From 62fda3e3e660302c3f70f61cf141594aced1d9cd Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Mon, 11 Feb 2019 10:30:28 -0800
Subject: [PATCH] transformer docs tweaks
---
README.md | 2 +-
docs/state/transforms.md | 54 ++++++++++++++++++++++++++++++++++------
src/mol-plugin/layout.ts | 11 +++++---
3 files changed, 55 insertions(+), 12 deletions(-)
diff --git a/README.md b/README.md
index 1ad2a6da9..d35442edd 100644
--- a/README.md
+++ b/README.md
@@ -119,7 +119,7 @@ Run the image
**State Transformer Docs**
- node build/state-docs
+ export NODE_PATH="build/src"; node build/state-docs
## Contributing
Just open an issue or make a pull request. All contributions are welcome.
diff --git a/docs/state/transforms.md b/docs/state/transforms.md
index 5c97d1e98..f02e38b68 100644
--- a/docs/state/transforms.md
+++ b/docs/state/transforms.md
@@ -5,6 +5,7 @@
* [ms-plugin.read-file](#ms-plugin-read-file)
* [ms-plugin.parse-cif](#ms-plugin-parse-cif)
* [ms-plugin.parse-ccp4](#ms-plugin-parse-ccp4)
+* [ms-plugin.parse-dsn6](#ms-plugin-parse-dsn6)
* [ms-plugin.trajectory-from-mmcif](#ms-plugin-trajectory-from-mmcif)
* [ms-plugin.model-from-trajectory](#ms-plugin-model-from-trajectory)
* [ms-plugin.structure-from-model](#ms-plugin-structure-from-model)
@@ -13,6 +14,7 @@
* [ms-plugin.structure-complex-element](#ms-plugin-structure-complex-element)
* [ms-plugin.custom-model-properties](#ms-plugin-custom-model-properties)
* [ms-plugin.volume-from-ccp4](#ms-plugin-volume-from-ccp4)
+* [ms-plugin.volume-from-dsn6](#ms-plugin-volume-from-dsn6)
* [ms-plugin.representation-highlight-loci](#ms-plugin-representation-highlight-loci)
* [ms-plugin.representation-select-loci](#ms-plugin-representation-select-loci)
* [ms-plugin.default-loci-label-provider](#ms-plugin-default-loci-label-provider)
@@ -63,7 +65,11 @@
----------------------------
## <a name="ms-plugin-parse-ccp4"></a>ms-plugin.parse-ccp4 :: Binary -> Ccp4
-*Parse CCP4 from Binary data*
+*Parse CCP4/MRC from Binary data*
+
+----------------------------
+## <a name="ms-plugin-parse-dsn6"></a>ms-plugin.parse-dsn6 :: Binary -> Dsn6
+*Parse CCP4/BRIX from Binary data*
----------------------------
## <a name="ms-plugin-trajectory-from-mmcif"></a>ms-plugin.trajectory-from-mmcif :: Cif -> Trajectory
@@ -98,13 +104,11 @@
*Create a molecular structure assembly.*
### Parameters
-- **id**: String *(Assembly Id. If none specified (undefined or empty string), the asymmetric unit is used.)*
+- **id**?: String *(Assembly Id. If none specified (undefined or empty string), the asymmetric unit is used.)*
### Default Parameters
```js
-{
- "id": ""
-}
+{}
```
----------------------------
## <a name="ms-plugin-structure-selection"></a>ms-plugin.structure-selection :: Structure -> Structure
@@ -150,6 +154,23 @@
### Parameters
- **voxelSize**: 3D vector [x, y, z]
+### Default Parameters
+```js
+{
+ "voxelSize": [
+ 1,
+ 1,
+ 1
+ ]
+}
+```
+----------------------------
+## <a name="ms-plugin-volume-from-dsn6"></a>ms-plugin.volume-from-dsn6 :: Dsn6 -> Data
+*Create Volume from DSN6/BRIX data*
+
+### Parameters
+- **voxelSize**: 3D vector [x, y, z]
+
### Default Parameters
```js
{
@@ -445,7 +466,12 @@ Object with:
- **doubleSided**: true/false
- **flipSided**: true/false
- **flatShaded**: true/false
- - **isoValue**: Numeric value
+ - **isoValue**: - **absolute**: Numeric value
+ - **relative**: Numeric value
+
+ - **sizeFactor**: Numeric value
+ - **lineSizeAttenuation**: true/false
+ - **visuals**: Array of 'solid', 'wireframe'
- **direct-volume**:
Object with:
@@ -540,7 +566,21 @@ Object with:
"doubleSided": false,
"flipSided": false,
"flatShaded": false,
- "isoValue": 0.22
+ "isoValue": {
+ "kind": "relative",
+ "stats": {
+ "min": 0,
+ "max": 0,
+ "mean": 0,
+ "sigma": 0
+ },
+ "relativeValue": 2
+ },
+ "sizeFactor": 1,
+ "lineSizeAttenuation": false,
+ "visuals": [
+ "solid"
+ ]
}
},
"colorTheme": {
diff --git a/src/mol-plugin/layout.ts b/src/mol-plugin/layout.ts
index e4b32f576..bca2e2cd1 100644
--- a/src/mol-plugin/layout.ts
+++ b/src/mol-plugin/layout.ts
@@ -172,9 +172,12 @@ export class PluginLayout extends PluginComponent<PluginLayoutStateProps> {
PluginCommands.Layout.Update.subscribe(context, e => this.updateProps(e.state));
- // <meta name='viewport' content='width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=0' />
- this.expandedViewport = document.createElement('meta') as any;
- this.expandedViewport.name = 'viewport';
- this.expandedViewport.content = 'width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=0';
+ // TODO how best make sure it runs on node.js as well as in the browser?
+ if (typeof document !== 'undefined') {
+ // <meta name='viewport' content='width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=0' />
+ this.expandedViewport = document.createElement('meta') as any;
+ this.expandedViewport.name = 'viewport';
+ this.expandedViewport.content = 'width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=0';
+ }
}
}
\ No newline at end of file
--
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