add ability to upload a cif to be converted (#59)

* add ability to upload a cif to be converted

Author: jacobfilik

web-conexs-api/src/web_conexs_api/jobfilebuilders.py

@@ -1,9 +1,13 @@
 import io
+import logging
 from pathlib import Path
 from typing import List
 
 import numpy as np
+from pymatgen.analysis.graphs import StructureGraph
+from pymatgen.analysis.local_env import JmolNN
 from pymatgen.core import Lattice, Structure
+from pymatgen.io.cif import CifParser
 
 from .models.models import (
     ChemicalSite,
@@ -20,6 +24,8 @@
 from .models.models import Lattice as CrystalLattice
 from .periodictable import elements, periodic_table_by_z
 
+logger = logging.getLogger(__name__)
+
 
 def sites_to_string(sites: List[ChemicalSite], use_symbol=True, absorbing_index=None):
     structure_string = ""
@@ -411,3 +417,50 @@ def pymatstruct_to_crystal(structure: Structure, label="materials project struct
     s = CrystalStructureInput(label=label, sites=site_list, lattice=lattice)
 
     return s
+
+
+def cif_string_to_molecule(cif_string: str):
+    try:
+        cif_file = io.StringIO(cif_string)
+        parser = CifParser(cif_file)
+        structure = parser.parse_structures(primitive=True)
+        structure = structure[0]
+        sg = StructureGraph.from_local_env_strategy(structure, JmolNN())
+        my_molecules = sg.get_subgraphs_as_molecules()
+
+        if len(my_molecules) == 0 or len(my_molecules[0]) == 0:
+            return None
+
+        new_sites = []
+
+        for i, s in enumerate(my_molecules[0]):
+            new_sites.append(
+                ChemicalSite(
+                    element_z=s.specie.number,
+                    x=s.x,
+                    y=s.y,
+                    z=s.z,
+                    index=i,
+                )
+            )
+
+        molecule: ChemicalStructure = ChemicalStructure(
+            label="Generated from cif",
+            sites=new_sites,
+        )
+        return molecule
+    except Exception as e:
+        logger.exception(f"Could not parse cif to molecule {e}")
+        return None
+
+
+def cif_string_to_crystal(cif_string: str):
+    try:
+        cif_file = io.StringIO(cif_string)
+        parser = CifParser(cif_file)
+        structure = parser.parse_structures(primitive=True)
+        structure = structure[0]
+        print(structure.sites[0].species.elements[0])
+        return pymatstruct_to_crystal(structure, label="Generated from cif")
+    except Exception as e:
+        logger.exception(f"Could not parse cif to crystal {e}")

web-conexs-api/src/web_conexs_api/routers/structures.py

@@ -1,6 +1,6 @@
 from typing import List
 
-from fastapi import APIRouter, Depends
+from fastapi import APIRouter, Depends, HTTPException, Request
 from sqlmodel import Session
 
 from ..auth import get_current_user
@@ -10,6 +10,7 @@
     upload_structure,
 )
 from ..database import get_session
+from ..jobfilebuilders import cif_string_to_crystal, cif_string_to_molecule
 from ..models.models import (
     CrystalStructure,
     CrystalStructureInput,
@@ -49,3 +50,35 @@ def get_structure_list_endpoint(
 ) -> List[StructureWithMetadata]:
     output = get_structures(session, user_id, type)
     return output
+
+
+@router.post("/convert/molecule")
+async def convert_to_molecule(
+    request: Request,
+    user_id: str = Depends(get_current_user),
+) -> MolecularStructureInput:
+    body = await request.body()
+    molecule = cif_string_to_molecule(body.decode())
+
+    if molecule is None:
+        raise HTTPException(
+            status_code=422, detail="Could not extract structure from file"
+        )
+
+    return molecule
+
+
+@router.post("/convert/crystal")
+async def convert_to_crystal(
+    request: Request,
+    user_id: str = Depends(get_current_user),
+) -> CrystalStructureInput:
+    body = await request.body()
+    crystal = cif_string_to_crystal(body.decode())
+
+    if not crystal:
+        raise HTTPException(
+            status_code=422, detail="Could not extract structure from file"
+        )
+
+    return crystal

