ichinorm.c File Reference

#include <stdlib.h>
#include <string.h>
#include "mode.h"
#include "ichinorm.h"
#include "ichierr.h"
#include "bcf_s.h"

Include dependency graph for ichinorm.c:

Data Structures
struct	tagAtPair
struct	tagDerivAttachment
struct	tagRing2Chain

Macros
#define	DERIV_BRIDGE_O   0x0001 /* R1-O-R2 => R1-OH + HO-R2 */
#define	DERIV_BRIDGE_NH   0x0002 /* R1-NH-R2 amine */
#define	DERIV_AMINE_tN   0x0004 /* R1-N(-R2)-R3 tertiary amine */
#define	DERIV_RING_O_OUTSIDE_PRECURSOR   0x0008 /* -O- in a ring */
#define	DERIV_RING_NH_OUTSIDE_PRECURSOR   0x0010 /* -NH- in a ring */
#define	DERIV_X_OXIME   0x0020 /* comment out to disable */
#define	DERIV_UNMARK   0x0040 /* unmark the cut */
#define	DERIV_DUPLIC   0x0080 /* duplicated disconnection */
#define	DERIV_RO_COX   0x0100 /* alcohol derivatives: R-O--C(=O)C[n]F[2n+1] 0<n<4, R-O--C(=O)CH3, R-O--C(=O)-Phenyl */
#define	DERIV_RING_DMOX_DEOX_N   0x0200 /* =N- in a ring: /-O--CH2-\ DMOX, DEOX */
#define	DERIV_RING_DMOX_DEOX_O   0x0400 /* -O- in a ring: R-C=N--------C<2Me or 2Et */
#define	DERIV_RING2_PRRLDD_OUTSIDE_PRECUR   0x0800 /* alcohol derivatives: R(=O)-N<C4H4 5-memb ring Pyrrolidides; replace -N< with -OH */
#define	DERIV_RING2_PPRDN_OUTSIDE_PRECUR   0x1000 /* alcohol derivatives: R(=O)-N<C5H5 6-memb ring Piperidines; replace -N< with -OH */
#define	DERIV_DANSYL   0x2000 /* alcohol derivatives: R-O--SO2-C10H5-N(CH3)2 => R-OH */
#define	DERIV_RING_DMOX_DEOX   (DERIV_RING_DMOX_DEOX_O | DERIV_RING_DMOX_DEOX_N)
#define	DERIV_RING_OUTSIDE_PRECURSOR   (DERIV_RING_O_OUTSIDE_PRECURSOR | DERIV_RING_NH_OUTSIDE_PRECURSOR)
#define	DERIV_RING2_OUTSIDE_PRECUR   (DERIV_RING2_PRRLDD_OUTSIDE_PRECUR | DERIV_RING2_PPRDN_OUTSIDE_PRECUR)
#define	DERIV_AT_LEN   4
#define	DERIV_NOT   0x1000 /* cannot be a derivatization agent atom */
#define	MAX_AT_DERIV   13 /* max. num of heavy atoms in removed derivatizing agent: RO-C(O)PheF5 */
#define	NOT_AT_DERIV   99 /* DERIV_AT::num; rejected as > MAX_AT_DERIV */
#define	MIN_AT_LEFT_DERIV   2 /* was 3 before 2013-11-12; min num heavy atoms in derivative precursor = MIN_AT_LEFT_DERIV-1 */
#define	NO_ORD_VAL   0x0037 /* not used */
#define	CFLAG_MARK_BRANCH   1 /* for main derivative traversal */
#define	CFLAG_MARK_BLOCK   2 /* for block detection */
#define	CFLAG_MARK_BLOCK_INV   ((char)~(CFLAG_MARK_BLOCK)) /* for block detection */
#define	COUNT_ALL_NOT_DERIV   1 /* 1=> count ALL atoms that are not in deriv. agents */
#define	IS_DA_NUM_LE(DA, I, MX)   (((DA)->typ[I] && ((DA)->typ[I] & DERIV_UNEXPADABLE) == (DA)->typ[I]) || (DA)->num[I] <= (MX))
#define	OX_RING_SIZE   5
#define	PRRLDD_RING_SIZE   5
#define	PPRDN_RING_SIZE   6
#define	MIN_PRRLDD_PPRDN_RING_SIZE   PRRLDD_RING_SIZE
#define	MAX_PRRLDD_PPRDN_RING_SIZE   PPRDN_RING_SIZE
#define	DERIV_RING   DERIV_RING_OUTSIDE_PRECURSOR
#define	UNDERIV_MAX_NUM   512 /*max. number of records in szUnderivList */
#define	UNDERIV_LEN   128
#define	UNDERIV_LEN2   128
#define	ALLOC_AP
#define	UNDERIV_LIST_LEN   2048
#define	UNDERIV_LIST_LEN2   2048
#define	R2C_EMPTY   127

Typedefs
typedef struct tagAtPair	R2C_ATPAIR
typedef struct tagDerivAttachment	DERIV_AT
typedef enum tagDerivId	DerivId
typedef enum tagDerivBit	DerivBit
typedef int	BIT_UNDERIV
typedef struct tagRing2Chain	R2C_AT

