mol_fmt.h

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/*
 * International Chemical Identifier (InChI)
 * Version 1
 * Software version 1.07
 * April 30, 2024
 *
 * MIT License
 *
 * Copyright (c) 2024 IUPAC and InChI Trust
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in all
 * copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 * SOFTWARE.
 *
 * The InChI library and programs are free software developed under the
 * auspices of the International Union of Pure and Applied Chemistry (IUPAC).
 * Originally developed at NIST.
 * Modifications and additions by IUPAC and the InChI Trust.
 * Some portions of code were developed/changed by external contributors
 * (either contractor or volunteer) which are listed in the file
 * 'External-contributors' included in this distribution.
 *
 * info@inchi-trust.org
 *
 */
 
#ifndef _MOL_FMT_H_
#define _MOL_FMT_H_
 
#include <stdio.h>
 
#include "ichisize.h"
#include "mode.h" /* djb-rwth: necessary header file */
 
/*
    Data structures and constants
*/
 
/*************************** read MOL file V2000.************************/
/* ref: A.Dalby et al, "Description of Several Chemical Structure
 * File Formats Used by Computer Programs Developed at Molecular
 * Design Limited", J. Chem. Inf. Comput. Sci., 1992, 32, 244-255.
 */
 
/* ************************** read MOL file V3000.************************ */
/* http://download.accelrys.com/freeware/ctfile-formats/CTFile-formats.zip
 * Last accessed 2013-06-11
 */
 
/*-----------*/
/* CONSTANTS */
/*-----------*/
 
#define SD_FMT_END_OF_DATA "$$$$"
 
#define MOL_FMT_INPLINELEN 204 /* add cr, lf, double zero termination */
#ifndef MOL_FMT_MAXLINELEN
#define MOL_FMT_MAXLINELEN 200
#endif
 
#define MOL_FMT_PRESENT 1
#define MOL_FMT_ABSENT 0
 
/* configuration */
#define MOL_FMT_QUERY MOL_FMT_ABSENT
#define MOL_FMT_CPSS MOL_FMT_ABSENT
#define MOL_FMT_REACT MOL_FMT_ABSENT
 
#define MOL_FMT_STRING_DATA 'S'
#define MOL_FMT_CHAR_INT_DATA 'C'
#define MOL_FMT_SHORT_INT_DATA 'N'
#define MOL_FMT_LONG_INT_DATA 'L'
#define MOL_FMT_DOUBLE_DATA 'D'
#define MOL_FMT_FLOAT_DATA 'F'
#define MOL_FMT_JUMP_TO_RIGHT 'J'
#define MOL_FMT_INT_DATA 'I'
 
#define MOL_FMT_MAX_VALUE_LEN 32 /* max length of string containing a numerical value */
 
#define MOL_FMT_M_STY_NON 0 
#define MOL_FMT_M_STY_SRU 1 
#define MOL_FMT_M_STY_MON 2 
#define MOL_FMT_M_STY_COP 3 
#define MOL_FMT_M_STY_MOD 4 
#define MOL_FMT_M_STY_CRO 5 
#define MOL_FMT_M_STY_MER 6 
#define MOL_FMT_M_SST_NON 0 
#define MOL_FMT_M_SST_ALT 1 
#define MOL_FMT_M_SST_RAN 2 
#define MOL_FMT_M_SST_BLK 3 
#define MOL_FMT_M_CONN_NON 0
#define MOL_FMT_M_CONN_HT 1
#define MOL_FMT_M_CONN_HH 2
#define MOL_FMT_M_CONN_EU 3
 
/* V3000 specific constants */
#define MOL_FMT_V3000_STENON -1
#define MOL_FMT_V3000_STEABS 1
#define MOL_FMT_V3000_STEREL 2
#define MOL_FMT_V3000_STERAC 3
 
/* provisional limits for V3000 */
#define MOL_FMT_V3000_INPLINELEN 32004 /* add cr, lf, double zero termination */
#ifndef MOL_FMT_V3000_MAXLINELEN
#define MOL_FMT_V3000_MAXLINELEN 32000
#endif
#define MOL_FMT_V3000_MAXFIELDLEN 4096
 
