Doc updates (#18)

* refactor docs

Cargo.toml

@@ -4,7 +4,7 @@ version = "0.1.0"
 edition = "2021"
 
 [dependencies]
-clap = { version = "4.5.9", features = ["derive"] }
+clap = { version = "4.5.11", features = ["derive"] }
 serde = { version = "1.0", features = ["derive"] }
 serde_json = "1.0"
 serde-pickle = "1.1"

docs/_quarto.yml

@@ -10,9 +10,14 @@ website:
     left:
       - href: index.qmd
         text: Home
-      - about.qmd
+      - href: examples.qmd
+        text: Examples
       - href: doc/pseutils/index.html
         text: RustDoc
+    right:
+      - icon: github
+        href: https://github.com/zachcp/pseutils
+        aria-label: GitHub
 
 format:
   html:

docs/examples.qmd

@@ -0,0 +1,29 @@
+---
+title: "Examples"
+format:
+  html:
+    page-layout: full
+---
+
+PSE utils: Conversion of python session files to Molviewspec.
+
+
+## Example PSE
+
+This is a simple example PSE that has a protein object and a selection object. The pymol `PSE` is on the left and the resulting molviewspec is on the right.
+
+```sh
+pseutils --psefile docs/examples/example.pse --outputdir docs/examples/example
+```
+
+:::: {.columns .column-page}
+
+::: {.column width="40%"}
+![](./examples/images/example_pse.png)
+:::
+
+::: {.column width="60%"}
+{{< mol-json ./examples/example/state.mvsj >}}
+:::
+
+::::

docs/index.qmd

@@ -1,16 +1,45 @@
 ---
 title: "pseutils"
-
 ---
 
 
-PSE utils: Conversion of python sessionfiles to Molviewspec.
+PSEutils: Conversion of python session files to Molviewspec.
+
+
+
+## Convert PSE
+
+```sh
+
+# build the binary and test
+cargo build --release
+./target/release/pseutils  --psefile tests/data/example.pse --outputdir binary_test
+
+# outputs a complete directory
+> tree binary_test
+binary_test
+├── index.html
+├── molstar.css
+├── molstar.js
+├── pdb
+│   └── 1pdb.pdb
+├── pdb_contents.txt
+└── state.mvsj
+
+```
+
 
+## Docs and Links
 
-## Example PSE
+PSEUtils:
 
-This is a simple example PSE that has a protein object and a selection object.
+- High Level [Rust Docs](./doc/pseutils)
+- PSE [Rust Parser](./doc/pseutils/pymolparsing/psedata/index.html)
+- MVSJ [Nodes](./doc/pseutils/molviewspec/nodes/index.html)
 
-![](./examples/images/example_pse.png)
+Related:
 
-{{< mol-json ./examples/example/state.mvsj >}}
+- [Pymol-Open-source](https://github.com/schrodinger/pymol-open-source)
+- [mol-view-spec](https://molstar.org/mol-view-spec/)
+- [molstar](https://molstar.org)
+- [molstar-quarto](https://github.com/jmbuhr/quarto-molstar). Used to embed the MVSJ widgets in the page.