Enumerations
enum	tagDerivId {   DERIV_ID_Acentonate , DERIV_ID_Benzlidene , DERIV_ID_BenzOX , DERIV_ID_BuBorate ,   DERIV_ID_Dansyl , DERIV_ID_DEOX , DERIV_ID_DMOX , DERIV_ID_EtBorate ,   DERIV_ID_EtOX , DERIV_ID_HFB , DERIV_ID_MeBorate , DERIV_ID_MOX ,   DERIV_ID_PFB , DERIV_ID_PFP , DERIV_ID_Piperidine , DERIV_ID_Pyrrolidide ,   DERIV_ID_TBDMS , DERIV_ID_TFA , DERIV_ID_TMS , DERIV_ID_Unknown ,   DERIV_ID_Acetate , DERIV_ID_Benzoate }
enum	tagDerivBit {   DERIV_BIT_Acentonate = 1 << DERIV_ID_Acentonate , DERIV_BIT_Benzlidene = 1 << DERIV_ID_Benzlidene , DERIV_BIT_BenzOX = 1 << DERIV_ID_BenzOX , DERIV_BIT_BuBorate = 1 << DERIV_ID_BuBorate ,   DERIV_BIT_Dansyl = 1 << DERIV_ID_Dansyl , DERIV_BIT_DEOX = 1 << DERIV_ID_DEOX , DERIV_BIT_DMOX = 1 << DERIV_ID_DMOX , DERIV_BIT_EtBorate = 1 << DERIV_ID_EtBorate ,   DERIV_BIT_EtOX = 1 << DERIV_ID_EtOX , DERIV_BIT_HFB = 1 << DERIV_ID_HFB , DERIV_BIT_MeBorate = 1 << DERIV_ID_MeBorate , DERIV_BIT_MOX = 1 << DERIV_ID_MOX ,   DERIV_BIT_PFB = 1 << DERIV_ID_PFB , DERIV_BIT_PFP = 1 << DERIV_ID_PFP , DERIV_BIT_Piperidine = 1 << DERIV_ID_Piperidine , DERIV_BIT_Pyrrolidide = 1 << DERIV_ID_Pyrrolidide ,   DERIV_BIT_TBDMS = 1 << DERIV_ID_TBDMS , DERIV_BIT_TFA = 1 << DERIV_ID_TFA , DERIV_BIT_TMS = 1 << DERIV_ID_TMS , DERIV_BIT_Unknown = 1 << DERIV_ID_Unknown ,   DERIV_BIT_Acetate = 1 << DERIV_ID_Acetate , DERIV_BIT_Benzoate = 1 << DERIV_ID_Benzoate , DERIV_ID_NUMBER }

