rino 0.1.0

data/ext/src/inchi_dll.h

@@ -0,0 +1,34 @@
+/*
+ * 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_DLL_H__
+#define __INCHI_DLL_H__
+
+
+#ifndef INCHI_ALL_CPP
+#ifdef  __cplusplus
+extern "C" {
+#endif
+#endif
+
+
+int ExtractOneStructure( STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle,
+         inchi_Input *inp, INCHI_FILE *log_file, INCHI_FILE *output_file, INCHI_FILE *prb_file,
+         ORIG_ATOM_DATA *orig_inp_data, int *num_inp, char *pStr, int nStrLen );
+
+
+
+#ifndef INCHI_ALL_CPP
+#ifdef  __cplusplus
+}
+#endif
+#endif
+
+
+#endif /* __INCHI_DLL_H__ */

data/ext/src/inchi_dll_main.c

@@ -0,0 +1,23 @@
+/*
+ * International Union of Pure and Applied Chemistry (IUPAC)
+ * International Chemical Identifier (InChI)
+ * Version 1
+ * Software version 1.00
+ * April 13, 2005
+ * Developed at NIST
+ */
+
+/* inchi_dll_main.c : Defines the entry point for the DLL application. */
+#if defined(_WIN32) && defined(_USRDLL) && defined(_DEBUG)
+#include "inchi_dll_main.h"
+int INCHI_DLLMAIN_TYPE DllMain( HANDLE hModule, 
+                       DWORD  ul_reason_for_call, 
+                       LPVOID lpReserved
+					 )
+{
+    return TRUE;
+}
+#else
+int dummy_inchi_dll_main=0;  /* avoid empty module to keep C compiler happy */
+#endif
+

data/ext/src/inchi_dll_main.h

@@ -0,0 +1,31 @@
+/*
+ * 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_DLL_MAIN_H__
+#define __INCHI_DLL_MAIN_H__
+
+#if _MSC_VER > 1000
+#pragma once
+#endif /* _MSC_VER > 1000 */
+
+#if defined(_WIN32) && defined(_MSC_VER) && defined(_USRDLL)
+
+/*#define WIN32_LEAN_AND_MEAN */  /* Exclude rarely-used stuff from Windows headers */
+#include <windows.h>
+
+#define  INCHI_DLLMAIN_TYPE APIENTRY
+
+#else  /* not a Win32 DLL under MS VC++ */
+
+#define  INCHI_DLLMAIN_TYPE
+
+#endif
+
+
+#endif /* __INCHI_DLL_MAIN_H__ */

data/ext/src/inpdef.h

@@ -0,0 +1,328 @@
+/*
+ * 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__
+
+#include "mode.h"
+#include "comdef.h"
+#include "ichidrp.h"
+
+
+#define bDrawingLabelLeftShift endpoint    /* for drawing only */
+typedef S_SHORT ST_CAP_FLOW;
+
+/* inp_ATOM::at_type */
+#define ATT_NONE         0x0000
+#define ATT_ACIDIC_CO    0x0001
+#define ATT_ACIDIC_S     0x0002
+#define ATT_OO           0x0004
+#define ATT_ZOO          0x0008
+#define ATT_NO           0x0010
+#define ATT_N_O          0x0020
+#define ATT_ATOM_N       0x0040
+#define ATT_ATOM_P       0x0080
+#define ATT_OTHER_NEG_O  0x0100
+#define ATT_OTHER_ZO     0x0200   /* -Z=O or =Z=O */
+#define ATT_OH_MINUS     0x0400   /* OH(-), O=O,S,Se,Te */
+#define ATT_O_PLUS       0x0800   /* -OH2(+), =OH(+), -OH(+)-, OH3(+), =O(+)-, etc; O=O,S,Se,Te */
+#define ATT_PROTON       0x1000
+#define ATT_HalAnion     0x2000
+#define ATT_HalAcid      0x4000
+
+#define AT_FLAG_ISO_H_POINT 0x01  /* may have isotopic H */
+
+#define PERIODIC_NUMBER_H  1
+
+#ifndef NUMH
+#define NUM_ISO_H(AT,N) (AT[N].num_iso_H[0]+AT[N].num_iso_H[1]+AT[N].num_iso_H[2])
+#define NUMH(AT,N)     (AT[N].num_H+NUM_ISO_H(AT,N))
+#endif
+
+#define FlagSC_0D  1  /* bUsed0DParity */
+#define FlagSB_0D  2  /* bUsed0DParity */
+
+#define SB_PARITY_FLAG  0x38 /* mask for disconnected metal parity if it is different */
