Contains classes and functions related to conformer ensemble generation. More...

Namespaces
	ConformerSamplingMode
	Provides constants used to specify the employed conformer sampling method.

	ControlParameter
	Provides keys for built-in control-parameters.

	ControlParameterDefault
	Provides default values for built-in control-parameters.

	DataFormat
	Provides preinitialized Base::DataFormat objects for all supported data formats.

	ForceFieldType
	Provides constants used to specify the forcefield that shall be used for 3D coordinates refinement and energy calculations.

	FragmentType
	Provides constants that are used to describe the nature of fragments used to build-up molecule 3D models.

	NitrogenEnumerationMode
	Provides constants for specifying the mode of invertible nitrogen enumeration.

	ReturnCode
	Provides constants that are used to describe the result of operations related to conformer generation.

	StructureGenerationMode
	Provides constants used to specify the 3D structure generation method that shall be employed.

Classes
class	CanonicalFragment
	Data structure representing a canonicalized molecular fragment. More...

class	CFLMoleculeReader
	Reader for molecule fragment data stored in the CDPL Conformer Generator Fragment Library (CFL) format. More...

class	ConformerData
	Container for the 3D coordinates of a generated conformer plus its associated energy value. More...

class	ConformerGenerator
	High-level driver for the generation of low-energy conformer ensembles of molecular graphs. More...

class	ConformerGeneratorSettings
	Bundle of configuration parameters for conformer ensemble generation via class ConfGen::ConformerGenerator. More...

class	DGConstraintGenerator
	Constructs geometric constraints (distance, planarity, volume) for distance-geometry-based 3D structure generation. More...

class	DGConstraintGeneratorSettings
	Bundle of configuration parameters for distance-geometry constraint generation via class ConfGen::DGConstraintGenerator. More...

class	DGStructureGenerator
	Distance-geometry-based generation of raw 3D structures for molecular graphs. More...

class	DGStructureGeneratorSettings
	Bundle of configuration parameters for raw coordinates generation via class ConfGen::DGStructureGenerator. More...

class	FragmentAssembler
	Driver for the fragment-based generation of 3D starting conformers. More...

class	FragmentAssemblerSettings
	Bundle of configuration parameters for fragment conformer assembly via class ConfGen::FragmentAssembler. More...

class	FragmentConformerGenerator
	Driver for the generation of low-energy conformer ensembles for single molecular fragments (chain, small ring system or macrocycle) More...

class	FragmentConformerGeneratorSettings
	Bundle of configuration parameters for fragment conformer ensemble generation via class ConfGen::FragmentConformerGenerator. More...

class	FragmentLibrary
	Data structure representing a library of pre-generated molecular fragment conformer ensembles. More...

class	FragmentLibraryEntry
	Data structure representing a single entry of a conformer generation fragment library. More...

class	FragmentLibraryGenerator
	Driver for populating a ConfGen::FragmentLibrary with conformers of canonicalized molecular fragments. More...

class	RMSDConformerSelector
	Greedy RMSD-based conformer-diversity filter. More...

class	StructureGenerator
	High-level driver for the generation of a single low-energy 3D structure from a molecular graph. More...

class	StructureGeneratorSettings
	Bundle of configuration parameters for single 3D structure generation via class ConfGen::StructureGenerator. More...

class	TorsionCategory
	Represents a node of a hierarchical torsion library. More...

class	TorsionDriver
	Driver for the systematic enumeration of conformers obtained by rotating around rotatable bonds of a molecular graph, using preferred torsion angles taken from configured ConfGen::TorsionLibrary instances. More...

class	TorsionDriverSettings
	Bundle of configuration parameters for systematic conformer enumeration via class ConfGen::TorsionDriver. More...

class	TorsionLibrary
	Data structure representing a hierarchical library of torsion rules organized into categories. More...

class	TorsionRule
	Data structure for the representation of single torsion library rules. More...

class	TorsionRuleMatch
	A single match of a ConfGen::TorsionRule against a rotatable bond: the rule, the bond and the four atoms that span the torsion. More...

class	TorsionRuleMatcher
	Finds torsion rules from a TorsionLibrary that apply to a given rotatable bond. More...

