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Functionality for calling the InChI library from Java. Requires an appropriate InChI binary on the classpath to use
/**
* JNA-InChI - Library for calling InChI from Java
* Copyright © 2018 Daniel Lowe
*
* This library is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public
* License as published by the Free Software Foundation; either
* version 2.1 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program. If not, see
* This file was autogenerated by JNAerator,
* a tool written by Olivier Chafik that uses a few opensource projects..
* For help, please visit NativeLibs4Java , Rococoa, or JNA.
*/
public class InchiLibrary implements Library {
public static final String JNA_LIBRARY_NAME = "jnainchi";
public static final NativeLibrary JNA_NATIVE_LIB = NativeLibrary.getInstance(InchiLibrary.JNA_LIBRARY_NAME);
static {
Native.register(InchiLibrary.class, InchiLibrary.JNA_NATIVE_LIB);
}
/** enum values */
public static interface tagINCHIRadical {
public static final int INCHI_RADICAL_NONE = 0;
public static final int INCHI_RADICAL_SINGLET = 1;
public static final int INCHI_RADICAL_DOUBLET = 2;
public static final int INCHI_RADICAL_TRIPLET = 3;
};
/** enum values */
public static interface tagINCHIBondType {
public static final int INCHI_BOND_TYPE_NONE = 0;
public static final int INCHI_BOND_TYPE_SINGLE = 1;
public static final int INCHI_BOND_TYPE_DOUBLE = 2;
public static final int INCHI_BOND_TYPE_TRIPLE = 3;
/**
* avoid by all means
*/
public static final int INCHI_BOND_TYPE_ALTERN = 4;
};
/** enum values */
public static interface tagINCHIBondStereo2D {
public static final int INCHI_BOND_STEREO_NONE = 0;
public static final int INCHI_BOND_STEREO_SINGLE_1UP = 1;
public static final int INCHI_BOND_STEREO_SINGLE_1EITHER = 4;
public static final int INCHI_BOND_STEREO_SINGLE_1DOWN = 6;
public static final int INCHI_BOND_STEREO_SINGLE_2UP = -1;
public static final int INCHI_BOND_STEREO_SINGLE_2EITHER = -4;
public static final int INCHI_BOND_STEREO_SINGLE_2DOWN = -6;
/**
* unknown stereobond geometry
*/
public static final int INCHI_BOND_STEREO_DOUBLE_EITHER = 3;
};
/** enum values */
public static interface tagINCHIStereoType0D {
public static final int INCHI_StereoType_None = 0;
public static final int INCHI_StereoType_DoubleBond = 1;
public static final int INCHI_StereoType_Tetrahedral = 2;
public static final int INCHI_StereoType_Allene = 3;
};
/** enum values */
public static interface tagINCHIStereoParity0D {
public static final int INCHI_PARITY_NONE = 0;
/**
* 'o'
*/
public static final int INCHI_PARITY_ODD = 1;
/**
* 'e'
*/
public static final int INCHI_PARITY_EVEN = 2;
/**
* 'u'
*/
public static final int INCHI_PARITY_UNKNOWN = 3;
/**
* '?' -- should not be used; however, see Note above
*/
public static final int INCHI_PARITY_UNDEFINED = 4;
};
/** enum values */
public static interface tagRetValGetINCHI {
public static final int inchi_Ret_BREAK = -100;
/**
* not used in InChI library
*/
public static final int inchi_Ret_SKIP = -2;
/**
* no structural data has been provided
*/
public static final int inchi_Ret_EOF = -1;
/**
* Success; no errors or warnings
*/
public static final int inchi_Ret_OKAY = 0;
/**
* Success; warning(s) issued
*/
public static final int inchi_Ret_WARNING = 1;
/**
* Error: no InChI has been created
*/
public static final int inchi_Ret_ERROR = 2;
/**
* Severe error: no InChI has been created (typically, memory allocation failure)
*/
public static final int inchi_Ret_FATAL = 3;
/**
* Unknown program error
*/
public static final int inchi_Ret_UNKNOWN = 4;
/**
* Previuos call to InChI has not returned yet
*/
public static final int inchi_Ret_BUSY = 5;
};
/** enum values */
public static interface tagRetValMOL2INCHI {
/**
* Success; no errors or warnings
*/
public static final int mol2inchi_Ret_OKAY = 0;
/**
* Success; warning(s) issued
*/
public static final int mol2inchi_Ret_WARNING = 1;
/**
* generic Error: no InChI has been created
*/
public static final int mol2inchi_Ret_EOF = -1;
/**
* generic Error: no InChI has been created
*/
public static final int mol2inchi_Ret_ERROR = 2;
/**
* get structure Error: no InChI has been created
*/
public static final int mol2inchi_Ret_ERROR_get = 4;
/**
* compute InChI Error: no InChI has been created
*/
public static final int mol2inchi_Ret_ERROR_comp = 5;
};
/** enum values */
public static interface tagRetValCheckINCHI {
public static final int INCHI_VALID_STANDARD = 0;
public static final int INCHI_VALID_NON_STANDARD = 1;
public static final int INCHI_VALID_BETA = 2;
public static final int INCHI_INVALID_PREFIX = 3;
public static final int INCHI_INVALID_VERSION = 4;
public static final int INCHI_INVALID_LAYOUT = 5;
public static final int INCHI_FAIL_I2I = 6;
};
/** enum values */
public static interface tagRetValGetINCHIKey {
public static final int INCHIKEY_VALID_STANDARD = 0;
public static final int INCHIKEY_VALID_NON_STANDARD = -1;
public static final int INCHIKEY_INVALID_LENGTH = 1;
public static final int INCHIKEY_INVALID_LAYOUT = 2;
public static final int INCHIKEY_INVALID_VERSION = 3;
};
public static final int FIND_RING_SYSTEMS = (int)1;
public static final int FIND_RINS_SYSTEMS_DISTANCES = (int)0;
public static final int FIX_DOCANON_RETCODE_RESET_BUG = (int)1;
public static final int MAXVAL = (int)20;
public static final int ATOM_EL_LEN = (int)6;
public static final int NUM_H_ISOTOPES = (int)3;
public static final int ISOTOPIC_SHIFT_FLAG = (int)10000;
public static final int ISOTOPIC_SHIFT_MAX = (int)100;
public static final int NO_ATOM = (int)(-1);
public static final String INCHI_STRING_PREFIX = (String)"InChI=";
public static final int LEN_INCHI_STRING_PREFIX = (int)6;
public static final int STR_ERR_LEN = (int)256;
public static final int INCHIKEY_OK = (int)0;
public static final int INCHIKEY_UNKNOWN_ERROR = (int)1;
public static final int INCHIKEY_EMPTY_INPUT = (int)2;
public static final int INCHIKEY_INVALID_INCHI_PREFIX = (int)3;
public static final int INCHIKEY_NOT_ENOUGH_MEMORY = (int)4;
public static final int INCHIKEY_INVALID_INCHI = (int)20;
public static final int INCHIKEY_INVALID_STD_INCHI = (int)21;
public static final int MAX_NUM_STEREO_ATOM_NEIGH = (int)4;
public static final int MAX_NUM_STEREO_BONDS = (int)3;
public static final int INCHI_NUM = (int)2;
/**
* Original signature : void FreeInChIExtInput(inchi_Input_Polymer*, inchi_Input_V3000*)
*/
//public static native void FreeInChIExtInput(inchi_Input_Polymer polymer, inchi_Input_V3000 v3000);
