Canon Namespace Reference

Classes
union	MolStackUnion
	used to store components in the molecular stack More...
class	MolStackElem
	these are the actual elements in the molecular stack More...
Typedefs
typedef std::vector< MolStackElem >	MolStack
typedef std::pair< int, std::pair< int, RDKit::Bond * > >	PossibleType
	used to represent possible branches from an atom
Enumerations
enum	AtomColors { WHITE_NODE = 0, GREY_NODE, BLACK_NODE }
	used in traversals of the molecule More...
enum	MolStackTypes {   MOL_STACK_ATOM = 0, MOL_STACK_BOND, MOL_STACK_RING, MOL_STACK_BRANCH_OPEN,   MOL_STACK_BRANCH_CLOSE }
	used to indicate types of entries in the molecular stack: More...
Functions
PossibleType	makePossible (int rank, int atomIdx, RDKit::Bond *bond)
	returns a PossibleType
int	_possibleComp (const PossibleType &arg1, const PossibleType &arg2)
	compare two PossibleTypes
void	canonicalizeFragment (RDKit::ROMol &mol, int atomIdx, std::vector< AtomColors > &colors, std::vector< int > &ranks, MolStack &molStack)
	constructs the canonical traversal order for a molecular fragment
Variables
const int	MAX_NATOMS = 5000
	used in the canonical traversal code
const int	MAX_CYCLES = 99
	used in the canonical traversal code

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Typedef Documentation

typedef std::vector<MolStackElem> Canon::MolStack

Definition at line 88 of file Canon.h.

typedef std::pair< int, std::pair< int, RDKit::Bond * > > Canon::PossibleType

used to represent possible branches from an atom

Definition at line 92 of file Canon.h.

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Enumeration Type Documentation

enum Canon::AtomColors

used in traversals of the molecule

Enumerator:

WHITE_NODE
GREY_NODE	not visited
BLACK_NODE	visited, but not finished

Definition at line 24 of file Canon.h.

enum Canon::MolStackTypes

used to indicate types of entries in the molecular stack:

Enumerator:

MOL_STACK_ATOM	an Atom
MOL_STACK_BOND	a Bond
MOL_STACK_RING	a ring closure
MOL_STACK_BRANCH_OPEN	beginning of a branch
MOL_STACK_BRANCH_CLOSE	end of a branch

Definition at line 31 of file Canon.h.

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Function Documentation

int Canon::_possibleComp	(	const PossibleType &	arg1,
		const PossibleType &	arg2
	)

compare two PossibleTypes

void Canon::canonicalizeFragment	(	RDKit::ROMol &	mol,
		int	atomIdx,
		std::vector< AtomColors > &	colors,
		std::vector< int > &	ranks,
		MolStack &	molStack
	)

constructs the canonical traversal order for a molecular fragment

Parameters:

	mol	the ROMol we're working on
	atomIdx	the index of the atom to start the traversal from
	colors	the traversal status of each atom in mol
	ranks	the assigned rank of each atom in mol
	molStack	the current traversal stack (used to return the results)

Notes

• mol will, in general, be modified by this operation as bond directions and the like are changed to fit the canonical traversal order

PossibleType Canon::makePossible	(	int	rank,
		int	atomIdx,
		RDKit::Bond *	bond
	)

returns a PossibleType

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Variable Documentation

const int Canon::MAX_CYCLES = 99

used in the canonical traversal code

Definition at line 21 of file Canon.h.

const int Canon::MAX_NATOMS = 5000

used in the canonical traversal code

Definition at line 20 of file Canon.h.