+#define SB_PARITY_SHFT  3    /* number of right shift bits to get disconnected metal parity */
+#define SB_PARITY_MASK  0x07
+#define SB_PARITY_1(X) (X & SB_PARITY_MASK)  /* refers to connected structure */
+#define SB_PARITY_2(X) (((X) >> SB_PARITY_SHFT) & SB_PARITY_MASK) /* refers to connected structure */
+
+
+
+typedef struct tagInputAtom {
+    char          elname[ATOM_EL_LEN]; /* chem. element name */
+    U_CHAR        el_number;               /* number of the element in the Periodic Table */
+    AT_NUMB       neighbor[MAXVAL];        /* positions (from 0) of the neighbors in the inp_ATOM array */
+    AT_NUMB       orig_at_number;          /* original atom number */
+    AT_NUMB       orig_compt_at_numb;      /* atom number within the component before terminal H removal */
+    S_CHAR        bond_stereo[MAXVAL];     /* 1=Up,4=Either,6=Down; this atom is at the pointing wedge,
+                                              negative => on the opposite side; 3=Either double bond  */
+    U_CHAR        bond_type[MAXVAL];       /* 1..4; 4="aromatic", should be discouraged on input */
+
+    S_CHAR        valence;                 /* number of bonds = number of neighbors */
+    S_CHAR        chem_bonds_valence;      /* sum of bond types (type 4 needs special treatment) */
+    S_CHAR        num_H;                   /* number of implicit hydrogens including D and T    */
+    S_CHAR        num_iso_H[NUM_H_ISOTOPES]; /* number of implicit 1H, 2H(D), 3H(T) < 16 */
+    S_CHAR        iso_atw_diff;            /* =0 => natural isotopic abundances  */
+                                           /* >0 => (mass) - (mass of the most abundant isotope) + 1 */
+                                           /* <0 => (mass) - (mass of the most abundant isotope) */
+    S_CHAR        charge;                  /* charge */
+    S_CHAR        radical;                 /* RADICAL_SINGLET, RADICAL_DOUBLET, or RADICAL_TRIPLET */
+    S_CHAR        bAmbiguousStereo;
+    S_CHAR        cFlags;                  /* AT_FLAG_ISO_H_POINT */
+    AT_NUMB       at_type;                 /* ATT_NONE, ATT_ACIDIC */
+    AT_NUMB       component;               /* number of the structure component > 0 */
+    AT_NUMB       endpoint;                /* id of a tautomeric group */
+    AT_NUMB       c_point;                 /* id of a positive charge group */
+    double        x;
+    double        y;
+    double        z;
+    /* cml 0D parities */
+    S_CHAR        bUsed0DParity;          /* bit=1 => stereobond; bit=2 => stereocenter */
+    /* cml tetrahedral parity */
+    S_CHAR        p_parity;
+    AT_NUMB       p_orig_at_num[MAX_NUM_STEREO_ATOM_NEIGH];
+    /* cml bond parities */
+    S_CHAR        sb_ord[MAX_NUM_STEREO_BONDS];  /* stereo bond/neighbor ordering number, starts from 0 */
+    /* neighbors on both sides of stereobond have same sign=> trans/T/E, diff. signs => cis/C/Z */
+    S_CHAR        sn_ord[MAX_NUM_STEREO_BONDS]; /* ord. num. of the neighbor adjacent to the SB; starts from 0;
+                                                   -1 means removed explicit H */
+    /* neighbors on both sides of stereobond have same parity => trans/T/E/2, diff. parities => cis/C/Z/1 */
