structure.Structure property) (parmed.structure.StructureView property) (parmed.StructureView property) coordinatesold() (parmed.charmm.charmmcrds.CharmmRstFile property) (parmed.charmm.CharmmRstFile property) copy() (parmed.gromacs.gromacstop.GromacsTopologyFile method) (parmed.gromacs.GromacsTopologyFile method) (parmed.Structure method) (parmed.structure.Structure method) copy_from() (parmed.amber.readparm.Rst7 class method) (parmed.amber.Rst7 class method) copyatoms() (parmed.namd.namdbinfiles.NamdBinFile method) cos() (in module parmed.unit.unit_math) cosh() (in module parmed.unit.unit_math) count() (parmed.unit.quantity.Quantity method) cpin_pointers() (parmed.amber.titratable_residues.TitratableResidue method) CRDS_PER_LINE (parmed.amber.AmberAsciiRestart attribute) (parmed.amber.AmberMdcrd attribute) (parmed.amber.asciicrd.AmberAsciiRestart attribute) (parmed.amber.asciicrd.AmberMdcrd attribute) create_dataframe() (in module parmed.utils.pandautils) create_unit() (parmed.unit.unit.Unit method) createDimension() (parmed.utils.netcdf.netcdf_file method) createSystem() (parmed.charmm.CharmmPsfFile method) (parmed.charmm.psf.CharmmPsfFile method) (parmed.Structure method) (parmed.structure.Structure method) createVariable() (parmed.utils.netcdf.netcdf_file method)

D

DataCategory (class in parmed.formats.pdbx.PdbxContainers) DataCategoryBase (class in parmed.formats.pdbx.PdbxContainers) DataContainer (class in parmed.formats.pdbx.PdbxContainers) default() (parmed.tools.parmed_cmd.ParmedCmd method) (parmed.tools.parmed_cmd.PythonCmd method) DEFAULT_TITLE (parmed.amber.AmberAsciiRestart attribute) (parmed.amber.AmberMdcrd attribute) (parmed.amber.asciicrd.AmberAsciiRestart attribute) (parmed.amber.asciicrd.AmberMdcrd attribute) define_conversion_factor_to() (parmed.unit.baseunit.BaseUnit method) define_prefixed_units() (in module parmed.unit.prefix) defineSolvent (class in parmed.tools.actions) DefinitionContainer (class in parmed.formats.pdbx.PdbxContainers) delatoms() (parmed.namd.namdbinfiles.NamdBinFile method) delete() (parmed.Angle method) (parmed.Bond method) (parmed.Cmap method) (parmed.Dihedral method) (parmed.Improper method) (parmed.topologyobjects.Angle method) (parmed.topologyobjects.Bond method) (parmed.topologyobjects.Cmap method) (parmed.topologyobjects.Dihedral method) (parmed.topologyobjects.Improper method) (parmed.topologyobjects.TorsionTorsion method) (parmed.topologyobjects.UreyBradley method) (parmed.TorsionTorsion method) (parmed.UreyBradley method) delete_atom() (parmed.modeller.residue.ResidueTemplate method) (parmed.modeller.ResidueTemplate method) (parmed.Residue method) (parmed.topologyobjects.Residue method) delete_bond() (parmed.modeller.residue.ResidueTemplate method) (parmed.modeller.ResidueTemplate method) delete_flag() (parmed.amber.AmberFormat method) (parmed.amber.amberformat.AmberFormat method) (parmed.amber.readparm.AmberFormat method) deleteBond (class in parmed.tools.actions) deleteDihedral (class in parmed.tools.actions) DeleteDihedralError deletePDB (class in parmed.tools.actions) describeNextReport() (parmed.openmm.EnergyMinimizerReporter method) (parmed.openmm.MdcrdReporter method) (parmed.openmm.NetCDFReporter method) (parmed.openmm.ProgressReporter method) (parmed.openmm.reporters.EnergyMinimizerReporter method) (parmed.openmm.reporters.MdcrdReporter method) (parmed.openmm.reporters.NetCDFReporter method) (parmed.openmm.reporters.ProgressReporter method) (parmed.openmm.reporters.RestartReporter method) (parmed.openmm.reporters.StateDataReporter method) (parmed.openmm.RestartReporter method) (parmed.openmm.StateDataReporter method)

Dihedral (class in parmed) (class in parmed.tools.coarsegrain) (class in parmed.topologyobjects), [1] dihedral() (in module parmed.geometry) DIHEDRAL_FORCE_GROUP (parmed.Structure attribute) (parmed.structure.Structure attribute) dihedral_partners() (parmed.Atom property) (parmed.ExtraPoint property) (parmed.topologyobjects.Atom property) (parmed.topologyobjects.ExtraPoint property) dihedral_to() (parmed.Atom method) (parmed.topologyobjects.Atom method) dihedrals_inc_h() (parmed.amber.AmberParm property) (parmed.amber.readparm.AmberParm property) dihedrals_without_h() (parmed.amber.AmberParm property) (parmed.amber.readparm.AmberParm property) DihedralType (class in parmed) (class in parmed.topologyobjects), [1] DihedralTypeList (class in parmed) (class in parmed.topologyobjects), [1] DipolePolarizability (class in parmed.tinker.topologyobjects) DipolePolarizabilityList (class in parmed.tinker.topologyobjects) distance2() (in module parmed.geometry) DNAResidue (class in parmed.residue) do_EOF() (parmed.tools.parmed_cmd.ParmedCmd method) (parmed.tools.parmed_cmd.PythonCmd method) do_go() (parmed.tools.parmed_cmd.ParmedCmd method) do_help() (parmed.tools.parmed_cmd.ParmedCmd method) do_history() (parmed.tools.parmed_cmd.ParmedCmd method) do_parmout() (parmed.tools.parmed_cmd.ParmedCmd method) do_quit() (parmed.tools.parmed_cmd.ParmedCmd method) do_shell() (parmed.tools.parmed_cmd.ParmedCmd method) (parmed.tools.parmed_cmd.PythonCmd method) do_source() (parmed.tools.parmed_cmd.ParmedCmd method) done() (parmed.utils.timer.Timer method) dot() (in module parmed.unit.unit_math) download() (parmed.formats.CIFFile static method) (parmed.formats.pdb.CIFFile static method) (parmed.formats.pdb.PDBFile static method) (parmed.formats.PDBFile static method) download_CIF() (in module parmed) download_PDB() (in module parmed) drude_charge() (parmed.DrudeAtom property) (parmed.topologyobjects.DrudeAtom property) DrudeAnisotropy (class in parmed) (class in parmed.topologyobjects) DrudeAtom (class in parmed) (class in parmed.topologyobjects) dump() (parmed.tools.exceptions.WarningList method) dumpIt() (parmed.formats.pdbx.PdbxContainers.DataCategory method) DuplicateParamWarning DuplicateParm DynFile (class in parmed.tinker.tinkerfiles)

E

element() (parmed.Atom property) (parmed.topologyobjects.Atom property) element_by_mass() (in module parmed.periodic_table) element_by_name() (in module parmed.periodic_table) element_name() (parmed.Atom property) (parmed.topologyobjects.Atom property) empirical_chemical_formula() (parmed.modeller.residue.ResidueTemplate property) (parmed.modeller.ResidueTemplate property) empty() (parmed.tools.ParmList method) (parmed.tools.parmlist.ParmList method) emptyline() (parmed.tools.parmed_cmd.ParmedCmd method) (parmed.tools.parmed_cmd.PythonCmd method) end_all() (parmed.utils.timer.Timer method) energy (class in parmed.tools.actions) energy() (in module parmed.tools.simulations.openmm) (in module parmed.tools.simulations.sanderapi) (parmed.Angle method) (parmed.Bond method) (parmed.Dihedral method) (parmed.Improper method) (parmed.topologyobjects.Angle method) (parmed.topologyobjects.Bond method) (parmed.topologyobjects.Dihedral method) (parmed.topologyobjects.Improper method) energy_decomposition() (in module parmed.openmm), [1] (in module parmed.openmm.utils) energy_decomposition_system() (in module parmed.openmm) (in module parmed.openmm.utils) EnergyMinimizerReporter (class in parmed.openmm) (class in parmed.openmm.reporters) epsilon() (parmed.Atom property) (parmed.topologyobjects.Atom property) epsilon_14() (parmed.Atom property) (parmed.topologyobjects.Atom property) error (parmed.utils.six.Module_six_moves_urllib attribute) ewald (class in parmed.amber.mdin.ewald) exclude() (parmed.Atom method) (parmed.topologyobjects.Atom method) exclusion_partners() (parmed.Atom property) (parmed.ExtraPoint property) (parmed.topologyobjects.Atom property) (parmed.topologyobjects.ExtraPoint property) execute() (parmed.tools.actions.Action method) (parmed.tools.actions.add12_6_4 method) (parmed.tools.actions.addAtomicNumber method) (parmed.tools.actions.addDihedral method) (parmed.tools.actions.addExclusions method) (parmed.tools.actions.addLJType method) (parmed.tools.actions.addPDB method) (parmed.tools.actions.cd method) (parmed.tools.actions.chamber method) (parmed.tools.actions.change method) (parmed.tools.actions.changeLJ14Pair method) (parmed.tools.actions.changeLJPair method) (parmed.tools.actions.changeLJSingleType method) (parmed.tools.actions.changeProtState method) (parmed.tools.actions.changeRadii method) (parmed.tools.actions.changeRedoxState method) (parmed.tools.actions.checkValidity method) (parmed.tools.actions.deleteBond method) (parmed.tools.actions.deleteDihedral method) (parmed.tools.actions.deletePDB method) (parmed.tools.actions.energy method) (parmed.tools.actions.gromber method) (parmed.tools.actions.HMassRepartition method) (parmed.tools.actions.interpolate method) (parmed.tools.actions.lmod method) (parmed.tools.actions.loadCoordinates method) (parmed.tools.actions.loadRestrt method) (parmed.tools.actions.minimize method) (parmed.tools.actions.netCharge method) (parmed.tools.actions.OpenMM method) (parmed.tools.actions.outCIF method) (parmed.tools.actions.outPDB method) (parmed.tools.actions.parm method) (parmed.tools.actions.parmout method) (parmed.tools.actions.scale method) (parmed.tools.actions.scee method) (parmed.tools.actions.scnb method) (parmed.tools.actions.setAngle method) (parmed.tools.actions.setBond method) (parmed.tools.actions.setMolecules method) (parmed.tools.actions.setOverwrite method) (parmed.tools.actions.source method) (parmed.tools.actions.strip method) (parmed.tools.actions.tiMerge method) (parmed.tools.actions.writeCoordinates method) (parmed.tools.actions.writeFrcmod method) (parmed.tools.actions.writeOFF method) (parmed.tools.gui.guitools.ActionButton method)

exists() (parmed.formats.pdbx.PdbxContainers.ContainerBase method) express_unit() (parmed.unit.unit.UnitSystem method) extend() (parmed.AtomList method) (parmed.tools.exceptions.WarningList method) (parmed.topologyobjects.AtomList method) (parmed.topologyobjects.TrackedList method) (parmed.TrackedList method) (parmed.unit.quantity.Quantity method) extended() (parmed.Cmap class method) (parmed.topologyobjects.Cmap class method) extra_args (parmed.amber.AmberMdcrd attribute) (parmed.amber.asciicrd.AmberMdcrd attribute) ExtraPoint (class in parmed) (class in parmed.topologyobjects) eye() (in module parmed.unit.mymatrix)