Functions
int	MarkRingSystemsInp (inp_ATOM *at, int num_atoms, int start)
int	mark_arom_bonds (struct tagINCHI_CLOCK *ic, struct tagCANON_GLOBALS *pCG, inp_ATOM *at, int num_atoms)
void	set_R2C_el_numbers (void)
int	subtract_DT_from_num_H (int num_atoms, inp_ATOM *at)
int	add_inp_ATOM (inp_ATOM *at, int len_at, int len_cur, inp_ATOM *add, int len_add)
int	cmp_r2c_atpair (const void *p1, const void *p2)
int	has_atom_pair (R2C_ATPAIR *ap, int num_ap, AT_NUMB at1, AT_NUMB at2)
int	mark_atoms_ap (inp_ATOM *at, AT_NUMB start, R2C_ATPAIR *ap, int num_ap, int num, AT_NUMB cFlags)
int	UnMarkDisconnectedComponents (ORIG_ATOM_DATA *orig_inp_data)
int	UnMarkOtherIndicators (inp_ATOM *at, int num_atoms)
int	UnMarkOneComponent (inp_ATOM *at, int num_atoms)
int	DisconnectInpAtBond (inp_ATOM *at, AT_NUMB *nOldCompNumber, int iat, int neigh_ord)
int	ExtractConnectedComponent (inp_ATOM *at, int num_at, int component_number, inp_ATOM *component_at)
int	UnMarkRingSystemsInp (inp_ATOM *at, int num_atoms)
int	has_atom_pair_seq (R2C_ATPAIR *ap, int num_ap, AT_NUMB at1, AT_NUMB at2)
int	mark_atoms_cFlags (inp_ATOM *at, int start, int num, char cFlags)
int	unmark_atoms_cFlags (inp_ATOM *at, int start, int num, char cFlags, char cInvFlags)
int	is_C_or_S_DB_O (inp_ATOM *at, int i)
int	is_C_DB_O (inp_ATOM *at, int i)
int	is_C_unsat_not_arom (inp_ATOM *at, int i)
int	is_Aryl (inp_ATOM *at, int outside_point, int attachment_pont)
int	is_Saturated_C (inp_ATOM *at, int attachment_pont)
int	is_C_Alk (inp_ATOM *at, int i, char cFlags)
int	is_Phenyl (inp_ATOM *at, int outside_point, int attachment_point)
int	is_PentaFluoroPhenyl (inp_ATOM *at, int outside_point, int attachment_point)
int	is_Methyl (inp_ATOM *at, int attachment_point)
int	is_Ethyl (inp_ATOM *at, int outside_point, int attachment_point)
int	is_Methyl_or_Etyl (inp_ATOM *at, int outside_point, int attachment_point)
int	is_Si_IV (inp_ATOM *at, int i)
int	is_P_TB_N (inp_ATOM *at, int i)
int	is_DERIV_RING2_PRRLDD_PPRDN (inp_ATOM *at, int cur_atom, int from_ord, DERIV_AT *da, DERIV_AT *da1)
int	check_arom_chain (inp_ATOM *at, int first, int first_from, int last, int len)
int	is_Dansyl (inp_ATOM *at, int cur_atom, int from_ord, DERIV_AT *da, DERIV_AT *da1)
int	is_possibly_deriv_neigh (inp_ATOM *at, int iat, int iord, int type, char cFlags)
int	get_traversed_deriv_type (inp_ATOM *at, DERIV_AT *da, int k, DERIV_AT *da1, char cFlags)
int	add_to_da (DERIV_AT *da, DERIV_AT *add)
int	mark_atoms_deriv (inp_ATOM *at, DERIV_AT *da, int start, int num, char cFlags, int *pbFound)
int	count_one_bond_atoms (inp_ATOM *at, DERIV_AT *da, int start, int ord, char cFlags, int *bFound)
int	is_silyl (inp_ATOM *at, int start, int ord_prev)
int	is_silyl2 (inp_ATOM *at, int start, int from_at)
int	is_Me_or_Et (inp_ATOM *at, int start, int ord_prev)
int	is_nButyl (inp_ATOM *at, int start, int ord_prev)
int	is_CF3_or_linC3F7a (inp_ATOM *at, int start, int iat_prev)
int	is_CF3_or_linC3F7 (inp_ATOM *at, int start, int ord_prev)
int	is_phenyl (inp_ATOM *at, int start, int ord_prev)
int	is_DERIV_RING_O_or_NH_OUTSIDE_PRECURSOR (inp_ATOM *at, int start, int num_atoms, DERIV_AT *da1, int idrv, char *szUnderiv, int lenUnderiv, char *szUnderiv2, int lenUnderiv2, BIT_UNDERIV *bitUnderiv)
int	is_deriv_chain (inp_ATOM *at, int start, int num_atoms, DERIV_AT *da1, int idrv, char *szUnderiv, int lenUnderiv, char *szUnderiv2, int lenUnderiv2, BIT_UNDERIV *bitUnderiv)
int	is_deriv_chain2 (inp_ATOM *at, int start, int type, int num, int ord, int idrv, char *szUnderiv, int lenUnderiv, char *szUnderiv2, int lenUnderiv2, BIT_UNDERIV *bitUnderiv)
int	is_deriv_chain_or_ring (inp_ATOM *at, int start, int num_atoms, DERIV_AT *da1, int *idrv)
int	remove_deriv (DERIV_AT *da1, int idrv)
int	remove_deriv_mark (DERIV_AT *da1, int idrv)
int	underiv_compare (const void *p1, const void *p2)
int	underiv_list_add_two_cuts (char *szUnderivList, int lenUnderivList, char *szUnderiv, const char cDelim)
int	sort_merge_underiv (char *pSdfValue, int bOutputSdf, char *szUnderivList, char cDerivSeparator, const char *pszUnderivPrefix, const char *pszUnderivPostfix)
int	eliminate_deriv_not_in_list (inp_ATOM *at, DERIV_AT *da, int num_atoms, char *szUnderivList, int lenUnderivList, char *szUnderivList2, int lenUnderivList2, BIT_UNDERIV *bitUnderivList)
void	underiv_buf_clear (char *szUnderiv)
int	underiv_list_add (char *szUnderivList, int lenUnderivList, const char *szUnderiv, char cDelimiter)
const char *	underiv_list_get_last (const char *szUnderivList, char cDelimiter)
int	make_single_cut (inp_ATOM *at, DERIV_AT *da, int iat, int icut)
int	fill_out_bond_cuts (inp_ATOM *at, DERIV_AT *da, int num_atoms, R2C_ATPAIR *ap, int num_cuts_to_check)
int	mark_deriv_agents (inp_ATOM *at, DERIV_AT *da, int num_atoms, R2C_ATPAIR *ap, int num_cuts_to_check, AT_NUMB *pnum_comp, int *pcur_num_at)
int	replace_arom_bonds (inp_ATOM *at, int num_atoms, inp_ATOM *at2, int num_atoms2)
int	add_explicit_H (INP_ATOM_DATA *inp_cur_data)
void	free_underiv_temp_data (R2C_ATPAIR *ap, DERIV_AT *da, inp_ATOM *at2, INP_ATOM_DATA *inp_cur_data, int num_components)
void	remove_cut_derivs (int num_atoms, inp_ATOM *at, INP_ATOM_DATA *inp_cur_data, int i_component, int *errcode)
int	get_CO_opposite (inp_ATOM *at, int iat, int iord, int *iat_opposite, int *iord_opposite)
int	is_DERIV_RING_DMOX_DEOX_O (inp_ATOM *at, int cur_atom, int from_ord, DERIV_AT *da, DERIV_AT *da1)
int	is_DERIV_RING_DMOX_DEOX_N (inp_ATOM *at, int cur_atom, int from_ord, DERIV_AT *da, DERIV_AT *da1)
int	OAD_Edit_Underivatize (struct tagINCHI_CLOCK *ic, struct tagCANON_GLOBALS *pCG, ORIG_ATOM_DATA *orig_inp_data, int bOutputSdf, int bOutputReport, char *pSdfValue)
	Underivatize the original atom data (main underivatization procedure)
int	detect_r2c_Zatom (inp_ATOM *at, R2C_AT *da, int iZ)
int	cut_ring_to_chain (inp_ATOM *at, R2C_AT *da, int iZ)
int	Ring2Chain (struct tagINCHI_CLOCK *ic, struct tagCANON_GLOBALS *pCG, ORIG_ATOM_DATA *orig_inp_data)
	Convert rings to chains in the original atom data.
void	OAD_Edit_MergeComponentsAndRecreateOAD (ORIG_ATOM_DATA *orig_OrigAtomData, INP_ATOM_DATA *curr_InpAtomData, int num_components, int *errcode)
	Merge components and recreate original atom data.

