inpdef.h File Reference

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

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Data Structures
struct	tagInputAtom
struct	OAD_PolymerUnit
struct	OAD_Polymer
struct	OAD_AtProps
struct	OAD_V3000
struct	tagOrigAtom
struct	tagOriginalStruct
struct	tagAtomParmsForDrawing
struct	tagInfoAtomData
struct	tagInputAtomData
struct	tagNormCanonFlags
struct	tagCompositeAtomData
struct	tagStructFptrs
struct	tagOAD_StructureEdits

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 /* for drawing only */
#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 /* -Z=O or =Z=O */
#define	ATT_OH_MINUS   0x0400 /* OH(-), O=O,S,Se,Te */
#define	ATT_O_PLUS   0x0800 /* -OH2(+), =OH(+), -OH(+)-, OH3(+), =O(+)-, etc; O=O,S,Se,Te */
#define	ATT_PROTON   0x1000
#define	ATT_HalAnion   0x2000
#define	ATT_HalAcid   0x4000
#define	ATT_NP_MINUS_V23   0x8000 /* =N(-) or =P(-) where = previously was triple */
#define	AT_FLAG_ISO_H_POINT   0x01 /* may have isotopic H */
#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 /* bUsed0DParity */
#define	FlagSB_0D   2 /* bUsed0DParity */
#define	SB_PARITY_FLAG   0x38 /* mask for disconnected metal parity if it is different */
#define	SB_PARITY_SHFT   3 /* number of right shift bits to get disconnected metal parity */
#define	SB_PARITY_MASK   0x07
#define	SB_PARITY_1(X)   (X & SB_PARITY_MASK) /* refers to connected structure */
#define	SB_PARITY_2(X)   (((X) >> SB_PARITY_SHFT) & SB_PARITY_MASK) /* refers to connected structure */
#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 /* allow simultaneous presence of source-based and */
#define	POLYMER_STY_NON   0
#define	POLYMER_STY_SRU   1 /* structure-based unit or copolymer subunit */
#define	POLYMER_STY_MON   2 /* source-based polymer unit or copolymer subunit */
#define	POLYMER_STY_COP   3 /* copolymer unit embedding >1 subunits */
#define	POLYMER_STY_MOD   4 /* copolymer subunit only, designates chemical modification of SRU */
#define	POLYMER_STY_CRO   5 /* copolymer subunit only, designates cross-linked version of SRU */
#define	POLYMER_STY_MER   6 /* copolymer subunit only, source-based with no homopolymerize */
#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
typedef struct OAD_PolymerUnit	OAD_PolymerUnit
typedef struct OAD_Polymer	OAD_Polymer
typedef struct OAD_AtProps	OAD_AtProps
typedef struct OAD_V3000	OAD_V3000
typedef struct tagOrigAtom	ORIG_ATOM_DATA
typedef struct tagOriginalStruct	ORIG_STRUCT
typedef struct tagAtomParmsForDrawing	inf_ATOM
typedef struct tagInfoAtomData	INF_ATOM_DATA
typedef struct tagInputAtomData	INP_ATOM_DATA
typedef INP_ATOM_DATA	INP_ATOM_DATA2[TAUT_NUM]
typedef struct tagNormCanonFlags	NORM_CANON_FLAGS
typedef struct tagCompositeAtomData	COMP_ATOM_DATA
typedef long	INCHI_FPTR
typedef struct tagStructFptrs	STRUCT_FPTRS
typedef struct tagOAD_StructureEdits	OAD_StructureEdits