/**
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* 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
* /WMnumber Set time-out per structure in milliseconds; WM0 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)
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* Original signature : int GetINCHI(inchi_Input*, inchi_Output*)
* @param inp
* @param out
* @return
*/
public static native int GetINCHI(tagINCHI_Input inp, tagINCHI_Output out);
/**
* Original signature : int GetStdINCHI(inchi_Input*, inchi_Output*)
* @param inp
* @param out
* @return
*/
public static native int GetStdINCHI(tagINCHI_Input inp, tagINCHI_Output out);
/**
* Extended version of GetINCHI supporting v. 1.05+ extensions: V3000; polymers
* Original signature : int GetINCHIEx(inchi_InputEx*, inchi_Output*)
* @param inp
* @param out
* @return
*/
public static native int GetINCHIEx(inchi_InputEx inp, tagINCHI_Output out);
/**
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* FreeINCHI / FreeStdINCHI
* should be called to deallocate char* pointers
* obtained from each GetINCHI /GetStdINCHI call
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* Original signature : void FreeINCHI(inchi_Output*)
* @param out
*/
public static native void FreeINCHI(tagINCHI_Output out);
/**
* Original signature : void FreeStdINCHI(inchi_Output*)
* @param out
*/
public static native void FreeStdINCHI(tagINCHI_Output out);
/**
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* GetStructFromINCHI / GetStructFromStdINCHI / GetStructFromINCHIEx
* 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 initialized out to zeroes; see FreeStructFromStdINCHI() on how to deallocate it
* Option /Inchi2Struct is not needed for GetStructFromINCHI()/GetStructFromStdINCHI()
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* Original signature : int GetStructFromINCHI(inchi_InputINCHI*, inchi_OutputStruct*)
* @param inpInChI
* @param outStruct
* @return
*/
public static native int GetStructFromINCHI(tagINCHI_InputINCHI inpInChI, tagINCHI_OutputStruct outStruct);
/**
* Original signature : int GetStructFromStdINCHI(inchi_InputINCHI*, inchi_OutputStruct*)
* @param inpInChI
* @param outStruct
* @return
*/
public static native int GetStructFromStdINCHI(tagINCHI_InputINCHI inpInChI, tagINCHI_OutputStruct outStruct);
/**
* Original signature : int GetStructFromINCHIEx(inchi_InputINCHI*, inchi_OutputStructEx*)
* @param inpInChI
* @param outStruct
* @return
*/
public static native int GetStructFromINCHIEx(tagINCHI_InputINCHI inpInChI, tagINCHI_OutputStructEx outStruct);
/**
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* FreeStructFromINCHI / FreeStructFromStdINCHI / FreeStructFromINCHIEx
* should be called to deallocate pointers obtained from each
* GetStructFromStdINCHI / GetStructFromINCHI / GetStructFromINCHIEx
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* Original signature : void FreeStructFromINCHI(inchi_OutputStruct*)
* @param out
*/
public static native void FreeStructFromINCHI(tagINCHI_OutputStruct out);
/**
* Original signature : void FreeStructFromStdINCHI(inchi_OutputStruct*)
* @param out
*/
public static native void FreeStructFromStdINCHI(tagINCHI_OutputStruct out);
/**
* Original signature : void FreeStructFromINCHIEx(inchi_OutputStructEx*)
* @param out
*/
public static native void FreeStructFromINCHIEx(tagINCHI_OutputStructEx 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
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* Original signature : int GetINCHIfromINCHI(inchi_InputINCHI*, inchi_Output*)
* @param inpInChI
* @param out
* @return
*/
public static native int GetINCHIfromINCHI(tagINCHI_InputINCHI inpInChI, tagINCHI_Output out);
/**
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* 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
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* Original signature : int Get_inchi_Input_FromAuxInfo(char*, int, int, InchiInpData*)
* @param szInchiAuxInfo
* @param bDoNotAddH
* @param bDiffUnkUndfStereo
* @param pInchiInp
* @return
*/
public static native int Get_inchi_Input_FromAuxInfo(String szInchiAuxInfo, boolean bDoNotAddH, boolean bDiffUnkUndfStereo, tagInchiInpData pInchiInp);
/**
* Original signature : int Get_std_inchi_Input_FromAuxInfo(char*, int, InchiInpData*)
* @param szInchiAuxInfo
* @param bDoNotAddH
* @param pInchiInp
* @return
*/
public static native int Get_std_inchi_Input_FromAuxInfo(String szInchiAuxInfo, boolean bDoNotAddH, tagInchiInpData pInchiInp);
/**
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* Free_inchi_Input / Free_std_inchi_Input
* To deallocate and write zeroes into the changed members of pInchiInp->pInp call
* Free_inchi_Input( inchi_Input *pInp )
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* Original signature : void Free_inchi_Input(inchi_Input*)
* @param pInp
*/
public static native void Free_inchi_Input(tagINCHI_Input pInp);
/**
* Original signature : void Free_std_inchi_Input(inchi_Input*)
* @param pInp
*/
public static native void Free_std_inchi_Input(tagINCHI_Input pInp);
/**
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* CheckINCHI
* Check if the string represents valid InChI/standard
* 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
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* Original signature : int CheckINCHI(const char*, const int)
* @param szINCHI
* @param strict
* @return
*/
public static native int CheckINCHI(String szINCHI, boolean strict);
/**
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* 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
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* Original signature : int GetINCHIKeyFromINCHI(const char*, const int, const int, char*, char*, char*)
* @param szINCHISource
* @param xtra1
* @param xtra2
* @param szINCHIKey
* @param szXtra1
* @param szXtra2
* @return
*/
public static native int GetINCHIKeyFromINCHI(String szINCHISource, int xtra1, int xtra2, byte[] szINCHIKey, byte[] szXtra1, byte[] 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.
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* Original signature : int GetStdINCHIKeyFromStdINCHI(const char*, char*)
* @param szINCHISource
* @param szINCHIKey
* @return
*/
public static native int GetStdINCHIKeyFromStdINCHI(String szINCHISource, ByteBuffer szINCHIKey);
/**
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* CheckINCHIKey
* Check if the string represents valid InChIKey.