Variables
static const int	DERIV_UNEXPADABLE
static const int	DERIV_REPL_N_WITH_O
static const int	DERIV_REPL_N_WITH_OH
const char *	pszDerivName []

Macro Definition Documentation

ALLOC_AP

#define ALLOC_AP

Value:

        if ( 0 < num_cuts_to_check && (lenAllocated_ap < num_cuts_to_check || !ap) ) {\
            if ( ap )\
                inchi_free( ap );\
            ap = (R2C_ATPAIR *) inchi_malloc( num_cuts_to_check * sizeof(ap[0]) );\
            if ( !ap ) {\
                ret = -1;\
                goto exit_function; /* malloc failure */\
            }\
            lenAllocated_ap = num_cuts_to_check;\
        }

CFLAG_MARK_BLOCK

#define CFLAG_MARK_BLOCK   2 /* for block detection */

CFLAG_MARK_BLOCK_INV

#define CFLAG_MARK_BLOCK_INV   ((char)~(CFLAG_MARK_BLOCK)) /* for block detection */

CFLAG_MARK_BRANCH

#define CFLAG_MARK_BRANCH   1 /* for main derivative traversal */

COUNT_ALL_NOT_DERIV

#define COUNT_ALL_NOT_DERIV   1 /* 1=> count ALL atoms that are not in deriv. agents */

DERIV_AMINE_tN

#define DERIV_AMINE_tN   0x0004 /* R1-N(-R2)-R3 tertiary amine */

DERIV_AT_LEN

#define DERIV_AT_LEN   4

DERIV_BRIDGE_NH

#define DERIV_BRIDGE_NH   0x0002 /* R1-NH-R2 amine */

DERIV_BRIDGE_O

#define DERIV_BRIDGE_O   0x0001 /* R1-O-R2 => R1-OH + HO-R2 */

DERIV_DANSYL

#define DERIV_DANSYL   0x2000 /* alcohol derivatives: R-O--SO2-C10H5-N(CH3)2 => R-OH */

DERIV_DUPLIC

#define DERIV_DUPLIC   0x0080 /* duplicated disconnection */

DERIV_NOT

#define DERIV_NOT   0x1000 /* cannot be a derivatization agent atom */

DERIV_RING

#define DERIV_RING   DERIV_RING_OUTSIDE_PRECURSOR

DERIV_RING2_OUTSIDE_PRECUR

#define DERIV_RING2_OUTSIDE_PRECUR   (DERIV_RING2_PRRLDD_OUTSIDE_PRECUR | DERIV_RING2_PPRDN_OUTSIDE_PRECUR)

DERIV_RING2_PPRDN_OUTSIDE_PRECUR

#define DERIV_RING2_PPRDN_OUTSIDE_PRECUR   0x1000 /* alcohol derivatives: R(=O)-N<C5H5 6-memb ring Piperidines; replace -N< with -OH */

DERIV_RING2_PRRLDD_OUTSIDE_PRECUR

#define DERIV_RING2_PRRLDD_OUTSIDE_PRECUR   0x0800 /* alcohol derivatives: R(=O)-N<C4H4 5-memb ring Pyrrolidides; replace -N< with -OH */

DERIV_RING_DMOX_DEOX

#define DERIV_RING_DMOX_DEOX   (DERIV_RING_DMOX_DEOX_O | DERIV_RING_DMOX_DEOX_N)

DERIV_RING_DMOX_DEOX_N

#define DERIV_RING_DMOX_DEOX_N   0x0200 /* =N- in a ring: /-O--CH2-\ DMOX, DEOX */

