ConfGen/MolecularGraphFunctions.hpp File Reference

Declaration of functions that operate on Chem::MolecularGraph instances. More...

#include <cstddef>
#include "CDPL/ConfGen/APIPrefix.hpp"
#include "CDPL/ConfGen/ConformerDataArray.hpp"
#include "CDPL/Util/BitSet.hpp"

Go to the source code of this file.

Namespaces
	CDPL
	The namespace of the Chemical Data Processing Library.
	CDPL::Chem
	Contains classes and functions related to chemistry.
	CDPL::ForceField
	Contains classes and functions related to molecular force fields.
	CDPL::ConfGen
	Contains classes and functions related to conformer ensemble generation.

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

Detailed Description

Declaration of functions that operate on Chem::MolecularGraph instances.