Scine::Molassembler::DistanceGeometry::SpatialModel Class Reference

Class performing spatial modeling of molecules. More...

#include <SpatialModel.h>

Data Structures
struct	BoundsMatrixHelper

Public Types
Member types
template<unsigned size>
using	BoundsMapType = std::unordered_map< std::array< AtomIndex, size >, ValueBounds, boost::hash< std::array< AtomIndex, size > > >
	ValueBounds container for various internal coordinates.
using	FixedPositionsMapType = std::unordered_map< AtomIndex, Utils::Position >
	Type used to store fixed positions in angstrom.
using	BoundsMatrix = Eigen::MatrixXd
	Type used to represent atom-pairwise distance bounds constructed from bounds on internal coordinates. More...

Public Member Functions
Special member functions
	SpatialModel (const Molecule &molecule, const Configuration &configuration)
	Model a molecule into internal coordinate bounds stored internally. More...
Modifiers
void	setBondBoundsIfEmpty (std::array< AtomIndex, 2 > bondIndices, ValueBounds bounds)
	Sets bond bounds to exact value bounds if unset. More...
void	setAngleBoundsIfEmpty (std::array< AtomIndex, 3 > angleIndices, ValueBounds bounds)
	Adds angle bounds to the model if unset. More...
void	setDihedralBoundsIfEmpty (std::array< AtomIndex, 4 > dihedralIndices, ValueBounds bounds)
	Adds the dihedral bounds to the model if unset. More...
void	addAtomStereopermutatorInformation (const AtomStereopermutator &permutator, const PrivateGraph &graph, double looseningMultiplier, const std::unordered_map< AtomIndex, Utils::Position > &fixedAngstromPositions, bool forceChiralConstraintEmission)
	Adds angle information to the internal coordinate bounds and collects chiral constraints. More...
void	addBondStereopermutatorInformation (const BondStereopermutator &permutator, const AtomStereopermutator &stereopermutatorA, const AtomStereopermutator &stereopermutatorB, double looseningMultiplier, const std::unordered_map< AtomIndex, Utils::Position > &fixedAngstromPositions)
	Adds dihedral information to the internal coordinate bounds and collects dihedral constraints. More...
bool	modelPartiallyFixedBond (const BondStereopermutator &permutator, const std::pair< const AtomStereopermutator &, const AtomStereopermutator & > &atomPermutators, const std::unordered_map< AtomIndex, Utils::Position > &fixedAngstromPositions)
	Sets bond bounds to exact value bounds if unset. More...
Information
std::vector< ChiralConstraint >	getChiralConstraints () const
	Yields all collected chiral constraints. More...
std::vector< DihedralConstraint >	getDihedralConstraints () const
	Yields all collected dihedral constraints. More...
BoundsMatrix	makePairwiseBounds () const
	Generate unsmoothed atom-pairwise distance bounds matrix. More...
std::string	dumpGraphviz () const
	Generates a string graphviz representation of the modeled molecule. More...
void	writeGraphviz (const std::string &filename) const
	Writes a graphviz representation of a modeled molecule to a file. More...

Private Member Functions
Private methods
void	addDefaultAngles_ ()
	Adds [0, π] default angle bounds for all bonded atom triples.
void	addDefaultDihedrals_ ()
	Adds [0, π] default dihedrals to the model (of connected sequences) More...
void	instantiateMissingAtomStereopermutators_ (Random::Engine &engine)
void	modelBondDistances_ (const FixedPositionsMapType &fixedAngstromPositions, double looseningFactor)
	Add bond distances to the underlying model.
void	modelFlatCycles_ (const FixedPositionsMapType &fixedAngstromPositions, double looseningFactor)
	Add precise information to the model for cycles that are flat.
void	modelSpirocenters_ (const FixedPositionsMapType &fixedAngstromPositions)
	Adds spirocenter modelling to the data set. More...

