rino 0.1.0 → 0.2.0

data/ext/src/e_ichisize.h

@@ -1,43 +0,0 @@
-/*
- * International Union of Pure and Applied Chemistry (IUPAC)
- * International Chemical Identifier (InChI)
- * Version 1
- * Software version 1.00
- * April 13, 2005
- * Developed at NIST
- */
-
-#ifndef ___INCHISIZE_H__
-#define ___INCHISIZE_H__
-
-
-typedef unsigned short AT_NUMB;
-typedef unsigned short AT_RANK;
-#define AT_RANK_MASK   ((AT_RANK)~0)
-
-typedef signed short NUM_H;
-#define MAX_ATOMS  1024
-
-#define CHAR_MASK  0xFF
-
-typedef unsigned long INCHI_MODE;
-
-#define LEN_COORD 10
-#define NUM_COORD 3
-typedef char MOL_COORD[LEN_COORD*NUM_COORD + NUM_COORD-1]; /*copied 30 bytes from MOLfile */
-
-typedef enum tagInputType { INPUT_NONE=0, INPUT_MOLFILE=1, INPUT_SDFILE=2, INPUT_INCHI_XML=3, INPUT_INCHI_PLAIN=4, INPUT_CMLFILE=5, INPUT_MAX } INPUT_TYPE;
-
-/* other types */
-
-#define UCINT  (int)(unsigned char)
-#ifndef INCHI_US_CHAR_DEF
-typedef signed char   S_CHAR;
-typedef unsigned char U_CHAR;
-#define INCHI_US_CHAR_DEF
-#endif
-
-
-
-#endif /* ___INCHISIZE_H__ */
-

data/ext/src/e_inchi_atom.c

@@ -1,75 +0,0 @@
-/*
- * International Union of Pure and Applied Chemistry (IUPAC)
- * International Chemical Identifier (InChI)
- * Version 1
- * Software version 1.00
- * April 13, 2005
- * Developed at NIST
- */
-
-#include <stdio.h>
-#include <string.h>
-
-#include "e_mode.h"
-#include "inchi_api.h"
-#include "e_inchi_atom.h"
-#include "e_ichisize.h"
-#include "e_util.h"
-/******************************************************************************************************/
-void e_FreeInchi_Atom( inchi_Atom **at )
-{
-    if ( at && *at ) {
-        e_inchi_free( *at );
-        *at = NULL;
-    }
-}
-/******************************************************************************************************/
-void e_FreeInchi_Stereo0D( inchi_Stereo0D **stereo0D )
-{
-    if ( stereo0D && *stereo0D ) {
-        e_inchi_free( *stereo0D );
-        *stereo0D = NULL;
-    }
-}
-/******************************************************************************************************/
-inchi_Atom *e_CreateInchi_Atom( int num_atoms )
-{
-   inchi_Atom *p = (inchi_Atom* ) e_inchi_calloc(num_atoms, sizeof(inchi_Atom) );
-   return p;
-}
-/******************************************************************************************************/
-inchi_Stereo0D *e_CreateInchi_Stereo0D( int num_stereo0D )
-{
-   return (inchi_Stereo0D* ) e_inchi_calloc(num_stereo0D, sizeof(inchi_Stereo0D) );
-}
-/******************************************************************************************************/
-void e_FreeInchi_Input( inchi_Input *inp_at_data )
-{
-    e_FreeInchi_Atom( &inp_at_data->atom );
-    e_FreeInchi_Stereo0D( &inp_at_data->stereo0D );
-    memset( inp_at_data, 0, sizeof(*inp_at_data) );
-}
-/*********************************************************/
-int e_RemoveRedundantNeighbors( inchi_Input *inp_at_data )
-{
-    int i, j, k;
-    inchi_Atom *at        = inp_at_data->atom;
-    int         num_atoms = inp_at_data->num_atoms;
-    for ( i = 0; i < num_atoms; i ++ ) {
-        for ( j = k = 0; j < at[i].num_bonds; j ++ ) {
-            if (  at[i].neighbor[j] < i ) {
-                at[i].neighbor[k]    = at[i].neighbor[j];
-                at[i].bond_type[k]   = at[i].bond_type[j];
-                at[i].bond_stereo[k] = at[i].bond_stereo[j];
-                k ++;
-            }
-        }
-        for ( j = k; j < at[i].num_bonds; j ++ ) {
-            at[i].neighbor[j]    = 0;
-            at[i].bond_type[j]   = 0;
-            at[i].bond_stereo[j] = 0;
-        }
-        at[i].num_bonds = k;
-    }
-    return 0;
-}

data/ext/src/e_inchi_atom.h

@@ -1,33 +0,0 @@
-/*
- * International Union of Pure and Applied Chemistry (IUPAC)
- * International Chemical Identifier (InChI)
- * Version 1
- * Software version 1.00
- * April 13, 2005
- * Developed at NIST
- */
-
-#ifndef __INCHI_ATOM_H__
-#define __INCHI_ATOM_H__
-
-#ifndef INCHI_ALL_CPP
-#ifdef __cplusplus
-extern "C" {
-#endif
-#endif
-
-void           e_FreeInchi_Atom( inchi_Atom **at );
-void           e_FreeInchi_Stereo0D( inchi_Stereo0D **stereo0D );
-inchi_Atom     *e_CreateInchi_Atom( int num_atoms );
-inchi_Stereo0D *e_CreateInchi_Stereo0D( int num_stereo0D );
-void           e_FreeInchi_Input( inchi_Input *inp_at_data );
-int            e_RemoveRedundantNeighbors( inchi_Input *inp_at_data );
-
-#ifndef INCHI_ALL_CPP
-#ifdef __cplusplus
-}
-#endif
-#endif
-
-
-#endif /* __INCHI_ATOM_H__ */

data/ext/src/e_inpdef.h

@@ -1,41 +0,0 @@
-/*
- * International Union of Pure and Applied Chemistry (IUPAC)
- * International Chemical Identifier (InChI)
- * Version 1
- * Software version 1.00
- * April 13, 2005
- * Developed at NIST
- */
-
-/* input/output format */
-#ifndef __INPDEF_H__
-#define __INPDEF_H__
-
-
-/* BILLY 8/6/04 */
-#ifndef INCHI_ALL_CPP