web-conexs-api/tests/test_cif_to_structure.py

@@ -0,0 +1,22 @@
+from web_conexs_api.jobfilebuilders import cif_string_to_crystal, cif_string_to_molecule
+
+cif_h_string = (
+    "data_1\n\n_symmetry_space_group_name_H-M   P-1\n"
+    + "loop_\n_symmetry_equiv_pos_site_id\n_symmetry_equiv_pos_as_xyz\n1 +x,+y,+z\n\n"
+    + "_cell_angle_alpha 90\n_cell_angle_beta 90\n_cell_angle_gamma 90\n "
+    + "_cell_length_a 4.1043564\n_cell_length_b 4.1043564"
+    + "\n_cell_length_c 4.1043564\n\n\n"
+    + "loop_\n_atom_site_label\n_atom_site_type_symbol\n_atom_site_fract_x\n"
+    + "_atom_site_fract_y\n_atom_site_fract_z\nH_0 H 0 0 0\nH_1 H 0.1 0.1 0.1"
+)
+
+
+def test_cif_string_to_molecule():
+    molecule = cif_string_to_molecule(cif_h_string)
+    assert len(molecule.sites) == 2
+
+
+def test_cif_string_to_crystal():
+    crystal = cif_string_to_crystal(cif_h_string)
+    print(crystal)
+    assert crystal.lattice.alpha == 90

web-conexs-api/tests/test_jobfile_builder.py

@@ -42,8 +42,6 @@ def test_orca_scf_filebuilder():
 
     jobfile = build_orca_input_file(test_model, test_structure)
 
-    print(jobfile)
-
     assert "P_ReducedOrbPopMO_L" in jobfile
     assert "!ReducedPop UNO" in jobfile
 
@@ -174,7 +172,6 @@ def test_qe_filebuilder():
     assert "nat = 2" in jobfile
     assert "ntyp = 2" in jobfile
 
-    print(jobfile)
     jobfile_array = jobfile.split("\n")
 
     species_line = -1

web-conexs-client/src/components/ConvertFromCif.tsx

@@ -0,0 +1,112 @@
+import {
+  Button,
+  Card,
+  CircularProgress,
+  Stack,
+  Typography,
+} from "@mui/material";
+import VisuallyHiddenInput from "./VisuallyHiddenInput";
+import { useMutation } from "@tanstack/react-query";
+import { postConvertCrystal, postConvertMolecule } from "../queryfunctions";
+import { CrystalInput, MoleculeInput } from "../models";
+import { useState } from "react";
+import CheckCircleIcon from "@mui/icons-material/CheckCircle";
+import ErrorIcon from "@mui/icons-material/Error";
+import GrainIcon from "./icons/GrainIcon";
+import MoleculeIcon from "./icons/MoleculeIcon";
+
+function getConvertIcon(state: string, molecule: boolean) {
+  if (state == "ok") {
+    return <CheckCircleIcon />;
+  } else if (state == "failed") {
+    return <ErrorIcon />;
+  } else if (state == "running") {
+    return <CircularProgress size="1em" />;
+  }
+
+  return molecule ? <MoleculeIcon /> : <GrainIcon />;
+}
+
+export default function ConvertFromCif(props: {
+  isFractional: boolean;
+  setStructure: (moleculeInput: MoleculeInput | CrystalInput | null) => void;
+}) {
+  const [textFile, setTextFile] = useState<string | null>(null);
+  const [filename, setFileName] = useState<string | null>(null);
+
+  const [convertState, setConvertState] = useState<
+    "default" | "ok" | "failed" | "running"
+  >("default");
+
+  const mutation = useMutation({
+    mutationFn: props.isFractional ? postConvertCrystal : postConvertMolecule,
+    onSuccess: (data) => {
+      props.setStructure(data);
+      setConvertState("ok");
+      setTimeout(() => setConvertState("default"), 2000);
+    },
+    onError: () => {
+      setConvertState("failed");
+      setTimeout(() => setConvertState("default"), 2000);
+    },
+  });
+
+  //   mutation.data
+  const handleFile = (event: React.ChangeEvent<HTMLInputElement>) => {
+    if (!event.target.files) return;
+    const file = event.target.files[0];
+    setFileName(file.name);
+
+    if (file.name.endsWith(".cif")) {
+      const reader = new FileReader();
+      reader.onload = function () {
+        const content = reader.result as string;
+
+        setTextFile(content);
+      };
+      reader.readAsText(file); // Read the file as text
+    }
+  };
+
+  const title = props.isFractional
+    ? "Convert from Crystal Cif File"
+    : "Convert from Molecular Crystal Cif File";
+
+  return (
+    <Card>
+      <Stack>
+        <Typography>{title}</Typography>
+        <Stack direction="row" spacing="5px" margin="5px">
+          <Button
+            variant="contained"
+            type="submit"
+            role={undefined}
+            tabIndex={-1}
+            component="label"
+          >
+            Upload
+            <VisuallyHiddenInput
+              type="file"
+              name="file1"
+              onChange={handleFile}
+            />
+          </Button>
+          <Button
+            variant="outlined"
+            disabled={textFile == null}
+            onClick={() => {
+              if (textFile != null) {
+                setConvertState("running");
+                mutation.mutate(textFile);
+              }
+            }}
+            endIcon={getConvertIcon(convertState, !props.isFractional)}
+          >
+            Run Convert
+          </Button>
+          <Typography>{filename ? filename : "No file"}</Typography>
+        </Stack>
+      </Stack>
+    </Card>
+  );
+}