Private Attributes
const Molecule &	molecule_
std::unordered_map< AtomIndex, Stereopermutators::LocalSpatialModel >	localModels_
	Local models of atom stereopermutators.
BoundsMapType< 2 >	constraints_
	Constraints by fixed positions.
BoundsMapType< 2 >	bondBounds_
	Bond distance value bounds on index pairs.
BoundsMapType< 3 >	angleBounds_
	Angle value bounds on index triples.
BoundsMapType< 4 >	dihedralBounds_
	Dihedral value bounds on index quadruplets.
std::vector< ChiralConstraint >	chiralConstraints_
	Chiral constraints.
std::vector< DihedralConstraint >	dihedralConstraints_

Static members
static constexpr double	bondRelativeVariance = 0.01
	Relative bond distance variance 0.0x mean x% variance. Must fulfill 0 < x << 1.
static constexpr double	angleRelativeVariance = 0.02
	Relative angle variance. More...
static constexpr double	dihedralAbsoluteVariance = M_PI / 90
	Absolute dihedral angle variance in radians.
static constexpr ValueBounds	angleClampBounds {0.0, M_PI}
	Defines clamping bounds on angles.
static const ValueBounds	defaultDihedralBounds
	Defines the range (-π,π] using std::nextafter (not constexpr)
static double	modelDistance (AtomIndex i, AtomIndex j, const PrivateGraph &graph)
	Models the equilibrium distance between two bonded atoms. More...
static double	modelDistance (const BondIndex &bond, const PrivateGraph &graph)
static std::vector< BondIndex >	cycleConsistingOfExactly (const std::vector< AtomIndex > &atoms, const PrivateGraph &graph)
	Tries to find a cycle that consists of a particular set of atoms. More...
static boost::optional < ValueBounds >	coneAngle (const std::vector< AtomIndex > &baseConstituents, const ValueBounds &coneHeightBounds, const PrivateGraph &graph)
	Tries to calculate the cone angle for a possibly haptic ligand site. More...
static double	spiroCrossAngle (double alpha, double beta)
	Calculates the cross angle between opposite cycle atoms in a spirocenter. More...
static ValueBounds	siteDistanceFromCenter (const std::vector< AtomIndex > &siteAtomList, AtomIndex placement, const PrivateGraph &graph)
	Calculates bounds on the distance of a (possibly haptic) ligand site to a central index. More...
static ValueBounds	makeBoundsFromCentralValue (double centralValue, double absoluteVariance)
	Yields central value plus/minus some absolute variance bounds. More...
static double	smallestCycleDistortionMultiplier (AtomIndex i, const Cycles &cycles)
	Idealization strictness loosening multiplier due to small cycles. More...
static BoundsMatrix	makePairwiseBounds (unsigned N, const BoundsMapType< 2 > &fixedPositionBounds, const BoundsMapType< 2 > &bondBounds, const BoundsMapType< 3 > &angleBounds, const BoundsMapType< 4 > &dihedralBounds)
	Relative bond distance variance 0.0x mean x% variance. Must fulfill 0 < x << 1.
static double	siteCentralAngle (AtomIndex placement, const Shapes::Shape &shape, const RankingInformation &ranking, const AtomStereopermutator::ShapeMap &shapeVertexMap, const std::pair< SiteIndex, SiteIndex > &sites, const PrivateGraph &inner)
	Determines the central value of the angle between AtomStereopermutator sites. More...
static double	siteCentralAngle (const AtomStereopermutator &permutator, const std::pair< SiteIndex, SiteIndex > &sites, const PrivateGraph &inner)
static ValueBounds	modelSiteAngleBounds (const AtomStereopermutator &permutator, const Stereopermutators::LocalSpatialModel &localModel, const std::pair< SiteIndex, SiteIndex > &sites, double looseningMultiplier, const PrivateGraph &inner)
	Models bounds on the angle between AtomStereopermutator sites. More...
static ChiralConstraint	makeChiralConstraint (const AtomStereopermutator::MinimalChiralConstraint &minimalConstraint, const AtomStereopermutator &permutator, const Stereopermutators::LocalSpatialModel &localModel, double looseningMultiplier)
	Creates a volume-specific chiral constraint from a list of. More...
static ValueBounds	clamp (ValueBounds bounds, const ValueBounds &clampBounds)
	Analogous to C++17's clamp, reduces ValueBounds to the maximal extent specified by some clamping bounds. More...
static void	checkFixedPositionsPreconditions (const Molecule &molecule, const Configuration &configuration)
	Ensures that the preconditions for fixed positions in Distance Geometry detailed in the Configuration object are met. More...