-#ifdef __cplusplus
-extern "C" {
-#endif
-#endif
-
-int e_MolfileToInchi_Input( FILE *inp_molfile, inchi_Input *orig_at_data, int bMergeAllInputStructures,
-                       int bDoNotAddH, int bAllowEmptyStructure,
-                       const char *pSdfLabel, char *pSdfValue, long *lSdfId,
-                       long *lMolfileNumber, INCHI_MODE *pInpAtomFlags, int *err, char *pStrErr );
-int e_INChIToInchi_Input( FILE *inp_molfile, inchi_Input *orig_at_data, int bMergeAllInputStructures,
-                       int bDoNotAddH, INPUT_TYPE nInputType,
-                       char *pSdfLabel, char *pSdfValue, long *lSdfId, INCHI_MODE *pInpAtomFlags,
-                       int *err, char *pStrErr );
-
-int e_CopyMOLfile(FILE *inp_file, long fPtrStart, long fPtrEnd, FILE *prb_file, long nNumb);
-
-
-/* BILLY 8/6/04 */
-#ifndef INCHI_ALL_CPP
-#ifdef __cplusplus
-}
-#endif
-#endif
-
-#endif  /* __INPDEF_H__ */

data/ext/src/e_mode.h

@@ -1,706 +0,0 @@
-/*
- * International Union of Pure and Applied Chemistry (IUPAC)
- * International Chemical Identifier (InChI)
- * Version 1
- * Software version 1.00
- * April 13, 2005
- * Developed at NIST
- */
-
-#ifndef __MODE_H__
-#define __MODE_H__
-
-/* uncomment to unconditionally force ANSI-89 C, no Win32 specific code */
-#define INCHI_ANSI_ONLY
-
-/* uncomment to create a library for using INChI API described in inchi_api.h */
-/* #define INCHI_LIBRARY */
-
-/* uncomment to use INChI library as a Win32 DLL or to eliminate stricmp duplication */
-/* #define INCHI_LINK_AS_DLL */
-
-/* Uncomment to compile INCHI_MAIN.exe that calls INCHI_DLL.dll */
-#define INCHI_MAIN
-
-#if(!defined(_MSC_VER) || defined(INCHI_LIBRARY))  /* non-Microsoft GNU C, BCC, etc. compilers */
-#ifndef INCHI_ANSI_ONLY
-#define INCHI_ANSI_ONLY
-#endif
-#endif
-
-/* #define INCHI_ALL_CPP */   /* uncomment to allow C++ compilation/linkage of functions prototyped in .h files */
-
-#ifdef _MSC_VER
-/*
-========== disable MS VC++ 6.0 Level 4 compiler warnings: ==============
- C4706: assignment within conditional expression
- C4127: conditional expression is constant
- C4244: '=' : conversion from 'int ' to '???', possible loss of data
- C4701: local variable '???' may be used without having been initialized (removed)
- C4514: unreferenced inline/local function has been removed (C++)
- C4100: 'identifier' : unreferenced formal parameter
- C4786: 'identifier' : identifier was truncated to 'number' characters in the debug information
-========================================================================
-*/
-   #pragma warning( disable : 4706 4127 4514 4100 4786 )
-#endif
-
-/* Release */
-#define bRELEASE_VERSION  1    /* 1=> release version; comment out to disable */
-/* Debug */
-#ifndef bRELEASE_VERSION 
-#define bRELEASE_VERSION  0    /* 0=> debug version */
-#endif
-
-#define ACD_LABS_VERSION 0    /* always 0 */
-
-#ifndef ADD_CMLPP
-/* this allows ADD_CMLPP be #defined in a makefile */
-#define ADD_CMLPP        0    /* 1 => add CMLPP input */
-#endif
-
-#if ( ADD_CMLPP == 1 )
-#ifdef USE_CMLPPDLL
-/* 1200 is VC++ 6.0 version, 1300 is VC++ .NET; USE_CMLPPDLL may be #defined in a makefile*/
-#if ( defined(_WIN32) && defined(_MSC_VER) && _MSC_VER >= 1200 )
-#define MSC_DELAY_LOAD_CMLPPDLL
-#endif
-#endif
-#endif
-
-/* display (non-canonical) c-groups, display orig at numbers */
-#if( bRELEASE_VERSION == 1 )
-#define DISPLAY_DEBUG_DATA_C_POINT 0  /* disabled release version for now */
-#define DISPLAY_ORIG_AT_NUMBERS    1  /* 1 => in an uncanonicalized components display orig. atom numbers (default) */
-#else
-#define DISPLAY_DEBUG_DATA_C_POINT 1  /* debug: 1=>display (non-canonically numbered) c-groups, 0=>do not display */
-#define DISPLAY_ORIG_AT_NUMBERS    1  /* 0 => in an uncanonicalized components display ordering atom numbers (debug) */
-#endif
-
-#if ( DISPLAY_DEBUG_DATA_C_POINT > 0 )
-#define DISPLAY_DEBUG_DATA         DISPLAY_DEBUG_DATA_C_POINT
-#endif
-
-/**************************/
-/* Normalization settings */
-/**************************/
-
-/* post-2004-04-27 features */
-#define HAL_ACID_H_XCHG            1 /* allow iso H exchange to HX (X=halogen) and H2Y (Y=halcogen) */
-#define CANON_FIXH_TRANS           1 /* produce canonical fixed-H transposition */
-#define STEREO_WEDGE_ONLY          0 /* 1=> only pointed ends stereo bonds define stereo; 0=> both ends */
-
-/* current new (with respect to v1.12 Beta) preprocessing */
-#define REMOVE_ION_PAIRS_EARLY     1 /* 1=> new preprocessing: step 1 before disconnecting metals in fix_odd_things() */
-#define REMOVE_ION_PAIRS_DISC_STRU 1 /* 1=> new post-preprocessing: remove charhes after metal disconnection */
-#define REMOVE_ION_PAIRS_FIX_BONDS 1 /* 1=> step2: set unchangeable bonds around removed ion pairs */
-#define S_VI_O_PLUS_METAL_FIX_BOND 1 /* 1=> count double bond M-O(+)=S  as O=S in S(VI) ans S(VIII) fixing bonds */