* Input:
* szINCHIKey
* source InChIKey string
* Returns:
* success/errors codes
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* Original signature : int CheckINCHIKey(const char*)
* @param szINCHIKey
* @return
*/
public static native int CheckINCHIKey(String szINCHIKey);
/**
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* INCHIGEN_Create / STDINCHIGEN_Create
* InChI Generator: create generator
* Returns handle of generator object or NULL on failure
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* Original signature : INCHIGEN_HANDLE INCHIGEN_Create()
* @return
*/
public static native Pointer INCHIGEN_Create();
/**
* Original signature : INCHIGEN_HANDLE STDINCHIGEN_Create()
* @return
*/
public static native Pointer STDINCHIGEN_Create();
/**
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* INCHIGEN_Setup / STDINCHIGEN_Setup
* InChI Generator: setup
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* Original signature : int INCHIGEN_Setup(INCHIGEN_HANDLE, INCHIGEN_DATA*, inchi_Input*)
* @param HGen
* @param pGenData
* @param pInp
* @return
*/
public static native int INCHIGEN_Setup(Pointer HGen, tagINCHIGEN_DATA pGenData, tagINCHI_Input pInp);
/**
* Original signature : int STDINCHIGEN_Setup(INCHIGEN_HANDLE, INCHIGEN_DATA*, inchi_Input*)
* @param HGen
* @param pGenData
* @param pInp
* @return
*/
public static native int STDINCHIGEN_Setup(Pointer HGen, tagINCHIGEN_DATA pGenData, tagINCHI_Input pInp);
/**
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* INCHIGEN_DoNormalization / STDINCHIGEN_DoNormalization
* InChI Generator: structure normalization stage
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* Original signature : int INCHIGEN_DoNormalization(INCHIGEN_HANDLE, INCHIGEN_DATA*)
* @param HGen
* @param pGenData
* @return
*/
public static native int INCHIGEN_DoNormalization(Pointer HGen, tagINCHIGEN_DATA pGenData);
/**
* Original signature : int STDINCHIGEN_DoNormalization(INCHIGEN_HANDLE, INCHIGEN_DATA*)
* @param HGen
* @param pGenData
* @return
*/
public static native int STDINCHIGEN_DoNormalization(Pointer HGen, tagINCHIGEN_DATA pGenData);
/**
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* INCHIGEN_DoCanonicalization / STDINCHIGEN_DoCanonicalization
* InChI Generator: structure canonicalization stage
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* Original signature : int INCHIGEN_DoCanonicalization(INCHIGEN_HANDLE, INCHIGEN_DATA*)
* @param HGen
* @param pGenData
* @return
*/
public static native int INCHIGEN_DoCanonicalization(Pointer HGen, tagINCHIGEN_DATA pGenData);
/**
* Original signature : int STDINCHIGEN_DoCanonicalization(INCHIGEN_HANDLE, INCHIGEN_DATA*)
* @param HGen
* @param pGenData
* @return
*/
public static native int STDINCHIGEN_DoCanonicalization(Pointer HGen, tagINCHIGEN_DATA pGenData);
/**
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* INCHIGEN_DoSerialization / STDINCHIGEN_DoSerialization
* InChI Generator: InChI serialization stage
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* Original signature : int INCHIGEN_DoSerialization(INCHIGEN_HANDLE, INCHIGEN_DATA*, inchi_Output*)
* @param HGen
* @param pGenData
* @param pResults
* @return
*/
public static native int INCHIGEN_DoSerialization(Pointer HGen, tagINCHIGEN_DATA pGenData, tagINCHI_Output pResults);
/**
* Original signature : int STDINCHIGEN_DoSerialization(INCHIGEN_HANDLE, INCHIGEN_DATA*, inchi_Output*)
* @param HGen
* @param pGenData
* @param pResults
* @return
*/
public static native int STDINCHIGEN_DoSerialization(Pointer HGen, tagINCHIGEN_DATA pGenData, tagINCHI_Output pResults);
/**
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* INCHIGEN_Reset / STDINCHIGEN_Reset
* InChI Generator: reset stage (use before get next structure)
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* Original signature : void INCHIGEN_Reset(INCHIGEN_HANDLE, INCHIGEN_DATA*, inchi_Output*)
* @param HGen
* @param pGenData
* @param pResults
*/
public static native void INCHIGEN_Reset(Pointer HGen, tagINCHIGEN_DATA pGenData, tagINCHI_Output pResults);
/**
* Original signature : void STDINCHIGEN_Reset(INCHIGEN_HANDLE, INCHIGEN_DATA*, inchi_Output*)
* @param HGen
* @param pGenData
* @param pResults
*/
public static native void STDINCHIGEN_Reset(Pointer HGen, tagINCHIGEN_DATA pGenData, tagINCHI_Output pResults);
/**
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* INCHIGEN_Destroy / STDINCHIGEN_Destroy
* InChI Generator: destroy generator
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* Original signature : void INCHIGEN_Destroy(INCHIGEN_HANDLE)
* @param HGen
*/
public static native void INCHIGEN_Destroy(Pointer HGen);
/**
* Original signature : void STDINCHIGEN_Destroy(INCHIGEN_HANDLE)
* @param HGen
*/
public static native void STDINCHIGEN_Destroy(Pointer HGen);
/**
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* MakeINCHIFromMolfileText
* Direct generation of InChI from Molfile supplied as text
* ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* Original signature : int MakeINCHIFromMolfileText(const char*, char*, inchi_Output*)
* @param moltext
* @param options
* @param result
* @return
*/
public static native int MakeINCHIFromMolfileText(String moltext, String options, tagINCHI_Output result);
/** enum values */
public static interface IXA_STATUS {
public static final int IXA_STATUS_SUCCESS = 0;
public static final int IXA_STATUS_WARNING = 1;
public static final int IXA_STATUS_ERROR = 2;
};
/** enum values */
public static interface IXA_ATOM_RADICAL {
public static final int IXA_ATOM_RADICAL_NONE = 0;