Detailed Description

Class performing spatial modeling of molecules.

Keeps a record of the internal coordinate bounds that a molecular graph is interpreted as and generates a list of atom-pairwise bounds from which classes performing smoothing can be constructed.

Member Typedef Documentation

using Scine::Molassembler::DistanceGeometry::SpatialModel::BoundsMatrix = Eigen::MatrixXd

Type used to represent atom-pairwise distance bounds constructed from bounds on internal coordinates.

Diagonal entries are undefined. Strict lower triangle contains lower bounds, strict upper triangle contains upper bounds.

Constructor & Destructor Documentation

Scine::Molassembler::DistanceGeometry::SpatialModel::SpatialModel	(	const Molecule &	molecule,
		const Configuration &	configuration
	)

Model a molecule into internal coordinate bounds stored internally.

Main space where modeling is performed. This is where a molecule's graph and list of stereopermutators are transformed into explicit bounds on 1-2 (bonds), 1-3 (angles) and 1-4 (dihedral) internal coordinates. This determines which conformations are accessible.

Complexity At least \(O(P_2 + P_3 + P_4)\) where \(P_i\) is the number of distinct paths of length \(i\) in the graph. That should scale at least linearly in the number of vertices.

Parameters

molecule	The molecule that is to be modeled. This may not contain stereopermutators with zero assignments or unassigned stereopermutators.
configuration	The Distance Geometry configuration object. Relevant for this stage of the process are the loosening multiplier and fixed positions, if set.

Member Function Documentation

void Scine::Molassembler::DistanceGeometry::SpatialModel::addAtomStereopermutatorInformation	(	const AtomStereopermutator &	permutator,
		const PrivateGraph &	graph,
		double	looseningMultiplier,
		const std::unordered_map< AtomIndex, Utils::Position > &	fixedAngstromPositions,
		bool	forceChiralConstraintEmission
	)

Adds angle information to the internal coordinate bounds and collects chiral constraints.

Complexity \(O(S^2)\) where \(S\) is the size of the modeled shape

Parameters

permutator	The AtomStereopermutator to collect information from
graph	The graph context
looseningMultiplier	A loosening factor for the overall model
fixedAngstromPositions	A mapping between atom indices and fixed spatial positions
forceChiralConstraintEmission	If set, the stereopermutator emits chiral constraints even if the stereopermutator does not have chiral state, i.e. numAssignments() <= 1, as long as it is assigned.

void Scine::Molassembler::DistanceGeometry::SpatialModel::addBondStereopermutatorInformation	(	const BondStereopermutator &	permutator,
		const AtomStereopermutator &	stereopermutatorA,
		const AtomStereopermutator &	stereopermutatorB,
		double	looseningMultiplier,
		const std::unordered_map< AtomIndex, Utils::Position > &	fixedAngstromPositions
	)

Adds dihedral information to the internal coordinate bounds and collects dihedral constraints.

Complexity \(O(S^2)\) where \(S\) is the size of the larger modeled shape

Parameters

permutator	The BondStereopermutator to collect information from
stereopermutatorA	One AtomStereopermutator constituting the BondStereopermutator
stereopermutatorB	The other AtomStereopermutator constituting the BondStereopermutator
looseningMultiplier	A loosening factor for the overall model
fixedAngstromPositions	A mapping between atom indices and fixed spatial positions

void Scine::Molassembler::DistanceGeometry::SpatialModel::addDefaultDihedrals_ ( )

private

Adds [0, π] default dihedrals to the model (of connected sequences)

Adds [0, π] default dihedrals to the model. Avoids treating 1-4 pairs as nonbonded.

static void Scine::Molassembler::DistanceGeometry::SpatialModel::checkFixedPositionsPreconditions ( const Molecule &  molecule, const Configuration &  configuration  )

static

Ensures that the preconditions for fixed positions in Distance Geometry detailed in the Configuration object are met.

