Class with static functions providing higher-level molecule operations. More...

#include <Editing.h>

Static Public Member Functions
static std::pair< Molecule, Molecule >	cleave (const Molecule &a, BondIndex bridge)
	Splits a molecule along a bridge edge. More...

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

static Molecule	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...

static Molecule	substitute (const Molecule &left, const Molecule &right, BondIndex leftBond, BondIndex rightBond)
	Connect two molecules by substituting away the lighter side of a pair of bonds of separate molecules. More...

static Molecule	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...

static Molecule	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

Class with static functions providing higher-level molecule operations.

Member Function Documentation

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

static

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

static std::pair<Molecule, Molecule> Scine::Molassembler::Editing::cleave	(	const Molecule &	a,
		BondIndex	bridge
	)

static

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)

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

static

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

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

static

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

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

static

Connect two molecules by substituting away the lighter 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 heavy 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.

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

static

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

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

Molassembler/Editing.h

Static Public Member Functions

Detailed Description

Member Function Documentation