File BondDetector.h

Copyright

This code is licensed under the 3-clause BSD license.

Copyright ETH Zurich, Laboratory for Physical Chemistry, Reiher Group.

See LICENSE.txt for details.

namespace Scine

This header file contains functions that allow for common notation for common things that can be done at a different degree of derivatives.

This header contains alias definitions defining which classes to use for the different degrees of derivatives.

namespace Utils
class BondDetector
#include <BondDetector.h>

Detecting bonds from 3D structures using covalent radii.

The radii are stored in Scine::Utils::BondDetectorRadii .

References:

  • DOI: 10.1002/jcc.540120716

  • DOI: 10.1186/1758-2946-4-26

  • DOI: 10.1002/jcc.24309

Public Functions

BondDetector()

Static functions only.

Public Static Functions

static BondOrderCollection detectBonds(const AtomCollection &atoms)

Detect all bonds in an AtomCollection.

Return

BondOrderCollection The bonds.

Parameters

  • atoms: The collection of atoms.

static BondOrderCollection detectBonds(const ElementTypeCollection &elements, const PositionCollection &positions)

Detect all bonds based on elements and positions.

Return

BondOrderCollection The bonds.

Parameters

  • elements: The collection of elements.

  • positions: The collection of positions.

static bool bondExists(const ElementType &e1, const ElementType &e2, const Position &p1, const Position &p2)

Check if a bond exists between two atoms.

Return

true If a bond exists.

false If no bond exists.

Parameters

  • e1: The element of the first atom.

  • e2: The element of the second atom.

  • p1: The position of the first atom.

  • p2: The position of the second atom.

Private Static Functions

static double getCovalentRadius(ElementType e)

Get the covalent radius for a given element.

Return

double The covalent radius.

Parameters

  • e: The element.