Class containing a fragment of a molecule that has already been embedded. More...

#include <EmbeddedFrag.h>

Public Member Functions
	EmbeddedFrag ()
	Default constructor.

	EmbeddedFrag (unsigned int aid, const RDKit::ROMol *mol)
	Initializer from a single atom id.

	EmbeddedFrag (const RDKit::ROMol *mol, const RDGeom::INT_POINT2D_MAP &coordMap)
	Constructor when the coordinates have been specified for a set of atoms.

	EmbeddedFrag (const RDKit::ROMol *mol, const RDKit::VECT_INT_VECT &fusedRings, bool useRingTemplates)
	Initializer from a set of fused rings.

	EmbeddedFrag (const RDKit::Bond *dblBond)
	Initializer for a cis/trans system using the double bond.

void	expandEfrag (RDKit::INT_LIST &nratms, std::list< EmbeddedFrag > &efrags)

void	addNonRingAtom (unsigned int aid, unsigned int toAid)
	Add a new non-ring atom to this object.

void	mergeNoCommon (EmbeddedFrag &embObj, unsigned int toAid, unsigned int nbrAid)
	Merge this embedded object with another embedded fragment.

void	mergeWithCommon (EmbeddedFrag &embObj, RDKit::INT_VECT &commAtms)
	Merge this embedded object with another embedded fragment.

void	mergeFragsWithComm (std::list< EmbeddedFrag > &efrags)

void	markDone ()
	Mark this fragment to be done for final embedding.

bool	isDone ()
	If this fragment done for the final embedding.

const RDKit::ROMol *	getMol () const
	Get the molecule that this embedded fragment belongs to.

RDKit::INT_VECT	findCommonAtoms (const EmbeddedFrag &efrag2)
	Find the common atom ids between this fragment and a second one.

int	findNeighbor (unsigned int aid)
	Find a neighbor to a non-ring atom among the already embedded atoms.

void	Transform (const RDGeom::Transform2D &trans)
	Transform this object to a new coordinates system.

void	Reflect (const RDGeom::Point2D &loc1, const RDGeom::Point2D &loc2)

const INT_EATOM_MAP &	GetEmbeddedAtoms () const

void	Translate (const RDGeom::Point2D &shift)

EmbeddedAtom	GetEmbeddedAtom (unsigned int aid) const

int	Size () const
	the number of atoms in the embedded system

void	computeBox ()
	compute a box that encloses the fragment

void	flipAboutBond (unsigned int bondId, bool flipEnd=true)
	Flip atoms on one side of a bond - used in removing collisions.

void	openAngles (const double *dmat, unsigned int aid1, unsigned int aid2)

std::vector< PAIR_I_I >	findCollisions (const double *dmat, bool includeBonds=1)

void	computeDistMat (DOUBLE_SMART_PTR &dmat)

double	mimicDistMatAndDensityCostFunc (const DOUBLE_SMART_PTR *dmat, double mimicDmatWt)

void	permuteBonds (unsigned int aid, unsigned int aid1, unsigned int aid2)

void	randomSampleFlipsAndPermutations (unsigned int nBondsPerSample=3, unsigned int nSamples=100, int seed=100, const DOUBLE_SMART_PTR *dmat=nullptr, double mimicDmatWt=0.0, bool permuteDeg4Nodes=false)

void	removeCollisionsBondFlip ()

void	removeCollisionsOpenAngles ()
	Remove collision by opening angles at the offending atoms.

void	removeCollisionsShortenBonds ()

void	setupNewNeighs ()
	helpers functions to

void	updateNewNeighs (unsigned int aid)
	update the unembedded neighbor atom list for a specified atom

int	findNumNeigh (const RDGeom::Point2D &pt, double radius)
	Find all atoms in this embedded system that are within a specified distant of a point.

double	getBoxPx ()

double	getBoxNx ()

double	getBoxPy ()

double	getBoxNy ()

void	canonicalizeOrientation ()

Detailed Description

Class containing a fragment of a molecule that has already been embedded.

