rino 0.1.0

data/ext/src/e_readinch.c

@@ -0,0 +1,58 @@
+/*
+ * 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 <stdlib.h>
+#include <limits.h>
+#include <math.h>
+#include <float.h>
+#include <string.h>
+#include <ctype.h>
+
+/* for use in the main program */
+
+
+#include "e_mode.h"
+#include "inchi_api.h"
+#include "e_ctl_data.h"
+#include "e_inchi_atom.h"
+#include "e_ichi_io.h"
+
+#include "e_ichisize.h"
+#include "e_comdef.h"
+#include "e_util.h"
+#include "e_ichierr.h"
+#include "e_ichicomp.h"
+#include "e_readstru.h"
+#include "e_inpdef.h"
+
+/* rename to avoid duplicated entry points */
+
+#define mystrncpy            e_mystrncpy       
+#define LtrimRtrim           e_LtrimRtrim      
+#define FreeInchi_Atom       e_FreeInchi_Atom
+#define FreeInchi_Stereo0D   e_FreeInchi_Stereo0D
+#define CreateInchi_Atom     e_CreateInchi_Atom
+#define CreateInchi_Stereo0D e_CreateInchi_Stereo0D
+#define FreeInchi_Input      e_FreeInchi_Input
+#define AddMOLfileError      e_AddMOLfileError
+#define my_fgets             e_my_fgets
+#define my_fgetsTab          e_my_fgetsTab 
+#define my_fgetsTab1         e_my_fgetsTab1 
+#define is_in_the_slist      e_is_in_the_slist
+#define is_element_a_metal   e_is_element_a_metal
+#define INChIToInchi_Atom    e_INChIToInchi_Atom
+#define INChIToInchi_Input   e_INChIToInchi_Input
+
+#define IGNORE_HEADERS
+#define STATIC
+
+/* This contains executable code. Included in lReadAux.c, e_ReadINCH.c, ReadINCH.c,  */
+#include "aux2atom.h"
+

data/ext/src/e_readmol.c

@@ -0,0 +1,54 @@
+/*
+ * 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 <stdlib.h>
+#include <limits.h>
+#include <math.h>
+#include <float.h>
+#include <string.h>
+#include <ctype.h>
+
+#include "e_mode.h"
+#include "inchi_api.h"
+#include "e_ctl_data.h"
+
+#include "e_ichisize.h"
+#include "e_comdef.h"
+#include "e_util.h"
+#include "e_readmol.h"
+#include "e_ichicomp.h"
+#include "e_ichi_io.h"
+#include "e_readstru.h"
+#include "e_inpdef.h"
+
+#define AddMOLfileError        e_AddMOLfileError
+#define remove_one_lf          e_remove_one_lf
+#define RemoveNonPrintable     e_RemoveNonPrintable
+#define mystrncpy              e_mystrncpy
+#define read_mol_file          e_read_mol_file
+#define bypass_sdf_data_items  e_bypass_sdf_data_items
+#define extract_ChargeRadical  e_extract_ChargeRadical
+#define delete_mol_data        e_delete_mol_data
+#define remove_trailing_spaces e_remove_trailing_spaces
+#define normalize_name         e_normalize_name
+#define read_sdfile_segment    e_read_sdfile_segment
+#define CopyMOLfile            e_CopyMOLfile
+#define LtrimRtrim             e_LtrimRtrim
+
+#ifndef inchi_calloc
+#define inchi_calloc            e_inchi_calloc
+#endif
+
+#ifndef inchi_free
+#define inchi_free              e_inchi_free
+#endif
+
+#include "lreadmol.h"
+

data/ext/src/e_readmol.h

@@ -0,0 +1,180 @@
+/*
+ * 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 __READMOL_H__
+#define __READMOL_H__
+
+/*************** 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.
