added random-coil-index coloring based on validation report xml file

ngl.sublime-project

@@ -1,42 +1,42 @@
 {
-    "folders":
-    [
-        {
-            "path": "."
-        }
-    ],
-    "settings":
-    {
-        "tab_size": 4,
-        "translate_tabs_to_spaces": false,
-        "trim_trailing_white_space_on_save": true
-    },
-    "build_systems":
-    [
-        {
-            "name": "Lint",
-            "shell_cmd": "npm run-script lint",
-            "working_dir": "${project_path}",
-        },
-        {
-            "name": "Test",
-            "shell_cmd": "npm test",
-            "working_dir": "${project_path}",
-        },
-        {
-            "name": "Build",
-            "shell_cmd": "npm run-script build",
-            "working_dir": "${project_path}",
-        },
-        {
-            "name": "Watch",
-            "shell_cmd": "npm run-script watch",
-            "working_dir": "${project_path}",
-        },
-        {
-            "name": "Rollup",
-            "shell_cmd": "rollup -c",
-            "working_dir": "${project_path}",
-        }
-    ]
+	"build_systems":
+	[
+		{
+			"name": "Lint",
+			"shell_cmd": "npm run-script lint",
+			"working_dir": "${project_path}"
+		},
+		{
+			"name": "Test",
+			"shell_cmd": "npm test",
+			"working_dir": "${project_path}"
+		},
+		{
+			"name": "Build",
+			"shell_cmd": "npm run-script build",
+			"working_dir": "${project_path}"
+		},
+		{
+			"name": "Watch",
+			"shell_cmd": "npm run-script watch",
+			"working_dir": "${project_path}"
+		},
+		{
+			"name": "Rollup",
+			"shell_cmd": "rollup -c",
+			"working_dir": "${project_path}"
+		}
+	],
+	"folders":
+	[
+		{
+			"path": "."
+		}
+	],
+	"settings":
+	{
+		"tab_size": 4,
+		"translate_tabs_to_spaces": false,
+		"trim_trailing_white_space_on_save": true
+	}
 }

src/color/randomcoilindex-colormaker.ts

@@ -0,0 +1,43 @@
+/**
+ * @file Randomcoilindex Colormaker
+ * @author Alexander Rose <[email protected]>
+ * @private
+ */
+
+import { ColormakerRegistry } from '../globals'
+import Colormaker, { StuctureColormakerParams, ColormakerScale } from './colormaker'
+import AtomProxy from '../proxy/atom-proxy'
+
+/**
+ * Color by random coil index
+ */
+class RandomcoilindexColormaker extends Colormaker {
+  rciScale: ColormakerScale
+  rciDict: { [k: string]: number|undefined } = {}
+
+  constructor (params: StuctureColormakerParams) {
+    super(params)
+
+    if (!params.scale) {
+      this.parameters.scale = 'RdYlBu'
+    }
+
+    this.rciScale = this.getScale({ domain: [ 1, 0 ] })
+
+    const val = params.structure.validation
+    if (val) this.rciDict = val.rciDict
+
+  }
+
+  atomColor (atom: AtomProxy) {
+    let sele = `[${atom.resname}]${atom.resno}`
+    if (atom.chainname) sele += ':' + atom.chainname
+
+    const rci = this.rciDict[ sele ]
+    return rci !== undefined ? this.rciScale(rci) : 0x909090
+  }
+}
+
+ColormakerRegistry.add('randomcoilindex', RandomcoilindexColormaker as any)
+
+export default RandomcoilindexColormaker

src/ngl.ts

@@ -62,6 +62,7 @@ import './color/moleculetype-colormaker'
 import './color/occupancy-colormaker'
 import './color/partialcharge-colormaker'
 import './color/random-colormaker'
+import './color/randomcoilindex-colormaker'
 import './color/residueindex-colormaker'
 import './color/resname-colormaker'
 import './color/sstruc-colormaker'