Typedefs
typedef std::function< bool()>	CallbackFunction
	Generic wrapper for storing user-defined callback functions returning a `bool` status flag (see [FUNWRP]). More...

typedef Util::DefaultDataInputHandler< CFLMoleculeReader, DataFormat::CFL >	CFLMoleculeInputHandler
	Handler for the input of molecule fragments stored in the CDPL Conformer Generator Fragment Library (CFL) format. More...

typedef std::vector< ConformerData::SharedPointer >	ConformerDataArray
	Dynamically-sized array of shared pointers to ConfGen::ConformerData objects. More...

typedef std::function< void(const std::string &)>	LogMessageCallbackFunction
	Generic wrapper for storing user-defined log message callback functions (see [FUNWRP]). More...

Functions
CDPL_CONFGEN_API bool	isFragmentLinkBond (const Chem::Bond &bond, const Chem::MolecularGraph &molgraph)
	Tells whether bond is a link bond between two fragments under the fragment-based conformer generation heuristics. More...

CDPL_CONFGEN_API bool	isRotatableBond (const Chem::Bond &bond, const Chem::MolecularGraph &molgraph, bool het_h_rotors)
	Tells whether bond is rotatable under the conformer generation rotatable bond heuristics. More...

CDPL_CONFGEN_API bool	getStrictErrorCheckingParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the ConfGen::ControlParameter::STRICT_ERROR_CHECKING parameter stored in cntnr. More...

CDPL_CONFGEN_API void	setStrictErrorCheckingParameter (Base::ControlParameterContainer &cntnr, bool strict)
	Sets the value of the ConfGen::ControlParameter::STRICT_ERROR_CHECKING parameter stored in cntnr. More...

CDPL_CONFGEN_API bool	hasStrictErrorCheckingParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the ConfGen::ControlParameter::STRICT_ERROR_CHECKING parameter is set on cntnr. More...

CDPL_CONFGEN_API void	clearStrictErrorCheckingParameter (Base::ControlParameterContainer &cntnr)
	Removes the ConfGen::ControlParameter::STRICT_ERROR_CHECKING parameter from cntnr. More...

CDPL_CONFGEN_API std::size_t	createFragmentLinkBondMask (const Chem::MolecularGraph &molgraph, Util::BitSet &bond_mask, bool reset=true)
	Sets bits in bond_mask for every fragment-link bond of molgraph (see ConfGen::isFragmentLinkBond()). More...

CDPL_CONFGEN_API std::size_t	createRotatableBondMask (const Chem::MolecularGraph &molgraph, Util::BitSet &bond_mask, bool het_h_rotors, bool reset=true)
	Sets bits in bond_mask for every rotatable bond of molgraph (see ConfGen::isRotatableBond()). More...

CDPL_CONFGEN_API std::size_t	createRotatableBondMask (const Chem::MolecularGraph &molgraph, const Util::BitSet &excl_bond_mask, Util::BitSet &bond_mask, bool het_h_rotors, bool reset=true)
	Sets bits in bond_mask for every rotatable bond of molgraph that is not already marked in excl_bond_mask. More...

CDPL_CONFGEN_API std::size_t	getRotatableBondCount (const Chem::MolecularGraph &molgraph, bool het_h_rotors)
	Returns the number of rotatable bonds in molgraph (see ConfGen::isRotatableBond()). More...

CDPL_CONFGEN_API unsigned int	perceiveFragmentType (const Chem::MolecularGraph &molgraph)
	Classifies molgraph as a ConfGen::FragmentType (chain, flexible ring, rigid ring, etc.). More...

