Public Member Functions
	Atom ()
	Default constructor for Atom.

	Atom (const std::string &pdbLine)
	Constructor for Atom with PDB line.

	Atom (const std::string &pdbLine, int atomIndex)
	Constructor for Atom with PDB line and atom index.

int	index () const
	Get the atom index.

std::string	name ()
	Get the atom name.

std::string	element ()
	Get the atom element.

std::string	residueName ()
	Get the residue name.

int	residueId () const
	Get the residue ID.

std::string	chainId ()
	Get the chain ID.

std::string	segmentId ()
	Get the segment ID.

float	temperatureFactor () const
	Get the temperature factor.

float	occupancy () const
	Get the occupancy.

int	serial () const
	Get the serial number.

std::string	tag ()
	Get the atom tag.

float	mass () const
	Get the mass of the atom.

unsigned int	hash () const
	Get the hash of the atom.

float	x (CuArray< float > *coordinates, int frame, int numFrames) const
	Get the x-coordinate of the atom.

float	y (CuArray< float > *coordinates, int frame, int numFrames) const
	Get the y-coordinate of the atom.

float	z (CuArray< float > *coordinates, int frame, int numFrames) const
	Get the z-coordinate of the atom.

void	load (const std::string &jsonFile)
	Load atom information from a JSON file.

Private Attributes
int	_index

std::string	_name

std::string	_element

std::string	_residueName

int	_residueId

std::string	_chainId

std::string	_segmentId

float	_temperatureFactor

float	_occupancy

int	_serial

std::string	_tag

float	_mass

unsigned int	_hash

Constructor & Destructor Documentation

◆ Atom() [1/3]

Atom::Atom ( )

Default constructor for Atom.

Constructs an empty Atom object.

◆ Atom() [2/3]

Atom::Atom ( const std::string & pdbLine )

explicit

Constructor for Atom with PDB line.

Constructs an Atom object using the provided PDB line. The constructor parses the PDB line to extract the relevant atom information, such as index, name, element, residue name, residue ID, chain ID, segment ID, temperature factor, occupancy, serial number, atom tag, mass, and hash.

The PDB line should follow the standard PDB format for ATOM records as described in Section 9 of the PDB file format documentation:

See also: https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM

Parameters

pdbLine The PDB line containing atom information in the standard PDB format.

◆ Atom() [3/3]

Atom::Atom	(	const std::string &	pdbLine,
		int	atomIndex
	)

Constructor for Atom with PDB line and atom index.

Constructs an Atom object using the provided PDB line and atom index.

Parameters

pdbLine	The PDB line containing atom information.
atomIndex	The atom index.

Member Function Documentation

◆ chainId()

std::string Atom::chainId ( )

Get the chain ID.

Returns the chain ID.

Returns: The chain ID.

Python Example

from netchem import Network, data_files
 
"""
1000 frame Molecular Dynamics trajectory of a pyrophosphatase system.
The dcd is a binary coordinate file, and the pdb is a single frame 
topology file.
"""
dcd, pdb = data_files('pyro')
 
"""
Construct a network using the entire trajectory.
If you want to use only a subset of the trajectory, you can specify
the first frame, last frame, and stride.
"""
network = Network()
network.init(
    trajectoryFile=str(dcd), # Convert the dcd Path object to a string
    topologyFile=str(pdb), # Convert the pdb Path object to a string
    firstFrame=0,
    lastFrame=999,
    stride=1
)
 
"""
We will use the first atom in the first node for this example.
"""
atom = network.nodes()[0].atoms()[0]
 
"""
Use the Atom chainId method to get the chain ID of the atom.
"""
print(atom.chainId())

◆ element()

std::string Atom::element ( )

Get the atom element.

Returns the atom element.

Returns: The atom element.

Python Example

from netchem import Network, data_files
 
"""
1000 frame Molecular Dynamics trajectory of a pyrophosphatase system.
The dcd is a binary coordinate file, and the pdb is a single frame 
topology file.
"""
dcd, pdb = data_files('pyro')
 
"""
Construct a network using the entire trajectory.
If you want to use only a subset of the trajectory, you can specify
the first frame, last frame, and stride.
"""
network = Network()
network.init(
    trajectoryFile=str(dcd), # Convert the dcd Path object to a string
    topologyFile=str(pdb), # Convert the pdb Path object to a string
    firstFrame=0,
    lastFrame=999,
    stride=1
)
 
"""
We will use the first atom in the first node for this example.
"""
atom = network.nodes()[0].atoms()[0]
 
"""
Use the Atom element method to get the atom's element symbol. 
"""
print(atom.element())

◆ hash()

unsigned int Atom::hash ( ) const

Get the hash of the atom.