F

FancyURLopener (parmed.utils.six.Module_six_moves_urllib_request attribute) file_chooser() (in module parmed.tools.gui.guifiletools) FileDoesNotExist FileExists FileFormatType (class in parmed.formats.registry) FileHandler (parmed.utils.six.Module_six_moves_urllib_request attribute) fill_LJ() (parmed.amber.AmberParm method) (parmed.amber.ChamberParm method) (parmed.amber.readparm.AmberParm method) (parmed.amber.readparm.ChamberParm method) finalize() (parmed.openmm.EnergyMinimizerReporter method) (parmed.openmm.MdcrdReporter method) (parmed.openmm.NetCDFReporter method) (parmed.openmm.reporters.EnergyMinimizerReporter method) (parmed.openmm.reporters.MdcrdReporter method) (parmed.openmm.reporters.NetCDFReporter method) (parmed.openmm.reporters.RestartReporter method) (parmed.openmm.reporters.StateDataReporter method) (parmed.openmm.RestartReporter method) (parmed.openmm.StateDataReporter method) find_atom_pairs() (in module parmed.utils) (in module parmed.utils.pairlist) find_original_index() (parmed.AtomList method) (parmed.topologyobjects.AtomList method) fix_charges() (parmed.modeller.residue.ResidueTemplate method) (parmed.modeller.residue.ResidueTemplateContainer method) (parmed.modeller.ResidueTemplate method) (parmed.modeller.ResidueTemplateContainer method) FixableParmWarning floatre (parmed.amber.amberformat.FortranFormat attribute) (parmed.amber.FortranFormat attribute) floatre2 (parmed.amber.amberformat.FortranFormat attribute) (parmed.amber.FortranFormat attribute) flush() (parmed.amber.netcdffiles.NetCDFRestart method) (parmed.amber.netcdffiles.NetCDFTraj method) (parmed.amber.NetCDFRestart method) (parmed.amber.NetCDFTraj method) (parmed.utils.netcdf.netcdf_file method) forces() (parmed.amber.netcdffiles.NetCDFTraj property) (parmed.amber.NetCDFTraj property) format() (parmed.unit.quantity.Quantity method) (parmed.utils.fortranformat.FortranRecordReader.FortranRecordReader property) (parmed.utils.fortranformat.FortranRecordWriter.FortranRecordWriter property) FormatNotFound FortranFormat (class in parmed.amber) (class in parmed.amber.amberformat)

FortranRecordReader (class in parmed.utils.fortranformat.FortranRecordReader) FortranRecordWriter (class in parmed.utils.fortranformat.FortranRecordWriter) frame() (parmed.amber.AmberMdcrd property) (parmed.amber.asciicrd.AmberMdcrd property) frame_type() (parmed.ExtraPoint property) (parmed.topologyobjects.ExtraPoint property) from_leaprc() (parmed.amber.AmberParameterSet class method) (parmed.amber.parameters.AmberParameterSet class method) from_library() (parmed.modeller.residue.ResidueTemplateContainer class method) (parmed.modeller.ResidueTemplateContainer class method) from_parameterset() (parmed.charmm.CharmmParameterSet class method) (parmed.charmm.parameters.CharmmParameterSet class method) (parmed.openmm.OpenMMParameterSet class method) (parmed.openmm.parameters.OpenMMParameterSet class method) from_rawdata() (parmed.amber.AmberParm class method) (parmed.amber.BeemanRestart class method) (parmed.amber.readparm.AmberParm class method) from_rbtorsion() (parmed.DihedralTypeList class method) (parmed.topologyobjects.DihedralTypeList class method) from_residue() (parmed.modeller.residue.ResidueTemplate class method) (parmed.modeller.ResidueTemplate class method) from_sdf() (in module parmed.rdkit) (parmed.rdkit.rdkit.RDKit static method) from_smiles() (in module parmed.rdkit) (parmed.rdkit.rdkit.RDKit static method) from_structure() (parmed.amber.AmberParameterSet class method) (parmed.amber.AmberParm class method) (parmed.amber.ChamberParm class method) (parmed.amber.parameters.AmberParameterSet class method) (parmed.amber.readparm.AmberParm class method) (parmed.amber.readparm.ChamberParm class method) (parmed.charmm.CharmmParameterSet class method) (parmed.charmm.CharmmPsfFile class method) (parmed.charmm.parameters.CharmmParameterSet class method) (parmed.charmm.psf.CharmmPsfFile class method) (parmed.gromacs.gromacstop.GromacsTopologyFile class method) (parmed.gromacs.GromacsTopologyFile class method) (parmed.modeller.residue.ResidueTemplateContainer class method) (parmed.modeller.ResidueTemplateContainer class method) (parmed.parameters.ParameterSet class method) (parmed.ParameterSet class method) from_weights() (parmed.ThreeParticleExtraPointFrame static method) (parmed.topologyobjects.ThreeParticleExtraPointFrame static method) FTPHandler (parmed.utils.six.Module_six_moves_urllib_request attribute) funct() (parmed.Dihedral property) (parmed.topologyobjects.Dihedral property)

G

genBorn() (parmed.amber.mdin.Mdin method) (parmed.amber.mdin.mdin.Mdin method) genopen() (in module parmed.utils.io) get() (parmed.formats.pdbx.PdbxContainers.DataCategoryBase method) (parmed.residue.AminoAcidResidue class method) (parmed.residue.DNAResidue class method) (parmed.residue.RNAResidue class method) get_angle_type() (in module parmed.tinker.parameterfile) get_atom_type() (in module parmed.tinker.parameterfile) get_atoms() (parmed.OutOfPlaneExtraPointFrame method) (parmed.ThreeParticleExtraPointFrame method) (parmed.topologyobjects.OutOfPlaneExtraPointFrame method) (parmed.topologyobjects.ThreeParticleExtraPointFrame method) (parmed.topologyobjects.TwoParticleExtraPointFrame method) (parmed.TwoParticleExtraPointFrame method) get_box() (parmed.Structure method) (parmed.structure.Structure method) get_conversion_factor_to_base_units() (parmed.unit.unit.ScaledUnit method) (parmed.unit.unit.Unit method) get_coordinates() (parmed.Structure method) (parmed.structure.Structure method) get_dimension_tuple() (parmed.unit.baseunit.BaseUnit method) (parmed.unit.unit.ScaledUnit method) get_format() (parmed.utils.fortranformat.FortranRecordReader.FortranRecordReader method) (parmed.utils.fortranformat.FortranRecordWriter.FortranRecordWriter method) get_key_float() (parmed.tools.argumentlist.ArgumentList method) get_key_int() (parmed.tools.argumentlist.ArgumentList method) get_key_mask() (parmed.tools.argumentlist.ArgumentList method) get_key_string() (parmed.tools.argumentlist.ArgumentList method) get_name() (parmed.unit.unit.Unit method) get_next_float() (parmed.tools.argumentlist.ArgumentList method) get_next_int() (parmed.tools.argumentlist.ArgumentList method) get_next_mask() (parmed.tools.argumentlist.ArgumentList method) get_next_string() (parmed.tools.argumentlist.ArgumentList method) get_symbol() (parmed.unit.unit.Unit method) get_unbound_function() (in module parmed.utils.six) get_weights() (parmed.OutOfPlaneExtraPointFrame method) (parmed.ThreeParticleExtraPointFrame method) (parmed.topologyobjects.OutOfPlaneExtraPointFrame method) (parmed.topologyobjects.ThreeParticleExtraPointFrame method) (parmed.topologyobjects.TwoParticleExtraPointFrame method) (parmed.TwoParticleExtraPointFrame method)

getAttributeCount() (parmed.formats.pdbx.PdbxContainers.DataCategory method) getAttributeIndex() (parmed.formats.pdbx.PdbxContainers.DataCategory method) getAttributeLengthMaximumList() (parmed.formats.pdbx.PdbxContainers.DataCategory method) getAttributeList() (parmed.formats.pdbx.PdbxContainers.DataCategory method) getAttributeListWithOrder() (parmed.formats.pdbx.PdbxContainers.DataCategory method) getAttributeValueMaxLengthList() (parmed.formats.pdbx.PdbxContainers.DataCategory method) getCurrentAttribute() (parmed.formats.pdbx.PdbxContainers.DataCategory method) getFormatTypeList() (parmed.formats.pdbx.PdbxContainers.DataCategory method) getFormatTypeListX() (parmed.formats.pdbx.PdbxContainers.DataCategory method) getFullRow() (parmed.formats.pdbx.PdbxContainers.DataCategory method) getGlobal() (parmed.formats.pdbx.PdbxContainers.DataContainer method) getIndex() (parmed.formats.pdbx.PdbxContainers.DataCategory method) getItemNameList() (parmed.formats.pdbx.PdbxContainers.DataCategory method) getName() (parmed.formats.pdbx.PdbxContainers.ContainerBase method) (parmed.formats.pdbx.PdbxContainers.DataCategory method) getObj() (parmed.formats.pdbx.PdbxContainers.ContainerBase method) getObjNameList() (parmed.formats.pdbx.PdbxContainers.ContainerBase method) getproxies (parmed.utils.six.Module_six_moves_urllib_request attribute) getRow() (parmed.formats.pdbx.PdbxContainers.DataCategory method) getRowCount() (parmed.formats.pdbx.PdbxContainers.DataCategory method) getRowIndex() (parmed.formats.pdbx.PdbxContainers.DataCategory method) getRowList() (parmed.formats.pdbx.PdbxContainers.DataCategory method) getType() (parmed.formats.pdbx.PdbxContainers.ContainerBase method) getValue() (parmed.formats.pdbx.PdbxContainers.DataCategory method) (parmed.utils.netcdf.netcdf_variable method) getValueFormatted() (parmed.formats.pdbx.PdbxContainers.DataCategory method) getValueFormattedByIndex() (parmed.formats.pdbx.PdbxContainers.DataCategory method) GromacsError GromacsGroFile (class in parmed.gromacs), [1], [2] (class in parmed.gromacs.gromacsgro) GromacsTopologyFile (class in parmed.gromacs), [1], [2] (class in parmed.gromacs.gromacstop) GromacsWarning gromber (class in parmed.tools.actions) Group (class in parmed) (class in parmed.topologyobjects) gui_action_dispatcher() (in module parmed.tools.gui.guiactions) guiapp() (in module parmed.scripts)

