#include "ichidrp.h"
#include "mode.h"
#include "mol_fmt.h"

Include dependency graph for inpdef.h:

This graph shows which files directly or indirectly include this file:

Data Structures
struct	tagInputAtom
	Structure describing an input atom. More...

struct	OAD_PolymerUnit
	Structure describing a polymer unit. More...

struct	OAD_Polymer
	Structure describing a polymer. More...

struct	OAD_AtProps
	Structure describing atom properties for OAD. More...

struct	OAD_V3000
	Structure describing v. 1.05 extended input supporting V3000; polymers. More...

struct	tagOrigAtom
	Structure describing original atom data. More...

struct	tagOriginalStruct
	Structure describing the original structure. More...

struct	tagAtomParmsForDrawing
	Structure describing atom parameters for drawing. More...

struct	tagInfoAtomData
	Structure describing information about atoms for InChI generation. More...

struct	tagInputAtomData
	Structure describing input atom data for InChI generation. More...

struct	tagNormCanonFlags
	Structure describing normalization and canonicalization flags. More...

struct	tagCompositeAtomData
	Structure describing composite atom data for InChI generation. More...

struct	tagStructFptrs
	Structure describing file pointers for structures. More...

struct	tagOAD_StructureEdits
	Structure describing structure edits. More...

Macros
#define	CLOSING_STARRED_SRU_IS_A_MUST 1

#define	ALLOW_CLOSING_SRU_VIA_HIGHER_ORDER_BOND 1

#define	ALLOW_CLOSING_SRU_VIA_DIRADICAL 1

#define	CLOSING_SRU_NOT_APPLICABLE 0

#define	CLOSING_SRU_RING 1

#define	CLOSING_SRU_HIGHER_ORDER_BOND 2

#define	CLOSING_SRU_DIRADICAL 3

#define	CLOSING_SRU_RING_OPENED 4

#define	CLOSING_SRU_MOVED_BRACKETS 5

#define	bDrawingLabelLeftShift endpoint

#define	ATT_NONE 0x0000

#define	ATT_ACIDIC_CO 0x0001

#define	ATT_ACIDIC_S 0x0002

#define	ATT_OO 0x0004

#define	ATT_ZOO 0x0008

#define	ATT_NO 0x0010

#define	ATT_N_O 0x0020

#define	ATT_ATOM_N 0x0040

#define	ATT_ATOM_P 0x0080

#define	ATT_OTHER_NEG_O 0x0100

#define	ATT_OTHER_ZO 0x0200

#define	ATT_OH_MINUS 0x0400

#define	ATT_O_PLUS 0x0800

#define	ATT_PROTON 0x1000

#define	ATT_HalAnion 0x2000

#define	ATT_HalAcid 0x4000

#define	ATT_NP_MINUS_V23 0x8000

#define	AT_FLAG_ISO_H_POINT 0x01

#define	PERIODIC_NUMBER_H 1

#define	NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2])

#define	NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N))

#define	FlagSC_0D 1

#define	FlagSB_0D 2

#define	SB_PARITY_FLAG 0x38

#define	SB_PARITY_SHFT 3

#define	SB_PARITY_MASK 0x07

#define	SB_PARITY_1(X) (X & SB_PARITY_MASK)

#define	SB_PARITY_2(X) (((X) >> SB_PARITY_SHFT) & SB_PARITY_MASK)

#define	NO_POLYMER -1

#define	POLYMER_REPRESENTATION_SOURCE_BASED 1

#define	POLYMER_REPRESENTATION_STRUCTURE_BASED 2

#define	POLYMER_REPRESENTATION_MIXED 3

#define	POLYMER_REPRESENTATION_UNRECOGNIZED 4

#define	ALLOW_MIXED_SRU_AND_MON 1

#define	POLYMER_STY_NON 0

#define	POLYMER_STY_SRU 1

#define	POLYMER_STY_MON 2

#define	POLYMER_STY_COP 3

#define	POLYMER_STY_MOD 4

#define	POLYMER_STY_CRO 5

#define	POLYMER_STY_MER 6

#define	POLYMER_SST_NON 0

#define	POLYMER_SST_ALT 1

#define	POLYMER_SST_RAN 2

#define	POLYMER_SST_BLK 3

#define	POLYMER_CONN_NON 0

#define	POLYMER_CONN_HT 1

#define	POLYMER_CONN_HH 2

#define	POLYMER_CONN_EU 3

#define	INF_STEREO_ABS 0x0001

#define	INF_STEREO_REL 0x0002

#define	INF_STEREO_RAC 0x0004

#define	INF_STEREO_NORM 0x0008

#define	INF_STEREO_INV 0x0010

#define	INF_STEREO 0x0020

#define	INF_STEREO_ABS_REL_RAC (INF_STEREO_ABS \| INF_STEREO_REL \| INF_STEREO_RAC)

#define	INF_STEREO_NORM_INV (INF_STEREO_NORM \| INF_STEREO_INV)

#define	MAX_LEN_REMOVED_PROTONS 128

#define	ADD_LEN_STRUCT_FPTRS 100 /* allocation increments */

#define	FLAG_INP_AT_CHIRAL 1

#define	FLAG_INP_AT_NONCHIRAL 2

#define	FLAG_SET_INP_AT_CHIRAL 4

#define	FLAG_SET_INP_AT_NONCHIRAL 8

#define	FLAG_SET_INP_LARGE_MOLS 16

Typedefs
typedef S_SHORT	ST_CAP_FLOW

typedef struct tagInputAtom	inp_ATOM
	Structure describing an input atom.

typedef struct OAD_PolymerUnit	OAD_PolymerUnit
	Structure describing a polymer unit.

typedef struct OAD_Polymer	OAD_Polymer
	Structure describing a polymer.

typedef struct OAD_AtProps	OAD_AtProps
	Structure describing atom properties for OAD.

typedef struct OAD_V3000	OAD_V3000
	Structure describing v. 1.05 extended input supporting V3000; polymers.

typedef struct tagOrigAtom	ORIG_ATOM_DATA
	Structure describing original atom data.

typedef struct tagOriginalStruct	ORIG_STRUCT
	Structure describing the original structure.

typedef struct tagAtomParmsForDrawing	inf_ATOM
	Structure describing atom parameters for drawing.

typedef struct tagInfoAtomData	INF_ATOM_DATA
	Structure describing information about atoms for InChI generation.

typedef struct tagInputAtomData	INP_ATOM_DATA
	Structure describing input atom data for InChI generation.

typedef INP_ATOM_DATA	INP_ATOM_DATA2[TAUT_NUM]

typedef struct tagNormCanonFlags	NORM_CANON_FLAGS
	Structure describing normalization and canonicalization flags.

typedef struct tagCompositeAtomData	COMP_ATOM_DATA
	Structure describing composite atom data for InChI generation.

typedef long	INCHI_FPTR

typedef struct tagStructFptrs	STRUCT_FPTRS
	Structure describing file pointers for structures.

typedef struct tagOAD_StructureEdits	OAD_StructureEdits
	Structure describing structure edits.

Functions
int	bInchiTimeIsOver (struct tagINCHI_CLOCK ic, struct tagInchiTime TickEnd)

int	CreateOrigInpDataFromMolfile (INCHI_IOSTREAM inp_file, ORIG_ATOM_DATA orig_at_data, int bMergeAllInputStructures, int bGetOrigCoord, int bDoNotAddH, int treat_polymers, int treat_NPZz, const char pSdfLabel, char pSdfValue, unsigned long lSdfId, long lMolfileNumber, INCHI_MODE pInpAtomFlags, int err, char *pStrErr, int bNoWarnings)
	Create original input data from molfile.

int	InchiToOrigAtom (INCHI_IOSTREAM infile, ORIG_ATOM_DATA orig_at_data, int bMergeAllInputStructures, int bGetOrigCoord, int bDoNotAddH, int vABParityUnknown, INPUT_TYPE nInputType, char pSdfLabel, char pSdfValue, unsigned long lSdfId, INCHI_MODE pInpAtomFlags, int err, char pStrErr)
	Convert InChI representation to original atom data.

int	MarkDisconnectedComponents (ORIG_ATOM_DATA *orig_at_data, int bProcessOldCompNumbers)
	Mark disconnected components in the original atom data.

int	DisconnectSalts (ORIG_ATOM_DATA *orig_inp_data, int bDisconnect)
	Disconnect salts in the original atom data.

int	DisconnectMetals (ORIG_ATOM_DATA orig_inp_data, int bCheckMetalValence, INCHI_MODE bTautFlagsDone)
	Disconnect metals in the original atom data.

int	bMayDisconnectMetals (ORIG_ATOM_DATA orig_inp_data, int bCheckMetalValence, INCHI_MODE bTautFlagsDone)
	Check if metals may be disconnected in the original atom data.

int	bHasMetalAtom (ORIG_ATOM_DATA *orig_inp_data)
	Check if there is a metal atom in the original atom data.

int	FixAdjacentRadicals (int num_inp_atoms, inp_ATOM *at)
	Fix adjacent radicals in the input atoms.

int	fix_odd_things (int num_atoms, inp_ATOM *at, int bFixBug, int bFixNonUniformDraw)
	Fix odd things in the input atoms.

int	post_fix_odd_things (int num_atoms, inp_ATOM *at)
	Post-fix odd things in the input atoms (does nothing, returns 0)

int	remove_ion_pairs (int num_atoms, inp_ATOM *at)
	Remove ion pairs from the input atoms.

int	bFoundFeature (inp_ATOM *at, int num_atoms)
	Check if a feature is found in the input atoms ???

int	UnMarkRingSystemsInp (inp_ATOM *at, int num_atoms)
	Unmark ring systems in the input atoms.

int	OrigAtData_WriteToSDfile (const ORIG_ATOM_DATA inp_at_data, INCHI_IOSTREAM fcb, const char name, const char comment, int bChiralFlag, int bAtomsDT, const char szLabel, const char szValue)
	Write original atom data to SD file.

void	FreeInpAtom (inp_ATOM **at)
	Free input atom array.

void	FreeInfAtom (inf_ATOM **at)
	Free information atom array (same as FreeInpAtom)

void	FreeOrigAtData (ORIG_ATOM_DATA *orig_at_data)
	Free original atom data.

void	FreeExtOrigAtData (OAD_Polymer pd, OAD_V3000 v3k)
	Free extended original atom data (polymers and V3000)

void	FreeInpAtomData (INP_ATOM_DATA *inp_at_data)
	Free input atom data.

void	FreeCompAtomData (COMP_ATOM_DATA *inp_at_data)
	Free composite atom data.

void	FreeInfoAtomData (INF_ATOM_DATA *inf_at_data)
	Free information atom data.

int	OAD_StructureEdits_Init (OAD_StructureEdits *ed)
	Initialize structure edits.

void	OAD_StructureEdits_Clear (OAD_StructureEdits *ed)
	Clear structure edits.

void	OAD_StructureEdits_DebugPrint (OAD_StructureEdits *ed)
	Debug print structure edits.

