Node Class Reference

Represents a node in a graph. More...

#include <node.h>

Public Member Functions
	Node ()
	Default constructor for Node.
	~Node ()
	Destructor for Node.
	Node (unsigned int numFrames, unsigned int index_)
	Constructor for Node with specified number of frames and index.
void	addAtom (Atom *atom, CuArray< float > *coordinates, CuArray< float > *nodeCoordinates)
	Add an Atom to the Node.
std::string	tag ()
	Get the tag of the Node.
unsigned int	numAtoms () const
	Get the number of Atoms in the Node.
unsigned int	index () const
	Get the index of the Node.
float	totalMass () const
	Get the total mass of the Node.
unsigned int	hash () const
	Get the hash value of the Node.
std::vector< Atom * >	atoms () const
	Get a vector of pointers to the Atoms in the Node.

Private Attributes
unsigned int	_numAtoms
std::vector< int >	atomIndices_
unsigned int	_index
float	_totalMass
std::string	_tag
std::vector< Atom * >	atoms_
unsigned int	_hash = 0
unsigned int	_numFrames

Friends
class	Network

Detailed Description

Represents a node in a graph.

Constructor & Destructor Documentation

Node()

Node::Node	(	unsigned int	numFrames,
		unsigned int	index_
	)

Constructor for Node with specified number of frames and index.

Parameters

numFrames	Number of frames.
index_	Index of the node.

Member Function Documentation

addAtom()

void Node::addAtom	(	Atom *	atom,
		CuArray< float > *	coordinates,
		CuArray< float > *	nodeCoordinates
	)

Add an Atom to the Node.

Adds the specified Atom to the Node along with its corresponding coordinates.

Parameters

atom	Pointer to the Atom object.
coordinates	Pointer to the coordinates array.
nodeCoordinates	Pointer to the node coordinates array.

atoms()

std::vector< Atom * > Node::atoms

(

)

const

Get a vector of pointers to the Atoms in the Node.

Returns a vector of pointers to the Atoms contained in the Node.

Returns

A vector of pointers to the Atoms in the Node.

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
)
 
"""
For this example, we will use the first node in the network.
"""
node = network.nodes()[0]
 
"""
To get a vector of all Atom objects in the node, use the atoms() method.
Unlike the atoms method in the Network class, this method returns a vector
of Atom objects instead of an Atoms object. This is for memory efficiency.
"""
atoms = node.atoms()
 
"""
The Atom object vector is iterable, indexable, and can be converted 
to a built-in Python list/tuple using the explicit list and tuple constructors.
"""
atoms_list = list(atoms)
atoms_tuple = tuple(atoms)
 
"""
Iterate over all atoms in the node and print their information. 
For more information on the Atom class, see the Atom class documentation.
"""
for atom in atoms:
    print(atom)
    print("-" * 80)

hash()

unsigned int Node::hash

(

)

const

Get the hash value of the Node.

Returns the hash value of the Node, which is a unique identifier based on its tag and index.

Returns

The hash value of the Node.

index()

unsigned int Node::index

(

)

const

Get the index of the Node.

Returns the index of the Node.

Returns

The index of the Node.

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
)
 
"""
For this example, we will use the first node in the network.
"""
node = network.nodes()[0]
 
"""
Use the Node index method to get the index of the node.
"""
node_index = node.index()
print(node_index)

numAtoms()

unsigned int Node::numAtoms

(

)

const

Get the number of Atoms in the Node.

Returns the number of Atoms contained in the Node.

Returns

The number of Atoms in the Node.

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
)
 
"""
For this example, we will use the first node in the network.
"""
node = network.nodes()[0]
 
"""
Use the Node numAtoms method to get the number of atoms in the node.
"""
num_atoms = node.numAtoms()
print(num_atoms)

tag()

std::string Node::tag

(

)

Get the tag of the Node.

Returns the tag of the Node, which represents its unique identifier.

Returns

The tag of the Node.

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
)
 
"""
For this example, we will use the first node in the network.
"""
node = network.nodes()[0]
 
"""
Use the Node tag method to get the key used to 
identify Node atoms. By default, the tag is defined
as the concatenation of the residue name and residue
index, chain id, and fragment id an atom belongs to.
"""
node_tag = node.tag()
print(node_tag)

totalMass()

float Node::totalMass

(

)

const

Get the total mass of the Node.

Returns the total mass of the Node, calculated as the sum of the masses of all the Atoms in the Node.

Returns

The total mass of the Node.

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
)
 
"""
For this example, we will use the first node in the network.
"""
node = network.nodes()[0]
 
"""
Use the Node totalMass method to get the total mass of the node. 
"""
total_mass = node.totalMass()
print(total_mass)

---

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

• node.h