H

has_1012() (parmed.amber.AmberParm method) (parmed.amber.readparm.AmberParm method) has_cmap() (parmed.amber.AmberParm property) (parmed.amber.readparm.AmberParm property) has_key() (parmed.tools.argumentlist.ArgumentList method) has_NBFIX() (parmed.amber.AmberParm method) (parmed.amber.readparm.AmberParm method) (parmed.Structure method) (parmed.structure.Structure method) hasAttribute() (parmed.formats.pdbx.PdbxContainers.DataCategory method) hasbox() (parmed.amber.readparm.Rst7 property) (parmed.amber.Rst7 property) hasvels() (parmed.amber.readparm.Rst7 property) (parmed.amber.Rst7 property)

heat() (parmed.amber.mdin.Mdin method) (parmed.amber.mdin.mdin.Mdin method) HMassRepartition (class in parmed.tools.actions) HMassRepartitionError HTTPBasicAuthHandler (parmed.utils.six.Module_six_moves_urllib_request attribute) HTTPCookieProcessor (parmed.utils.six.Module_six_moves_urllib_request attribute) HTTPDefaultErrorHandler (parmed.utils.six.Module_six_moves_urllib_request attribute) HTTPDigestAuthHandler (parmed.utils.six.Module_six_moves_urllib_request attribute) HTTPErrorProcessor (parmed.utils.six.Module_six_moves_urllib_request attribute) HTTPHandler (parmed.utils.six.Module_six_moves_urllib_request attribute) HTTPPasswordMgr (parmed.utils.six.Module_six_moves_urllib_request attribute) HTTPPasswordMgrWithDefaultRealm (parmed.utils.six.Module_six_moves_urllib_request attribute) HTTPRedirectHandler (parmed.utils.six.Module_six_moves_urllib_request attribute) HTTPSHandler (parmed.utils.six.Module_six_moves_urllib_request attribute)

I

id_format() (parmed.amber.AmberAsciiRestart static method) (parmed.amber.AmberFormat static method) (parmed.amber.amberformat.AmberFormat static method) (parmed.amber.AmberMdcrd static method) (parmed.amber.AmberOFFLibrary static method) (parmed.amber.AmberParameterSet static method) (parmed.amber.asciicrd.AmberAsciiRestart static method) (parmed.amber.asciicrd.AmberMdcrd static method) (parmed.amber.netcdffiles.NetCDFRestart static method) (parmed.amber.netcdffiles.NetCDFTraj static method) (parmed.amber.NetCDFRestart static method) (parmed.amber.NetCDFTraj static method) (parmed.amber.offlib.AmberOFFLibrary static method) (parmed.amber.parameters.AmberParameterSet static method) (parmed.amber.readparm.AmberFormat static method) (parmed.charmm.CharmmCrdFile static method) (parmed.charmm.charmmcrds.CharmmCrdFile static method) (parmed.charmm.charmmcrds.CharmmRstFile static method) (parmed.charmm.CharmmRstFile static method) (parmed.formats.CIFFile static method) (parmed.formats.mol2.Mol2File static method) (parmed.formats.Mol2File static method) (parmed.formats.pdb.CIFFile static method) (parmed.formats.pdb.PDBFile static method) (parmed.formats.PDBFile static method) (parmed.formats.pqr.PQRFile static method) (parmed.formats.PQRFile static method) (parmed.formats.psf.PSFFile static method) (parmed.formats.PSFFile static method) (parmed.formats.sdf.SDFFile static method) (parmed.formats.SDFFile static method) (parmed.gromacs.gromacsgro.GromacsGroFile static method) (parmed.gromacs.GromacsGroFile static method) (parmed.gromacs.gromacstop.GromacsTopologyFile static method) (parmed.gromacs.GromacsTopologyFile static method) (parmed.modeller.AmberOFFLibrary static method) (parmed.openmm.OpenMMParameterSet static method) (parmed.openmm.parameters.OpenMMParameterSet static method) (parmed.openmm.XmlFile static method) (parmed.openmm.xmlfile.XmlFile static method) (parmed.tinker.tinkerfiles.XyzFile static method) (parmed.tinker.XyzFile static method) Improper (class in parmed) (class in parmed.topologyobjects), [1] IMPROPER_FORCE_GROUP (parmed.Structure attribute) (parmed.structure.Structure attribute) ImproperType (class in parmed) (class in parmed.topologyobjects), [1] in_unit_system() (parmed.unit.quantity.Quantity method) (parmed.unit.unit.Unit method) in_units_of() (parmed.unit.quantity.Quantity method) IncompatibleParmsError IncompatiblePatchError index() (parmed.tools.ParmList method) (parmed.tools.parmlist.ParmList method) (parmed.unit.quantity.Quantity method) index_members() (parmed.topologyobjects.TrackedList method) (parmed.TrackedList method) init() (parmed.tools.actions.Action method) (parmed.tools.actions.add12_6_4 method) (parmed.tools.actions.addAtomicNumber method) (parmed.tools.actions.addDihedral method) (parmed.tools.actions.addExclusions method) (parmed.tools.actions.addLJType method) (parmed.tools.actions.addPDB method) (parmed.tools.actions.cd method) (parmed.tools.actions.chamber method) (parmed.tools.actions.change method) (parmed.tools.actions.changeLJ14Pair method) (parmed.tools.actions.changeLJPair method) (parmed.tools.actions.changeLJSingleType method) (parmed.tools.actions.changeProtState method) (parmed.tools.actions.changeRadii method) (parmed.tools.actions.changeRedoxState method) (parmed.tools.actions.checkValidity method) (parmed.tools.actions.defineSolvent method) (parmed.tools.actions.deleteBond method) (parmed.tools.actions.deleteDihedral method) (parmed.tools.actions.deletePDB method) (parmed.tools.actions.energy method) (parmed.tools.actions.gromber method) (parmed.tools.actions.HMassRepartition method) (parmed.tools.actions.interpolate method) (parmed.tools.actions.listParms method) (parmed.tools.actions.lmod method) (parmed.tools.actions.loadCoordinates method) (parmed.tools.actions.loadRestrt method) (parmed.tools.actions.ls method) (parmed.tools.actions.minimize method) (parmed.tools.actions.netCharge method) (parmed.tools.actions.OpenMM method) (parmed.tools.actions.outCIF method) (parmed.tools.actions.outPDB method) (parmed.tools.actions.parm method) (parmed.tools.actions.parmout method) (parmed.tools.actions.printAngles method) (parmed.tools.actions.printBonds method) (parmed.tools.actions.printDetails method) (parmed.tools.actions.printDihedrals method) (parmed.tools.actions.printFlags method) (parmed.tools.actions.printInfo method) (parmed.tools.actions.printLJMatrix method) (parmed.tools.actions.printLJTypes method) (parmed.tools.actions.printPointers method) (parmed.tools.actions.scale method) (parmed.tools.actions.scee method) (parmed.tools.actions.scnb method) (parmed.tools.actions.setAngle method) (parmed.tools.actions.setBond method) (parmed.tools.actions.setMolecules method) (parmed.tools.actions.setOverwrite method) (parmed.tools.actions.source method) (parmed.tools.actions.strip method) (parmed.tools.actions.summary method) (parmed.tools.actions.tiMerge method) (parmed.tools.actions.writeCoordinates method) (parmed.tools.actions.writeFrcmod method) (parmed.tools.actions.writeOFF method)

initialize_topology() (parmed.amber.AmberParm method) (parmed.amber.AmoebaParm method) (parmed.amber.ChamberParm method) (parmed.amber.readparm.AmberParm method) (parmed.amber.readparm.ChamberParm method) InputError, [1] insert() (parmed.AtomList method) (parmed.topologyobjects.AtomList method) (parmed.topologyobjects.TrackedList method) (parmed.TrackedList method) (parmed.unit.quantity.Quantity method) insertatoms() (parmed.namd.namdbinfiles.NamdBinFile method) insertion_code() (parmed.formats.pdb.PDBFile.AtomLookupKey property) (parmed.formats.PDBFile.AtomLookupKey property) install_opener (parmed.utils.six.Module_six_moves_urllib_request attribute) interpolate (class in parmed.tools.actions) InterpreterError intre (parmed.amber.amberformat.FortranFormat attribute) (parmed.amber.FortranFormat attribute) invokeAttributeMethod() (parmed.formats.pdbx.PdbxContainers.DataCategory method) invokeCategoryMethod() (parmed.formats.pdbx.PdbxContainers.DataCategory method) invokeDataBlockMethod() (parmed.formats.pdbx.PdbxContainers.DataContainer method) is_changed() (parmed.amber.AmberParm method) (parmed.amber.readparm.AmberParm method) (parmed.Structure method) (parmed.structure.Structure method) is_compatible() (parmed.unit.unit.Unit method) is_dimensionless() (in module parmed.unit.quantity) (parmed.unit.unit.Unit method) is_empty() (parmed.Residue method) (parmed.topologyobjects.Residue method) is_float() (in module parmed.tinker.tinkerfiles) is_quantity() (in module parmed.unit) (in module parmed.unit.quantity) is_square() (parmed.unit.mymatrix.MyMatrix method) is_unit() (in module parmed.unit.unit) isAttribute() (parmed.formats.pdbx.PdbxContainers.DefinitionContainer method) isCategory() (parmed.formats.pdbx.PdbxContainers.DefinitionContainer method) isfloat() (parmed.tools.argumentlist.Argument method) isint() (parmed.tools.argumentlist.Argument method) ismask() (parmed.tools.argumentlist.Argument method) isrec() (parmed.utils.netcdf.netcdf_variable property) itemsize() (parmed.utils.netcdf.netcdf_variable method) iter_all_base_units() (parmed.unit.unit.Unit method) iter_base_dimensions() (parmed.unit.baseunit.BaseUnit method) (parmed.unit.unit.ScaledUnit method) (parmed.unit.unit.Unit method) iter_base_or_scaled_units() (parmed.unit.unit.Unit method) iter_base_units() (parmed.unit.baseunit.BaseUnit method) (parmed.unit.unit.ScaledUnit method) iter_scaled_units() (parmed.unit.unit.Unit method) iter_top_base_units() (parmed.unit.unit.Unit method) iteritems() (in module parmed.utils.six) iterkeys() (in module parmed.utils.six) iterlists() (in module parmed.utils.six) itervalues() (in module parmed.utils.six)

J

join_dihedrals() (parmed.Structure method) (parmed.structure.Structure method)

K

KeywordControlFile (class in parmed.tinker.tinkerfiles)