+ */
+
+/*
+#define MOLFILEINPLINELEN   84  // add cr, lf, double zero termination
+#ifndef MOLFILEMAXLINELEN
+#define MOLFILEMAXLINELEN   80
+#endif
+*/
+
+#define MOLFILEINPLINELEN   204  /* add cr, lf, double zero termination */
+#ifndef MOLFILEMAXLINELEN
+#define MOLFILEMAXLINELEN   200
+#endif
+
+
+#define MOL_PRESENT 1
+#define MOL_ABSENT  0
+
+/* configuration */
+#define MOL_QUERY   MOL_ABSENT
+#define MOL_CPSS    MOL_ABSENT
+#define MOL_REACT   MOL_ABSENT
+
+#define MOL_STRING_DATA      'S'
+#define MOL_CHAR_INT_DATA    'C'
+#define MOL_SHORT_INT_DATA   'N'
+#define MOL_LONG_INT_DATA    'L'
+#define MOL_DOUBLE_DATA      'D'
+#define MOL_FLOAT_DATA       'F'
+#define MOL_JUMP_TO_RIGHT    'J'
+#define MOL_MAX_VALUE_LEN    32    /* max length of string containing a numerical value */
+
+
+#define SDF_END_OF_DATA "$$$$"
+
+/****************************************************************************/
+typedef struct tagMOL_HEADER_BLOCK {
+    /* Line #1 */
+    char    szMoleculeName[MOLFILEMAXLINELEN+1]; /* up to 80 characters */
+    /* Line #2: optional */
+    char    szMoleculeLine2[MOLFILEMAXLINELEN+1]; /* the whole line2 -- up to 80 characters */
+    char    szUserInitials[3];      /* 2 bytes; char */
+    char    szProgramName[9];       /* 8 bytes; char */
+    char    cMonth;                 /* 2 bytes; integral */
+    char    cDay;                   /* 2 bytes; integral */
+    char    cYear;                  /* 2 bytes; integral */
+    char    cHour;                  /* 2 bytes; integral */
+    char    cMinute;                /* 2 bytes; integral */
+    char    szDimCode[3];           /* 2 bytes: dimensional code; char */
+    short   nScalingFactor1;        /* 2 bytes;  I2    */
+    double  dScalingFactor2;        /* 10 bytes, F10.5 */
+    double  dEnergy;                /* 10 bytes, F10.5 */
+    long    lInternalRegistryNumber;/* 6 bytes, integral */
+    /* Line #3: comment */
+    char    szComment[81];
+}MOL_HEADER_BLOCK;
+
+/****************************************************************************/
+typedef struct tagMOL_ATOM {
+    double   fX;                       /* F10.5;       Generic */
+    double   fY;                       /* F10.5;       Generic */
+    double   fZ;                       /* F10.5;       Generic */
+    char     szAtomSymbol[6];          /* aaa;         Generic */ /* changed from 4 to 6 to match STDATA */
+    S_SHORT  cMassDifference;   /* dd;  (M_ISO) Generic: -3..+4 otherwise 0 or 127=most abund. isotope */
+    S_CHAR   cCharge;           /* ccc; (M CHG), Generic: 1=+3,2=+2,3=+1,4=doublet,5=-1,6=-2,7=-3 */
+    char     cRadical;                 /*      (M RAD) */
+    char     cStereoParity;            /* sss;         Generic */
+#if ( MOL_QUERY == MOL_PRESENT )
+    char     cH_countPlus1;            /* hhh;         Query; Hn means >= n H; H0 means no H */
+    char     cStereoCare;              /* bbb;         Query: 0=ignore; 1=must match */
+#endif
+    char     cValence;                 /* vvv:         0=no marking; (1..14)=(1..14); 15=zero valence */
+                                       /*              number of bonds including bonds to implies H's */
+#if ( MOL_CPSS == MOL_PRESENT )
+    char     cH0_designator;           /* HHH:         CPSS */
+    char     cReactionComponentType;   /* rrr:         CPSS: 1=reactant, 2=product, 3=intermediate */
+    char     cReactionComponentNumber; /* iii:         CPSS: 0 to (n-1) */
+#endif
+
+#if ( MOL_REACT == MOL_PRESENT )
+    short    nAtomAtomMappingNumber;   /* mmm:         Reaction: 1..255 */