public static final int IXA_ATOM_RADICAL_SINGLET = 1;
public static final int IXA_ATOM_RADICAL_DOUBLET = 2;
public static final int IXA_ATOM_RADICAL_TRIPLET = 3;
};
/** enum values */
public static interface IXA_BOND_TYPE {
public static final int IXA_BOND_TYPE_SINGLE = 1;
public static final int IXA_BOND_TYPE_DOUBLE = 2;
public static final int IXA_BOND_TYPE_TRIPLE = 3;
public static final int IXA_BOND_TYPE_AROMATIC = 4;
};
/** enum values */
public static interface IXA_BOND_WEDGE {
public static final int IXA_BOND_WEDGE_NONE = 0;
public static final int IXA_BOND_WEDGE_UP = 1;
public static final int IXA_BOND_WEDGE_DOWN = 2;
public static final int IXA_BOND_WEDGE_EITHER = 3;
};
/** enum values */
public static interface IXA_DBLBOND_CONFIG {
public static final int IXA_DBLBOND_CONFIG_PERCEIVE = 0;
public static final int IXA_DBLBOND_CONFIG_EITHER = 1;
};
/** enum values */
public static interface IXA_STEREO_TOPOLOGY {
public static final int IXA_STEREO_TOPOLOGY_INVALID = 0;
public static final int IXA_STEREO_TOPOLOGY_TETRAHEDRON = 2;
public static final int IXA_STEREO_TOPOLOGY_RECTANGLE = 3;
public static final int IXA_STEREO_TOPOLOGY_ANTIRECTANGLE = 4;
};
/** enum values */
public static interface IXA_STEREO_PARITY {
public static final int IXA_STEREO_PARITY_NONE = 0;
public static final int IXA_STEREO_PARITY_ODD = 1;
public static final int IXA_STEREO_PARITY_EVEN = 2;
public static final int IXA_STEREO_PARITY_UNKNOWN = 3;
};
/** enum values */
public static interface IXA_INCHIBUILDER_OPTION {
public static final int IXA_INCHIBUILDER_OPTION_NewPsOff = 0;
public static final int IXA_INCHIBUILDER_OPTION_DoNotAddH = 1;
public static final int IXA_INCHIBUILDER_OPTION_SUU = 2;
public static final int IXA_INCHIBUILDER_OPTION_SLUUD = 3;
public static final int IXA_INCHIBUILDER_OPTION_FixedH = 4;
public static final int IXA_INCHIBUILDER_OPTION_RecMet = 5;
public static final int IXA_INCHIBUILDER_OPTION_KET = 6;
public static final int IXA_INCHIBUILDER_OPTION_15T = 7;
public static final int IXA_INCHIBUILDER_OPTION_SaveOpt = 8;
public static final int IXA_INCHIBUILDER_OPTION_AuxNone = 9;
public static final int IXA_INCHIBUILDER_OPTION_WarnOnEmptyStructure = 10;
public static final int IXA_INCHIBUILDER_OPTION_LargeMolecules = 11;
public static final int IXA_INCHIBUILDER_OPTION_Polymers = 12;
public static final int IXA_INCHIBUILDER_OPTION_Polymers105 = 13;
public static final int IXA_INCHIBUILDER_OPTION_Polymers105Plus = 14;
public static final int IXA_INCHIBUILDER_OPTION_FilterSS = 15;
public static final int IXA_INCHIBUILDER_OPTION_InvFilterSS = 16;
public static final int IXA_INCHIBUILDER_OPTION_NPZZ = 17;
public static final int IXA_INCHIBUILDER_OPTION_SATZZ = 18;
public static final int IXA_INCHIBUILDER_OPTION_NoFrameShift = 19;
public static final int IXA_INCHIBUILDER_OPTION_FoldCRU = 20;
public static final int IXA_INCHIBUILDER_OPTION_NoEdits = 21;
public static final int IXA_INCHIBUILDER_OPTION_LooseTSACheck = 22;
public static final int IXA_INCHIBUILDER_OPTION_OutErrInChI = 23;
public static final int IXA_INCHIBUILDER_OPTION_NoWarnings = 24;
};
/** enum values */
public static interface IXA_INCHIBUILDER_STEREOOPTION {
public static final int IXA_INCHIBUILDER_STEREOOPTION_SAbs = 0;
public static final int IXA_INCHIBUILDER_STEREOOPTION_SNon = 1;
public static final int IXA_INCHIBUILDER_STEREOOPTION_SRel = 2;
public static final int IXA_INCHIBUILDER_STEREOOPTION_SRac = 3;
public static final int IXA_INCHIBUILDER_STEREOOPTION_SUCF = 4;
};
public static final int IXA_ATOM_NATURAL_MASS = (int)0;
public static final int IXA_EXT_MOLDATA_INVALID = (int)(-1);
public static final int IXA_EXT_POLYMER_INVALID = (int)(-1);
public static final int IXA_EXT_V3000_INVALID = (int)(-1);
public static final int IXA_USES_SMART_ALLOCS = (int)1;
/*
* Functions handling IXA Status Objects
*/
/**
* Original signature : INCHI_DECL IXA_STATUS_Create()
* @return
*/
static native Pointer IXA_STATUS_Create();
/**
* Original signature : INCHI_DECL IXA_STATUS_Clear(Pointer)
* @param hStatus
*/
static native void IXA_STATUS_Clear(Pointer hStatus);
/**
* Original signature : INCHI_DECL IXA_STATUS_Destroy(Pointer)
* @param hStatus
*/
static native void IXA_STATUS_Destroy(Pointer hStatus);
/**
* Original signature : INCHI_DECL IXA_STATUS_HasError(Pointer)
* @param hStatus
* @return
*/
static native boolean IXA_STATUS_HasError(Pointer hStatus);
/**
* Original signature : INCHI_DECL IXA_STATUS_HasWarning(Pointer)
* @param hStatus
* @return
*/
static native boolean IXA_STATUS_HasWarning(Pointer hStatus);
/**
* Original signature : INCHI_DECL IXA_STATUS_GetCount(Pointer)
* @param hStatus
* @return
*/
static native int IXA_STATUS_GetCount(Pointer hStatus);
/**
* Original signature : INCHI_DECL IXA_STATUS_GetSeverity(Pointer, int)
* @param hStatus
* @param vIndex
* @return
*/
static native int IXA_STATUS_GetSeverity(Pointer hStatus, int vIndex);
/**
* Original signature : INCHI_DECL IXA_STATUS_GetMessage(Pointer, int)
* @param hStatus
* @param vIndex
* @return
*/
static native String IXA_STATUS_GetMessage(Pointer hStatus, int vIndex);
/*
* Functions to Create, Clear and Destroy Molecule Objects
*/
/**
* Original signature : INCHI_DECL IXA_MOL_Create(Pointer)
* @param hStatus
* @return
*/
static native Pointer IXA_MOL_Create(Pointer hStatus);
/**
* Original signature : INCHI_DECL IXA_MOL_Clear(Pointer, Pointer)
* @param hStatus
* @param hMolecule
*/
static native void IXA_MOL_Clear(Pointer hStatus, Pointer hMolecule);
/**
* Original signature : INCHI_DECL IXA_MOL_Destroy(Pointer, Pointer)
