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Support chemical JSON (#50)
- implement basic reader for chemical JSON - implement writer for chemical JSON - test if chemical JSON produced by mctc-lib round-trips - document implemented format - implementation matches https://github.com/OpenChemistry/avogadrolibs/blob/c707a49/avogadro/io/cjsonformat.cpp
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‎doc/format-cjson.md‎

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---
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title: Chemical JSON
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---
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## Specification
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@Note [Reference](https://github.com/OpenChemistry/avogadrolibs/blob/master/avogadro/io/cjsonformat.cpp)
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Chemical JSON files are identified by the extension ``cjson`` and parsed following the format implemented in Avogadro 2.
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The entries *name*, *atoms.elements.number*, *atoms.coords.3d*, *atoms.coords.3d fractional*, *unit cell*, *atoms.formalCharges*, *bonds.connections.index*, and *bonds.order* are recognized by the reader.
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## Example
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Caffeine molecule in ``qcschema_molecule`` format.
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```json
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{
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"chemicalJson": 1,
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"atoms": {
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"elements": {
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"number": [
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6, 7, 6, 7, 6, 6, 6, 8, 7, 6, 8, 7, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
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]
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},
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"coords": {
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"3d": [
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1.0731997649702911E+00, 4.8899989290949721E-02, -7.5699983421776973E-02,
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2.5136994495022558E+00, 1.2599997240612813E-02, -7.5799983399877077E-02,
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3.3519992659154081E+00, 1.0958997599990143E+00, -7.5299983509376570E-02,
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4.6189989884436962E+00, 7.3029984006504256E-01, -7.5499983465576764E-02,
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4.5790989971817559E+00, -6.3139986172404194E-01, -7.5299983509376570E-02,
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3.3012992770186567E+00, -1.1025997585317211E+00, -7.5199983531276451E-02,
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2.9806993472297307E+00, -2.4868994553714288E+00, -7.3799983837875047E-02,
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1.8252996002611557E+00, -2.9003993648153492E+00, -7.5799983399877077E-02,
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4.1143990989505834E+00, -3.3042992763616597E+00, -6.9399984801470568E-02,
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5.4516988060832432E+00, -2.8561993744951040E+00, -7.2399984144473614E-02,
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6.3892986007497967E+00, -3.6596991985294207E+00, -7.2299984166373524E-02,
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5.6623987599401575E+00, -1.4767996765823013E+00, -7.4899983596976152E-02,
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7.0094984649266268E+00, -9.3649979490745228E-01, -7.5199983531276451E-02,
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3.9205991413925863E+00, -4.7408989617477202E+00, -6.1599986509662634E-02,
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7.3399983925474632E-01, 1.0878997617510062E+00, -7.4999983575076257E-02,
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7.1239984398512435E-01, -4.5699989991746470E-01, 8.2339981967623732E-01,
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7.1239984398512435E-01, -4.5579990018026340E-01, -9.7549978636649193E-01,
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2.9929993445360430E+00, 2.1175995362477531E+00, -7.4799983618876062E-02,
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7.7652982994071955E+00, -1.7262996219420552E+00, -7.5899983377977168E-02,
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7.1485984344638682E+00, -3.2179992952612718E-01, 8.1969982048653345E-01,
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7.1479984345952676E+00, -3.2079992974512617E-01, -9.6949978768048573E-01,
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2.8649993725679135E+00, -5.0231988999243073E+00, -5.8299987232359275E-02,
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4.4022990359007768E+00, -5.1591988701404459E+00, 8.2839981858124223E-01,
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4.4001990363606742E+00, -5.1692988679285561E+00, -9.4779979243276369E-01
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]
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}
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},
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"bonds": {
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"connections": {
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"index": [
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0, 1,
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1, 2,
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2, 3,
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3, 4,
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1, 5,
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4, 5,
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5, 6,
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6, 7,
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6, 8,
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8, 9,
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9, 10,
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4, 11,
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9, 11,
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11, 12,
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8, 13,
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0, 14,
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0, 15,
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0, 16,
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2, 17,
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12, 18,
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12, 19,
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12, 20,
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13, 21,
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13, 22,
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13, 23
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]
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},
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"order": [
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1, 4, 4, 4, 1, 4, 1, 2, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
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]
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}
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}
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```
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## Missing features
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The schema is not verified on completeness and not all data is stored in the final structure type.
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@Note Feel free to contribute support for missing features
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or bring missing features to our attention by opening an issue.

‎doc/index.md‎

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- [a subset of PDB format](./format-pdb.html)
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- [DFTB+ general format](./format-gen.html)
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- [Gaussian external format](./format-ein.html)
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- [Chemical JSON format](./format-cjson.html)
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- [QCSchema JSON format](./format-qcschema.html)
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- [FHI-aims geometry.in](./format-aims.html)
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- [Q-Chem molecule format](./format-qchem.html)

‎man/mctc-convert.1.adoc‎

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- Connection table files, molfile (mol) and structure data format (sdf)
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- Gaussian's external program input (ein)
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- JSON input with `qcschema_molecule` or `qcschema_input` structure (json)
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- Chemical JSON input (cjson)
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- FHI-AIMS' input files (geometry.in)
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- Q-Chem molecule block inputs (qchem)
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‎src/mctc/io/filetype.f90‎

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!> Q-Chem molecule format
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integer :: qchem = 11
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!> Chemical JSON format (avogadro)
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integer :: cjson = 12
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end type enum_filetype
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!> File type enumerator
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ftype = filetype%gaussian
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case('json')
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ftype = filetype%qcschema
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case('cjson')
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ftype = filetype%cjson
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case('qchem')
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ftype = filetype%qchem
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end select

‎src/mctc/io/read.f90‎

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use mctc_env_error, only : error_type, fatal_error
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use mctc_io_filetype, only : filetype, get_filetype
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use mctc_io_read_aims, only : read_aims
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use mctc_io_read_cjson, only : read_cjson
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use mctc_io_read_ctfile, only : read_molfile, read_sdf
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use mctc_io_read_gaussian, only : read_gaussian_external
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use mctc_io_read_genformat, only : read_genformat
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case(filetype%qcschema)
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reader => read_qcschema
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case(filetype%cjson)
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reader => read_cjson
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case(filetype%pdb)
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reader => read_pdb
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‎src/mctc/io/read/CMakeLists.txt‎

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list(
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APPEND srcs
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"${dir}/aims.f90"
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"${dir}/cjson.F90"
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"${dir}/ctfile.f90"
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"${dir}/gaussian.f90"
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"${dir}/genformat.f90"

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