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)
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)
int	MarkDisconnectedComponents (ORIG_ATOM_DATA *orig_at_data, int bProcessOldCompNumbers)
int	DisconnectSalts (ORIG_ATOM_DATA *orig_inp_data, int bDisconnect)
int	DisconnectMetals (ORIG_ATOM_DATA *orig_inp_data, int bCheckMetalValence, INCHI_MODE *bTautFlagsDone)
int	bMayDisconnectMetals (ORIG_ATOM_DATA *orig_inp_data, int bCheckMetalValence, INCHI_MODE *bTautFlagsDone)
int	bHasMetalAtom (ORIG_ATOM_DATA *orig_inp_data)
int	FixAdjacentRadicals (int num_inp_atoms, inp_ATOM *at)
int	fix_odd_things (int num_atoms, inp_ATOM *at, int bFixBug, int bFixNonUniformDraw)
int	post_fix_odd_things (int num_atoms, inp_ATOM *at)
int	remove_ion_pairs (int num_atoms, inp_ATOM *at)
int	bFoundFeature (inp_ATOM *at, int num_atoms)
int	UnMarkRingSystemsInp (inp_ATOM *at, int num_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)
void	FreeInpAtom (inp_ATOM **at)
void	FreeInfAtom (inf_ATOM **at)
void	FreeOrigAtData (ORIG_ATOM_DATA *orig_at_data)
void	FreeExtOrigAtData (OAD_Polymer *pd, OAD_V3000 *v3k)
void	FreeInpAtomData (INP_ATOM_DATA *inp_at_data)
void	FreeCompAtomData (COMP_ATOM_DATA *inp_at_data)
void	FreeInfoAtomData (INF_ATOM_DATA *inf_at_data)
int	OAD_StructureEdits_Init (OAD_StructureEdits *ed)
void	OAD_StructureEdits_Clear (OAD_StructureEdits *ed)
void	OAD_StructureEdits_DebugPrint (OAD_StructureEdits *ed)
int	Ring2Chain (struct tagINCHI_CLOCK *ic, struct tagCANON_GLOBALS *pCG, ORIG_ATOM_DATA *orig_inp_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)
void	OAD_Edit_MergeComponentsAndRecreateOAD (ORIG_ATOM_DATA *orig_OrigAtomData, INP_ATOM_DATA *curr_InpAtomData, int num_components, int *errcode)
int	OAD_ValidatePolymerAndPseudoElementData (ORIG_ATOM_DATA *orig_at_data, int treat_polymers, int bNPZz, char *pStrErr, int bNoWarnings)
void	OAD_ValidateAndSortOutPseudoElementAtoms (ORIG_ATOM_DATA *orig_at_data, int treat_polymers, int use_zz, int *err, char *pStrErr)
int	OAD_Polymer_GetRepresentation (OAD_Polymer *p)
int	OAD_Polymer_CyclizeCloseableUnits (ORIG_ATOM_DATA *orig_at_data, int use_zz, char *pStrErr, int bNoWarnings)
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)
void	OAD_Polymer_SetAtProps (OAD_Polymer *pd, inp_ATOM *at, int nat, int *num_inp_bonds, OAD_AtProps *aprops, int *cano_nums)
int	OAD_Polymer_CompareBackboneBondsSeniority (int *b1, int *b2, OAD_AtProps *aprops)
int	OAD_Polymer_CompareRanksOfTwoAtoms (int atom1, int atom2, OAD_AtProps *aprops)
int	OAD_Polymer_IsFirstAtomRankLower (int atom1, int atom2, OAD_AtProps *aprops)
int	OAD_PolymerUnit_SetReopeningDetails (OAD_PolymerUnit *u, inp_ATOM *at)
void	OAD_PolymerUnit_SortBackboneBondsAndSetSeniors (OAD_PolymerUnit *u, inp_ATOM *at, OAD_AtProps *aprops, int *senior_bond)
void	OAD_Polymer_FindBackbones (ORIG_ATOM_DATA *where_to_look, COMP_ATOM_DATA *composite_norm_data, int *err, char *pStrErr)
int	OAD_Polymer_PrepareWorkingSet (OAD_Polymer *p, int *cano_nums, int *compnt_nums, OAD_PolymerUnit **units2, int *unum)
void	OAD_Polymer_Free (OAD_Polymer *p)
void	OAD_Polymer_DebugTrace (OAD_Polymer *p)
void	OAD_Polymer_SmartReopenCyclizedUnits (OAD_Polymer *p, inp_ATOM *at, int nat, int *num_inp_bonds)
int	OAD_Polymer_PrepareFoldCRUEdits (ORIG_ATOM_DATA *orig_at_data, char *sinchi_noedits, char *saux_noedits, char *sinchi, char *saux, OAD_StructureEdits *ed)
int	OAD_Polymer_PrepareFrameShiftEdits (ORIG_ATOM_DATA *orig_at_data, char *sinchi, char *saux, OAD_StructureEdits *ed)
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)
OAD_PolymerUnit *	OAD_PolymerUnit_CreateCopy (OAD_PolymerUnit *u)
void	OAD_PolymerUnit_Free (OAD_PolymerUnit *unit)
void	OAD_PolymerUnit_DebugTrace (OAD_PolymerUnit *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)
void	OAD_PolymerUnit_SetEndsAndCaps (OAD_PolymerUnit *unit, ORIG_ATOM_DATA *orig_at_data, int *err, char *pStrErr)
void	OAD_PolymerUnit_UnlinkCapsAndConnectEndAtoms (OAD_PolymerUnit *unit, ORIG_ATOM_DATA *orig_at_data, int *err, char *pStrErr)
void	OAD_PolymerUnit_PrepareToFrameShift (OAD_PolymerUnit *unit, ORIG_ATOM_DATA *orig_at_data, int *err, char *pStrErr)
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)
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)
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)
void	OAD_PolymerUnit_DelistIntraRingBackboneBonds (OAD_PolymerUnit *unit, ORIG_ATOM_DATA *orig_at_data, int *err, char *pStrErr)
void	OAD_PolymerUnit_DelistHighOrderBackboneBonds (OAD_PolymerUnit *unit, ORIG_ATOM_DATA *orig_at_data, COMP_ATOM_DATA *composite_norm_data, int *err, char *pStrErr)
void	OAD_PolymerUnit_SortBackboneBonds (OAD_PolymerUnit *u, OAD_AtProps *aprops, int *bnum)
void	OAD_PolymerUnit_ReopenCyclized (OAD_PolymerUnit *u, inp_ATOM *at, OAD_AtProps *aprops, int nat, int *num_inp_bonds)
int	OAD_PolymerUnit_CompareAtomLists (OAD_PolymerUnit *u1, OAD_PolymerUnit *u2)
int	OAD_PolymerUnit_CompareAtomListsMod (OAD_PolymerUnit *u1, OAD_PolymerUnit *u2)
int	OAD_PolymerUnit_OrderBondAtomsAndBondsThemselves (OAD_PolymerUnit *u, int n_stars, int *stars)
int	OAD_PolymerUnit_HasMetal (OAD_PolymerUnit *u, inp_ATOM *at)
int	FixUnkn0DStereoBonds (inp_ATOM *at, int num_at)
inf_ATOM *	CreateInfAtom (int num_atoms)
inp_ATOM *	CreateInpAtom (int num_atoms)
int	CreateInfoAtomData (INF_ATOM_DATA *inf_at_data, int num_atoms, int num_components)
int	AllocateInfoAtomData (INF_ATOM_DATA *inf_at_data, int num_atoms, int num_components)
int	DuplicateInfoAtomData (INF_ATOM_DATA *inf_at_data_to, const INF_ATOM_DATA *inf_at_data_from)
int	CreateInpAtomData (INP_ATOM_DATA *inp_at_data, int num_atoms, int create_at_fixed_bonds)
int	CreateCompAtomData (COMP_ATOM_DATA *inp_at_data, int num_atoms, int num_components, int bIntermediateTaut)
void	PrintFileName (const char *fmt, FILE *out_file, const char *szFname)
void	MySleep (unsigned long ms)
int	ReconcileAllCmlBondParities (inp_ATOM *at, int num_atoms, int bDisconnected)