* @param hStatus
* @param hMolecule
*/
static native void IXA_MOL_Destroy(Pointer hStatus, Pointer hMolecule);
/*
* Functions Operating on Complete Molecules
*/
/**
* Original signature : INCHI_DECL IXA_MOL_ReadMolfile(Pointer, Pointer, const char*)
* @param hStatus
* @param hMolecule
* @param pBytes
*/
static native void IXA_MOL_ReadMolfile(Pointer hStatus, Pointer hMolecule, byte[] pBytes);
/**
* Original signature : INCHI_DECL IXA_MOL_ReadInChI(Pointer, Pointer, const char*)
* @param hStatus
* @param hMolecule
* @param pInChI
*/
static native void IXA_MOL_ReadInChI(Pointer hStatus, Pointer hMolecule, byte[] pInChI);
/**
* Original signature : INCHI_DECL IXA_MOL_SetChiral(Pointer, Pointer, IXA_BOOL)
* @param hStatus
* @param hMolecule
* @param vChiral
*/
static native void IXA_MOL_SetChiral(Pointer hStatus, Pointer hMolecule, boolean vChiral);
/**
* Original signature : INCHI_DECL IXA_MOL_GetChiral(Pointer, Pointer)
* @param hStatus
* @param hMolecule
* @return
*/
static native boolean IXA_MOL_GetChiral(Pointer hStatus, Pointer hMolecule);
/*
* Functions to Add and Define Atoms
*/
/**
* Original signature : INCHI_DECL IXA_MOL_CreateAtom(Pointer, Pointer)
* @param hStatus
* @param hMolecule
* @return
*/
static native Pointer IXA_MOL_CreateAtom(Pointer hStatus, Pointer hMolecule);
/**
* Original signature : INCHI_DECL IXA_MOL_SetAtomElement(Pointer, Pointer, Pointer, const char*)
* @param hStatus
* @param hMolecule
* @param vAtom
* @param pElement
*/
static native void IXA_MOL_SetAtomElement(Pointer hStatus, Pointer hMolecule, Pointer vAtom, byte[] pElement);
/**
* Original signature : INCHI_DECL IXA_MOL_SetAtomAtomicNumber(Pointer, Pointer, Pointer, int)
* @param hStatus
* @param hMolecule
* @param vAtom
* @param vAtomicNumber
*/
static native void IXA_MOL_SetAtomAtomicNumber(Pointer hStatus, Pointer hMolecule, Pointer vAtom, int vAtomicNumber);
/**
* Original signature : INCHI_DECL IXA_MOL_SetAtomMass(Pointer, Pointer, Pointer, int)
* @param hStatus
* @param hMolecule
* @param vAtom
* @param vMassNumber
*/
static native void IXA_MOL_SetAtomMass(Pointer hStatus, Pointer hMolecule, Pointer vAtom, int vMassNumber);
/**
* Original signature : INCHI_DECL IXA_MOL_SetAtomCharge(Pointer, Pointer, Pointer, int)
* @param hStatus
* @param hMolecule
* @param vAtom
* @param vCharge
*/
static native void IXA_MOL_SetAtomCharge(Pointer hStatus, Pointer hMolecule, Pointer vAtom, int vCharge);
/**
* Original signature : INCHI_DECL IXA_MOL_SetAtomRadical(Pointer, Pointer, Pointer, IXA_ATOM_RADICAL)
* @param hStatus
* @param hMolecule
* @param vAtom
* @param vRadical
*/
static native void IXA_MOL_SetAtomRadical(Pointer hStatus, Pointer hMolecule, Pointer vAtom, int vRadical);
/**
* Original signature : INCHI_DECL IXA_MOL_SetAtomHydrogens(Pointer, Pointer, Pointer, int, int)
* @param hStatus
* @param hMolecule
* @param vAtom
* @param vHydrogenMassNumber
* @param vHydrogenCount
*/
static native void IXA_MOL_SetAtomHydrogens(Pointer hStatus, Pointer hMolecule, Pointer vAtom, int vHydrogenMassNumber, int vHydrogenCount);
/**
* Original signature : INCHI_DECL IXA_MOL_SetAtomX(Pointer, Pointer, Pointer, double)
* @param hStatus
* @param hMolecule
* @param vAtom
* @param vX
*/
static native void IXA_MOL_SetAtomX(Pointer hStatus, Pointer hMolecule, Pointer vAtom, double vX);
/**
* Original signature : INCHI_DECL IXA_MOL_SetAtomY(Pointer, Pointer, Pointer, double)
* @param hStatus
* @param hMolecule
* @param vAtom
* @param vY
*/
static native void IXA_MOL_SetAtomY(Pointer hStatus, Pointer hMolecule, Pointer vAtom, double vY);
/**
* Original signature : INCHI_DECL IXA_MOL_SetAtomZ(Pointer, Pointer, Pointer, double)
* @param hStatus
* @param hMolecule
* @param vAtom
* @param vZ
*/
static native void IXA_MOL_SetAtomZ(Pointer hStatus, Pointer hMolecule, Pointer vAtom, double vZ);
/*
* Functions to Add and Define Bonds
*/
/**
* Original signature : INCHI_DECL IXA_MOL_CreateBond(Pointer, Pointer, Pointer, Pointer)
* @param hStatus
* @param hMolecule
* @param vAtom1
* @param vAtom2
* @return
*/
static native Pointer IXA_MOL_CreateBond(Pointer hStatus, Pointer hMolecule, Pointer vAtom1, Pointer vAtom2);
/**
* Original signature : INCHI_DECL IXA_MOL_SetBondType(Pointer, Pointer, Pointer, IXA_BOND_TYPE)
* @param hStatus
* @param hMolecule
* @param vBond
* @param vType
*/
static native void IXA_MOL_SetBondType(Pointer hStatus, Pointer hMolecule, Pointer vBond, int vType);
/**
* Original signature : INCHI_DECL IXA_MOL_SetBondWedge(Pointer, Pointer, Pointer, Pointer, IXA_BOND_WEDGE)
* @param hStatus
* @param hMolecule
* @param vBond
* @param vRefAtom
* @param vDirection
*/
static native void IXA_MOL_SetBondWedge(Pointer hStatus, Pointer hMolecule, Pointer vBond, Pointer vRefAtom, int vDirection);
/**
* Original signature : INCHI_DECL IXA_MOL_SetDblBondConfig(Pointer, Pointer, Pointer, IXA_DBLBOND_CONFIG)
* @param hStatus
* @param hMolecule
* @param vBond
* @param vConfig
*/
static native void IXA_MOL_SetDblBondConfig(Pointer hStatus, Pointer hMolecule, Pointer vBond, int vConfig);
/*
* Functions to Add and Define Stereodescriptors
*/
/**
* Original signature : INCHI_DECL IXA_MOL_CreateStereoTetrahedron(Pointer, Pointer, Pointer, Pointer, Pointer, Pointer, Pointer)
* @param hStatus
* @param hMolecule
* @param vCentralAtom
* @param vVertex1
* @param vVertex2
* @param vVertex3
* @param vVertex4
* @return
*/
static native Pointer IXA_MOL_CreateStereoTetrahedron(Pointer hStatus, Pointer hMolecule, Pointer vCentralAtom, Pointer vVertex1, Pointer vVertex2, Pointer vVertex3, Pointer vVertex4);