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.

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)

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.

int	OAD_ValidatePolymerAndPseudoElementData (ORIG_ATOM_DATA orig_at_data, int treat_polymers, int bNPZz, char pStrErr, int bNoWarnings)
	Validate polymer and pseudo-element data in the original atom data.

void	OAD_ValidateAndSortOutPseudoElementAtoms (ORIG_ATOM_DATA orig_at_data, int treat_polymers, int use_zz, int err, char *pStrErr)
	Validate and sort out pseudo-element atoms in the original atom data.

int	OAD_Polymer_GetRepresentation (OAD_Polymer *p)
	Get polymer representation type.

int	OAD_Polymer_CyclizeCloseableUnits (ORIG_ATOM_DATA orig_at_data, int use_zz, char pStrErr, int bNoWarnings)
	Cyclize closeable units in the original atom data.

int	OAD_Polymer_FindRingSystems (OAD_Polymer pd, inp_ATOM at, int nat, int num_inp_bonds, int num_ring_sys, int *size_ring_sys, int start)
	Find ring systems in the polymer data.

void	OAD_Polymer_SetAtProps (OAD_Polymer pd, inp_ATOM at, int nat, int num_inp_bonds, OAD_AtProps aprops, int *cano_nums)
	Set atom properties for the polymer data.

int	OAD_Polymer_CompareBackboneBondsSeniority (int b1, int b2, OAD_AtProps *aprops)
	Compare backbone bonds seniority (for sorting SRU cyclizing bonds (PS=='frame-shift') in descending order)

int	OAD_Polymer_CompareRanksOfTwoAtoms (int atom1, int atom2, OAD_AtProps *aprops)
	Compare ranks of two atoms (compare seniority of two atoms in polymer SRU)

int	OAD_Polymer_IsFirstAtomRankLower (int atom1, int atom2, OAD_AtProps *aprops)
	Check if the first atom has a lower rank than the second atom (check seniority of two atoms in polymer SRU)

int	OAD_PolymerUnit_SetReopeningDetails (OAD_PolymerUnit u, inp_ATOM at)
	Set reopening details for a polymer unit.

void	OAD_PolymerUnit_SortBackboneBondsAndSetSeniors (OAD_PolymerUnit u, inp_ATOM at, OAD_AtProps aprops, int senior_bond)
	Sort backbone bonds and set seniors for a polymer unit.

void	OAD_Polymer_FindBackbones (ORIG_ATOM_DATA where_to_look, COMP_ATOM_DATA composite_norm_data, int err, char pStrErr)
	Find backbones in the original atom data.

int	OAD_Polymer_PrepareWorkingSet (OAD_Polymer p, int cano_nums, int compnt_nums, OAD_PolymerUnit units2, int unum)
	Prepare working set for polymer processing (replace original atom numbers in polymer data with (canonical num + 1))

void	OAD_Polymer_Free (OAD_Polymer *p)
	Free polymer data structure.

void	OAD_Polymer_DebugTrace (OAD_Polymer *p)
	Debug trace for polymer data structure (print the whole polymer data)

void	OAD_Polymer_SmartReopenCyclizedUnits (OAD_Polymer p, inp_ATOM at, int nat, int *num_inp_bonds)
	Smartly reopen cyclized units in the original atom data (open pre-cyclized CRUs appropriately (i.e., make frame shift))

int	OAD_Polymer_PrepareFoldCRUEdits (ORIG_ATOM_DATA orig_at_data, char sinchi_noedits, char saux_noedits, char sinchi, char saux, OAD_StructureEdits ed)
	Prepare CRU edits for polymer data structure (prepare CRU fold edits as suggested by the strings with preliminary generated interim (1.05+ flavoured) InChI and AuxInfo)

int	OAD_Polymer_PrepareFrameShiftEdits (ORIG_ATOM_DATA orig_at_data, char sinchi, char saux, OAD_StructureEdits ed)
	Prepare frame shift edits for polymer data structure (prepare frame shift edits as suggested by the strings with preliminary generated interim (1.05+ flavoured) InChI and AuxInfo)

OAD_PolymerUnit *	OAD_PolymerUnit_New (int maxatoms, int maxbonds, int id, int label, int type, int subtype, int conn, char smt, int na, INT_ARRAY alist, int nb, INT_ARRAY blist, int nbkbonds, int *bkbonds)
	Create a new polymer unit.

OAD_PolymerUnit *	OAD_PolymerUnit_CreateCopy (OAD_PolymerUnit *u)
	Create a copy of a polymer unit.

void	OAD_PolymerUnit_Free (OAD_PolymerUnit *unit)
	Free a polymer unit.

void	OAD_PolymerUnit_DebugTrace (OAD_PolymerUnit *unit)
	Debug trace for a polymer unit (print the whole polymer unit)

void	OAD_PolymerUnit_FindEndsAndCaps (OAD_PolymerUnit unit, ORIG_ATOM_DATA orig_at_data, int end1, int cap1, int cap1_is_undef, int end2, int cap2, int cap2_is_undef, int err, char pStrErr)
	Find the ends and caps of a polymer unit.

void	OAD_PolymerUnit_SetEndsAndCaps (OAD_PolymerUnit unit, ORIG_ATOM_DATA orig_at_data, int err, char pStrErr)
	Set the ends and caps of a polymer unit.

void	OAD_PolymerUnit_UnlinkCapsAndConnectEndAtoms (OAD_PolymerUnit unit, ORIG_ATOM_DATA orig_at_data, int err, char pStrErr)
	Unlink caps and connect end atoms of a polymer unit.

void	OAD_PolymerUnit_PrepareToFrameShift (OAD_PolymerUnit unit, ORIG_ATOM_DATA orig_at_data, int err, char pStrErr)
	Prepare a polymer unit for frame shifting.

int	OAD_CollectReachableAtoms (ORIG_ATOM_DATA orig_at_data, int start_atom, int nforbidden_bonds, int forbidden_bonds, int n_reachable, int reachable, int err, char pStrErr)
	Find reachable atoms from a given start atom.

void	OAD_CollectBackboneAtoms (ORIG_ATOM_DATA at_data, int na, int alist, int end_atom1, int end_atom2, int nbkatoms, int bkatoms, int err, char pStrErr)
	Collect backbone atoms from a polymer unit.

void	OAD_CollectBackboneBonds (ORIG_ATOM_DATA at_data, int na, int alist, int end_atom1, int end_atom2, int nbkbonds, int bkbonds, int err, char *pStrErr)
	Collect backbone bonds from a polymer unit.

void	OAD_PolymerUnit_DelistIntraRingBackboneBonds (OAD_PolymerUnit unit, ORIG_ATOM_DATA orig_at_data, int err, char pStrErr)
	Collect backbone bonds from a polymer unit and delist intra-ring backbone bonds.

void	OAD_PolymerUnit_DelistHighOrderBackboneBonds (OAD_PolymerUnit unit, ORIG_ATOM_DATA orig_at_data, COMP_ATOM_DATA composite_norm_data, int err, char *pStrErr)
	Collect high-order backbone bonds from a polymer unit.

void	OAD_PolymerUnit_SortBackboneBonds (OAD_PolymerUnit u, OAD_AtProps aprops, int *bnum)
	Collect backbone bonds from a polymer unit and sort them.

void	OAD_PolymerUnit_ReopenCyclized (OAD_PolymerUnit u, inp_ATOM at, OAD_AtProps aprops, int nat, int num_inp_bonds)
	Collect backbone atoms from a polymer unit.

int	OAD_PolymerUnit_CompareAtomLists (OAD_PolymerUnit u1, OAD_PolymerUnit u2)
	Compare two polymer units based on their atom lists.

int	OAD_PolymerUnit_CompareAtomListsMod (OAD_PolymerUnit u1, OAD_PolymerUnit u2)
	Compare two polymer units based on their atom lists with modifications.

int	OAD_PolymerUnit_OrderBondAtomsAndBondsThemselves (OAD_PolymerUnit u, int n_stars, int stars)
	Order bond atoms and bonds themselves in a polymer unit.

int	OAD_PolymerUnit_HasMetal (OAD_PolymerUnit u, inp_ATOM at)
	Check if a polymer unit has a specific atom (e.g., metal)

int	FixUnkn0DStereoBonds (inp_ATOM *at, int num_at)
	Fix unknown stereo bonds in the input atoms.

inf_ATOM *	CreateInfAtom (int num_atoms)
	Create/allocate a Inf Atom structure.

inp_ATOM *	CreateInpAtom (int num_atoms)
	Create/allocate a Inp Atom structure.

int	CreateInfoAtomData (INF_ATOM_DATA *inf_at_data, int num_atoms, int num_components)
	Create a Info Atom Data structure.

int	AllocateInfoAtomData (INF_ATOM_DATA *inf_at_data, int num_atoms, int num_components)
	Allocate memory for Info Atom Data structure.

int	DuplicateInfoAtomData (INF_ATOM_DATA inf_at_data_to, const INF_ATOM_DATA inf_at_data_from)
	Duplicate Info Atom Data structure.

int	CreateInpAtomData (INP_ATOM_DATA *inp_at_data, int num_atoms, int create_at_fixed_bonds)
	Create a Inp Atom Data structure.

int	CreateCompAtomData (COMP_ATOM_DATA *inp_at_data, int num_atoms, int num_components, int bIntermediateTaut)
	Create a Comp Atom Data structure.

void	PrintFileName (const char fmt, FILE out_file, const char *szFname)
	Print the file name.

void	MySleep (unsigned long ms)
	Sleep for a specified amount of time.

int	ReconcileAllCmlBondParities (inp_ATOM *at, int num_atoms, int bDisconnected)
	Reconcile all CML bond parities in the input atoms.