+    S_CHAR        sb_parity[MAX_NUM_STEREO_BONDS];
+    AT_NUMB       sn_orig_at_num[MAX_NUM_STEREO_BONDS]; /* orig. at number of sn_ord[] neighbors */
+
+#if( FIND_RING_SYSTEMS == 1 )
+    S_CHAR  bCutVertex;
+    AT_NUMB nRingSystem;
+    AT_NUMB nNumAtInRingSystem;
+    AT_NUMB nBlockSystem;
+
+#if( FIND_RINS_SYSTEMS_DISTANCES == 1 )
+    AT_NUMB nDistanceFromTerminal;       /* terminal atom or ring system has 1, next has 2, etc. */
+#endif
+
+#endif
+} inp_ATOM;
+
+typedef struct tagOrigAtom {
+    /* initially filled out by MolfileToOrigAtom */
+    /* may be changed by disconnecting salts and disconnecting metals */
+    inp_ATOM *at;
+    int num_dimensions;
+    int num_inp_bonds;
+    int num_inp_atoms;
+    /* may be changed by disconnecting salts and disconnecting metals */
+    int num_components;    /* set by MarkDisconnectedComponents() and disconnecting metals */
+    int bDisconnectSalts;  /* whether salt disconnection is possible */
+    int bDisconnectCoord;  /* 0 if no disconnection needed else (Num Implicit H to disconnect)+1 */
+#if( bRELEASE_VERSION == 0 )
+    int bExtract;
+#endif
+    AT_NUMB *nCurAtLen;      /* has max_num_components elements */
+    AT_NUMB *nOldCompNumber; /* 0 or component number in previous numbering */
+    int      nNumEquSets;  /* number of found component equivalence sets */
+    AT_NUMB *nEquLabels; /* num_inp_atoms elements, value>0 marks atoms in the set #value  */
+    AT_NUMB *nSortedOrder; /* num_components elements, values = 1..num_components; only if num_components > 1  */
+    int bSavedInINCHI_LIB[INCHI_NUM];
+    int bPreprocessed[INCHI_NUM];
+    MOL_COORD *szCoord;
+} ORIG_ATOM_DATA;
+
+typedef struct tagOriginalStruct {
+    int num_atoms;
+    char *szAtoms;
+    char *szBonds;
+    char *szCoord;
+} ORIG_STRUCT;
+
+typedef struct tagAtomParmsForDrawing {
+    char      at_string[ATOM_INFO_LEN];
+    int       DrawingLabelLeftShift;
+    int       DrawingLabelLength;
+    AT_NUMB   nCanonNbr;               /* if zero then do not use all data for the atom */
+    AT_NUMB   nCanonEquNbr;
+    AT_NUMB   nTautGroupCanonNbr;
+    AT_NUMB   nTautGroupEquNbr;
+    S_CHAR    cFlags;                  /* AT_FLAG_ISO_H_POINT */
+#ifdef DISPLAY_DEBUG_DATA
+    int       nDebugData;
+#endif
+    S_CHAR    cHighlightTheAtom;
+    S_CHAR    cStereoCenterParity;
+    S_CHAR    cStereoBondParity[MAX_STEREO_BONDS];
+    S_CHAR    cStereoBondWarning[MAX_STEREO_BONDS];
+    S_CHAR    cStereoBondNumber[MAX_STEREO_BONDS];
+} inf_ATOM;
+
+
+#define INF_STEREO_ABS         0x0001
+#define INF_STEREO_REL         0x0002
+#define INF_STEREO_RAC         0x0004
+#define INF_STEREO_NORM        0x0008
+#define INF_STEREO_INV         0x0010
+#define INF_STEREO             0x0020
+#define INF_STEREO_ABS_REL_RAC (INF_STEREO_ABS | INF_STEREO_REL | INF_STEREO_RAC)
+#define INF_STEREO_NORM_INV    (INF_STEREO_NORM | INF_STEREO_INV)
+
+#define MAX_LEN_REMOVED_PROTONS 128
+
+typedef struct tagInfoAtomData {
+    inf_ATOM  *at;
+    int        num_at;
+    AT_NUMB    StereoFlags;
+    AT_NUMB    num_components;
+    AT_NUMB    *pStereoFlags;
+
+    int        nNumRemovedProtons;
+    int        num_removed_iso_H; /* number of exchangable isotopic H */