+    char     cInversionRetentionFlag;  /* nnn:         1=inverted,2=retained config.; 0=property not applied */
+#endif
+#if ( MOL_REACT == MOL_PRESENT || MOL_QUERY == MOL_PRESENT )
+    char     cExactChargeFlag;         /* eee:         1=charge on atom must match exactly, 0=property not applied */
+#endif
+    char cMyNumImpH;                 /* number of implicit H calculated for adding H to strings in STDATA */
+    char cDisplayAtom;               /* Do not hide element's name ( applies to C 7-25-98 DCh */
+    char cAtomAliasedFlag;           /* Do not remove charge/radical/isotope if it is in the alias. 9-3-99 DCh */
+} MOL_ATOM;
+
+/****************************************************************************/
+typedef struct tagMOL_BONDS {
+    short nAtomNo1;                  /* 111:     First atom number:  Generic */
+    short nAtomNo2;                  /* 222:     Second atom number: Generic */
+    char  cBondType;                 /* 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 cBondStereo;                /* 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_QUERY == MOL_PRESENT )
+    char cBondTopology;              /* rrr:     0=either, 1=ring, 2=chain: SSS queries only */
+#endif
+#if ( MOL_REACT == MOL_PRESENT )
+    char cReactingCenterStatus;      /* 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 are also possible      */
+#endif
+} MOL_BONDS;
+/****************************************************************************/
+typedef struct tagMOL_CTAB {
+    /* Line #1: Counts line */
+    short nNumberOfAtoms;                  /* aaa; <= 999; Generic */
+    short nNumberOfBonds;                  /* bbb; <= 999; Generic */
+#if ( MOL_QUERY == MOL_PRESENT )
+    short nNumberOfAtomsLists;              /* lll; <=  30; Query   */
+#endif
+                                            /* fff; Obsolete */
+    char cChiralFlag;                       /* ccc; 0 or 1; Generic */
+    short nNumberOfStextEntries;            /* sss;         CPSS    */
+#if ( MOL_CPSS == MOL_PRESENT )
+    short nNumberOfReactionComponentsPlus1; /* xxx;         CPSS    */
+    short nNumberOfReactants;               /* rrr;         CPSS    */
+    short nNumberOfProducts;                /* ppp;         CPSS    */
+    short nNumberOfIntermediates;           /* iii;         CPSS    */
+#endif
+    short nNumberOfPropertyLines;            /* mmm;         Generic */
+    char  csCurrentCtabVersion[7];          /* vvvvvv;      Generic; 'V2000' */
+    /* The Atom Block */
+    MOL_ATOM  *MolAtom;
+    MOL_BONDS *MolBond;
+    MOL_COORD *szCoord;
+} MOL_CTAB;
+
+typedef struct tagMOL_DATA {
+    MOL_HEADER_BLOCK hdr;
+    MOL_CTAB         ctab;
+} MOL_DATA;
+
+#ifndef INCHI_ALL_CPP
+#ifdef __cplusplus
+extern "C" {
+#endif
+#endif
+
+
+MOL_DATA* e_delete_mol_data( MOL_DATA* mol_data );
+
+MOL_DATA* e_read_sdfile_segment(FILE* inp, MOL_HEADER_BLOCK *OnlyHeaderBlock, MOL_CTAB *OnlyCtab,
+                              int bGetOrigCoord,
+                              char *pname, int lname,
+                              long *Id, const char *pSdfLabel, char *pSdfValue,
+                              int *err, char *pStrErr );
+
+
+#ifndef INCHI_ALL_CPP
+#ifdef __cplusplus
+}
+#endif
+#endif
+
+#endif /*__READMOL_H__*/

data/ext/src/e_readstru.c

@@ -0,0 +1,251 @@
+/*
+ * 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 <stdlib.h>
+
+#include <string.h>
+#include <ctype.h>
+#include <stdarg.h>
+#include <errno.h>
+#include <limits.h>
+#include <float.h>
+
+#include "e_mode.h"
+#include "ichitime.h"
+#include "inchi_api.h"
+#include "e_ctl_data.h"
+#include "e_readstru.h"
+#include "e_ichi_io.h"
