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Port InCHI functions #8

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maneetgoyal opened this issue Jun 6, 2021 · 9 comments
Open

Port InCHI functions #8

maneetgoyal opened this issue Jun 6, 2021 · 9 comments
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enhancement New feature or request good first issue Good for newcomers help wanted Extra attention is needed

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@maneetgoyal
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maneetgoyal commented Jun 6, 2021 •
edited by qur786
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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

  • MakeINCHIFromMolfileText

D. Restoring structure from InChI or AuxInfo

  • GetStructFromINCHI
  • GetStructFromINCHIEx
  • FreeStructFromINCHI
  • GetStructFromStdINCHI
  • FreeStructFromStdINCHI

E. InChIKey

  • GetINCHIKeyFromINCHI
  • CheckINCHIKey
  • GetStdINCHIKeyFromStdINCHI

F. Test and utlity procedures

  • GetINCHIfromINCHI
  • CheckINCHI
  • 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 maneetgoyal added enhancement New feature or request good first issue Good for newcomers help wanted Extra attention is needed labels Jun 6, 2021
@maneetgoyal
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maneetgoyal commented Jun 6, 2021 •
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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.

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maneetgoyal commented Aug 4, 2021 •
edited by qur786
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@qur786 In the first phase, try to port the following functions only:

D. Restoring structure from InChI or AuxInfo

  • GetStructFromINCHI
  • GetStructFromINCHIEx
  • FreeStructFromINCHI
  • GetStructFromStdINCHI
  • FreeStructFromStdINCHI

maneetgoyal added a commit that referenced this issue Aug 23, 2021
@maneetgoyal
Merge branch 'main' into qur786/#8-Port-InCHI-functions-Batch1
8032b2b
@maneetgoyal
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@qur786 Please make the necessary updates now as mentioned during the morning call.

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qur786 commented Aug 23, 2021

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

working on it sir

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

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qur786 commented Aug 24, 2021

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

done sir

qur786 pushed a commit that referenced this issue Aug 24, 2021
@sumitnegi7
Merge branch 'main' of github.com:manufac-analytics/perry into sumitn…
7bfa368 
…egi7/#8-Migrate-vapor-pressure-data
qur786 pushed a commit that referenced this issue Aug 24, 2021
@sumitnegi7
Merge branch 'main' of github.com:manufac-analytics/perry into sumitn…
9197aaa 
…egi7/#8-Migrate-vapor-pressure-data
qur786 pushed a commit that referenced this issue Aug 24, 2021
@sumitnegi7
Merge pull request #18 from manufac-analytics/sumitnegi7/#8-Migrate-v…
b30da33 
…apor-pressure-data

Migrate vapor pressure data batch1
qur786 pushed a commit that referenced this issue Aug 24, 2021
@sumitnegi7
Merge branch 'main' of github.com:manufac-analytics/perry into sumitn…
715ffaa 
…egi7/#8-Migrate-vapor-pressure-data-bath2
qur786 pushed a commit that referenced this issue Aug 24, 2021
@sumitnegi7
Merge pull request #21 from manufac-analytics/sumitnegi7/#8-Migrate-v…
27e0bc2 
…apor-pressure-data-bath2

Migrate vapor pressure data batch2
qur786 pushed a commit that referenced this issue Aug 24, 2021
@sumitnegi7
Merge branch 'main' of github.com:manufac-analytics/perry into sumitn…
d1c45b7 
…egi7/#8-Migrate-vapor-pressure-daata-batch3
qur786 pushed a commit that referenced this issue Aug 24, 2021
@sumitnegi7
Merge pull request #23 from manufac-analytics/sumitnegi7/#8-Migrate-v…
2341492 
…apor-pressure-daata-batch3

Add vapor pressure for compounds batch3
qur786 pushed a commit that referenced this issue Aug 24, 2021
@sumitnegi7
Merge branch 'main' of github.com:manufac-analytics/perry into sumitn…
fe61073 
…egi7/#8-Migrate-vapor-pressure-batch4
qur786 pushed a commit that referenced this issue Aug 24, 2021
@sumitnegi7
Merge pull request #27 from manufac-analytics/sumitnegi7/#8-Migrate-v…
82462c4 
…apor-pressure-batch4

Add compounds to vapor-pressure batch4
qur786 pushed a commit that referenced this issue Aug 24, 2021
@sumitnegi7
Merge branch 'main' of github.com:manufac-analytics/perry into sumitn…
9fd5cb7 
…egi7/#8-Migrate-vapor-pressure-data-batch5
qur786 pushed a commit that referenced this issue Aug 24, 2021
@sumitnegi7
Merge branch 'sumitnegi7/#8-Migrate-vapor-pressure-data-batch5' of gi…
cb5afb9 
…thub.com:manufac-analytics/perry into sumitnegi7/#8-Migrate-vapor-pressure-data-batch5
qur786 pushed a commit that referenced this issue Aug 24, 2021
@sumitnegi7
Merge pull request #32 from manufac-analytics/sumitnegi7/#8-Migrate-v…
b0ef540 
…apor-pressure-data-batch5