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 */

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 */

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

INCHI_FPTR

typedef long INCHI_FPTR

inf_ATOM

typedef struct tagAtomParmsForDrawing inf_ATOM

INF_ATOM_DATA

typedef struct tagInfoAtomData INF_ATOM_DATA

inp_ATOM

typedef struct tagInputAtom inp_ATOM

INP_ATOM_DATA

typedef struct tagInputAtomData INP_ATOM_DATA

INP_ATOM_DATA2

typedef INP_ATOM_DATA INP_ATOM_DATA2[TAUT_NUM]

NORM_CANON_FLAGS

typedef struct tagNormCanonFlags NORM_CANON_FLAGS

OAD_AtProps

typedef struct OAD_AtProps OAD_AtProps

OAD_Polymer

typedef struct OAD_Polymer OAD_Polymer

OAD_PolymerUnit

typedef struct OAD_PolymerUnit OAD_PolymerUnit

OAD_StructureEdits

typedef struct tagOAD_StructureEdits OAD_StructureEdits

OAD_V3000

typedef struct OAD_V3000 OAD_V3000

ORIG_ATOM_DATA

typedef struct tagOrigAtom ORIG_ATOM_DATA

ORIG_STRUCT

typedef struct tagOriginalStruct ORIG_STRUCT

ST_CAP_FLOW

typedef S_SHORT ST_CAP_FLOW

STRUCT_FPTRS

typedef struct tagStructFptrs STRUCT_FPTRS

Function Documentation

AllocateInfoAtomData()

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

bFoundFeature()

int bFoundFeature	(	inp_ATOM *	at,
		int	num_atoms
	)

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bHasMetalAtom()

int bHasMetalAtom

(

ORIG_ATOM_DATA *

orig_inp_data

)

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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
	)

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CreateCompAtomData()

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

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CreateInfAtom()

inf_ATOM * CreateInfAtom

(

int

num_atoms

)

CreateInfoAtomData()

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

CreateInpAtom()

inp_ATOM * CreateInpAtom

(

int

num_atoms

)

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CreateInpAtomData()

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

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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
	)

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DisconnectMetals()

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

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DisconnectSalts()

int DisconnectSalts	(	ORIG_ATOM_DATA *	orig_inp_data,
		int	bDisconnect
	)

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DuplicateInfoAtomData()

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

fix_odd_things()

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

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FixAdjacentRadicals()

int FixAdjacentRadicals	(	int	num_inp_atoms,
		inp_ATOM *	at
	)

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FixUnkn0DStereoBonds()

int FixUnkn0DStereoBonds	(	inp_ATOM *	at,
		int	num_at
	)

