Port InCHI functions

[maneetgoyal]

API Porting Status

We are slowly working towards exposing all the InCHI functions. PRs welcome.

A. Generation of InChI from structure

• [ ] GetINCHI | int INCHI_DECL GetINCHI(inchi_Input *inp, inchi_Output *out)
• [ ] GetINCHIEx
• [ ] FreeINCHI
• [ ] Free_inchi_Input
• [ ] Get_inchi_Input_FromAuxInfo
• [ ] GetStdINCHI
• [ ] FreeStdINCHI
• [ ] Free_std_inchi_Input
• [ ] Get_std_inchi_Input_FromAuxInfo

B. Generation of InChI from structure, step-by-step way

• [ ] INCHIGEN_Create
• [ ] INCHIGEN_Setup
• [ ] INCHIGEN_DoNormalization
• [ ] INCHIGEN_DoCanonicalization
• [ ] INCHIGEN_DoSerialization
• [ ] INCHIGEN_Reset
• [ ] INCHIGEN_Destroy
• [ ] STDINCHIGEN_Create
• [ ] STDINCHIGEN_Setup
• [ ] STDINCHIGEN_DoNormalization
• [ ] STDINCHIGEN_DoCanonicalization
• [ ] STDINCHIGEN_DoSerialization
• [ ] STDINCHIGEN_Reset
• [ ] STDINCHIGEN_Destroy

C. Generation of InChI directly from Molfile

• [x] MakeINCHIFromMolfileText

D. Restoring structure from InChI or AuxInfo

• [x] GetStructFromINCHI
• [x] GetStructFromINCHIEx
• [x] FreeStructFromINCHI
• [x] GetStructFromStdINCHI
• [x] FreeStructFromStdINCHI

E. InChIKey

• [x] GetINCHIKeyFromINCHI
• [x] CheckINCHIKey
• [x] GetStdINCHIKeyFromStdINCHI

F. Test and utlity procedures

• [x] GetINCHIfromINCHI
• [x] CheckINCHI
• [x] GetStringLength

G. Status Objects

• [ ] IXA_STATUS_Create
• [ ] IXA_STATUS_Clear
• [ ] IXA_STATUS_Destroy
• [ ] IXA_STATUS_HasError
• [ ] IXA_STATUS_HasWarning
• [ ] IXA_STATUS_GetCount
• [ ] IXA_STATUS_GetSeverity
• [ ] IXA_STATUS_GetMessage

H. Molecule Objects

• [ ] IXA_MOL_Create
• [ ] IXA_MOL_Clear
• [ ] IXA_MOL_Destroy
• [ ] IXA_MOL_ReadMolfile
• [ ] IXA_MOL_ReadInChI
• [ ] IXA_MOL_SetChiral
• [ ] IXA_MOL_GetChiral
• [ ] IXA_MOL_CreateAtom
• [ ] IXA_MOL_SetAtomElement
• [ ] IXA_MOL_SetAtomAtomicNumber
• [ ] IXA_MOL_SetAtomMass
• [ ] IXA_MOL_SetAtomCharge
• [ ] IXA_MOL_SetAtomRadical
• [ ] IXA_MOL_SetAtomHydrogens
• [ ] IXA_MOL_SetAtomX
• [ ] IXA_MOL_SetAtomY
• [ ] IXA_MOL_SetAtomZ
• [ ] IXA_MOL_CreateBond
• [ ] IXA_MOL_SetBondType
• [ ] IXA_MOL_SetBondWedge
• [ ] IXA_MOL_SetDblBondConfig
• [ ] IXA_MOL_CreateStereoTetrahedron
• [ ] IXA_MOL_CreateStereoRectangle
• [ ] IXA_MOL_CreateStereoAntiRectangle
• [ ] IXA_MOL_SetStereoParity
• [ ] IXA_MOL_CreatePolymerUnit (new in v. 1.06)
• [ ] IXA_MOL_GetPolymerUnitId (new in v. 1.06)
• [ ] IXA_MOL_GetPolymerUnitIndex (new in v. 1.06)
• [ ] IXA_MOL_SetPolymerUnit (new in v. 1.06)
• [ ] IXA_MOL_GetNumAtoms
• [ ] IXA_MOL_GetNumBonds
• [ ] IXA_MOL_GetAtomId
• [ ] IXA_MOL_GetBondId
• [ ] IXA_MOL_GetAtomIndex
• [ ] IXA_MOL_GetBondIndex
• [ ] IXA_MOL_GetAtomNumBonds
• [ ] IXA_MOL_GetAtomBond
• [ ] IXA_MOL_GetCommonBond
• [ ] IXA_MOL_GetBondAtom1
• [ ] IXA_MOL_GetBondAtom2
• [ ] IXA_MOL_GetBondOtherAtom (new in v. 1.06)
• [ ] IXA_MOL_GetAtomElement
• [ ] IXA_MOL_GetAtomAtomicNumber
• [ ] IXA_MOL_GetAtomMass
• [ ] IXA_MOL_GetAtomCharge
• [ ] IXA_MOL_GetAtomRadical
• [ ] IXA_MOL_GetAtomHydrogens
• [ ] IXA_MOL_GetAtomX
• [ ] IXA_MOL_GetAtomY
• [ ] IXA_MOL_GetAtomZ
• [ ] IXA_MOL_GetBondType
• [ ] IXA_MOL_GetBondWedge
• [ ] IXA_MOL_GetDblBondConfig
• [ ] IXA_MOL_GetNumStereos
• [ ] IXA_MOL_GetStereoId
• [ ] IXA_MOL_GetStereoIndex
• [ ] IXA_MOL_GetStereoTopology
• [ ] IXA_MOL_GetStereoCentralAtom
• [ ] IXA_MOL_GetStereoCentralBond
• [ ] IXA_MOL_GetStereoNumVertices
• [ ] IXA_MOL_GetStereoVertex
• [ ] IXA_MOL_GetStereoParity