L

Link (class in parmed) (class in parmed.topologyobjects) listParms (class in parmed.tools.actions) LJ12_6_4Error LJ_TypeError lmod (class in parmed.tools.actions) load() (parmed.rdkit.rdkit.RDKit static method) (parmed.rosetta.pose.RosettaPose static method) (parmed.rosetta.RosettaPose static method) load_atom_info() (parmed.amber.AmberParm method) (parmed.amber.AmoebaParm method) (parmed.amber.readparm.AmberParm method) load_dataframe() (in module parmed.utils.pandautils) (parmed.Structure method) (parmed.structure.Structure method) (parmed.structure.StructureView method) (parmed.StructureView method) load_file() (in module parmed) (in module parmed.formats) (in module parmed.formats.registry), [1], [2] load_parameter_file() (parmed.tinker.parameterfile.AmoebaParameterSet method) load_parameters() (parmed.amber.AmberParameterSet method) (parmed.amber.parameters.AmberParameterSet method) (parmed.charmm.CharmmPsfFile method) (parmed.charmm.psf.CharmmPsfFile method) load_pointers() (parmed.amber.AmberParm method) (parmed.amber.ChamberParm method) (parmed.amber.readparm.AmberParm method) (parmed.amber.readparm.ChamberParm method)

load_rdkit() (in module parmed) (in module parmed.rdkit) load_rosetta() (in module parmed), [1] load_rst7() (parmed.amber.AmberParm method) (parmed.amber.readparm.AmberParm method) load_set() (parmed.charmm.CharmmParameterSet class method) (parmed.charmm.parameters.CharmmParameterSet class method) load_structure() (parmed.amber.AmberParm method) (parmed.amber.AmoebaParm method) (parmed.amber.ChamberParm method) (parmed.amber.readparm.AmberParm method) (parmed.amber.readparm.ChamberParm method) load_topology() (in module parmed.openmm), [1] (in module parmed.openmm.topsystem) loadCoordinates (class in parmed.tools.actions) LoadParm() (in module parmed.amber), [1] (in module parmed.amber.readparm) loadRestrt (class in parmed.tools.actions) log_commands() (in module parmed.tools.parmed_cmd) Logo (class in parmed.tools.logos) LongBondWarning lower() (parmed.tools.argumentlist.Argument method) ls (class in parmed.tools.actions)

M

map() (parmed.modeller.residue.ResidueTemplate property) (parmed.modeller.ResidueTemplate property) mark() (parmed.tinker.parameterfile.BookmarkedFile method) (parmed.tools.argumentlist.Argument method) MaskError match() (parmed.utils.fortranformat.FortranRecordReader.FortranRecordReader method) match_improper_type() (parmed.charmm.parameters.CharmmImproperMatchingMixin method) max() (parmed.unit.quantity.Quantity method) mbondi() (in module parmed.tools.changeradii) mbondi2() (in module parmed.tools.changeradii) mbondi3() (in module parmed.tools.changeradii) MdcrdReporter (class in parmed.openmm), [1] (class in parmed.openmm.reporters) Mdin (class in parmed.amber.mdin) (class in parmed.amber.mdin.mdin) mdin_skeleton() (parmed.amber.AmoebaParm method) mean() (parmed.unit.quantity.Quantity method) measure() (parmed.Angle method) (parmed.Bond method) (parmed.Dihedral method) (parmed.Improper method) (parmed.topologyobjects.Angle method) (parmed.topologyobjects.Bond method) (parmed.topologyobjects.Dihedral method) (parmed.topologyobjects.Improper method) min() (parmed.unit.quantity.Quantity method) minimization() (parmed.amber.mdin.Mdin method) (parmed.amber.mdin.mdin.Mdin method) minimize (class in parmed.tools.actions) minimize() (in module parmed.tools.simulations.openmm) (in module parmed.tools.simulations.sanderapi) MissingDisulfide module parmed parmed.amber parmed.amber.amberformat parmed.amber.asciicrd parmed.amber.mask parmed.amber.mdin parmed.amber.mdin.cntrl parmed.amber.mdin.ewald parmed.amber.mdin.mdin parmed.amber.mdin.pb parmed.amber.mdin.qmmm parmed.amber.netcdffiles parmed.amber.offlib parmed.amber.parameters parmed.amber.readparm parmed.amber.titratable_residues parmed.charmm parmed.charmm.charmmcrds parmed.charmm.parameters parmed.charmm.psf parmed.constants parmed.exceptions parmed.formats parmed.formats.mol2 parmed.formats.pdb parmed.formats.pdbx parmed.formats.pdbx.PdbxContainers parmed.formats.pdbx.PdbxReader parmed.formats.pdbx.PdbxWriter parmed.formats.pqr parmed.formats.psf parmed.formats.registry parmed.formats.sdf parmed.geometry parmed.gromacs parmed.gromacs.gromacsgro parmed.gromacs.gromacstop parmed.modeller parmed.modeller.residue parmed.modeller.standardtemplates parmed.namd parmed.namd.namdbinfiles parmed.openmm parmed.openmm.parameters parmed.openmm.reporters parmed.openmm.topsystem parmed.openmm.utils parmed.openmm.xmlfile parmed.parameters parmed.periodic_table parmed.rdkit parmed.rdkit.rdkit parmed.residue parmed.rosetta parmed.rosetta.pose parmed.scripts parmed.structure parmed.symmetry parmed.tinker parmed.tinker.parameterfile parmed.tinker.system parmed.tinker.tinkerfiles parmed.tinker.topologyobjects parmed.tools parmed.tools.actions parmed.tools.add1264 parmed.tools.addljtype parmed.tools.argumentlist parmed.tools.changeradii parmed.tools.checkvalidity parmed.tools.coarsegrain parmed.tools.exceptions parmed.tools.gui parmed.tools.gui.guiactions parmed.tools.gui.guifiletools parmed.tools.gui.guitools parmed.tools.logos parmed.tools.parmed_cmd parmed.tools.parmlist parmed.tools.simulations parmed.tools.simulations.openmm parmed.tools.simulations.sanderapi parmed.topologyobjects parmed.unit parmed.unit.basedimension parmed.unit.baseunit parmed.unit.constants parmed.unit.mymatrix parmed.unit.prefix parmed.unit.quantity parmed.unit.standard_dimensions parmed.unit.unit parmed.unit.unit_definitions parmed.unit.unit_math parmed.unit.unit_operators parmed.utils parmed.utils.decorators parmed.utils.fortranformat parmed.utils.fortranformat.config parmed.utils.fortranformat.FortranRecordReader parmed.utils.fortranformat.FortranRecordWriter parmed.utils.io parmed.utils.netcdf parmed.utils.pairlist parmed.utils.pandautils parmed.utils.six parmed.utils.timer parmed.vec3

Module_six_moves_urllib (class in parmed.utils.six) Module_six_moves_urllib_error (class in parmed.utils.six) Module_six_moves_urllib_parse (class in parmed.utils.six) Module_six_moves_urllib_request (class in parmed.utils.six) Module_six_moves_urllib_response (class in parmed.utils.six) Module_six_moves_urllib_robotparser (class in parmed.utils.six) Mol2Error Mol2File (class in parmed.formats) (class in parmed.formats.mol2) MoleculeError MovedAttribute (class in parmed.utils.six) MovedModule (class in parmed.utils.six) MultipoleFrame (class in parmed) (class in parmed.topologyobjects), [1] MyMatrix (class in parmed.unit.mymatrix) MyMatrixTranspose (class in parmed.unit.mymatrix) MyVector (class in parmed.unit.mymatrix)

N

NamdBinCoor (class in parmed.namd) (class in parmed.namd.namdbinfiles) NamdBinFile (class in parmed.namd.namdbinfiles) NamdBinVel (class in parmed.namd) (class in parmed.namd.namdbinfiles) name() (parmed.formats.pdb.PDBFile.AtomLookupKey property) (parmed.formats.PDBFile.AtomLookupKey property) natom() (parmed.amber.BeemanRestart property) (parmed.namd.namdbinfiles.NamdBinFile property) needs_lxml() (in module parmed.openmm.parameters) needs_openmm() (in module parmed.utils.decorators) needs_parm (parmed.tools.actions.Action attribute) (parmed.tools.actions.cd attribute) (parmed.tools.actions.chamber attribute) (parmed.tools.actions.gromber attribute) (parmed.tools.actions.listParms attribute) (parmed.tools.actions.ls attribute) (parmed.tools.actions.parm attribute) (parmed.tools.actions.setOverwrite attribute) (parmed.tools.actions.source attribute) net_charge() (parmed.modeller.residue.ResidueTemplate property) (parmed.modeller.ResidueTemplate property) netcdf_file (class in parmed.utils.netcdf) netcdf_variable (class in parmed.utils.netcdf) NetCDFReporter (class in parmed.openmm), [1] (class in parmed.openmm.reporters) NetCDFRestart (class in parmed.amber), [1] (class in parmed.amber.netcdffiles) NetCDFTraj (class in parmed.amber), [1] (class in parmed.amber.netcdffiles) netCharge (class in parmed.tools.actions)

new() (parmed.tinker.topologyobjects.TorsionTorsionGrid class method) NoArgument nonbonded_exclusions() (parmed.Atom method) (parmed.topologyobjects.Atom method) NONBONDED_FORCE_GROUP (parmed.Structure attribute) (parmed.structure.Structure attribute) NonbondedException (class in parmed) (class in parmed.topologyobjects), [1] NonbondedExceptionType (class in parmed) (class in parmed.topologyobjects), [1] NonexistentParm NonfatalWarning NonUniversalWarning norm() (in module parmed.unit.unit_math) not_supported (parmed.tools.actions.Action attribute) (parmed.tools.actions.addDihedral attribute) (parmed.tools.actions.addExclusions attribute) (parmed.tools.actions.changeRadii attribute) (parmed.tools.actions.deleteDihedral attribute) (parmed.tools.actions.minimize attribute) (parmed.tools.actions.OpenMM attribute) (parmed.tools.actions.scee attribute) (parmed.tools.actions.scnb attribute) (parmed.tools.actions.setAngle attribute) (parmed.tools.actions.setBond attribute) number() (parmed.formats.pdb.PDBFile.AtomLookupKey property) (parmed.formats.PDBFile.AtomLookupKey property) numCols() (parmed.unit.mymatrix.MyMatrix method) (parmed.unit.mymatrix.MyMatrixTranspose method) numRows() (parmed.unit.mymatrix.MyMatrix method) (parmed.unit.mymatrix.MyMatrixTranspose method)