/*#ifdef TARGET_EXE_USING_API*/
#ifndef ISOTOPIC_SHIFT_FLAG
#define ISOTOPIC_SHIFT_FLAG 10000 /* add to isotopic mass if isotopic_mass = */
#endif
/*#endif*/
 
/*-------------------*/
/* SIMPLE DATA TYPES */
/*-------------------*/
 
#ifndef INCHI_US_CHAR_DEF
typedef signed char S_CHAR;
typedef unsigned char U_CHAR;
#define INCHI_US_CHAR_DEF
#endif
 
#ifndef LEN_COORD
#define LEN_COORD 10
#endif
#ifndef NUM_COORD
#define NUM_COORD 3
#endif
 
/*-----------------*/
/* DATA STRUCTURES */
/*-----------------*/
typedef struct A_NUM_LISTS
{
    int **lists;
    int allocated;
    int used;
    int increment;
} NUM_LISTS;
 
int NumLists_Alloc(NUM_LISTS *num_lists, int nlists);
 
int NumLists_ReAlloc(NUM_LISTS *num_lists);
 
int NumLists_Append(NUM_LISTS *num_lists, int *list);
 
void NumLists_Free(NUM_LISTS *num_lists);
 
typedef struct tagINT_ARRAY
{
    int *item;
    int allocated;
    int used;
    int increment;
} INT_ARRAY;
 
int IntArray_Alloc(INT_ARRAY *items, int nitems);
 
int IntArray_ReAlloc(INT_ARRAY *items);
 
int IntArray_Append(INT_ARRAY *items, int new_item);
 
int IntArray_AppendIfAbsent(INT_ARRAY *items, int new_item);
 
void IntArray_Reset(INT_ARRAY *items);
 
void IntArray_Free(INT_ARRAY *items);
 
void IntArray_DebugPrint(INT_ARRAY *items);
 
typedef struct A_MOL_FMT_SGROUP
{
    int id;
    int type;
    int subtype;
    int conn;
    int label;
    double xbr1[4];
    double xbr2[4];
    char smt[80];
    INT_ARRAY alist;
    INT_ARRAY blist;
} MOL_FMT_SGROUP;
 
int MolFmtSgroup_Create(MOL_FMT_SGROUP **sgroup,
                        int id,
                        int type);
 
void MolFmtSgroup_Free(MOL_FMT_SGROUP *sgroup);
 
typedef struct A_MOL_FMT_SGROUPS
{
    MOL_FMT_SGROUP **group;
    int allocated;
    int used;
    int increment;
} MOL_FMT_SGROUPS;
 
int MolFmtSgroups_Alloc(MOL_FMT_SGROUPS *items, int nitems);
 
int MolFmtSgroups_ReAlloc(MOL_FMT_SGROUPS *items);
 
int MolFmtSgroups_Append(MOL_FMT_SGROUPS *items, int id, int type);
 
void MolFmtSgroups_Free(MOL_FMT_SGROUPS *items);
 
int MolFmtSgroups_GetIndexBySgroupId(int id, MOL_FMT_SGROUPS *items);
 
typedef struct A_MOL_FMT_HEADER_BLOCK
{
    char molname[MOL_FMT_MAXLINELEN + 1];
    char line2[MOL_FMT_MAXLINELEN + 1];
    char user_initls[3];
    char prog_name[9];
    char month;
    char day;
    char year;
    char hour;
    char minute;
    char dim_code[3];
    short scaling_factor1;
    double scaling_factor2;
    double energy;
    long internal_regno;
    char comment[81];
} MOL_FMT_HEADER_BLOCK;
 
typedef struct A_MOL_FMT_ATOM
{
    double fx;      /* F10.5;       Generic             */
    double fy;      /* F10.5;       Generic             */
    double fz;      /* F10.5;       Generic             */
    char symbol[6]; /* aaa;         Generic             */
 
