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Package: Molecule

    Covalent structure of molecules; sequence of linear poymers (DNA. RNA, and proteins).
Data Types
Data Obj Types

Imported Packages:

ChemComp,   ChemCompCoord,   ccp.api.general.Citation,   ccp.api.general.DbRef,   ccp.api.general.Taxonomy,   memops.api.AccessControl,   memops.api.Implementation

Packages Importing ccp.api.molecule.Molecule:

LabeledMolecule,   MolSystem,   cambridge.api.Dangle,   ccp.api.general.Annotation,   ccp.api.lims.ExpBlueprint,   ccp.api.lims.RefSampleComponent,   ccp.api.nmr.Nmr,   ccp.api.nmr.NmrEntry,   ccp.api.nmr.NmrScreen,   ccpnmr.api.Analysis,   ccpnmr.api.NameMapping


Class Description
Alignment Alignment of molecule with database reference
MolResLink Link (bond) between two molResidues, through their MolResLinkEnds. MolResLinks that are valid for a Molecule are implicitly valid also for Chains linked to that Molecule. Unlike MolResLinkEnds, MolResLinks can be created (or modified) for existing molecules, even if the Molecule is linked to one or more Chains. This allows linkages to be redefined, or to be left as initially unknown (as in the case of a protein with unknown disulfide binding topology).
MolResLinkEnd The MolResidue end (Link End) of a bond to another MolResidue
The MolResLinkEnds corresponding to a MolResidue are created automatically when the MolResidue is created.
Note that MolResLinkEnds can neither be created nor deleted while their ancestor Molecule is linked to one or more chains.
MolResidue Monomer/Residue belonging to a Molecule, e.g. in the sequence for Insulin A-chain as such, as opposed to a specific Insulin A-chain molecule with coordinates.

Note that MolResidues can neither be created nor deleted while their parent Molecule is linked to one or more chains. When creating a Molecule all relevant MolResLinkEnds are created automatically.
Note also that MolResidues can not be deleted, except as a consequence of deleting their molecule.

It is guaranteed that the serials of molResidues form a continuous range, and that all linear polymer type links are between MolResidues with consecutive serials. The Molesidue.serials must start at one. This constraint is not checked (for technical reasons), but it can only be broken if someone has modified the data bypassing the API.
MolSeqFragment Block of molResidues with consecutive serials in a molecule . For linear polymers this is guaranteed to be a connected fragment of the molecule. For other molecules the set of Molresidues selected may or may not be connected, depending on how the molecule was created. MolSeqFragments are disjoint and no residue can be a member of more than one.
Molecule Abstract molecule, with defined topology but no location, coordinates, etc.
MoleculeSysName Molecule systematic name in a given naming system.

Data Obj Types:

Type Description

Data Types:

Type Description
LinkDihedralAngle Data Type for approximate dihedral angle across an interresidue bond, in degrees. Serves to specify the conformation across rotationally hindered bonds.
MolType This is an open enumeration for the type of Molecule and MolComponent.
SecStrucCode Secondary Structure Code, or DSSP code (Kabsch and Sander)
Values are :
H: 4-membered (alpha) helix
B: beta bridge
E: (extended) beta strand.
G: three-membered helix (3/01 helix)
I: five-membered (pi) helix
T: hydrogen-bonded turn
S: Bend (non-hydrogen bonded)
C: Random coil - not in a stable coformation
U: Undefined.
SmilesType Type of smiles string

Package guid:
  Data Model Version 2.0.5
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  Autogenerated by  PyApiDocGen  revision 1.3   on  Mon Mar 26 16:58:15 2012    from data model package  ccp.api.molecule.Molecule   revision 1.46  
  Work done by the CCPN team.