Atoms Class Reference

Public Member Functions
	Atoms ()
	Default constructor for Atoms.
void	addAtom (Atom *atom)
	Add an Atom to the Atoms collection.
int	numAtoms () const
	Get the number of Atoms in the collection.
Atom *	at (int atomIndex)
	Get the Atom with the specified index.
int	numUniqueTags () const
	Get the number of unique Atom tags.
std::vector< Atom * > &	atoms ()
	Get a reference to the vector of Atoms.

Private Attributes
std::vector< Atom * >	atoms_
std::set< std::string >	uniqueTags_

Constructor & Destructor Documentation

Atoms()

Atoms::Atoms

(

)

Default constructor for Atoms.

Constructs an empty Atoms object.

Member Function Documentation

addAtom()

void Atoms::addAtom

(

Atom *

atom

)

Add an Atom to the Atoms collection.

Adds the specified Atom to the collection of Atoms.

Parameters

atom	Pointer to the Atom to add.

at()

Atom * Atoms::at

(

int

atomIndex

)

Get the Atom with the specified index.

Returns a pointer to the Atom with the specified index.

Parameters

atomIndex

The index of the Atom.

Returns

A pointer to the Atom with the specified 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
)
 
"""
Get the Network's Atoms class object using the Network atoms method.
"""
atoms = network.atoms()
 
"""
The Atoms class is a container like class for Atom objects.
The reason for using a custom container class to store Atom objects
instead of using an Atom vector is to have more control over memory
management.
"""
 
"""
The Atoms at method can be used to get the Atom object with an 
atom index equal to the provided index.
"""
atom = atoms.at(0)
print(atom)

atoms()

std::vector< Atom * > & Atoms::atoms

(

)

Get a reference to the vector of Atoms.

Returns a reference to the vector of Atoms.

Returns

A reference to the vector of Atoms.

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
)
 
"""
Get the Network's Atoms class object using the Network atoms method.
The Atoms class is a container like class for Atom objects.
The reason for using a custom container class to store Atom objects
instead of using an Atom vector is to have more control over memory
management.
"""
atoms = network.atoms()
 
"""
Use the Atoms atoms method to return a vector of Atom objects.
"""
atom_vector = atoms.atoms()
for atom in atom_vector:
    print(atom)
    print("-"*80)

numAtoms()

int Atoms::numAtoms

(

)

const

Get the number of Atoms in the collection.

Returns the number of Atoms in the collection.

Returns

The number of Atoms.

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
)
 
"""
Get the Network's Atoms class object using the Network atoms method.
The Atoms class is a container like class for Atom objects.
The reason for using a custom container class to store Atom objects
instead of using an Atom vector is to have more control over memory
management.
"""
atoms = network.atoms()
 
"""
Use the Atoms numAtoms method to get the number of atoms in the Atoms
object.
"""
num_atoms = atoms.numAtoms()
print(num_atoms)

numUniqueTags()

int Atoms::numUniqueTags

(

)

const

Get the number of unique Atom tags.

Returns the number of unique Atom tags. Atoms with the same tag belong to the same Node.

Returns

The number of unique Atom tags.

---

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

• atoms.h