DERIV_RING_DMOX_DEOX_O

#define DERIV_RING_DMOX_DEOX_O   0x0400 /* -O- in a ring: R-C=N--------C<2Me or 2Et */

DERIV_RING_NH_OUTSIDE_PRECURSOR

#define DERIV_RING_NH_OUTSIDE_PRECURSOR   0x0010 /* -NH- in a ring */

DERIV_RING_O_OUTSIDE_PRECURSOR

#define DERIV_RING_O_OUTSIDE_PRECURSOR   0x0008 /* -O- in a ring */

DERIV_RING_OUTSIDE_PRECURSOR

#define DERIV_RING_OUTSIDE_PRECURSOR   (DERIV_RING_O_OUTSIDE_PRECURSOR | DERIV_RING_NH_OUTSIDE_PRECURSOR)

DERIV_RO_COX

#define DERIV_RO_COX   0x0100 /* alcohol derivatives: R-O--C(=O)C[n]F[2n+1] 0<n<4, R-O--C(=O)CH3, R-O--C(=O)-Phenyl */

DERIV_UNMARK

#define DERIV_UNMARK   0x0040 /* unmark the cut */

DERIV_X_OXIME

#define DERIV_X_OXIME   0x0020 /* comment out to disable */

IS_DA_NUM_LE

#define IS_DA_NUM_LE	(		DA,
			I,
			MX
	)		(((DA)->typ[I] && ((DA)->typ[I] & DERIV_UNEXPADABLE) == (DA)->typ[I]) || (DA)->num[I] <= (MX))

MAX_AT_DERIV

#define MAX_AT_DERIV   13 /* max. num of heavy atoms in removed derivatizing agent: RO-C(O)PheF5 */

MAX_PRRLDD_PPRDN_RING_SIZE

#define MAX_PRRLDD_PPRDN_RING_SIZE   PPRDN_RING_SIZE

MIN_AT_LEFT_DERIV

#define MIN_AT_LEFT_DERIV   2 /* was 3 before 2013-11-12; min num heavy atoms in derivative precursor = MIN_AT_LEFT_DERIV-1 */

MIN_PRRLDD_PPRDN_RING_SIZE

#define MIN_PRRLDD_PPRDN_RING_SIZE   PRRLDD_RING_SIZE

NO_ORD_VAL

#define NO_ORD_VAL   0x0037 /* not used */

NOT_AT_DERIV

#define NOT_AT_DERIV   99 /* DERIV_AT::num; rejected as > MAX_AT_DERIV */

OX_RING_SIZE

#define OX_RING_SIZE   5

PPRDN_RING_SIZE

#define PPRDN_RING_SIZE   6

PRRLDD_RING_SIZE

#define PRRLDD_RING_SIZE   5

R2C_EMPTY

#define R2C_EMPTY   127

UNDERIV_LEN

#define UNDERIV_LEN   128

UNDERIV_LEN2

#define UNDERIV_LEN2   128

UNDERIV_LIST_LEN

#define UNDERIV_LIST_LEN   2048

UNDERIV_LIST_LEN2

#define UNDERIV_LIST_LEN2   2048

UNDERIV_MAX_NUM

#define UNDERIV_MAX_NUM   512 /*max. number of records in szUnderivList */

Typedef Documentation

BIT_UNDERIV

typedef int BIT_UNDERIV

DERIV_AT

typedef struct tagDerivAttachment DERIV_AT

DerivBit

typedef enum tagDerivBit DerivBit

DerivId

typedef enum tagDerivId DerivId

R2C_AT

typedef struct tagRing2Chain R2C_AT

R2C_ATPAIR

typedef struct tagAtPair R2C_ATPAIR

Enumeration Type Documentation

tagDerivBit

enum tagDerivBit

Enumerator
DERIV_BIT_Acentonate
DERIV_BIT_Benzlidene
DERIV_BIT_BenzOX
DERIV_BIT_BuBorate
DERIV_BIT_Dansyl
DERIV_BIT_DEOX
DERIV_BIT_DMOX
DERIV_BIT_EtBorate
DERIV_BIT_EtOX
DERIV_BIT_HFB
DERIV_BIT_MeBorate
DERIV_BIT_MOX
DERIV_BIT_PFB
DERIV_BIT_PFP
DERIV_BIT_Piperidine
DERIV_BIT_Pyrrolidide
DERIV_BIT_TBDMS
DERIV_BIT_TFA
DERIV_BIT_TMS
DERIV_BIT_Unknown
DERIV_BIT_Acetate
DERIV_BIT_Benzoate
DERIV_ID_NUMBER

tagDerivId

enum tagDerivId

Enumerator
DERIV_ID_Acentonate
DERIV_ID_Benzlidene
DERIV_ID_BenzOX
DERIV_ID_BuBorate
DERIV_ID_Dansyl
DERIV_ID_DEOX
DERIV_ID_DMOX
DERIV_ID_EtBorate
DERIV_ID_EtOX
DERIV_ID_HFB
DERIV_ID_MeBorate
DERIV_ID_MOX
DERIV_ID_PFB
DERIV_ID_PFP
DERIV_ID_Piperidine
DERIV_ID_Pyrrolidide
DERIV_ID_TBDMS
DERIV_ID_TFA
DERIV_ID_TMS
DERIV_ID_Unknown
DERIV_ID_Acetate
DERIV_ID_Benzoate