/**
* Original signature : INCHI_DECL IXA_MOL_CreateStereoRectangle(Pointer, Pointer, Pointer, Pointer, Pointer, Pointer, Pointer)
* @param hStatus
* @param hMolecule
* @param vCentralBond
* @param vVertex1
* @param vVertex2
* @param vVertex3
* @param vVertex4
* @return
*/
static native Pointer IXA_MOL_CreateStereoRectangle(Pointer hStatus, Pointer hMolecule, Pointer vCentralBond, Pointer vVertex1, Pointer vVertex2, Pointer vVertex3, Pointer vVertex4);
/**
* Original signature : INCHI_DECL IXA_MOL_CreateStereoAntiRectangle(Pointer, Pointer, Pointer, Pointer, Pointer, Pointer, Pointer)
* @param hStatus
* @param hMolecule
* @param vCentralAtom
* @param vVertex1
* @param vVertex2
* @param vVertex3
* @param vVertex4
* @return
*/
static native Pointer IXA_MOL_CreateStereoAntiRectangle(Pointer hStatus, Pointer hMolecule, Pointer vCentralAtom, Pointer vVertex1, Pointer vVertex2, Pointer vVertex3, Pointer vVertex4);
/**
* Original signature : INCHI_DECL IXA_MOL_SetStereoParity(Pointer, Pointer, Pointer, IXA_STEREO_PARITY)
* @param hStatus
* @param hMolecule
* @param vStereo
* @param vParity
*/
static native void IXA_MOL_SetStereoParity(Pointer hStatus, Pointer hMolecule, Pointer vStereo, int vParity);
/**
* Original signature : INCHI_DECL IXA_MOL_ReserveSpace(IXA_STATUS_HANDLE, IXA_MOL_HANDLE, int, int, int)
* @param hStatus
* @param hMolecule
* @param num_atoms
* @param num_bonds
* @param num_stereos
* @return
*/
static native int IXA_MOL_ReserveSpace(Pointer hStatus, Pointer hMolecule, int num_atoms, int num_bonds, int num_stereos);
/*
* Functions to to Treat Extended molecular data
*/
//FIXME IXA_MOL_CreatePolymerUnit and IXA_MOL_SetPolymerUnit are missing from Linux build
/**
* Original signature : INCHI_DECL IXA_MOL_CreatePolymerUnit(IXA_STATUS_HANDLE, IXA_MOL_HANDLE)
* @param hStatus
* @param hMolecule
* @return
*/
//static native Pointer IXA_MOL_CreatePolymerUnit(Pointer hStatus, Pointer hMolecule);
/**
* Original signature : INCHI_DECL IXA_MOL_SetPolymerUnit(IXA_STATUS_HANDLE, IXA_MOL_HANDLE, IXA_POLYMERUNITID, int, int, int, int, int, int, int, double[4], double[4], char[80], int*, int*)
* @param hStatus
* @param hMolecule
* @param vPunit
* @param vid
* @param vtype
* @param vsubtype
* @param vconn
* @param vlabel
* @param vna
* @param vnb
* @param vxbr1
* @param vxbr2
* @param vsmt
* @param valist
* @param vblist
*/
//static native void IXA_MOL_SetPolymerUnit(Pointer hStatus, Pointer hMolecule, Pointer vPunit, int vid, int vtype, int vsubtype, int vconn, int vlabel, int vna, int vnb, DoubleBuffer vxbr1, DoubleBuffer vxbr2, ByteBuffer vsmt, IntBuffer valist, IntBuffer vblist);
/*
* Functions to Navigate Within a Molecule
*/
/**
* Original signature : INCHI_DECL IXA_MOL_GetNumAtoms(Pointer, Pointer)
* @param hStatus
* @param hMolecule
* @return
*/
static native int IXA_MOL_GetNumAtoms(Pointer hStatus, Pointer hMolecule);
/**
* Original signature : INCHI_DECL IXA_MOL_GetNumBonds(Pointer, Pointer)
* @param hStatus
* @param hMolecule
* @return
*/
static native int IXA_MOL_GetNumBonds(Pointer hStatus, Pointer hMolecule);
/**
* Original signature : INCHI_DECL IXA_MOL_GetAtomId(Pointer, Pointer, int)
* @param hStatus
* @param hMolecule
* @param vAtomIndex
* @return
*/
static native Pointer IXA_MOL_GetAtomId(Pointer hStatus, Pointer hMolecule, int vAtomIndex);
/**
* Original signature : INCHI_DECL IXA_MOL_GetBondId(Pointer, Pointer, int)
* @param hStatus
* @param hMolecule
* @param vBondIndex
* @return
*/
static native Pointer IXA_MOL_GetBondId(Pointer hStatus, Pointer hMolecule, int vBondIndex);
/**
* Original signature : INCHI_DECL IXA_MOL_GetAtomIndex(Pointer, Pointer, Pointer)
* @param hStatus
* @param hMolecule
* @param vAtom
* @return
*/
static native int IXA_MOL_GetAtomIndex(Pointer hStatus, Pointer hMolecule, Pointer vAtom);
/**
* Original signature : INCHI_DECL IXA_MOL_GetBondIndex(Pointer, Pointer, Pointer)
* @param hStatus
* @param hMolecule
* @param vBond
* @return
*/
static native int IXA_MOL_GetBondIndex(Pointer hStatus, Pointer hMolecule, Pointer vBond);
/**
* Original signature : INCHI_DECL IXA_MOL_GetAtomNumBonds(Pointer, Pointer, Pointer)
* @param hStatus
* @param hMolecule
* @param vAtom
* @return
*/
static native int IXA_MOL_GetAtomNumBonds(Pointer hStatus, Pointer hMolecule, Pointer vAtom);
//FIXME IXA_MOL_GetPolymerUnitId and IXA_MOL_GetPolymerUnitIndex are missing from Linux build
/**
* Original signature : INCHI_DECL IXA_MOL_GetPolymerUnitId(IXA_STATUS_HANDLE, IXA_MOL_HANDLE, int)
* @param hStatus
* @param hMolecule
* @param vPolymerUnitIndex
* @return
*/
//static native Pointer IXA_MOL_GetPolymerUnitId(Pointer hStatus, Pointer hMolecule, int vPolymerUnitIndex);
/**
* Original signature : INCHI_DECL IXA_MOL_GetPolymerUnitIndex(IXA_STATUS_HANDLE, IXA_MOL_HANDLE, IXA_POLYMERUNITID)
* @param hStatus
* @param hMolecule
* @param vPolymerUnit
* @return
*/
//static native int IXA_MOL_GetPolymerUnitIndex(Pointer hStatus, Pointer hMolecule, Pointer vPolymerUnit);
/**
* Original signature : INCHI_DECL IXA_MOL_GetAtomBond(Pointer, Pointer, Pointer, int)
* @param hStatus
* @param hMolecule
* @param vAtom
* @param vBondIndex
* @return
*/
static native Pointer IXA_MOL_GetAtomBond(Pointer hStatus, Pointer hMolecule, Pointer vAtom, int vBondIndex);
/**
* Original signature : INCHI_DECL IXA_MOL_GetCommonBond(Pointer, Pointer, Pointer, Pointer)
* @param hStatus
* @param hMolecule
* @param vAtom1
* @param vAtom2
* @return
*/
static native Pointer IXA_MOL_GetCommonBond(Pointer hStatus, Pointer hMolecule, Pointer vAtom1, Pointer vAtom2);
/**
