mol
β Molecular structures and surfacesΒΆ
The mol module implements data structures to work with molecular datasets. At its heart lie the EntityHandle
and EntityView
classes which represent molecular structures such as proteins, DNA, RNA and small molecules. There are also classes to deal with molecular surfaces.
- The Molecular Entity
- The Handle Classes
CreateEntity()
EntityHandle
EntityHandle.chains
EntityHandle.chain_count
EntityHandle.residues
EntityHandle.residue_count
EntityHandle.atoms
EntityHandle.atom_count
EntityHandle.bounds
EntityHandle.mass
EntityHandle.center_of_mass
EntityHandle.center_of_atoms
EntityHandle.positions
EntityHandle.valid
EntityHandle.GetName()
EntityHandle.SetName()
EntityHandle.FindChain()
EntityHandle.GetChainList()
EntityHandle.GetChainCount()
EntityHandle.FindResidue()
EntityHandle.GetResidueList()
EntityHandle.GetResidueCount()
EntityHandle.FindAtom()
EntityHandle.GetAtomList()
EntityHandle.GetAtomCount()
EntityHandle.EditXCS()
EntityHandle.EditICS()
EntityHandle.Select()
EntityHandle.CreateFullView()
EntityHandle.CreateEmptyView()
EntityHandle.Copy()
EntityHandle.GetCenterOfAtoms()
EntityHandle.GetCenterOfMass()
EntityHandle.GetGeometricCenter()
EntityHandle.GetMass()
EntityHandle.GetPositions()
EntityHandle.FindWithin()
EntityHandle.IsValid()
ChainHandle
ChainHandle.atoms
ChainHandle.bounds
ChainHandle.center_of_atoms
ChainHandle.center_of_mass
ChainHandle.description
ChainHandle.in_sequence
ChainHandle.is_oligosaccharide
ChainHandle.is_polymer
ChainHandle.is_polynucleotide
ChainHandle.is_polypeptide
ChainHandle.is_polysaccharide
ChainHandle.mass
ChainHandle.name
ChainHandle.residue_count
ChainHandle.residues
ChainHandle.type
ChainHandle.valid
ChainHandle.FindResidue()
ChainHandle.GetResidueList()
ChainHandle.GetResidueCount()
ChainHandle.FindAtom()
ChainHandle.GetAtomList()
ChainHandle.GetName()
ChainHandle.GetType()
ChainHandle.IsOligosaccharide()
ChainHandle.IsPolymer()
ChainHandle.IsPolynucleotide()
ChainHandle.IsPolypeptide()
ChainHandle.IsPolysaccharide()
ChainHandle.GetDescription()
ChainHandle.IsValid()
ResidueHandle
ResidueHandle.name
ResidueHandle.number
ResidueHandle.one_letter_code
ResidueHandle.atoms
ResidueHandle.bounds
ResidueHandle.mass
ResidueHandle.center_of_mass
ResidueHandle.center_of_atoms
ResidueHandle.chain
ResidueHandle.phi_torsion
ResidueHandle.psi_torsion
ResidueHandle.chem_class
ResidueHandle.chem_type
ResidueHandle.sec_structure
ResidueHandle.is_ligand
ResidueHandle.is_protein
ResidueHandle.peptide_linking
ResidueHandle.index
ResidueHandle.central_atom
ResidueHandle.central_normal
ResidueHandle.valid
ResidueHandle.next
ResidueHandle.prev
ResidueHandle.FindAtom()
ResidueHandle.HasAltAtoms()
ResidueHandle.HasAltAtomGroup()
ResidueHandle.GetAltAtomGroupNames()
ResidueHandle.GetCurrentAltGroupName()
ResidueHandle.SwitchAtomPos()
ResidueHandle.GetAtomList()
ResidueHandle.IsPeptideLinking()
ResidueHandle.GetChain()
ResidueHandle.GetCenterOfAtoms()
ResidueHandle.GetCenterOfMass()
ResidueHandle.GetPhiTorsion()
ResidueHandle.GetPsiTorsion()
ResidueHandle.GetChemType()
ResidueHandle.GetIndex()
ResidueHandle.GetCentralAtom()
ResidueHandle.SetCentralAtom()
ResidueHandle.GetCentralNormal()
ResidueHandle.IsValid()
AtomHandle
AtomHandle.name
AtomHandle.qualified_name
AtomHandle.element
AtomHandle.mass
AtomHandle.pos
AtomHandle.original_pos
AtomHandle.radius
AtomHandle.occupancy
AtomHandle.b_factor
AtomHandle.charge
AtomHandle.residue
AtomHandle.is_hetatom
AtomHandle.bonds
AtomHandle.index
AtomHandle.hash_code
AtomHandle.valid
AtomHandle.FindBondToAtom()
AtomHandle.GetBondCount()
AtomHandle.GetBondList()
AtomHandle.GetBondPartners()
AtomHandle.GetCharge()
AtomHandle.GetElement()
AtomHandle.GetEntity()
AtomHandle.GetHashCode()
AtomHandle.GetIndex()
AtomHandle.GetMass()
AtomHandle.GetName()
AtomHandle.GetOriginalPos()
AtomHandle.GetPos()
AtomHandle.GetQualifiedName()
AtomHandle.GetRadius()