-#define N_V_STEREOBONDS            1 /* 1=> detect stereobonds incident to N(V); 0 => don't */
-/* for testing */
-#define REMOVE_ION_PAIRS_ORIG_STRU 0 /* 0=> normal mode (default)
-                                      * 1=> testing mode only: remove ion pairs from the original structure 
-                                      *     to save the changes in the output Molfile (/OutputSDF) or AuxInfo
-                                      *     NIP=No Ion Pairs
-                                      */
-/* salts treatment */
-#define DISCONNECT_SALTS            1  /* 1=>disconnect metal atoms from salts, 0=>dont */
-#define TEST_REMOVE_S_ATOMS         1  /* 1=>default: after merging into one group test &
-                                        *    remove unreachable,
-                                        * 0=> old version: test only before merging into one t-group */
-#define CHARGED_SALTS_ONLY          1  /* 1=>(default)do not test far salts tautomerism if
-                                        *     no negative charge(s) present */
-#define BNS_PROTECT_FROM_TAUT       1  /* 1=> do not allow testing of bonds to acetyl or nitro */
-#define BNS_MARK_EDGE_2_DISCONNECT  1  /* 1=> mark edge as temp forbidden instead of disconnection */
-
-#define REPLACE_ALT_WITH_TAUT       1  /* 1 => replace alt bonds with tautomeric bonds in case of standard t-groups */
-#define MOVE_CHARGES                1  /* 1 => take moveable charges into account */
-#define NEUTRALIZE_ENDPOINTS        1  /* 1 => before checking whether an H is moveable make 2 endpoints neutral */
-                                       /*      implemented only if CHECK_TG_ALT_PATH = 0, defined in ichi_bns.c  */
-#define FIX_H_CHECKING_TAUT         1  /* 1 => Fix moveable H or (-) before checking if taut. exchange is possible */
-#define ALWAYS_ADD_TG_ON_THE_FLY    1  /* 1 => disables radical calcellation by taut-charge movement */
-#define IGNORE_SINGLE_ENDPOINTS     1  /* 1 => see FindAccessibleEndPoints() in INChITaut.c */
-
-/* recently added -- begin */
-#define INCL_NON_SALT_CANDIDATATES   1  /* 1=> allow H and (-) migrate between "acidic" O and
-                                         *     other possible endpoints */
-#define SALT_WITH_PROTONS            1  /* 1=> (new new) include proton migrarion C-SH, =C-OH, NH+ */
-#define OPPOSITE_CHARGE_IN_CGROUP    1  /* 1=> allow N(-) in (+) c-group, 0=> disallow */
-#define MOVE_PPLUS_TO_REMOVE_PROTONS 0  /* 0=> default; 1=> (disabled) add P/P+ charge group during
-                                         *     'hard' proton removal */
-#define ADD_MOVEABLE_O_PLUS          1  /* 1=> allow charges on O(+) to move */
-/* recently added -- end */
-
-#define DISCONNECT_METALS           1  /* make main layer disconnected */
-#define RECONNECT_METALS            0  /* 1=> by default add reconnected layer in case of coord.
-                                        *     compound disconnection */  
-#define CHECK_METAL_VALENCE         0  /* 1=> disconnect only metals that have abnormal valence */
-#define bREUSE_INCHI                1  /* 1=> do not recalulate INChI for components in reconnected
-                                        *     structure that are same as in the connected one */
-#define OUTPUT_CONNECTED_METAL_ONLY 0  /* 0=> default; 1 => (debug) create only reconnected or
-                                        *     initial struct. output */
-#define EMBED_REC_METALS_INCHI      1  /* 1=> (default) output Reconnected embedded in Disconnected INChI;
-                                        * 0=> separate output */
-
-#define bOUTPUT_ONE_STRUCT_TIME     1  /* 1 => output each structure time (non-release only) */
-
-
-/*#define INCHI_VERSION     "0.9Beta"  */
-/*#define INCHI_VERSION     "0.91Beta" */  /* 10-10-2002: sent to Jonathan Goodman */
-/*#define INCHI_VERSION     "0.92Beta" */  /* 11-15-2002: added Hill notation; sent to S.Heller & S.Stein */
-/*#define INCHI_VERSION     "0.93Beta" */  /* 12-09-2002: Fixed isotopic canon. bug & chiralanes; sent to S.Heller & A. McNaught */
-/*#define INCHI_VERSION     "0.931Beta" */  /* Non-BNS without salts released to PMR 01-2003 */
-/*#define INCHI_VERSION     "0.932Beta" */      /* Released to CAS 04-01-2003:
-                                            * - Improved taut. definitions as compared to 01-2003;
-                                            * - fixed bug: non-isotopic components' stereo missing from isotopic stereo
-                                            * - fixed bug: couldn't properly read Unix files (EOL = LF instead of CR/LF)
-                                            *   (effective only for MS VC++, Borland and MinGW/GCC compiles that accept "rb" mode of fopen)
-                                            *   DJGPP/GCC does not seem to need this fix.