Function Documentation

add_explicit_H()

int add_explicit_H

(

INP_ATOM_DATA *

inp_cur_data

)

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add_inp_ATOM()

int add_inp_ATOM	(	inp_ATOM *	at,
		int	len_at,
		int	len_cur,
		inp_ATOM *	add,
		int	len_add
	)

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add_to_da()

int add_to_da	(	DERIV_AT *	da,
		DERIV_AT *	add
	)

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check_arom_chain()

int check_arom_chain	(	inp_ATOM *	at,
		int	first,
		int	first_from,
		int	last,
		int	len
	)

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cmp_r2c_atpair()

int cmp_r2c_atpair	(	const void *	p1,
		const void *	p2
	)

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count_one_bond_atoms()

int count_one_bond_atoms	(	inp_ATOM *	at,
		DERIV_AT *	da,
		int	start,
		int	ord,
		char	cFlags,
		int *	bFound
	)

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cut_ring_to_chain()

int cut_ring_to_chain	(	inp_ATOM *	at,
		R2C_AT *	da,
		int	iZ
	)

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detect_r2c_Zatom()

int detect_r2c_Zatom	(	inp_ATOM *	at,
		R2C_AT *	da,
		int	iZ
	)

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DisconnectInpAtBond()

int DisconnectInpAtBond	(	inp_ATOM *	at,
		AT_NUMB *	nOldCompNumber,
		int	iat,
		int	neigh_ord
	)

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eliminate_deriv_not_in_list()

int eliminate_deriv_not_in_list	(	inp_ATOM *	at,
		DERIV_AT *	da,
		int	num_atoms,
		char *	szUnderivList,
		int	lenUnderivList,
		char *	szUnderivList2,
		int	lenUnderivList2,
		BIT_UNDERIV *	bitUnderivList
	)

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ExtractConnectedComponent()

int ExtractConnectedComponent	(	inp_ATOM *	at,
		int	num_at,
		int	component_number,
		inp_ATOM *	component_at
	)

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fill_out_bond_cuts()

int fill_out_bond_cuts	(	inp_ATOM *	at,
		DERIV_AT *	da,
		int	num_atoms,
		R2C_ATPAIR *	ap,
		int	num_cuts_to_check
	)

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free_underiv_temp_data()

void free_underiv_temp_data	(	R2C_ATPAIR *	ap,
		DERIV_AT *	da,
		inp_ATOM *	at2,
		INP_ATOM_DATA *	inp_cur_data,
		int	num_components
	)

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get_CO_opposite()

int get_CO_opposite	(	inp_ATOM *	at,
		int	iat,
		int	iord,
		int *	iat_opposite,
		int *	iord_opposite
	)

get_traversed_deriv_type()

int get_traversed_deriv_type	(	inp_ATOM *	at,
		DERIV_AT *	da,
		int	k,
		DERIV_AT *	da1,
		char	cFlags
	)

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has_atom_pair()

int has_atom_pair	(	R2C_ATPAIR *	ap,
		int	num_ap,
		AT_NUMB	at1,
		AT_NUMB	at2
	)

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has_atom_pair_seq()

int has_atom_pair_seq	(	R2C_ATPAIR *	ap,
		int	num_ap,
		AT_NUMB	at1,
		AT_NUMB	at2
	)

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is_Aryl()

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

is_C_Alk()

int is_C_Alk	(	inp_ATOM *	at,
		int	i,
		char	cFlags
	)

is_C_DB_O()

int is_C_DB_O	(	inp_ATOM *	at,
		int	i
	)

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is_C_or_S_DB_O()

int is_C_or_S_DB_O	(	inp_ATOM *	at,
		int	i
	)

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is_C_unsat_not_arom()

int is_C_unsat_not_arom	(	inp_ATOM *	at,
		int	i
	)

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is_CF3_or_linC3F7()

int is_CF3_or_linC3F7	(	inp_ATOM *	at,
		int	start,
		int	ord_prev
	)

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is_CF3_or_linC3F7a()

int is_CF3_or_linC3F7a	(	inp_ATOM *	at,
		int	start,
		int	iat_prev
	)

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is_Dansyl()

int is_Dansyl	(	inp_ATOM *	at,
		int	cur_atom,
		int	from_ord,
		DERIV_AT *	da,
		DERIV_AT *	da1
	)

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is_deriv_chain()

int is_deriv_chain	(	inp_ATOM *	at,
		int	start,
		int	num_atoms,
		DERIV_AT *	da1,
		int	idrv,
		char *	szUnderiv,
		int	lenUnderiv,
		char *	szUnderiv2,
		int	lenUnderiv2,
		BIT_UNDERIV *	bitUnderiv
	)

