Atom {SMRUCC.genomics.Data.RCSB.PDB.Structures}

.NET clr documentation

Atom

Description

The unified molecular atom model for the PDB/SDF structure readers.

This class is the single merged atom model of this library: it only carries the general physico-chemical fields (coordinates, element, partial charge, residue and chain annotations). Domain specific fields (e.g. the AutoDock Vina atom typing) should be placed on a derived type instead of polluting this base model.

Both of the legacy keyword level atom models (AtomUnit for ATOM records and HETATMRecord for HETATM records) are inherited from this class, so that the fixed-column parsing logic can be shared in one place.

Declare

            
# namespace SMRUCC.genomics.Data.RCSB.PDB.Structures
export class Atom {
   # The alternate location indicator (PDB column 17).
   AltLoc: string;
   # The atom name (PDB column 13-16).
   AtomName: string;
   # The chain identifier (PDB column 22).
   ChainID: string;
   # The partial charge of current atom site.
   Charge: double;
   # The normalized element symbol, e.g. C/N/O/Cl/FE.
   Element: string;
   # Is current atom comes from a HETATM record? (False means the ATOM record)
   IsHet: boolean;
   # Is current atom a water molecule? (residue name is HOH or WAT)
   IsWater: boolean;
   # Get/set the atom spatial position as a point tuple in 3D space.
   Location: Point3D;
   # The occupancy value (PDB column 55-60).
   Occupancy: double;
   # The residue name (PDB column 18-20), in upper case.
   ResName: string;
   # The residue sequence number (PDB column 23-26).
   ResSeq: integer;
   # The atom serial number (PDB column 7-11).
   Serial: integer;
   # The temperature factor, aka B-factor (PDB column 61-66).
   TempFactor: double;
   # The X axis coordinate value in angstrom.
   X: double;
   # The Y axis coordinate value in angstrom.
   Y: double;
   # The Z axis coordinate value in angstrom.
   Z: double;
}

        

.NET clr type reference tree

1. use by property member Location: Point3D

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