+    NUM_H      num_iso_H[NUM_H_ISOTOPES]; /* number of exchangable isotopic H */
+    char       szRemovedProtons[MAX_LEN_REMOVED_PROTONS];
+} INF_ATOM_DATA;
+
+typedef struct tagInputAtomData {
+    inp_ATOM *at;
+    inp_ATOM *at_fixed_bonds; /* tautomeric case, added or removed H */
+    int       num_at;
+    int       num_removed_H;
+    int       num_bonds;
+    int       num_isotopic;
+    int       bExists;
+    int       bDeleted;
+    int       bHasIsotopicLayer;
+    int       bTautomeric;
+    int       bTautPreprocessed;
+    int       nNumRemovedProtons;
+    NUM_H     nNumRemovedProtonsIsotopic[NUM_H_ISOTOPES]; /* isotopic composition of removed protons, not included in num_iso_H[] */
+    NUM_H     num_iso_H[NUM_H_ISOTOPES]; /* isotopic H on tautomeric atoms and those in nIsotopicEndpointAtomNumber */
+    INCHI_MODE  bTautFlags;
+    INCHI_MODE  bTautFlagsDone;
+    INCHI_MODE  bNormalizationFlags;
+} INP_ATOM_DATA;
+typedef INP_ATOM_DATA INP_ATOM_DATA2[TAUT_NUM];
+
+typedef struct tagNormCanonFlags {
+    INCHI_MODE  bTautFlags[INCHI_NUM][TAUT_NUM];
+    INCHI_MODE  bTautFlagsDone[INCHI_NUM][TAUT_NUM];
+    INCHI_MODE  bNormalizationFlags[INCHI_NUM][TAUT_NUM];
+    int        nCanonFlags[INCHI_NUM][TAUT_NUM];
+} NORM_CANON_FLAGS;
+
+typedef struct tagCompositeAtomData {
+    inp_ATOM *at;
+    int       num_at;
+    int       num_removed_H;
+    int       num_bonds;
+    int       num_isotopic;
+    int       bExists;
+    int       bDeleted;    /* unused */
+    int       bHasIsotopicLayer;
+    int       bTautomeric;
+    int       nNumRemovedProtons;
+    NUM_H     nNumRemovedProtonsIsotopic[NUM_H_ISOTOPES]; /* isotopic composition of removed protons, not included in num_iso_H[] */
+    NUM_H     num_iso_H[NUM_H_ISOTOPES]; /* isotopic H on tautomeric atoms and those in nIsotopicEndpointAtomNumber */
+
+    AT_NUMB   *nOffsetAtAndH;
+    int       num_components;
+} COMP_ATOM_DATA;
+/*
+typedef COMP_ATOM_DATA COMP_ATOM_DATA3[TAUT_NUM+1];
+*/
+#define ADD_LEN_STRUCT_FPTRS 100  /* allocation increments */
+typedef long INCHI_FPTR;
+typedef struct tagStructFptrs {
+    INCHI_FPTR *fptr;      /* input:  fptr[cur_fptr]   = file pointer to the structure to read */
+                          /* output: fptr[cur_fptr+1] = file pointer to the next structure or EOF */
+    int        len_fptr;  /* allocated length of fptr */
+    int        cur_fptr;  /* input: k-1 to read the kth struct, k = 1, 2, 3,...; left unchanged; struct number := cur_fptr+1 */
+    int        max_fptr;  /* length of the filled out portion of fptr */
+} STRUCT_FPTRS;
+
+#define FLAG_INP_AT_CHIRAL         1
+#define FLAG_INP_AT_NONCHIRAL      2
+#define FLAG_SET_INP_AT_CHIRAL     4
+#define FLAG_SET_INP_AT_NONCHIRAL  8
+
+/* BILLY 8/6/04 */
+#ifndef INCHI_ALL_CPP
+#ifdef __cplusplus
+extern "C" {
+#endif
+#endif
+
+int MolfileToInpAtom( FILE *inp_molfile, int bDoNotAddH, inp_ATOM **at, MOL_COORD **szCoord, int max_num_at,
+                      int *num_dimensions, int *num_bonds, const char *pSdfLabel, char *pSdfValue,
+                      long *Id, long *lMolfileNumber, INCHI_MODE *pInpAtomFlags, int *err, char *pStrErr );
