util.h

Go to the documentation of this file.

/*
 * 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 _UTIL_H_
#define _UTIL_H_
 
#include "inpdef.h"
 
#define EL_NUMBER_H  ((U_CHAR)1)
#define EL_NUMBER_B  ((U_CHAR)5)
#define EL_NUMBER_C  ((U_CHAR)6)
#define EL_NUMBER_N  ((U_CHAR)7)
#define EL_NUMBER_O  ((U_CHAR)8)
#define EL_NUMBER_F  ((U_CHAR)9)
#define EL_NUMBER_SI ((U_CHAR)14)
#define EL_NUMBER_P  ((U_CHAR)15)
#define EL_NUMBER_S  ((U_CHAR)16)
#define EL_NUMBER_CL ((U_CHAR)17)
#define EL_NUMBER_GE ((U_CHAR)32)
#define EL_NUMBER_AS ((U_CHAR)33)
#define EL_NUMBER_SE ((U_CHAR)34)
#define EL_NUMBER_BR ((U_CHAR)35)
#define EL_NUMBER_SB ((U_CHAR)51)
#define EL_NUMBER_TE ((U_CHAR)52)
#define EL_NUMBER_I  ((U_CHAR)53)
#define EL_NUMBER_PO ((U_CHAR)84)
#define EL_NUMBER_AT ((U_CHAR)85)
 
#define EL_NUMBER_ZY ((U_CHAR)119)
#define EL_NUMBER_ZZ ((U_CHAR)120)
 
#ifndef COMPILE_ALL_CPP
#ifdef __cplusplus
extern "C" {
#endif
#endif
 
int get_atomic_mass(const char *elname);
 
int get_atomic_mass_from_elnum(int nAtNum);
 
int get_num_H(const char *elname, int inp_num_H, S_CHAR num_iso_H[], int charge, int radical, int chem_bonds_valence, int atom_input_valence, int bAliased, int bDoNotAddH, int bHasMetalNeighbor);
 
int extract_charges_and_radicals(char *elname, int *pnRadical, int *pnCharge);
 
int extract_H_atoms(char *elname, S_CHAR num_iso_H[]);
 
int normalize_string(char *name);
 
int read_upto_delim(char **pstring, char *field, int maxlen, char *delims);
 
int is_matching_any_delim(char c, char *delims);
 
int dotify_non_printable_chars(char *line);
 
char *lrtrim(char *p, int *nLen);
 
void remove_trailing_spaces(char *p);
 
void remove_one_lf(char *p);
 
int mystrncpy(char *target, const char *source, unsigned maxlen);
 
void mystrrev(char *p);
 
#define ALPHA_BASE 27
 
int inchi_memicmp(const void *p1, const void *p2, size_t length);
 
int inchi_stricmp(const char *s1, const char *s2);
 
char *inchi__strnset(char *s, int val, size_t length);
 
char *inchi__strdup(const char *string);
 
long inchi_strtol(const char *str, const char **p, int base);
 
double inchi_strtod(const char *str, const char **p);
 
AT_NUMB *is_in_the_list(AT_NUMB *pathAtom, AT_NUMB nNextAtom, int nPathLen);
 
int *is_in_the_ilist(int *pathAtom, int nNextAtom, int nPathLen);
 
int is_ilist_inside(int *ilist, int nlist, int *ilist2, int nlist2);
 
void extract_inchi_substring(char **buf, const char *str, size_t slen);
 
void extract_auxinfo_substring(char **buf, const char *str, size_t slen);
 
int extract_orig_nums_from_auxinfo_string(char *saux, int *orig);
 
int extract_nonstereo_eq_classes_from_auxinfo_string(char *saux, int nat, int *orig, int *have_eclass_info, int *eclass, int *eclass_by_origs);
 
int extract_stereo_info_from_inchi_string(char *sinchi, int nat, int *orig, int *at_stereo_mark);
 
int extract_all_backbone_bonds_from_inchi_string(char *sinchi, int *n_all_bkb_orig, int *orig, int *all_bkb_orig);
 
int get_periodic_table_number(const char *elname);
 
int is_el_a_metal(int nPeriodicNum);
 
int get_el_valence(int nPeriodicNum, int charge, int val_num);
 
int get_unusual_el_valence(int nPeriodicNum, int charge, int radical, int bonds_valence, int num_H, int num_bonds);
 
/*  Output valence that does not fit any known valences */
 
int detect_unusual_el_valence(int nPeriodicNum, int charge, int radical, int bonds_valence, int num_H, int num_bonds);
 
int needed_unusual_el_valence(int nPeriodicNum, int charge, int radical, int bonds_valence, int actual_bonds_val, int num_H, int num_bonds);
 
int get_el_type(int nPeriodicNum);
 
int if_skip_add_H(int nPeriodicNum);
 
int get_element_chemical_symbol(int nAtNum, char *szElement);
 
int get_element_or_pseudoelement_symbol(int nAtNum, char *szElement);
 
int MakeRemovedProtonsString(int nNumRemovedProtons, NUM_H *nNumExchgIsotopicH, NUM_H *nNumRemovedProtonsIsotopic, int bIsotopic, char *szRemovedProtons, int *num_removed_iso_H);
 
/*
    Ion pairs and fixing bonds
*/
 
int num_of_H(inp_ATOM *at, int iat);
 
