Editing of molecules past low-level member functions. More...

#include "Molassembler/Molecule.h"
#include "Molassembler/RankingInformation.h"
#include <tuple>

Include dependency graph for Editing.h:

Data Structures
struct	Scine::Molassembler::Editing::Cleaved

Namespaces
	Scine::Molassembler
	Central library namespace.

Typedefs
using	Scine::Molassembler::Editing::AtomSitePair = std::pair< AtomIndex, SiteIndex >
	Descriptor for an entire haptic site connected to an atom.

Functions
Cleaved	Scine::Molassembler::Editing::cleave (const Molecule &a, BondIndex bridge)
	Splits a molecule along a bridge edge. More...

Cleaved	Scine::Molassembler::Editing::cleave (const Molecule &a, AtomSitePair hapticSite)
	Splits a molecule at a haptic site. More...

Molecule	Scine::Molassembler::Editing::insert (Molecule log, const Molecule &wedge, BondIndex logBond, AtomIndex firstWedgeAtom, AtomIndex secondWedgeAtom)
	Inserts a molecule into a bond of another molecule. More...

Molecule	Scine::Molassembler::Editing::superpose (Molecule top, const Molecule &bottom, AtomIndex topAtom, AtomIndex bottomAtom)
	Fuses two molecules, adding all adjacencies and continuations of one Molecule's atoms to another. More...

Molecule	Scine::Molassembler::Editing::substitute (const Molecule &left, const Molecule &right, BondIndex leftBond, BondIndex rightBond)
	Connect two molecules by substituting away the smaller side of a pair of bonds of separate molecules. More...

Molecule	Scine::Molassembler::Editing::substitute (const Molecule &left, const Molecule &right, BondIndex leftBond, BondIndex rightBond, AtomIndex leftSubstituteIndex, AtomIndex rightSubstituteIndex)
	Connect two molecules by substituting away the defined side of a pair of bonds of separate molecules. More...

Molecule	Scine::Molassembler::Editing::connect (Molecule a, const Molecule &b, AtomIndex aConnectAtom, AtomIndex bConnectAtom, BondType bondType)
	Connect molecules by creating a new bond between two atoms from separate molecules. More...

Molecule	Scine::Molassembler::Editing::addLigand (Molecule a, const Molecule &ligand, AtomIndex complexatingAtom, const std::vector< AtomIndex > &ligandBindingAtoms)
	Connects two molecules by connecting multiple atoms from one to a single atom of the other via single bonds. More...

Detailed Description

Editing of molecules past low-level member functions.

Copyright: This code is licensed under the 3-clause BSD license. Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group. See LICENSE.txt for details.

Function Documentation

◆ addLigand()

Molecule Scine::Molassembler::Editing::addLigand	(	Molecule	a,
		const Molecule &	ligand,
		AtomIndex	complexatingAtom,
		const std::vector< AtomIndex > &	ligandBindingAtoms
	)

Connects two molecules by connecting multiple atoms from one to a single atom of the other via single bonds.

Complexity \(\Theta(N)\)

Parameters

a	The molecule the ligand is being connected to
ligand	The ligand molecule being bound to `complexatingAtom`
complexatingAtom	The atom in `a` that `ligand` is being bound to
ligandBindingAtoms	The atoms of `ligand` that should be connected to `a`

Returns: A joined molecule

◆ cleave() [1/2]

Cleaved Scine::Molassembler::Editing::cleave	(	const Molecule &	a,
		AtomSitePair	hapticSite
	)

Splits a molecule at a haptic site.

Parameters

hapticSite The haptic site to cleave the molecule at. Does not check if the site is conceptually a bridge of the graph. If it is not, splitting is not undefined.

Note: The first molecule always contains the atom to which the haptic site belonged.

Complexity \(\Theta(N)\)

Exceptions

std::invalid_argument If there is no stereopermutator on the specified atom.

◆ cleave() [2/2]

Cleaved Scine::Molassembler::Editing::cleave	(	const Molecule &	a,
		BondIndex	bridge
	)

Splits a molecule along a bridge edge.

Complexity \(\Theta(N)\)

Exceptions

std::logic_error

If bridge is not a bridge edge, i.e. the graph is not disconnected by cleaving the indicated bonds. This can be tested for using

a.graph().canRemove(bridge) == false)

.

