inpdef.h

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/*
 * SPDX-License-Identifier: MIT
 * Copyright (c) 2024 IUPAC and InChI Trust
 */
 
#ifndef _INPDEF_H_
#define _INPDEF_H_
 
/* input/output format */
 
#include "ichidrp.h"
#include "mode.h"
#include "mol_fmt.h"
 
#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 
typedef S_SHORT ST_CAP_FLOW;
 
/* inp_ATOM::at_type */
#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
#if (FIX_NP_MINUS_BUG == 1)
#define ATT_NP_MINUS_V23 0x8000 
#endif
 
#define AT_FLAG_ISO_H_POINT 0x01 
#define PERIODIC_NUMBER_H 1
 
#ifndef NUMH
#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))
#endif
 
#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) 
typedef struct tagInputAtom
{
    char elname[ATOM_EL_LEN];         /* name of chemical element                                 */
    U_CHAR el_number;                 /* number of the element in the Periodic Table              */
    AT_NUMB neighbor[MAXVAL];         /* positions (from 0) of the neighbors in the inp_ATOM array*/
    AT_NUMB orig_at_number;           /* original atom number                                     */
    AT_NUMB orig_compt_at_numb;       /* original atom number within the component                */
                                      /* before terminal H removal                                */
    S_CHAR bond_stereo[MAXVAL];       /* 1=Up,4=Either,6=Down; this atom is at the pointing wedge,*/
                                      /*   negative => on the opposite side; 3=Either double bond */
    U_CHAR bond_type[MAXVAL];         /* 1..4; 4="aromatic", should be discouraged on input       */
    S_CHAR valence;                   /* for most chemists, it is coordination number, CN;        */
                                      /* number of bonds = number of neighbors                  */
    S_CHAR chem_bonds_valence;        /* for most chemists, it is what usually called valence;    */
                                      /* sum of bond types (type 4 needs special treatment)       */
    S_CHAR num_H;                     /* number of implicit hydrogens, including D and T          */
    S_CHAR num_iso_H[NUM_H_ISOTOPES]; /* number of implicit 1H, 2H(D), 3H(T) < 16                */
    S_CHAR iso_atw_diff;              /* =0 => natural isotopic abundances                        */
                                      /* >0 => (mass) - (mass of the most abundant isotope) + 1   */
                                      /* <0 => (mass) - (mass of the most abundant isotope)       */
    S_CHAR charge;                    /* charge                                                   */
    S_CHAR radical;                   /* RADICAL_SINGLET, RADICAL_DOUBLET, or RADICAL_TRIPLET     */
    S_CHAR bAmbiguousStereo;
    S_CHAR cFlags;     /* AT_FLAG_ISO_H_POINT                                      */
    AT_NUMB at_type;   /* ATT_NONE, ATT_ACIDIC                                     */
    AT_NUMB component; /* number of the structure component > 0                    */
    AT_NUMB endpoint;  /* id of a tautomeric group                                 */
    AT_NUMB c_point;   /* id of a positive charge group                            */
    double x;
    double y;
    double z;
    /* 0D parities (originally were used with CML) */
    S_CHAR bUsed0DParity; /* bit=1 => stereobond; bit=2 => stereocenter               */
    /* 0D tetrahedral parity */
    S_CHAR p_parity;
    AT_NUMB p_orig_at_num[MAX_NUM_STEREO_ATOM_NEIGH];
    /* 0D bond parities */
    S_CHAR sb_ord[MAX_NUM_STEREO_BONDS]; /* stereo bond/neighbor ordering number, starts from 0  */
    /* neighbors on both sides of stereobond have same sign=> trans/T/E, diff. signs => cis/C/Z         */
    S_CHAR sn_ord[MAX_NUM_STEREO_BONDS]; /* ord. num. of the neighbor adjacent to the SB;        */
                                         /* starts from 0;                                       */
                                         /* -1 means removed explicit H                          */
    /* neighbors on both sides of stereobond have same parity => trans/T/E/2, diff. parities => cis/C/Z/1 */
    S_CHAR sb_parity[MAX_NUM_STEREO_BONDS];
    AT_NUMB sn_orig_at_num[MAX_NUM_STEREO_BONDS]; /* orig. at number of sn_ord[] neighbors        */
 
#if (FIND_RING_SYSTEMS == 1)
    S_CHAR bCutVertex;
    AT_NUMB nRingSystem;
    AT_NUMB nNumAtInRingSystem;
    AT_NUMB nBlockSystem;
 