* Original signature : INCHI_DECL IXA_MOL_GetBondAtom1(Pointer, Pointer, Pointer)
* @param hStatus
* @param hMolecule
* @param vBond
* @return
*/
static native Pointer IXA_MOL_GetBondAtom1(Pointer hStatus, Pointer hMolecule, Pointer vBond);
/**
* Original signature : INCHI_DECL IXA_MOL_GetBondAtom2(Pointer, Pointer, Pointer)
* @param hStatus
* @param hMolecule
* @param vBond
* @return
*/
static native Pointer IXA_MOL_GetBondAtom2(Pointer hStatus, Pointer hMolecule, Pointer vBond);
/**
* Original signature : INCHI_DECL IXA_MOL_GetBondOtherAtom(IXA_STATUS_HANDLE, IXA_MOL_HANDLE, IXA_BONDID, IXA_ATOMID)
* @param hStatus
* @param hMolecule
* @param vBond
* @param vAtom
* @return
*/
static native Pointer IXA_MOL_GetBondOtherAtom(Pointer hStatus, Pointer hMolecule, Pointer vBond, Pointer vAtom);
/*
* Functions to Return Information About Atoms
*/
/**
* Original signature : INCHI_DECL IXA_MOL_GetAtomElement(Pointer, Pointer, Pointer)
* @param hStatus
* @param hMolecule
* @param vAtom
* @return
*/
static native String IXA_MOL_GetAtomElement(Pointer hStatus, Pointer hMolecule, Pointer vAtom);
/**
* Original signature : INCHI_DECL IXA_MOL_GetAtomAtomicNumber(Pointer, Pointer, Pointer)
* @param hStatus
* @param hMolecule
* @param vAtom
* @return
*/
static native int IXA_MOL_GetAtomAtomicNumber(Pointer hStatus, Pointer hMolecule, Pointer vAtom);
/**
* Original signature : INCHI_DECL IXA_MOL_GetAtomMass(Pointer, Pointer, Pointer)
* @param hStatus
* @param hMolecule
* @param vAtom
* @return
*/
static native int IXA_MOL_GetAtomMass(Pointer hStatus, Pointer hMolecule, Pointer vAtom);
/**
* Original signature : INCHI_DECL IXA_MOL_GetAtomCharge(Pointer, Pointer, Pointer)
* @param hStatus
* @param hMolecule
* @param vAtom
* @return
*/
static native int IXA_MOL_GetAtomCharge(Pointer hStatus, Pointer hMolecule, Pointer vAtom);
/**
* Original signature : INCHI_DECL IXA_MOL_GetAtomRadical(Pointer, Pointer, Pointer)
* @param hStatus
* @param hMolecule
* @param vAtom
* @return
*/
static native int IXA_MOL_GetAtomRadical(Pointer hStatus, Pointer hMolecule, Pointer vAtom);
/**
* Original signature : INCHI_DECL IXA_MOL_GetAtomHydrogens(Pointer, Pointer, Pointer, int)
* @param hStatus
* @param hMolecule
* @param vAtom
* @param vHydrogenMassNumber
* @return
*/
static native int IXA_MOL_GetAtomHydrogens(Pointer hStatus, Pointer hMolecule, Pointer vAtom, int vHydrogenMassNumber);
/**
* Original signature : INCHI_DECL IXA_MOL_GetAtomX(Pointer, Pointer, Pointer)
* @param hStatus
* @param hMolecule
* @param vAtom
* @return
*/
static native double IXA_MOL_GetAtomX(Pointer hStatus, Pointer hMolecule, Pointer vAtom);
/**
* Original signature : INCHI_DECL IXA_MOL_GetAtomY(Pointer, Pointer, Pointer)
* @param hStatus
* @param hMolecule
* @param vAtom
* @return
*/
static native double IXA_MOL_GetAtomY(Pointer hStatus, Pointer hMolecule, Pointer vAtom);
/**
* Original signature : INCHI_DECL IXA_MOL_GetAtomZ(Pointer, Pointer, Pointer)
* @param hStatus
* @param hMolecule
* @param vAtom
* @return
*/
static native double IXA_MOL_GetAtomZ(Pointer hStatus, Pointer hMolecule, Pointer vAtom);
/*
* Functions to Return Information About Bonds
*/
/**
* Original signature : INCHI_DECL IXA_MOL_GetBondType(Pointer, Pointer, Pointer)
* @param hStatus
* @param hMolecule
* @param vBond
* @return
*/
static native int IXA_MOL_GetBondType(Pointer hStatus, Pointer hMolecule, Pointer vBond);
/**
* Original signature : INCHI_DECL IXA_MOL_GetBondWedge(Pointer, Pointer, Pointer, Pointer)
* @param hStatus
* @param hMolecule
* @param vBond
* @param vRefAtom
* @return
*/
static native int IXA_MOL_GetBondWedge(Pointer hStatus, Pointer hMolecule, Pointer vBond, Pointer vRefAtom);
/**
* Original signature : INCHI_DECL IXA_MOL_GetDblBondConfig(Pointer, Pointer, Pointer)
* @param hStatus
* @param hMolecule
* @param vBond
* @return
*/
static native int IXA_MOL_GetDblBondConfig(Pointer hStatus, Pointer hMolecule, Pointer vBond);
/*
* Functions to return Information About Stereodescriptors
*/
/**
* Original signature : INCHI_DECL IXA_MOL_GetNumStereos(Pointer, Pointer)
* @param hStatus
* @param hMolecule
* @return
*/
static native int IXA_MOL_GetNumStereos(Pointer hStatus, Pointer hMolecule);
/**
* Original signature : INCHI_DECL IXA_MOL_GetStereoId(Pointer, Pointer, int)
* @param hStatus
* @param hMolecule
* @param vStereoIndex
* @return
*/
static native Pointer IXA_MOL_GetStereoId(Pointer hStatus, Pointer hMolecule, int vStereoIndex);
/**
* Original signature : INCHI_DECL IXA_MOL_GetStereoIndex(Pointer, Pointer, Pointer)
* @param hStatus
* @param hMolecule
* @param vStereo
* @return
*/
static native int IXA_MOL_GetStereoIndex(Pointer hStatus, Pointer hMolecule, Pointer vStereo);
/**
* Original signature : INCHI_DECL IXA_MOL_GetStereoTopology(Pointer, Pointer, Pointer)
* @param hStatus
* @param hMolecule
* @param vStereo
* @return
*/
static native int IXA_MOL_GetStereoTopology(Pointer hStatus, Pointer hMolecule, Pointer vStereo);
/**
* Original signature : INCHI_DECL IXA_MOL_GetStereoCentralAtom(Pointer, Pointer, Pointer)
* @param hStatus
* @param hMolecule
* @param vStereo
* @return
*/
static native Pointer IXA_MOL_GetStereoCentralAtom(Pointer hStatus, Pointer hMolecule, Pointer vStereo);
/**
* Original signature : INCHI_DECL IXA_MOL_GetStereoCentralBond(Pointer, Pointer, Pointer)
* @param hStatus
* @param hMolecule
* @param vStereo
* @return
*/
static native Pointer IXA_MOL_GetStereoCentralBond(Pointer hStatus, Pointer hMolecule, Pointer vStereo);
/**
* Original signature : INCHI_DECL IXA_MOL_GetStereoNumVertices(Pointer, Pointer, Pointer)