Macro Definition Documentation

◆ ADD_LEN_STRUCT_FPTRS

#define ADD_LEN_STRUCT_FPTRS 100 /* allocation increments */

◆ ALLOW_CLOSING_SRU_VIA_DIRADICAL

#define ALLOW_CLOSING_SRU_VIA_DIRADICAL 1

◆ ALLOW_CLOSING_SRU_VIA_HIGHER_ORDER_BOND

#define ALLOW_CLOSING_SRU_VIA_HIGHER_ORDER_BOND 1

◆ ALLOW_MIXED_SRU_AND_MON

#define ALLOW_MIXED_SRU_AND_MON 1

allow simultaneous presence of source-based and structure-based units in embedding copolymer unit

◆ AT_FLAG_ISO_H_POINT

#define AT_FLAG_ISO_H_POINT 0x01

may have isotopic H

◆ ATT_ACIDIC_CO

#define ATT_ACIDIC_CO 0x0001

◆ ATT_ACIDIC_S

#define ATT_ACIDIC_S 0x0002

◆ ATT_ATOM_N

#define ATT_ATOM_N 0x0040

◆ ATT_ATOM_P

#define ATT_ATOM_P 0x0080

◆ ATT_HalAcid

#define ATT_HalAcid 0x4000

◆ ATT_HalAnion

#define ATT_HalAnion 0x2000

◆ ATT_N_O

#define ATT_N_O 0x0020

◆ ATT_NO

#define ATT_NO 0x0010

◆ ATT_NONE

#define ATT_NONE 0x0000

◆ ATT_NP_MINUS_V23

#define ATT_NP_MINUS_V23 0x8000

=N(-) or =P(-) where = previously was triple

◆ ATT_O_PLUS

#define ATT_O_PLUS 0x0800

-OH2(+), =OH(+), -OH(+)-, OH3(+), =O(+)-, etc; O=O,S,Se,Te

◆ ATT_OH_MINUS

#define ATT_OH_MINUS 0x0400

OH(-), O=O,S,Se,Te

◆ ATT_OO

#define ATT_OO 0x0004

◆ ATT_OTHER_NEG_O

#define ATT_OTHER_NEG_O 0x0100

◆ ATT_OTHER_ZO

#define ATT_OTHER_ZO 0x0200

-Z=O or =Z=O

◆ ATT_PROTON

#define ATT_PROTON 0x1000

◆ ATT_ZOO

#define ATT_ZOO 0x0008

◆ bDrawingLabelLeftShift

#define bDrawingLabelLeftShift endpoint

for drawing only

◆ CLOSING_SRU_DIRADICAL

#define CLOSING_SRU_DIRADICAL 3

◆ CLOSING_SRU_HIGHER_ORDER_BOND

#define CLOSING_SRU_HIGHER_ORDER_BOND 2

◆ CLOSING_SRU_MOVED_BRACKETS

#define CLOSING_SRU_MOVED_BRACKETS 5

◆ CLOSING_SRU_NOT_APPLICABLE

#define CLOSING_SRU_NOT_APPLICABLE 0

◆ CLOSING_SRU_RING

#define CLOSING_SRU_RING 1

◆ CLOSING_SRU_RING_OPENED

#define CLOSING_SRU_RING_OPENED 4

◆ CLOSING_STARRED_SRU_IS_A_MUST

#define CLOSING_STARRED_SRU_IS_A_MUST 1

◆ FLAG_INP_AT_CHIRAL

#define FLAG_INP_AT_CHIRAL 1

◆ FLAG_INP_AT_NONCHIRAL

#define FLAG_INP_AT_NONCHIRAL 2

◆ FLAG_SET_INP_AT_CHIRAL

#define FLAG_SET_INP_AT_CHIRAL 4

◆ FLAG_SET_INP_AT_NONCHIRAL

#define FLAG_SET_INP_AT_NONCHIRAL 8

◆ FLAG_SET_INP_LARGE_MOLS

#define FLAG_SET_INP_LARGE_MOLS 16

◆ FlagSB_0D

#define FlagSB_0D 2

bUsed0DParity

◆ FlagSC_0D

#define FlagSC_0D 1

bUsed0DParity

◆ INF_STEREO

#define INF_STEREO 0x0020

◆ INF_STEREO_ABS

#define INF_STEREO_ABS 0x0001

◆ INF_STEREO_ABS_REL_RAC

#define INF_STEREO_ABS_REL_RAC (INF_STEREO_ABS | INF_STEREO_REL | INF_STEREO_RAC)

◆ INF_STEREO_INV

#define INF_STEREO_INV 0x0010

◆ INF_STEREO_NORM

#define INF_STEREO_NORM 0x0008

◆ INF_STEREO_NORM_INV

#define INF_STEREO_NORM_INV (INF_STEREO_NORM | INF_STEREO_INV)

◆ INF_STEREO_RAC

#define INF_STEREO_RAC 0x0004

◆ INF_STEREO_REL

#define INF_STEREO_REL 0x0002

◆ MAX_LEN_REMOVED_PROTONS

#define MAX_LEN_REMOVED_PROTONS 128

◆ NO_POLYMER

#define NO_POLYMER -1

◆ NUM_ISO_H

#define NUM_ISO_H	(	AT,
		N
	)	(AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2])

◆ NUMH

#define NUMH	(	AT,
		N
	)	(AT[N].num_H + NUM_ISO_H(AT, N))

◆ PERIODIC_NUMBER_H

#define PERIODIC_NUMBER_H 1

◆ POLYMER_CONN_EU

#define POLYMER_CONN_EU 3

◆ POLYMER_CONN_HH

#define POLYMER_CONN_HH 2

◆ POLYMER_CONN_HT

#define POLYMER_CONN_HT 1

◆ POLYMER_CONN_NON

#define POLYMER_CONN_NON 0

◆ POLYMER_REPRESENTATION_MIXED

#define POLYMER_REPRESENTATION_MIXED 3

◆ POLYMER_REPRESENTATION_SOURCE_BASED

#define POLYMER_REPRESENTATION_SOURCE_BASED 1

◆ POLYMER_REPRESENTATION_STRUCTURE_BASED

#define POLYMER_REPRESENTATION_STRUCTURE_BASED 2

◆ POLYMER_REPRESENTATION_UNRECOGNIZED

#define POLYMER_REPRESENTATION_UNRECOGNIZED 4

◆ POLYMER_SST_ALT

#define POLYMER_SST_ALT 1

◆ POLYMER_SST_BLK

#define POLYMER_SST_BLK 3

◆ POLYMER_SST_NON

#define POLYMER_SST_NON 0

◆ POLYMER_SST_RAN

#define POLYMER_SST_RAN 2

◆ POLYMER_STY_COP

#define POLYMER_STY_COP 3

copolymer unit embedding >1 subunits (may be SRU, MON, MER, CRO, MOD; others not supported yet)

◆ POLYMER_STY_CRO

#define POLYMER_STY_CRO 5

copolymer subunit only, designates cross-linked version of SRU

◆ POLYMER_STY_MER

#define POLYMER_STY_MER 6

copolymer subunit only, source-based with no homopolymerize

◆ POLYMER_STY_MOD

#define POLYMER_STY_MOD 4

copolymer subunit only, designates chemical modification of SRU

◆ POLYMER_STY_MON

#define POLYMER_STY_MON 2

source-based polymer unit or copolymer subunit

◆ POLYMER_STY_NON

#define POLYMER_STY_NON 0

◆ POLYMER_STY_SRU

#define POLYMER_STY_SRU 1

structure-based unit or copolymer subunit

◆ SB_PARITY_1

#define SB_PARITY_1 ( X ) (X & SB_PARITY_MASK)

refers to connected structure

◆ SB_PARITY_2

#define SB_PARITY_2 ( X ) (((X) >> SB_PARITY_SHFT) & SB_PARITY_MASK)

refers to connected structure

◆ SB_PARITY_FLAG

#define SB_PARITY_FLAG 0x38

mask for disconnected metal parity if it is different

◆ SB_PARITY_MASK

#define SB_PARITY_MASK 0x07

◆ SB_PARITY_SHFT

#define SB_PARITY_SHFT 3

number of right shift bits to get disconnected metal parity

Typedef Documentation

◆ COMP_ATOM_DATA

typedef struct tagCompositeAtomData COMP_ATOM_DATA

Structure describing composite atom data for InChI generation.

