diff --git a/README.md b/README.md index e9124e4..2dda34a 100644 --- a/README.md +++ b/README.md @@ -21,3 +21,10 @@ represntations for chemistry, and to document those representations more formally than has been done in the past. [Chemical_JSON]: http://wiki.openchemistry.org/Chemical_JSON + +## Documentation + +Project documentation is available in the [docs directory](./docs). +This content is migrated from the archived Open Chemistry wiki and +serves as a centralized reference until a dedicated documentation +site is available. diff --git "a/and examples links clickable in documentation\357\200\242" "b/and examples links clickable in documentation\357\200\242" new file mode 100644 index 0000000..fd40b87 --- /dev/null +++ "b/and examples links clickable in documentation\357\200\242" @@ -0,0 +1,25 @@ +diff --git a/README.md b/README.md +index 0d32498..2f670cd 100644 +--- a/README.md ++++ b/README.md +@@ -25,7 +25,7 @@ formally than has been done in the past. +  + ## Documentation +  +-Project documentation is available in the `docs/` directory.  ++Project documentation is available in the [docs/](docs/) directory.  + This content is migrated from the archived Open Chemistry wiki and will + serve as a centralized reference until a dedicated documentation site + is available. +diff --git a/docs/overview.md b/docs/overview.md +index 8eb64d2..dbac41e 100644 +--- a/docs/overview.md ++++ b/docs/overview.md +@@ -28,6 +28,5 @@ The format is designed to be extensible, allowing new properties to be + added without breaking existing tools. +  + ## Example +- +-See the `examples/` directory in this repository for concrete examples ++See the [examples/](../examples/) directory in this repository for concrete examples + of ChemicalJSON files, including small molecules and periodic systems. diff --git a/docs/coordinate-sets.md b/docs/coordinate-sets.md new file mode 100644 index 0000000..ba39f9b --- /dev/null +++ b/docs/coordinate-sets.md @@ -0,0 +1,18 @@ +## Multiple Coordinate Sets (3dSets) + +ChemicalJSON supports multiple coordinate sets using `coords.3dSets`, represented as an array of coordinate arrays. + +Each entry in `3dSets` contains a complete set of Cartesian coordinates for all atoms in the system. This can be used to represent conformers, geometry optimization steps, or simple animations. + +### Example + +See `examples/multiple-coordinate-sets.json` for a minimal example demonstrating two coordinate frames. + +### Current Limitations + +The current format does not standardize: +- time steps for coordinate series (e.g., molecular dynamics) +- per-frame energies or forces +- an explicit default coordinate set index + +Consumers typically interpret the first entry in `3dSets` as the initial frame, but this behavior is not formally defined. diff --git a/docs/overview.md b/docs/overview.md new file mode 100644 index 0000000..47d2c8c --- /dev/null +++ b/docs/overview.md @@ -0,0 +1,24 @@ +# ChemicalJSON + +## Purpose + +ChemicalJSON is a JSON-based format for representing chemical data +in a structured and machine-readable way. It is designed to support +storage, exchange, and processing of chemical information across +different tools and programming languages. + +## Basic Structure + +A ChemicalJSON document typically includes: + +- Metadata such as molecule name and formula +- Atomic information (elements, coordinates) +- Optional properties such as unit cells, energies, or orbitals + +The format is designed to be extensible, allowing new properties +to be added without breaking existing tools. + +## Examples + +See the [examples directory](../examples) for concrete examples of +ChemicalJSON files, including small molecules and periodic systems. diff --git a/examples/multiple-coordinate-sets.json b/examples/multiple-coordinate-sets.json new file mode 100644 index 0000000..0b114a8 --- /dev/null +++ b/examples/multiple-coordinate-sets.json @@ -0,0 +1,21 @@ +{ + "chemicalJson": 1, + "atoms": { + "elements": { "number": [8, 1, 1] } + }, + "coords": { + "3dSets": [ + [ + [0.000, 0.000, 0.000], + [0.957, 0.000, 0.000], + [-0.239, 0.927, 0.000] + ], + [ + [0.000, 0.000, 0.010], + [0.957, 0.000, 0.010], + [-0.239, 0.927, 0.010] + ] + ] + } + } + \ No newline at end of file