I. InChI Builder Objects

• [ ] IXA_INCHIBUILDER_Create
• [ ] IXA_INCHIBUILDER_SetMolecule
• [ ] IXA_INCHIBUILDER_GetInChI
• [ ] IXA_INCHIBUILDER_GetAuxInfo
• [ ] IXA_INCHIBUILDER_GetLog
• [ ] IXA_INCHIBUILDER_Destroy
• [ ] IXA_INCHIBUILDER_SetOption
• [ ] IXA_INCHIBUILDER_SetOption_Stereo
• [ ] IXA_INCHIBUILDER_SetOption_Timeout
• [ ] IXA_INCHIBUILDER_SetOption_Timeout_Milliseconds (new in v. 1.06)
• [ ] IXA_INCHIBUILDER_CheckOption (new in v. 1.06)
• [ ] IXA_INCHIBUILDER_CheckOption_Stereo (new in v. 1.06)
• [ ] IXA_INCHIBUILDER_IXA_INCHIBUILDER_GetOption_Timeout_MilliSeconds (new in v. 1.06)

J. InChIKey Builder Objects

• [ ] IXA_INCHIKEYBUILDER_Create
• [ ] IXA_INCHIKEYBUILDER_SetInChI
• [ ] IXA_INCHIKEYBUILDER_GetInChIKey
• [ ] IXA_INCHIKEYBUILDER_Destroy

[maneetgoyal]

How to port the functions?

• This InCHI API manual can help in determining the function signature: InChI_API_Reference.pdf
• The input/output types of the function signatures are already ported.
• Simply functions need to be ported now. This tutorial can teach you all that is needed.
• These ported functions reside in ffis.ts.
• Wrap the functions such that end users don't need to worry about ref/ref-napi and expose them via src/api.ts.
• Add appropriate unit tests in ffis.test.ts and api.test.ts.
• Expose src/api.ts functions via server.ts as well.
• Add JSDOc comments for the functions added to src/api.ts to showcase how to use them.

[maneetgoyal]

• [ ] Expose ported InCHI functions via server.js as well.

[maneetgoyal]

• [ ] Wrap the functions such that end users don't need to worry about ref/ref-napi.

[maneetgoyal]

@qur786 In the first phase, try to port the following functions only:

D. Restoring structure from InChI or AuxInfo

• [x] GetStructFromINCHI
• [x] GetStructFromINCHIEx
• [x] FreeStructFromINCHI
• [x] GetStructFromStdINCHI
• [x] FreeStructFromStdINCHI

[maneetgoyal]

@qur786 Please make the necessary updates now as mentioned during the morning call.

[qur786]

@qur786 Please make the necessary updates now as mentioned during the morning call.

working on it sir

[maneetgoyal]

@qur786 Update the task list in the above comment (https://github.com/manufac-analytics/inchi/issues/8#issue-912617166) also as mentioned earlier.

[qur786]

@qur786 Update the task list in the above comment (#8 (comment)) also as mentioned earlier.

done sir

[maneetgoyal]

@qur786 Here's the next batch of functions that should be ported in Milestone 2

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A. Generation of InChI from structure

• [ ] GetINCHI | int INCHI_DECL GetINCHI(inchi_Input *inp, inchi_Output *out)
• [ ] GetINCHIEx
• [ ] FreeINCHI
• [ ] Free_inchi_Input
• [ ] Get_inchi_Input_FromAuxInfo
• [ ] GetStdINCHI
• [ ] FreeStdINCHI
• [ ] Free_std_inchi_Input
• [ ] Get_std_inchi_Input_FromAuxInfo

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