Definition at line 146 of file EmbeddedFrag.h.

Constructor & Destructor Documentation

◆ EmbeddedFrag() [1/5]

RDDepict::EmbeddedFrag::EmbeddedFrag ( )

inline

Default constructor.

Definition at line 153 of file EmbeddedFrag.h.

◆ EmbeddedFrag() [2/5]

RDDepict::EmbeddedFrag::EmbeddedFrag	(	unsigned int	aid,
		const RDKit::ROMol *	mol
	)

Initializer from a single atom id.

A single Embedded Atom with this atom ID is added and placed at the origin

◆ EmbeddedFrag() [3/5]

RDDepict::EmbeddedFrag::EmbeddedFrag	(	const RDKit::ROMol *	mol,
		const RDGeom::INT_POINT2D_MAP &	coordMap
	)

Constructor when the coordinates have been specified for a set of atoms.

This simply initialized a set of EmbeddedAtom to have the same coordinates as the one's specified. No testing is done to verify any kind of correctness. Also this fragment is less ready (to expand and add new neighbors) than when using other constructors. This is because:

the user may have specified coords for only a part of the atoms in a fused ring systems in which case we need to find these atoms and merge these ring systems to this fragment
The atoms are not yet aware of their neighbor (what is left to add etc.) this again depends on atoms properly so that new neighbors can be added to them

◆ EmbeddedFrag() [4/5]

RDDepict::EmbeddedFrag::EmbeddedFrag	(	const RDKit::ROMol *	mol,
		const RDKit::VECT_INT_VECT &	fusedRings,
		bool	useRingTemplates
	)

Initializer from a set of fused rings.

ARGUMENTS:

Parameters

mol	the molecule of interest
fusedRings	a vector of rings, each ring is a list of atom ids
useRingTemplates	whether to use ring system templates for generating initial coordinates

◆ EmbeddedFrag() [5/5]

RDDepict::EmbeddedFrag::EmbeddedFrag ( const RDKit::Bond * dblBond )

explicit

Initializer for a cis/trans system using the double bond.

ARGUMENTS:

Parameters

dblBond the double bond that is involved in the cis/trans configuration

Member Function Documentation

◆ addNonRingAtom()

void RDDepict::EmbeddedFrag::addNonRingAtom	(	unsigned int	aid,
		unsigned int	toAid
	)

Add a new non-ring atom to this object.

◆ canonicalizeOrientation()

void RDDepict::EmbeddedFrag::canonicalizeOrientation ( )

◆ computeBox()

void RDDepict::EmbeddedFrag::computeBox ( )

compute a box that encloses the fragment

◆ computeDistMat()

void RDDepict::EmbeddedFrag::computeDistMat ( DOUBLE_SMART_PTR & dmat )

◆ expandEfrag()

void RDDepict::EmbeddedFrag::expandEfrag	(	RDKit::INT_LIST &	nratms,
		std::list< EmbeddedFrag > &	efrags
	)

Expand this embedded system by adding neighboring atoms or other embedded systems

Note that both nratms and efrags are modified in this function as we start merging them with the current fragment

◆ findCollisions()

std::vector< PAIR_I_I > RDDepict::EmbeddedFrag::findCollisions	(	const double *	dmat,
		bool	includeBonds = `1`
	)

◆ findCommonAtoms()

RDKit::INT_VECT RDDepict::EmbeddedFrag::findCommonAtoms ( const EmbeddedFrag & efrag2 )

Find the common atom ids between this fragment and a second one.

◆ findNeighbor()

int RDDepict::EmbeddedFrag::findNeighbor ( unsigned int aid )

Find a neighbor to a non-ring atom among the already embedded atoms.

ARGUMENTS:

Parameters

aid	the atom id of interest

RETURNS:

Returns: the id of the atom if we found a neighbor -1 otherwise

NOTE: by definition we can have only one neighbor in the embedded system.