U_CHAR ion_el_group(int el);
 
int has_other_ion_neigh(inp_ATOM *at, int iat, int iat_ion_neigh);
 
int has_other_ion_in_sphere_2(inp_ATOM *at, int iat, int iat_ion_neigh);
 
int nNoMetalNumBonds(inp_ATOM *at, int at_no);
 
int nNoMetalBondsValence(inp_ATOM *at, int at_no);
 
int nNoMetalNeighIndex(inp_ATOM *at, int at_no);
 
int nNoMetalOtherNeighIndex(inp_ATOM *at, int at_no, int cur_neigh);
 
int nNoMetalOtherNeighIndex2(inp_ATOM *at, int at_no, int cur_neigh, int cur_neigh2);
 
int nBondsValToMetal(inp_ATOM *at, int iat);
 
int nBondsValenceInpAt(const inp_ATOM *at, int *nNumAltBonds, int *nNumWrongBonds);
 
int bHeteroAtomMayHaveXchgIsoH(inp_ATOM *atom, int iat);
 
int get_endpoint_valence(U_CHAR el_number);
#if (KETO_ENOL_TAUT == 1)
 
int get_endpoint_valence_KET(U_CHAR el_number);
#endif
 
#define MIN_ATOM_CHARGE        (-2)
#define MAX_ATOM_CHARGE         2
#define NEUTRAL_STATE          (-MIN_ATOM_CHARGE)
#define NUM_ATOM_CHARGES       (MAX_ATOM_CHARGE - MIN_ATOM_CHARGE + 1)
#define MAX_NUM_VALENCES        5                /* max. number + 1 to provide zero termination */
 
/*    CHEMICAL ELEMENTS & ATOMIC VALENCE MODEL
      FOR VARIOUS OXIDATION STATES
*/
typedef struct tagElData
{
    /*    Element chemical symbol */
    const char* szElName;
    /*    Average atomic mass from the Periodic Chart of the Elements
        (Fisher cat. no. 05-702-10) */
    int     nAtMass;
    /*    (not used currently) Atomic mass of the most abundant isotope */
    int     nNormAtMass;
    /*    (not used currently) Exact mw of the most abundant isotope (not used)    */
    double  dAtMass;
    /*    METAL or METAL2 */
    int     nType;
    /*    (not used currently) Pauling electronegativity x 10; 0 means unknown    */
    int     nElNegPauling10;
    /*    InChI does not add implicit H to atoms that have non-zero bSkipAddingH */
    /*    NB: was called bDoNotAddH, renamed to avoid confusion with other procedures */
    int     bSkipAddingH;
    S_CHAR  cValence[NUM_ATOM_CHARGES][MAX_NUM_VALENCES];
} ELDATA;
 
/* Forward declaration */
struct tagCANON_GLOBALS;
 
int SetBitFree(struct tagCANON_GLOBALS *pCG);
 
void WriteCoord(char *str, double x);
extern const int ERR_ELEM;
extern const int nElDataLen;
 
#ifndef COMPILE_ALL_CPP
#ifdef __cplusplus
}
#endif
#endif
 
#ifndef INCHI_BUILD_PLATFORM
 
#if defined(_WIN32)
 
#if defined(_WIN64)
#define INCHI_BUILD_PLATFORM "Windows 64-bit"
#else
#define INCHI_BUILD_PLATFORM "Windows 32-bit"
#endif
 
#elif defined(__linux__)
 
#if defined(__x86_64__) || defined(__ppc64__) || defined(__aarch64__) /* djb-rwth: macro added for 64-bit ARM CPUs -- GH issue #10, thanks to Vincent F. Scalfani */
#define INCHI_BUILD_PLATFORM "Linux 64-bit"
#else
#define INCHI_BUILD_PLATFORM "Linux 32-bit"
#endif
 
#elif defined(__APPLE__)
#define INCHI_BUILD_PLATFORM "OSX"
 
#else
#define INCHI_BUILD_PLATFORM ""
#endif
#endif
 
#ifndef INCHI_BUILD_DEBUG
#if defined(_DEBUG)
#define INCHI_BUILD_DEBUG " Debug"
#else
#define INCHI_BUILD_DEBUG ""
#endif
#endif
 
#ifndef INCHI_SRC_REV
#if defined(_DEBUG)
#define INCHI_SRC_REV "rev. 9b6f1414ebf3+"
#else
#define INCHI_SRC_REV ""
#endif
#endif
 
#ifndef INCHI_BUILD_COMPILER
 
#if defined(_MSC_VER)
 
#if _MSC_VER > 1900
#define INCHI_BUILD_COMPILER "MS VS 2017 or later"
#elif _MSC_VER == 1900
#define INCHI_BUILD_COMPILER "MS VS 2015"
#elif _MSC_VER == 1800
#define INCHI_BUILD_COMPILER "MS VS 2013"
#elif _MSC_VER == 1700
#define INCHI_BUILD_COMPILER "MS VS 2012"
#elif _MSC_VER == 1600
#define INCHI_BUILD_COMPILER "MS VS 2010"
#elif _MSC_VER == 1500
#define INCHI_BUILD_COMPILER "MS VS 2008"
#elif _MSC_VER == 1400
#define INCHI_BUILD_COMPILER "MS VS 2005"
#elif _MSC_VER == 1310
#define INCHI_BUILD_COMPILER "MS VS 2003"
#elif _MSC_VER == 1300
#define INCHI_BUILD_COMPILER "MS VS 2002"
#elif _MSC_VER == 1200
#define INCHI_BUILD_COMPILER "MS VS 6.0"
#else
#define INCHI_BUILD_COMPILER "MS VC++ 5.0 or earlier"
#endif
 
#else
 
#if defined(__GNUC__)
#define INCHI_BUILD_COMPILER "gcc " __VERSION__ ""
#else
#define INCHI_BUILD_COMPILER ""
#endif
#endif
 
#endif
 
#endif /* _UTIL_H_ */