Parameters

at	Array of input atoms
num_at	Number of atoms
num_removed_H	Number of removed hydrogens
num_bonds	Number of bonds
num_isotopic	Number of isotopic atoms
bExists	Flag indicating if the atom data exists
bDeleted	Flag indicating if the atom data is deleted
bHasIsotopicLayer	Flag indicating if the atom data has isotopic layer
bTautomeric	Flag indicating if the atom data is tautomeric
nNumRemovedProtons	Number of removed protons
nNumRemovedProtonsIsotopic	Array with number of removed isotopic protons per isotope
num_iso_H	Array with number of isotopic hydrogens per isotope
nOffsetAtAndH	Array with offsets for atoms and hydrogens
num_components	Number of components

◆ INCHI_FPTR

typedef long INCHI_FPTR

◆ inf_ATOM

typedef struct tagAtomParmsForDrawing inf_ATOM

Structure describing atom parameters for drawing.

Parameters

at_string	Atom string for drawing
DrawingLabelLeftShift	Left shift for drawing label
DrawingLabelLength	Length of drawing label
nCanonNbr	Canonical number; if zero then do not use all data for the atom
nCanonEquNbr	Canonical equivalence number
nTautGroupCanonNbr	Tautomeric group canonical number
nTautGroupEquNbr	Tautomeric group equivalence number
cFlags	Additional flags (e.g., AT_FLAG_ISO_H_POINT)
nDebugData	Debug data (only if DISPLAY_DEBUG_DATA is defined)
cHighlightTheAtom	Flag indicating whether to highlight the atom
cStereoCenterParity	Stereo center parity
cStereoBondParity	Stereo bond parities
cStereoBondWarning	Stereo bond warnings
cStereoBondNumber	Stereo bond numbers

◆ INF_ATOM_DATA

typedef struct tagInfoAtomData INF_ATOM_DATA

Structure describing information about atoms for InChI generation.

Parameters

at	Array of atoms for InChI generation
num_at	Number of atoms
StereoFlags	Stereo flags
num_components	Number of components
pStereoFlags	Pointer to stereo flags per component
nNumRemovedProtons	Number of removed protons
num_removed_iso_H	Number of removed/exchangeable isotopic hydrogens
num_iso_H	Array with number of removed isotopic hydrogens per isotope
szRemovedProtons	String with removed protons

◆ inp_ATOM

typedef struct tagInputAtom inp_ATOM

Structure describing an input atom.

Parameters

elname	Name of chemical element
el_number	Number of the element in the Periodic Table
neighbor	Positions (from 0) of the neighbors in the inp_ATOM array
orig_at_number	Original atom number
orig_compt_at_numb	Original atom number within the component before terminal H removal
bond_stereo	Bond stereo information (1=Up,4=Either,6=Down; this atom is at the pointing wedge, negative => on the opposite side; 3=Either double bond)
bond_type	Bond type (1..4; 4="aromatic", should be discouraged on input)
valence	Valence (for most chemists, it is coordination number, CN; number of bonds = number of neighbors)
chem_bonds_valence	Chemical bonds valence (for most chemists, it is what usually called valence; sum of bond types (type 4 needs special treatment))
num_H	Number of implicit hydrogens, including D and T
num_iso_H	Number of implicit 1H, 2H(D), 3H(T) < 16
iso_atw_diff	Isotopic atomic weight difference (=0 => natural isotopic abundances; >0 => (mass) - (mass of the most abundant isotope) + 1; <0 => (mass) - (mass of the most abundant isotope))
charge	Charge
radical	Radical type (RADICAL_SINGLET, RADICAL_DOUBLET, or RADICAL_TRIPLET)
bAmbiguousStereo	Flag indicating ambiguous stereochemistry
cFlags	Additional flags (e.g., AT_FLAG_ISO_H_POINT)
at_type	Atom type (ATT_NONE, ATT_ACIDIC, etc.)
component	Number of the structure component > 0
endpoint	ID of a tautomeric group
c_point	ID of a positive charge group
x,y,z	3D coordinates
bUsed0DParity	Bit flags for 0D parities (bit=1 => stereobond; bit=2 => stereocenter)
p_parity	0D tetrahedral parity
p_orig_at_num	Original atom numbers of neighbors for tetrahedral stereochemistry
sb_ord	Stereo bond/neighbor ordering number, starts from 0
sn_ord	Ord. num. of the neighbor adjacent to the SB; starts from 0; -1 means removed explicit H
sb_parity	Stereo bond parities
sn_orig_at_num	Original atom numbers of neighbors for stereobonds
bCutVertex	Flag indicating if the atom is a cut vertex (part of ring system analysis)
nRingSystem	Ring system number (part of ring system analysis)
nNumAtInRingSystem	Number of atoms in the ring system (part of ring system analysis)
nBlockSystem	Block system number (part of ring system analysis)
nDistanceFromTerminal	Distance from terminal atom or ring system (terminal atom or ring system has 1, next has 2, etc.)

◆ INP_ATOM_DATA

typedef struct tagInputAtomData INP_ATOM_DATA

Structure describing input atom data for InChI generation.

Parameters

at	Array of input atoms
at_fixed_bonds	Array of input atoms with fixed bonds (tautomeric case, added or removed H)
num_at	Number of atoms
num_removed_H	Number of removed hydrogens
num_bonds	Number of bonds
num_isotopic	Number of isotopic atoms
bExists	Flag indicating if the atom data exists
bDeleted	Flag indicating if the atom data is deleted
bHasIsotopicLayer	Flag indicating if the atom data has isotopic layer
bTautomeric	Flag indicating if the atom data is tautomeric
bTautPreprocessed	Flag indicating if the atom data is tautomeric and preprocessed
nNumRemovedProtons	Number of removed protons
nNumRemovedProtonsIsotopic	Array with number of removed isotopic protons per isotope
num_iso_H	Array with number of isotopic hydrogens per isotope
bTautFlags	Tautomeric flags
bTautFlagsDone	Tautomeric flags done
bNormalizationFlags	Normalization flags

◆ INP_ATOM_DATA2

typedef INP_ATOM_DATA INP_ATOM_DATA2[TAUT_NUM]

◆ NORM_CANON_FLAGS

typedef struct tagNormCanonFlags NORM_CANON_FLAGS

Structure describing normalization and canonicalization flags.

Parameters

bTautFlags	Tautomeric flags
bTautFlagsDone	Tautomeric flags done
bNormalizationFlags	Normalization flags
nCanonFlags	Canonicalization flags

◆ OAD_AtProps

typedef struct OAD_AtProps OAD_AtProps

Structure describing atom properties for OAD.

Parameters

erank	Rank of element; 2 - C, >2 - rank of heteroatom in chain, O > S > Se > Te > N ...., Rule 4
ring_erank	0 - not ring or just carbocycle, >2 - rank of senior heteroatom in this cycle, according to Rule 2 ( N > O >... )
ring_num	Ring number
ring_size	0 or ring system size that is: ring_erank != 0 heterocycle of ring_size ring_erank==0 && ring_size>0 carbocycle of ring_size

◆ OAD_Polymer

typedef struct OAD_Polymer OAD_Polymer

Structure describing a polymer.

Parameters

units	array of pointers to units
n	number of units
n_pzz	number of polymeric Zz atoms
pzz	polymeric Zz atoms
really_do_frame_shift	flag indicating whether to do frame shift
frame_shift_scheme	frame shift analysis scheme
treat	treatment flag
representation	representation type
is_in_reconn	flag indicating whether polymer is in reconnection mode
edit_repeats	flag indicating whether repeats need to be edited (-1 unknown, to be checked; 0 no, no edits required; 1 yes, edits are necessary)

◆ OAD_PolymerUnit

typedef struct OAD_PolymerUnit OAD_PolymerUnit

Structure describing a polymer unit.

Parameters

id	It is what is called 'Sgroup number' in CTFILE
type	Type as by MDL format (STY)
subtype	Subtype as by MDL format (SST)
conn	Connection scheme as by MDL format (SCN)
label	It is what is called 'unique Sgroup identifier' CTFILE
na	Number of atoms in the unit
nb	Number of bonds in the unit
cyclizable	=1 if frame shift via CRU 'cyclization' is applicable
cyclized	=1 if CRU already was frame_shift' treated
xbr1	Bracket ends coordinates (SDI)
xbr2	Bracket ends coordinates (SDI)
smt	Sgroup Subscript (SMT)
representation
cap1	Cap atom 1
end_atom1	End atom 1
end_atom2	End atom 2
cap2	Cap atom 2
cap1_is_undef	=1 if cap1 is undefined (star)
cap2_is_undef	=1 if cap2 is undefined (star)
alist	List of atoms in the unit (SAL)
blist	Bonds in the unit as list [atom1, atom2; atom1, atom2,..] for crossing bonds (S)
maxbkbonds	Max (allocd) number of frame_shift involved bonds
nbkbonds	Number of bkbonds in CRU main chain bkbonds are [breakable at possible frame shift] backbone bonds in between "left" end_atom1 and "right" end_atom2 ends (they may be only single-order non-intraring bonds)
bkbonds	List of [breakable] backbone bonds [(a1,a2), (a3,a4),...]

◆ OAD_StructureEdits

typedef struct tagOAD_StructureEdits OAD_StructureEdits

Structure describing structure edits.

Parameters

del_atom	Array of deleted atom indices
del_bond	Array of deleted bond indices
new_bond	Array of new bond indices
mod_bond	Array of modified bond indices
mod_coord	Array of modified coordinate indices
del_side_chains	Flag indicating whether to delete side chains

◆ OAD_V3000

typedef struct OAD_V3000 OAD_V3000

Structure describing v. 1.05 extended input supporting V3000; polymers.