-                                            */
-/*==== Release version ===*/
-/*#define INCHI_VERSION     "0.94Beta" */       /* 02-27-2003: Balanced network search to find alt paths and non-stereo bonds;
-                                                      Implemented salts disconnection; added (-) to taut groups */
-/*#define INCHI_VERSION     "1.12Beta" */       /* 1.12: 07-06-2004: sort order: No H formula,..; Pointed end stereo ON, Aggressive (de)protonation OFF */
-                                                /* 1.11: 05-19-2004: annotated plain text output, fixed bugs */
-                                                /* 1.1:  04-08-2004: variable protonation version */
-                                                /* 1.01: 12-23-2003 protected bonds, isotopic canonicalization in GetBaseCanonRanking() */
-                                                /* 1.02: 01-26-2004 fixed new isotopic tgroup canon bug, molfile merge bug */
-
-/*#define INCHI_VERSION       "1.0RC"*/             /* 02-07-2005 v1.0 Release Candidate */
-#define INCHI_VERSION       "1"
-#define INCHI_NAME          "InChI"
-#define INCHI_NAM_VER_DELIM "="
-
-/* constants and array sizes */
-
-#define INCHI_NUM            2    /* = array size; member indexes: */
-#define INCHI_BAS            0    /* 0 => disconnected or normal */
-#define INCHI_REC            1    /* 1 => reconnected */
-
-#define TAUT_NUM            2    /* = array size; member indexes: */
-#define TAUT_NON            0    /* 0 => normal structure */
-#define TAUT_YES            1    /* 1 => tautomeric */
-#define TAUT_INI            2    /* 2 => intermediate tautomeric structure */
-#define ALT_TAUT(X)        ((X)>TAUT_YES? TAUT_YES : 1-(X))  /* was (1-(X)) */
-
-/* INChI output modes */
-#define OUT_N1              0    /* non-tautomeric only */
-#define OUT_T1              1    /* tautomeric if present otherwise non-tautomeric */
-#define OUT_NT              2    /* only non-taut representations of tautomeric */
-#define OUT_TN              3    /* tautomeric if present otherwise non-tautomeric;
-                                    separately output non-taut representations of tautomeric if present */
-#define OUT_NN              4    /* only non-taut representations: non-taut else tautomeric */
-
-/* OUT_TN = OUT_T1 + OUT_NT */
-
-/* torture test */
-
-#define TEST_RENUMB_ATOMS           0    /* 1 => heavy duty test by multiple renumbering of atoms */
-#define TEST_RENUMB_NEIGH           1    /* 1 => randomly permutate neighbors */
-#define TEST_RENUMB_SWITCH          0    /* 1 => output another (different) picture */
-#define TEST_RENUMB_ATOMS_SAVE_LONGEST 0 /* 1 => save the component with largest processing time into the problem file */
-
-#if ( defined(_WIN32) && defined(_DEBUG) && defined(_MSC_VER) /*&& !defined(INCHI_ANSI_ONLY)*/ )
-/* debug: memory leaks tracking */
-#ifndef INCHI_LIB
-#define TRACE_MEMORY_LEAKS          1    /* 1=>trace, 0 => do not trace (Debug only) */
-#else
-#define TRACE_MEMORY_LEAKS          1    /* 1=>trace, **ALWAYS** =1 for INCHI_LIB */
-#endif
-
-#else /* not MSC and not Debug */
-
-#define TRACE_MEMORY_LEAKS          0    /* 0: do not change */
-
-#endif
-
-/* stereo */
-
-#define NEW_STEREOCENTER_CHECK      1    /* 1 => add new stereocenter categories (see bCanInpAtomBeAStereoCenter(...)) */
-#define MIN_SB_RING_SIZE            8    /* do not assume stereo bonds in rings containing 3..MIN_SB_RING_SIZE-1 atoms */
-
-#define REMOVE_KNOWN_NONSTEREO      1 /* 1=> check in advance known stereo to remove parities from non-stereogenic elements */
-#define REMOVE_CALC_NONSTEREO       1 /* 1=> check new stereo numberings to remove parities from non-stereogenic elements */
-#define PROPAGATE_ILL_DEF_STEREO    1 /* 1=> if at least one of the pair of constitutionally identical (far) neighbors */
-                                      /*     (of the tested atom) has ill-defined stereo parity and another has any */
-                                      /*     stereo parity then set the parity of the tested atom to ill-defined value. */
-
-#define ONLY_DOUBLE_BOND_STEREO     0  /* 1=> no alt bond stereo, no taut. bond attachment to stereo bond */
-                                       /* 0=> allow other definitions (below) to be active */
-#define ONE_BAD_SB_NEIGHBOR         1  /* 1 => allow 1 "bad" bond type neighbor to a stereobond atom. 2004-06-02 */
-
-/* more stereo settings */
-#define BREAK_ONE_MORE_SC_TIE       1   /* break one more tie when comparing possible stereocenter neighbors */
-#define BREAK_ALSO_NEIGH_TIE        0   /* post 1.12Beta 2004-08-20: if fixed neighbor has equ neighbors, fix the one with smaller canon. rank */
-#define BREAK_ALSO_NEIGH_TIE_ROTATE 1   /* post 1.12Beta 2004-09-02: break the second in 2nd psition; 1 works, 0 does not (example:MFCD01085607) */
-
-#define STEREO_CENTER_BONDS_NORM   1   /* set length of the bonds around a stereocenter = 1 before getting the parity  */
-#define STEREO_CENTER_BOND4_NORM   0   /* set length of the added bond around a stereocenter = 1 before getting the parity  */
-#define NORMALIZE_INP_COORD        0   /* 0=>keep unchanged, 1 => make atom coordinates integer values, avg bond len=20 */
-
-/* recent stereo */