#if (FIND_RINS_SYSTEMS_DISTANCES == 1)
    AT_NUMB nDistanceFromTerminal; /* terminal atom or ring system has 1, next has 2, etc. */
#endif
 
#endif
} inp_ATOM;
 
/*  v. 1.05 extensions: extended input supporting V3000; polymers   */
/*  OAD stands for OrigAtData                                       */
 
/* v. 1.05 Polymer stuff                                            */
 
/* Polymer representation type */
#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
 
typedef struct OAD_PolymerUnit
{
    int id;         /* it is what is called 'Sgroup number' in CTFILE           */
    int type;       /* type as by MDL format (STY)                              */
    int subtype;    /* subtype as by MDL format (SST)                           */
    int conn;       /* connection scheme  as by MDL format (SCN)                */
    int label;      /* it is what is called 'unique Sgroup identifier' CTFILE   */
    int na;         /* number of atoms in the unit                              */
    int nb;         /* number of bonds in the unit                              */
    int cyclizable; /* =1 if frame shift via CRU 'cyclization' is applicable    */
    int cyclized;   /* =1 if CRU already was frame_shift' treated                 */
    double xbr1[4]; /* bracket ends coordinates (SDI)                           */
    double xbr2[4]; /* bracket ends coordinates (SDI)                           */
    char smt[80];   /* Sgroup Subscript (SMT)                                   */
    int representation;
    /* CRU structure is:            cap1-[-end_atom1/\/\/\end_atom2-]-cap2              */
    int cap1;
    int end_atom1;
    int end_atom2;
    int cap2;
    int cap1_is_undef;
    int cap2_is_undef;
    int *alist;     /* list of atoms in the unit (SAL)                          */
    int *blist;     /* bonds in the unit as list [atom1, atom2; atom1, atom2,..]*/
                    /* for crossing bonds (S)                                   */
    int maxbkbonds; /* max (allocd) number of frame_shift involved bonds        */
    int 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) */
    int **bkbonds;  /* list of [breakable] backbone bonds [(a1,a2), (a3,a4),...}*/
} OAD_PolymerUnit;
 
typedef struct OAD_Polymer
{
    OAD_PolymerUnit **units; /* array of pointers to units               */
    int n;
    int n_pzz; /* number of polymeric Zz atoms             */
               /* paired undefined-nature caps/stars around*/
               /* CRY's (must be even)                     */
    int *pzz;  /* polymeric Zz atoms                       */
    int really_do_frame_shift;
    int frame_shift_scheme; /* frame shift analysis scheme              */
    int treat;
    int representation;
    int is_in_reconn;
    int edit_repeats; /*  -1 unknown, to be checked               */
                      /*   0 no, no edits required                */
                      /*   1 yes, edits are necessary             */
} OAD_Polymer;
 
typedef struct OAD_AtProps
{
    int erank;      /* rank of element; 2 - C, >2 - rank of heteroatom in chain,    */
                    /* O > S > Se > Te > N ...., Rule 4                             */
    int ring_erank; /* 0 - not ring or just carbocycle,
                       >2 - rank of senior heteroatom in this cycle                 */
                    /* according to Rule 2 ( N > O >... )                           */
    int ring_num;
    int 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_AtProps;
 
/* Extended input supports v. 1.05 extensions: V3000; polymers  */
typedef struct OAD_V3000
{
    int n_non_star_atoms;
    int n_star_atoms;
    int *atom_index_orig; /* index as supplied for atoms                                  */
    int *atom_index_fin;  /* = index or -1 for star atom                                  */
    int n_sgroups;        /* currently, we do not use this.                               */
    int n_3d_constraints; /* currently, we do not use this.                               */
    int n_collections;
    int n_non_haptic_bonds;
    int n_haptic_bonds;
    int **lists_haptic_bonds;
    /* haptic_bonds[i] is pointer to int* which contains:           */
    /* bond_type, non-star atom number, nendpts,                    */
    /* then endpts themselves                                       */
    /* Enhanced stereo */
    int n_steabs;
    int **lists_steabs; /* steabs[k][0] - not used                                      */
                        /* steabs[k][1] -  number of members in collection              */
                        /* steabs[k][2..] - member atom numbers                         */
    int n_sterel;
    int **lists_sterel; /* sterel[k][0] - n from "STERELn" tag                          */
                        /* sterel[k][1] -  number of members in collection              */
                        /* sterel[k][2..] - member atom numbers                         */
    int n_sterac;
    int **lists_sterac; /* sterac[k][0] - n from "STERACn" tag                          */
                        /* sterac[k][1] -  number of members in collection              */
                        /* sterac[k][2..] - member atom numbers                      */
} OAD_V3000;
 