web-conexs-client/src/components/VisuallyHiddenInput.tsx

@@ -0,0 +1,15 @@
+import { styled } from "@mui/material/styles";
+
+const VisuallyHiddenInput = styled("input")({
+  clip: "rect(0 0 0 0)",
+  clipPath: "inset(50%)",
+  height: 1,
+  overflow: "hidden",
+  position: "absolute",
+  bottom: 0,
+  left: 0,
+  whiteSpace: "nowrap",
+  width: 1,
+});
+
+export default VisuallyHiddenInput;

web-conexs-client/src/components/XYZEditor.tsx

@@ -1,6 +1,7 @@
-import { TextField } from "@mui/material";
+import { Stack, TextField } from "@mui/material";
 import { useState } from "react";
-import { validateMoleculeData } from "../utils";
+import { inputToXYZNoHeader, validateMoleculeData } from "../utils";
+import ConvertFromCif from "./ConvertFromCif";
 
 export default function XYZEditor(props: {
   structure: string;
@@ -26,22 +27,37 @@ export default function XYZEditor(props: {
   };
 
   return (
-    <TextField
-      error={errorMessage.length != 0}
-      sx={{ width: "100%" }}
-      id="datafilebox"
-      label={
-        props.isFractional
-          ? "Atomic Coordinates (Fractional)"
-          : "Atomic Coordinates (Angstroms)"
-      }
-      rows={12}
-      multiline
-      value={data}
-      helperText={errorMessage}
-      onChange={(e) => {
-        onChange(e.target.value);
-      }}
-    />
+    <Stack spacing="10px">
+      <TextField
+        error={errorMessage.length != 0}
+        sx={{ width: "100%" }}
+        id="datafilebox"
+        label={
+          props.isFractional
+            ? "Atomic Coordinates (Fractional)"
+            : "Atomic Coordinates (Angstroms)"
+        }
+        rows={12}
+        multiline
+        value={data}
+        helperText={errorMessage}
+        onChange={(e) => {
+          onChange(e.target.value);
+        }}
+      />
+
+      <ConvertFromCif
+        setStructure={(structure) => {
+          if (structure == null) {
+            return;
+          }
+          const s = inputToXYZNoHeader(structure);
+          props.setStructure(s);
+          setData(s);
+          setErrorMessage("");
+        }}
+        isFractional={props.isFractional}
+      ></ConvertFromCif>
+    </Stack>
   );
 }

web-conexs-client/src/components/crystals/CreateCrystalPage.tsx

@@ -66,23 +66,25 @@ export default function CreateCystalPage() {
             Create Crystal
           </Typography>
         </Toolbar>
-        <Stack direction={"row"} spacing="5px" margin="5px">
-          <CrystalEditor crystal={crystal} setCrystal={setCrytal} />
+        <Stack direction={"row"} margin="10px">
+          <Stack spacing="10px" margin="10px">
+            <CrystalEditor crystal={crystal} setCrystal={setCrytal} />
+            <Button
+              variant="contained"
+              onClick={() => {
+                if (crystal != null) {
+                  mutation.mutate(crystal);
+                }
+              }}
+            >
+              Create
+            </Button>
+          </Stack>
           <MolStarCrystalWrapper
             cif={crystal == null ? null : crystalInputToCIF(crystal)}
             labelledAtomIndex={undefined}
           />
         </Stack>
-        <Button
-          variant="contained"
-          onClick={() => {
-            if (crystal != null) {
-              mutation.mutate(crystal);
-            }
-          }}
-        >
-          Create
-        </Button>
       </Stack>
     </MainPanel>
   );