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

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

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

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

class	CanonicalFragment
	Data structure representing a canonicalized molecular fragment. 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	ConformerSamplingMode
	Provides constants used to specify the employed conformer sampling method. More...

class	ControlParameter
	Provides keys for built-in control-parameters. More...

class	ControlParameterDefault
	Provides default values for built-in control-parameters. 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	DataFormat
	Provides preinitialized Base.DataFormat objects for all supported data formats. More...

class	FileCFLMoleculeReader

class	ForceFieldType
	Provides constants used to specify the forcefield that shall be used for 3D coordinates refinement and energy calculations. 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	FragmentType
	Provides constants that are used to describe the nature of fragments used to build-up molecule 3D models. More...

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

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

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

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

class	StructureGenerationMode
	Provides constants used to specify the 3D structure generation method that shall be employed. 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 ConfGen.TorsionLibrary instance that match a given rotatable bond. More...

Functions
int	getRotatableBondCount (Chem.MolecularGraph molgraph, bool het_h_rotors)
	Returns the number of rotatable bonds in molgraph (see ConfGen.isRotatableBond()). More...

int	createFragmentLinkBondMask (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...

int	createRotatableBondMask (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...

int	createRotatableBondMask (Chem.MolecularGraph molgraph, 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...

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

None	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...

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

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

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

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

None	prepareForConformerGeneration (Chem.Molecule mol, bool canonicalize=False)
	Prepares the molecule mol for conformer generation. More...

int	setupFixedSubstructureData (Chem.CommonConnectedSubstructureSearch sub_search, int max_num_matches, Chem.MolecularGraph molgraph, Chem.Fragment fixed_substr, Math.Vector3DArray fixed_substr_coords=0)
	Configures the fixed-substructure handling of molgraph using the matches produced by sub_search. More...

int	setupFixedSubstructureData (Chem.SubstructureSearch sub_search, int max_num_matches, Chem.MolecularGraph molgraph, Chem.Fragment fixed_substr, Math.Vector3DArray fixed_substr_coords=0)
	Configures the fixed-substructure handling of molgraph using the matches produced by sub_search. More...

None	setStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr, bool strict)
	Sets the value of the ConfGen.ControlParameter.STRICT_ERROR_CHECKING parameter stored in cntnr. More...

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

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

None	clearStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr)
	Removes the ConfGen.ControlParameter.STRICT_ERROR_CHECKING parameter from cntnr. More...

Detailed Description

Contains classes and functions related to conformer ensemble generation.

Function Documentation

◆ getRotatableBondCount()

int CDPL.ConfGen.getRotatableBondCount	(	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.

◆ createFragmentLinkBondMask()

int CDPL.ConfGen.createFragmentLinkBondMask	(	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]

int CDPL.ConfGen.createRotatableBondMask	(	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]

int CDPL.ConfGen.createRotatableBondMask	(	Chem.MolecularGraph	molgraph,
		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.

◆ initFixedSubstructurePattern()

bool CDPL.ConfGen.initFixedSubstructurePattern	(	Chem.MolecularGraph	molgraph,
		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

◆ initFixedSubstructureTemplate()

None 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

◆ isFragmentLinkBond()

bool CDPL.ConfGen.isFragmentLinkBond	(	Chem.Bond	bond,
		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()

bool CDPL.ConfGen.isRotatableBond	(	Chem.Bond	bond,
		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.

◆ parameterizeMMFF94Interactions()

int CDPL.ConfGen.parameterizeMMFF94Interactions	(	Chem.MolecularGraph	molgraph,
		ForceField.MMFF94InteractionParameterizer	parameterizer,
		ForceField.MMFF94InteractionData	param_data,
		int	ff_type,
		bool	strict,
		float	estat_de_const,
		float	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.

◆ perceiveFragmentType()

int CDPL.ConfGen.perceiveFragmentType ( 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.

◆ prepareForConformerGeneration()

None CDPL.ConfGen.prepareForConformerGeneration	(	Chem.Molecule	mol,
		bool	canonicalize = `False`
	)

Prepares the molecule mol for conformer generation.

The molecules gets prepared by completing its hydrogens, perceiving the 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.

◆ setupFixedSubstructureData() [1/2]

int CDPL.ConfGen.setupFixedSubstructureData	(	Chem.CommonConnectedSubstructureSearch	sub_search,
		int	max_num_matches,
		Chem.MolecularGraph	molgraph,
		Chem.Fragment	fixed_substr,
		Math.Vector3DArray	fixed_substr_coords = `0`
	)

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

◆ setupFixedSubstructureData() [2/2]

int CDPL.ConfGen.setupFixedSubstructureData	(	Chem.SubstructureSearch	sub_search,
		int	max_num_matches,
		Chem.MolecularGraph	molgraph,
		Chem.Fragment	fixed_substr,
		Math.Vector3DArray	fixed_substr_coords = `0`
	)

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

◆ setStrictErrorCheckingParameter()

None 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.
strict	The new STRICT_ERROR_CHECKING value.

◆ hasStrictErrorCheckingParameter()

bool CDPL.ConfGen.hasStrictErrorCheckingParameter ( Base.ControlParameterContainer cntnr )

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

Parameters

cntnr The control-parameter container.

Returns: True if the parameter is set, and False otherwise.

◆ getStrictErrorCheckingParameter()

bool CDPL.ConfGen.getStrictErrorCheckingParameter ( 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).

◆ clearStrictErrorCheckingParameter()

None CDPL.ConfGen.clearStrictErrorCheckingParameter ( Base.ControlParameterContainer cntnr )

Removes the ConfGen.ControlParameter.STRICT_ERROR_CHECKING parameter from cntnr.

Parameters

cntnr The control-parameter container.

Classes

Functions

Detailed Description

Function Documentation

◆ getRotatableBondCount()

◆ createFragmentLinkBondMask()

◆ createRotatableBondMask() [1/2]

◆ createRotatableBondMask() [2/2]

◆ initFixedSubstructurePattern()

◆ initFixedSubstructureTemplate()

◆ isFragmentLinkBond()

◆ isRotatableBond()

◆ parameterizeMMFF94Interactions()

◆ perceiveFragmentType()

◆ prepareForConformerGeneration()

◆ setupFixedSubstructureData() [1/2]

◆ setupFixedSubstructureData() [2/2]

◆ setStrictErrorCheckingParameter()

◆ hasStrictErrorCheckingParameter()

◆ getStrictErrorCheckingParameter()

◆ clearStrictErrorCheckingParameter()