    S_CHAR mass_difference; /* dd;  (M_ISO)                     */
                            /*   Generic: -3..+4 otherwise 0 or */
                            /*   127=most abund. isotope        */
    S_CHAR charge;          /* ccc; (M CHG),                    */
                            /*  Generic: 1=+3, 2=+2,3=+1,       */
                            /*  4=doublet,5=-1,6=-2,7=-3        */
    char radical;           /*      (M RAD)                     */
    char stereo_parity;     /*   sss;         Generic           */
#if (MOL_FMT_QUERY == MOL_FMT_PRESENT)
    char H_count_plus_1; /* hhh;         Query;              */
                         /*   Hn means >= n H;               */
                         /*   H0 means no H                  */
    char stereo_care;    /* bbb;         Query: 0=ignore;    */
                         /*   1=must match                   */
#endif
    char valence; /* vvv:                             */
                  /*   0=no marking; (1..14)=(1..14); */
                  /*   15=zero valence.Number of bonds*/
                  /*   includes bonds to impl. H's    */
 
#if (MOL_FMT_CPSS == MOL_FMT_PRESENT)
    char H0_designator;           /* HHH:         CPSS                */
    char reaction_component_type; /* rrr:                             */
                                  /* CPSS: 1=reactant,                */
                                  /*       2=product,                 */
                                  /*       3=intermediate             */
    char reaction_component_num;  /* iii:         CPSS: 0 to (n-1)    */
#endif
#if (MOL_FMT_REACT == MOL_FMT_PRESENT)
    short atom_atom_mapping_num;  /* mmm:        Reaction: 1..255     */
    char cInversionRetentionFlag; /* nnn:                             */
                                  /*   1=inverted, 2=retained config.;*/
                                  /*   0=property not applied         */
#endif
#if (MOL_FMT_REACT == MOL_FMT_PRESENT || MOL_FMT_QUERY == MOL_FMT_PRESENT)
    char exact_change_flag; /* eee                              */
#endif
    char my_n_impH;         /* number of implicit H calculated  */
                            /* for adding H to strings in STDATA*/
    char display_tom;       /* Do not hide element's name       */
                            /*   (applies to C 7-25-98 DCh      */
    char atom_aliased_flag; /* Do not remove                    */
                            /* charge/radical/isotope if it     */
                            /*   is in the alias. 9-3-99 DCh    */
} MOL_FMT_ATOM;
 
typedef struct A_MOL_FMT_BOND
{
    short atnum1;     /* 111: First atom number: Generic  */
    short atnum2;     /* 222: Second atom number:Generic  */
    char bond_type;   /* ttt:                             */
                      /* 1,2,3=single, double, triple;    */
                      /* 4=aromatic;                      */
                      /* 5=single or double;              */
                      /* 6=single or aromatic;            */
                      /* 7=double or aromatic;            */
                      /* 8=any.                           */
                      /* Values 4-8 are for               */
                      /* SSS queries only                 */
    char bond_stereo; /* sss:                             */
                      /* Single bonds:                    */
                      /*   0=not stereo, 1=up,            */
                      /*   4=either, 6=down               */
                      /* Double bonds:                    */
                      /*   0=use x,y,z to                 */
                      /*     determine cis/trans,         */
                      /*   3=cis or trans (either)        */
                      /*   xxx:     not used              */
 
#if (MOL_FMT_QUERY == MOL_FMT_PRESENT)
    char bond_topology; /* rrr:                             */
                        /* 0=either, 1=ring, 2=chain:       */
                        /* SSS queries only                 */
#endif
#if (MOL_FMT_REACT == MOL_FMT_PRESENT)
    char react_center_status; /* ccc:                             */
                              /* 0 = unmarked,                    */
                              /* 1 = a center,                    */
                              /* -1 = not a center;               */
                              /* Additional:                      */
                              /* 2 = no charge,                   */
                              /* 4 = bond made/broken,            */
                              /* 8 = bond order changes           */
                              /*  12=4+8; 5=4+1, 9=8+1, 13=12+1   */
                              /*  12=4+8; 5=4+1, 9=8+1, 13=12+1   */
                              /*  are also possible               */
#endif
} MOL_FMT_BOND;
 
