Atom

Full name SMRUCC.genomics.Data.RCSB.PDB.Structures.Atom Assembly SMRUCC.genomics.Data.RCSB.PDB Members 18

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

00 Remarks

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.

01 Syntax

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

02 Methods

Name	Overloads	Summary
CopyFrom	1	Copy all of the general field values from another atom instance.
CopyTo	1	Copy all of the general field values of current atom into another atom instance.

03 Properties

Name	Overloads	Summary
X	1	The X axis coordinate value in angstrom.
Y	1	The Y axis coordinate value in angstrom.
Z	1	The Z axis coordinate value in angstrom.
Element	1	The normalized element symbol, e.g.
Charge	1	The partial charge of current atom site.
ChainID	1	The chain identifier (PDB column 22).
ResName	1	The residue name (PDB column 18-20), in upper case.
ResSeq	1	The residue sequence number (PDB column 23-26).
AtomName	1	The atom name (PDB column 13-16).
Serial	1	The atom serial number (PDB column 7-11).
AltLoc	1	The alternate location indicator (PDB column 17).
Occupancy	1	The occupancy value (PDB column 55-60).
TempFactor	1	The temperature factor, aka B-factor (PDB column 61-66).
IsHet	1	Is current atom comes from a HETATM record? (False means the ATOM record)
IsWater	1	Is current atom a water molecule? (residue name is HOH or WAT)
Location	1	Get/set the atom spatial position as a point tuple in 3D space.

04 Members

method CopyFrom #

CopyFrom(Atom)

Copy all of the general field values from another atom instance.

Parameters

Name	Type	Description
`atom`	Atom	The atom model that provides the source field values.

method CopyTo #

CopyTo(Atom)

Copy all of the general field values of current atom into another atom instance.

Parameters

Name	Type	Description
`atom`	Atom	The atom model that accepts the field values.

property X #

The X axis coordinate value in angstrom.

property Y #

The Y axis coordinate value in angstrom.

property Z #

The Z axis coordinate value in angstrom.

property Element #

Element

The normalized element symbol, e.g. C/N/O/Cl/FE.

property Charge #

Charge

The partial charge of current atom site.

property ChainID #

ChainID

The chain identifier (PDB column 22).

property ResName #

ResName

The residue name (PDB column 18-20), in upper case.

property ResSeq #

ResSeq

The residue sequence number (PDB column 23-26).

property AtomName #

AtomName

The atom name (PDB column 13-16).

property Serial #

Serial

The atom serial number (PDB column 7-11).

property AltLoc #

AltLoc

The alternate location indicator (PDB column 17).

property Occupancy #

Occupancy

The occupancy value (PDB column 55-60).

property TempFactor #

TempFactor

The temperature factor, aka B-factor (PDB column 61-66).

property IsHet #

IsHet

Is current atom comes from a HETATM record? (False means the ATOM record)

property IsWater #

IsWater

Is current atom a water molecule? (residue name is HOH or WAT)

property Location #

Location

Get/set the atom spatial position as a point tuple in 3D space.

Remarks

This property is a value type view of the Atom.X, Atom.Y and Atom.Z fields, which is kept for the backward compatibility with the legacy Atom.Location property.