+#include "e_util.h"
+#include "e_ichierr.h"
+#include "e_inpdef.h"
+
+int e_TreatReadTheStructureErrors(  STRUCT_DATA *sd, INPUT_PARMS *ip,
+                                  FILE *inp_file, FILE *log_file, FILE *output_file, FILE *prb_file,
+                                  inchi_Input *pInp, int *num_inp );
+int e_GetInpStructErrorType( INPUT_PARMS *ip, int err, char *pStrErrStruct, int num_inp_atoms );
+
+/*********************************************************************************************************/
+int e_ReadStructure( STRUCT_DATA *sd, INPUT_PARMS *ip,
+                     FILE *inp_file, FILE *log_file, FILE *output_file, FILE *prb_file,
+                     inchi_Input *pInp, int num_inp,  /* for CML:*/ int inp_index, int *out_index )
+{
+    inchiTime     ulTStart;
+    int           nRet = 0, nRet2 = 0;
+    int           bGetOrigCoord = 0;
+    INCHI_MODE    InpAtomFlags = 0;
+
+    memset( sd, 0, sizeof(*sd) );
+    switch ( ip->nInputType ) {
+    case INPUT_MOLFILE:
+    case INPUT_SDFILE:
+        if ( pInp ) {
+            if ( ip->pSdfValue && ip->pSdfValue[0] ) {
+                /* Added 07-29-2003 to avoid inheriting exact value from prev. structure
+                   and to make reference to a (bad) structure with unknown ID Value */
+                char *p, *q;  /* q shadows prev declaration of const char *q */
+                int  n;
+                if ( (p = strrchr( ip->pSdfValue, '+' )) &&
+                     '[' == *(p-1) && 0 < (n=strtol(p+1,&q,10)) && q[0] && ']'==q[0] && !q[1] ) {
+                    sprintf( p+1, "%d]", n+1 );
+                } else {
+                    strcat( ip->pSdfValue, " [+1]" );
+                }
+            }
+            e_InchiTimeGet( &ulTStart );
+            sd->fPtrStart = (inp_file == stdin)? -1 : ftell( inp_file );
+            /*  read the original structure */
+            nRet2 = e_MolfileToInchi_Input( inp_file, pInp, ip->bMergeAllInputStructures,
+                               ip->bDoNotAddH, ip->bAllowEmptyStructure,
+                               ip->pSdfLabel, ip->pSdfValue, &ip->lSdfId, &ip->lMolfileNumber,
+                               &InpAtomFlags, &sd->nStructReadError, sd->pStrErrStruct );
+
+            sd->bChiralFlag |= InpAtomFlags;
+            if ( !ip->bGetSdfileId || ip->lSdfId == 999999) ip->lSdfId = 0;
+            if ( !ip->bGetMolfileNumber || ip->lMolfileNumber < 0 ) ip->lMolfileNumber = 0;
+            sd->fPtrEnd = (inp_file == stdin)? -1 : ftell( inp_file );
+            sd->ulStructTime += e_InchiTimeElapsed( &ulTStart );
+        } else {
+            /*  read the next original structure */
+            int nStructReadError=0;
+            if ( !ip->bMergeAllInputStructures ) {
+                nRet2 = e_MolfileToInchi_Input( inp_file, NULL, 0, 0, 0,
+                                       NULL, NULL, NULL, NULL, NULL, &nStructReadError, NULL );
+                if ( nRet2 <= 0 && 10 < nStructReadError && nStructReadError < 20 ) {
+                    return _IS_EOF;
+                }
+            } else {
+                return _IS_EOF;
+            }
+        }
+        break;
+    case INPUT_INCHI_XML:
+    case INPUT_INCHI_PLAIN:
+        if ( pInp ) {
+            if ( ip->pSdfValue && ip->pSdfValue[0] ) {
+                /* Added 07-29-2003 to avoid inheriting exact value from prev. structure
+                   and to make reference to a (bad) structure with unknown ID Value */
+                char *p, *q;
+                int  n;
+                if ( (p = strrchr( ip->pSdfValue, '+' )) &&
