Merge branch 'develop' into trunk

.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 +1,7 @@
+Version 2.2.0
+- Added option to write out source of data into json file
+- Updated node modules
+
 Version 2.1.1
 - Fix a bug that caused too many residues being placed where
   they are not unique.

docroot/alphafill.json.schema

@@ -14,6 +14,11 @@
                     "description": "Date of AlphaFill run",
                     "type": "string"
                 },
+                "source": {
+                    "description": "Data source for input model",
+                    "type": "string",
+                    "enum": ["AFDB", "BFVD", "user"]
+                },
                 "file": {
                     "description": "Input file used for AlphaFill",
                     "type": "string"
@@ -277,4 +282,4 @@
     },
     "title": "Validation"
     }
-}}
+}}

docroot/model.html

@@ -45,10 +45,22 @@ <h5 z:text="${title}"></h5>
 				<td><a z:href="@{/v1/aff/${af_id}/json}"
 						z:text="|${af_id}/json|"></a></td>
 			</tr>
-			<tr>
-				<td>Original AlphaFold model</td>
-				<td><a z:href="|https://alphafold.ebi.ac.uk/entry/${id}|"
-						z:text="|https://alphafold.ebi.ac.uk/entry/${id}|" target="_BLANK"></a></td>
+
+			<tr z:switch="${source}">
+				<z:block z:case="BFVD">
+					<td>Original BFVD model</td>
+					<td>
+						<a z:href="|https://bfvd.foldseek.com/cluster/${id}|"
+							z:text="|https://bfvd.foldseek.com/cluster/${id}|" target="_BLANK"></a>
+					</td>
+				</z:block>
+				<z:block z:case="*">
+					<td>Original AlphaFold model</td>
+					<td>
+						<a z:href="|https://alphafold.ebi.ac.uk/entry/${id}|"
+							z:text="|https://alphafold.ebi.ac.uk/entry/${id}|" target="_BLANK"></a>
+					</td>
+				</z:block>
 			</tr>
 		</table>
 

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

@@ -492,7 +492,8 @@ void check_blast_index()
 
 // --------------------------------------------------------------------
 
-zeep::json::element alphafill(cif::datablock &db, const std::vector<PAE_matrix> &v_pae, alphafill_progress_cb &&progress)
+zeep::json::element alphafill(cif::datablock &db, const std::string &source,
+	const std::vector<PAE_matrix> &v_pae, alphafill_progress_cb &&progress)
 {
 	using namespace std::literals;
 	using namespace cif::literals;
@@ -542,7 +543,8 @@ zeep::json::element alphafill(cif::datablock &db, const std::vector<PAE_matrix>
 	json result = {
 		{ "id", afID },
 		{ "date", ss.str() },
-		{ "alphafill_version", kVersionNumber }
+		{ "alphafill_version", kVersionNumber },
+		{ "source", source }
 	};
 
 	json &hits = result["hits"] = json::array();
@@ -970,6 +972,11 @@ 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},
@@ -1071,6 +1078,12 @@ zeep::json::element alphafill(cif::datablock &db, const std::vector<PAE_matrix>
 								// now fix up the newly created residue
 								ligand.modify(af_structure, asym_id);
 
+								// Give all the atoms in the newly created residue an alt_id with the same
+								// value as the asym_id, improves rendering in molstar
+
+								for (auto atom : res.atoms())
+									atom.set_property("label_alt_id", asym_id);
+
 								// validation info?
 								if (hsp.identity() == 1)
 								{
@@ -1105,11 +1118,15 @@ zeep::json::element alphafill(cif::datablock &db, const std::vector<PAE_matrix>
 	af_structure.cleanup_empty_categories();
 
 	auto &software = af_structure.get_category("software");
-	software.emplace({ { "pdbx_ordinal", software.size() + 1 }, // TODO: should we check this ordinal number???
+	software.emplace({
+		//
+		{ "pdbx_ordinal", software.size() + 1 }, // TODO: should we check this ordinal number???
 		{ "name", "alphafill" },
 		{ "version", kVersionNumber },
 		{ "date", kRevisionDate },
-		{ "classification", "model annotation" } });
+		{ "classification", "model annotation" }
+		//
+	});
 
 	return result;
 }
@@ -1174,6 +1191,8 @@ int alphafill_main(int argc, char *const argv[])
 		mcfp::make_hidden_option<int>("blast-gap-open", 11, "Blast penalty for gap open"),
 		mcfp::make_hidden_option<int>("blast-gap-extend", 1, "Blast penalty for gap extend"),
 
+		mcfp::make_option("data-source", "user", "Data source for input model"),
+
 		mcfp::make_option<size_t>("threads,t", std::thread::hardware_concurrency(), "Number of threads to use, zero means all available cores"),
 
 		mcfp::make_hidden_option<std::string>("custom-dir", (fs::temp_directory_path() / "alphafill").string(), "Directory for custom built entries")
@@ -1215,6 +1234,12 @@ int alphafill_main(int argc, char *const argv[])
 		return 1;
 	}
 
