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inchi_api.h
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/*
* International Chemical Identifier (InChI)
* Version 1
* Software version 1.04
* September 9, 2011
*
* 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.
*
* IUPAC/InChI-Trust Licence No.1.0 for the
* International Chemical Identifier (InChI) Software version 1.04
* Copyright (C) IUPAC and InChI Trust Limited
*
* This library is free software; you can redistribute it and/or modify it
* under the terms of the IUPAC/InChI Trust InChI Licence No.1.0,
* or any later version.
*
* Please note that this library is distributed WITHOUT ANY WARRANTIES
* whatsoever, whether expressed or implied. See the IUPAC/InChI Trust
* Licence for the International Chemical Identifier (InChI) Software
* version 1.04, October 2011 ("IUPAC/InChI-Trust InChI Licence No.1.0")
* for more details.
*
* You should have received a copy of the IUPAC/InChI Trust InChI
* Licence No. 1.0 with this library; if not, please write to:
*
* The InChI Trust
* c/o FIZ CHEMIE Berlin
*
* Franklinstrasse 11
* 10587 Berlin
* GERMANY
*
* or email to: ulrich@inchi-trust.org.
*
*/
#ifndef __INHCH_API_H__
#define __INHCH_API_H__
/*^^^ Post-1.02b fix - thanks to David Foss */
#ifndef FIND_RING_SYSTEMS
#define FIND_RING_SYSTEMS 1
#endif
#ifndef FIND_RINS_SYSTEMS_DISTANCES
#define FIND_RINS_SYSTEMS_DISTANCES 0
#endif
/* radical definitions */
typedef enum tagINCHIRadical {
INCHI_RADICAL_NONE = 0,
INCHI_RADICAL_SINGLET = 1,
INCHI_RADICAL_DOUBLET = 2,
INCHI_RADICAL_TRIPLET = 3
} inchi_Radical;
/* bond type definitions */
typedef enum tagINCHIBondType {
INCHI_BOND_TYPE_NONE = 0,
INCHI_BOND_TYPE_SINGLE = 1,
INCHI_BOND_TYPE_DOUBLE = 2,
INCHI_BOND_TYPE_TRIPLE = 3,
INCHI_BOND_TYPE_ALTERN = 4 /* avoid by all means */
} inchi_BondType;
/* 2D stereo definitions */
typedef enum tagINCHIBondStereo2D {
/* stereocenter-related; positive: the sharp end points to this atom */
INCHI_BOND_STEREO_NONE = 0,
INCHI_BOND_STEREO_SINGLE_1UP = 1,
INCHI_BOND_STEREO_SINGLE_1EITHER = 4,
INCHI_BOND_STEREO_SINGLE_1DOWN = 6,
/* stereocenter-related; negative: the sharp end points to the opposite atom */
INCHI_BOND_STEREO_SINGLE_2UP = -1,
INCHI_BOND_STEREO_SINGLE_2EITHER = -4,
INCHI_BOND_STEREO_SINGLE_2DOWN = -6,
/* stereobond-related */
INCHI_BOND_STEREO_DOUBLE_EITHER = 3 /* unknown stereobond geometry */
} inchi_BondStereo2D;
/*************************************************************************
* Notes on using INCHI_BOND_STEREO_SINGLE_* from inchi_BondStereo2D *
* *
* These stereo markings are used by InChI to characterize a stereogenic *
* atom if and only if all neighbors of this atom have same z-coordinate *
* as this atom (that is, in case of 2D fragment). *
* The only exception is INCHI_BOND_STEREO_SINGLE_?EITHER marking which *
* always assigns to the atom an "unknown" parity (u). *
* *
* Note the behavior which is default for InChI software v.1.04/03/02std *
* (at -NEWPSOFF option is not supplied) 2D stereo interpretation: *
* only bonds that have sharp end pointing to the stereogenic atom are *
* considered as being out of plane and only sharp ends of *
* INCHI_BOND_STEREO_SINGLE_?EITHER bonds are considered to determine *
* whether the stereochemistry is unknown. *
*************************************************************************/
/* sizes definitions */
#define MAXVAL 20 /* max number of bonds per atom */
#define ATOM_EL_LEN 6 /* length of ASCIIZ element symbol field */
#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */
#define ISOTOPIC_SHIFT_FLAG 10000 /* add to isotopic mass if isotopic_mass = */
/* (isotopic mass - average atomic mass) */
#define ISOTOPIC_SHIFT_MAX 100 /* max abs(isotopic mass - average atomic mass) */
#ifndef INCHI_US_CHAR_DEF
typedef signed char S_CHAR;
typedef unsigned char U_CHAR;
#define INCHI_US_CHAR_DEF
#endif
#ifndef INCHI_US_SHORT_DEF