O

old_accelerations() (parmed.amber.BeemanRestart property) omm_add_constraints() (parmed.Structure method) (parmed.structure.Structure method) omm_angle_force() (parmed.Structure method) (parmed.structure.Structure method) omm_bond_force() (parmed.Structure method) (parmed.structure.Structure method) omm_cmap_force() (parmed.Structure method) (parmed.structure.Structure method) omm_dihedral_force() (parmed.Structure method) (parmed.structure.Structure method) omm_gbsa_force() (parmed.Structure method) (parmed.structure.Structure method) omm_improper_force() (parmed.Structure method) (parmed.structure.Structure method) omm_nonbonded_force() (parmed.amber.AmberParm method) (parmed.amber.readparm.AmberParm method) (parmed.Structure method) (parmed.structure.Structure method) omm_out_of_plane_bend_force() (parmed.Structure method) (parmed.structure.Structure method) omm_pi_torsion_force() (parmed.Structure method) (parmed.structure.Structure method) omm_rb_torsion_force() (parmed.Structure method) (parmed.structure.Structure method) omm_set_virtual_sites() (parmed.Structure method) (parmed.structure.Structure method) omm_stretch_bend_force() (parmed.Structure method) (parmed.structure.Structure method) omm_torsion_torsion_force() (parmed.Structure method) (parmed.structure.Structure method) omm_trigonal_angle_force() (parmed.Structure method) (parmed.structure.Structure method) omm_urey_bradley_force() (parmed.Structure method) (parmed.structure.Structure method) open() (parmed.amber.readparm.Rst7 class method) (parmed.amber.Rst7 class method)

open_new() (parmed.amber.netcdffiles.NetCDFRestart class method) (parmed.amber.netcdffiles.NetCDFTraj class method) (parmed.amber.NetCDFRestart class method) (parmed.amber.NetCDFTraj class method) open_old() (parmed.amber.netcdffiles.NetCDFRestart class method) (parmed.amber.netcdffiles.NetCDFTraj class method) (parmed.amber.NetCDFRestart class method) (parmed.amber.NetCDFTraj class method) OpenerDirector (parmed.utils.six.Module_six_moves_urllib_request attribute) OpenMM (class in parmed.tools.actions) OpenMMError OpenMMParameterSet (class in parmed.openmm) (class in parmed.openmm.parameters) OpenMMWarning order() (parmed.Bond property) (parmed.topologyobjects.Bond property) OUT_OF_PLANE_BEND_FORCE_GROUP (parmed.Structure attribute) (parmed.structure.Structure attribute) outCIF (class in parmed.tools.actions) outfile (parmed.tools.actions.netCharge attribute) (parmed.tools.actions.printInfo attribute) OutOfPlaneBend (class in parmed) (class in parmed.tinker.topologyobjects) (class in parmed.topologyobjects), [1] OutOfPlaneBendList (class in parmed.tinker.topologyobjects) OutOfPlaneBendType (class in parmed) (class in parmed.topologyobjects), [1] OutOfPlaneDist (class in parmed.tinker.topologyobjects) OutOfPlaneDistList (class in parmed.tinker.topologyobjects) OutOfPlaneExtraPointFrame (class in parmed) (class in parmed.topologyobjects) outparm (class in parmed.tools.actions) OutparmButton (class in parmed.tools.gui.guitools) outPDB (class in parmed.tools.actions) output (parmed.tools.actions.checkValidity attribute) (parmed.tools.actions.energy attribute) (parmed.tools.actions.tiMerge attribute) overwrite (parmed.tools.actions.Action attribute)

P

ParameterError ParameterSet (class in parmed) (class in parmed.parameters) ParameterWarning parametrize() (parmed.gromacs.gromacstop.GromacsTopologyFile method) (parmed.gromacs.GromacsTopologyFile method) params1264() (in module parmed.tools.add1264) parent() (parmed.ExtraPoint property) (parmed.topologyobjects.ExtraPoint property) parm (class in parmed.tools.actions) parmed module parmed.amber module parmed.amber.amberformat module parmed.amber.asciicrd module parmed.amber.mask module parmed.amber.mdin module parmed.amber.mdin.cntrl module parmed.amber.mdin.ewald module parmed.amber.mdin.mdin module parmed.amber.mdin.pb module parmed.amber.mdin.qmmm module parmed.amber.netcdffiles module parmed.amber.offlib module parmed.amber.parameters module parmed.amber.readparm module parmed.amber.titratable_residues module parmed.charmm module parmed.charmm.charmmcrds module parmed.charmm.parameters module parmed.charmm.psf module parmed.constants module parmed.exceptions module parmed.formats module parmed.formats.mol2 module parmed.formats.pdb module parmed.formats.pdbx module parmed.formats.pdbx.PdbxContainers module parmed.formats.pdbx.PdbxReader module parmed.formats.pdbx.PdbxWriter module parmed.formats.pqr module parmed.formats.psf module parmed.formats.registry module parmed.formats.sdf module parmed.geometry module parmed.gromacs module parmed.gromacs.gromacsgro module parmed.gromacs.gromacstop module parmed.modeller module parmed.modeller.residue module parmed.modeller.standardtemplates module parmed.namd module parmed.namd.namdbinfiles module parmed.openmm module parmed.openmm.parameters module parmed.openmm.reporters module parmed.openmm.topsystem module parmed.openmm.utils module parmed.openmm.xmlfile module parmed.parameters module parmed.periodic_table module parmed.rdkit module parmed.rdkit.rdkit module parmed.residue module parmed.rosetta module parmed.rosetta.pose module parmed.scripts module parmed.structure module parmed.symmetry module parmed.tinker module parmed.tinker.parameterfile module parmed.tinker.system module parmed.tinker.tinkerfiles module parmed.tinker.topologyobjects module parmed.tools module parmed.tools.actions module parmed.tools.add1264 module parmed.tools.addljtype module parmed.tools.argumentlist module parmed.tools.changeradii module parmed.tools.checkvalidity module parmed.tools.coarsegrain module parmed.tools.exceptions module parmed.tools.gui module parmed.tools.gui.guiactions module parmed.tools.gui.guifiletools module parmed.tools.gui.guitools module parmed.tools.logos module parmed.tools.parmed_cmd module parmed.tools.parmlist module parmed.tools.simulations module parmed.tools.simulations.openmm module parmed.tools.simulations.sanderapi module parmed.topologyobjects module parmed.unit module parmed.unit.basedimension module

parmed.unit.baseunit module parmed.unit.constants module parmed.unit.mymatrix module parmed.unit.prefix module parmed.unit.quantity module parmed.unit.standard_dimensions module parmed.unit.unit module parmed.unit.unit_definitions module parmed.unit.unit_math module parmed.unit.unit_operators module parmed.utils module parmed.utils.decorators module parmed.utils.fortranformat module parmed.utils.fortranformat.config module parmed.utils.fortranformat.FortranRecordReader module parmed.utils.fortranformat.FortranRecordWriter module parmed.utils.io module parmed.utils.netcdf module parmed.utils.pairlist module parmed.utils.pandautils module parmed.utils.six module parmed.utils.timer module parmed.vec3 module ParmedAddLJTypeError ParmedApp (class in parmed.tools.gui.guitools) ParmedChangeError ParmedCmd (class in parmed.tools.parmed_cmd) ParmedError, [1] ParmedMoleculeError ParmedUtilsError ParmedWarning, [1] ParmError ParmFileNotFound ParmIndexError ParmList (class in parmed.tools) (class in parmed.tools.parmlist) parmout (class in parmed.tools.actions) ParmWarning parse (parmed.utils.six.Module_six_moves_urllib attribute) parse() (parmed.amber.AmberAsciiRestart class method) (parmed.amber.AmberFormat static method) (parmed.amber.amberformat.AmberFormat static method) (parmed.amber.AmberOFFLibrary static method) (parmed.amber.asciicrd.AmberAsciiRestart class method) (parmed.amber.netcdffiles.NetCDFRestart class method) (parmed.amber.NetCDFRestart class method) (parmed.amber.offlib.AmberOFFLibrary static method) (parmed.amber.readparm.AmberFormat static method) (parmed.formats.CIFFile static method) (parmed.formats.mol2.Mol2File static method) (parmed.formats.Mol2File static method) (parmed.formats.pdb.CIFFile static method) (parmed.formats.pdb.PDBFile class method) (parmed.formats.PDBFile class method) (parmed.formats.pqr.PQRFile static method) (parmed.formats.PQRFile static method) (parmed.formats.psf.PSFFile static method) (parmed.formats.PSFFile static method) (parmed.formats.sdf.SDFFile static method) (parmed.formats.SDFFile static method) (parmed.gromacs.gromacsgro.GromacsGroFile static method) (parmed.gromacs.GromacsGroFile static method) (parmed.modeller.AmberOFFLibrary static method) (parmed.openmm.XmlFile static method) (parmed.openmm.xmlfile.XmlFile static method) parse_qs (parmed.utils.six.Module_six_moves_urllib_parse attribute) parse_qsl (parmed.utils.six.Module_six_moves_urllib_parse attribute) parseline() (parmed.tools.parmed_cmd.ParmedCmd method) (parmed.tools.parmed_cmd.PythonCmd method) ParseResult (parmed.utils.six.Module_six_moves_urllib_parse attribute) ParsingError patch_is_compatible() (parmed.modeller.residue.ResidueTemplate method) (parmed.modeller.ResidueTemplate method) PatchTemplate (class in parmed.modeller) (class in parmed.modeller.residue) pathname2url (parmed.utils.six.Module_six_moves_urllib_request attribute) pb (class in parmed.amber.mdin.pb) PDBError PDBFile (class in parmed.formats) (class in parmed.formats.pdb) PDBFile.AtomLookupKey (class in parmed.formats) (class in parmed.formats.pdb) PDBWarning PdbxError PdbxReader (class in parmed.formats.pdbx) (class in parmed.formats.pdbx.PdbxReader) PdbxSyntaxError PdbxWriter (class in parmed.formats.pdbx) (class in parmed.formats.pdbx.PdbxWriter) penalty() (parmed.DihedralTypeList property) (parmed.topologyobjects.DihedralTypeList property) PI_TORSION_FORCE_GROUP (parmed.Structure attribute) (parmed.structure.Structure attribute) PiTorsion (class in parmed) (class in parmed.tinker.topologyobjects) (class in parmed.topologyobjects), [1] PiTorsionList (class in parmed.tinker.topologyobjects) pop() (parmed.AtomList method) (parmed.topologyobjects.AtomList method) (parmed.topologyobjects.TrackedList method) (parmed.TrackedList method) (parmed.unit.quantity.Quantity method) populate_actions() (parmed.tools.parmed_cmd.ParmedCmd class method) positional_restraints() (in module parmed.tools.simulations.openmm) positions() (parmed.amber.readparm.Rst7 property) (parmed.amber.Rst7 property) (parmed.charmm.CharmmCrdFile property) (parmed.charmm.charmmcrds.CharmmCrdFile property) (parmed.charmm.charmmcrds.CharmmRstFile property) (parmed.charmm.CharmmRstFile property) (parmed.Structure property) (parmed.structure.Structure property) (parmed.structure.StructureView property) (parmed.StructureView property) positionsold() (parmed.charmm.charmmcrds.CharmmRstFile property) (parmed.charmm.CharmmRstFile property) PQRFile (class in parmed.formats) (class in parmed.formats.pqr) precmd() (parmed.tools.parmed_cmd.ParmedCmd method) (parmed.tools.parmed_cmd.PythonCmd method) PreProcessorError PreProcessorWarning pretty_print() (in module parmed.openmm.parameters) print_() (parmed.utils.timer.Timer method) printAngles (class in parmed.tools.actions) printBonds (class in parmed.tools.actions) printDetails (class in parmed.tools.actions) printDihedrals (class in parmed.tools.actions) printFlags (class in parmed.tools.actions) printInfo (class in parmed.tools.actions) printIt() (parmed.formats.pdbx.PdbxContainers.ContainerBase method) (parmed.formats.pdbx.PdbxContainers.DataCategory method) (parmed.formats.pdbx.PdbxContainers.DefinitionContainer method) printLJMatrix (class in parmed.tools.actions) printLJTypes (class in parmed.tools.actions) printPointers (class in parmed.tools.actions) ProgressReporter (class in parmed.openmm), [1] (class in parmed.openmm.reporters) prompt (parmed.tools.parmed_cmd.ParmedCmd attribute) (parmed.tools.parmed_cmd.PythonCmd attribute) proxy_bypass (parmed.utils.six.Module_six_moves_urllib_request attribute) ProxyBasicAuthHandler (parmed.utils.six.Module_six_moves_urllib_request attribute) ProxyDigestAuthHandler (parmed.utils.six.Module_six_moves_urllib_request attribute) ProxyHandler (parmed.utils.six.Module_six_moves_urllib_request attribute) prune() (parmed.ResidueList method) (parmed.topologyobjects.ResidueList method) prune_empty_terms() (parmed.Structure method) (parmed.structure.Structure method) prune_exclusions() (parmed.Atom method) (parmed.topologyobjects.Atom method) prune_unused() (parmed.topologyobjects.TrackedList method) (parmed.TrackedList method) PSFFile (class in parmed.formats) (class in parmed.formats.psf) ptr() (parmed.amber.AmberParm method) (parmed.amber.readparm.AmberParm method) python_2_unicode_compatible() (in module parmed.utils.six) PythonCmd (class in parmed.tools.parmed_cmd)

