aromaticity.h File Reference

#include "mode.h"
#include "inpdef.h"

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Functions
int	fix_aromatic_oxygen_and_sulfur (inp_ATOM *atom)
	Charge a neutral, divalent aromatic oxygen or sulfur so it can be kekulized.
int	is_C_unsat_not_arom (inp_ATOM *at, int i)
	Test whether an atom is an unsaturated but non-aromatic carbon.
int	is_Aryl (inp_ATOM *at, int outside_point, int attachment_pont)
	Test whether an atom is an aromatic aryl attachment carbon.
int	check_arom_chain (inp_ATOM *at, int cur, int from, int last, int len)
	Verify a chain of aromatic CH carbons of a given length.
int	replace_arom_bonds (inp_ATOM *at, int num_atoms, inp_ATOM *at2, int num_atoms2)
	Restore resolved bond orders onto residual aromatic bonds from a reference.
int	mark_arom_bonds (struct tagINCHI_CLOCK *ic, struct tagCANON_GLOBALS *pCG, inp_ATOM *at, int num_atoms)
	Mark alternating (aromatic) bonds via the balanced-network kekulizer.

Function Documentation

check_arom_chain()

int check_arom_chain	(	inp_ATOM *	at,
		int	cur,
		int	from,
		int	last,
		int	len
	)

Verify a chain of aromatic CH carbons of a given length.

Walks from cur toward last following aromatic (BOND_TYPE_ALTERN) bonds. Every atom visited before last must be an aromatic CH carbon (carbon, valence 2, chem_bonds_valence 3, one implicit H) joined to the next atom by an aromatic bond. Succeeds only if the walk reaches last with exactly len atoms validated.

Parameters

at	Atom array.
cur	Index of the first atom of the chain.
from	Index of the atom preceding cur (fixes the walk direction).
last	Index of the terminal atom the chain must reach.
len	Required chain length (number of validated atoms).

Returns

Non-zero if a valid aromatic chain of length len reaches last; 0 otherwise.

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fix_aromatic_oxygen_and_sulfur()

int fix_aromatic_oxygen_and_sulfur

(

inp_ATOM *

atom

)

Charge a neutral, divalent aromatic oxygen or sulfur so it can be kekulized.

Matches a two-coordinate, uncharged, non-radical O or S whose two bond types sum to 3 (one single + one double bond – the Kekule form of a divalent -O-/-S- in an aromatic ring). Setting a formal +1 charge marks such an atom so the surrounding ring can be kekulized.

Parameters

atom	Atom to inspect; its charge is set to 1 in place on a match.

Returns

1 if the atom matched and was modified; 0 otherwise (atom untouched).

is_Aryl()

int is_Aryl	(	inp_ATOM *	at,
		int	outside_point,
		int	attachment_pont
	)

Test whether an atom is an aromatic aryl attachment carbon.

True when attachment_pont is a neutral, non-radical, three-coordinate carbon (chem_bonds_valence 4, no implicit H) whose two bonds other than the one to outside_point are aromatic (BOND_TYPE_ALTERN) bonds to carbon or nitrogen.

Parameters

at	Atom array.
outside_point	Index of the substituent-side neighbor (outside the ring).
attachment_pont	Index of the candidate aryl attachment carbon.

Returns

Non-zero if attachment_pont is an aromatic aryl carbon; 0 otherwise.

is_C_unsat_not_arom()

int is_C_unsat_not_arom	(	inp_ATOM *	at,
		int	i
	)

Test whether an atom is an unsaturated but non-aromatic carbon.

True when at[i] is a neutral, non-radical carbon of total valence 4 that carries at least one genuine double bond (double bonds to a terminal =O or =S are not counted) and no aromatic (BOND_TYPE_ALTERN) bonds.

Parameters

at	Atom array.
i	Index of the atom to test.

Returns

Non-zero if the carbon is unsaturated and not aromatic; 0 otherwise.

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mark_arom_bonds()

int mark_arom_bonds	(	struct tagINCHI_CLOCK *	ic,
		struct tagCANON_GLOBALS *	pCG,
		inp_ATOM *	at,
		int	num_atoms
	)

Mark alternating (aromatic) bonds via the balanced-network kekulizer.

Thin convenience wrapper around mark_alt_bonds_and_taut_groups() invoked with default (zeroed) tautomer flags and no fixed-bond/tautomer-group output — i.e. normalize alternating bonds without collecting tautomer info.

Parameters

ic	InChI clock / timeout context.
pCG	Canonicalization globals.
at	Atom array to process (modified in place).
num_atoms	Number of atoms in at.

Returns

Status from mark_alt_bonds_and_taut_groups() (0 on success, non-zero error code otherwise).

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replace_arom_bonds()

int replace_arom_bonds	(	inp_ATOM *	at,
		int	num_atoms,
		inp_ATOM *	at2,
		int	num_atoms2
	)

Restore resolved bond orders onto residual aromatic bonds from a reference.

For every bond in at still typed above BOND_TRIPLE (an unresolved type-4/aromatic bond), finds the same atom pair in reference array at2 by original atom number and copies the reference's concrete bond type onto both endpoints in at.

Parameters

at	Atom array to fix up (modified in place).
num_atoms	Number of atoms in at.
at2	Reference atom array carrying resolved bond types.
num_atoms2	Number of atoms in at2.

Returns

Count of residual aromatic bonds that could not be resolved (0 on full success).

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