typedef signed short S_SHORT;
typedef unsigned short U_SHORT;
#define INCHI_US_SHORT_DEF
#endif
typedef S_SHORT AT_NUM; /* atom number; starts from 0 */
/*************************************************
*
*
* A T O M S a n d C O N N E C T I V I T Y
*
*
*************************************************/
typedef struct tagInchiAtom {
/* atom coordinates */
double x;
double y;
double z;
/* connectivity */
AT_NUM neighbor[MAXVAL]; /* adjacency list: ordering numbers of */
/* the adjacent atoms, >= 0 */
S_CHAR bond_type[MAXVAL]; /* inchi_BondType */
/* 2D stereo */
S_CHAR bond_stereo[MAXVAL]; /* inchi_BondStereo2D; negative if the */
/* sharp end points to opposite atom */
/* other atom properties */
char elname[ATOM_EL_LEN]; /* zero-terminated chemical element name:*/
/* "H", "Si", etc. */
AT_NUM num_bonds; /* number of neighbors, bond types and bond*/
/* stereo in the adjacency list */
S_CHAR num_iso_H[NUM_H_ISOTOPES+1]; /* implicit hydrogen atoms */
/* [0]: number of implicit non-isotopic H
(exception: num_iso_H[0]=-1 means INCHI
adds implicit H automatically),
[1]: number of implicit isotopic 1H (protium),
[2]: number of implicit 2H (deuterium),
[3]: number of implicit 3H (tritium) */
AT_NUM isotopic_mass; /* 0 => non-isotopic; isotopic mass or */
/* ISOTOPIC_SHIFT_FLAG + mass - (average atomic mass) */
S_CHAR radical; /* inchi_Radical */
S_CHAR charge; /* positive or negative; 0 => no charge */
}inchi_Atom;
/*******************************************************************
* Notes: 1. Atom ordering numbers (i, k, and atom[i].neighbor[j] below)
* start from zero; max. ordering number is (num_atoms-1).
* 2. inchi_Atom atom[i] is connected to the atom[atom[i].neighbor[j]]
* by a bond that has type atom[i].bond_type[j] and 2D stereo type
* atom[i].bond_stereo[j] (in case of no stereo
* atom[i].bond_stereo[j] = INCHI_BOND_STEREO_NONE)
* Index j is in the range 0 <= j <= (atom[i].num_bonds-1)
* 3. Any connection (represented by atom[i].neighbor[j],
* atom[i].bond_type[j], and atom[i].bond_stereo[j])
* should be present in one or both adjacency list:
* if k = atom[i].neighbor[j] then i may or may not be present in
* atom[k].neighbor[] list. For example, the adjacency lists may be
* populated with only such neighbors that atom[i].neighbor[j] < i
* All elements of an adjacency list must be different, that is,
* a bond must be specified in an adjacency list only once.
* 4. in Molfiles usually
* (number of implicit H) = Valence - SUM(bond_type[])
* 5. Seemingly illogical order of the inchi_Atom members was
* chosen in an attempt to avoid alignment problems when
* accessing inchi_Atom from unrelated to C programming
* languages such as Visual Basic.
*******************************************************************/
/*******************************************************************
0D Stereo Parity and Type definitions
*******************************************************************
Note:
=====
o Below #A is the ordering number of atom A, starting from 0
o See parity values corresponding to 'o', 'e', and 'u' in
inchi_StereoParity0D definition below)
=============================================
stereogenic bond >A=B< or cumulene >A=C=C=B<
=============================================
neighbor[4] : {#X,#A,#B,#Y} in this order
X central_atom : NO_ATOM
\ X Y type : INCHI_StereoType_DoubleBond
A==B \ /
\ A==B
Y
parity= 'e' parity= 'o' unknown parity = 'u'
Limitations:
============
o Atoms A and B in cumulenes MUST be connected by a chain of double bonds;
atoms A and B in a stereogenic 'double bond' may be connected by a double,
single, or alternating bond.
o One atom may belong to up to 3 stereogenic bonds (i.g. in a fused
aromatic structure).
o Multiple stereogenic bonds incident to any given atom should
either all except possibly one have (possibly different) defined
parities ('o' or 'e') or should all have an unknown parity 'u'.