CDPL_CONFGEN_API unsigned int	parameterizeMMFF94Interactions (const Chem::MolecularGraph &molgraph, ForceField::MMFF94InteractionParameterizer &parameterizer, ForceField::MMFF94InteractionData &param_data, unsigned int ff_type, bool strict, double estat_de_const, double estat_dist_expo)
	Parameterizes the MMFF94 interactions of molgraph via parameterizer and stores them in param_data. More...

CDPL_CONFGEN_API void	setConformers (Chem::MolecularGraph &molgraph, const ConformerDataArray &conf_array)
	Transfers the conformer ensemble stored in conf_array onto molgraph (sets the per-atom 3D coordinates and conformer energies). More...

CDPL_CONFGEN_API std::size_t	setupFixedSubstructureData (const Chem::SubstructureSearch &sub_search, std::size_t max_num_matches, Chem::MolecularGraph &molgraph, Chem::Fragment &fixed_substr, Math::Vector3DArray *fixed_substr_coords)
	Configures the fixed-substructure handling of molgraph using the matches produced by sub_search. More...

CDPL_CONFGEN_API std::size_t	setupFixedSubstructureData (const Chem::CommonConnectedSubstructureSearch &sub_search, std::size_t max_num_matches, Chem::MolecularGraph &molgraph, Chem::Fragment &fixed_substr, Math::Vector3DArray *fixed_substr_coords)
	Configures the fixed-substructure handling of molgraph using the matches produced by sub_search. More...

CDPL_CONFGEN_API void	initFixedSubstructureTemplate (Chem::MolecularGraph &molgraph, bool init_match_expr)
	Initializes molgraph as a fixed-substructure template (perception of atom/bond properties and optionally match expressions). More...

CDPL_CONFGEN_API bool	initFixedSubstructurePattern (Chem::MolecularGraph &molgraph, const Chem::MolecularGraph *tmplt)
	Initializes molgraph as a fixed-substructure pattern matched against the supplied tmplt template. More...

CDPL_CONFGEN_API void	prepareForConformerGeneration (Chem::Molecule &mol, bool canonicalize=false)
	Prepares mol for conformer generation by completing its hydrogens, perceiving SSSR, ring flags, implicit hydrogen counts, hybridization states, aromaticity and (optionally) canonicalizing the atom ordering. More...

Detailed Description

Contains classes and functions related to conformer ensemble generation.

Typedef Documentation

◆ CallbackFunction

typedef std::function<bool()> CDPL::ConfGen::CallbackFunction

Generic wrapper for storing user-defined callback functions returning a bool status flag (see [FUNWRP]).

Used by the conformer generation pipeline (Chem::ConformerGenerator, Chem::TorsionDriver, etc.) for the periodic abort and timeout-check callbacks: returning false signals the pipeline to abort.

◆ CFLMoleculeInputHandler

typedef Util::DefaultDataInputHandler<CFLMoleculeReader, DataFormat::CFL> CDPL::ConfGen::CFLMoleculeInputHandler

Handler for the input of molecule fragments stored in the CDPL Conformer Generator Fragment Library (CFL) format.

◆ ConformerDataArray

typedef std::vector<ConformerData::SharedPointer> CDPL::ConfGen::ConformerDataArray

Dynamically-sized array of shared pointers to ConfGen::ConformerData objects.

◆ LogMessageCallbackFunction

typedef std::function<void(const std::string&)> CDPL::ConfGen::LogMessageCallbackFunction

Generic wrapper for storing user-defined log message callback functions (see [FUNWRP]).

Used by the conformer generation pipeline (Chem::ConformerGenerator, Chem::FragmentConformerGenerator, Chem::FragmentLibraryGenerator) to forward textual log messages to the caller.

Function Documentation

◆ isFragmentLinkBond()

CDPL_CONFGEN_API bool CDPL::ConfGen::isFragmentLinkBond	(	const Chem::Bond &	bond,
		const Chem::MolecularGraph &	molgraph
	)

Tells whether bond is a link bond between two fragments under the fragment-based conformer generation heuristics.

