Chemical Data Processing Library C++ API - Version 1.1.1
Namespaces | Classes | Typedefs | Functions
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::CFLCFLMoleculeInputHandler
 A handler for the input of molecule data from conformer generator fragment libraries. More...
 
typedef std::vector< ConformerData::SharedPointerConformerDataArray
 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

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

◆ 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 
)