Skip to content

Latest commit

 

History

History
265 lines (210 loc) · 12.9 KB

README.md

File metadata and controls

265 lines (210 loc) · 12.9 KB
Raw

@manufac-analytics/inchi Logo

NodeJS/TypeScript Port of InChI 1.06

Build & Tests

What does Line Notation refer to in the field Cheminformatics?

Cheminformatics can be defined as the field of solving chemistry problems with the help of computers. It is the field of science where computational methods and information science models, like machine learning, are used to solve problems in chemistry, biology and related molecular fields. These methods can also be used to tackle difficulties in chemical and allied industries, where chemical processes are involved and studied. Information is fed in a way that is flexible to the computers. Line notations, here, represent the structure of chemical compounds and nomenclature as a linear sequence of letters and numbers. Examples of line notations include the Wiswesser Line-Formula Notation (WLN), Sybyl Line Notation (SLN), and Representation of structure diagram arranged linearly (ROSDAL). Currently, the most widely used linear notations are the Simplified Molecular-Input Line-Entry System (SMILES), and the IUPAC International Chemical Identifier (InChI).

References : Cheminformatics - Wikipedia, Line Notations - ChemLibreTexts

What are some features of the InChI notation?

  1. Structure-based approach. Anybody anywhere should be able to produce InChI from just the structural formula of a chemical substance.
  2. Strict uniqueness of identifier. The same label always means the same substance, and the same substance always receives the same label (under the same labelling conditions). This is achieved through a well-defined procedure of obtaining canonical numbering of atoms.
  3. Non-proprietary, Open Source, free and open approach.* Free access to developed computer programs. No payment is assumed under any circumstances.* Open access to the source code. Everybody is free to read and use the source code.
  4. Applicability to the entire domain of “classic organic chemistry” and, to a significant extent, to inorganic compounds, bearing in mind the eventual goal to extend InChI to cover all of chemistry.
  5. Ability to generate the same InChI for structures drawn under (reasonably) different styles and conventions, specifically those represented by mesomers.
  6. Hierarchical approach allowing encoding of molecular structure with different levels of “granularity”, dependent on algorithms and software switches. In particular, the ability to include/exclude stereochemical, isotopic and tautomeric information was considered necessary.
  7. Ability to produce an identifier with some “default” switches, targeted to a fixed level of granularity and ensuring interoperability in large databases.

Reference: InChI, the IUPAC International Chemical Identifier

How would you differentiate between InChI and SMILES line notations?

The Simplified Molecular-Input Line-Entry System (SMILES) is a line notation for describing the structure of chemical species using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules. SMILES was designed to be read and written by humans and is therefore relatively straightforward to read, provided the user knows the basic principles of the format. InChIs are meant to contain molecular information that computers can read within the layers and express more information, so unlike SMILES, users can't really read InChI.

Unlike SMILES, InChI is a canonical line notation and so is a unique identifier that is built upon a set of nomenclature rules. That is, although there are canonical SMILES built through a canonicalization algorithm, there can be more than one canonicalization algorithm for SMILES, and so you can have more than one SMILES string for the same structure. Therefore, InChI aims to provide a unique, or canonical, identifier for chemical structures, while SMILES strings are widely used for storage and interchange of chemical structures, but no standard exists to generate a canonical SMILES string.

References : SMILES - Wikipedia, SMILES and InChI, SMILES representation from InChI

How to use this library?

  1. Using the library in your source code.

    • This library has a dependency on ffi-napi so you may need to install some necessary build tools for it to work.
    • Alternately, you can also use Docker to automatically set up your dev environment with required dependencies. Here's the Dockerfile that we are using for the same.

  2. Running a JSON-RPC 2.0 server.

    • This library exposes a Docker image which you can run to spin off a JSON-RPC 2.0 server.
    • You can interact with that server from your source code by making a HTTP POST request.
    • The request's body should be JSON-RPC 2.0 compliant. For e.g.,
    {
  "jsonrpc": "2.0",
  "method": "GetStringLength",
  "params": ["my-string"],
  "id": 1
}
    • The response can look like:
    {
  "jsonrpc": "2.0",
  "id": 1,
  "result": 9
}
    • In case of an error, the response can look like:
    {
  "jsonrpc": "2.0",
  "id": 1,
  "error": {
    "message": "Expected 1 arguments, got 2",
    "code": -32602
  }
}

API Porting Status

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

A. Generation of InChI from structure

  • GetINCHI
  • 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

Contributors' Notes

Intro

  • This library is a NodeJS/TypeScript port of InChI 1.06. API documentation of the original C based library is present here. Derived some inspiration from smikes/inchi.
  • The Shared Object file, libinchi.so.1.06.00, contains all the InChI related business logic, is installed from InChITRUST, and is licensed under IUPAC/InChI Trust Licence.

Which porting approach is used?

  • Here's a cool overview of integrating native modules with NodeJS applications: N-API - The new native in Node.JS by Atishay Jain.
  • This library uses foreign function interface to access the native InChI module. The decision was mainly taken to achieve an ease of development that ffi provides as compared to using nan, Node-API, or node-addon-api.
  • One can port the InChI library using the above tools also. These examples may provide you a good idea on how to move forward.
  • For using ffi, 2 libraries were considered: ffi and ffi-napi. ffi-napi was adopted because it supports the latest/recent versions of NodeJS; it is tested to run on Node 6 and above, whereas ffi is only tested to run on Node v0.6, v0.8, v0.9 and v0.10.
  • You can learn more about ffi-napi/ffi via this tutorial.

How are the types ported?