* @param hStatus
* @param hMolecule
* @param vStereo
* @return
*/
static native int IXA_MOL_GetStereoNumVertices(Pointer hStatus, Pointer hMolecule, Pointer vStereo);
/**
* Original signature : INCHI_DECL IXA_MOL_GetStereoVertex(Pointer, Pointer, Pointer, int)
* @param hStatus
* @param hMolecule
* @param vStereo
* @param vVertexIndex
* @return
*/
static native Pointer IXA_MOL_GetStereoVertex(Pointer hStatus, Pointer hMolecule, Pointer vStereo, int vVertexIndex);
/**
* Original signature : INCHI_DECL IXA_MOL_GetStereoParity(Pointer, Pointer, Pointer)
* @param hStatus
* @param hMolecule
* @param vStereo
* @return
*/
static native int IXA_MOL_GetStereoParity(Pointer hStatus, Pointer hMolecule, Pointer vStereo);
/*
* Functions for Generating InChIs
*/
/**
* Original signature : INCHI_DECL IXA_INCHIBUILDER_Create(Pointer)
* @param hStatus
* @return
*/
static native Pointer IXA_INCHIBUILDER_Create(Pointer hStatus);
/**
* Original signature : INCHI_DECL IXA_INCHIBUILDER_SetMolecule(Pointer, Pointer, Pointer)
* @param hStatus
* @param hInChIBuilder
* @param hMolecule
*/
static native void IXA_INCHIBUILDER_SetMolecule(Pointer hStatus, Pointer hInChIBuilder, Pointer hMolecule);
/**
* Original signature : INCHI_DECL IXA_INCHIBUILDER_GetInChI(Pointer, Pointer)
* @param hStatus
* @param hInChIBuilder
* @return
*/
static native String IXA_INCHIBUILDER_GetInChI(Pointer hStatus, Pointer hInChIBuilder);
/**
* Original signature : INCHI_DECL IXA_INCHIBUILDER_GetInChIEx(Pointer, Pointer)
* @param hStatus
* @param hBuilder
* @return
*/
static native String IXA_INCHIBUILDER_GetInChIEx(Pointer hStatus, Pointer hBuilder);
/**
* Original signature : INCHI_DECL IXA_INCHIBUILDER_GetAuxInfo(Pointer, Pointer)
* @param hStatus
* @param hInChIBuilder
* @return
*/
static native String IXA_INCHIBUILDER_GetAuxInfo(Pointer hStatus, Pointer hInChIBuilder);
/**
* Original signature : INCHI_DECL IXA_INCHIBUILDER_GetLog(Pointer, Pointer)
* @param hStatus
* @param hInChIBuilder
* @return
*/
static native String IXA_INCHIBUILDER_GetLog(Pointer hStatus, Pointer hInChIBuilder);
/**
* Original signature : INCHI_DECL IXA_INCHIBUILDER_Destroy(Pointer, Pointer)
* @param hStatus
* @param hInChIBuilder
*/
static native void IXA_INCHIBUILDER_Destroy(Pointer hStatus, Pointer hInChIBuilder);
/*
* Functions for Specifying InChI Generation Options
*/
/**
* Original signature : INCHI_DECL IXA_INCHIBUILDER_SetOption(Pointer, Pointer, IXA_INCHIBUILDER_OPTION, IXA_BOOL)
* @param hStatus
* @param hInChIBuilder
* @param vOption
* @param vValue
*/
static native void IXA_INCHIBUILDER_SetOption(Pointer hStatus, Pointer hInChIBuilder, int vOption, boolean vValue);
/**
* Original signature : INCHI_DECL IXA_INCHIBUILDER_SetOption_Stereo(Pointer, Pointer, IXA_INCHIBUILDER_STEREOOPTION)
* @param hStatus
* @param hInChIBuilder
* @param vValue
*/
static native void IXA_INCHIBUILDER_SetOption_Stereo(Pointer hStatus, Pointer hInChIBuilder, int vValue);
/**
* Original signature : INCHI_DECL IXA_INCHIBUILDER_SetOption_Timeout(Pointer, Pointer, int)
* @param hStatus
* @param hInChIBuilder
* @param vValue
*/
static native void IXA_INCHIBUILDER_SetOption_Timeout(Pointer hStatus, Pointer hInChIBuilder, int vValue);
/**
* Original signature : INCHI_DECL IXA_INCHIBUILDER_SetOption_Timeout_MilliSeconds(IXA_STATUS_HANDLE, IXA_INCHIBUILDER_HANDLE, long)
* @param hStatus
* @param hInChIBuilder
* @param vValue
*/
static native void IXA_INCHIBUILDER_SetOption_Timeout_MilliSeconds(Pointer hStatus, Pointer hInChIBuilder, long vValue);
/**
* Original signature : INCHI_DECL IXA_INCHIBUILDER_CheckOption(IXA_STATUS_HANDLE, IXA_INCHIBUILDER_HANDLE, IXA_INCHIBUILDER_OPTION)
* @param hStatus
* @param hInChIBuilder
* @param vOption
* @return
*/
static native boolean IXA_INCHIBUILDER_CheckOption(Pointer hStatus, Pointer hInChIBuilder, int vOption);
/**
* Original signature : INCHI_DECL IXA_INCHIBUILDER_CheckOption_Stereo(IXA_STATUS_HANDLE, IXA_INCHIBUILDER_HANDLE, IXA_INCHIBUILDER_STEREOOPTION)
* @param hStatus
* @param hInChIBuilder
* @param vValue
* @return
*/
static native boolean IXA_INCHIBUILDER_CheckOption_Stereo(Pointer hStatus, Pointer hInChIBuilder, int vValue);
//FIXME IXA_INCHIBUILDER_GetOption_Timeout_MilliSeconds is missing from Linux build
/**
* Original signature : long INCHI_DECL IXA_INCHIBUILDER_GetOption_Timeout_MilliSeconds(IXA_STATUS_HANDLE, IXA_INCHIBUILDER_HANDLE)
* @param hStatus
* @param hInChIBuilder
* @return
*/
//static native long IXA_INCHIBUILDER_GetOption_Timeout_MilliSeconds(Pointer hStatus, Pointer hInChIBuilder);
/*
* Functions for Generating InChI Keys
*/
/**
* Original signature : INCHI_DECL IXA_INCHIKEYBUILDER_Create(Pointer)
* @param hStatus
* @return
*/
static native Pointer IXA_INCHIKEYBUILDER_Create(Pointer hStatus);
/**
* Original signature : INCHI_DECL IXA_INCHIKEYBUILDER_SetInChI(Pointer, Pointer, const char*)
* @param hStatus
* @param hInChIKeyBuilder
* @param pInChI
*/
static native void IXA_INCHIKEYBUILDER_SetInChI(Pointer hStatus, Pointer hInChIKeyBuilder, byte[] pInChI);
/**
* Original signature : INCHI_DECL IXA_INCHIKEYBUILDER_GetInChIKey(Pointer, Pointer)
* @param hStatus
* @param hInChIKeyBuilder
* @return
*/
static native String IXA_INCHIKEYBUILDER_GetInChIKey(Pointer hStatus, Pointer hInChIKeyBuilder);
/**
* Original signature : INCHI_DECL IXA_INCHIKEYBUILDER_Destroy(Pointer, Pointer)
* @param hStatus
* @param hInChIKeyBuilder
*/
static native void IXA_INCHIKEYBUILDER_Destroy(Pointer hStatus, Pointer hInChIKeyBuilder);
}
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