Parameters

bond	The bond to test.
molgraph	The parent molecular graph.

Returns: true if bond connects two fragments, and false otherwise.

◆ isRotatableBond()

CDPL_CONFGEN_API bool CDPL::ConfGen::isRotatableBond	(	const Chem::Bond &	bond,
		const Chem::MolecularGraph &	molgraph,
		bool	het_h_rotors
	)

Tells whether bond is rotatable under the conformer generation rotatable bond heuristics.

Parameters

bond	The bond to test.
molgraph	The parent molecular graph.
het_h_rotors	If `true`, rotors involving only heteroatom-bound hydrogens are also counted as rotatable.

Returns: true if bond is rotatable, and false otherwise.

◆ getStrictErrorCheckingParameter()

CDPL_CONFGEN_API bool CDPL::ConfGen::getStrictErrorCheckingParameter ( const Base::ControlParameterContainer & cntnr )

Returns the value of the ConfGen::ControlParameter::STRICT_ERROR_CHECKING parameter stored in cntnr.

Parameters

cntnr The control-parameter container to query.

Returns: The current value of the STRICT_ERROR_CHECKING parameter (the ConfGen::ControlParameterDefault::STRICT_ERROR_CHECKING value if the parameter is unset).

◆ setStrictErrorCheckingParameter()

CDPL_CONFGEN_API void CDPL::ConfGen::setStrictErrorCheckingParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	strict
	)

Sets the value of the ConfGen::ControlParameter::STRICT_ERROR_CHECKING parameter stored in cntnr.

Parameters

cntnr	The control-parameter container to update.
strict	The new STRICT_ERROR_CHECKING value.

◆ hasStrictErrorCheckingParameter()

CDPL_CONFGEN_API bool CDPL::ConfGen::hasStrictErrorCheckingParameter ( const Base::ControlParameterContainer & cntnr )

Tells whether the ConfGen::ControlParameter::STRICT_ERROR_CHECKING parameter is set on cntnr.

Parameters

cntnr The control-parameter container to query.

Returns: true if the parameter is set, and false otherwise.

◆ clearStrictErrorCheckingParameter()

CDPL_CONFGEN_API void CDPL::ConfGen::clearStrictErrorCheckingParameter ( Base::ControlParameterContainer & cntnr )

Removes the ConfGen::ControlParameter::STRICT_ERROR_CHECKING parameter from cntnr.

Parameters

cntnr The control-parameter container to update.

◆ createFragmentLinkBondMask()

CDPL_CONFGEN_API std::size_t CDPL::ConfGen::createFragmentLinkBondMask	(	const Chem::MolecularGraph &	molgraph,
		Util::BitSet &	bond_mask,
		bool	reset = `true`
	)

Sets bits in bond_mask for every fragment-link bond of molgraph (see ConfGen::isFragmentLinkBond()).

Parameters

molgraph	The molecular graph.
bond_mask	The output bit mask sized to the number of bonds in molgraph.
reset	If `true`, the output mask is cleared before bits are set.

Returns: The number of fragment-link bonds encountered.

◆ createRotatableBondMask() [1/2]

CDPL_CONFGEN_API std::size_t CDPL::ConfGen::createRotatableBondMask	(	const Chem::MolecularGraph &	molgraph,
		Util::BitSet &	bond_mask,
		bool	het_h_rotors,
		bool	reset = `true`
	)

Sets bits in bond_mask for every rotatable bond of molgraph (see ConfGen::isRotatableBond()).

Parameters

molgraph	The molecular graph.
bond_mask	The output bit mask sized to the number of bonds in molgraph.
het_h_rotors	If `true`, rotors involving only heteroatom-bound hydrogens are also counted as rotatable.
reset	If `true`, the output mask is cleared before bits are set.

Returns: The number of rotatable bonds encountered.

