CDPL::ConfGen Namespace Reference

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 that are 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 that are used to specify 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 employed structure generation method.

Classes
class	CanonicalFragment
	CanonicalFragment. More...
class	CFLMoleculeReader
	A reader for molecule data in the native I/O format of the CDPL. More...
class	ConformerData
class	ConformerGenerator
class	ConformerGeneratorSettings
class	DGConstraintGenerator
class	DGConstraintGeneratorSettings
class	DGStructureGenerator
class	DGStructureGeneratorSettings
class	FragmentAssembler
class	FragmentAssemblerSettings
class	FragmentConformerGenerator
class	FragmentConformerGeneratorSettings
class	FragmentLibrary
class	FragmentLibraryEntry
	FragmentLibraryEntry. More...
class	FragmentLibraryGenerator
	FragmentLibraryGenerator. More...
class	RMSDConformerSelector
class	StructureGenerator
class	StructureGeneratorSettings
class	TorsionCategory
class	TorsionDriver
class	TorsionDriverSettings
class	TorsionLibrary
class	TorsionRule
class	TorsionRuleMatch
class	TorsionRuleMatcher

Typedefs
typedef std::function< bool()>	CallbackFunction
	A generic wrapper class used to store a user-defined callback functions (see [FUNWRP]). More...
typedef Util::DefaultDataInputHandler< CFLMoleculeReader, DataFormat::CFL >	CFLMoleculeInputHandler
	A handler for the input of molecule data from conformer generator fragment libraries. More...
typedef std::vector< ConformerData::SharedPointer >	ConformerDataArray
	A data type for the storage of dyn. allocated ConfGen::ConformerData objects. More...
typedef std::function< void(const std::string &)>	LogMessageCallbackFunction
	A generic wrapper class used to store a user-defined callback functions. More...

Functions
CDPL_CONFGEN_API bool	isFragmentLinkBond (const Chem::Bond &bond, const Chem::MolecularGraph &molgraph)
CDPL_CONFGEN_API bool	isRotatableBond (const Chem::Bond &bond, const Chem::MolecularGraph &molgraph, bool het_h_rotors)
CDPL_CONFGEN_API bool	getStrictErrorCheckingParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CONFGEN_API void	setStrictErrorCheckingParameter (Base::ControlParameterContainer &cntnr, bool strict)
CDPL_CONFGEN_API bool	hasStrictErrorCheckingParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CONFGEN_API void	clearStrictErrorCheckingParameter (Base::ControlParameterContainer &cntnr)
CDPL_CONFGEN_API std::size_t	createFragmentLinkBondMask (const Chem::MolecularGraph &molgraph, Util::BitSet &bond_mask, bool reset=true)
CDPL_CONFGEN_API std::size_t	createRotatableBondMask (const Chem::MolecularGraph &molgraph, Util::BitSet &bond_mask, bool het_h_rotors, bool reset=true)
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)
CDPL_CONFGEN_API std::size_t	getRotatableBondCount (const Chem::MolecularGraph &molgraph, bool het_h_rotors)
CDPL_CONFGEN_API unsigned int	perceiveFragmentType (const Chem::MolecularGraph &molgraph)
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)
CDPL_CONFGEN_API void	setConformers (Chem::MolecularGraph &molgraph, const ConformerDataArray &conf_array)
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)
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)
CDPL_CONFGEN_API void	initFixedSubstructureTemplate (Chem::MolecularGraph &molgraph, bool init_match_expr)
CDPL_CONFGEN_API bool	initFixedSubstructurePattern (Chem::MolecularGraph &molgraph, const Chem::MolecularGraph *tmplt)
CDPL_CONFGEN_API void	prepareForConformerGeneration (Chem::Molecule &mol, bool canonicalize=false)

Detailed Description

Contains classes and functions related to conformer ensemble generation.

Typedef Documentation

CallbackFunction

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

A generic wrapper class used to store a user-defined callback functions (see [FUNWRP]).

CFLMoleculeInputHandler

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

A handler for the input of molecule data from conformer generator fragment libraries.

ConformerDataArray

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

A data type for the storage of dyn. allocated ConfGen::ConformerData objects.

LogMessageCallbackFunction

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

A generic wrapper class used to store a user-defined callback functions.

Function Documentation

isFragmentLinkBond()

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

isRotatableBond()

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

getStrictErrorCheckingParameter()

CDPL_CONFGEN_API bool CDPL::ConfGen::getStrictErrorCheckingParameter

(

const Base::ControlParameterContainer &

cntnr

)

setStrictErrorCheckingParameter()

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

hasStrictErrorCheckingParameter()

CDPL_CONFGEN_API bool CDPL::ConfGen::hasStrictErrorCheckingParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearStrictErrorCheckingParameter()

CDPL_CONFGEN_API void CDPL::ConfGen::clearStrictErrorCheckingParameter

(

Base::ControlParameterContainer &

cntnr

)

createFragmentLinkBondMask()

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

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
	)

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
	)

getRotatableBondCount()

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

perceiveFragmentType()

CDPL_CONFGEN_API unsigned int CDPL::ConfGen::perceiveFragmentType

(

const Chem::MolecularGraph &

molgraph

)

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
	)

setConformers()

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

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
	)

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
	)

Since

1.1

initFixedSubstructureTemplate()

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

Since

1.1

initFixedSubstructurePattern()

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

Since

1.1

prepareForConformerGeneration()

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