Note on parities of alternating stereobonds
===========================================
D--E
In large rings (see Fig. 1, all // \\
atoms are C) all alternating bonds B--C F--G
are treated as stereogenic. // \\
To avoid "undefined" bond parities A H
for bonds BC, DE, FG, HI, JK, LM, AN \ /
it is recommended to mark them with N==M J==I
parities. \ /
L==K Fig. 1
Such a marking will make
the stereochemical layer unambiguous
and it will be different from the B--C F--G
stereochemical layer of the second // \\ // \\
structure (Fig. 2). A D--E H
\ /
N==M J==I
By default, double and alternating \ /
bonds in 8-member and greater rings L==K Fig. 2
are treated by InChI as stereogenic.
=============================================
tetrahedral atom
=============================================
4 neighbors
X neighbor[4] : {#W, #X, #Y, #Z}
| central_atom: #A
W--A--Y type : INCHI_StereoType_Tetrahedral
|
Z
parity: if (X,Y,Z) are clockwize when seen from W then parity is 'e' otherwise 'o'
Example (see AXYZW above): if W is above the plane XYZ then parity = 'e'
3 neighbors
Y Y neighbor[4] : {#A, #X, #Y, #Z}
/ / central_atom: #A
X--A (e.g. O=S ) type : INCHI_StereoType_Tetrahedral
\ \
Z Z
parity: if (X,Y,Z) are clockwize when seen from A then parity is 'e',
otherwise 'o'
unknown parity = 'u'
Example (see AXYZ above): if A is above the plane XYZ then parity = 'e'
This approach may be used also in case of an implicit H attached to A.
=============================================
allene
=============================================
X Y neighbor[4] : {#X,#A,#B,#Y}
\ / central_atom : #C
A=C=B type : INCHI_StereoType_Allene
Y X
| |
when seen from A along A=C=B: X-A Y-A
parity: 'e' 'o'
parity: if A, B, Y are clockwise when seen from X then parity is 'e',
otherwise 'o'
unknown parity = 'u'
Example (see XACBY above): if X on the diagram is above the plane ABY
then parity is 'o'
Limitations
===========
o Atoms A and B in allenes MUST be connected by a chain of double bonds;
==============================================
Note. Correspondence to CML 0D stereo parities
==============================================
a list of 4 atoms corresponds to CML atomRefs4
tetrahedral atom
================
CML atomParity > 0 <=> INCHI_PARITY_EVEN
CML atomParity < 0 <=> INCHI_PARITY_ODD
| 1 1 1 1 | where xW is x-coordinate of
| xW xX xY xZ | atom W, etc. (xyz is a
CML atomParity = determinant | yW yX yY yZ | 'right-handed' Cartesian
| zW zX xY zZ | coordinate system)
allene (not yet defined in CML)
===============================
the parity corresponds to the sign of the following determinant
in exactly same way as for tetrahedral atoms:
| 1 1 1 1 | where bonds and neighbor[4] array are
| xX xA xB xY | same as defined above for allenes
| yX yA yB yY | Obviously, the parity is same for
| zX zA xB zY | {#X,#A,#B,#Y} and {#Y,#B,#A,#X}
because of the even number of column permutations.
stereogenic double bond and (not yet defined in CML) cumulenes
==============================================================
CML 'C' (cis) <=> INCHI_PARITY_ODD
CML 'T' (trans) <=> INCHI_PARITY_EVEN
How InChI uses 0D parities
==========================
1. 0D parities are used if all atom coordinates are zeroes.
In addition to that:
2. 0D parities are used for Stereobonds, Allenes, or Cumulenes if:
2a. A bond to the end-atom is shorter than MIN_BOND_LEN=0.000001
2b. A ratio of two bond lengths to the end-atom is smaller than MIN_SINE=0.03
2c. In case of a linear fragment X-A=B end-atom A is treated as satisfying 2a-b
0D parities are used if 2a or 2b or 2c applies to one or both end-atoms.
