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()
- Entity Handle
EntityHandle
EntityHandle.properties
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()
- Chain Handle
ChainHandle
ChainHandle.properties
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()
- Residue Handle
ResidueHandle
ResidueHandle.properties
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()
- Atom Handle
AtomHandle
AtomHandle.properties
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()
- Bond Handle
BondHandle
BondHandle.properties
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
- Entity View
EntityView
EntityView.properties
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.ViewForHandle()
EntityView.ExtendViewToResidues()
EntityView.ExtendViewToSurrounding()
EntityView.Select()
EntityView.Copy()
EntityView.Dump()
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()
- Chain View
ChainView
ChainView.properties
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.ViewForHandle()
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()
- Residue View
ResidueView
ResidueView.properties
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.ViewForHandle()
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()
- Atom View
- Entity View
- 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.AddAltAtomPos()
EditorBase.AddTorsion()
EditorBase.DeleteAtom()
EditorBase.DeleteAllAtoms()
EditorBase.DeleteAtoms()
EditorBase.DeleteResidue()
EditorBase.DeleteResidues()
EditorBase.DeleteChain()
EditorBase.ReorderResidues()
EditorBase.ReorderAllResidues()
EditorBase.RenumberAllResidues()
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