Parameters

molecule	The molecule for which the Configuration is valid
configuration	The Configuration object detailing fixed positions

Exceptions

std::runtime_error

If the preconditions are not met

static ValueBounds Scine::Molassembler::DistanceGeometry::SpatialModel::clamp ( ValueBounds  bounds, const ValueBounds &  clampBounds  )

static

Analogous to C++17's clamp, reduces ValueBounds to the maximal extent specified by some clamping bounds.

Complexity \(\Theta(1)\)

Parameters

bounds	The bounds to be clamped
clampBounds	The range in which bounds may exist

Returns

New bounds that are within the clamp bounds

static boost::optional<ValueBounds> Scine::Molassembler::DistanceGeometry::SpatialModel::coneAngle ( const std::vector< AtomIndex > &  baseConstituents, const ValueBounds &  coneHeightBounds, const PrivateGraph &  graph  )

static

Tries to calculate the cone angle for a possibly haptic ligand site.

Complexity \(O(C)\) where \(C\) is the number of cycles in the molecule

Parameters

baseConstituents	Atom indices constituting the ligand site
coneHeightBounds	Bounds on the distance of the ligand site to the central atom
graph	The molecular graph to model

Returns

If calculable, bounds on the cone angle spanned by the ligand site

static std::vector<BondIndex> Scine::Molassembler::DistanceGeometry::SpatialModel::cycleConsistingOfExactly ( const std::vector< AtomIndex > &  atoms, const PrivateGraph &  graph  )

static

Tries to find a cycle that consists of a particular set of atoms.

Complexity \(\Theta(C)\) where \(C\) is the number of cycles in the molecule

Parameters

atoms	The exact set of atoms that constitute the cycle.
graph	The graph context

Returns

A vector of bond indices of exactly the matching cycle if found. An empty vector is returned otherwise.

std::string Scine::Molassembler::DistanceGeometry::SpatialModel::dumpGraphviz

(

)

const

Generates a string graphviz representation of the modeled molecule.

The graph contains basic connectivity, stereopermutator information and internal coordinate bounds.

Complexity \(\Theta(N)\)

Returns

A string that can be converted into an image using graphviz of the molecule being modeled.

std::vector<ChiralConstraint> Scine::Molassembler::DistanceGeometry::SpatialModel::getChiralConstraints

(

)

const

Yields all collected chiral constraints.

Complexity \(\Theta(1)\)

std::vector<DihedralConstraint> Scine::Molassembler::DistanceGeometry::SpatialModel::getDihedralConstraints

(

)

const

Yields all collected dihedral constraints.

Complexity \(\Theta(1)\)

void Scine::Molassembler::DistanceGeometry::SpatialModel::instantiateMissingAtomStereopermutators_ ( Random::Engine &  engine )

private

It is permissible in some circumstances not to have AtomStereopermutators even on non-terminal atoms. These have to be re-added in order for us to be able to model everywhere.

static ValueBounds Scine::Molassembler::DistanceGeometry::SpatialModel::makeBoundsFromCentralValue ( double  centralValue, double  absoluteVariance  )

static

Yields central value plus/minus some absolute variance bounds.

Complexity \(\Theta(1)\)

Parameters

centralValue	The central value
absoluteVariance	The value to subtract and add to yield new bounds

Returns

bounds with median central value and width 2 * absoluteVariance

static ChiralConstraint Scine::Molassembler::DistanceGeometry::SpatialModel::makeChiralConstraint ( const AtomStereopermutator::MinimalChiralConstraint &  minimalConstraint, const AtomStereopermutator &  permutator, const Stereopermutators::LocalSpatialModel &  localModel, double  looseningMultiplier  )

static

Creates a volume-specific chiral constraint from a list of.

Complexity \(\Theta(1)\)

Parameters

minimalConstraint	Site index sequence defining a chiral constraint
permutator	The AtomStereopermutator from which the minimalConstraint has been generated
looseningMultiplier	Describes the spatial modeling loosening of bounds

Returns

A volume constraint on the site index sequence in a final conformation

BoundsMatrix Scine::Molassembler::DistanceGeometry::SpatialModel::makePairwiseBounds

(

)

const

Generate unsmoothed atom-pairwise distance bounds matrix.

Generates a matrix of atom-pairwise distance bounds from the internal coordinate bounds and fixed positions from which this was constructed.