AtomHandle.GetResidue()
AtomHandle.IsHetAtom()
AtomHandle.IsValid()
- The View Classes
EntityView
EntityView.chains
EntityView.chain_count
EntityView.residues
EntityView.residue_count
EntityView.atoms
EntityView.atom_count
EntityView.bounds
EntityView.handle
EntityView.valid
EntityView.GetName()
EntityView.SetName()
EntityView.CreateEmptyView()
EntityView.CreateFullView()
EntityView.AddChain()
EntityView.AddResidue()
EntityView.AddAtom()
EntityView.AddBond()
EntityView.AddAllInclusiveBonds()
EntityView.RemoveChain()
EntityView.RemoveResidue()
EntityView.RemoveAtom()
EntityView.GetAngle()
EntityView.FindWithin()
EntityView.FindChain()
EntityView.FindResidue()
EntityView.FindAtom()
EntityView.Select()
EntityView.Copy()
EntityView.GetMass()
EntityView.GetCenterOfMass()
EntityView.GetGeometricCenter()
EntityView.GetGeometricStart()
EntityView.GetCenterOfAtoms()
EntityView.GetBondCount()
EntityView.GetBondList()
EntityView.GetHandle()
EntityView.GetGeometricEnd()
EntityView.GetChainList()
EntityView.GetChainCount()
EntityView.GetResidueList()
EntityView.GetResidueCount()
EntityView.GetAtomList()
EntityView.GetAtomCount()
EntityView.IsValid()
ChainView
ChainView.name
ChainView.residues
ChainView.in_sequence
ChainView.atoms
ChainView.bounds
ChainView.mass
ChainView.center_of_mass
ChainView.center_of_atoms
ChainView.handle
ChainView.in_sequence
ChainView.geometric_center
ChainView.valid
ChainView.AddAtom()
ChainView.AddResidue()
ChainView.FindAtom()
ChainView.FindResidue()
ChainView.GetCenterOfAtoms()
ChainView.GetCenterOfMass()
ChainView.GetEntity()
ChainView.GetGeometricCenter()
ChainView.GetHandle()
ChainView.GetMass()
ChainView.GetName()
ChainView.GetResidueByIndex()
ChainView.GetResidueList()
ChainView.InSequence()
ChainView.IsValid()
ChainView.RemoveResidue()
ChainView.RemoveResidues()
ChainView.Select()
ResidueView
ResidueView.handle
ResidueView.name
ResidueView.number
ResidueView.one_letter_code
ResidueView.bounds
ResidueView.mass
ResidueView.center_of_mass
ResidueView.center_of_atoms
ResidueView.chain
ResidueView.handle
ResidueView.atoms
ResidueView.index
ResidueView.RemoveAtom()
ResidueView.GetHandle()
ResidueView.GetMass()
ResidueView.GetChain()
ResidueView.FindAtom()
ResidueView.GetIndex()
ResidueView.GetCenterOfMass()
ResidueView.IsAtomIncluded()
ResidueView.GetGeometricCenter()
ResidueView.AddAtom()
ResidueView.GetCenterOfAtoms()
ResidueView.GetAtomList()
ResidueView.Select()
AtomView
- Functions
- Residue Numbering
- ChainType
- ViewAddFlag
- SecStructure
- ChemClass
- ChemType
- The Handle Classes
- Editors
- Edit Modes
- Basic Editing Operations
EditorBase
EditorBase.InsertChain()
EditorBase.AppendResidue()
EditorBase.RenameResidue()
EditorBase.RenameChain()
EditorBase.SetChainType()
EditorBase.SetChainDescription()
EditorBase.InsertAtom()
EditorBase.InsertAltAtom()
EditorBase.InsertAltAtom()
EditorBase.AddAltAtomPos()
EditorBase.AddTorsion()
EditorBase.DeleteAtom()
EditorBase.DeleteAllAtoms()
EditorBase.DeleteAtoms()
EditorBase.DeleteResidue()
EditorBase.DeleteResidues()
EditorBase.DeleteChain()
EditorBase.ReorderResidues()
EditorBase.ReorderAllResidues()
EditorBase.RenumberAllResidues()
EditorBase.RenumberChain()
EditorBase.RenumberChain()
EditorBase.GetMode()
EditorBase.RenameAtom()
EditorBase.SetResidueNumber()
EditorBase.Connect()
EditorBase.Prune()
- Editor for the External Coordinate System
- Editor for the Internal Coordinate System
- Queries
- Surfaces
- Trajectories
CreateCoordGroup()
CoordGroupHandle
CoordGroupHandle.entity
CoordGroupHandle.atoms
CoordGroupHandle.AddFrames()
CoordGroupHandle.Capture()
CoordGroupHandle.CaptureInto()
CoordGroupHandle.CopyFrame()
CoordGroupHandle.Filter()
CoordGroupHandle.GetAtomCount()
CoordGroupHandle.GetAtomList()
CoordGroupHandle.GetAtomPos()
CoordGroupHandle.GetEntity()
CoordGroupHandle.GetFrameCount()
CoordGroupHandle.IsValid()
CoordGroupHandle.SetAtomPos()
CoordGroupHandle.SetFramePositions()
CoordFrame