typedef struct tagOrigAtom
{
    /* Initially filled out by CreateOrigInpDataFromMolfile()                               */
    /* may be changed by disconnecting salts and disconnecting metals                       */
    inp_ATOM *at;
    int num_dimensions;
    int num_inp_bonds;
    int num_inp_atoms;
    /* may be changed by disconnecting salts and disconnecting metals                       */
    int num_components;   /* set by MarkDisconnectedComponents and disconn. metals*/
    int bDisconnectSalts; /* whether salt disconnection is possible               */
    int bDisconnectCoord; /* 0 if no disconnection needed                         */
                          /* else (NumImplicitH to disconnect)+1                  */
#if (bRELEASE_VERSION == 0)
    int bExtract;
#endif
    AT_NUMB *nCurAtLen;      /* has max_num_components elements                      */
    AT_NUMB *nOldCompNumber; /* 0 or component number in previous numbering          */
    int nNumEquSets;         /* number of found component equivalence sets           */
    AT_NUMB *nEquLabels;     /* num_inp_atoms elements, value>0 marks atoms          */
                             /* in the set #value                                    */
    AT_NUMB *nSortedOrder;   /* num_components elements, values = 1..num_components; */
                             /* only if num_components > 1                           */
    int bSavedInINCHI_LIB[INCHI_NUM];
    int bPreprocessed[INCHI_NUM];
    MOL_COORD *szCoord;
    /* v. 1.05 extensions                                                                   */
    OAD_Polymer *polymer;
    OAD_V3000 *v3000;
    int valid_polymer;
    int n_zy; /* number of non-polymeric pseudoatoms (Zy)             */
 
} ORIG_ATOM_DATA;
 
typedef struct tagOriginalStruct
{
    int num_atoms;
    char *szAtoms;
    char *szBonds;
    char *szCoord;
    /* v. 1.05 extensions                                                                   */
    OAD_Polymer *polymer; /* uses pointer copy from orig_inp_data, do not free after use! */
    OAD_V3000 *v3000;     /* uses pointer copy from orig_inp_data, do not free after use! */
    int n_zy;             /* number of non-polymeric pseudoatoms (Zy) */
 
} ORIG_STRUCT;
 
typedef struct tagAtomParmsForDrawing
{
    char at_string[ATOM_INFO_LEN];
    int DrawingLabelLeftShift;
    int DrawingLabelLength;
    AT_NUMB nCanonNbr; /* if zero then do not use all data for the atom                */
    AT_NUMB nCanonEquNbr;
    AT_NUMB nTautGroupCanonNbr;
    AT_NUMB nTautGroupEquNbr;
    S_CHAR cFlags; /* AT_FLAG_ISO_H_POINT                                          */
#ifdef DISPLAY_DEBUG_DATA
    int nDebugData;
#endif
    S_CHAR cHighlightTheAtom;
    S_CHAR cStereoCenterParity;
    S_CHAR cStereoBondParity[MAX_STEREO_BONDS];
    S_CHAR cStereoBondWarning[MAX_STEREO_BONDS];
    S_CHAR cStereoBondNumber[MAX_STEREO_BONDS];
} inf_ATOM;
 
#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
 
typedef struct tagInfoAtomData
{
    inf_ATOM *at;
    int num_at;
    AT_NUMB StereoFlags;
    AT_NUMB num_components;
    AT_NUMB *pStereoFlags;
 
    int nNumRemovedProtons;
    int num_removed_iso_H;           /* number of exchangable isotopic H     */
    NUM_H num_iso_H[NUM_H_ISOTOPES]; /* number of exchangable isotopic H     */
    char szRemovedProtons[MAX_LEN_REMOVED_PROTONS];
} INF_ATOM_DATA;
 
typedef struct tagInputAtomData
{
    inp_ATOM *at;
    inp_ATOM *at_fixed_bonds; /* tautomeric case, added or removed H  */
    unsigned char *keep_explicit_HDT;
    int num_at;
    int num_removed_H;
    int num_bonds;
    int num_isotopic;
    int bExists;
    int bDeleted;
    int bHasIsotopicLayer;
    int bTautomeric;
    int bTautPreprocessed;
    int nNumRemovedProtons;
    NUM_H nNumRemovedProtonsIsotopic[NUM_H_ISOTOPES];
    /* isotopic composition of removed protons, not included in num_iso_H[] */
    NUM_H num_iso_H[NUM_H_ISOTOPES];
    /* isotopic H on tautomerIC atoms and those in nIsotopicEndpointAtomNumber */
    INCHI_MODE bTautFlags;
    INCHI_MODE bTautFlagsDone;
    INCHI_MODE bNormalizationFlags;
} INP_ATOM_DATA;
 