-#define STEREO_WEDGE_ONLY          0 /* 1=> only pointed ends stereo bonds define stereo; 0=> both ends 1.12Beta */
-#define CHECK_C2v_S4_SYMM          0 /* post-1.12Beta 1=> check if a stereocenter has C2v or S4 symmetry; 0=>old mode */
-
-#define EQL_H_NUM_TOGETHER          1 /* 1=> output 1-3,5H2 intead of 1-3H2,5H2 (CT_MODE_EQL_H_TOGETHER)  */
-#define ABC_CT_NUM_CLOSURES         1 /* 1=> in coinnections compressed format output decimal number of closures instead of '-' */
-
-/* temporary fix */
-#define SINGLET_IS_TRIPLET          1 /* 'singlet' means two electrons make a lone pair instead of 2 bonds
-                                         its effect on valence is same as the effect of a triplet */
-
-/* defug: find structures where canonical partition is different from equitable */
-#define FIND_CANON_NE_EQUITABLE     0  /* 0=>normal mode */
-                                       /* 1=> extract (set EXTR_FLAGS = (EXTR_CANON_NE_EQUITABLE)*/
-                                       /*     set cmd line options: /onlynonTAUT /: /UNCHARGEDACIDS:1 /DISCONSALT:0 /MOVEPOS:0 /DISCONMETAL:0 */
-
-/* Debug: definitions for the extraction of the structures to the problem file */
-
-/* definition of the flags for structure extraction to the
-   problem file (for debugging and non-standard searching) */
-#define EXTR_KNOWN_USED_TO_REMOVE_PARITY  0x000001
-#define EXTR_CALC_USED_TO_REMOVE_PARITY   0x000002
-#define EXTR_2EQL2CENTER_TO_REMOVE_PARITY 0x000004
-#define EXTR_HAS_ATOM_WITH_DEFINED_PARITY 0x000008
-#define EXTR_REMOVE_PARITY_WARNING        0x000010
-#define EXTR_SALT_WAS_DISCONNECTED        0x000020
-#define EXTR_SALT_PROTON_MOVED            0x000040
-#define EXTR_SALT_PROTON_MOVE_ERR_WARN    0x000080
-#define EXTR_METAL_WAS_DISCONNECTED       0x000100
-#define EXTR_METAL_WAS_NOT_DISCONNECTED   0x000200
-#define EXTR_NON_TRIVIAL_STEREO           0x000400 /* (Inv != Abs stereo) && (parities can't be obtained by inverting them) */
-#define EXTR_UNUSUAL_VALENCES             0x000800
-#define EXTR_HAS_METAL_ATOM               0x001000
-#define EXTR_TEST_TAUT3_SALTS_DONE        0x002000 /* non-oxygen t-points used to discover tautomerism of merged t-groups */
-#define EXTR_CANON_NE_EQUITABLE           0x004000 /* find structures where canonical partition is different from equitable */
-#define EXTR_HAS_PROTON_PN                0x008000 /* has movable H+ attached to N or P */
-#define EXTR_HAS_FEATURE                  0x010000 /* found a feature */
-#define EXTR_TAUT_TREATMENT_CHARGES       0x020000 /* tautomeric treatment of charges */
-#define EXTR_TRANSPOSITION_EXAMPLES       0x040000 /* extract structures that have different mobile-H and fixed-H orders */
-
-/* define conditions of structure extraction to the problem file */
-#define EXTR_MASK                        0 /*EXTR_TAUT_TREATMENT_CHARGES*/ /*(EXTR_HAS_FEATURE)*/ /*(EXTR_UNUSUAL_VALENCES | EXTR_HAS_METAL_ATOM)*/ /* 0 to disable */
-#define EXTR_FLAGS                       0 /*EXTR_TAUT_TREATMENT_CHARGES*/ /*(EXTR_HAS_FEATURE)*/ /*(EXTR_HAS_PROTON_PN)*/ /*(EXTR_UNUSUAL_VALENCES)*/ /*(EXTR_CANON_NE_EQUITABLE)*/ /*(EXTR_TEST_TAUT3_SALTS_DONE)*/ /*(EXTR_HAS_METAL_ATOM)*/ /* (EXTR_NON_TRIVIAL_STEREO)*/ /*(EXTR_METAL_WAS_DISCONNECTED)*/ /* (EXTR_REMOVE_PARITY_WARNING)*/ /*(EXTR_HAS_ATOM_WITH_DEFINED_PARITY) */
-
-
-#define ENTITY_REFS_IN_XML_MESSAGES 1 /* 1=> replace ' " < > & in error/warning messages with xml entity references */
-
-/* added tautomeric structures */
-
-#define TAUT_TROPOLONE_7            1  /* 1=> tautomeric 7-member rings ON */
-#define TAUT_TROPOLONE_5            1  /* 1=> taut. similar to tropolone, 5-member ring */
-#define TAUT_4PYRIDINOL_RINGS       1  /* 1=> OH-C5H4N rings tautomerism */
-#define TAUT_PYRAZOLE_RINGS         1  /* 1=> tautomerizm in pyrazole rings */
-/* limitation on tautomerism detection: */
-#define TAUT_IGNORE_EQL_ENDPOINTS   0  /* 0=> even though 2 endpoints belong to same t-group check
-                                              them to find more alt bonds (new)
-                                          1=> ignore and do not check (old mode) */
-#define TAUT_RINGS_ATTACH_CHAIN     1  /* 1=> allow only chain attachments to tautomeric endpoints */
-                                       /*     (except pyrazole, where is no tautomeric attachment) */
-                                       /* 0=> allow taut. attachments from same ring system. Default=1 */
-
-#define FIND_RING_SYSTEMS           1  /* 1 => find and mark ring systems, blocks, cut-vertices */
-                                       /* Needed for 5- and 6-member ring tautomers and in other places */
-
-#define FIND_RINS_SYSTEMS_DISTANCES 0  /* 1 => find ring system and atom distance from terminal */
-#define USE_DISTANCES_FOR_RANKING   0  /* 1 => rank ring systems according to distances from terminal */
-
-#define DISPLAY_RING_SYSTEMS        0  /* 1 => for debug only; displays: */
-                                       /* "block no"/"ring system no"/"cut-vertex (num. intersecting blocks-1)" */
-                                       /* instead of ranks */
-/* consistency */
-
-#if( bRELEASE_VERSION==1 && bOUTPUT_ONE_STRUCT_TIME==1)
-#undef bOUTPUT_ONE_STRUCT_TIME
-#define bOUTPUT_ONE_STRUCT_TIME 0
-#endif
-