+int MolfileToOrigAtom( FILE *inp_molfile, ORIG_ATOM_DATA *orig_at_data, int bMergeAllInputStructures,
+                       int bGetOrigCoord, int bDoNotAddH,
+                       const char *pSdfLabel, char *pSdfValue, long *lSdfId, long *lMolfileNumber,
+                       INCHI_MODE *pInpAtomFlags, int *err, char *pStrErr );
+int INChIToOrigAtom( FILE *inp_molfile, ORIG_ATOM_DATA *orig_at_data, int bMergeAllInputStructures,
+                       int bGetOrigCoord, int bDoNotAddH, INPUT_TYPE nInputType,
+                       char *pSdfLabel, char *pSdfValue, long *lSdfId,
+                       INCHI_MODE *pInpAtomFlags, int *err, char *pStrErr );
+
+int MarkDisconnectedComponents( ORIG_ATOM_DATA *orig_at_data, int bProcessOldCompNumbers );
+int DisconnectSalts( ORIG_ATOM_DATA *orig_inp_data, int bDisconnect );
+int DisconnectMetals( ORIG_ATOM_DATA *orig_inp_data, int bCheckMetalValence, INCHI_MODE *bTautFlagsDone );
+int bMayDisconnectMetals( ORIG_ATOM_DATA *orig_inp_data, int bCheckMetalValence, INCHI_MODE *bTautFlagsDone );
+int bHasMetalAtom( ORIG_ATOM_DATA *orig_inp_data );
+int fix_odd_things( int num_atoms, inp_ATOM *at );
+int post_fix_odd_things( int num_atoms, inp_ATOM *at );
+int remove_ion_pairs( int num_atoms, inp_ATOM *at );
+
+int bFoundFeature( inp_ATOM *at, int num_atoms );
+int CopyMOLfile(FILE *inp_file, long fPtrStart, long fPtrEnd, INCHI_FILE *prb_file, long nNumb);
+
+void FreeInpAtom( inp_ATOM **at );
+void FreeInfAtom( inf_ATOM **at );
+void FreeOrigAtData( ORIG_ATOM_DATA *orig_at_data );
+void FreeInpAtomData( INP_ATOM_DATA *inp_at_data );
+void FreeCompAtomData( COMP_ATOM_DATA *inp_at_data );
+void FreeInfoAtomData( INF_ATOM_DATA *inf_at_data );
+
+inf_ATOM *CreateInfAtom( int num_atoms );
+inp_ATOM *CreateInpAtom( int num_atoms );
+
+int CreateInfoAtomData( INF_ATOM_DATA *inf_at_data, int num_atoms, int num_components );
+int AllocateInfoAtomData( INF_ATOM_DATA *inf_at_data, int num_atoms, int num_components );
+int DuplicateInfoAtomData( INF_ATOM_DATA *inf_at_data_to, const INF_ATOM_DATA *inf_at_data_from);
+int CreateInpAtomData( INP_ATOM_DATA *inp_at_data, int num_atoms, int create_at_fixed_bonds );
+int CreateCompAtomData( COMP_ATOM_DATA *inp_at_data, int num_atoms, int num_components, int bIntermediateTaut );
+#ifndef INCHI_ANSI_ONLY
+int DisplayInputStructure( char *szOutputString, inp_ATOM  *at, INF_ATOM_DATA *inf_at_data, int num_at, DRAW_PARMS *dp );
+#endif
+void PrintFileName( const char *fmt, INCHI_FILE *output_file, const char *szFname );
+void MySleep( unsigned long ms );
+
+#ifndef __ICHITIME_H__
+struct tagInchiTime;
+int bInchiTimeIsOver( struct tagInchiTime *TickEnd );
+#endif
+
+int get_endpoint_valence( U_CHAR el_number );
+
+#if( TEST_RENUMB_ATOMS == 1 )  /*  { */
+int CopyInpAtomData( INP_ATOM_DATA *dest_inp_at_data, INP_ATOM_DATA *src_inp_at_data );
+void RenumbInpAtomData( INP_ATOM_DATA *dest_inp_at_data, INP_ATOM_DATA *src_inp_at_data, AT_RANK *new_ord );
+void MakeNewOrd( int num_atoms, AT_RANK *new_ord );
+#endif
+
+int ReconcileAllCmlBondParities( inp_ATOM *at, int num_atoms, int bDisconnected );
+
+
+/* BILLY 8/6/04 */
+#ifndef INCHI_ALL_CPP
+#ifdef __cplusplus
+}
+#endif
+#endif
+
+#endif  /* __INPDEF_H__ */