Returns the hash of the atom, which is calculated from the atom tag concatenated with the atom index.

Returns: The hash of the atom.

◆ index()

int Atom::index ( ) const

Get the atom index.

Returns the atom index.

Returns: The atom index.

Python Example

from netchem import Network, data_files
 
"""
1000 frame Molecular Dynamics trajectory of a pyrophosphatase system.
The dcd is a binary coordinate file, and the pdb is a single frame 
topology file.
"""
dcd, pdb = data_files('pyro')
 
"""
Construct a network using the entire trajectory.
If you want to use only a subset of the trajectory, you can specify
the first frame, last frame, and stride.
"""
network = Network()
network.init(
    trajectoryFile=str(dcd), # Convert the dcd Path object to a string
    topologyFile=str(pdb), # Convert the pdb Path object to a string
    firstFrame=0,
    lastFrame=999,
    stride=1
)
 
"""
We will use the first atom in the first node for this example.
"""
atom = network.nodes()[0].atoms()[0]
 
"""
Use the Atom index method to get the atom's index. 
"""
print(atom.index())

◆ load()

void Atom::load ( const std::string & jsonFile )

Load atom information from a JSON file.

Loads atom information from the specified JSON file.

Parameters

jsonFile The name of the JSON file to load.

◆ mass()

float Atom::mass ( ) const

Get the mass of the atom.

Returns the mass of the atom.

Returns: The mass of the atom.

Python Example

from netchem import Network, data_files
 
"""
1000 frame Molecular Dynamics trajectory of a pyrophosphatase system.
The dcd is a binary coordinate file, and the pdb is a single frame 
topology file.
"""
dcd, pdb = data_files('pyro')
 
"""
Construct a network using the entire trajectory.
If you want to use only a subset of the trajectory, you can specify
the first frame, last frame, and stride.
"""
network = Network()
network.init(
    trajectoryFile=str(dcd), # Convert the dcd Path object to a string
    topologyFile=str(pdb), # Convert the pdb Path object to a string
    firstFrame=0,
    lastFrame=999,
    stride=1
)
 
"""
We will use the first atom in the first node for this example.
"""
atom = network.nodes()[0].atoms()[0]
 
"""
Use the Atom mass method to get the atom's mass. 
"""
print(atom.mass())

◆ name()

std::string Atom::name ( )

Get the atom name.

Returns the atom name.

Returns: The atom name.

Python Example

from netchem import Network, data_files
 
"""
1000 frame Molecular Dynamics trajectory of a pyrophosphatase system.
The dcd is a binary coordinate file, and the pdb is a single frame 
topology file.
"""
dcd, pdb = data_files('pyro')
 
"""
Construct a network using the entire trajectory.
If you want to use only a subset of the trajectory, you can specify
the first frame, last frame, and stride.
"""
network = Network()
network.init(
    trajectoryFile=str(dcd), # Convert the dcd Path object to a string
    topologyFile=str(pdb), # Convert the pdb Path object to a string
    firstFrame=0,
    lastFrame=999,
    stride=1
)
 
"""
We will use the first atom in the first node for this example.
"""
atom = network.nodes()[0].atoms()[0]
 
"""
Use the Atom name method to get the PDB name of the atom. 
"""
print(atom.name())

◆ occupancy()

float Atom::occupancy ( ) const

Get the occupancy.

Returns the occupancy.

Returns: The occupancy.