-/* consistency: bRELEASE_VERSION==1 needs FIND_RING_SYSTEMS=1 */
-#if( bRELEASE_VERSION==1 && FIND_RING_SYSTEMS!=1 )
-#ifdef FIND_RING_SYSTEMS
-#undef FIND_RING_SYSTEMS
-#endif
-#define FIND_RING_SYSTEMS 1
-#endif
-
-/* consistency: FIND_RINS_SYSTEMS_DISTANCES needs FIND_RING_SYSTEMS  */
-#if( FIND_RING_SYSTEMS != 1 )
-
-#if( FIND_RINS_SYSTEMS_DISTANCES == 1 )
-#undef  FIND_RINS_SYSTEMS_DISTANCES
-#define FIND_RINS_SYSTEMS_DISTANCES 0
-#endif
-
-#endif
-
-/* consistency: USE_DISTANCES_FOR_RANKING and DISPLAY_RING_SYSTEMS need FIND_RINS_SYSTEMS_DISTANCES */
-#if( FIND_RINS_SYSTEMS_DISTANCES != 1 )
-
-#if( USE_DISTANCES_FOR_RANKING == 1 )
-#undef  USE_DISTANCES_FOR_RANKING
-#define USE_DISTANCES_FOR_RANKING 0
-#endif
-
-#if( DISPLAY_RING_SYSTEMS == 1 )
-#undef  DISPLAY_RING_SYSTEMS
-#define DISPLAY_RING_SYSTEMS 0
-#endif
-
-#endif
-
-
-#if( FIND_RING_SYSTEMS==1 && (TAUT_TROPOLONE_7==1 || TAUT_TROPOLONE_5==1 || TAUT_4PYRIDINOL_RINGS==1 || TAUT_PYRAZOLE_RINGS) )
-#define TAUT_OTHER 1
-#else
-#define TAUT_OTHER 0
-#endif
-
-#define APPLY_IMPLICIT_H_DOWN_RULE 0   /* 1=> if 3 non-H atoms around stereocenter are in same plane */
-                                       /*     then add "down" hydrogen to obtain sterecenter oparity */
-                                       /* 0=> Implicit H stereo is unknown if all bonds to 3 non-H atoms */
-                                       /*     are in XY plane */
-#define ALLOW_TAUT_ATTACHMENTS_TO_STEREO_BONDS 1 /* 1=> consider bond in an alternating circuit stereogenic */
-                                                 /*     even though it has adjacent tautomeric atom(s) */
-
-#define IGNORE_TGROUP_WITHOUT_H   1    /* ignore tautomeric groups containing charges only */
-
-#if ( DISCONNECT_SALTS == 1 )
-#define REMOVE_TGROUP_CHARGE      0    /* 0: do not remove charge information from tautomeric groups */
-#else
-#define REMOVE_TGROUP_CHARGE      1    /* 1: remove charge information from tautomeric groups */
-#endif
-
-#if ( REMOVE_TGROUP_CHARGE == 1 )
-#define INCHI_T_NUM_MOVABLE  1
-#else
-#define INCHI_T_NUM_MOVABLE  2
-#endif
-
-/******************************************/
-/*   define canonicalization modes here   */
-/******************************************/
-
-#define USE_AUX_RANKING        1 /* 1=> get auxiliary ranking to accelerate canonicalization of H layers */
-#define USE_AUX_RANKING_ALL    1 /* 1=> include all vertices in CellGetMinNode() selection 0=> only vertices with highest ranks */
-
-#define USE_ISO_SORT_KEY_HFIXED  0  /* 0=> normal mode: merge isotopic taut H to isotopic atom sorting key in
-                                           taut H-fixed canonicalization;
-                                       1=> add one more "string" iso_sort_Hfixed to the canonicalization */
-
-/************************
-  questionable behavior
- ************************/
-#define REL_RAC_STEREO_IGN_1_SC  0 /* 1=> drop from InChI sp3 stereo in components that have a single stereocenter */
-                                   /* 0=> old-old mode (all such sp3 stereo is in the Identifier) */
-/* internal definitions; see also REQ_MODE_BASIC etc in ichi.h */
-#define CMODE_CT                 0x000001
-#define CMODE_ISO                0x000002
-#define CMODE_ISO_OUT            0x000004 /* obsolete ? */
-#define CMODE_STEREO             0x000008
-#define CMODE_ISO_STEREO         0x000010
-#define CMODE_TAUT               0x000020
-#define CMODE_NOEQ_STEREO        0x000040 /* 5-24-2002: do not use stereo equivalence to accelerate */
-#define CMODE_REDNDNT_STEREO     0x000080 /* 6-11-2002: do not check for redundant stereo elements */
-#define CMODE_NO_ALT_SBONDS      0x000100 /* 6-14-2002: do not assign stereo to alternating bonds */
-/* new 10-10-2003 */
-#define CMODE_RELATIVE_STEREO    0x000200    /* REL All Relative Stereo */
-#define CMODE_RACEMIC_STEREO     0x000400    /* RAC All Racemic Stereo */
-#define CMODE_SC_IGN_ALL_UU      0x000800    /* IAUSC Ignore stereocenters if All Undef/Unknown */
-#define CMODE_SB_IGN_ALL_UU      0x001000    /* IAUSC Ignore stereobonds if All Undef/Unknown */
-/* end of 10-10-2003 */
-
-/* external definitions */
-#define CANON_MODE_CT         (CMODE_CT)
-#define CANON_MODE_TAUT       (CMODE_CT|CMODE_TAUT)
-#define CANON_MODE_ISO        (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT)
-#define CANON_MODE_STEREO     (CMODE_CT|CMODE_STEREO)
-#define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO)
-
-#define CANON_MODE_MASK       0x00FF  /* used to determine canonicalization mode */
-
-/*************************************************
- * from d_norm.c
- */
-
-/* implemented definitions for CT_ATOMID */
-#define CT_ATOMID_DONTINCLUDE   1
-#define CT_ATOMID_IS_INITRANK   2
-#define CT_ATOMID_IS_CURRANK    3
-
-/***************************************
- * canonicalization settings  I
- ***************************************/
-
-#define CANON_TAUTOMERS                1  /* 1=> process tautomers */
-#define HYDROGENS_IN_INIT_RANKS        1  /* 1=> include num_H in initial ranking */
-
-#define DOUBLE_BOND_NEIGH_LIST    0  /* 1 => include double bond neighbor in NeighList 2 times */
-#define INCL_NON_6AROM            1  /* 1 => mark all arom. bonds; 0=>mark arom. bonds only in 6-member rings */
-