Q

qmmm (class in parmed.amber.mdin.qmmm) Quantity (class in parmed.unit) (class in parmed.unit.quantity)

quote (parmed.utils.six.Module_six_moves_urllib_parse attribute) quote_plus (parmed.utils.six.Module_six_moves_urllib_parse attribute)

R

radii() (parmed.ExtraPoint property) (parmed.topologyobjects.ExtraPoint property) raise_from() (in module parmed.utils.six) RB_TORSION_FORCE_GROUP (parmed.Structure attribute) (parmed.structure.Structure attribute) RBTorsionType (class in parmed) (class in parmed.topologyobjects) RDKit (class in parmed.rdkit.rdkit) rdparm() (parmed.amber.AmberFormat method) (parmed.amber.amberformat.AmberFormat method) (parmed.amber.readparm.AmberFormat method) rdparm_old() (parmed.amber.AmberFormat method) (parmed.amber.amberformat.AmberFormat method) (parmed.amber.readparm.AmberFormat method) rdparm_slow() (parmed.amber.AmberFormat method) (parmed.amber.amberformat.AmberFormat method) (parmed.amber.readparm.AmberFormat method) read() (parmed.amber.amberformat.FortranFormat method) (parmed.amber.FortranFormat method) (parmed.amber.mdin.Mdin method) (parmed.amber.mdin.mdin.Mdin method) (parmed.formats.pdbx.PdbxReader method) (parmed.formats.pdbx.PdbxReader.PdbxReader method) (parmed.gromacs.gromacstop.GromacsTopologyFile method) (parmed.gromacs.GromacsTopologyFile method) (parmed.namd.namdbinfiles.NamdBinFile class method) (parmed.tinker.system.TinkerAnalout method) (parmed.tinker.tinkerfiles.DynFile method) (parmed.utils.fortranformat.FortranRecordReader.FortranRecordReader method) read_CIF() (in module parmed) read_parameter_file() (parmed.charmm.CharmmParameterSet method) (parmed.charmm.parameters.CharmmParameterSet method) read_PDB() (in module parmed) read_stream_file() (parmed.charmm.CharmmParameterSet method) (parmed.charmm.parameters.CharmmParameterSet method) read_topology_file() (parmed.charmm.CharmmParameterSet method) (parmed.charmm.parameters.CharmmParameterSet method) recalculate_LJ() (parmed.amber.AmberParm method) (parmed.amber.ChamberParm method) (parmed.amber.readparm.AmberParm method) (parmed.amber.readparm.ChamberParm method) rediscover_molecules() (parmed.amber.AmberParm method) (parmed.amber.readparm.AmberParm method) reduce_box_vectors() (in module parmed.geometry) reduce_unit() (parmed.unit.quantity.Quantity method) remake_parm() (parmed.amber.AmberParm method) (parmed.amber.AmoebaParm method) (parmed.amber.ChamberParm method) (parmed.amber.readparm.AmberParm method) (parmed.amber.readparm.ChamberParm method) remd_dimtype() (parmed.amber.netcdffiles.NetCDFRestart property) (parmed.amber.netcdffiles.NetCDFTraj property) (parmed.amber.NetCDFRestart property) (parmed.amber.NetCDFTraj property) remd_indices() (parmed.amber.netcdffiles.NetCDFRestart property) (parmed.amber.netcdffiles.NetCDFTraj property) (parmed.amber.NetCDFRestart property) (parmed.amber.NetCDFTraj property) remove() (parmed.AtomList method) (parmed.formats.pdbx.PdbxContainers.ContainerBase method) (parmed.topologyobjects.AtomList method) (parmed.topologyobjects.TrackedList method) (parmed.TrackedList method) (parmed.unit.quantity.Quantity method)

remove_move() (in module parmed.utils.six) removeRow() (parmed.formats.pdbx.PdbxContainers.DataCategory method) rename() (parmed.formats.pdbx.PdbxContainers.ContainerBase method) renameAttribute() (parmed.formats.pdbx.PdbxContainers.DataCategory method) replace() (parmed.formats.pdbx.PdbxContainers.ContainerBase method) replaceSubstring() (parmed.formats.pdbx.PdbxContainers.DataCategory method) replaceValue() (parmed.formats.pdbx.PdbxContainers.DataCategory method) report() (parmed.openmm.EnergyMinimizerReporter method) (parmed.openmm.MdcrdReporter method) (parmed.openmm.NetCDFReporter method) (parmed.openmm.ProgressReporter method) (parmed.openmm.reporters.EnergyMinimizerReporter method) (parmed.openmm.reporters.MdcrdReporter method) (parmed.openmm.reporters.NetCDFReporter method) (parmed.openmm.reporters.ProgressReporter method) (parmed.openmm.reporters.RestartReporter method) (parmed.openmm.reporters.StateDataReporter method) (parmed.openmm.RestartReporter method) (parmed.openmm.StateDataReporter method) request (parmed.utils.six.Module_six_moves_urllib attribute) Request (parmed.utils.six.Module_six_moves_urllib_request attribute) reraise() (in module parmed.utils.six) reset() (in module parmed.tinker.parameterfile) (in module parmed.utils.fortranformat.config) (parmed.amber.titratable_residues.TitratableResidue method) reshape() (parmed.unit.quantity.Quantity method) Residue (class in parmed) (class in parmed.topologyobjects), [1] residue_name() (parmed.formats.pdb.PDBFile.AtomLookupKey property) (parmed.formats.PDBFile.AtomLookupKey property) residue_number() (parmed.formats.pdb.PDBFile.AtomLookupKey property) (parmed.formats.PDBFile.AtomLookupKey property) ResidueError ResidueList (class in parmed) (class in parmed.topologyobjects), [1] ResidueTemplate (class in parmed.modeller) (class in parmed.modeller.residue) ResidueTemplateContainer (class in parmed.modeller) (class in parmed.modeller.residue) response (parmed.utils.six.Module_six_moves_urllib attribute) restart() (parmed.amber.mdin.Mdin method) (parmed.amber.mdin.mdin.Mdin method) RestartReporter (class in parmed.openmm), [1] (class in parmed.openmm.reporters) restrainBackbone() (parmed.amber.mdin.Mdin method) (parmed.amber.mdin.mdin.Mdin method) restrainHeavyAtoms() (parmed.amber.mdin.Mdin method) (parmed.amber.mdin.mdin.Mdin method) REVERSE_BOND_ORDER_MAP (parmed.formats.mol2.Mol2File attribute) (parmed.formats.Mol2File attribute) rewind() (parmed.tinker.parameterfile.BookmarkedFile method) rmin() (parmed.Atom property) (parmed.topologyobjects.Atom property) rmin_14() (parmed.Atom property) (parmed.topologyobjects.Atom property) RNAResidue (class in parmed.residue) RobotFileParser (parmed.utils.six.Module_six_moves_urllib_robotparser attribute) robotparser (parmed.utils.six.Module_six_moves_urllib attribute) RosettaError RosettaPose (class in parmed.rosetta) (class in parmed.rosetta.pose) Rst7 (class in parmed.amber), [1] (class in parmed.amber.readparm)

S

same_atoms() (parmed.Cmap method) (parmed.Dihedral method) (parmed.Improper method) (parmed.topologyobjects.Cmap method) (parmed.topologyobjects.Dihedral method) (parmed.topologyobjects.Improper method) save() (parmed.modeller.residue.ResidueTemplate method) (parmed.modeller.residue.ResidueTemplateContainer method) (parmed.modeller.ResidueTemplate method) (parmed.modeller.ResidueTemplateContainer method) (parmed.Structure method) (parmed.structure.Structure method) save_file_chooser() (in module parmed.tools.gui.guifiletools) scale (class in parmed.tools.actions) ScaledUnit (class in parmed.unit.unit) scan() (parmed.charmm.charmmcrds.CharmmRstFile method) (parmed.charmm.CharmmRstFile method) scee (class in parmed.tools.actions) scnb (class in parmed.tools.actions) SDFFile (class in parmed.formats) (class in parmed.formats.sdf) segment_id() (parmed.formats.pdb.PDBFile.AtomLookupKey property) (parmed.formats.PDBFile.AtomLookupKey property) Selected() (parmed.amber.AmberMask method) (parmed.amber.mask.AmberMask method) Selection() (parmed.amber.AmberMask method) (parmed.amber.mask.AmberMask method) SeriousParmWarning set_first_charge() (parmed.amber.titratable_residues.TitratableResidue method) set_first_state() (parmed.amber.titratable_residues.TitratableResidue method) set_format() (parmed.utils.fortranformat.FortranRecordReader.FortranRecordReader method) (parmed.utils.fortranformat.FortranRecordWriter.FortranRecordWriter method) set_lj_params() (parmed.AtomType method) (parmed.topologyobjects.AtomType method) set_molecules() (in module parmed.charmm.psf) set_new_active() (parmed.tools.ParmList method) (parmed.tools.parmlist.ParmList method) set_states() (parmed.amber.titratable_residues.TitratableResidueList method) set_version() (parmed.amber.AmberFormat method) (parmed.amber.amberformat.AmberFormat method) (parmed.amber.readparm.AmberFormat method) setAngle (class in parmed.tools.actions) setAttributeNameList() (parmed.formats.pdbx.PdbxContainers.DataCategoryBase method) setBond (class in parmed.tools.actions) setGlobal() (parmed.formats.pdbx.PdbxContainers.DataContainer method) setlog() (parmed.tools.parmed_cmd.ParmedCmd method) (parmed.tools.parmed_cmd.PythonCmd method) setMolecules (class in parmed.tools.actions) setName() (parmed.formats.pdbx.PdbxContainers.ContainerBase method) (parmed.formats.pdbx.PdbxContainers.DataCategoryBase method) setOverwrite (class in parmed.tools.actions) setRowList() (parmed.formats.pdbx.PdbxContainers.DataCategoryBase method) setRowPartition() (parmed.formats.pdbx.PdbxWriter method) (parmed.formats.pdbx.PdbxWriter.PdbxWriter method) setType() (parmed.formats.pdbx.PdbxContainers.ContainerBase method) setValue() (parmed.formats.pdbx.PdbxContainers.DataCategory method) SHAKE() (parmed.amber.mdin.Mdin method) (parmed.amber.mdin.mdin.Mdin method) shape() (parmed.utils.netcdf.netcdf_variable property) sigma() (parmed.Atom property) (parmed.AtomType property) (parmed.NonbondedExceptionType property) (parmed.topologyobjects.Atom property) (parmed.topologyobjects.AtomType property) (parmed.topologyobjects.NonbondedExceptionType property) sigma_14() (parmed.Atom property) (parmed.AtomType property) (parmed.topologyobjects.Atom property) (parmed.topologyobjects.AtomType property) simulate() (in module parmed.tools.simulations.openmm) SimulationError SimulationWarning sin() (in module parmed.unit.unit_math) sinh() (in module parmed.unit.unit_math) SiPrefix (class in parmed.unit.prefix)