3. 0D parities are used for Tetrahedral Atoms if at least one of 3a-c is true:
3a. One of bonds to the central atom is shorter than MIN_BOND_LEN=0.000001
3b. A ratio of two bond lengths to the central atom is smaller than MIN_SINE=0.03
3c. The four neighbors are almost in one plane or the central atom and
its only 3 explicit neighbors are almost in one plane
Notes on 0D parities and 'undefined' stereogenic elements
=========================================================
If 0D parity is to be used according to 1-3 but CH3 CH3
has not been provided then the corresponding \ /
stereogenic element is considered 'undefined'. C=CH
/
For example, if in the structure (Fig. 3) H
the explicit H has been moved so that it Fig. 3
has same coordinates as atom >C= (that is,
the length of the bond H-C became zero)
then the double bond is assigned 'undefined' CH3 CH3
parity which by default is omitted from the \ /
Identifier. CH=CH
However, the structure on Fig. 4 will have double Fig. 4
bond parity 'o' and its parity in the Identifier is (-).
Notes on 0D parities in structures containing metals
====================================================
Since InChI disconnects bonds to metals the 0D parities upon the
disconnection may change in several different ways:
1) previously non-stereogenic bond may become stereogenic:
\ / \ /
CH==CH disconnection CH==CH
\ / ======>
M M
before the disconnection: after the disconnection:
atoms C have valence=5 and the double bond may become
the double bond is not stereogenic
recognized as stereogenic
2) previously stereogenic bond may become non-stereogenic:
M M(+)
\ / /
N==C disconnection (-)N==C
\ ======> \
3) Oddball structures, usually resulting from projecting 3D
structures on the plane, may contain fragment like that
depicted on Fig. 5:
M A M A
|\ / B / B
| X / disconnection / /
|/ \ / ======> / /
C===C C===C
Fig. 5
(X stands for bond intersection)
A-C=C-B parity is A-C=C-B parity is
trans (e) cis (o) or undefined
because the bond because C valence = 3,
orientation is same not 4.
as on Fig, 6 below:
A M
\ / Removal of M from the structure
C===C on Fig. 5 changes the geometry from trans
/ \ to cis.
M' B Removal of M and M' from the structure
Fig. 6 on Fig. 6 does not change the A-C=C-B
geometry: it is trans.
To resolve the problem InChI API accepts the second parity
corresponding to the metal-disconnected structure.
To store both bond parities use left shift by 3 bits:
inchi_Stereo0D::parity = ParityOfConnected | (ParityOfDisconnected<<3)
In case when only disconnected structure parity exists set
ParityOfConnected = INCHI_PARITY_UNDEFINED.
This is the only case when INCHI_PARITY_UNDEFINED parity
may be fed to the InChI.
In cases when the bond parity in a disconnected structure exists and
differs from the parity in the connected structure the atoms A and B
should be non-metals.
****************************************************************************/
#define NO_ATOM (-1) /* non-existent (central) atom */
/* 0D parity types */
typedef enum tagINCHIStereoType0D {
INCHI_StereoType_None = 0,
INCHI_StereoType_DoubleBond = 1,
INCHI_StereoType_Tetrahedral = 2,
INCHI_StereoType_Allene = 3
} inchi_StereoType0D;
/* 0D parities */
typedef enum tagINCHIStereoParity0D {
INCHI_PARITY_NONE = 0,
INCHI_PARITY_ODD = 1, /* 'o' */
INCHI_PARITY_EVEN = 2, /* 'e' */
INCHI_PARITY_UNKNOWN = 3, /* 'u' */ /* (see also readinch.c)
used in: Extract0DParities, INChITo_Atom */
INCHI_PARITY_UNDEFINED = 4 /* '?' -- should not be used; however, see Note above */
} inchi_StereoParity0D;
/*************************************************
*
*
* 0D - S T E R E O (if no coordinates given)
*
*
*************************************************/
typedef struct tagINCHIStereo0D {
AT_NUM neighbor[4]; /* 4 atoms always */
AT_NUM central_atom; /* central tetrahedral atom or a central */
/* atom of allene; otherwise NO_ATOM */
S_CHAR type; /* inchi_StereoType0D */
