Adding conformations ui

BasedLabs · Dec 3, 2023 · a4f63be · a4f63be
1 parent c601edf
commit a4f63be
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Showing 5 changed files with 371 additions and 205 deletions.
diff --git a/src/server/api_handlers/conformations.py b/src/server/api_handlers/conformations.py
@@ -1,6 +1,6 @@
 from flask import Request
 
-#from src.server.services.conformations.conformations_pipeline import permute_simulation
+from src.server.services.conformations.conformations_pipeline import pipeline
 from src.server.services.experiments_structure_loader import ConformationsExperimentsLoader
 from src.server.api_handlers.api_handler import ApiHandler
 
@@ -41,15 +41,35 @@ def inference(self, request: Request) -> dict:
         protein_files = request.files.getlist('proteinFileInput')
         experiment_name = request.form['experimentName']
         experiment_id = request.form['experimentId']
+        total_frames = int(request.form['totalFramesInput'])
+        system_temp = float(request.form['tempInput'])
+        take_frame_every = int(request.form['takeFrameEveryInput'])
+        step_size = float(request.form['stepSizeInput'])
+        replace_nonstandard_residues = True if request.form['replaceNonstandardResiduesInput'] == 'on' else False
+        integrator = request.form['integratorSelect']
+        friction_coeff = float(request.form['frictionCoeffInput'])
+        add_missing_hydrogens = True if request.form['addMissingHydrogensCheckbox'] == 'on' else False
+        add_missing_atoms = True if request.form['addMissingAtomsCheckbox'] == 'on' else False
+        ignore_missing_atoms = True if request.form['ignoreMissingAtomsCheckbox'] == 'on' else False
 
-        #simulation_result = permute_simulation(protein_files[0])
-        simulation_result = ''
+        (simulation_result, errors) = pipeline(pdb_content=protein_files[0],
+                                     total_frames=total_frames,
+                                     take_frame_every=take_frame_every,
+                                     integrator=integrator,
+                                     friction_coeff=friction_coeff,
+                                     step_size=step_size,
+                                     temperature_kelvin=system_temp,
+                                     replace_nonstandard_residues=replace_nonstandard_residues,
+                                     add_missing_atoms=add_missing_atoms,
+                                     add_missing_hydrogens=add_missing_hydrogens,
+                                     ignore_missing=ignore_missing_atoms)
         if simulation_result:
             self.experiments_loader.store_experiment(experiment_id, simulation_result)
             self.experiments_loader.save_experiment_metadata(experiment_id, experiment_name)
 
         return {
             'id': experiment_id,
             'name': experiment_name,
-            'data': {'pdb': simulation_result}
+            'data': {'pdb': simulation_result},
+            'errors': errors
         }
diff --git a/src/server/frontend/src/storage.js b/src/server/frontend/src/storage.js
@@ -167,6 +167,7 @@ const store = createStore({
         },
         async conformations_inference({ commit }, { payload }) {
             const { form, experiment } = payload;
+            debugger;
             const formData = new FormData(form);
             formData.append('experimentId', experiment.id ?? '');
             formData.append('experimentName', experiment.name);

diff --git a/src/server/frontend/src/views/ConformationsFormView.vue b/src/server/frontend/src/views/ConformationsFormView.vue
@@ -5,24 +5,110 @@ export default {
 </script>
 