skipped_actions (parmed.tools.gui.guitools.ParmedApp attribute) softcore_TI() (parmed.amber.mdin.Mdin method) (parmed.amber.mdin.mdin.Mdin method) sort() (parmed.amber.titratable_residues.TitratableResidueList method) (parmed.Residue method) (parmed.topologyobjects.Residue method) source (class in parmed.tools.actions) split() (parmed.Structure method) (parmed.structure.Structure method) splitquery (parmed.utils.six.Module_six_moves_urllib_parse attribute) SplitResidueWarning SplitResult (parmed.utils.six.Module_six_moves_urllib_parse attribute) splittag (parmed.utils.six.Module_six_moves_urllib_parse attribute) splituser (parmed.utils.six.Module_six_moves_urllib_parse attribute) sqrt() (in module parmed.unit.unit_math) (parmed.unit.quantity.Quantity method) (parmed.unit.unit.Unit method) start_timer() (parmed.utils.timer.Timer method) StateDataReporter (class in parmed.openmm), [1] (class in parmed.openmm.reporters) std() (parmed.unit.quantity.Quantity method) stderr (parmed.tools.actions.Action attribute) stop_timer() (parmed.utils.timer.Timer method) STRETCH_BEND_FORCE_GROUP (parmed.Structure attribute) (parmed.structure.Structure attribute) StretchBend (class in parmed) (class in parmed.tinker.topologyobjects) (class in parmed.topologyobjects), [1] StretchBendList (class in parmed.tinker.topologyobjects) StretchBendType (class in parmed) (class in parmed.topologyobjects), [1] strictly_supported (parmed.tools.actions.Action attribute) (parmed.tools.actions.add12_6_4 attribute) (parmed.tools.actions.addLJType attribute) (parmed.tools.actions.changeLJ14Pair attribute) (parmed.tools.actions.changeLJPair attribute) (parmed.tools.actions.changeLJSingleType attribute) (parmed.tools.actions.changeProtState attribute) (parmed.tools.actions.changeRedoxState attribute) (parmed.tools.actions.checkValidity attribute) (parmed.tools.actions.interpolate attribute) (parmed.tools.actions.lmod attribute) (parmed.tools.actions.printLJMatrix attribute) (parmed.tools.actions.printLJTypes attribute) (parmed.tools.actions.tiMerge attribute) (parmed.tools.actions.writeFrcmod attribute) (parmed.tools.actions.writeOFF attribute) strip (class in parmed.tools.actions) strip() (parmed.amber.AmberParm method) (parmed.amber.readparm.AmberParm method) (parmed.Structure method) (parmed.structure.Structure method) strre (parmed.amber.amberformat.FortranFormat attribute) (parmed.amber.FortranFormat attribute) Structure (class in parmed) (class in parmed.structure), [1] StructureView (class in parmed) (class in parmed.structure) sum() (in module parmed.unit.unit_math) (parmed.unit.quantity.Quantity method) summary (class in parmed.tools.actions) supported_subclasses (parmed.tools.actions.Action attribute) (parmed.tools.actions.addAtomicNumber attribute) (parmed.tools.actions.addPDB attribute) (parmed.tools.actions.defineSolvent attribute) (parmed.tools.actions.deletePDB attribute) (parmed.tools.actions.loadRestrt attribute) (parmed.tools.actions.parmout attribute) (parmed.tools.actions.printFlags attribute) (parmed.tools.actions.printInfo attribute) (parmed.tools.actions.printPointers attribute) (parmed.tools.actions.scale attribute) (parmed.tools.actions.setMolecules attribute) Symmetry (class in parmed.symmetry) sync() (parmed.utils.netcdf.netcdf_file method)

T

tag_molecules() (in module parmed.utils) tan() (in module parmed.unit.unit_math) tanh() (in module parmed.unit.unit_math) temp0() (parmed.amber.netcdffiles.NetCDFRestart property) (parmed.amber.netcdffiles.NetCDFTraj property) (parmed.amber.NetCDFRestart property) (parmed.amber.NetCDFTraj property) ThreeParticleExtraPointFrame (class in parmed) (class in parmed.topologyobjects) TI() (parmed.amber.mdin.Mdin method) (parmed.amber.mdin.mdin.Mdin method) time() (parmed.amber.mdin.Mdin method) (parmed.amber.mdin.mdin.Mdin method) (parmed.amber.netcdffiles.NetCDFRestart property) (parmed.amber.netcdffiles.NetCDFTraj property) (parmed.amber.NetCDFRestart property) (parmed.amber.NetCDFTraj property) Timer (class in parmed.utils.timer) tiMerge (class in parmed.tools.actions) TiMergeError TinkerAnalout (class in parmed.tinker.system) TinkerError TinkerWarning TitratableResidue (class in parmed.amber.titratable_residues) TitratableResidueList (class in parmed.amber.titratable_residues) to_dataframe() (parmed.modeller.residue.ResidueTemplate method) (parmed.modeller.ResidueTemplate method) (parmed.Structure method) (parmed.structure.Structure method) (parmed.structure.StructureView method) (parmed.StructureView method) to_library() (parmed.modeller.residue.ResidueTemplateContainer method) (parmed.modeller.ResidueTemplateContainer method) to_networkx() (parmed.modeller.residue.ResidueTemplate method) (parmed.modeller.ResidueTemplate method) to_structure() (parmed.modeller.residue.ResidueTemplate method) (parmed.modeller.ResidueTemplate method) tokenize() (parmed.tools.argumentlist.ArgumentList method) topology() (parmed.Structure property) (parmed.structure.Structure property) TORSION_TORSION_FORCE_GROUP (parmed.Structure attribute) (parmed.structure.Structure attribute)

TorsionAngle (class in parmed.tinker.topologyobjects) TorsionAngleList (class in parmed.tinker.topologyobjects) TorsionTorsion (class in parmed) (class in parmed.tinker.topologyobjects) (class in parmed.topologyobjects), [1] TorsionTorsionGrid (class in parmed.tinker.topologyobjects) TorsionTorsionList (class in parmed.tinker.topologyobjects) TorsionTorsionType (class in parmed) (class in parmed.topologyobjects), [1] tortor_partners() (parmed.Atom property) (parmed.ExtraPoint property) (parmed.topologyobjects.Atom property) (parmed.topologyobjects.ExtraPoint property) tortor_to() (parmed.Atom method) (parmed.topologyobjects.Atom method) TrackedList (class in parmed) (class in parmed.topologyobjects) transpose() (parmed.unit.mymatrix.MyMatrix method) (parmed.unit.mymatrix.MyMatrixTranspose method) TRIGONAL_ANGLE_FORCE_GROUP (parmed.Structure attribute) (parmed.structure.Structure attribute) TrigonalAngle (class in parmed) (class in parmed.topologyobjects), [1] try_convert() (in module parmed.formats.pdb) TwoParticleExtraPointFrame (class in parmed) (class in parmed.topologyobjects) typeclass (parmed.tinker.topologyobjects.AngleList attribute) (parmed.tinker.topologyobjects.AtomicMultipoleList attribute) (parmed.tinker.topologyobjects.AtomList attribute) (parmed.tinker.topologyobjects.BondList attribute) (parmed.tinker.topologyobjects.DipolePolarizabilityList attribute) (parmed.tinker.topologyobjects.OutOfPlaneBendList attribute) (parmed.tinker.topologyobjects.OutOfPlaneDistList attribute) (parmed.tinker.topologyobjects.PiTorsionList attribute) (parmed.tinker.topologyobjects.StretchBendList attribute) (parmed.tinker.topologyobjects.TorsionAngleList attribute) (parmed.tinker.topologyobjects.TorsionTorsionList attribute) (parmed.tinker.topologyobjects.UreyBradleyList attribute) typecode() (parmed.utils.netcdf.netcdf_variable method) typeify_templates() (parmed.parameters.ParameterSet method) (parmed.ParameterSet method)

U

u() (in module parmed.utils.six) uc0() (parmed.RBTorsionType property) (parmed.topologyobjects.RBTorsionType property) uc1() (parmed.RBTorsionType property) (parmed.topologyobjects.RBTorsionType property) uc2() (parmed.RBTorsionType property) (parmed.topologyobjects.RBTorsionType property) uc3() (parmed.RBTorsionType property) (parmed.topologyobjects.RBTorsionType property) uc4() (parmed.RBTorsionType property) (parmed.topologyobjects.RBTorsionType property) uc5() (parmed.RBTorsionType property) (parmed.topologyobjects.RBTorsionType property) ucharge() (parmed.Atom property) (parmed.topologyobjects.Atom property) uenergy() (parmed.Angle method) (parmed.Bond method) (parmed.Dihedral method) (parmed.Improper method) (parmed.topologyobjects.Angle method) (parmed.topologyobjects.Bond method) (parmed.topologyobjects.Dihedral method) (parmed.topologyobjects.Improper method) uepsilon() (parmed.Atom property) (parmed.AtomType property) (parmed.NonbondedExceptionType property) (parmed.topologyobjects.Atom property) (parmed.topologyobjects.AtomType property) (parmed.topologyobjects.NonbondedExceptionType property) uepsilon_14() (parmed.Atom property) (parmed.AtomType property) (parmed.topologyobjects.Atom property) (parmed.topologyobjects.AtomType property) uk() (parmed.AngleType property) (parmed.BondType property) (parmed.OutOfPlaneBendType property) (parmed.topologyobjects.AngleType property) (parmed.topologyobjects.BondType property) (parmed.topologyobjects.OutOfPlaneBendType property) uk1() (parmed.StretchBendType property) (parmed.topologyobjects.StretchBendType property) uk2() (parmed.StretchBendType property) (parmed.topologyobjects.StretchBendType property) umass() (parmed.Atom property) (parmed.topologyobjects.Atom property) umeasure() (parmed.Angle method) (parmed.Bond method) (parmed.Dihedral method) (parmed.Improper method) (parmed.topologyobjects.Angle method) (parmed.topologyobjects.Bond method) (parmed.topologyobjects.Dihedral method) (parmed.topologyobjects.Improper method) unchange() (parmed.Structure method) (parmed.structure.Structure method) UnhandledArgumentWarning Unit (class in parmed.unit) (class in parmed.unit.unit) UnitSystem (class in parmed.unit) (class in parmed.unit.unit) UnknownHandler (parmed.utils.six.Module_six_moves_urllib_request attribute) unmark() (parmed.AtomList method) (parmed.tools.argumentlist.Argument method) (parmed.topologyobjects.AtomList method) unmarked() (parmed.tools.argumentlist.ArgumentList method) unquote (parmed.utils.six.Module_six_moves_urllib_parse attribute) unquote_plus (parmed.utils.six.Module_six_moves_urllib_parse attribute) update_dihedral_exclusions() (parmed.Structure method) (parmed.structure.Structure method) uphase() (parmed.DihedralType property) (parmed.topologyobjects.DihedralType property) uphi_k() (parmed.DihedralType property) (parmed.topologyobjects.DihedralType property) upsi_eq() (parmed.ImproperType property) (parmed.topologyobjects.ImproperType property) upsi_k() (parmed.ImproperType property) (parmed.topologyobjects.ImproperType property) ureq() (parmed.BondType property) (parmed.topologyobjects.BondType property) ureq1() (parmed.StretchBendType property) (parmed.topologyobjects.StretchBendType property) ureq2() (parmed.StretchBendType property) (parmed.topologyobjects.StretchBendType property) UREY_BRADLEY_FORCE_GROUP (parmed.Structure attribute) (parmed.structure.Structure attribute) UreyBradley (class in parmed) (class in parmed.tinker.topologyobjects) (class in parmed.topologyobjects), [1] UreyBradleyList (class in parmed.tinker.topologyobjects) url2pathname (parmed.utils.six.Module_six_moves_urllib_request attribute) urlcleanup (parmed.utils.six.Module_six_moves_urllib_request attribute)

