Merge branch 'develop' of github.com:PDB-REDO/alphafill into develop

.gitignore

@@ -27,6 +27,7 @@ docs/conf.py
 new-alphafill.conf
 docroot/_sources/
 docroot/_static/
+docroot/dist/
 docroot/.doctrees/
 docroot/.buildinfo
 docroot/**/index.html

CMakeLists.txt

@@ -27,7 +27,7 @@ cmake_minimum_required(VERSION 3.21)
 # set the project name
 project(
   alphafill
-  VERSION 2.1.1
+  VERSION 2.2.0
   LANGUAGES C CXX)
 
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
@@ -132,7 +132,7 @@ if(NOT zeep_FOUND)
 	FetchContent_Declare(
 		zeep
 		GIT_REPOSITORY https://github.com/mhekkel/libzeep.git
-		GIT_TAG v6.0.11)
+		GIT_TAG v6.0.16)
 	FetchContent_MakeAvailable(zeep)
 endif()
 

changelog

@@ -1,3 +1,6 @@
+Version 2.2.0
+- Added support for 
+
 Version 2.1.1
 - Fix a bug that caused too many residues being placed where
   they are not unique.

package.json

@@ -10,7 +10,8 @@
 		"@babel/runtime-corejs3": "^7.16.0",
 		"bootstrap": "^5.1.3",
 		"core-js": "^3.19.1",
-		"molstar": "^2.3.5"
+		"gyp": "^0.5.0",
+		"molstar": "^4.10.0"
 	},
 	"scripts": {
 		"build": "webpack --config webpack.config.js",
@@ -21,17 +22,21 @@
 		"@babel/preset-env": "^7.16.0",
 		"@babel/preset-typescript": "^7.16.0",
 		"@popperjs/core": "^2.10.2",
-		"babel-loader": "^8.2.3",
+		"babel-loader": "^9.2.1",
 		"clean-webpack-plugin": "^4.0.0",
-		"css-loader": "^6.5.0",
+		"css-loader": "^7.1.2",
 		"mini-css-extract-plugin": "^2.4.3",
+		"postcss": "^8.4.49",
+		"postcss-loader": "^8.1.1",
+		"react": "^19.0.0",
+		"react-dom": "^19.0.0",
 		"sass": "^1.43.4",
-		"sass-loader": "^12.3.0",
+		"sass-loader": "^16.0.4",
 		"terser-webpack-plugin": "^5.2.5",
 		"ts-loader": "^9.2.6",
 		"uglifyjs-webpack-plugin": "^2.2.0",
 		"webpack": "^5.60.0",
-		"webpack-cli": "^4.9.1"
+		"webpack-cli": "^6.0.1"
 	},
 	"babel": {
 		"presets": [

src/alphafill.cpp

@@ -973,6 +973,11 @@ zeep::json::element alphafill(cif::datablock &db, const std::vector<PAE_matrix>
 								auto entity_id = af_structure.create_non_poly_entity(comp_id);
 								auto asym_id = af_structure.create_non_poly(entity_id, res.atoms());
 
+								// Hack to get better molstar rendering
+								auto &rres = af_structure.get_residue(asym_id);
+								for (auto &atom : rres.atoms())
+									atom.set_property("label_alt_id", asym_id);
+
 								auto &hsp_t = r_hsp["transplants"].emplace_back(json{
 									{ "compound_id", comp_id },
 									// {"entity_id", entity_id},

src/server.cpp

@@ -1202,7 +1202,7 @@ int server_main(int argc, char *const argv[])
 		if (config.has("no-daemon"))
 			result = server.run_foreground(address, port);
 		else
-			result = server.start(address, port, 1, 16, user);
+			result = server.start(address, port, 16, user);
 	}
 	else if (command == "stop")
 		result = server.stop();