Returns: A pair of molecules, ordered corresponding to the bond's atoms' position in the supplied bond index (i.e. .first contains the atom at bridge.first)

◆ connect()

Molecule Scine::Molassembler::Editing::connect	(	Molecule	a,
		const Molecule &	b,
		AtomIndex	aConnectAtom,
		AtomIndex	bConnectAtom,
		BondType	bondType
	)

Connect molecules by creating a new bond between two atoms from separate molecules.

Complexity \(\Theta(N)\)

Parameters

a	The first molecule to connect
b	The second molecule to connect
aConnectAtom	The atom index to connect to in `a`
bConnectAtom	The atom index to connect to in `b`
bondType	The type of the new bond

Note: This function is symmetric on exchanging the tuples (a, aConnectAtom), (b, bConnectAtom), i.e. the order of the molecule and atom index arguments does not matter as long as the atom indices are properly associated to their respective molecule.

Returns: A single molecule connected by the specified bond type at the indicated atoms

◆ insert()

Molecule Scine::Molassembler::Editing::insert	(	Molecule	log,
		const Molecule &	wedge,
		BondIndex	logBond,
		AtomIndex	firstWedgeAtom,
		AtomIndex	secondWedgeAtom
	)

Inserts a molecule into a bond of another molecule.

Complexity \(\Theta(N)\)

Parameters

log	The molecule being inserted into
wedge	The molecule being inserted
logBond	The bond in `log` into which `wedge` is being inserted into
firstWedgeAtom	The atom of wedge to bond to the first atom in `logBond`
secondWedgeAtom	The atom of wedge to bond to the second atom in `logBond`

Note: The bond type of the bond inserted into is reused in the new bonds to firstWedgeAtom and secondWedgeAtom.

Returns: A molecule inserted into the bond of another molecule

◆ substitute() [1/2]

Molecule Scine::Molassembler::Editing::substitute	(	const Molecule &	left,
		const Molecule &	right,
		BondIndex	leftBond,
		BondIndex	rightBond
	)

Connect two molecules by substituting away the smaller side of a pair of bonds of separate molecules.

Complexity \(\Theta(N)\)

Parameters

left	The first molecule
right	The second molecule
leftBond	`left's` bond from which to substitute the lighter part away
rightBond	`right's` bond from which to substitute the lighter part away

Note: The smaller side is chosen by number of atoms first, then molecular weight if the number of atoms is equal. Should both sides be equal in both, which side is picked is undefined.

◆ substitute() [2/2]

Molecule Scine::Molassembler::Editing::substitute	(	const Molecule &	left,
		const Molecule &	right,
		BondIndex	leftBond,
		BondIndex	rightBond,
		AtomIndex	leftSubstituteIndex,
		AtomIndex	rightSubstituteIndex
	)

Connect two molecules by substituting away the defined side of a pair of bonds of separate molecules.

Complexity \(\Theta(N)\)

Parameters

left	The first molecule
right	The second molecule
leftBond	`left's` bond from which to substitute the lighter part away
rightBond	`right's` bond from which to substitute the lighter part away
leftSubstituteIndex	The atom index of `left` to substitute away
rightSubstituteIndex	The atom index of `right` to substitute away

Note: The substituting indices must be contained in the respective bonds

◆ superpose()

Molecule Scine::Molassembler::Editing::superpose	(	Molecule	top,
		const Molecule &	bottom,
		AtomIndex	topAtom,
		AtomIndex	bottomAtom
	)

Fuses two molecules, adding all adjacencies and continuations of one Molecule's atoms to another.

Adds all adjacent atoms and continuations of bottomAtom in bottom to topAtom in top. topAtom's element type is unchanged as it is the 'top' of the superimposition / overlay.

Complexity \(\Theta(N)\)

Parameters

top	The molecule that is at the top of the superposition.
bottom	The molecule that is set at the bottom of the superposition.
topAtom	An atom index of `top` that is placed 'atop' `bottom's` `bottomAtom`
bottomAtom	An atom index of `bottom` that is placed 'beneath' `top's` `topAtom`

Returns: A single molecule fused at the specified atoms

Data Structures

Namespaces

Typedefs

Functions

Detailed Description

Function Documentation

◆ addLigand()

◆ cleave() [1/2]

◆ cleave() [2/2]

◆ connect()

◆ insert()

◆ substitute() [1/2]

◆ substitute() [2/2]

◆ superpose()