S_CHAR parity; /* inchi_StereoParity0D: may be a combination of two parities: */
/* ParityOfConnected | (ParityOfDisconnected << 3), see Note above */
}inchi_Stereo0D;
/*************************************************
*
*
* I N C h I D L L I n p u t
*
*
*************************************************/
/* Structure -> InChI, GetINCHI() / GetStdINCHI() */
typedef struct tagINCHI_Input {
/* the caller is responsible for the data allocation and deallocation */
inchi_Atom *atom; /* array of num_atoms elements */
inchi_Stereo0D *stereo0D; /* array of num_stereo0D 0D stereo elements or NULL */
char *szOptions; /* InChI options: space-delimited; each is preceded by */
/* '/' or '-' depending on OS and compiler */
AT_NUM num_atoms; /* number of atoms in the structure < 1024 */
AT_NUM num_stereo0D; /* number of 0D stereo elements */
}inchi_Input;
/* InChI -> Structure, GetStructFromINCHI()/GetStructFromStdINCHI() */
typedef struct tagINCHI_InputINCHI {
/* the caller is responsible for the data allocation and deallocation */
char *szInChI; /* InChI ASCIIZ string to be converted to a strucure */
char *szOptions; /* InChI options: space-delimited; each is preceded by */
/* '/' or '-' depending on OS and compiler */
} inchi_InputINCHI;
/*************************************************
*
*
* I N C h I D L L O u t p u t
*
*
*************************************************/
/* Structure -> InChI */
typedef struct tagINCHI_Output {
/* zero-terminated C-strings allocated by GetStdINCHI() */
/* to deallocate all of them call FreeStdINCHI() (see below) */
char *szInChI; /* InChI ASCIIZ string */
char *szAuxInfo; /* Aux info ASCIIZ string */
char *szMessage; /* Error/warning ASCIIZ message */
char *szLog; /* log-file ASCIIZ string, contains a human-readable list */
/* of recognized options and possibly an Error/warning message */
} inchi_Output;
/* InChI -> Structure */
typedef struct tagINCHI_OutputStruct {
/* 4 pointers are allocated by GetStructFromINCHI()/GetStructFromStdINCHI() */
/* to deallocate all of them call FreeStructFromStdINCHI()/FreeStructFromStdINCHI() */
inchi_Atom *atom; /* array of num_atoms elements */
inchi_Stereo0D *stereo0D; /* array of num_stereo0D 0D stereo elements or NULL */
AT_NUM num_atoms; /* number of atoms in the structure < 1024 */
AT_NUM num_stereo0D; /* number of 0D stereo elements */
char *szMessage; /* Error/warning ASCIIZ message */
char *szLog; /* log-file ASCIIZ string, contains a human-readable list */
/* of recognized options and possibly an Error/warning message */
unsigned long WarningFlags[2][2]; /* warnings, see INCHIDIFF in inchicmp.h */
/* [x][y]: x=0 => Reconnected if present in InChI otherwise Disconnected/Normal
x=1 => Disconnected layer if Reconnected layer is present
y=1 => Main layer or Mobile-H
y=0 => Fixed-H layer
*/
}inchi_OutputStruct;
/*************************************************
*
*
* I N C h I D L L I n t e r f a c e
*
*
*************************************************/
#if (defined( _WIN32 ) && defined( _MSC_VER ) && defined(BUILD_LINK_AS_DLL) )
/* Win32 & MS VC ++, compile and link as a DLL */
#ifdef _USRDLL
/* InChI library dll */
#define INCHI_API __declspec(dllexport)
#define EXPIMP_TEMPLATE
#define INCHI_DECL __stdcall
#else
/* calling the InChI dll program */
#define INCHI_API __declspec(dllimport)
#define EXPIMP_TEMPLATE extern
#define INCHI_DECL __stdcall
#endif
#else
/* create a statically linked InChI library or link to an executable */
#define INCHI_API
#define EXPIMP_TEMPLATE
#define INCHI_DECL
#endif
/*^^^ Return codes for
GetINCHI
GetStdINCHI
Get_inchi_Input_FromAuxInfo
Get_std_inchi_Input_FromAuxInfo
GetStructFromINCHI
GetStructFromStdINCHI
*/
typedef enum tagRetValGetINCHI {
inchi_Ret_SKIP = -2, /* not used in InChI library */
inchi_Ret_EOF = -1, /* no structural data has been provided */
inchi_Ret_OKAY = 0, /* Success; no errors or warnings */
inchi_Ret_WARNING = 1, /* Success; warning(s) issued */
