6.8. Scanning Interface

class pharmaforge.interfaces.scanning.Scan(interface)[source]

Bases: object

This is a class for performing cans on a molecule using a calculator of your choice.

Parameters:: calculator (object) – The calculator to use for the calculations. This should be an instance of a class that inherits from AbstractIO.

calculator

The calculator to use for the calculations. This should be an instance of a class that inherits from AbstractIO.

Type:: object

torsion_angles

A list of torsion angles for the scan.

Type:: list

energies

A list of energies for the scan.

Type:: list

forces

A list of forces for the scan.

Type:: list

coordinates

A list of coordinates for the scan.

Type:: list

dihedrals

A list of dihedrals for the scan.

Type:: list

unit

The unit of the dihedral angle. Default is None.

Type:: str

initial_structure

The initial structure of the molecule.

Type:: ase.Atoms

atom_types

A list of atom types in the molecule.

Type:: list

mask

A list of atom indices that should be rotated.

Type:: list

See also

ase.neighborlist.NeighborList: The ASE neighbor list object used to determine connectivity.
MDAnalysis: The MDAnalysis library used for molecular dynamics analysis.
multiprocessing: The multiprocessing library used for parallel processing.

Methods

`add_initial_coordinates`(structure)	Add the initial coordinates of the molecule to the torsional scan.
`plot_scan`([save])	Plot the scan results.
`scan`([atoms, scan_range, mask, verbose, ...])	Perform a scan on the molecule.
`write_xyz`([filename])	Write the scan results to an XYZ file.

process_angle_scan
process_bond_scan
process_structure

add_initial_coordinates(structure)[source]

Add the initial coordinates of the molecule to the torsional scan.

Parameters:: structure (ase.Atoms) – The ASE atoms object containing the initial coordinates of the molecule.

plot_scan(save=None)[source]

Plot the scan results.

Parameters:: save (str) – The filename to save the plot. If None, the plot will be shown but not saved.

static process_angle_scan(args)[source]

static process_bond_scan(args)[source]

static process_structure(args)[source]

scan(atoms=None, scan_range=(0, 10, 1), mask=None, verbose=False, num_workers=1, charge=0, schedule=None, constrain=None, optimize=True)[source]

Perform a scan on the molecule.

Parameters:

atoms (list) – A list of atoms indices to scan. Must be length 2, 3, or 4.
scan_range (tuple) – A tuple containing the start, end, and step size of the scan. Default is (0,10,1).
mask (list) – A list of atom indices that should be rotated. If None, the function will automatically select the mask.
verbose (bool) – If True, print the dihedral angle being scanned.
num_workers (int) – The number of workers to use for parallel processing. Default is 1.
charge (int) – The net charge of the system. Default is 0.
schedule (str) – The schedule for the scan. Can be “linear” or “iterative”. Default is None, which means no schedule is applied.

Returns:

energies (list) – A list of energies for each scan point.
forces (list) – A list of forces for each scan point.
coordinates (list) – A list of coordinates for each scan point.

Raises:

ValueError – If the number of atoms is not 2, 3, or 4.

write_xyz(filename='scan.xyz')[source]

Write the scan results to an XYZ file.

Parameters:: filename (str) – The filename to save the XYZ file. Default is “scan.xyz”.