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is_deriv_chain2()

int is_deriv_chain2	(	inp_ATOM *	at,
		int	start,
		int	type,
		int	num,
		int	ord,
		int	idrv,
		char *	szUnderiv,
		int	lenUnderiv,
		char *	szUnderiv2,
		int	lenUnderiv2,
		BIT_UNDERIV *	bitUnderiv
	)

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is_deriv_chain_or_ring()

int is_deriv_chain_or_ring	(	inp_ATOM *	at,
		int	start,
		int	num_atoms,
		DERIV_AT *	da1,
		int *	idrv
	)

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is_DERIV_RING2_PRRLDD_PPRDN()

int is_DERIV_RING2_PRRLDD_PPRDN	(	inp_ATOM *	at,
		int	cur_atom,
		int	from_ord,
		DERIV_AT *	da,
		DERIV_AT *	da1
	)

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is_DERIV_RING_DMOX_DEOX_N()

int is_DERIV_RING_DMOX_DEOX_N	(	inp_ATOM *	at,
		int	cur_atom,
		int	from_ord,
		DERIV_AT *	da,
		DERIV_AT *	da1
	)

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is_DERIV_RING_DMOX_DEOX_O()

int is_DERIV_RING_DMOX_DEOX_O	(	inp_ATOM *	at,
		int	cur_atom,
		int	from_ord,
		DERIV_AT *	da,
		DERIV_AT *	da1
	)

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is_DERIV_RING_O_or_NH_OUTSIDE_PRECURSOR()

int is_DERIV_RING_O_or_NH_OUTSIDE_PRECURSOR	(	inp_ATOM *	at,
		int	start,
		int	num_atoms,
		DERIV_AT *	da1,
		int	idrv,
		char *	szUnderiv,
		int	lenUnderiv,
		char *	szUnderiv2,
		int	lenUnderiv2,
		BIT_UNDERIV *	bitUnderiv
	)

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is_Ethyl()

int is_Ethyl	(	inp_ATOM *	at,
		int	outside_point,
		int	attachment_point
	)

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is_Me_or_Et()

int is_Me_or_Et	(	inp_ATOM *	at,
		int	start,
		int	ord_prev
	)

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is_Methyl()

int is_Methyl	(	inp_ATOM *	at,
		int	attachment_point
	)

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is_Methyl_or_Etyl()

int is_Methyl_or_Etyl	(	inp_ATOM *	at,
		int	outside_point,
		int	attachment_point
	)

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is_nButyl()

int is_nButyl	(	inp_ATOM *	at,
		int	start,
		int	ord_prev
	)

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is_P_TB_N()

int is_P_TB_N	(	inp_ATOM *	at,
		int	i
	)

is_PentaFluoroPhenyl()

int is_PentaFluoroPhenyl	(	inp_ATOM *	at,
		int	outside_point,
		int	attachment_point
	)

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is_Phenyl()

int is_Phenyl	(	inp_ATOM *	at,
		int	outside_point,
		int	attachment_point
	)

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is_phenyl()

int is_phenyl	(	inp_ATOM *	at,
		int	start,
		int	ord_prev
	)

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is_possibly_deriv_neigh()

int is_possibly_deriv_neigh	(	inp_ATOM *	at,
		int	iat,
		int	iord,
		int	type,
		char	cFlags
	)

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is_Saturated_C()

int is_Saturated_C	(	inp_ATOM *	at,
		int	attachment_pont
	)

is_Si_IV()

int is_Si_IV	(	inp_ATOM *	at,
		int	i
	)

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is_silyl()

int is_silyl	(	inp_ATOM *	at,
		int	start,
		int	ord_prev
	)

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is_silyl2()

int is_silyl2	(	inp_ATOM *	at,
		int	start,
		int	from_at
	)

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make_single_cut()

int make_single_cut	(	inp_ATOM *	at,
		DERIV_AT *	da,
		int	iat,
		int	icut
	)

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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
	)

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mark_atoms_ap()

int mark_atoms_ap	(	inp_ATOM *	at,
		AT_NUMB	start,
		R2C_ATPAIR *	ap,
		int	num_ap,
		int	num,
		AT_NUMB	cFlags
	)

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mark_atoms_cFlags()

int mark_atoms_cFlags	(	inp_ATOM *	at,
		int	start,
		int	num,
		char	cFlags
	)

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mark_atoms_deriv()

int mark_atoms_deriv	(	inp_ATOM *	at,
		DERIV_AT *	da,
		int	start,
		int	num,
		char	cFlags,
		int *	pbFound
	)

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mark_deriv_agents()

int mark_deriv_agents	(	inp_ATOM *	at,
		DERIV_AT *	da,
		int	num_atoms,
		R2C_ATPAIR *	ap,
		int	num_cuts_to_check,
		AT_NUMB *	pnum_comp,
		int *	pcur_num_at
	)

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MarkRingSystemsInp()

int MarkRingSystemsInp	(	inp_ATOM *	at,
		int	num_atoms,
		int	start
	)

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OAD_Edit_MergeComponentsAndRecreateOAD()

void OAD_Edit_MergeComponentsAndRecreateOAD	(	ORIG_ATOM_DATA *	orig_OrigAtomData,
		INP_ATOM_DATA *	curr_InpAtomData,
		int	num_components,
		int *	errcode
	)

Merge components and recreate original atom data.