+	if (config.get("data-source") != "AFDB" and config.get("data-source") != "BFVD" and config.get("data-source") != "user")
+	{
+		std::cerr << "Invalid data-source, allowed values are 'AFDB', 'BFVD' and 'user'\n";
+		return 1;
+	}
+
 	fs::path paein;
 
 	if (config.has("pae-file"))
@@ -1239,7 +1264,7 @@ int alphafill_main(int argc, char *const argv[])
 	if (fs::exists(paein))
 		v_pae = load_pae_from_file(paein);
 
-	json metadata = alphafill(f.front(), v_pae, my_progress{});
+	json metadata = alphafill(f.front(), config.get("data-source"), v_pae, my_progress{});
 
 	if (config.operands().size() == 2)
 	{

src/alphafill.hpp

@@ -44,7 +44,8 @@ struct alphafill_progress_cb
 
 using PAE_matrix = cif::matrix<uint8_t>;
 
-zeep::json::element alphafill(cif::datablock &db, const std::vector<PAE_matrix> &pae, alphafill_progress_cb &&progress);
+zeep::json::element alphafill(cif::datablock &db, const std::string &source,
+	const std::vector<PAE_matrix> &pae, alphafill_progress_cb &&progress);
 int alphafill_main(int argc, char *const argv[]);
 
 int create_index(int argc, char *const argv[]);

src/blast.cpp

@@ -1001,6 +1001,7 @@ struct DiagonalStartTable
 {
 	DiagonalStartTable()
 		: mTable(nullptr)
+		, mTableLength(0)
 	{
 	}
 	~DiagonalStartTable() { delete[] mTable; }

src/data-service.cpp

@@ -632,7 +632,7 @@ void data_service::process_queued(const std::filesystem::path &xyzin, const std:
 		fs::rename(paein, m_work_dir / paein.filename(), ec);
 	}
 
-	auto metadata = alphafill(f.front(), pae_data, data_service_progress{ m_progress });
+	auto metadata = alphafill(f.front(), "user", pae_data, data_service_progress{ m_progress });
 
 	try
 	{

src/main.cpp

@@ -24,9 +24,9 @@
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
+#include "main.hpp"
 #include "alphafill.hpp"
 #include "config.hpp"
-#include "main.hpp"
 #include "revision.hpp"
 #include "validate.hpp"
 
@@ -38,9 +38,9 @@
 #include <thread>
 
 #if defined(BUILD_WEB_APPLICATION)
-#include "data-service.hpp"
-#include "db-connection.hpp"
-#include "server.hpp"
+# include "data-service.hpp"
+# include "db-connection.hpp"
+# include "server.hpp"
 #endif
 
 namespace fs = std::filesystem;
@@ -76,8 +76,7 @@ int rebuild_db_main(int argc, char *const argv[])
 
 		mcfp::make_option<size_t>("threads,t", std::thread::hardware_concurrency(), "Number of threads to use, zero means all available cores"),
 
-		mcfp::make_hidden_option<std::string>("custom-dir", (fs::temp_directory_path() / "alphafill").string(), "Directory for custom built entries")
-		);
+		mcfp::make_hidden_option<std::string>("custom-dir", (fs::temp_directory_path() / "alphafill").string(), "Directory for custom built entries"));
 
 	parse_argv(argc, argv, config);
 
@@ -199,19 +198,19 @@ int main(int argc, char *const argv[])
 		else
 		{
 			const std::string usage =
-R"(usage: alphafill command [options]
+				R"(usage: alphafill command [options]
 
 where command is one of
 
     create-index   Create a FastA file based on data in the PDB files
                    (A FastA file is required to process files)
     process        Process an AlphaFill structure)"
 #if defined(BUILD_WEB_APPLICATION)
-R"(
+				R"(
     rebuild-db     Rebuild the databank
     server         Start a web server instance)"
 #endif
-R"(
+				R"(
 
 The following options are always recognized:
 )";
@@ -235,7 +234,7 @@ The following options are always recognized:
 
 				if (config.operands().empty())
 					std::cerr << "Missing command"
-							<< "\n\n";
+							  << "\n\n";
 
 				std::cerr << config << '\n';
 				return config.has("help") ? 0 : 1;

src/server.cpp

@@ -573,6 +573,9 @@ void affd_html_controller::model(const zh::request &request, const zh::scope &sc
 		sub.put("title", e.what());
 	}
 
+	// Add the source
+	sub.put("source", data["source"]);
+
 	// TODO: These magic numbers should of course be configurable parameters
 	// 11.43, 3.04 voor global, en 3.10 en 0.92 voor local
 	sub.put("cutoff", json{
@@ -1202,7 +1205,7 @@ 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);
-	// 		}
-	// 	}
-	// });
-
-
 })