Python Example

from netchem import Network, data_files
 
"""
1000 frame Molecular Dynamics trajectory of a pyrophosphatase system.
The dcd is a binary coordinate file, and the pdb is a single frame 
topology file.
"""
dcd, pdb = data_files('pyro')
 
"""
Construct a network using the entire trajectory.
If you want to use only a subset of the trajectory, you can specify
the first frame, last frame, and stride.
"""
network = Network()
network.init(
    trajectoryFile=str(dcd), # Convert the dcd Path object to a string
    topologyFile=str(pdb), # Convert the pdb Path object to a string
    firstFrame=0,
    lastFrame=999,
    stride=1
)
 
"""
We will use the first atom in the first node for this example.
"""
atom = network.nodes()[0].atoms()[0]
 
"""
Use the Atom occupancy method to get the atom's occupancy number. 
"""
print(atom.occupancy())

◆ residueId()

int Atom::residueId ( ) const

Get the residue ID.

Returns the residue ID.

Returns: The residue ID.

Python Example

from netchem import Network, data_files
 
"""
1000 frame Molecular Dynamics trajectory of a pyrophosphatase system.
The dcd is a binary coordinate file, and the pdb is a single frame 
topology file.
"""
dcd, pdb = data_files('pyro')
 
"""
Construct a network using the entire trajectory.
If you want to use only a subset of the trajectory, you can specify
the first frame, last frame, and stride.
"""
network = Network()
network.init(
    trajectoryFile=str(dcd), # Convert the dcd Path object to a string
    topologyFile=str(pdb), # Convert the pdb Path object to a string
    firstFrame=0,
    lastFrame=999,
    stride=1
)
 
"""
We will use the first atom in the first node for this example.
"""
atom = network.nodes()[0].atoms()[0]
 
"""
Use the Atom residueId method to get the residue ID that the atom belongs to. 
"""
print(atom.residueId())

◆ residueName()

std::string Atom::residueName ( )

Get the residue name.

Returns the residue name.

Returns: The residue name.

Python Example

from netchem import Network, data_files
 
"""
1000 frame Molecular Dynamics trajectory of a pyrophosphatase system.
The dcd is a binary coordinate file, and the pdb is a single frame 
topology file.
"""
dcd, pdb = data_files('pyro')
 
"""
Construct a network using the entire trajectory.
If you want to use only a subset of the trajectory, you can specify
the first frame, last frame, and stride.
"""
network = Network()
network.init(
    trajectoryFile=str(dcd), # Convert the dcd Path object to a string
    topologyFile=str(pdb), # Convert the pdb Path object to a string
    firstFrame=0,
    lastFrame=999,
    stride=1
)
 
"""
We will use the first atom in the first node for this example.
"""
atom = network.nodes()[0].atoms()[0]
 
"""
Use the Atom residueName method to get the name of the residue that the atom belongs to. 
"""
print(atom.residueName())

◆ segmentId()

std::string Atom::segmentId ( )

Get the segment ID.

Returns the segment ID.

Returns: The segment ID.

Python Example

from netchem import Network, data_files
 
"""
1000 frame Molecular Dynamics trajectory of a pyrophosphatase system.
The dcd is a binary coordinate file, and the pdb is a single frame 
topology file.
"""
dcd, pdb = data_files('pyro')
 
"""
Construct a network using the entire trajectory.
If you want to use only a subset of the trajectory, you can specify
the first frame, last frame, and stride.
"""
network = Network()
network.init(
    trajectoryFile=str(dcd), # Convert the dcd Path object to a string
    topologyFile=str(pdb), # Convert the pdb Path object to a string
    firstFrame=0,
    lastFrame=999,
    stride=1
)
 
"""
We will use the first atom in the first node for this example.
"""
atom = network.nodes()[0].atoms()[0]
 
"""
Use the Atom segmentId method to get the ID of the segment that the atom belongs to. 
"""
print(atom.segmentId())

◆ serial()

int Atom::serial ( ) const

Get the serial number.

Returns the serial number, which is one greater than the atom index.

Returns: The serial number.

Python Example

from netchem import Network, data_files
 
"""
1000 frame Molecular Dynamics trajectory of a pyrophosphatase system.
The dcd is a binary coordinate file, and the pdb is a single frame 
topology file.
"""
dcd, pdb = data_files('pyro')
 
"""
Construct a network using the entire trajectory.
If you want to use only a subset of the trajectory, you can specify
the first frame, last frame, and stride.
"""
network = Network()
network.init(
    trajectoryFile=str(dcd), # Convert the dcd Path object to a string
    topologyFile=str(pdb), # Convert the pdb Path object to a string
    firstFrame=0,
    lastFrame=999,
    stride=1
)
 
"""
We will use the first atom in the first node for this example.
"""
atom = network.nodes()[0].atoms()[0]
 
"""
Use the Atom serial method to get the atom's serial number, which is 1 greater than the atom's index. 
"""
print(atom.serial())

◆ tag()

std::string Atom::tag ( )

Get the atom tag.