Parameters

orig_OrigAtomData	Pointer to original atom data structure
curr_InpAtomData	Pointer to current input atom data structure
num_components	Number of components
errcode	Pointer to error code

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OAD_Edit_Underivatize()

int OAD_Edit_Underivatize	(	struct tagINCHI_CLOCK *	ic,
		struct tagCANON_GLOBALS *	pCG,
		ORIG_ATOM_DATA *	orig_inp_data,
		int	bOutputSdf,
		int	bOutputReport,
		char *	pSdfValue
	)

Underivatize the original atom data (main underivatization procedure)

Parameters

ic	Pointer to INCHI_CLOCK structure
pCG	Pointer to CANON_GLOBALS structure
orig_inp_data	Pointer to original atom data structure
bOutputSdf	Flag indicating whether to output SDF
bOutputReport	Flag indicating whether to output report
pSdfValue	Pointer to SDF value

Returns

int Status code

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remove_cut_derivs()

void remove_cut_derivs	(	int	num_atoms,
		inp_ATOM *	at,
		INP_ATOM_DATA *	inp_cur_data,
		int	i_component,
		int *	errcode
	)

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remove_deriv()

int remove_deriv	(	DERIV_AT *	da1,
		int	idrv
	)

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remove_deriv_mark()

int remove_deriv_mark	(	DERIV_AT *	da1,
		int	idrv
	)

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replace_arom_bonds()

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

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Ring2Chain()

int Ring2Chain	(	struct tagINCHI_CLOCK *	ic,
		struct tagCANON_GLOBALS *	pCG,
		ORIG_ATOM_DATA *	orig_inp_data
	)

Convert rings to chains in the original atom data.

Parameters

ic	Pointer to INCHI_CLOCK structure
pCG	Pointer to CANON_GLOBALS structure
orig_inp_data	Pointer to original atom data structure

Returns

int Status code or the number of ring cuts made

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set_R2C_el_numbers()

void set_R2C_el_numbers

(

void

)

sort_merge_underiv()

int sort_merge_underiv	(	char *	pSdfValue,
		int	bOutputSdf,
		char *	szUnderivList,
		char	cDerivSeparator,
		const char *	pszUnderivPrefix,
		const char *	pszUnderivPostfix
	)

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subtract_DT_from_num_H()

int subtract_DT_from_num_H	(	int	num_atoms,
		inp_ATOM *	at
	)

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underiv_buf_clear()

void underiv_buf_clear

(

char *

szUnderiv

)

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underiv_compare()

int underiv_compare	(	const void *	p1,
		const void *	p2
	)

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underiv_list_add()

int underiv_list_add	(	char *	szUnderivList,
		int	lenUnderivList,
		const char *	szUnderiv,
		char	cDelimiter
	)

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underiv_list_add_two_cuts()

int underiv_list_add_two_cuts	(	char *	szUnderivList,
		int	lenUnderivList,
		char *	szUnderiv,
		const char	cDelim
	)

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underiv_list_get_last()

const char * underiv_list_get_last	(	const char *	szUnderivList,
		char	cDelimiter
	)

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unmark_atoms_cFlags()

int unmark_atoms_cFlags	(	inp_ATOM *	at,
		int	start,
		int	num,
		char	cFlags,
		char	cInvFlags
	)

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UnMarkDisconnectedComponents()

int UnMarkDisconnectedComponents

(

ORIG_ATOM_DATA *

orig_inp_data

)

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UnMarkOneComponent()

int UnMarkOneComponent	(	inp_ATOM *	at,
		int	num_atoms
	)

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UnMarkOtherIndicators()

int UnMarkOtherIndicators	(	inp_ATOM *	at,
		int	num_atoms
	)

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UnMarkRingSystemsInp()

int UnMarkRingSystemsInp	(	inp_ATOM *	at,
		int	num_atoms
	)

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Variable Documentation

DERIV_REPL_N_WITH_O

const int DERIV_REPL_N_WITH_O

static

Initial value:

= 0
 
| DERIV_X_OXIME
 
 
| DERIV_RING_DMOX_DEOX_N

DERIV_REPL_N_WITH_OH

const int DERIV_REPL_N_WITH_OH

static

Initial value:

= 0
 
| DERIV_RING2_PRRLDD_OUTSIDE_PRECUR
 
 
| DERIV_RING2_PPRDN_OUTSIDE_PRECUR

DERIV_UNEXPADABLE

const int DERIV_UNEXPADABLE

static

Initial value:

= 0
 
| DERIV_X_OXIME
 
 
| ( DERIV_RING_DMOX_DEOX_O | DERIV_RING_DMOX_DEOX_N )
 
 
 
| DERIV_RING2_PRRLDD_OUTSIDE_PRECUR
 
 
| DERIV_RING2_PPRDN_OUTSIDE_PRECUR
 
 
| DERIV_DANSYL

pszDerivName

const char* pszDerivName[]