Complexity \(O(P_2 + P_3 + P_4)\) where \(P_i\) is the number of distinct paths of length \(i\) in the graph. That should scale at least linearly in the number of vertices.

Returns

A matrix of atom-pairwise distance bounds. Lower bounds are in the strict lower triangle of the matrix, upper bounds in the strict upper triangle.

static double Scine::Molassembler::DistanceGeometry::SpatialModel::modelDistance ( AtomIndex  i, AtomIndex  j, const PrivateGraph &  graph  )

static

Models the equilibrium distance between two bonded atoms.

Complexity \(\Theta(1)\)

Precondition

i and j are bonded

static double Scine::Molassembler::DistanceGeometry::SpatialModel::modelDistance ( const BondIndex &  bond, const PrivateGraph &  graph  )

static

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

bool Scine::Molassembler::DistanceGeometry::SpatialModel::modelPartiallyFixedBond	(	const BondStereopermutator &	permutator,
		const std::pair< const AtomStereopermutator &, const AtomStereopermutator & > &	atomPermutators,
		const std::unordered_map< AtomIndex, Utils::Position > &	fixedAngstromPositions
	)

Sets bond bounds to exact value bounds if unset.

Complexity \(\Theta(1)\)

Parameters

bondIndices	The atom pair on which to place bond distance bounds
bounds	The distance bounds to enforce

Precondition

bondIndices must be ordered (i.e. front() < back())

static ValueBounds Scine::Molassembler::DistanceGeometry::SpatialModel::modelSiteAngleBounds ( const AtomStereopermutator &  permutator, const Stereopermutators::LocalSpatialModel &  localModel, const std::pair< SiteIndex, SiteIndex > &  sites, double  looseningMultiplier, const PrivateGraph &  inner  )

static

Models bounds on the angle between AtomStereopermutator sites.

Complexity Varies. For most cases, \(\Omega(1)\)

Parameters

permutator	The permutator being modeled
sites	The two sites between which the angle is to be determined
looseningMultiplier	Loosening of that particular atom
inner	Graph instance being modeled

Returns

Bounds on the angle between two AtomStereopermutator sites

void Scine::Molassembler::DistanceGeometry::SpatialModel::modelSpirocenters_ ( const FixedPositionsMapType &  fixedAngstromPositions )

private

Adds spirocenter modelling to the data set.

The cross-angle in a spiro-atom is expliticly modeled if the disjoint cycles are both small, i.e. of size \(\le 5\). Only then is the additional variance when calculating cross-angle bounds particularly harmful for the overall 3D structure. We define:

\begin{align} \vec{a} &= R_z\left(\frac{\alpha}{2}\right)\begin{pmatrix} 1\\ 0\\ 0 \end{pmatrix} = \begin{pmatrix} \cos \frac{\alpha}{2}\\ \sin \frac{\alpha}{2}\\ 0 \end{pmatrix}\\ \vec{b} &= R_y\left(\frac{\beta}{2}\right)\begin{pmatrix} -1\\ 0\\ 0 \end{pmatrix} = \begin{pmatrix} - \cos \frac{\beta}{2}\\ 0\\ \sin \frac{\beta}{2} \end{pmatrix} \end{align}

Where \(R_y\) and \(R_z\) are the standard three-dimensional rotation matrices, \(\alpha\) is the cycle internal angle for the first cycle at the spiro-atom, and \(\beta\) is the cycle internal angle for the second cycle at the spiro-atom. The angle between these vectors \(\phi\) is then:

\begin{align} \vec{a}\vec{b} &= |\vec{a}||\vec{b}|\cos\phi\\ \phi &= \arccos \left\{ \left(\cos \frac{\alpha}{2} \right) \left(- \cos \frac{\beta}{2} \right) \right\} \end{align}

void Scine::Molassembler::DistanceGeometry::SpatialModel::setAngleBoundsIfEmpty	(	std::array< AtomIndex, 3 >	angleIndices,
		ValueBounds	bounds
	)

Adds angle bounds to the model if unset.