Returns the atom tag, which is the concatenation of the residue name, residue ID, chain ID, and segment ID.

Returns: The atom tag.

Python Example

from netchem import Network, data_files
 
"""
1000 frame Molecular Dynamics trajectory of a pyrophosphatase system.
The dcd is a binary coordinate file, and the pdb is a single frame 
topology file.
"""
dcd, pdb = data_files('pyro')
 
"""
Construct a network using the entire trajectory.
If you want to use only a subset of the trajectory, you can specify
the first frame, last frame, and stride.
"""
network = Network()
network.init(
    trajectoryFile=str(dcd), # Convert the dcd Path object to a string
    topologyFile=str(pdb), # Convert the pdb Path object to a string
    firstFrame=0,
    lastFrame=999,
    stride=1
)
 
"""
We will use the first atom in the first node for this example.
"""
atom = network.nodes()[0].atoms()[0]
 
"""
Use the Atom tag method to get the atom's node identifier tag, which is used to determine which 
node the atom belongs to. The tag is a concatenation of the atom's residue name, residue id, 
chain id, and segment id. 
"""
print(atom.residueId())

◆ temperatureFactor()

float Atom::temperatureFactor ( ) const

Get the temperature factor.

Returns the temperature factor.

Returns: The temperature factor.

Python Example

from netchem import Network, data_files
 
"""
1000 frame Molecular Dynamics trajectory of a pyrophosphatase system.
The dcd is a binary coordinate file, and the pdb is a single frame 
topology file.
"""
dcd, pdb = data_files('pyro')
 
"""
Construct a network using the entire trajectory.
If you want to use only a subset of the trajectory, you can specify
the first frame, last frame, and stride.
"""
network = Network()
network.init(
    trajectoryFile=str(dcd), # Convert the dcd Path object to a string
    topologyFile=str(pdb), # Convert the pdb Path object to a string
    firstFrame=0,
    lastFrame=999,
    stride=1
)
 
"""
We will use the first atom in the first node for this example.
"""
atom = network.nodes()[0].atoms()[0]
 
"""
Use the Atom temperatureFactor method to get the atom's temperature factor. 
"""
print(atom.temperatureFactor())

◆ x()

float Atom::x	(	CuArray< float > *	coordinates,
		int	frame,
		int	numFrames
	)		const

Get the x-coordinate of the atom.

Returns the x-coordinate of the atom at the specified frame.

Parameters

coordinates	The CuArray containing the coordinates.
frame	The frame index.
numFrames	The total number of frames.

Returns: The x-coordinate of the atom.

◆ y()

float Atom::y	(	CuArray< float > *	coordinates,
		int	frame,
		int	numFrames
	)		const

Get the y-coordinate of the atom.

Returns the y-coordinate of the atom at the specified frame.

Parameters

coordinates	The CuArray containing the coordinates.
frame	The frame index.
numFrames	The total number of frames.

Returns: The y-coordinate of the atom.

◆ z()

float Atom::z	(	CuArray< float > *	coordinates,
		int	frame,
		int	numFrames
	)		const

Get the z-coordinate of the atom.

Returns the z-coordinate of the atom at the specified frame.

Parameters

coordinates	The CuArray containing the coordinates.
frame	The frame index.
numFrames	The total number of frames.

Returns: The z-coordinate of the atom.

The documentation for this class was generated from the following file:

atom.h

Public Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ Atom() [1/3]

◆ Atom() [2/3]

◆ Atom() [3/3]

Member Function Documentation

◆ chainId()

◆ element()

◆ hash()

◆ index()

◆ load()

◆ mass()

◆ name()

◆ occupancy()

◆ residueId()

◆ residueName()

◆ segmentId()

◆ serial()

◆ tag()

◆ temperatureFactor()

◆ x()

◆ y()

◆ z()