Parameters

n_non_star_atoms	Number of non-star atoms
n_star_atoms	Number of star atoms
atom_index_orig	index as supplied for atoms
atom_index_fin	= index or -1 for star atom
n_sgroups	currently, we do not use this.
n_3d_constraints	currently, we do not use this.
n_collections	number of collections
n_non_haptic_bonds	number of non-haptic bonds
n_haptic_bonds	number of haptic bonds
lists_haptic_bonds	haptic_bonds[i] is pointer to int* which contains: bond_type, non-star atom number, nendpts, then endpts themselves
n_steabs	number of enhanced stereo absolute configurations
lists_steabs	steabs[k][0] - not used steabs[k][1] - number of members in collection steabs[k][2..] - member atom numbers
n_sterel	number of enhanced stereo relative configurations
lists_sterel	sterel[k][0] - n from "STERELn" tag sterel[k][1] - number of members in collection sterel[k][2..] - member atom numbers
n_sterac	number of enhanced stereo racemic configurations
lists_sterac	sterac[k][0] - n from "STERACn" tag sterac[k][1] - number of members in collection

◆ ORIG_ATOM_DATA

typedef struct tagOrigAtom ORIG_ATOM_DATA

Structure describing original atom data.

Parameters

at	Array of input atoms
num_dimensions	Number of dimensions (2D or 3D)
num_inp_bonds	Number of input bonds
num_inp_atoms	Number of input atoms
num_components	Number of components in the structure
bDisconnectSalts	Flag indicating whether salt disconnection is possible
bDisconnectCoord	Flag indicating whether coordinate disconnection is needed
nCurAtLen	Array with current atom counts per component
nOldCompNumber	Array with old component numbers
nNumEquSets	Number of found component equivalence sets
nEquLabels	Array with equivalence labels for atoms
nSortedOrder	Array with sorted order of components
bSavedInINCHI_LIB	Array indicating if saved in InChI library
bPreprocessed	Array indicating if preprocessed
szCoord	Array of molecular coordinates
polymer	Pointer to polymer data structure
v3000	Pointer to V3000 data structure
valid_polymer	Flag indicating if polymer data is valid
n_zy	Number of non-polymeric pseudoatoms (Zy)

◆ ORIG_STRUCT

typedef struct tagOriginalStruct ORIG_STRUCT

Structure describing the original structure.

Parameters

num_atoms	Number of atoms
szAtoms	String representation of atoms
szBonds	String representation of bonds
szCoord	String representation of coordinates
polymer	Pointer to polymer data structure (uses pointer copy from orig_inp_data, do not free after use!)
v3000	Pointer to V3000 data structure (uses pointer copy from orig_inp_data, do not free after use!)
n_zy	Number of non-polymeric pseudoatoms (Zy)

◆ ST_CAP_FLOW

typedef S_SHORT ST_CAP_FLOW

◆ STRUCT_FPTRS

typedef struct tagStructFptrs STRUCT_FPTRS

Structure describing file pointers for structures.

Parameters

fptr	Array of file pointers to structures (input: fptr[cur_fptr] =file ptr to the struct to read; output: fptr[cur_fptr+1]=file ptr to the next struct or EOF)
len_fptr	Allocated length of fptr
cur_fptr	Current file pointer index (input: k-1 to read the kth struct, k = 1, 2, 3,...; left unchanged; struct number := cur_fptr+1)
max_fptr	Length of the filled out portion of fptr

Function Documentation

◆ AllocateInfoAtomData()

int AllocateInfoAtomData	(	INF_ATOM_DATA *	inf_at_data,
		int	num_atoms,
		int	num_components
	)

Allocate memory for Info Atom Data structure.

Parameters

inf_at_data	Pointer to the Info Atom Data structure
num_atoms	Number of atoms
num_components	Number of components

Returns: int Status code (1 if successful, 0 otherwise)

◆ bFoundFeature()

int bFoundFeature	(	inp_ATOM *	at,
		int	num_atoms
	)

Check if a feature is found in the input atoms ???

Parameters

at	Array of input atoms
num_atoms	Number of input atoms

Returns: int Status code

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◆ bHasMetalAtom()

int bHasMetalAtom ( ORIG_ATOM_DATA * orig_inp_data )

Check if there is a metal atom in the original atom data.

Parameters

orig_inp_data Pointer to original atom data structure

Returns: int Status code

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◆ bInchiTimeIsOver()

int bInchiTimeIsOver	(	struct tagINCHI_CLOCK *	ic,
		struct tagInchiTime *	TickEnd
	)

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◆ bMayDisconnectMetals()

int bMayDisconnectMetals	(	ORIG_ATOM_DATA *	orig_inp_data,
		int	bCheckMetalValence,
		INCHI_MODE *	bTautFlagsDone
	)

Check if metals may be disconnected in the original atom data.

Parameters

orig_inp_data	Pointer to original atom data structure
bCheckMetalValence	Flag indicating whether to check metal valence
bTautFlagsDone	Pointer to tautomeric flags done

Returns: int Status code

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◆ CreateCompAtomData()

int CreateCompAtomData	(	COMP_ATOM_DATA *	inp_at_data,
		int	num_atoms,
		int	num_components,
		int	bIntermediateTaut
	)

Create a Comp Atom Data structure.

Parameters

inp_at_data	Pointer to the Comp Atom Data structure
num_atoms	Number of atoms
num_components	Number of components
bIntermediateTaut	Flag for intermediate tautomer

Returns: int Status code (1 if successful, 0 otherwise)

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◆ CreateInfAtom()

inf_ATOM * CreateInfAtom ( int num_atoms )

Create/allocate a Inf Atom structure.

Parameters

num_atoms Number of atoms

Returns: inf_ATOM* Pointer to the created Inf Atom structure

◆ CreateInfoAtomData()

int CreateInfoAtomData	(	INF_ATOM_DATA *	inf_at_data,
		int	num_atoms,
		int	num_components
	)

Create a Info Atom Data structure.

Parameters

inf_at_data	Pointer to the Info Atom Data structure
num_atoms	Number of atoms
num_components	Number of components

Returns: int Status code (1 if successful, 0 otherwise)

◆ CreateInpAtom()

inp_ATOM * CreateInpAtom ( int num_atoms )

Create/allocate a Inp Atom structure.

Parameters

num_atoms Number of atoms

Returns: inp_ATOM* Pointer to the created Inp Atom structure

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◆ CreateInpAtomData()

int CreateInpAtomData	(	INP_ATOM_DATA *	inp_at_data,
		int	num_atoms,
		int	create_at_fixed_bonds
	)

Create a Inp Atom Data structure.

Parameters

inp_at_data	Pointer to the Inp Atom Data structure
num_atoms	Number of atoms
create_at_fixed_bonds	Flag to create fixed bonds

Returns: int Status code (1 if successful, 0 otherwise)

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◆ CreateOrigInpDataFromMolfile()

int CreateOrigInpDataFromMolfile	(	INCHI_IOSTREAM *	inp_file,
		ORIG_ATOM_DATA *	orig_at_data,
		int	bMergeAllInputStructures,
		int	bGetOrigCoord,
		int	bDoNotAddH,
		int	treat_polymers,
		int	treat_NPZz,
		const char *	pSdfLabel,
		char *	pSdfValue,
		unsigned long *	lSdfId,
		long *	lMolfileNumber,
		INCHI_MODE *	pInpAtomFlags,
		int *	err,
		char *	pStrErr,
		int	bNoWarnings
	)

Create original input data from molfile.

Parameters

inp_file	Input file stream
orig_at_data	Pointer to original atom data structure to be filled
bMergeAllInputStructures	Flag indicating whether to merge all input structures
bGetOrigCoord	Flag indicating whether to get original coordinates
bDoNotAddH	Flag indicating whether to avoid adding hydrogens
treat_polymers	Flag indicating how to treat polymers
treat_NPZz	Flag indicating how to treat non-polymeric Zz atoms
pSdfLabel	Pointer to SDF label
pSdfValue	Pointer to SDF value
lSdfId	Pointer to SDF ID
lMolfileNumber	Pointer to molfile number
pInpAtomFlags	Pointer to input atom flags
err	Pointer to error code
pStrErr	Pointer to error string
bNoWarnings	Flag indicating whether to suppress warnings

Returns: int Status code

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◆ DisconnectMetals()

int DisconnectMetals	(	ORIG_ATOM_DATA *	orig_inp_data,
		int	bCheckMetalValence,
		INCHI_MODE *	bTautFlagsDone
	)

Disconnect metals in the original atom data.

Parameters

orig_inp_data	Pointer to original atom data structure
bCheckMetalValence	Flag indicating whether to check metal valence
bTautFlagsDone	Pointer to tautomeric flags done

Returns: int Status code

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◆ DisconnectSalts()

int DisconnectSalts	(	ORIG_ATOM_DATA *	orig_inp_data,
		int	bDisconnect
	)

Disconnect salts in the original atom data.

Parameters

orig_inp_data	Pointer to original atom data structure
bDisconnect	Flag indicating whether to disconnect salts

Returns: int Status code

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◆ DuplicateInfoAtomData()

int DuplicateInfoAtomData	(	INF_ATOM_DATA *	inf_at_data_to,
		const INF_ATOM_DATA *	inf_at_data_from
	)

Duplicate Info Atom Data structure.

Parameters

inf_at_data_to	Pointer to the destination Info Atom Data structure
inf_at_data_from	Pointer to the source Info Atom Data structure

Returns: int Status code (1 if successful, 0 otherwise)

◆ fix_odd_things()

int fix_odd_things	(	int	num_atoms,
		inp_ATOM *	at,
		int	bFixBug,
		int	bFixNonUniformDraw
	)

Fix odd things in the input atoms.

Parameters

num_atoms	Number of input atoms
at	Array of input atoms
bFixBug	Flag indicating whether to fix bugs
bFixNonUniformDraw	Flag indicating whether to fix non-uniform drawing

Returns: int Status code

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◆ FixAdjacentRadicals()

int FixAdjacentRadicals	(	int	num_inp_atoms,
		inp_ATOM *	at
	)

Fix adjacent radicals in the input atoms.

