molecule.h File Reference

#include "nuri/eigen_config.h"
#include "nuri/core/container/index_set.h"
#include "nuri/core/container/property_map.h"
#include "nuri/core/element.h"
#include "nuri/core/graph/graph.h"
#include "nuri/core/graph/subgraph.h"
#include "nuri/meta.h"
#include "nuri/utils.h"

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Classes
class	nuri::AtomData
class	nuri::BondData
class	nuri::Molecule
	Read-only molecule class. More...
class	nuri::MoleculeMutator
	A class to mutate a molecule. More...
class	nuri::MoleculeSanitizer

Namespaces
namespace	nuri
namespace	nuri::constants

Typedefs
using	nuri::Substructure = internal::Substructure<false>
using	nuri::ConstSubstructure = internal::Substructure<true>

Enumerations
enum	nuri::constants::Hybridization : int {   nuri::constants::kUnbound = 0 , nuri::constants::kTerminal = 1 , nuri::constants::kSP = 2 , nuri::constants::kSP2 = 3 ,   nuri::constants::kSP3 = 4 , nuri::constants::kSP3D = 5 , nuri::constants::kSP3D2 = 6 , nuri::constants::kOtherHyb = 7 }
	The hybridization state of an atom object. More...
enum	nuri::constants::BondOrder : int {   nuri::constants::kOtherBond = 0 , nuri::constants::kSingleBond = 1 , nuri::constants::kDoubleBond = 2 , nuri::constants::kTripleBond = 3 ,   nuri::constants::kQuadrupleBond = 4 , nuri::constants::kAromaticBond = 5 }
	The bond order of a bond object. More...
enum class	nuri::AtomFlags : std::uint32_t {   nuri::kAromatic = 0x1 , nuri::kConjugated = 0x2 , nuri::kRing = 0x4 , nuri::kChiral = 0x8 ,   nuri::kClockWise = 0x10 }
enum class	nuri::BondFlags : std::uint32_t {   nuri::kRing = 0x1 , nuri::kAromatic = 0x2 , nuri::kConjugated = 0x4 , nuri::kConfigSpecified = 0x8 ,   nuri::kTransConfig = 0x10 }
enum class	nuri::SubstructCategory { nuri::kUnknown , nuri::kResidue , nuri::kChain }

Functions
std::ostream &	nuri::constants::operator<< (std::ostream &os, Hybridization hyb)
std::ostream &	nuri::constants::operator<< (std::ostream &os, BondOrder bo)
constants::Hybridization	nuri::clamp_hyb (int hyb)
constants::BondOrder	nuri::clamp_ord (int ord)
bool	nuri::operator== (const AtomData &lhs, const AtomData &rhs)
int	nuri::all_neighbors (Molecule::Atom atom)
	Get the number of all neighbors of an atom.
int	nuri::count_heavy (Molecule::Atom atom)
	Get the number of heavy atoms bonded to an atom.
int	nuri::count_hydrogens (Molecule::Atom atom)
	Count the number of hydrogens of the atom.
int	nuri::sum_bond_order (Molecule::Atom atom)
	Get the approximate total bond order of the atom.
int	nuri::nonbonding_electrons (Molecule::Atom atom)
	Get the predicted non-bonding electron count of the atom.
int	nuri::steric_number (Molecule::Atom atom)
	Get the predicted steric number of the atom.
const Element *	nuri::effective_element (const AtomData &data)
	Get "effective" element of the atom.
const Element *	nuri::effective_element (Molecule::Atom atom)
	Get "effective" element of the atom.
std::vector< std::vector< int > >	nuri::fragments (const Molecule &mol)
	Get fragments of the molecule.

Variables
constexpr double	nuri::constants::kBondOrderToDouble [] = { 0.0, 1.0, 2.0, 3.0, 4.0, 1.5 }