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
grimme-lab · Jul 26, 2022 · abfbff1 · abfbff1
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diff --git a/doc/format-cjson.md b/doc/format-cjson.md
@@ -0,0 +1,99 @@
+---
+title: Chemical JSON
+---
+
+## Specification
+
+@Note [Reference](https://github.com/OpenChemistry/avogadrolibs/blob/master/avogadro/io/cjsonformat.cpp)
+
+Chemical JSON files are identified by the extension ``cjson`` and parsed following the format implemented in Avogadro 2.
+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.
+
+
+## Example
+
+Caffeine molecule in ``qcschema_molecule`` format.
+
+
+```json
+{
+  "chemicalJson": 1,
+  "atoms": {
+    "elements": {
+      "number": [
+        6, 7, 6, 7, 6, 6, 6, 8, 7, 6, 8, 7, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+      ]
+    },
+    "coords": {
+      "3d": [
+         1.0731997649702911E+00,  4.8899989290949721E-02, -7.5699983421776973E-02,
+         2.5136994495022558E+00,  1.2599997240612813E-02, -7.5799983399877077E-02,
+         3.3519992659154081E+00,  1.0958997599990143E+00, -7.5299983509376570E-02,
+         4.6189989884436962E+00,  7.3029984006504256E-01, -7.5499983465576764E-02,
+         4.5790989971817559E+00, -6.3139986172404194E-01, -7.5299983509376570E-02,
+         3.3012992770186567E+00, -1.1025997585317211E+00, -7.5199983531276451E-02,
+         2.9806993472297307E+00, -2.4868994553714288E+00, -7.3799983837875047E-02,
+         1.8252996002611557E+00, -2.9003993648153492E+00, -7.5799983399877077E-02,
+         4.1143990989505834E+00, -3.3042992763616597E+00, -6.9399984801470568E-02,
+         5.4516988060832432E+00, -2.8561993744951040E+00, -7.2399984144473614E-02,
+         6.3892986007497967E+00, -3.6596991985294207E+00, -7.2299984166373524E-02,
+         5.6623987599401575E+00, -1.4767996765823013E+00, -7.4899983596976152E-02,
+         7.0094984649266268E+00, -9.3649979490745228E-01, -7.5199983531276451E-02,
+         3.9205991413925863E+00, -4.7408989617477202E+00, -6.1599986509662634E-02,
+         7.3399983925474632E-01,  1.0878997617510062E+00, -7.4999983575076257E-02,
+         7.1239984398512435E-01, -4.5699989991746470E-01,  8.2339981967623732E-01,
+         7.1239984398512435E-01, -4.5579990018026340E-01, -9.7549978636649193E-01,
+         2.9929993445360430E+00,  2.1175995362477531E+00, -7.4799983618876062E-02,
+         7.7652982994071955E+00, -1.7262996219420552E+00, -7.5899983377977168E-02,
+         7.1485984344638682E+00, -3.2179992952612718E-01,  8.1969982048653345E-01,
+         7.1479984345952676E+00, -3.2079992974512617E-01, -9.6949978768048573E-01,
+         2.8649993725679135E+00, -5.0231988999243073E+00, -5.8299987232359275E-02,
+         4.4022990359007768E+00, -5.1591988701404459E+00,  8.2839981858124223E-01,
+         4.4001990363606742E+00, -5.1692988679285561E+00, -9.4779979243276369E-01
+      ]
+    }
+  },
+  "bonds": {
+    "connections": {
+      "index": [
+        0, 1,
+        1, 2,
+        2, 3,
+        3, 4,
+        1, 5,
+        4, 5,
+        5, 6,
+        6, 7,
+        6, 8,
+        8, 9,
+        9, 10,
+        4, 11,
+        9, 11,
+        11, 12,
+        8, 13,
+        0, 14,
+        0, 15,
+        0, 16,
+        2, 17,
+        12, 18,
+        12, 19,
+        12, 20,
+        13, 21,
+        13, 22,
+        13, 23
+      ]
+    },
+    "order": [
+      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
+    ]
+  }
+}
+```
+
+
+## Missing features
+
+The schema is not verified on completeness and not all data is stored in the final structure type.
+
+@Note Feel free to contribute support for missing features
+      or bring missing features to our attention by opening an issue.
diff --git a/doc/index.md b/doc/index.md
@@ -11,6 +11,7 @@ This library supports reading and writing of the following formats:
 - [a subset of PDB format](./format-pdb.html)
 - [DFTB+ general format](./format-gen.html)
 - [Gaussian external format](./format-ein.html)
+- [Chemical JSON format](./format-cjson.html)
 - [QCSchema JSON format](./format-qcschema.html)
 - [FHI-aims geometry.in](./format-aims.html)
 - [Q-Chem molecule format](./format-qchem.html)
diff --git a/man/mctc-convert.1.adoc b/man/mctc-convert.1.adoc
@@ -27,6 +27,7 @@ Supported formats:
 - Connection table files, molfile (mol) and structure data format (sdf)
 - Gaussian's external program input (ein)
 - JSON input with `qcschema_molecule` or `qcschema_input` structure (json)
+- Chemical JSON input (cjson)
 - FHI-AIMS' input files (geometry.in)
 - Q-Chem molecule block inputs (qchem)
 

diff --git a/src/mctc/io/filetype.f90 b/src/mctc/io/filetype.f90
@@ -59,6 +59,9 @@ module mctc_io_filetype
       !> Q-Chem molecule format
       integer :: qchem = 11
 
+      !> Chemical JSON format (avogadro)
+      integer :: cjson = 12
+
    end type enum_filetype
 
    !> File type enumerator
@@ -102,6 +105,8 @@ elemental function get_filetype(file) result(ftype)
          ftype = filetype%gaussian
       case('json')
          ftype = filetype%qcschema
+      case('cjson')
+         ftype = filetype%cjson
       case('qchem')
          ftype = filetype%qchem
       end select

diff --git a/src/mctc/io/read.f90 b/src/mctc/io/read.f90
@@ -16,6 +16,7 @@ module mctc_io_read
    use mctc_env_error, only : error_type, fatal_error
    use mctc_io_filetype, only : filetype, get_filetype
    use mctc_io_read_aims, only : read_aims
+   use mctc_io_read_cjson, only : read_cjson
    use mctc_io_read_ctfile, only : read_molfile, read_sdf
    use mctc_io_read_gaussian, only : read_gaussian_external
    use mctc_io_read_genformat, only : read_genformat
@@ -149,6 +150,9 @@ subroutine get_structure_reader(reader, ftype)
    case(filetype%qcschema)
       reader => read_qcschema
 
+   case(filetype%cjson)
+      reader => read_cjson
+
    case(filetype%pdb)
       reader => read_pdb
 

diff --git a/src/mctc/io/read/CMakeLists.txt b/src/mctc/io/read/CMakeLists.txt
@@ -17,6 +17,7 @@ set(dir "${CMAKE_CURRENT_SOURCE_DIR}")
 list(
   APPEND srcs
   "${dir}/aims.f90"
+  "${dir}/cjson.F90"
   "${dir}/ctfile.f90"
   "${dir}/gaussian.f90"
   "${dir}/genformat.f90"