 <template>
-    <form enctype="multipart/form-data" id="inferenceInputFormConformations"
-        v-on:submit.prevent="onFormSubmit">
-        <div class="row justify-content-center">
-            <div class="col-md-6">
-                <label for="proteinFileInput" class="col-form-label fs-4">.pdb file with molecule conformations</label>
-                <input type="file" multiple="multiple" accept="text/x-pdb" class="form-control" id="proteinFileInput"
-                    name="proteinFileInput">
+    <form enctype="multipart/form-data" id="inferenceInputFormConformations" class="row" v-on:submit.prevent="onFormSubmit">
+        <div class="justify-content-center col-md-5">
+            <label for="proteinFileInput" class="col-form-label fs-4">.pdb file with molecule conformations</label>
+            <input type="file" required multiple="multiple" accept="text/x-pdb" class="form-control" id="proteinFileInput"
+                name="proteinFileInput">
+        </div>
+        <div class="justify-content-center col-md-7 mt-2">
+            <h4>Simulation parameters</h4>
+            <div class="form-group row">
+                <label for="totalFramesInput" class="col-sm-4 col-form-label">Total frames</label>
+                <div class="col-sm-8">
+                    <input type="number" required min="0" step="1" class="form-control" id="totalFramesInput"
+                    name="totalFramesInput"
+                        aria-describedby="totalFramesInputHelp" placeholder="Total frames" value="20000">
+                </div>
+            </div>
+            <div class="mt-1 form-group row">
+                <label for="takeFrameEveryInput" class="col-sm-4 col-form-label">Take frame every</label>
+                <div class="col-sm-8">
+                    <input type="number" required min="0" step="1" class="form-control" id="takeFrameEveryInput"
+                    name="takeFrameEveryInput"
+                        aria-describedby="takeFrameEveryInputHelp" placeholder="Total frames" value="1000">
+                </div>
+            </div>
+            <div class="mt-1 form-group row">
+                <label for="integratorSelect" class="col-sm-4 col-form-label">Integrator</label>
+                <div class="col-sm-8">
+                    <select class="form-select" required aria-label="Default select example" id="integratorSelect"
+                    name="integratorSelect">
+                        <option selected value="LangevinIntegator">Langevin integator</option>
+                        <option value="LangevinMiddleIntegrator">Langevin middle integator</option>
+                        <option value="NoseHooverIntegrator">Nose hoover integrator</option>
+                        <option value="BrownianIntegrator">Brownian integrator</option>
+                        <option value="VariableVerletIntegrator">Variable verlet integrator</option>
+                    </select>
+                </div>
+            </div>
+            <div class="mt-1 form-group row">
+                <label for="frictionCoeffInput" class="col-sm-4 col-form-label">Friction coeff / 10<sup>-12</sup></label>
+                <div class="col-sm-8">
+                    <input type="number" min="0" required step="0.01" class="form-control" id="frictionCoeffInput"
+                    name="frictionCoeffInput"
+                        aria-describedby="takeFrameEveryInputHelp" placeholder="Friction coeff" value="1">
+                </div>
+            </div>
+            <div class="mt-1 form-group row">
+                <label for="stepSizeInput" class="col-sm-4 col-form-label">Step size / 10<sup>-12</sup></label>
+                <div class="col-sm-8">
+                    <input type="number" min="0" required step="0.001" class="form-control" id="stepSizeInput"
+                    name="stepSizeInput"
+                        aria-describedby="takeFrameEveryInputHelp" placeholder="Simulation step size" value="0.002">
+                </div>
+            </div>
+            <div class="mt-1 form-group row">
+                <label for="tempInput" class="col-sm-4 col-form-label">System temp in K</label>
+                <div class="col-sm-8">
+                    <input type="number" min="0" required step="0.001" class="form-control" id="tempInput"
+                    name="tempInput"
+                        aria-describedby="takeFrameEveryInputHelp" placeholder="Simulation step size" value="273.15">
+                </div>
+            </div>
+            <div class="mt-1 form-group row">
+                <label for="replaceNonstandardResiduesInput" class="col-sm-4 col-form-label">Replace nonstandard residues</label>
+                <div class="col-sm-8">
+                    <input type="checkbox" class="form-check-input" id="replaceNonstandardResiduesInput"
+                    name="replaceNonstandardResiduesInput"
+                        aria-describedby="takeFrameEveryInputHelp" placeholder="Simulation step size" checked>
+                </div>
+            </div>
+            <div class="mt-1 form-group row">
+                <label for="addMissingAtomsCheckbox" class="col-sm-4 col-form-label">Add missing atoms</label>
+                <div class="col-sm-8">
+                    <input type="checkbox" class="form-check-input" id="addMissingAtomsCheckbox"
+                    name="addMissingAtomsCheckbox"
+                        aria-describedby="takeFrameEveryInputHelp" placeholder="Simulation step size" checked>
+                </div>
+            </div>
+            <div class="mt-1 form-group row">
+                <label for="addMissingHydrogensCheckbox" class="col-sm-4 col-form-label">Add missing hydrogens</label>
+                <div class="col-sm-8">
+                    <input type="checkbox" class="form-check-input" id="addMissingHydrogensCheckbox"
+                    name="addMissingHydrogensCheckbox"
+                        aria-describedby="takeFrameEveryInputHelp" placeholder="Simulation step size" checked>
+                </div>
+            </div>
+            <div class="mt-1 form-group row">
+                <label for="ignoreMissingAtomsCheckbox" class="col-sm-4 col-form-label">Ignore missing atoms</label>
+                <div class="col-sm-8">
+                    <input type="checkbox" class="form-check-input" id="ignoreMissingAtomsCheckbox"
+                    name="ignoreMissingAtomsCheckbox"
+                        aria-describedby="takeFrameEveryInputHelp" placeholder="Simulation step size" checked>
+                </div>
             </div>
         </div>
         <div class="row justify-content-center m-4">
             <div class="col-md-4">
-                <div class="btn-group mt-4" role="group"
-                    aria-label="Basic checkbox toggle button group">
+                <div class="btn-group mt-4" role="group" aria-label="Basic checkbox toggle button group">
                     <button type="submit" id="submitInference" class="btn btn-lg btn-primary">
                         Submit
                     </button>
                 </div>
             </div>
         </div>
+<hr/>
+
     </form>
 </template>
diff --git a/src/server/frontend/src/views/ConformationsLab.vue b/src/server/frontend/src/views/ConformationsLab.vue
@@ -23,7 +23,7 @@ export default {
 <template>
     <ExperimentsView :state="experimentsState" :api="experimentsApi">
         <template v-slot:labTitle>
-            <h4>Conformations lab (pre-alpha)</h4>
+            <h2>Conformations lab (pre-alpha)</h2>
         </template>
         <template v-slot:labForm="labForm">
             <ConformationsFormView :onFormSubmit="labForm.onFormSubmit"/>