inchi_Ret_ERROR = 2, /* Error: no InChI has been created */
inchi_Ret_FATAL = 3, /* Severe error: no InChI has been created (typically, memory allocation failure) */
inchi_Ret_UNKNOWN = 4, /* Unknown program error */
inchi_Ret_BUSY = 5 /* Previuos call to InChI has not returned yet */
} RetValGetINCHI;
/*^^^ Return codes for CheckINCHI */
typedef enum tagRetValCheckINCHI
{
INCHI_VALID_STANDARD = 0,
INCHI_VALID_NON_STANDARD = -1,
INCHI_INVALID_PREFIX = 1,
INCHI_INVALID_VERSION = 2,
INCHI_INVALID_LAYOUT = 3,
INCHI_FAIL_I2I = 4
} RetValCheckINCHI;
/* to compile all InChI code as a C++ code #define COMPILE_ALL_CPP */
#ifndef COMPILE_ALL_CPP
#ifdef __cplusplus
extern "C" {
#endif
#endif
/*^^^ InChI PREFIX */
#define INCHI_STRING_PREFIX "InChI="
#define LEN_INCHI_STRING_PREFIX 6
/*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Format:
Standard InChI starts with: InChI=1S/
Non-standard one with: InChI=1/
Empty std InChI: InChI=1S//
Empty InChI: InChI=1//
AuxInfo=1//
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
/* EXPORTED FUNCTIONS */
/*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
GetINCHI / GetStdINCHI
inchi_Input is created by the user; strings in inchi_Output are allocated and deallocated by InChI
inchi_Output does not need to be initilized out to zeroes; see FreeNCHI()/FreeSTDINCHI() on how to deallocate it
Valid options for GetINCHI:
(use - instead of / for O.S. other than MS Windows)
Structure perception (compatible with stdInChI)
/NEWPSOFF /DoNotAddH /SNon
Stereo interpretation (lead to generation of non-standard InChI)
/SRel /SRac /SUCF /ChiralFlagON /ChiralFlagOFF
InChI creation options (lead to generation of non-standard InChI)
/SUU /SLUUD /FixedH /RecMet /KET /15T
GetINCHI produces standard InChI if no InChI creation/stereo modification options
are specified. Inveresely, if any of SUU/SLUUD/RecMet/FixedH/Ket/15T/SRel/SRac/SUCF
options are specified, generated InChI will be non-standard one.
GetStdINCHI produces standard InChI only.
The valid structure perception options are:
/NEWPSOFF /DoNotAddH /SNon
Other options are:
/AuxNone Omit auxiliary information (default: Include)
/Wnumber Set time-out per structure in seconds; W0 means unlimited
In InChI library the default value is unlimited
/OutputSDF Output SDfile instead of InChI
/WarnOnEmptyStructure
Warn and produce empty InChI for empty structure
/SaveOpt Save custom InChI creation options (non-standard InChI)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
EXPIMP_TEMPLATE INCHI_API int INCHI_DECL GetINCHI( inchi_Input *inp, inchi_Output *out );
EXPIMP_TEMPLATE INCHI_API int INCHI_DECL GetStdINCHI( inchi_Input *inp, inchi_Output *out );
/*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FreeINCHI / FreeStdINCHI
should be called to deallocate char* pointers
obtained from each GetINCHI /GetStdINCHI call
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
EXPIMP_TEMPLATE INCHI_API void INCHI_DECL FreeINCHI ( inchi_Output *out );
EXPIMP_TEMPLATE INCHI_API void INCHI_DECL FreeStdINCHI ( inchi_Output *out );
/*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
GetStringLength
helper: get string length
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
EXPIMP_TEMPLATE INCHI_API int INCHI_DECL GetStringLength( char *p );
/*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
GetStructFromINCHI / GetStructFromStdINCHI
inchi_Inputinchi_InputINCHI is created by the user; pointers in inchi_OutputStruct are allocated and deallocated by InChI
inchi_OutputStruct does not need to be initilized out to zeroes; see FreeStructFromStdINCHI() on how to deallocate it
Option /Inchi2Struct is not needed for GetStructFromINCHI()/GetStructFromStdINCHI()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
EXPIMP_TEMPLATE INCHI_API int INCHI_DECL GetStructFromINCHI( inchi_InputINCHI *inpInChI, inchi_OutputStruct *outStruct );
EXPIMP_TEMPLATE INCHI_API int INCHI_DECL GetStructFromStdINCHI( inchi_InputINCHI *inpInChI, inchi_OutputStruct *outStruct );