-#define CT_SMALLEST             /* minimal CT */
-
-#define CT_NEIGH_SMALLER        /* in CT, include neighbors with smaller ranks */
-
-#define CT_ATOMID          CT_ATOMID_IS_CURRANK /*CT_ATOMID_DONTINCLUDE */
-
-#define CT_NEIGH_INCREASE               /* in CT, neighbors ranks increase  */
-
-#define USE_SYMMETRY_TO_ACCELERATE 1   /*1 => for fast CT canonicalization, to avoid full enumeration */
-
-/* dependent definitions due to settings */
-
-#ifdef CT_SMALLEST
-#define CT_GREATER_THAN    >
-#define CT_INITVALUE      ~0
-#define BEST_PARITY        1  /* odd */
-#define WORSE_PARITY       2
-#else
-#define CT_GREATER_THAN    <
-#define CT_INITVALUE       0
-#define BEST_PARITY        2  /* even */
-#define WORSE_PARITY       1
-#endif
-
-#ifdef CT_NEIGH_SMALLER
-#define CT_NEIGH_SMALLER_THAN <
-#else
-#define CT_NEIGH_SMALLER_THAN >
-#endif
-
-/* verify corectness of dependent settings */
-#if !defined( CT_ATOMID )
-  #error  You have to #define CT_ATOMID
-#else
-#if( defined( CT_ATOMID ) && CT_ATOMID==CT_ATOMID_DONTINCLUDE )
-  #error  CT_DELIMITER should be #defined if CT_ATOMID is not included
-#endif
-#endif
-
-/***************************************
- * canonicalization settings  II
- ***************************************/
-/* from extr_ct.h */
-#define ALL_ALT_AS_AROMATIC         1  /* 1 => all altrnate bonds (even in cyclooctateraene) treat as aromatic */
-                                       /*      and set DOUBLE_BOND_NEIGH_LIST = 0 */
-#define ANY_ATOM_IN_ALT_CYCLE       1  /* 1=> accept any atom in alternating bond circuit, 0=>only some */
-
-#define EXCL_ALL_AROM_BOND_PARITY   0  /* 1 => any arom atom cannot belong to stereo bond. */
-                                       /*      This has presedence over ADD_6MEMB_AROM_BOND_PARITY=1 */
-                                       /* 0 => include arom bonds parities according to */
-                                       /*      ADD_6MEMB_AROM_BOND_PARITY definition */
-
-#if ( EXCL_ALL_AROM_BOND_PARITY == 0 )
-#define ADD_6MEMB_AROM_BOND_PARITY  1  /* 1 => all arom bonds are stereo bonds */
-                                       /* 0 => only those arom bonds which do not belong to */
-                                       /*      6-member arom rings are stereo bonds */
-#else
-#define ADD_6MEMB_AROM_BOND_PARITY  0  /* 0 => standard; 1 => meaningless: ignore parities of non-6-member ring alt. bonds */
-#endif
-
-#define CML_NUM_AT_IN_ATREF4      4
-#define MAX_NUM_STEREO_BONDS      3
-#define MAX_NUM_STEREO_BOND_NEIGH 3
-#define MIN_NUM_STEREO_BOND_NEIGH 2
-
-#define MAX_NUM_STEREO_ATOM_NEIGH 4
-#define STEREO_AT_MARK            8 /* > MAX_NUM_STEREO_BONDS */
-
-#if( ONLY_DOUBLE_BOND_STEREO == 1 )  /* { */
-
-#ifdef ALLOW_TAUT_ATTACHMENTS_TO_STEREO_BONDS
-#undef ALLOW_TAUT_ATTACHMENTS_TO_STEREO_BONDS
-#define ALLOW_TAUT_ATTACHMENTS_TO_STEREO_BONDS 0
-#endif
-
-#ifdef EXCL_ALL_AROM_BOND_PARITY
-#undef EXCL_ALL_AROM_BOND_PARITY
-#define EXCL_ALL_AROM_BOND_PARITY 1
-#endif
-
-#ifdef ADD_6MEMB_AROM_BOND_PARITY
-#undef ADD_6MEMB_AROM_BOND_PARITY
-#define ADD_6MEMB_AROM_BOND_PARITY 0
-#endif
-
-#endif /* } ONLY_DOUBLE_BOND_STEREO */
-
-/* dependent definitions due to settings */
-#if( ALL_ALT_AS_AROMATIC == 1 && DOUBLE_BOND_NEIGH_LIST != 0 )
-#undef DOUBLE_BOND_NEIGH_LIST
-#define DOUBLE_BOND_NEIGH_LIST 0
-#endif
-
-
-/*************************************
- * Drawing
- */
-
-#define DRAW_AROM_TAUT  1              /* 1=> draw distinct aromatic & tautomer bonds, 0=> don't */
-
-/******************************************************/
-/*       C O M M O N     D E F I N I T I O N S        */
-/******************************************************/
-
-
-/* input bTautFlags flags */
-#define TG_FLAG_TEST_TAUT__ATOMS         0x00000001   /* find regular tautomerism */
-#define TG_FLAG_DISCONNECT_SALTS         0x00000002   /* DISCONNECT_SALTS disconnect */
-#define TG_FLAG_TEST_TAUT__SALTS         0x00000004   /* DISCONNECT_SALTS if possible find long-range H/(-) taut. on =C-OH, >C=O    */
-#define TG_FLAG_MOVE_POS_CHARGES         0x00000008   /* MOVE_CHARGES allow long-range movement of N(+), P(+) charges           */
-#define TG_FLAG_TEST_TAUT2_SALTS         0x00000010   /* TEST_REMOVE_S_ATOMS multi-attachement long-range H/(-) taut. on =C-OH, >C=O   */
-#define TG_FLAG_ALLOW_NO_NEGTV_O         0x00000020   /* CHARGED_SALTS_ONLY=0 (debug) find long-range H-only tautomerism on =C-OH, >C=O */
-#define TG_FLAG_MERGE_TAUT_SALTS         0x00000040   /* DISCONNECT_SALTS merge all "salt"-t-groups and other =C-OH into one t-group */
-                                       
-#define TG_FLAG_ALL_TAUTOMERIC          (TG_FLAG_TEST_TAUT__ATOMS| \
-                                         TG_FLAG_TEST_TAUT__SALTS| \
-                                         TG_FLAG_TEST_TAUT2_SALTS| \
-                                         TG_FLAG_MERGE_TAUT_SALTS)
-                                       
-#define TG_FLAG_DISCONNECT_COORD         0x00000080   /* find "coord. centers" and disconnect them */
-#define TG_FLAG_RECONNECT_COORD          0x00000100   /* reconnect disconnected "coord. centers" */
-#define TG_FLAG_CHECK_VALENCE_COORD      0x00000200   /* do not disconnect "coord. centers" with usual valence */