typedef struct A_MOL_FMT_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;
    NUM_LISTS *haptic_bonds; /* haptic_bonds[i] is ptr to int* which contains    */
                             /* bond_type, non-star atom number,                 */
                             /* nendpts, then endpts themselves                  */
    /* Enhanced stereo */
    int n_steabs;
    NUM_LISTS *steabs; /* steabs[k][0] - not used                          */
                       /* steabs[k][1] -  number of members in collection  */
                       /* steabs[k][2..] - member atom numbers             */
    int n_sterel;
    NUM_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;
    NUM_LISTS *sterac; /* sterac[k][0] - n from "STERACn" tag              */
                       /* sterac[k][1] -  number of members in collection  */
                       /* sterac[k][2..] - member atom numbers          */
} MOL_FMT_v3000;
 
typedef struct A_MOL_FMT_CTAB
{
    /* Line #1: Counts line */
    int n_atoms; /* int accounts for possible V3000. Was: aaa; <= 255; Generic */
    int n_bonds; /* int accounts for possible V3000. Was: bbb; <= 255; Generic */
#if (MOL_FMT_QUERY == MOL_FMT_PRESENT)
    short n_atom_lists; /* lll; <=  30; Query                               */
#endif
 
    char chiral_flag;      /* ccc; 0 or 1; Generic                             */
    short n_stext_entries; /* sss;         CPSS                                */
#if (MOL_FMT_CPSS == MOL_FMT_PRESENT)
    short n_reaction_components_plus_1; /* xxx;         CPSS                    */
    short n_reactants;                  /* rrr;         CPSS                                */
    short n_products;                   /* ppp;         CPSS                                */
    short n_intermediates;              /* iii;         CPSS                                */
#endif
    short n_property_lines; /* mmm;         Generic                             */
    short follow_inchi_1_treating_iso_mass;
    char version_string[7]; /* vvvvvv;      Generic; 'V2000'                    */
    MOL_FMT_ATOM *atoms;    /* The Atom Block                                   */
    MOL_FMT_BOND *bonds;
    MOL_COORD *coords;
    MOL_FMT_SGROUPS sgroups; /*    growable array of pointers to Sgroup objects  */
    MOL_FMT_v3000 *v3000;
} MOL_FMT_CTAB;
 
typedef struct A_MOL_FMT_DATA
{
    MOL_FMT_HEADER_BLOCK hdr;
    MOL_FMT_CTAB ctab;
} MOL_FMT_DATA;
 
/*
    Functions
*/
 
static MOL_FMT_DATA* MolfileReadDataLines(INCHI_IOSTREAM* inp_file,
    MOL_FMT_HEADER_BLOCK* OnlyHeaderBlock,
    MOL_FMT_CTAB* OnlyCTab,
    int bGetOrigCoord,
    int treat_polymers,
    int* err, char* pStrErr, int bNoWarnings);
 
static int MolfileReadHeaderLines(MOL_FMT_HEADER_BLOCK* hdr, INCHI_IOSTREAM* inp_file, char* pStrErr);
 
static int MolfileReadCountsLine(MOL_FMT_CTAB* ctab, INCHI_IOSTREAM* inp_file, char* pStrErr);
 
static int MolfileReadAtomsBlock(MOL_FMT_CTAB* ctab, INCHI_IOSTREAM* inp_file,
    int err, char* pStrErr);
 
static int MolfileReadBondsBlock(MOL_FMT_CTAB* ctab, INCHI_IOSTREAM* inp_file,
    int err, char* pStrErr);
 