webapp/model.js

@@ -101,36 +101,4 @@ window.addEventListener('load', () => {
 
 		window.location = `v1/aff/${AF_ID}/stripped/${selected.join(',')}/${IDENTITY}`;
 	});
-
-	// // Update PAE matrices
-	// const cv = [...document.querySelectorAll("td.pae-matrix canvas")];
-	// cv.forEach(c => {
-	// 	const ctx = c.getContext("2d");
-
-	// 	const pae = JSON.parse(c.getAttribute("data-pae"));
-
-	// 	const dim = Math.sqrt(pae.length);
-	// 	const scale = 32.0 / dim;
-
-	// 	ctx.scale(scale, scale);
-
-	// 	let i = 0;
-	// 	for (let x = 0; x < dim; ++x)
-	// 	{
-	// 		for (let y = 0; y < dim; ++y)
-	// 		{
-	// 			const v = 1.0 * pae[i];
-	// 			i += 1;
-
-	// 			console.log(v);
-
-	// 			const clr = `hsl(220,60%,${Math.round(25 + 50 * (v / 32.0))}%)`;
-
-	// 			ctx.fillStyle = clr;
-	// 			ctx.fillRect(x, y, 1, 1);
-	// 		}
-	// 	}
-	// });
-
-
 })

webapp/molstar.tsx

@@ -1,31 +1,47 @@
 import "core-js/stable";
 import 'molstar/build/viewer/molstar.css';
 import { StructureSelection } from "molstar/lib/mol-model/structure";
-import { createPlugin } from 'molstar/lib/mol-plugin-ui';
+import { createPluginUI } from 'molstar/lib/mol-plugin-ui';
 import { PluginUIContext } from 'molstar/lib/mol-plugin-ui/context';
-import { DefaultPluginUISpec } from 'molstar/lib/mol-plugin-ui/spec';
+import { DefaultPluginUISpec, PluginUISpec } from 'molstar/lib/mol-plugin-ui/spec';
 import { Script } from "molstar/lib/mol-script/script";
 import { Asset } from 'molstar/lib/mol-util/assets';
+import { PluginConfig } from "molstar/lib/mol-plugin/config";
+import { renderReact18 } from 'molstar/lib/mol-plugin-ui/react18';
 import "regenerator-runtime/runtime";
 
 export { PLUGIN_VERSION as version } from 'molstar/lib/mol-plugin/version';
 export { setDebugMode, setProductionMode } from 'molstar/lib/mol-util/debug';
 
+const AlphaFillMolstarSpec: PluginUISpec = {
+	...DefaultPluginUISpec(),
+	config: [
+		[PluginConfig.VolumeStreaming.Enabled, false],
+	],
+	layout: {
+		initial: {
+			isExpanded: false,
+			showControls: false
+		}
+	},
+	components: {
+		remoteState: 'none'
+	}
+
+}
+
 export class Viewer {
 	plugin: PluginUIContext
 
 	constructor(element: HTMLElement) {
-		this.plugin = createPlugin(element, {
-			...DefaultPluginUISpec(),
-			layout: {
-				initial: {
-					isExpanded: false,
-					showControls: false
-				}
-			},
-			components: {
-				remoteState: 'none'
-			}
+		this.createPlugin(element);
+	}
+
+	async createPlugin(element: HTMLElement) {
+		this.plugin = await createPluginUI({
+			target: element,
+			spec: AlphaFillMolstarSpec,
+			render: renderReact18
 		});
 	}
 
@@ -35,16 +51,16 @@ export class Viewer {
 
 			const data = await this.plugin.builders.data.rawData({ data: model }, { state: { isGhost: true } });
 			const trajectory = await this.plugin.builders.structure.parseTrajectory(data, 'mmcif');
-	
+
 			await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default', {
 				structure: {
 					name: 'model',
-					params: { }
+					params: {}
 				},
 				showUnitcell: false,
 				representationPreset: 'auto'
 			});
-        });
+		});
 	}
 
 	loadStructureFromUrl(url: string) {
@@ -53,16 +69,16 @@ export class Viewer {
 
 			const data = await this.plugin.builders.data.download({ url: Asset.Url(url), isBinary: false }, { state: { isGhost: true } });
 			const trajectory = await this.plugin.builders.structure.parseTrajectory(data, 'mmcif');
-	
+
 			await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default', {
 				structure: {
 					name: 'model',
-					params: { }
+					params: {}
 				},
 				showUnitcell: false,
 				representationPreset: 'auto'
 			});
-        });
+		});
 	}
 
 	handleResize() {