◆ createRotatableBondMask() [2/2]

CDPL_CONFGEN_API std::size_t CDPL::ConfGen::createRotatableBondMask	(	const Chem::MolecularGraph &	molgraph,
		const Util::BitSet &	excl_bond_mask,
		Util::BitSet &	bond_mask,
		bool	het_h_rotors,
		bool	reset = `true`
	)

Sets bits in bond_mask for every rotatable bond of molgraph that is not already marked in excl_bond_mask.

Parameters

molgraph	The molecular graph.
excl_bond_mask	The bit mask of bonds to exclude from rotatable bond consideration.
bond_mask	The output bit mask sized to the number of bonds in molgraph.
het_h_rotors	If `true`, rotors involving only heteroatom-bound hydrogens are also counted as rotatable.
reset	If `true`, the output mask is cleared before bits are set.

Returns: The number of rotatable bonds encountered.

◆ getRotatableBondCount()

CDPL_CONFGEN_API std::size_t CDPL::ConfGen::getRotatableBondCount	(	const Chem::MolecularGraph &	molgraph,
		bool	het_h_rotors
	)

Returns the number of rotatable bonds in molgraph (see ConfGen::isRotatableBond()).

Parameters

molgraph	The molecular graph.
het_h_rotors	If `true`, rotors involving only heteroatom-bound hydrogens are also counted as rotatable.

Returns: The rotatable bond count.

◆ perceiveFragmentType()

CDPL_CONFGEN_API unsigned int CDPL::ConfGen::perceiveFragmentType ( const Chem::MolecularGraph & molgraph )

Classifies molgraph as a ConfGen::FragmentType (chain, flexible ring, rigid ring, etc.).

Parameters

molgraph The molecular graph.

Returns: The ConfGen::FragmentType identifier.

◆ parameterizeMMFF94Interactions()

CDPL_CONFGEN_API unsigned int CDPL::ConfGen::parameterizeMMFF94Interactions	(	const Chem::MolecularGraph &	molgraph,
		ForceField::MMFF94InteractionParameterizer &	parameterizer,
		ForceField::MMFF94InteractionData &	param_data,
		unsigned int	ff_type,
		bool	strict,
		double	estat_de_const,
		double	estat_dist_expo
	)

Parameterizes the MMFF94 interactions of molgraph via parameterizer and stores them in param_data.

Parameters

molgraph	The molecular graph.
parameterizer	The MMFF94 interaction parameterizer.
param_data	The output interaction-data structure.
ff_type	The MMFF94 force field variant (see ForceField::MMFF94InteractionParameterizer for valid values).
strict	If `true`, missing parameters are treated as fatal errors. Otherwise, in case of parameterization problems, suitable fallback parameters will be used.
estat_de_const	The dielectric constant used in the electrostatic energy term.
estat_dist_expo	The distance exponent used in the electrostatic energy term.

Returns: A ConfGen::ReturnCode value reporting the outcome of the parameterization.

◆ setConformers()

CDPL_CONFGEN_API void CDPL::ConfGen::setConformers	(	Chem::MolecularGraph &	molgraph,
		const ConformerDataArray &	conf_array
	)

Transfers the conformer ensemble stored in conf_array onto molgraph (sets the per-atom 3D coordinates and conformer energies).

Parameters

molgraph	The molecular graph receiving the conformer data.
conf_array	The conformer ensemble to attach.

◆ setupFixedSubstructureData() [1/2]

CDPL_CONFGEN_API std::size_t CDPL::ConfGen::setupFixedSubstructureData	(	const Chem::SubstructureSearch &	sub_search,
		std::size_t	max_num_matches,
		Chem::MolecularGraph &	molgraph,
		Chem::Fragment &	fixed_substr,
		Math::Vector3DArray *	fixed_substr_coords
	)

Configures the fixed-substructure handling of molgraph using the matches produced by sub_search.