MOL_FMT_DATA *ReadMolfile(INCHI_IOSTREAM *inp_file,
                          MOL_FMT_HEADER_BLOCK *OnlyHeaderBlock,
                          MOL_FMT_CTAB *OnlyCTab,
                          int bGetOrigCoord,
                          int treat_polymers,
                          int pseudos_allowed,
                          char *pname,
                          int lname,
                          unsigned long *Id,
                          const char *pSdfLabel,
                          char *pSdfValue,
                          int *err,
                          char *pStrErr,
                          int bNoWarnings);
 
int MolfileStrnread(char *dest,
                    char *source,
                    int len,
                    char **first_space);
 
int MolfileReadField(void *data,
                     int field_len,
                     int data_type,
                     char **line_ptr);
 
long MolfileExtractStrucNum(MOL_FMT_HEADER_BLOCK *pHdr);
 
int MolfileHasNoChemStruc(MOL_FMT_DATA *mfdata);
 
int MolfileSaveCopy(INCHI_IOSTREAM *inp_file,
                    long fPtrStart,
                    long fPtrEnd,
                    FILE *outfile,
                    long num);
 
int MolfileGetXYZDimAndNormFactors(MOL_FMT_DATA *mfdata,
                                   int find_norm_factors,
                                   double *x0,
                                   double *y0,
                                   double *z0,
                                   double *xmin,
                                   double *ymin,
                                   double *zmin,
                                   double *scaler,
                                   int *err,
                                   char *pStrErr);
 
MOL_FMT_DATA *FreeMolfileData(MOL_FMT_DATA *mfdata);
 
/*
    V3000 Molfile
*/
 
int MolfileV3000Init(MOL_FMT_CTAB *ctab,
                     char *pStrErr);
 
int MolfileV3000ReadCTABBeginAndCountsLine(MOL_FMT_CTAB *ctab,
                                           INCHI_IOSTREAM *inp_file,
                                           char *pStrErr);
 
int MolfileV3000ReadAtomsBlock(MOL_FMT_CTAB *ctab,
                               INCHI_IOSTREAM *inp_file,
                               int err,
                               char *pStrErr);
 
int MolfileV3000ReadBondsBlock(MOL_FMT_CTAB *ctab,
                               INCHI_IOSTREAM *inp_file,
                               int err,
                               char *pStrErr);
 
int MolfileV3000ReadTailOfCTAB(MOL_FMT_CTAB *ctab,
                               INCHI_IOSTREAM *inp_file,
                               int err,
                               char *pStrErr);
 
int MolfileV3000ReadHapticBond(MOL_FMT_CTAB *ctab,
                               char **line_ptr,
                               int **num_list,
                               char *pStrErr);
 
int MolfileV3000ReadStereoCollection(MOL_FMT_CTAB *ctab,
                                     char **line_ptr,
                                     int **num_list,
                                     char *pStrErr);
 
int MolfileV3000ReadSGroup(MOL_FMT_CTAB *ctab,
                           INCHI_IOSTREAM *inp_file,
                           int err,
                           char *pStrErr);
 
int MolfileV3000Read3DBlock(MOL_FMT_CTAB *ctab,
                            INCHI_IOSTREAM *inp_file,
                            int err,
                            char *pStrErr);
 
int MolfileV3000ReadCollections(MOL_FMT_CTAB *ctab,
                                INCHI_IOSTREAM *inp_file,
                                int err,
                                char *pStrErr);
/*    Clean V3000 stuff */
 
int DeleteMolfileV3000Info(MOL_FMT_v3000 *v3000);
 
char *inchi_fgetsLf_V3000(char *line,
                          INCHI_IOSTREAM *inp_stream);
 
int get_V3000_input_line_to_strbuf(INCHI_IOS_STRING *buf,
                                   INCHI_IOSTREAM *inp_stream);
 
int MolfileV3000ReadField(void *data,
                          int data_type,
                          char **line_ptr);
int MolfileV3000ReadKeyword(char *key,
                            char **line_ptr);
 
/*
    SDF
*/
 
int SDFileSkipExtraData(INCHI_IOSTREAM *inp_file,
                        unsigned long *CAS_num,
                        char *comment,
                        int lcomment,
                        char *name,
                        int lname,
                        int prev_err,
                        const char *pSdfLabel,
                        char *pSdfValue,
                        char *pStrErr,
                        int bNoWarnings);
 
int SDFileIdentifyLabel(char *inp_line, const char *pSdfLabel);
 
unsigned long SDFileExtractCASNo(char *line);
 
#endif /* _MOL_FMT_H_ */