mol – Molecular structures and surfaces

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_atoms
      • EntityHandle.center_of_mass
      • EntityHandle.geometric_center
      • 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.GetMass()
      • EntityHandle.GetCenterOfAtoms()
      • EntityHandle.GetCenterOfMass()
      • EntityHandle.GetGeometricCenter()
      • EntityHandle.GetPositions()
      • EntityHandle.FindWithin()
      • EntityHandle.IsValid()
    • ChainHandle
      • ChainHandle.atoms
      • ChainHandle.bounds
      • ChainHandle.center_of_atoms
      • ChainHandle.center_of_mass
      • ChainHandle.geometric_center
      • 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.hash_code
      • 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.GetHashCode()
      • ChainHandle.IsValid()
    • ResidueHandle
      • ResidueHandle.name
      • ResidueHandle.qualified_name
      • ResidueHandle.number
      • ResidueHandle.one_letter_code
      • ResidueHandle.atoms
      • ResidueHandle.atom_count
      • ResidueHandle.bond_count
      • ResidueHandle.bounds
      • ResidueHandle.mass
      • ResidueHandle.center_of_atoms
      • ResidueHandle.center_of_mass
      • ResidueHandle.geometric_center
      • ResidueHandle.chain
      • ResidueHandle.phi_torsion
      • ResidueHandle.psi_torsion
      • ResidueHandle.omega_torsion
      • ResidueHandle.chem_class
      • ResidueHandle.chem_type
      • ResidueHandle.sec_structure
      • ResidueHandle.is_ligand
      • ResidueHandle.is_protein
      • ResidueHandle.peptide_linking
      • ResidueHandle.nucleotide_linking
      • ResidueHandle.index
      • ResidueHandle.central_atom
      • ResidueHandle.central_normal
      • ResidueHandle.hash_code
      • ResidueHandle.valid
      • ResidueHandle.next
      • ResidueHandle.prev
      • ResidueHandle.FindAtom()
      • ResidueHandle.HasAltAtoms()
      • ResidueHandle.HasAltAtomGroup()
      • ResidueHandle.GetAltAtomGroupNames()
      • ResidueHandle.GetCurrentAltGroupName()
      • ResidueHandle.SwitchAtomPos()
      • ResidueHandle.GetName()
      • ResidueHandle.GetQualifiedName()
      • ResidueHandle.GetNumber()
      • ResidueHandle.GetOneLetterCode()
      • ResidueHandle.GetAtomList()
      • ResidueHandle.GetAtomCount()
      • ResidueHandle.GetBondCount()
      • ResidueHandle.GetBounds()
      • ResidueHandle.GetMass()
      • ResidueHandle.GetCenterOfAtoms()
      • ResidueHandle.GetCenterOfMass()
      • ResidueHandle.GetGeometricCenter()
      • ResidueHandle.GetChain()
      • ResidueHandle.GetPhiTorsion()
      • ResidueHandle.GetPsiTorsion()
      • ResidueHandle.GetOmegaTorsion()
      • ResidueHandle.GetChemClass()
      • ResidueHandle.GetChemType()
      • ResidueHandle.GetSecStructure()
      • ResidueHandle.IsLigand()
      • ResidueHandle.IsProtein()
      • ResidueHandle.IsPeptideLinking()
      • ResidueHandle.IsNucleotideLinking()
      • ResidueHandle.GetIndex()
      • ResidueHandle.GetCentralAtom()
      • ResidueHandle.SetCentralAtom()
      • ResidueHandle.GetCentralNormal()
      • ResidueHandle.GetHashCode()
      • ResidueHandle.IsValid()
      • ResidueHandle.SetIsLigand()
      • ResidueHandle.SetIsProtein()
      • ResidueHandle.GetNext()
      • ResidueHandle.GetPrev()
    • 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()
    • BondHandle
      • BondHandle.first
      • BondHandle.second
      • BondHandle.pos
      • BondHandle.length
      • BondHandle.bond_order
      • BondHandle.hash_code
      • BondHandle.valid
      • BondHandle.GetFirst()