src/structure/validation.ts

@@ -20,18 +20,27 @@ function getNamedItem(a: NamedNodeMap, name: string) {
 }
 
 function getSele (a: NamedNodeMap, atomname?: string, useAltcode = false) {
-  const icode = getNamedItem(a, 'icode')
-  const chain = getNamedItem(a, 'chain')
+  const icode = getNamedItem(a, 'icode').trim()
+  const chain = getNamedItem(a, 'chain').trim()
   const altcode = getNamedItem(a, 'altcode')
   let sele = getNamedItem(a, 'resnum')
-  if (icode.trim()) sele += '^' + icode
-  if (chain.trim()) sele += ':' + chain
+  if (icode) sele += '^' + icode
+  if (chain) sele += ':' + chain
   if (atomname) sele += '.' + atomname
   if (useAltcode && altcode.trim()) sele += '%' + altcode
   sele += '/' + (parseInt(getNamedItem(a, 'model')) - 1)
   return sele
 }
 
+function getResSele (a: NamedNodeMap) {
+  const chain = getNamedItem(a, 'chain').trim()
+  const rescode = getNamedItem(a, 'rescode')
+  const resnum = getNamedItem(a, 'resnum')
+  let sele = `[${rescode}]${resnum}`
+  if (chain) sele += `:${chain}`
+  return sele
+}
+
 function setBitDict (dict: { [k: string]: number }, key: string, bit: number) {
   if (dict[ key ] === undefined) {
     dict[ key ] = bit
@@ -102,14 +111,30 @@ function getProblemCount (clashDict: { [k: string]: { [k: string]: string } }, g
 class Validation {
   rsrzDict: { [k: string]: number } = {}
   rsccDict: { [k: string]: number } = {}
+  /**
+   * Random Coil Index (RCI) - evaluates the proximity of residue structural
+   * and dynamic properties to the properties of flexible random coil regions
+   * from NMR chemical shifts.
+   *
+   * Mark V. Berjanskii and David S. Wishart (2005)
+   * A Simple Method To Predict Protein Flexibility Using Secondary Chemical Shifts
+   * J. Am. Chem. Soc., 2005, 127 (43), pp 14970–14971
+   * http://pubs.acs.org/doi/abs/10.1021/ja054842f
+   *
+   * Mark V. Berjanskii and David S. Wishart (2008)
+   * Application of the random coil index to studying protein flexibility.
+   * J Biomol NMR. 2008 Jan;40(1):31-48. Epub 2007 Nov 6.
+   * http://www.springerlink.com/content/2966482w10306126/
+   */
+  rciDict: { [k: string]: number } = {}
   clashDict: { [k: string]: { [k: string]: string } } = {}
   clashArray: { [k: string]: string }[] = []
   geoDict: { [k: string]: number } = {}
   geoAtomDict: { [k: string]: { [k: string]: number } } = {}
   atomDict: { [k: string]: boolean|number } = {}
   clashSele = 'NONE'
 
-  constructor (readonly name: string, readonlypath: string) {}
+  constructor (readonly name: string, readonly path: string) {}
 
   get type () { return 'validation' }
 
@@ -118,12 +143,26 @@ class Validation {
 
     const rsrzDict = this.rsrzDict
     const rsccDict = this.rsccDict
+    const rciDict = this.rciDict
     const clashDict = this.clashDict
     const clashArray = this.clashArray
     const geoDict = this.geoDict
     const geoAtomDict = this.geoAtomDict
     const atomDict = this.atomDict
 
+    const entries = xml.getElementsByTagName('Entry')
+    if (entries.length === 1) {
+      const chemicalShiftLists = entries[0].getElementsByTagName('chemical_shift_list')
+      if (chemicalShiftLists.length === 1) {
+        const randomCoilIndices = chemicalShiftLists[0].getElementsByTagName('random_coil_index')
+        for (let j = 0, jl = randomCoilIndices.length; j < jl; ++j) {
+          const rcia = randomCoilIndices[ j ].attributes
+          const sele = getResSele(rcia)
+          rciDict[ sele ] = parseFloat(getNamedItem(rcia, 'value'))
+        }
+      }
+    }
+
     const groups = xml.getElementsByTagName('ModelledSubgroup')
 
     const _clashDict: { [k: string]: { [k: string]: string } } = {}