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FreeCompAtomData()

void FreeCompAtomData

(

COMP_ATOM_DATA *

inp_at_data

)

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FreeExtOrigAtData()

void FreeExtOrigAtData	(	OAD_Polymer *	pd,
		OAD_V3000 *	v3k
	)

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FreeInfAtom()

void FreeInfAtom

(

inf_ATOM **

at

)

FreeInfoAtomData()

void FreeInfoAtomData

(

INF_ATOM_DATA *

inf_at_data

)

FreeInpAtom()

void FreeInpAtom

(

inp_ATOM **

at

)

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FreeInpAtomData()

void FreeInpAtomData

(

INP_ATOM_DATA *

inp_at_data

)

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FreeOrigAtData()

void FreeOrigAtData

(

ORIG_ATOM_DATA *

orig_at_data

)

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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
	)

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MarkDisconnectedComponents()

int MarkDisconnectedComponents	(	ORIG_ATOM_DATA *	orig_at_data,
		int	bProcessOldCompNumbers
	)

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MySleep()

void MySleep

(

unsigned long

ms

)

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
	)

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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
	)

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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
	)

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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
	)

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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
	)

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OAD_Polymer_CompareBackboneBondsSeniority()

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

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OAD_Polymer_CompareRanksOfTwoAtoms()

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

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OAD_Polymer_CyclizeCloseableUnits()

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

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OAD_Polymer_DebugTrace()

void OAD_Polymer_DebugTrace

(

OAD_Polymer *

p

)

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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
	)

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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
	)

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OAD_Polymer_Free()

void OAD_Polymer_Free

(

OAD_Polymer *

p

)

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OAD_Polymer_GetRepresentation()

int OAD_Polymer_GetRepresentation

(

OAD_Polymer *

p

)

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OAD_Polymer_IsFirstAtomRankLower()

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

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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
	)

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OAD_Polymer_PrepareFrameShiftEdits()

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

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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
	)

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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
	)

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OAD_Polymer_SmartReopenCyclizedUnits()

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

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OAD_PolymerUnit_CompareAtomLists()

int OAD_PolymerUnit_CompareAtomLists	(	OAD_PolymerUnit *	u1,
		OAD_PolymerUnit *	u2
	)

OAD_PolymerUnit_CompareAtomListsMod()

int OAD_PolymerUnit_CompareAtomListsMod	(	OAD_PolymerUnit *	u1,
		OAD_PolymerUnit *	u2
	)

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OAD_PolymerUnit_CreateCopy()

OAD_PolymerUnit * OAD_PolymerUnit_CreateCopy

(

OAD_PolymerUnit *

u

)

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OAD_PolymerUnit_DebugTrace()

void OAD_PolymerUnit_DebugTrace

(

OAD_PolymerUnit *

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
	)

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OAD_PolymerUnit_DelistIntraRingBackboneBonds()

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

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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
	)

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OAD_PolymerUnit_Free()

void OAD_PolymerUnit_Free

(

OAD_PolymerUnit *

unit

)

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OAD_PolymerUnit_HasMetal()

int OAD_PolymerUnit_HasMetal	(	OAD_PolymerUnit *	u,
		inp_ATOM *	at
	)

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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
	)

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OAD_PolymerUnit_OrderBondAtomsAndBondsThemselves()

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

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OAD_PolymerUnit_PrepareToFrameShift()

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

OAD_PolymerUnit_ReopenCyclized()

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

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OAD_PolymerUnit_SetReopeningDetails()

int OAD_PolymerUnit_SetReopeningDetails	(	OAD_PolymerUnit *	u,
		inp_ATOM *	at
	)

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OAD_PolymerUnit_SortBackboneBonds()

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

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OAD_PolymerUnit_SortBackboneBondsAndSetSeniors()

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

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OAD_PolymerUnit_UnlinkCapsAndConnectEndAtoms()

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

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OAD_StructureEdits_Clear()

void OAD_StructureEdits_Clear

(

OAD_StructureEdits *

ed

)

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OAD_StructureEdits_DebugPrint()

void OAD_StructureEdits_DebugPrint

(

OAD_StructureEdits *

ed

)

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OAD_StructureEdits_Init()

int OAD_StructureEdits_Init

(

OAD_StructureEdits *

ed

)

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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
	)

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OAD_ValidatePolymerAndPseudoElementData()

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

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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
	)

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post_fix_odd_things()

int post_fix_odd_things	(	int	num_atoms,
		inp_ATOM *	at
	)

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PrintFileName()

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

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ReconcileAllCmlBondParities()

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

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remove_ion_pairs()

int remove_ion_pairs	(	int	num_atoms,
		inp_ATOM *	at
	)

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Ring2Chain()

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

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UnMarkRingSystemsInp()

int UnMarkRingSystemsInp	(	inp_ATOM *	at,
		int	num_atoms
	)

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