◆ findNumNeigh()

int RDDepict::EmbeddedFrag::findNumNeigh	(	const RDGeom::Point2D &	pt,
		double	radius
	)

Find all atoms in this embedded system that are within a specified distant of a point.

◆ flipAboutBond()

void RDDepict::EmbeddedFrag::flipAboutBond	(	unsigned int	bondId,
		bool	flipEnd = `true`
	)

Flip atoms on one side of a bond - used in removing collisions.

ARGUMENTS:

Parameters

bondId	- the bond used as the mirror to flip
flipEnd	- flip the atoms at the end of the bond

◆ getBoxNx()

double RDDepict::EmbeddedFrag::getBoxNx ( )

inline

Definition at line 365 of file EmbeddedFrag.h.

◆ getBoxNy()

double RDDepict::EmbeddedFrag::getBoxNy ( )

inline

Definition at line 367 of file EmbeddedFrag.h.

◆ getBoxPx()

double RDDepict::EmbeddedFrag::getBoxPx ( )

inline

Definition at line 364 of file EmbeddedFrag.h.

◆ getBoxPy()

double RDDepict::EmbeddedFrag::getBoxPy ( )

inline

Definition at line 366 of file EmbeddedFrag.h.

◆ GetEmbeddedAtom()

EmbeddedAtom RDDepict::EmbeddedFrag::GetEmbeddedAtom ( unsigned int aid ) const

inline

Definition at line 298 of file EmbeddedFrag.h.

References PRECONDITION.

◆ GetEmbeddedAtoms()

const INT_EATOM_MAP & RDDepict::EmbeddedFrag::GetEmbeddedAtoms ( ) const

inline

Definition at line 289 of file EmbeddedFrag.h.

◆ getMol()

const RDKit::ROMol * RDDepict::EmbeddedFrag::getMol ( ) const

inline

Get the molecule that this embedded fragment belongs to.

Definition at line 261 of file EmbeddedFrag.h.

◆ isDone()

bool RDDepict::EmbeddedFrag::isDone ( )

inline

If this fragment done for the final embedding.

Definition at line 258 of file EmbeddedFrag.h.

◆ markDone()

void RDDepict::EmbeddedFrag::markDone ( )

inline

Mark this fragment to be done for final embedding.

Definition at line 255 of file EmbeddedFrag.h.

◆ mergeFragsWithComm()

void RDDepict::EmbeddedFrag::mergeFragsWithComm ( std::list< EmbeddedFrag > & efrags )

◆ mergeNoCommon()

void RDDepict::EmbeddedFrag::mergeNoCommon	(	EmbeddedFrag &	embObj,
		unsigned int	toAid,
		unsigned int	nbrAid
	)

Merge this embedded object with another embedded fragment.

The transformation (rotation + translation required to attached the passed in object will be computed and applied. The coordinates of the atoms in this object will remain fixed We will assume that there are no common atoms between the two fragments to start with

ARGUMENTS:

Parameters

embObj	another EmbeddedFrag object to be merged with this object
toAid	the atom in this embedded fragment to which the new object will be attached
nbrAid	the atom in the other fragment to attach to

◆ mergeWithCommon()

void RDDepict::EmbeddedFrag::mergeWithCommon	(	EmbeddedFrag &	embObj,
		RDKit::INT_VECT &	commAtms
	)

Merge this embedded object with another embedded fragment.