Parameters

num_inp_atoms	Number of input atoms
at	Array of input atoms

Returns: int Status code

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◆ FixUnkn0DStereoBonds()

int FixUnkn0DStereoBonds	(	inp_ATOM *	at,
		int	num_at
	)

Fix unknown stereo bonds in the input atoms.

Parameters

at	Pointer to the atom data
num_at	Pointer to the number of atoms

Returns: int Number of fixed stereo bonds

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◆ FreeCompAtomData()

void FreeCompAtomData ( COMP_ATOM_DATA * inp_at_data )

Free composite atom data.

Parameters

inp_at_data Pointer to composite atom data structure

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◆ FreeExtOrigAtData()

void FreeExtOrigAtData	(	OAD_Polymer *	pd,
		OAD_V3000 *	v3k
	)

Free extended original atom data (polymers and V3000)

Parameters

pd	Pointer to polymer data structure
v3k	Pointer to V3000 data structure

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◆ FreeInfAtom()

void FreeInfAtom ( inf_ATOM ** at )

Free information atom array (same as FreeInpAtom)

Parameters

at	Pointer to information atom array

◆ FreeInfoAtomData()

void FreeInfoAtomData ( INF_ATOM_DATA * inf_at_data )

Free information atom data.

Parameters

inf_at_data Pointer to information atom data structure

◆ FreeInpAtom()

void FreeInpAtom ( inp_ATOM ** at )

Free input atom array.

Parameters

at	Pointer to input atom array

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◆ FreeInpAtomData()

void FreeInpAtomData ( INP_ATOM_DATA * inp_at_data )

Free input atom data.

Parameters

inp_at_data Pointer to input atom data structure

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◆ FreeOrigAtData()

void FreeOrigAtData ( ORIG_ATOM_DATA * orig_at_data )

Free original atom data.

Parameters

orig_at_data Pointer to original atom data structure

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◆ InchiToOrigAtom()

int InchiToOrigAtom	(	INCHI_IOSTREAM *	infile,
		ORIG_ATOM_DATA *	orig_at_data,
		int	bMergeAllInputStructures,
		int	bGetOrigCoord,
		int	bDoNotAddH,
		int	vABParityUnknown,
		INPUT_TYPE	nInputType,
		char *	pSdfLabel,
		char *	pSdfValue,
		unsigned long *	lSdfId,
		INCHI_MODE *	pInpAtomFlags,
		int *	err,
		char *	pStrErr
	)

Convert InChI representation to original atom data.

Parameters

infile	Input file stream
orig_at_data	Pointer to original atom data structure to be filled
bMergeAllInputStructures	Flag indicating whether to merge all input structures
bGetOrigCoord	Flag indicating whether to get original coordinates
bDoNotAddH	Flag indicating whether to avoid adding hydrogens
vABParityUnknown	Flag indicating whether to treat vAB parity as unknown
nInputType	Input type
pSdfLabel	Pointer to SDF label
pSdfValue	Pointer to SDF value
lSdfId	Pointer to SDF ID
pInpAtomFlags	Pointer to input atom flags
err	Pointer to error code
pStrErr	Pointer to error string

Returns: int Status code

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◆ MarkDisconnectedComponents()

int MarkDisconnectedComponents	(	ORIG_ATOM_DATA *	orig_at_data,
		int	bProcessOldCompNumbers
	)

Mark disconnected components in the original atom data.

Parameters

orig_at_data	Pointer to original atom data structure
bProcessOldCompNumbers	Flag indicating whether to process old component numbers

Returns: int Status code

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◆ MySleep()

void MySleep ( unsigned long ms )

Sleep for a specified amount of time.

Parameters

ms	Milliseconds to sleep

◆ OAD_CollectBackboneAtoms()

void OAD_CollectBackboneAtoms	(	ORIG_ATOM_DATA *	at_data,
		int	na,
		int *	alist,
		int	end_atom1,
		int	end_atom2,
		int *	nbkatoms,
		int *	bkatoms,
		int *	err,
		char *	pStrErr
	)

Collect backbone atoms from a polymer unit.

Parameters

at_data	Pointer to the original atom data
na	The number of atoms
alist	Array of atom indices
end_atom1	The first end atom
end_atom2	The second end atom
nbkatoms	Pointer to the number of backbone atoms
bkatoms	Pointer to the array of backbone atoms
err	Pointer to the error status
pStrErr	Pointer to the error string

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◆ OAD_CollectBackboneBonds()

void OAD_CollectBackboneBonds	(	ORIG_ATOM_DATA *	at_data,
		int	na,
		int *	alist,
		int	end_atom1,
		int	end_atom2,
		int *	nbkbonds,
		int **	bkbonds,
		int *	err,
		char *	pStrErr
	)

Collect backbone bonds from a polymer unit.

Parameters

at_data	Pointer to the original atom data
na	The number of atoms
alist	Array of atom indices
end_atom1	The first end atom
end_atom2	The second end atom
nbkbonds	Pointer to the number of backbone bonds
bkbonds	Pointer to the array of backbone bonds
err	Pointer to the error status
pStrErr	Pointer to the error string

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◆ OAD_CollectReachableAtoms()

int OAD_CollectReachableAtoms	(	ORIG_ATOM_DATA *	orig_at_data,
		int	start_atom,
		int	nforbidden_bonds,
		int *	forbidden_bonds,
		int *	n_reachable,
		int *	reachable,
		int *	err,
		char *	pStrErr
	)

Find reachable atoms from a given start atom.

Parameters

orig_at_data	Pointer to the original atom data
start_atom	The starting atom
nforbidden_bonds	The number of forbidden bonds
forbidden_bonds	Array of forbidden bonds
n_reachable	Pointer to the number of reachable atoms
reachable	Pointer to the array of reachable atoms
err	Pointer to the error status
pStrErr	Pointer to the error string

Returns: int Status code

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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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◆ OAD_Polymer_CompareBackboneBondsSeniority()

int OAD_Polymer_CompareBackboneBondsSeniority	(	int *	b1,
		int *	b2,
		OAD_AtProps *	aprops
	)

Compare backbone bonds seniority (for sorting SRU cyclizing bonds (PS=='frame-shift') in descending order)

Parameters

b1	Pointer to first backbone bond
b2	Pointer to second backbone bond
aprops	Pointer to atom properties structure

Returns: int Comparison result (-1 if b1 < b2, 0 if equal, 1 if b1 > b2)

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◆ OAD_Polymer_CompareRanksOfTwoAtoms()

int OAD_Polymer_CompareRanksOfTwoAtoms	(	int	atom1,
		int	atom2,
		OAD_AtProps *	aprops
	)

Compare ranks of two atoms (compare seniority of two atoms in polymer SRU)

Parameters

atom1	Index of the first atom
atom2	Index of the second atom
aprops	Pointer to atom properties structure

Returns: int Comparison result

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◆ OAD_Polymer_CyclizeCloseableUnits()

int OAD_Polymer_CyclizeCloseableUnits	(	ORIG_ATOM_DATA *	orig_at_data,
		int	use_zz,
		char *	pStrErr,
		int	bNoWarnings
	)

Cyclize closeable units in the original atom data.

Parameters

orig_at_data	Pointer to original atom data structure
use_zz	Flag indicating whether to use Zz atoms
pStrErr	Pointer to error string
bNoWarnings	Flag indicating whether to suppress warnings

Returns: int Status code

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◆ OAD_Polymer_DebugTrace()

void OAD_Polymer_DebugTrace ( OAD_Polymer * p )

Debug trace for polymer data structure (print the whole polymer data)

Parameters

p	Pointer to polymer data structure

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◆ OAD_Polymer_FindBackbones()

void OAD_Polymer_FindBackbones	(	ORIG_ATOM_DATA *	where_to_look,
		COMP_ATOM_DATA *	composite_norm_data,
		int *	err,
		char *	pStrErr
	)

Find backbones in the original atom data.

Parameters

where_to_look	Pointer to original atom data structure
composite_norm_data	Pointer to composite atom data structure
err	Pointer to error code
pStrErr	Pointer to error string

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◆ OAD_Polymer_FindRingSystems()

int OAD_Polymer_FindRingSystems	(	OAD_Polymer *	pd,
		inp_ATOM *	at,
		int	nat,
		int *	num_inp_bonds,
		int *	num_ring_sys,
		int *	size_ring_sys,
		int	start
	)

Find ring systems in the polymer data.

Parameters

pd	Pointer to polymer data structure
at	Array of input atoms
nat	Number of input atoms
num_inp_bonds	Pointer to number of input bonds
num_ring_sys	Pointer to number of ring systems found
size_ring_sys	Pointer to size of ring systems found
start	Starting atom index

Returns: int Status code

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◆ OAD_Polymer_Free()

void OAD_Polymer_Free ( OAD_Polymer * p )

Free polymer data structure.

Parameters

p	Pointer to polymer data structure

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◆ OAD_Polymer_GetRepresentation()

int OAD_Polymer_GetRepresentation ( OAD_Polymer * p )

Get polymer representation type.