Add compounds to vapor pressure batch5
qur786 pushed a commit that referenced this issue Aug 24, 2021
@sumitnegi7
Merge pull request #40 from manufac-analytics/sumitnegi7/#8-Migrate-v…
e37db21 
…apor-pressure-data-batch6

Add compounds to vapor pressure batch6
qur786 pushed a commit that referenced this issue Aug 24, 2021
@sumitnegi7
Merge branch 'main' of github.com:manufac-analytics/perry into sumitn…
0fed21e 
…egi7/#8-Migrate-vapor-pressure-data-batch7
qur786 pushed a commit that referenced this issue Aug 24, 2021
@sumitnegi7
Merge pull request #41 from manufac-analytics/sumitnegi7/#8-Migrate-v…
1dc4058 
…apor-pressure-data-batch7

Add some compounds to vapor pressure batch7
qur786 pushed a commit that referenced this issue Aug 24, 2021
@sumitnegi7
Merge branch 'main' of github.com:manufac-analytics/perry into sumitn…
83505bf 
…egi7/#8-Migrate-vapor-pressure-data-batch8
qur786 pushed a commit that referenced this issue Aug 24, 2021
@sumitnegi7
Merge branch 'sumitnegi7/#8-Migrate-vapor-pressure-data-batch8' of gi…
8b6ca8d 
…thub.com:manufac-analytics/perry into sumitnegi7/#8-Migrate-vapor-pressure-data-batch8
qur786 pushed a commit that referenced this issue Aug 24, 2021
@sumitnegi7
Merge pull request #43 from manufac-analytics/sumitnegi7/#8-Migrate-v…
682951b 
…apor-pressure-data-batch8

Add compounds to vapor pressure batch8
qur786 pushed a commit that referenced this issue Aug 24, 2021
@sumitnegi7
Merge pull request #61 from manufac-analytics/sumitnegi7/#8-vapor-pre…
ccca5ab 
…ssure-09

Migrate vapor pressure batch9
qur786 pushed a commit that referenced this issue Aug 24, 2021
@sumitnegi7
Merge branch 'main' of github.com:manufac-analytics/perry into sumitn…
6f9453f 
…egi7/#8-vapor-pressure-batch10
qur786 pushed a commit that referenced this issue Aug 24, 2021
@sumitnegi7
Merge branch 'main' of github.com:manufac-analytics/perry into sumitn…
ef19096 
…egi7/#8-vapor-pressure-batch10
qur786 pushed a commit that referenced this issue Aug 24, 2021
@sumitnegi7
Merge branch 'sumitnegi7/#8-vapor-pressure-batch10' of github.com:man…
e012c36 
…ufac-analytics/perry into sumitnegi7/#8-vapor-pressure-batch10
qur786 pushed a commit that referenced this issue Aug 24, 2021
@sumitnegi7
Merge pull request #65 from manufac-analytics/sumitnegi7/#8-vapor-pre…
bd82b2b 
…ssure-batch10

Add compounds to vapor pressure batch10
qur786 pushed a commit that referenced this issue Aug 24, 2021
@sumitnegi7
Merge pull request #66 from manufac-analytics/sumitnegi7/#8-vapor-pre…
a793570 
…ssure-batch-11

Migrate vapor pressure batch 11
maneetgoyal added a commit that referenced this issue Aug 26, 2021
@maneetgoyal
Merge branch 'main' into qur786/#8-Port-InCHI-functions-Batch1-Phase2
1987481
qur786 added a commit that referenced this issue Aug 26, 2021
@qur786
Merge branch 'qur786/#8-Port-InCHI-functions-Batch1-Phase2' of https:…
efb3713 
…//github.com/manufac-analytics/inchi into qur786/#8-Port-InCHI-functions-Batch1-Phase2
qur786 added a commit that referenced this issue Aug 26, 2021
@qur786
Merge branch 'qur786/#8-Port-InCHI-functions-Batch1-Phase2' of https:…
e4c454f 
…//github.com/manufac-analytics/inchi into qur786/#8-Port-InCHI-functions-Batch1-Phase2
qur786 added a commit that referenced this issue Aug 26, 2021
@qur786
Merge branch 'qur786/#8-Port-InCHI-functions-Batch1-Phase2' of https:…
386f4c0 
…//github.com/manufac-analytics/inchi into qur786/#8-Port-InCHI-functions-Batch1-Phase2
maneetgoyal added a commit that referenced this issue Aug 26, 2021
@maneetgoyal
Merge pull request #22 from manufac-analytics/qur786/#8-Port-InCHI-fu…
4f61a6e 
…nctions-Batch1-Phase2

Port Inchi Functions Phase 2
@maneetgoyal
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@qur786 Here's the next batch of functions that should be ported in Milestone 2

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

@maneetgoyal maneetgoyal mentioned this issue Sep 3, 2021
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