/*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FreeStructFromINCHI / FreeStructFromStdINCHI
should be called to deallocate pointers obtained from each
GetStructFromStdINCHI / GetStructFromINCHI
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
EXPIMP_TEMPLATE INCHI_API void INCHI_DECL FreeStructFromINCHI( inchi_OutputStruct *out );
EXPIMP_TEMPLATE INCHI_API void INCHI_DECL FreeStructFromStdINCHI( inchi_OutputStruct *out );
/*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
GetINCHIfromINCHI
GetINCHIfromINCHI does same as -InChI2InChI option: converts InChI into InChI for validation purposes
It may also be used to filter out specific layers. For instance, /Snon would remove stereochemical layer
Omitting /FixedH and/or /RecMet would remove Fixed-H or Reconnected layers
To keep all InChI layers use options string "/FixedH /RecMet"; option /InChI2InChI is not needed
inchi_InputINCHI is created by the user; strings in inchi_Output are allocated and deallocated by InChI
inchi_Output does not need to be initilized out to zeroes; see FreeINCHI() on how to deallocate it
Note: there is no explicit tool to conversion from/to standard InChI
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
EXPIMP_TEMPLATE INCHI_API int INCHI_DECL GetINCHIfromINCHI( inchi_InputINCHI *inpInChI, inchi_Output *out );
#ifndef COMPILE_ALL_CPP
#ifdef __cplusplus
}
#endif
#endif
/*****************************************************************
*
*
* C o n v e r s i o n: InChI AuxInfo string => inchi_Input
*
*
*****************************************************************/
#ifndef STR_ERR_LEN
#define STR_ERR_LEN 256
#endif
typedef struct tagInchiInpData {
inchi_Input *pInp; /* a pointer to pInp that has all items 0 or NULL */
int bChiral; /* 1 => the structure was marked as chiral, 2=> not chiral, 0=> not marked */
char szErrMsg[STR_ERR_LEN];
} InchiInpData;
/* to compile all InChI code as a C++ code #define COMPILE_ALL_CPP */
#ifndef COMPILE_ALL_CPP
#ifdef __cplusplus
extern "C" {
#endif
#endif
/*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Get_inchi_Input_FromAuxInfo / Get_std_inchi_Input_FromAuxInfo
Input:
szInchiAuxInfo: contains ASCIIZ string of InChI output for a single
structure or only the AuxInfo line
bDoNotAddH: if 0 then InChI will be allowed to add implicit H
bDiffUnkUndfStereo
if not 0, use different labels for unknown and undefined stereo
pInchiInp: should have a valid pointer pInchiInp->pInp to an empty
(all members = 0) inchi_Input structure
Output:
pInchiInp: The following members of pInp may be filled during the call:
atom, num_atoms, stereo0D, num_stereo0D
Return value: see RetValGetINCHI
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
EXPIMP_TEMPLATE INCHI_API int INCHI_DECL Get_inchi_Input_FromAuxInfo(
char *szInchiAuxInfo,
int bDoNotAddH,
int bDiffUnkUndfStereo,
InchiInpData *pInchiInp );
EXPIMP_TEMPLATE INCHI_API int INCHI_DECL Get_std_inchi_Input_FromAuxInfo( char *szInchiAuxInfo,
int bDoNotAddH,
InchiInpData *pInchiInp );
/*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Free_inchi_Input / Free_std_inchi_Input
To deallocate and write zeroes into the changed members of pInchiInp->pInp call
Free_std_inchi_Input( inchi_Input *pInp )
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
EXPIMP_TEMPLATE INCHI_API void INCHI_DECL Free_inchi_Input( inchi_Input *pInp );
EXPIMP_TEMPLATE INCHI_API void INCHI_DECL Free_std_inchi_Input( inchi_Input *pInp );
/*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
CheckINCHI
Check if the string represents valid InChI/standard InChI.
Input:
szINCHI source InChI
strict if 0, just briefly check for proper layout (prefix, version, etc.)
The result may not be strict.
If not 0, try to perform InChI2InChI conversion and
returns success if a resulting InChI string exactly match source.
The result may be 'false alarm' due to imperfectness of conversion.