-#define TG_FLAG_MOVE_HPLUS2NEUTR         0x00000400   /* move protons to neutralize */
-#define TG_FLAG_VARIABLE_PROTONS         0x00000800   /* add/remove protons to neutralize */
-#define TG_FLAG_HARD_ADD_REM_PROTONS     0x00001000   /* add/remove protons to neutralize in hard way */
-#define TG_FLAG_POINTED_EDGE_STEREO      0x00002000   /* only pointed edge of stereo bond defines stereo */
-                                       
-/* output bTautFlags flags */          
-                                       
-#define TG_FLAG_MOVE_HPLUS2NEUTR_DONE    0x00000001   /* protons have been moved to neutralize */
-#define TG_FLAG_TEST_TAUT__ATOMS_DONE    0x00000002 
-#define TG_FLAG_DISCONNECT_SALTS_DONE    0x00000004
-#define TG_FLAG_TEST_TAUT__SALTS_DONE    0x00000008   /* multiple H tautomerism */
-#define TG_FLAG_MOVE_POS_CHARGES_DONE    0x00000010
-#define TG_FLAG_TEST_TAUT2_SALTS_DONE    0x00000020   /* merged t-groups */
-#define TG_FLAG_ALLOW_NO_NEGTV_O_DONE    0x00000040
-#define TG_FLAG_MERGE_TAUT_SALTS_DONE    0x00000080   /* added non-taut O to taut groups */
-
-#define TG_FLAG_ALL_SALT_DONE          (TG_FLAG_TEST_TAUT__SALTS_DONE | \
-                                        TG_FLAG_TEST_TAUT2_SALTS_DONE | \
-                                        TG_FLAG_MERGE_TAUT_SALTS_DONE )
-
-#define TG_FLAG_DISCONNECT_COORD_DONE    0x00000100   /* found and disconnected "coord. centers" */
-#define TG_FLAG_CHECK_VALENCE_COORD_DONE 0x00000200   /* did not disconnect "coord. centers" with usual valence */
-#define TG_FLAG_MOVE_CHARGE_COORD_DONE   0x00000400   /* changed charge of a disconnected ligand to fit its valence */
-#define TG_FLAG_FIX_ODD_THINGS_DONE      0x00000800   /* fixed drawing ambiguities in fix_odd_things */
-#define TG_FLAG_TEST_TAUT3_SALTS_DONE    0x00001000   /* merged t-groups + non-O taut atoms */
-#define TG_FLAG_FOUND_SALT_CHARGES_DONE  0x00002000   /* not assigned: preprocessing detected possibility of salt-type tautomerism */
-#define TG_FLAG_FOUND_ISOTOPIC_H_DONE    0x00004000   /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */
-#define TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE 0x00008000   /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */
-
-
-#ifdef _WIN32
-
-#define   INCHI_OPTION_PREFX  '/'
-#define   INCHI_PATH_DELIM    '\\'
-
-#else
-
-#define   INCHI_OPTION_PREFX  '-'
-#define   INCHI_PATH_DELIM    '/'
-
-#endif
-
-#define   INCHI_ALT_OPT_PREFIX  '-'
-#define   INCHI_ACD_LABS_PREFIX '-'
-
-#ifdef INCHI_LIBRARY
-typedef struct tagOutputString {
-    char *pStr;
-    int  nAllocatedLength;
-    int  nUsedLength;
-    int  nPtr;
-} INCHI_OUTPUT;
-#define INCHI_FILE INCHI_OUTPUT
-#else
-#define INCHI_FILE FILE
-#endif
-
-
-/* memory leaks tracking */
-
-#if( TRACE_MEMORY_LEAKS == 1 )
-#ifdef _DEBUG
-
-#define   inchi_malloc(s)         _malloc_dbg(s, _NORMAL_BLOCK, __FILE__, __LINE__)
-#define   inchi_calloc(c, s)      _calloc_dbg(c, s, _NORMAL_BLOCK, __FILE__, __LINE__)
-#define   inchi_free(p)           _free_dbg(p, _NORMAL_BLOCK)
-
-#ifdef INCHI_MAIN
-/* INChI_MAIN specific */
-#define e_inchi_malloc(a)   inchi_malloc(a)
-#define e_inchi_calloc(a,b) inchi_calloc(a,b)
-#define e_inchi_free(a)     inchi_free(a)
-#endif
-
-/*#define  _CRTDBG_MAP_ALLOC*/
-
-#include <crtdbg.h>
-
-#else
-#undef  TRACE_MEMORY_LEAKS
-#define TRACE_MEMORY_LEAKS 0
-#endif  /* _DEBUG */
-#endif  /* TRACE_MEMORY_LEAKS */
-
-#ifdef INCHI_MAIN
-/* INChI_MAIN specific */
-#ifndef inchi_malloc
-#define inchi_malloc   e_inchi_malloc
-#endif
-#ifndef inchi_calloc
-#define inchi_calloc   e_inchi_calloc
-#endif
-#ifndef inchi_free
-#define inchi_free     e_inchi_free
-#endif
-#endif /* INCHI_MAIN */
-
-/* allocation/deallocation */
-#define USE_ALLOCA 0
-
-#if( USE_ALLOCA == 1 )
-#define qmalloc(X) _alloca(X)
-#define qfree(X)   do{(X)=NULL;}while(0)
-#else
-#define qmalloc(X) inchi_malloc(X)
-#define qfree(X)   do{if(X){inchi_free(X);(X)=NULL;}}while(0)
-#endif
-
-#if( defined(_MSC_VER) && _MSC_VER >= 800 )
-#define fast_alloc(X) _alloca(X)
-#define fast_free(X)
-#else
-#define fast_alloc(X) inchi_malloc(X)
-#define fast_free(X)  inchi_free(X)
-#endif
-
-#define qzfree(X)   do{if(X){inchi_free(X);(X)=NULL;}}while(0)
-
-/* rellocation */
-
-#define MYREALLOC2(PTRTYPE1, PTRTYPE2, PTR1, PTR2, LEN1, LEN2, ERR) \
-    do { \
-        if( (LEN1) <= (LEN2) ) {\
-            PTRTYPE1 * newPTR1 = (PTRTYPE1 *)inchi_calloc( (LEN2)+1, sizeof(PTRTYPE1) );\
-            PTRTYPE2 * newPTR2 = (PTRTYPE2 *)inchi_calloc( (LEN2)+1, sizeof(PTRTYPE2) );\
-            if ( newPTR1 && newPTR2 ) { \
-                if ( (PTR1) && (LEN1) > 0 ) \
-                    (memcpy) ( newPTR1, (PTR1), (LEN1) * sizeof(PTRTYPE1) ); \
-                if ( (PTR2) && (LEN1) > 0 ) \
-                    (memcpy) ( newPTR2, (PTR2), (LEN1) * sizeof(PTRTYPE2) ); \
-                if ( PTR1 ) \
-                    inchi_free(PTR1);  \
-                if ( PTR2 ) \
-                    inchi_free(PTR2);  \
-                (PTR1) = newPTR1; \
-                (PTR2) = newPTR2; \
-                (LEN1) = (LEN2);  \
-                (ERR)  = 0; \
-            } else {        \
-                (ERR)  = 1; \
-            }               \
-        } else { (ERR) = 0; } \
-    } while(0)
-
-
-#endif /* __MODE_H__ */