| Atom {SMRUCC.genomics.Data.RCSB.PDB.Structures} | .NET clr documentation |
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 @T:SMRUCC.genomics.Data.RCSB.PDB.Keywords.HETATM.HETATMRecord for HETATM records) are inherited from this class, so that the fixed-column parsing logic can be shared in one place.
# 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;
}
Location: Point3D