Returns:
success/errors codes
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
EXPIMP_TEMPLATE INCHI_API int INCHI_DECL CheckINCHI(const char *szINCHI, const int strict);
#ifndef COMPILE_ALL_CPP
#ifdef __cplusplus
}
#endif
#endif
/*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
InChIKey API
InChIKey description
The InChIKey is a character signature based on a hash code of the InChI string.
Standard InChIKey is produced out of standard InChI.
Non-standard InChIKey is produced out of non-standard InChI.
AAAAAAAAAAAAAA-BBBBBBBBCD-P
InChIKey layout is as follows:
AAAAAAAAAAAAAA
First block (14 letters)
Encodes molecular skeleton (connectivity)
BBBBBBBB
Second block (8 letters)
Encodes tautomers, stereochemistry, isotopomers, reconnected layer
C
'S' for standard
'N' for non-standard
D
InChI version ('A' for 1)
P - (de)protonation flag
Protonization encoding:
N 0
O +1 P +2 Q +3 R +4 S +5 T +6 U +7 V +8 W +9 X +10 Y +11 Z +12
M -1 L-2 K -3 J -4 I -5 H -6 G -7 F -8 E -9 D -10 C -11 B -12
A < -12 or > +12
All symbols except delimiter (dash, that is, minus) are uppercase English
letters representing a "base 26" encoding.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
/*^^^ Return codes for key generation procedure */
#define INCHIKEY_OK 0
#define INCHIKEY_UNKNOWN_ERROR 1
#define INCHIKEY_EMPTY_INPUT 2
#define INCHIKEY_INVALID_INCHI_PREFIX 3
#define INCHIKEY_NOT_ENOUGH_MEMORY 4
#define INCHIKEY_INVALID_INCHI 20
#define INCHIKEY_INVALID_STD_INCHI 21
/*^^^ Return codes for CheckINCHIKey */
typedef enum tagRetValGetINCHIKey
{
INCHIKEY_VALID_STANDARD = 0,
INCHIKEY_VALID_NON_STANDARD = -1,
INCHIKEY_INVALID_LENGTH = 1,
INCHIKEY_INVALID_LAYOUT = 2,
INCHIKEY_INVALID_VERSION = 3
} RetValCheckINCHIKeyv;
/* EXPORTED FUNCTIONS */
/* To compile all InChI code as a C++ code #define COMPILE_ALL_CPP */
#ifndef COMPILE_ALL_CPP
#ifdef __cplusplus
extern "C" {
#endif
#endif
/*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
GetINCHIKeyFromINCHI
Calculate InChIKey by InChI string.
Input:
szINCHISource
source InChI string
xtra1
=1 calculate hash extension (up to 256 bits; 1st block)
xtra2
=1 calculate hash extension (up to 256 bits; 2nd block)
Output:
szINCHIKey
InChIKey string
The user-supplied buffer szINCHIKey should be at least 28 bytes long.
szXtra1
hash extension (up to 256 bits; 1st block) string
Caller should allocate space for 64 characters + trailing NULL
szXtra2
hash extension (up to 256 bits; 2nd block) string
Caller should allocate space for 64 characters + trailing NULL
Returns:
success/errors codes
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
EXPIMP_TEMPLATE INCHI_API int INCHI_DECL GetINCHIKeyFromINCHI(const char* szINCHISource,
const int xtra1,
const int xtra2,
char* szINCHIKey,
char* szXtra1,
char* szXtra2);
/*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
GetStdINCHIKeyFromStdINCHI
"Standard" counterpart
For compatibility with v. 1.02std, no extra hash calculation is allowed.
To calculate extra hash(es), use GetINCHIKeyFromINCHI with stdInChI as input.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
EXPIMP_TEMPLATE INCHI_API int INCHI_DECL GetStdINCHIKeyFromStdINCHI(const char* szINCHISource,
char* szINCHIKey);
/*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
CheckINCHIKey
Check if the string represents valid InChIKey.
Input:
szINCHIKey
source InChIKey string
Returns:
success/errors codes
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
EXPIMP_TEMPLATE INCHI_API int INCHI_DECL CheckINCHIKey(const char *szINCHIKey);
#ifndef COMPILE_ALL_CPP
#ifdef __cplusplus
}
#endif
#endif
/*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Modularized InChI generation API
Note. Functions with STDINCHIGEN prefix are
retained for compatibility with v. 1.02std