Parameters

sub_search	The substructure search engine providing the matches.
max_num_matches	The maximum number of matches to process (0 means unlimited).
molgraph	The molecular graph that holds the input atoms (modified in place).
fixed_substr	The output fragment receiving the matched atoms/bonds.
fixed_substr_coords	Optional output array receiving the 3D coordinates of the fixed substructure atoms.

Returns: The number of matches processed.

Since: 1.1

◆ setupFixedSubstructureData() [2/2]

CDPL_CONFGEN_API std::size_t CDPL::ConfGen::setupFixedSubstructureData	(	const Chem::CommonConnectedSubstructureSearch &	sub_search,
		std::size_t	max_num_matches,
		Chem::MolecularGraph &	molgraph,
		Chem::Fragment &	fixed_substr,
		Math::Vector3DArray *	fixed_substr_coords
	)

Configures the fixed-substructure handling of molgraph using the matches produced by sub_search.

Parameters

sub_search	The common-connected-substructure search engine providing the matches.
max_num_matches	The maximum number of matches to process (0 means unlimited).
molgraph	The molecular graph that holds the input atoms (modified in place).
fixed_substr	The output fragment receiving the matched atoms/bonds.
fixed_substr_coords	Optional output array receiving the 3D coordinates of the fixed substructure atoms.

Returns: The number of matches processed.

Since: 1.1

◆ initFixedSubstructureTemplate()

CDPL_CONFGEN_API void CDPL::ConfGen::initFixedSubstructureTemplate	(	Chem::MolecularGraph &	molgraph,
		bool	init_match_expr
	)

Initializes molgraph as a fixed-substructure template (perception of atom/bond properties and optionally match expressions).

Parameters

molgraph	The molecular graph that will serve as the template.
init_match_expr	If `true`, atom/bond match expressions are also generated.

Since: 1.1

◆ initFixedSubstructurePattern()

CDPL_CONFGEN_API bool CDPL::ConfGen::initFixedSubstructurePattern	(	Chem::MolecularGraph &	molgraph,
		const Chem::MolecularGraph *	tmplt
	)

Initializes molgraph as a fixed-substructure pattern matched against the supplied tmplt template.

Parameters

molgraph	The molecular graph to initialize.
tmplt	The template molecular graph (may be `nullptr`).

Returns: true if the initialization succeeded, and false otherwise.

Since: 1.1

◆ prepareForConformerGeneration()

CDPL_CONFGEN_API void CDPL::ConfGen::prepareForConformerGeneration	(	Chem::Molecule &	mol,
		bool	canonicalize = `false`
	)

Prepares mol for conformer generation by completing its hydrogens, perceiving SSSR, ring flags, implicit hydrogen counts, hybridization states, aromaticity and (optionally) canonicalizing the atom ordering.

Parameters

mol	The molecule to prepare (modified in place).
canonicalize	If `true`, the atom ordering of mol is canonicalized.

Namespaces

Classes

Typedefs

Functions

Detailed Description

Typedef Documentation

◆ CallbackFunction

◆ CFLMoleculeInputHandler

◆ ConformerDataArray

◆ LogMessageCallbackFunction

Function Documentation

◆ isFragmentLinkBond()

◆ isRotatableBond()

◆ getStrictErrorCheckingParameter()

◆ setStrictErrorCheckingParameter()

◆ hasStrictErrorCheckingParameter()

◆ clearStrictErrorCheckingParameter()

◆ createFragmentLinkBondMask()

◆ createRotatableBondMask() [1/2]

◆ createRotatableBondMask() [2/2]

◆ getRotatableBondCount()

◆ perceiveFragmentType()

◆ parameterizeMMFF94Interactions()

◆ setConformers()

◆ setupFixedSubstructureData() [1/2]

◆ setupFixedSubstructureData() [2/2]

◆ initFixedSubstructureTemplate()

◆ initFixedSubstructurePattern()

◆ prepareForConformerGeneration()