Parameters

p	Pointer to polymer data structure

Returns: int Polymer representation type (NO_POLYMER, POLYMER_REPRESENTATION_SOURCE_BASED, POLYMER_REPRESENTATION_STRUCTURE_BASED, POLYMER_REPRESENTATION_MIXED,POLYMER_REPRESENTATION_UNRECOGNIZED)

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◆ OAD_Polymer_IsFirstAtomRankLower()

int OAD_Polymer_IsFirstAtomRankLower	(	int	atom1,
		int	atom2,
		OAD_AtProps *	aprops
	)

Check if the first atom has a lower rank than the second atom (check seniority of two atoms in polymer SRU)

Parameters

atom1	Index of the first atom
atom2	Index of the second atom
aprops	Pointer to atom properties structure

Returns: int 1 if atom1 has a lower rank than atom2, 0 otherwise

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◆ OAD_Polymer_PrepareFoldCRUEdits()

int OAD_Polymer_PrepareFoldCRUEdits	(	ORIG_ATOM_DATA *	orig_at_data,
		char *	sinchi_noedits,
		char *	saux_noedits,
		char *	sinchi,
		char *	saux,
		OAD_StructureEdits *	ed
	)

Prepare CRU edits for polymer data structure (prepare CRU fold edits as suggested by the strings with preliminary generated interim (1.05+ flavoured) InChI and AuxInfo)

Parameters

orig_at_data	Pointer to original atom data structure
sinchi_noedits	Pointer to InChI string without edits
saux_noedits	Pointer to auxiliary InChI string without edits
sinchi	Pointer to InChI string with edits
saux	Pointer to auxiliary InChI string with edits
ed	Pointer to structure edits to be filled

Returns: int Status code

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◆ OAD_Polymer_PrepareFrameShiftEdits()

int OAD_Polymer_PrepareFrameShiftEdits	(	ORIG_ATOM_DATA *	orig_at_data,
		char *	sinchi,
		char *	saux,
		OAD_StructureEdits *	ed
	)

Prepare frame shift edits for polymer data structure (prepare frame shift edits as suggested by the strings with preliminary generated interim (1.05+ flavoured) InChI and AuxInfo)

Parameters

orig_at_data	Pointer to original atom data structure
sinchi	Pointer to InChI string with edits
saux	Pointer to auxiliary InChI string with edits
ed	Pointer to structure edits to be filled

Returns: int Status code

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◆ OAD_Polymer_PrepareWorkingSet()

int OAD_Polymer_PrepareWorkingSet	(	OAD_Polymer *	p,
		int *	cano_nums,
		int *	compnt_nums,
		OAD_PolymerUnit **	units2,
		int *	unum
	)

Prepare working set for polymer processing (replace original atom numbers in polymer data with (canonical num + 1))

Parameters

p	Pointer to polymer data structure
cano_nums	Pointer to canonical numbers array
compnt_nums	Pointer to component numbers array
units2	Pointer to array of polymer units (a copy of original polymer units with updated atom numbers)
unum	Pointer to number of polymer units

Returns: int Status code

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◆ OAD_Polymer_SetAtProps()

void OAD_Polymer_SetAtProps	(	OAD_Polymer *	pd,
		inp_ATOM *	at,
		int	nat,
		int *	num_inp_bonds,
		OAD_AtProps *	aprops,
		int *	cano_nums
	)

Set atom properties for the polymer data.

Parameters

pd	Pointer to polymer data structure
at	Array of input atoms
nat	Number of input atoms
num_inp_bonds	Pointer to number of input bonds
aprops	Pointer to atom properties structure
cano_nums	Pointer to canonical numbers array

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◆ OAD_Polymer_SmartReopenCyclizedUnits()

void OAD_Polymer_SmartReopenCyclizedUnits	(	OAD_Polymer *	p,
		inp_ATOM *	at,
		int	nat,
		int *	num_inp_bonds
	)

Smartly reopen cyclized units in the original atom data (open pre-cyclized CRUs appropriately (i.e., make frame shift))

Parameters

p	Pointer to polymer data structure
at	Pointer to input atom data
nat	Number of input atoms
num_inp_bonds	Pointer to number of input bonds

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◆ OAD_PolymerUnit_CompareAtomLists()

int OAD_PolymerUnit_CompareAtomLists	(	OAD_PolymerUnit *	u1,
		OAD_PolymerUnit *	u2
	)

Compare two polymer units based on their atom lists.

Parameters

u1	Pointer to the first polymer unit
u2	Pointer to the second polymer unit

Returns: int comparison result (-1, 0, 1)

◆ OAD_PolymerUnit_CompareAtomListsMod()

int OAD_PolymerUnit_CompareAtomListsMod	(	OAD_PolymerUnit *	u1,
		OAD_PolymerUnit *	u2
	)

Compare two polymer units based on their atom lists with modifications.

Parameters

u1	Pointer to the first polymer unit
u2	Pointer to the second polymer unit

Returns: int comparison result (-1, 0, 1)

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◆ OAD_PolymerUnit_CreateCopy()

OAD_PolymerUnit * OAD_PolymerUnit_CreateCopy ( OAD_PolymerUnit * u )

Create a copy of a polymer unit.

Parameters

u	Pointer to the original polymer unit

Returns: OAD_PolymerUnit* Pointer to the new polymer unit

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◆ OAD_PolymerUnit_DebugTrace()

void OAD_PolymerUnit_DebugTrace ( OAD_PolymerUnit * unit )

Debug trace for a polymer unit (print the whole polymer unit)

Parameters

unit	Pointer to the polymer unit

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◆ OAD_PolymerUnit_DelistHighOrderBackboneBonds()

void OAD_PolymerUnit_DelistHighOrderBackboneBonds	(	OAD_PolymerUnit *	unit,
		ORIG_ATOM_DATA *	orig_at_data,
		COMP_ATOM_DATA *	composite_norm_data,
		int *	err,
		char *	pStrErr
	)

Collect high-order backbone bonds from a polymer unit.

Parameters

unit	Pointer to the polymer unit
orig_at_data	Pointer to the original atom data
composite_norm_data	Pointer to the composite atom data
err	Pointer to the error status
pStrErr	Pointer to the error string

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◆ OAD_PolymerUnit_DelistIntraRingBackboneBonds()

void OAD_PolymerUnit_DelistIntraRingBackboneBonds	(	OAD_PolymerUnit *	unit,
		ORIG_ATOM_DATA *	orig_at_data,
		int *	err,
		char *	pStrErr
	)

Collect backbone bonds from a polymer unit and delist intra-ring backbone bonds.

Parameters

unit	Pointer to the polymer unit
orig_at_data	Pointer to the original atom data
err	Pointer to the error status
pStrErr	Pointer to the error string

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◆ OAD_PolymerUnit_FindEndsAndCaps()

void OAD_PolymerUnit_FindEndsAndCaps	(	OAD_PolymerUnit *	unit,
		ORIG_ATOM_DATA *	orig_at_data,
		int *	end1,
		int *	cap1,
		int *	cap1_is_undef,
		int *	end2,
		int *	cap2,
		int *	cap2_is_undef,
		int *	err,
		char *	pStrErr
	)

Find the ends and caps of a polymer unit.

Parameters

unit	Pointer to the polymer unit
orig_at_data	Pointer to the original atom data
end1	Pointer to the first end atom
cap1	Pointer to the first cap atom
cap1_is_undef	Pointer to the first cap atom's undefined status
end2	Pointer to the second end atom
cap2	Pointer to the second cap atom
cap2_is_undef	Pointer to the second cap atom's undefined status
err	Pointer to the error status
pStrErr	Pointer to the error string

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◆ OAD_PolymerUnit_Free()

void OAD_PolymerUnit_Free ( OAD_PolymerUnit * unit )

Free a polymer unit.

Parameters

unit	Pointer to the polymer unit to free

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◆ OAD_PolymerUnit_HasMetal()

int OAD_PolymerUnit_HasMetal	(	OAD_PolymerUnit *	u,
		inp_ATOM *	at
	)

Check if a polymer unit has a specific atom (e.g., metal)

Parameters

u	Pointer to the polymer unit
at	Pointer to the atom data

Returns: int Status code (1 if an atom is found, 0 otherwise)

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◆ OAD_PolymerUnit_New()

OAD_PolymerUnit * OAD_PolymerUnit_New	(	int	maxatoms,
		int	maxbonds,
		int	id,
		int	label,
		int	type,
		int	subtype,
		int	conn,
		char *	smt,
		int	na,
		INT_ARRAY *	alist,
		int	nb,
		INT_ARRAY *	blist,
		int	nbkbonds,
		int **	bkbonds
	)

Create a new polymer unit.

Parameters

maxatoms	Maximum number of atoms
maxbonds	Maximum number of bonds
id	Unique identifier for the polymer unit
label	Label for the polymer unit
type	Type of the polymer unit
subtype	Subtype of the polymer unit
conn	Connection type
smt	SMARTS pattern?
na	Number of atoms
alist	Pointer to the atom list
nb	Number of bonds
blist	Pointer to the bond list
nbkbonds	Number of backbone bonds
bkbonds	Pointer to the backbone bond list

Returns: OAD_PolymerUnit* Pointer to the new polymer unit

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◆ OAD_PolymerUnit_OrderBondAtomsAndBondsThemselves()

int OAD_PolymerUnit_OrderBondAtomsAndBondsThemselves	(	OAD_PolymerUnit *	u,
		int	n_stars,
		int *	stars
	)

Order bond atoms and bonds themselves in a polymer unit.

Parameters

u	Pointer to the polymer unit
n_stars	Pointer to the number of stars
stars	Pointer to the array of star atoms

Returns: int

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◆ OAD_PolymerUnit_PrepareToFrameShift()

void OAD_PolymerUnit_PrepareToFrameShift	(	OAD_PolymerUnit *	unit,
		ORIG_ATOM_DATA *	orig_at_data,
		int *	err,
		char *	pStrErr
	)

Prepare a polymer unit for frame shifting.

Parameters

unit	Pointer to the polymer unit
orig_at_data	Pointer to the original atom data
err	Pointer to the error status
pStrErr	Pointer to the error string

◆ OAD_PolymerUnit_ReopenCyclized()

void OAD_PolymerUnit_ReopenCyclized	(	OAD_PolymerUnit *	u,
		inp_ATOM *	at,
		OAD_AtProps *	aprops,
		int	nat,
		int *	num_inp_bonds
	)

Collect backbone atoms from a polymer unit.