Complexity \(\Theta(1)\)

Parameters

angleIndices	The atom index sequence specifying an angle
bounds	The angle bounds to enforce

Precondition

angleIndices must be ordered (i.e. front() < back())

Note

Passed angle bounds are clamped against the angleClampBounds

void Scine::Molassembler::DistanceGeometry::SpatialModel::setBondBoundsIfEmpty	(	std::array< AtomIndex, 2 >	bondIndices,
		ValueBounds	bounds
	)

Sets bond bounds to exact value bounds if unset.

Complexity \(\Theta(1)\)

Parameters

bondIndices	The atom pair on which to place bond distance bounds
bounds	The distance bounds to enforce

Precondition

bondIndices must be ordered (i.e. front() < back())

void Scine::Molassembler::DistanceGeometry::SpatialModel::setDihedralBoundsIfEmpty	(	std::array< AtomIndex, 4 >	dihedralIndices,
		ValueBounds	bounds
	)

Adds the dihedral bounds to the model if unset.

Complexity \(\Theta(1)\)

Parameters

dihedralIndices	The atom index sequence specifying a dihedral
bounds	The dihedral bounds to enforce

Precondition

dihedralIndices must be ordered (i.e. front() < back())

static double Scine::Molassembler::DistanceGeometry::SpatialModel::siteCentralAngle ( AtomIndex  placement, const Shapes::Shape &  shape, const RankingInformation &  ranking, const AtomStereopermutator::ShapeMap &  shapeVertexMap, const std::pair< SiteIndex, SiteIndex > &  sites, const PrivateGraph &  inner  )

static

Determines the central value of the angle between AtomStereopermutator sites.

Complexity Varies. For most cases, \(\Omega(1)\)

Parameters

placement	The atom index of the central index of the angle
shape	The local shape at placement
ranking	The ranking of substituents at placement
shapeVertexMap	The mapping from site indices to shape vertices
sites	The two sites between which the angle is to be determined
inner	Graph instance being modeled

Returns

The central value of the angle between the sites

static double Scine::Molassembler::DistanceGeometry::SpatialModel::siteCentralAngle ( const AtomStereopermutator &  permutator, const std::pair< SiteIndex, SiteIndex > &  sites, const PrivateGraph &  inner  )

static

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

static ValueBounds Scine::Molassembler::DistanceGeometry::SpatialModel::siteDistanceFromCenter ( const std::vector< AtomIndex > &  siteAtomList, AtomIndex  placement, const PrivateGraph &  graph  )

static

Calculates bounds on the distance of a (possibly haptic) ligand site to a central index.

Complexity \(\Theta(A)\) where \(A\) is the number of atoms comprising the site

Parameters

siteAtomList	Atom indices constituting the ligand site
placement	The central index to which the ligand is bound
graph	The molecular graph to model

Returns

Bounds on the distance of the ligand site to the central index

static double Scine::Molassembler::DistanceGeometry::SpatialModel::smallestCycleDistortionMultiplier ( AtomIndex  i, const Cycles &  cycles  )

static

Idealization strictness loosening multiplier due to small cycles.

Returns

A multiplier intended for the absolute angle variance for a particular atom. If that atom is part of a cycle of size < 6, the multiplier is > 1.

static double Scine::Molassembler::DistanceGeometry::SpatialModel::spiroCrossAngle ( double  alpha, double  beta  )

static

Calculates the cross angle between opposite cycle atoms in a spirocenter.

Complexity \(\Theta(1)\)

Parameters

alpha	The left cycle-internal angle
beta	The right cycle-internal angle

Returns

The cross angle between cycle atoms in the spirocenter

void Scine::Molassembler::DistanceGeometry::SpatialModel::writeGraphviz

(

const std::string &

filename

)

const

Writes a graphviz representation of a modeled molecule to a file.

The graph contains basic connectivity, stereopermutator information and internal coordinate bounds.

Complexity \(\Theta(N)\)

Parameters

filename

The filename to which to write the graphviz representation

Field Documentation

constexpr double Scine::Molassembler::DistanceGeometry::SpatialModel::angleRelativeVariance = 0.02

static

Relative angle variance.

0.0x mean x& variance. Must fulfill 0 < x << 1

---

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

• Molassembler/DistanceGeometry/SpatialModel.h