      • BondHandle.GetSecond()
      • BondHandle.GetPos()
      • BondHandle.GetLength()
      • BondHandle.GetBondOrder()
      • BondHandle.GetOther()
      • BondHandle.SetBondOrder()
      • BondHandle.IsValid()
      • BondHandle.GetHashCode()
  • The View Classes
    • EntityView
      • EntityView.handle
      • EntityView.chains
      • EntityView.chain_count
      • EntityView.residues
      • EntityView.residue_count
      • EntityView.atoms
      • EntityView.atom_count
      • EntityView.bounds
      • EntityView.mass
      • EntityView.center_of_atoms
      • EntityView.center_of_mass
      • EntityView.geometric_center
      • 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.handle
      • ChainView.hash_code
      • ChainView.name
      • ChainView.residues
      • ChainView.in_sequence
      • ChainView.atoms
      • ChainView.bounds
      • ChainView.mass
      • ChainView.center_of_atoms
      • ChainView.center_of_mass
      • ChainView.geometric_center
      • ChainView.valid
      • ChainView.AddAtom()
      • ChainView.AddResidue()
      • ChainView.FindAtom()
      • ChainView.FindResidue()
      • ChainView.GetCenterOfAtoms()
      • ChainView.GetCenterOfMass()
      • ChainView.GetEntity()
      • ChainView.GetGeometricCenter()
      • ChainView.GetHandle()
      • ChainView.GetHashCode()
      • ChainView.GetMass()
      • ChainView.GetName()
      • ChainView.GetResidueByIndex()
      • ChainView.GetResidueList()
      • ChainView.InSequence()
      • ChainView.IsValid()
      • ChainView.RemoveResidue()
      • ChainView.RemoveResidues()
      • ChainView.Select()
    • ResidueView
      • ResidueView.handle
      • ResidueView.hash_code
      • ResidueView.name
      • ResidueView.qualified_name
      • ResidueView.number
      • ResidueView.one_letter_code
      • ResidueView.bounds
      • ResidueView.mass
      • ResidueView.center_of_atoms
      • ResidueView.center_of_mass
      • ResidueView.geometric_center
      • ResidueView.phi_torsion
      • ResidueView.psi_torsion
      • ResidueView.omega_torsion
      • ResidueView.chem_class
      • ResidueView.chem_type
      • ResidueView.sec_structure
      • ResidueView.is_ligand
      • ResidueView.is_protein
      • ResidueView.peptide_linking
      • ResidueView.nucleotide_linking
      • ResidueView.central_atom
      • ResidueView.central_normal
      • ResidueView.valid
      • ResidueView.next
      • ResidueView.prev
      • ResidueView.atoms
      • ResidueView.atom_count
      • ResidueView.chain
      • ResidueView.index
      • ResidueView.RemoveAtom()
      • ResidueView.GetHandle()
      • ResidueView.GetHashCode()
      • ResidueView.GetName()
      • ResidueView.GetQualifiedName()
      • ResidueView.GetNumber()
      • ResidueView.GetOneLetterCode()
      • ResidueView.GetBounds()
      • ResidueView.GetMass()
      • ResidueView.GetCenterOfAtoms()
      • ResidueView.GetCenterOfMass()
      • ResidueView.GetGeometricCenter()
      • ResidueView.GetPhiTorsion()
      • ResidueView.GetPsiTorsion()
      • ResidueView.GetOmegaTorsion()
      • ResidueView.GetChemClass()
      • ResidueView.GetChemType()
      • ResidueView.GetSecStructure()
      • ResidueView.IsLigand()
      • ResidueView.SetIsLigand()
      • ResidueView.IsProtein()
      • ResidueView.IsPeptideLinking()
      • ResidueView.IsNucleotideLinking()
      • ResidueView.GetCentralAtom()
      • ResidueView.SetCentralAtom()
      • ResidueView.GetCentralNormal()
      • ResidueView.IsValid()
      • ResidueView.GetNext()