typedef INP_ATOM_DATA INP_ATOM_DATA2[TAUT_NUM];
 
typedef struct tagNormCanonFlags
{
    INCHI_MODE bTautFlags[INCHI_NUM][TAUT_NUM];
    INCHI_MODE bTautFlagsDone[INCHI_NUM][TAUT_NUM];
    INCHI_MODE bNormalizationFlags[INCHI_NUM][TAUT_NUM];
    int nCanonFlags[INCHI_NUM][TAUT_NUM];
} NORM_CANON_FLAGS;
 
typedef struct tagCompositeAtomData
{
    inp_ATOM *at;
    int num_at;
    int num_removed_H;
    int num_bonds;
    int num_isotopic;
    int bExists;
    int bDeleted; /* unused */
    int bHasIsotopicLayer;
    int bTautomeric;
    int nNumRemovedProtons;
    NUM_H nNumRemovedProtonsIsotopic[NUM_H_ISOTOPES];
    /* isotopic composition of removed protons, not included in num_iso_H[] */
    NUM_H num_iso_H[NUM_H_ISOTOPES];
    /* isotopic H on tautomeric atoms and those                             */
    /* in nIsotopicEndpointAtomNumber                                       */
    AT_NUMB *nOffsetAtAndH;
    int num_components;
} COMP_ATOM_DATA;
 
/*
typedef COMP_ATOM_DATA COMP_ATOM_DATA3[TAUT_NUM+1];
*/
 
#define ADD_LEN_STRUCT_FPTRS 100 /* allocation increments                                  */
 
typedef long INCHI_FPTR;
 
typedef struct tagStructFptrs
{
    INCHI_FPTR *fptr; /* input:  fptr[cur_fptr]  =file ptr to the struct to read      */
                      /* output: fptr[cur_fptr+1]=file ptr to the next struct or EOF  */
    int len_fptr;     /* allocated length of fptr                                     */
    int cur_fptr;     /* input: k-1 to read the kth struct, k = 1, 2, 3,...;          */
                      /* left unchanged; struct number := cur_fptr+1                  */
    int max_fptr;     /* length of the filled out portion of fptr                     */
} STRUCT_FPTRS;
 
/* forward declaration */
struct tagCANON_GLOBALS;
 
#ifndef __ICHITIME_H__
struct tagInchiTime;
struct tagINCHI_CLOCK;
int bInchiTimeIsOver(struct tagINCHI_CLOCK *ic, struct tagInchiTime *TickEnd);
#endif
 
#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
 
#ifndef COMPILE_ALL_CPP
#ifdef __cplusplus
extern "C"
{
#endif
#endif
 
    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); /* FIX_ADJ_RAD == 1 */
 
    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);
 
    /*
        ORIG_ATOM_DATA
            functions
    */
 
    /* OAD_Edit */
 
    typedef struct tagOAD_StructureEdits
    {
        INT_ARRAY *del_atom;
        INT_ARRAY *del_bond;
        INT_ARRAY *new_bond;
        INT_ARRAY *mod_bond;
        INT_ARRAY *mod_coord;
        int del_side_chains;
    } OAD_StructureEdits;
 
    int OAD_StructureEdits_Init(OAD_StructureEdits *ed);
 
    void OAD_StructureEdits_Clear(OAD_StructureEdits *ed);
 
    void OAD_StructureEdits_DebugPrint(OAD_StructureEdits *ed);
 
#if (RING2CHAIN == 1)
 
    int Ring2Chain(struct tagINCHI_CLOCK *ic, struct tagCANON_GLOBALS *pCG, ORIG_ATOM_DATA *orig_inp_data);
#endif
 
#if (UNDERIVATIZE == 1)
    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);
 
#endif
 
    /* OAD misc. */
 
    int OAD_ValidatePolymerAndPseudoElementData(ORIG_ATOM_DATA *orig_at_data, int treat_polymers, int bNPZz, char *pStrErr, int bNoWarnings);
 
    /* OAD_Polymer */
    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 *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);
 
#ifndef COMPILE_ANSI_ONLY
    int DisplayInputStructure(char *szOutputString, inp_ATOM *at, INF_ATOM_DATA *inf_at_data, int num_at, DRAW_PARMS *dp);
#endif
 
    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);
 
#ifndef COMPILE_ALL_CPP
#ifdef __cplusplus
}
#endif
#endif
 
#endif /* _INPDEF_H_ */