Parameters

u	Pointer to the polymer unit
at	Pointer to the atom data
aprops	Pointer to the atom properties
nat	Pointer to the number of atoms
num_inp_bonds	Pointer to the number of input bonds

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◆ OAD_PolymerUnit_SetEndsAndCaps()

void OAD_PolymerUnit_SetEndsAndCaps	(	OAD_PolymerUnit *	unit,
		ORIG_ATOM_DATA *	orig_at_data,
		int *	err,
		char *	pStrErr
	)

Set the ends and caps of a polymer unit.

Parameters

unit	Pointer to the polymer unit
orig_at_data	Pointer to the original atom data
err	Pointer to the error status
pStrErr	Pointer to the error string

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◆ OAD_PolymerUnit_SetReopeningDetails()

int OAD_PolymerUnit_SetReopeningDetails	(	OAD_PolymerUnit *	u,
		inp_ATOM *	at
	)

Set reopening details for a polymer unit.

Parameters

u	Pointer to polymer unit
at	Array of input atoms

Returns: int Number of breakable bonds

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◆ OAD_PolymerUnit_SortBackboneBonds()

void OAD_PolymerUnit_SortBackboneBonds	(	OAD_PolymerUnit *	u,
		OAD_AtProps *	aprops,
		int *	bnum
	)

Collect backbone bonds from a polymer unit and sort them.

Parameters

u	Pointer to the polymer unit
aprops	Pointer to the atom properties
bnum	Pointer to the number of backbone bonds

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◆ OAD_PolymerUnit_SortBackboneBondsAndSetSeniors()

void OAD_PolymerUnit_SortBackboneBondsAndSetSeniors	(	OAD_PolymerUnit *	u,
		inp_ATOM *	at,
		OAD_AtProps *	aprops,
		int *	senior_bond
	)

Sort backbone bonds and set seniors for a polymer unit.

Parameters

u	Pointer to polymer unit
at	Array of input atoms
aprops	Pointer to atom properties structure
senior_bond	Pointer to array to store senior bond indices

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◆ OAD_PolymerUnit_UnlinkCapsAndConnectEndAtoms()

void OAD_PolymerUnit_UnlinkCapsAndConnectEndAtoms	(	OAD_PolymerUnit *	unit,
		ORIG_ATOM_DATA *	orig_at_data,
		int *	err,
		char *	pStrErr
	)

Unlink caps and connect end atoms of a polymer unit.

Parameters

unit	Pointer to the polymer unit
orig_at_data	Pointer to the original atom data
err	Pointer to the error status
pStrErr	Pointer to the error string

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◆ OAD_StructureEdits_Clear()

void OAD_StructureEdits_Clear ( OAD_StructureEdits * ed )

Clear structure edits.

Parameters

ed	Pointer to structure edits

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◆ OAD_StructureEdits_DebugPrint()

void OAD_StructureEdits_DebugPrint ( OAD_StructureEdits * ed )

Debug print structure edits.

Parameters

ed	Pointer to structure edits

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◆ OAD_StructureEdits_Init()

int OAD_StructureEdits_Init ( OAD_StructureEdits * ed )

Initialize structure edits.

Parameters

ed	Pointer to structure edits

Returns: int Error status code

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◆ OAD_ValidateAndSortOutPseudoElementAtoms()

void OAD_ValidateAndSortOutPseudoElementAtoms	(	ORIG_ATOM_DATA *	orig_at_data,
		int	treat_polymers,
		int	use_zz,
		int *	err,
		char *	pStrErr
	)

Validate and sort out pseudo-element atoms in the original atom data.

Parameters

orig_at_data	Pointer to original atom data structure
treat_polymers	Flag indicating how to treat polymers (POLYMER_NO, POLYMER_MODERN, POLYMER_LEGACY, POLYMER_LEGACY_PLUS)
use_zz	Flag indicating whether to use Zz atoms
err	Pointer to error code
pStrErr	Pointer to error string

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◆ OAD_ValidatePolymerAndPseudoElementData()

int OAD_ValidatePolymerAndPseudoElementData	(	ORIG_ATOM_DATA *	orig_at_data,
		int	treat_polymers,
		int	bNPZz,
		char *	pStrErr,
		int	bNoWarnings
	)

Validate polymer and pseudo-element data in the original atom data.

Parameters

orig_at_data	Pointer to original atom data structure
treat_polymers	Flag indicating how to treat polymers
bNPZz	Flag indicating whether to treat non-polymeric Zz atoms
pStrErr	Pointer to error string
bNoWarnings	Flag indicating whether to suppress warnings

Returns: int Status code

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◆ OrigAtData_WriteToSDfile()

int OrigAtData_WriteToSDfile	(	const ORIG_ATOM_DATA *	inp_at_data,
		INCHI_IOSTREAM *	fcb,
		const char *	name,
		const char *	comment,
		int	bChiralFlag,
		int	bAtomsDT,
		const char *	szLabel,
		const char *	szValue
	)

Write original atom data to SD file.

Parameters

inp_at_data	Pointer to original atom data structure
fcb	File stream to write to
name	Name of the structure
comment	Comment to include
bChiralFlag	Flag indicating for chiral information
bAtomsDT	Flag indicating how H isotopes (D/T) are represented in the SD output
szLabel	SDF label
szValue	SDF value

Returns: int Status code

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◆ post_fix_odd_things()

int post_fix_odd_things	(	int	num_atoms,
		inp_ATOM *	at
	)

Post-fix odd things in the input atoms (does nothing, returns 0)

Parameters

num_atoms	Number of input atoms
at	Array of input atoms

Returns: int Status code

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◆ PrintFileName()

void PrintFileName	(	const char *	fmt,
		FILE *	out_file,
		const char *	szFname
	)

Print the file name.

Parameters

fmt	Format string
out_file	Output file pointer
szFname	File name string

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◆ ReconcileAllCmlBondParities()

int ReconcileAllCmlBondParities	(	inp_ATOM *	at,
		int	num_atoms,
		int	bDisconnected
	)

Reconcile all CML bond parities in the input atoms.

Parameters

at	Pointer to the atom data
num_atoms	Number of atoms
bDisconnected	Flag for disconnected atoms

Returns: int Status code

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◆ remove_ion_pairs()

int remove_ion_pairs	(	int	num_atoms,
		inp_ATOM *	at
	)

Remove ion pairs from the input atoms.

Parameters

num_atoms	Number of input atoms
at	Array of input atoms

Returns: int Status code

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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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◆ UnMarkRingSystemsInp()

int UnMarkRingSystemsInp	(	inp_ATOM *	at,
		int	num_atoms
	)

Unmark ring systems in the input atoms.

Parameters

at	Array of input atoms
num_atoms	Number of input atoms

Returns: int Status code

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Data Structures

Macros

Typedefs

Functions

Macro Definition Documentation

◆ ADD_LEN_STRUCT_FPTRS

◆ ALLOW_CLOSING_SRU_VIA_DIRADICAL

◆ ALLOW_CLOSING_SRU_VIA_HIGHER_ORDER_BOND

◆ ALLOW_MIXED_SRU_AND_MON

◆ AT_FLAG_ISO_H_POINT

◆ ATT_ACIDIC_CO

◆ ATT_ACIDIC_S

◆ ATT_ATOM_N

◆ ATT_ATOM_P

◆ ATT_HalAcid

◆ ATT_HalAnion

◆ ATT_N_O

◆ ATT_NO

◆ ATT_NONE

◆ ATT_NP_MINUS_V23

◆ ATT_O_PLUS

◆ ATT_OH_MINUS

◆ ATT_OO

◆ ATT_OTHER_NEG_O

◆ ATT_OTHER_ZO

◆ ATT_PROTON

◆ ATT_ZOO

◆ bDrawingLabelLeftShift

◆ CLOSING_SRU_DIRADICAL

◆ CLOSING_SRU_HIGHER_ORDER_BOND

◆ CLOSING_SRU_MOVED_BRACKETS

◆ CLOSING_SRU_NOT_APPLICABLE

◆ CLOSING_SRU_RING

◆ CLOSING_SRU_RING_OPENED

◆ CLOSING_STARRED_SRU_IS_A_MUST

◆ FLAG_INP_AT_CHIRAL

◆ FLAG_INP_AT_NONCHIRAL

◆ FLAG_SET_INP_AT_CHIRAL

◆ FLAG_SET_INP_AT_NONCHIRAL

◆ FLAG_SET_INP_LARGE_MOLS

◆ FlagSB_0D

◆ FlagSC_0D

◆ INF_STEREO

◆ INF_STEREO_ABS

◆ INF_STEREO_ABS_REL_RAC

◆ INF_STEREO_INV

◆ INF_STEREO_NORM

◆ INF_STEREO_NORM_INV

◆ INF_STEREO_RAC

◆ INF_STEREO_REL

◆ MAX_LEN_REMOVED_PROTONS

◆ NO_POLYMER

◆ NUM_ISO_H

◆ NUMH

◆ PERIODIC_NUMBER_H

◆ POLYMER_CONN_EU

◆ POLYMER_CONN_HH

◆ POLYMER_CONN_HT

◆ POLYMER_CONN_NON

◆ POLYMER_REPRESENTATION_MIXED

◆ POLYMER_REPRESENTATION_SOURCE_BASED

◆ POLYMER_REPRESENTATION_STRUCTURE_BASED

◆ POLYMER_REPRESENTATION_UNRECOGNIZED

◆ POLYMER_SST_ALT

◆ POLYMER_SST_BLK

◆ POLYMER_SST_NON

◆ POLYMER_SST_RAN

◆ POLYMER_STY_COP

◆ POLYMER_STY_CRO

◆ POLYMER_STY_MER

◆ POLYMER_STY_MOD

◆ POLYMER_STY_MON

◆ POLYMER_STY_NON

◆ POLYMER_STY_SRU

◆ SB_PARITY_1

◆ SB_PARITY_2

◆ SB_PARITY_FLAG

◆ SB_PARITY_MASK

◆ SB_PARITY_SHFT

Typedef Documentation