+                     '[' == *(p-1) && 0 < (n=strtol(p+1,&q,10)) && q[0] && ']'==q[0] && !q[1] ) {
+                    sprintf( p+1, "%d]", n+1 );
+                } else {
+                    strcat( ip->pSdfValue, " [+1]" );
+                }
+            }
+            e_InchiTimeGet( &ulTStart );
+            sd->fPtrStart = (inp_file == stdin)? -1 : ftell( inp_file );
+            /*  read the original structure */
+            nRet2 = e_INChIToInchi_Input( inp_file, pInp, ip->bMergeAllInputStructures, ip->bDoNotAddH,
+                               ip->nInputType, ip->pSdfLabel, ip->pSdfValue, &ip->lMolfileNumber,
+                               &InpAtomFlags, &sd->nStructReadError, sd->pStrErrStruct );
+            /*if ( !ip->bGetSdfileId || ip->lSdfId == 999999) ip->lSdfId = 0;*/
+            sd->bChiralFlag |= InpAtomFlags;
+            sd->fPtrEnd = (inp_file == stdin)? -1 : ftell( inp_file );
+            sd->ulStructTime += e_InchiTimeElapsed( &ulTStart );
+        } else {
+            /*  read the next original structure */
+            int           nStructReadError=0;
+            if ( !ip->bMergeAllInputStructures ) {
+                nRet2 = e_INChIToInchi_Input( inp_file, NULL, 0, 0,
+                                    ip->nInputType, NULL, NULL, NULL, NULL, &nStructReadError, NULL );
+                if ( nRet2 <= 0 && 10 < nStructReadError && nStructReadError < 20 ) {
+                    return _IS_EOF;
+                }
+            } else {
+                return _IS_EOF;
+            }
+        }
+        break;
+
+#if( ADD_CMLPP == 1 )
+    /* BILLY 8/6/04 */
+    case INPUT_CMLFILE:
+        if ( pInp ) {
+
+            e_InchiTimeGet( &ulTStart );
+            /*
+            if ( inp_index >= 0 ) {
+                sd->fPtrStart = inp_index;
+            } else {
+                sd->fPtrStart = GetCmlStructIndex();
+            }
+            */
+            sd->fPtrStart = -1; /* disable "e_CopyMOLfile() for CML input files */
+            sd->fPtrEnd = -1;
+            /*  read the original structure */
+            nRet = CmlfileToOrigAtom( inp_file, pInp, ip->bMergeAllInputStructures,
+                               bGetOrigCoord, ip->bDoNotAddH, inp_index, out_index,
+                               ip->pSdfLabel, ip->pSdfValue, &ip->lSdfId,
+                               &sd->nStructReadError, sd->pStrErrStruct );
+
+
+            sd->ulStructTime += e_InchiTimeElapsed( &ulTStart );
+#if( bRELEASE_VERSION == 0 )
+            sd->bExtract |= pInp->bExtract;
+#endif
+        } else {
+            /*  read the next original structure */
+            int nStructReadError=0;
+            if ( !ip->bMergeAllInputStructures ) {
+                nRet2 = CmlfileToOrigAtom( inp_file, NULL, 0, 0, 0, inp_index, out_index,
+                                       NULL, NULL, NULL, &nStructReadError, NULL );
+
+                if ( nRet2 <= 0 && 10 < nStructReadError && nStructReadError < 20 ) {
+                    return _IS_EOF;
+                }
+            } else {
+                return _IS_EOF;
+            }
+        }
+        break;
+#endif
+
+    default:
+        nRet = _IS_FATAL; /*  wrong file type */
+    }
+    nRet2 = e_TreatReadTheStructureErrors( sd, ip, inp_file, log_file, output_file, prb_file,
+                                         pInp, &num_inp );
+    if ( (!nRet || nRet == _IS_WARNING) && nRet2 )
+        nRet = nRet2;
+
+    return nRet;
+}
+/*****************************************************************************************************/
+int e_TreatReadTheStructureErrors(  STRUCT_DATA *sd, INPUT_PARMS *ip,
