CDPL.ConfGen Package Reference

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

Classes
class	CallbackFunction
	A generic wrapper class used to store a user-defined callback functions (see [FUNWRP]). More...
class	CanonicalFragment
	CanonicalFragment. More...
class	CFLMoleculeInputHandler
	A handler for the input of molecule data from conformer generator fragment libraries. 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	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	DataFormat
	Provides preinitialized Base.DataFormat objects for all supported data formats. More...
class	DGConstraintGenerator
class	DGConstraintGeneratorSettings
class	DGStructureGenerator
class	DGStructureGeneratorSettings
class	FileCFLMoleculeReader
class	ForceFieldType
	Provides constants that are used to specify the forcefield that shall be used for 3D coordinates refinement and energy calculations. More...
class	FragmentAssembler
class	FragmentAssemblerSettings
class	FragmentConformerGenerator
class	FragmentConformerGeneratorSettings
class	FragmentLibrary
class	FragmentLibraryEntry
	FragmentLibraryEntry. More...
class	FragmentLibraryGenerator
	FragmentLibraryGenerator. More...
class	FragmentType
	Provides constants that are used to describe the nature of fragments used to build-up molecule 3D models. More...
class	LogMessageCallbackFunction
	A generic wrapper class used to store a user-defined callback functions. More...
class	NitrogenEnumerationMode
	Provides constants that are used to specify the mode of invertible nitrogen enumeration. More...
class	ReturnCode
	Provides constants that are used to describe the result of operations related to conformer generation. More...
class	RMSDConformerSelector
class	StructureGenerationMode
	Provides constants used to specify the employed structure generation method. More...
class	StructureGenerator
class	StructureGeneratorSettings
class	TorsionCategory
class	TorsionDriver
class	TorsionDriverSettings
class	TorsionLibrary
class	TorsionRule
class	TorsionRuleMatch
class	TorsionRuleMatcher

Functions
bool	isRotatableBond (Chem.Bond bond, Chem.MolecularGraph molgraph, bool het_h_rotors)
bool	isFragmentLinkBond (Chem.Bond bond, Chem.MolecularGraph molgraph)
int	setupFixedSubstructureData (Chem.CommonConnectedSubstructureSearch sub_search, int max_num_matches, Chem.MolecularGraph molgraph, Chem.Fragment fixed_substr, Math.Vector3DArray fixed_substr_coords=0)
None	clearStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr)
bool	hasStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr)
bool	getStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr)
None	setStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr, bool strict)
int	perceiveFragmentType (Chem.MolecularGraph molgraph)
None	initFixedSubstructureTemplate (Chem.MolecularGraph molgraph, bool init_match_expr)
int	createRotatableBondMask (Chem.MolecularGraph molgraph, Util.BitSet bond_mask, bool het_h_rotors, bool reset=True)
int	createRotatableBondMask (Chem.MolecularGraph molgraph, Util.BitSet excl_bond_mask, Util.BitSet bond_mask, bool het_h_rotors, bool reset=True)
int	createFragmentLinkBondMask (Chem.MolecularGraph molgraph, Util.BitSet bond_mask, bool reset=True)
bool	initFixedSubstructurePattern (Chem.MolecularGraph molgraph, Chem.MolecularGraph tmplt)
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)
int	getRotatableBondCount (Chem.MolecularGraph molgraph, bool het_h_rotors)
None	prepareForConformerGeneration (Chem.Molecule mol, bool canonicalize=False)
int	setupFixedSubstructureData (Chem.SubstructureSearch sub_search, int max_num_matches, Chem.MolecularGraph molgraph, Chem.Fragment fixed_substr, Math.Vector3DArray fixed_substr_coords=0)

Detailed Description

Contains classes and functions related to conformer ensemble generation.

Function Documentation

isRotatableBond()

bool CDPL.ConfGen.isRotatableBond	(	Chem.Bond	bond,
		Chem.MolecularGraph	molgraph,
		bool	het_h_rotors
	)

Parameters

bond
molgraph
het_h_rotors

Returns

isFragmentLinkBond()

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

Parameters

bond
molgraph

Returns

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
	)

Parameters

sub_search
max_num_matches
molgraph
fixed_substr
fixed_substr_coords

Returns

clearStrictErrorCheckingParameter()

None CDPL.ConfGen.clearStrictErrorCheckingParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasStrictErrorCheckingParameter()

bool CDPL.ConfGen.hasStrictErrorCheckingParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getStrictErrorCheckingParameter()

bool CDPL.ConfGen.getStrictErrorCheckingParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setStrictErrorCheckingParameter()

None CDPL.ConfGen.setStrictErrorCheckingParameter	(	Base.ControlParameterContainer	cntnr,
		bool	strict
	)

Parameters

cntnr
strict

perceiveFragmentType()

int CDPL.ConfGen.perceiveFragmentType

(

Chem.MolecularGraph

molgraph

)

Parameters

molgraph

Returns

initFixedSubstructureTemplate()

None CDPL.ConfGen.initFixedSubstructureTemplate	(	Chem.MolecularGraph	molgraph,
		bool	init_match_expr
	)

Parameters

molgraph
init_match_expr

createRotatableBondMask() [1/2]

int CDPL.ConfGen.createRotatableBondMask	(	Chem.MolecularGraph	molgraph,
		Util.BitSet	bond_mask,
		bool	het_h_rotors,
		bool	reset = True
	)

Parameters

molgraph
bond_mask
het_h_rotors
reset

Returns

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
	)

Parameters

molgraph
excl_bond_mask
bond_mask
het_h_rotors
reset

Returns

createFragmentLinkBondMask()

int CDPL.ConfGen.createFragmentLinkBondMask	(	Chem.MolecularGraph	molgraph,
		Util.BitSet	bond_mask,
		bool	reset = True
	)

Parameters

molgraph
bond_mask
reset

Returns

initFixedSubstructurePattern()

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

Parameters

molgraph
tmplt

Returns

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
	)

Parameters

molgraph
parameterizer
param_data
ff_type
strict
estat_de_const
estat_dist_expo

Returns

getRotatableBondCount()

int CDPL.ConfGen.getRotatableBondCount	(	Chem.MolecularGraph	molgraph,
		bool	het_h_rotors
	)

Parameters

molgraph
het_h_rotors

Returns

prepareForConformerGeneration()

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

Parameters

mol
canonicalize

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
	)

Parameters

sub_search
max_num_matches
molgraph
fixed_substr
fixed_substr_coords

Returns