The transformation (rotation + translation required to attached the passed in object will be computed and applied. The coordinates of the atoms in this object will remain fixed This already know there are a atoms in common and we will use them to merge things

ARGUMENTS:

Parameters

embObj	another EmbeddedFrag object to be merged with this object
commAtms	a vector of ids of the common atoms

◆ mimicDistMatAndDensityCostFunc()

double RDDepict::EmbeddedFrag::mimicDistMatAndDensityCostFunc	(	const DOUBLE_SMART_PTR *	dmat,
		double	mimicDmatWt
	)

◆ openAngles()

void RDDepict::EmbeddedFrag::openAngles	(	const double *	dmat,
		unsigned int	aid1,
		unsigned int	aid2
	)

◆ permuteBonds()

void RDDepict::EmbeddedFrag::permuteBonds	(	unsigned int	aid,
		unsigned int	aid1,
		unsigned int	aid2
	)

◆ randomSampleFlipsAndPermutations()

void RDDepict::EmbeddedFrag::randomSampleFlipsAndPermutations	(	unsigned int	nBondsPerSample = `3`,
		unsigned int	nSamples = `100`,
		int	seed = `100`,
		const DOUBLE_SMART_PTR *	dmat = `nullptr`,
		double	mimicDmatWt = `0.0`,
		bool	permuteDeg4Nodes = `false`
	)

◆ Reflect()

void RDDepict::EmbeddedFrag::Reflect	(	const RDGeom::Point2D &	loc1,
		const RDGeom::Point2D &	loc2
	)

◆ removeCollisionsBondFlip()

void RDDepict::EmbeddedFrag::removeCollisionsBondFlip ( )

Remove collisions in a structure by flipping rotatable bonds along the shortest path between two colliding atoms

◆ removeCollisionsOpenAngles()

void RDDepict::EmbeddedFrag::removeCollisionsOpenAngles ( )

Remove collision by opening angles at the offending atoms.

◆ removeCollisionsShortenBonds()

void RDDepict::EmbeddedFrag::removeCollisionsShortenBonds ( )

Remove collisions by shortening bonds along the shortest path between the atoms

◆ setupNewNeighs()

void RDDepict::EmbeddedFrag::setupNewNeighs ( )

helpers functions to

make list of neighbors for each atom in the embedded system that still need to be embedded

◆ Size()

int RDDepict::EmbeddedFrag::Size ( ) const

inline

the number of atoms in the embedded system

Definition at line 307 of file EmbeddedFrag.h.

◆ Transform()

void RDDepict::EmbeddedFrag::Transform ( const RDGeom::Transform2D & trans )

Transform this object to a new coordinates system.

ARGUMENTS:

Parameters

trans : the transformation that need to be applied to the atoms in this object

◆ Translate()

void RDDepict::EmbeddedFrag::Translate ( const RDGeom::Point2D & shift )

inline

Definition at line 291 of file EmbeddedFrag.h.

◆ updateNewNeighs()

void RDDepict::EmbeddedFrag::updateNewNeighs ( unsigned int aid )

update the unembedded neighbor atom list for a specified atom

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

EmbeddedFrag.h

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ EmbeddedFrag() [1/5]

◆ EmbeddedFrag() [2/5]

◆ EmbeddedFrag() [3/5]

◆ EmbeddedFrag() [4/5]

◆ EmbeddedFrag() [5/5]

Member Function Documentation

◆ addNonRingAtom()

◆ canonicalizeOrientation()

◆ computeBox()

◆ computeDistMat()

◆ expandEfrag()

◆ findCollisions()

◆ findCommonAtoms()

◆ findNeighbor()

◆ findNumNeigh()

◆ flipAboutBond()

◆ getBoxNx()

◆ getBoxNy()

◆ getBoxPx()

◆ getBoxPy()

◆ GetEmbeddedAtom()

◆ GetEmbeddedAtoms()

◆ getMol()

◆ isDone()

◆ markDone()

◆ mergeFragsWithComm()

◆ mergeNoCommon()

◆ mergeWithCommon()

◆ mimicDistMatAndDensityCostFunc()

◆ openAngles()

◆ permuteBonds()

◆ randomSampleFlipsAndPermutations()

◆ Reflect()

◆ removeCollisionsBondFlip()

◆ removeCollisionsOpenAngles()

◆ removeCollisionsShortenBonds()

◆ setupNewNeighs()

◆ Size()

◆ Transform()

◆ Translate()

◆ updateNewNeighs()