urldefrag (parmed.utils.six.Module_six_moves_urllib_parse attribute) urlencode (parmed.utils.six.Module_six_moves_urllib_parse attribute) urljoin (parmed.utils.six.Module_six_moves_urllib_parse attribute) URLopener (parmed.utils.six.Module_six_moves_urllib_request attribute) urlparse (parmed.utils.six.Module_six_moves_urllib_parse attribute) urlretrieve (parmed.utils.six.Module_six_moves_urllib_request attribute) urlsplit (parmed.utils.six.Module_six_moves_urllib_parse attribute) urlunparse (parmed.utils.six.Module_six_moves_urllib_parse attribute) urlunsplit (parmed.utils.six.Module_six_moves_urllib_parse attribute) urmin() (parmed.Atom property) (parmed.AtomType property) (parmed.NonbondedExceptionType property) (parmed.topologyobjects.Atom property) (parmed.topologyobjects.AtomType property) (parmed.topologyobjects.NonbondedExceptionType property) urmin_14() (parmed.Atom property) (parmed.AtomType property) (parmed.topologyobjects.Atom property) (parmed.topologyobjects.AtomType property) usage (parmed.tools.actions.add12_6_4 attribute) (parmed.tools.actions.addDihedral attribute) (parmed.tools.actions.addExclusions attribute) (parmed.tools.actions.addLJType attribute) (parmed.tools.actions.addPDB attribute) (parmed.tools.actions.cd attribute) (parmed.tools.actions.chamber attribute) (parmed.tools.actions.change attribute) (parmed.tools.actions.changeLJ14Pair attribute) (parmed.tools.actions.changeLJPair attribute) (parmed.tools.actions.changeLJSingleType attribute) (parmed.tools.actions.changeProtState attribute) (parmed.tools.actions.changeRadii attribute) (parmed.tools.actions.changeRedoxState attribute) (parmed.tools.actions.defineSolvent attribute) (parmed.tools.actions.deleteBond attribute) (parmed.tools.actions.deleteDihedral attribute) (parmed.tools.actions.energy attribute) (parmed.tools.actions.gromber attribute) (parmed.tools.actions.HMassRepartition attribute) (parmed.tools.actions.interpolate attribute) (parmed.tools.actions.loadCoordinates attribute) (parmed.tools.actions.loadRestrt attribute) (parmed.tools.actions.ls attribute) (parmed.tools.actions.minimize attribute) (parmed.tools.actions.netCharge attribute) (parmed.tools.actions.OpenMM attribute) (parmed.tools.actions.outCIF attribute) (parmed.tools.actions.outparm attribute) (parmed.tools.actions.outPDB attribute) (parmed.tools.actions.parm attribute) (parmed.tools.actions.parmout attribute) (parmed.tools.actions.printAngles attribute) (parmed.tools.actions.printBonds attribute) (parmed.tools.actions.printDetails attribute) (parmed.tools.actions.printDihedrals attribute) (parmed.tools.actions.printInfo attribute) (parmed.tools.actions.printLJMatrix attribute) (parmed.tools.actions.printLJTypes attribute) (parmed.tools.actions.scale attribute) (parmed.tools.actions.scee attribute) (parmed.tools.actions.scnb attribute) (parmed.tools.actions.setAngle attribute) (parmed.tools.actions.setBond attribute) (parmed.tools.actions.setMolecules attribute) (parmed.tools.actions.setOverwrite attribute) (parmed.tools.actions.source attribute) (parmed.tools.actions.strip attribute) (parmed.tools.actions.tiMerge attribute) (parmed.tools.actions.writeCoordinates attribute) (parmed.tools.actions.writeFrcmod attribute) (parmed.tools.actions.writeOFF attribute) uses_fragment (parmed.utils.six.Module_six_moves_urllib_parse attribute) uses_netloc (parmed.utils.six.Module_six_moves_urllib_parse attribute) uses_params (parmed.utils.six.Module_six_moves_urllib_parse attribute) uses_query (parmed.utils.six.Module_six_moves_urllib_parse attribute) uses_relative (parmed.utils.six.Module_six_moves_urllib_parse attribute) usigma() (parmed.Atom property) (parmed.AtomType property) (parmed.NonbondedExceptionType property) (parmed.topologyobjects.Atom property) (parmed.topologyobjects.AtomType property) (parmed.topologyobjects.NonbondedExceptionType property) usigma_14() (parmed.Atom property) (parmed.AtomType property) (parmed.topologyobjects.Atom property) (parmed.topologyobjects.AtomType property) usolvent_radius() (parmed.Atom property) (parmed.topologyobjects.Atom property) utheteq() (parmed.AngleType property) (parmed.StretchBendType property) (parmed.topologyobjects.AngleType property) (parmed.topologyobjects.StretchBendType property)

V

value_in_unit() (parmed.unit.quantity.Quantity method) value_in_unit_system() (parmed.unit.quantity.Quantity method) Vec3 (class in parmed) (class in parmed.vec3) velocities() (parmed.amber.AmberAsciiRestart property) (parmed.amber.asciicrd.AmberAsciiRestart property) (parmed.amber.BeemanRestart property) (parmed.amber.netcdffiles.NetCDFRestart property) (parmed.amber.netcdffiles.NetCDFTraj property) (parmed.amber.NetCDFRestart property) (parmed.amber.NetCDFTraj property) (parmed.amber.readparm.Rst7 property) (parmed.amber.Rst7 property) (parmed.charmm.charmmcrds.CharmmRstFile property) (parmed.charmm.CharmmRstFile property) (parmed.namd.namdbinfiles.NamdBinVel property) (parmed.namd.NamdBinVel property) (parmed.Structure property) (parmed.structure.Structure property)

view() (parmed.Structure property) (parmed.structure.Structure property) view_as() (parmed.amber.AmberFormat method) (parmed.amber.amberformat.AmberFormat method) (parmed.amber.readparm.AmberFormat method) visualize() (parmed.Structure method) (parmed.structure.Structure method)

W

warn() (parmed.tools.exceptions.WarningList method) WarningList (class in parmed.tools.exceptions) which() (in module parmed.utils) with_metaclass() (in module parmed.utils.six) write() (parmed.amber.amberformat.FortranFormat method) (parmed.amber.AmberOFFLibrary static method) (parmed.amber.AmberParameterSet method) (parmed.amber.FortranFormat method) (parmed.amber.mdin.Mdin method) (parmed.amber.mdin.mdin.Mdin method) (parmed.amber.offlib.AmberOFFLibrary static method) (parmed.amber.parameters.AmberParameterSet method) (parmed.amber.readparm.Rst7 method) (parmed.amber.Rst7 method) (parmed.charmm.CharmmCrdFile static method) (parmed.charmm.charmmcrds.CharmmCrdFile static method) (parmed.charmm.CharmmParameterSet method) (parmed.charmm.parameters.CharmmParameterSet method) (parmed.formats.CIFFile static method) (parmed.formats.mol2.Mol2File static method) (parmed.formats.Mol2File static method) (parmed.formats.pdb.CIFFile static method) (parmed.formats.pdb.PDBFile static method) (parmed.formats.PDBFile static method) (parmed.formats.pdbx.PdbxWriter method) (parmed.formats.pdbx.PdbxWriter.PdbxWriter method) (parmed.formats.pqr.PQRFile static method) (parmed.formats.PQRFile static method) (parmed.formats.psf.PSFFile static method) (parmed.formats.PSFFile static method) (parmed.gromacs.gromacsgro.GromacsGroFile static method) (parmed.gromacs.GromacsGroFile static method) (parmed.gromacs.gromacstop.GromacsTopologyFile method) (parmed.gromacs.GromacsTopologyFile method) (parmed.modeller.AmberOFFLibrary static method) (parmed.namd.namdbinfiles.NamdBinFile method) (parmed.openmm.OpenMMParameterSet method) (parmed.openmm.parameters.OpenMMParameterSet method) (parmed.utils.fortranformat.FortranRecordWriter.FortranRecordWriter method)

write_CIF() (in module parmed) write_cif() (parmed.Structure method) (parmed.structure.Structure method) write_cpin() (parmed.amber.titratable_residues.TitratableResidueList method) write_parm() (parmed.amber.AmberFormat method) (parmed.amber.amberformat.AmberFormat method) (parmed.amber.AmberParm method) (parmed.amber.readparm.AmberFormat method) (parmed.amber.readparm.AmberParm method) write_PDB() (in module parmed) write_pdb() (parmed.Structure method) (parmed.structure.Structure method) write_psf() (parmed.Structure method) (parmed.structure.Structure method) write_rst7() (parmed.amber.AmberParm method) (parmed.amber.readparm.AmberParm method) writeContainer() (parmed.formats.pdbx.PdbxWriter method) (parmed.formats.pdbx.PdbxWriter.PdbxWriter method) writeCoordinates (class in parmed.tools.actions) writeFrcmod (class in parmed.tools.actions) writeOFF (class in parmed.tools.actions) WriteOFFError

X

XmlFile (class in parmed.openmm), [1] (class in parmed.openmm.xmlfile)

XyzFile (class in parmed.tinker) (class in parmed.tinker.tinkerfiles)

Z

zeros() (in module parmed.unit.mymatrix)