+                                  FILE *inp_file, FILE *log_file, FILE *output_file, FILE *prb_file,
+                                  inchi_Input *pInp, int *num_inp )
+{
+    int nRet = _IS_OKAY;
+    /*  End of file */
+    if ( 10 < sd->nStructReadError && sd->nStructReadError < 20 ) {
+        nRet = _IS_EOF;
+        goto exit_function; /*  end of file */
+    }
+    /*  Skipping the structures */
+    if ( *num_inp < ip->first_struct_number ) {
+        if ( log_file != stderr ) {
+            //e_my_fprintf( stderr, "\rSkipping structure #%d.%s%s%s%s...\r", *num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue));
+        }
+        nRet = sd->nErrorType = _IS_SKIP;
+        goto exit_function;
+    }
+
+    sd->nErrorType = e_GetInpStructErrorType( ip, sd->nStructReadError, sd->pStrErrStruct, pInp->num_atoms );
+
+    /*  Fatal error */
+    if ( sd->nErrorType == _IS_FATAL ) {
+        e_my_fprintf( log_file, "Fatal Error %d (aborted; %s) inp structure #%d.%s%s%s%s\n",
+                    sd->nStructReadError, sd->pStrErrStruct, *num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
+#if( bRELEASE_VERSION == 1 || EXTR_FLAGS == 0 )
+        if ( prb_file && 0L <= sd->fPtrStart && sd->fPtrStart < sd->fPtrEnd && !ip->bSaveAllGoodStructsAsProblem ) {
+            e_CopyMOLfile(inp_file, sd->fPtrStart, sd->fPtrEnd, prb_file, *num_inp);
+        }
+#endif
+        /* goto exit_function; */
+    }
+    /*  Non-fatal errors: do not produce INChI */
+    if ( sd->nErrorType == _IS_ERROR ) {  /*  70 => too many atoms */
+        e_my_fprintf( log_file, "Error %d (no INChI; %s) inp structure #%d.%s%s%s%s\n",
+                    sd->nStructReadError, sd->pStrErrStruct, *num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
+#if( bRELEASE_VERSION == 1 || EXTR_FLAGS == 0 )
+        if ( prb_file && 0L <= sd->fPtrStart && sd->fPtrStart < sd->fPtrEnd && !ip->bSaveAllGoodStructsAsProblem) {
+            e_CopyMOLfile(inp_file, sd->fPtrStart, sd->fPtrEnd, prb_file, *num_inp);
+        }
+#endif
+    }
+    /*  Warnings: try to produce INChI */
+    if ( sd->nErrorType == _IS_WARNING ) {
+        e_my_fprintf( log_file, "Warning: (%s) inp structure #%d.%s%s%s%s\n",
+                    sd->pStrErrStruct, *num_inp, SDF_LBL_VAL(ip->pSdfLabel,ip->pSdfValue) );
+    }
+exit_function:
+    if ( nRet <= _IS_OKAY && sd->nErrorType > 0 ) {
+        nRet = sd->nErrorType;
+    }
+    return nRet;
+}
+/**********************************************************************************************/
+int e_GetInpStructErrorType( INPUT_PARMS *ip, int err, char *pStrErrStruct, int num_inp_atoms )
+{
+    if ( err && err == 9 )
+        return _IS_ERROR; /*  sdfile bypassed to $$$$ */
+    if ( err && err < 30 )
+        return _IS_FATAL;
+    if ( num_inp_atoms <= 0 || err ) {
+        if ( 98 == err && 0 == num_inp_atoms && ip->bAllowEmptyStructure )
+            return _IS_OKAY /* _IS_WARNING*/; /* the warning will be issued by the dll */
+        return _IS_ERROR;
+    }
+    if ( pStrErrStruct[0] )
+        return _IS_WARNING;
+    return _IS_OKAY;
+}

data/ext/src/e_readstru.h

@@ -0,0 +1,33 @@
+/*
+ * 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 __READSTRU_H__
+#define __READSTRU_H__
+
+
+#ifndef INCHI_ALL_CPP
+#ifdef __cplusplus
+extern "C" {
+#endif
+#endif
+
+
+
+int e_ReadStructure( STRUCT_DATA *sd, INPUT_PARMS *ip, FILE *inp_file, FILE *log_file, FILE *output_file, FILE *prb_file,
+                   inchi_Input *pInp, int num_inp,  /* for CML:*/ int inp_index, int *out_index );
+
+
+#ifndef INCHI_ALL_CPP
+#ifdef __cplusplus
+}
+#endif
+#endif
+
+
+#endif /* __READSTRU_H__ */