Merge pull request #98 from glycojones/alphafold-update

Update Web App to allow AlphaFold 3 Structure Input
glycojones · May 22, 2024 · a2a9e84 · a2a9e84
2 parents 71c0022 + e53f81b
commit a2a9e84
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Showing 3 changed files with 14 additions and 6 deletions.
diff --git a/src/privateer/cpp/privateer-bind.cpp b/src/privateer/cpp/privateer-bind.cpp
@@ -50,14 +50,19 @@ clipper::MiniMol read_molecule(const std::string &file, const std::string &name)
   }
   ::gemmi::Structure structure = ::gemmi::read_structure_from_char_array(c_data, size, name);
   std::cout << "[Privateer] Successfully read structure" << std::endl;
+
+  if (structure.spacegroup_hm == "") {
+    std::cout << "[Privateer] This structure has no spacegroup specified, setting to P1." << std::endl;
+    structure.spacegroup_hm = "P 1";
+  }
+
   clipper::GEMMIFile gemmi_file;
   clipper::GemmiStructure *gemmi_structure = &gemmi_file;
   gemmi_structure->structure_ = structure;
   clipper::MiniMol mol;
   gemmi_file.import_minimol(mol);
 
-   clipper::Cell cell = mol.cell();
-   std::cout << cell.format() << std::endl;
+  clipper::Cell cell = mol.cell();
   if (cell.a() == 1.0 && cell.b() == 1.0 && cell.c() == 1.0 ) {
       std::cout << "[Privateer] This cell is 1A, inflating the cell but this will lose crystal contact information" << std::endl;
       mol.init ( clipper::Spacegroup::p1(), clipper::Cell(clipper::Cell_descr ( 300, 300, 300, 90, 90, 90 )) );

diff --git a/webapp/src/modals/Citations/Citations.tsx b/webapp/src/modals/Citations/Citations.tsx
@@ -76,10 +76,13 @@ export default function CitationModal(props: {
                     </strong>
                 </div>
 
-                {/* <div className="mt-4 flex flex-col space-y-2"> */}
-                {/*    <h3>If you have used the <b><i>Privateer Database</i></b>, please cite: </h3> */}
-                {/*    <span>Dialpuri, J. S., Bagdonas, H., Schofield, L. C., Pham, P. T., Holland, L., Bond, P. S., Sánchez Rodríguez, F., McNicholas, S. J. & Agirre, J. (2024). Online carbohydrate 3D structure validation with the Privateer web app. Acta Cryst. F80. https://doi.org/10.1107/S2053230X24000359</span> */}
-                {/* </div> */}
+                 <div className="mt-4 flex flex-col space-y-2">
+                    <h3>If you have used the <b><i>Privateer Database</i></b>, please cite: </h3>
+
+                    <strong>Dialpuri, J. S.; Bagdonas, H.; Schofield, L. C.; Pham, P. T.; Holland, L.; Agirre, J. Beilstein J. Org. Chem. 2024, 20, 931–939.
+                        <p><a href="https://doi.org/10.3762/bjoc.20.83" target="_blank">https://doi.org/10.3762/bjoc.20.83</a></p>
+                    </strong>
+                 </div>
 
                 <div className="mt-4 flex flex-col space-y-2 font text-sm sm:text-base">
                     <h3>

diff --git a/webapp/src/wasm/privateer.wasm b/webapp/src/wasm/privateer.wasm