      • ResidueView.GetPrev()
      • ResidueView.GetChain()
      • ResidueView.FindAtom()
      • ResidueView.IsAtomIncluded()
      • ResidueView.AddAtom()
      • ResidueView.GetAtomList()
      • ResidueView.GetAtomCount()
      • ResidueView.GetIndex()
      • ResidueView.Select()
    • AtomView
      • AtomView.handle
      • AtomView.hash_code
      • AtomView.GetHandle()
      • AtomView.GetHashCode()
  • Functions
    • Boolean Operators
      • Intersection()
      • Difference()
      • Union()
    • Other Entity-Related Functions
      • CreateViewFromAtomList()
      • CreateEntityFromView()
      • InSequence()
      • BondExists()
  • Residue Numbering
    • ResNum
      • ResNum.num
      • ResNum.ins_code
      • ResNum.GetNum()
      • ResNum.GetInsCode()
  • ChainType
    • ChainType
    • ChainTypeFromString()
    • StringFromChainType()
  • ViewAddFlag
    • ViewAddFlag
  • SecStructure
    • SecStructure
      • SecStructure.IsHelical()
      • SecStructure.IsExtended()
      • SecStructure.IsCoil()
      • SecStructure.__str__()
      • SecStructure.Type
  • ChemClass
    • ChemClass
      • ChemClass.IsPeptideLinking()
      • ChemClass.IsNucleotideLinking()
  • ChemType
    • ChemType
      • ChemType.IsIon()
      • ChemType.IsNucleotide()
      • ChemType.IsSaccharide()
      • ChemType.IsAminoAcid()
      • ChemType.IsCoenzyme()
      • ChemType.IsDrug()
      • ChemType.IsNonCanonical()
      • ChemType.IsWater()
      • ChemType.IsKnown()
• 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
    • XCSEditor
      • XCSEditor.ApplyTransform()
      • XCSEditor.ApplyTransform()
      • XCSEditor.SetTransform()
      • XCSEditor.SetTransform()
      • XCSEditor.FixTransform()
      • XCSEditor.UpdateICS()
      • XCSEditor.ForceUpdate()
      • XCSEditor.SetAtomPos()
      • XCSEditor.SetAtomTransformedPos()
      • XCSEditor.SetAtomOriginalPos()
  • Editor for the Internal Coordinate System
    • ICSEditor
      • ICSEditor.SetTorsionAngle()
      • ICSEditor.SetTorsionAngle()
      • ICSEditor.RotateTorsionAngle()
      • ICSEditor.RotateTorsionAngle()
      • ICSEditor.UpdateXCS()
      • ICSEditor.SetBondLength()
      • ICSEditor.SetAngle()
• Queries
  • The Basics
    • Combining predicates
    • Distance Queries
    • Bonds and Queries
    • Whole Residue Queries
    • More Query Usage
    • Generic Properties in Queries
  • Available Properties
    • Properties of Chains
    • Properties of Residues
    • Properties of Atoms
  • Query API documentation
    • Query
      • Query.string
      • Query.valid
      • Query.error
      • Query.IsAtomSelected()
      • Query.IsChainSelected()
      • Query.IsResidueSelected()
    • QueryFlag
    • QueryQuoteName()
• Surfaces
  • SurfaceHandle
    • SurfaceHandle.Attach()
    • SurfaceHandle.FindWithin()
    • SurfaceHandle.GetTriIDList()
    • SurfaceHandle.GetVertex()
    • SurfaceHandle.GetVertexIDList()
    • SurfaceHandle.Invert()
  • SurfaceVertex
    • SurfaceVertex.SurfaceVertex()
    • SurfaceVertex.Atom
    • SurfaceVertex.Normal
    • SurfaceVertex.Position
  • SurfaceVertexList
    • SurfaceVertexList.append()
    • SurfaceVertexList.extend()
  • SurfaceTriIDList
    • SurfaceTriIDList.append()
    • SurfaceTriIDList.extend()
• 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
    • CoordFrame.GetAngle()
    • CoordFrame.GetAtomPos()
    • CoordFrame.GetCenterOfMassPos()
    • CoordFrame.GetDihedralAngle()
    • CoordFrame.GetDistanceBetwAtoms()
    • CoordFrame.GetDistanceBetwCenterOfMass()
    • CoordFrame.GetRMSD()