def select_api(args): db = SLDDB(DB_FILE) res = db.search_material(filter_invalid=False, ID=int(args['ID'])) try: material = db.select_material(res[0]) except IndexError: return '## ID not found in database' except Exception as e: return repr( e) + '<br >' + "Raised when tried to parse material = %s" % res[0] out = material.export(xray_units=args.get('xray_unit', 'edens')) return json.dumps(out, indent=' ')
def collect_combination(ids, name_dict): db = SLDDB(DB_FILE) elements=[] loaded_ids={} for id in ids: if not id in loaded_ids: try: entry=db.search_material(name=ExactString(name_dict[id]))[0] except KeyError: possible_ids=name_dict.keys() raise SequenceParseError(f"Not a valid identifier {id}, options are {''.join(possible_ids)}") except IndexError: raise SequenceParseError(f"Molecule {name_dict[id]} not found in database") m=db.select_material(entry) loaded_ids[id]=m elements.append(loaded_ids[id]) result=elements[0] for element in elements[1:]: # combine molecule matierials result+=element return result
def collect_blendIDs(formula): db = SLDDB(DB_FILE) elements=[] loaded_ids={} items=[] while '(' in clean_str(formula): pre, formula=formula.split(')',1) number=float(pre.split('*',1)[0].strip('(').strip()) ID=int(pre.split('*',1)[1].strip()) items.append((number, ID)) for number, ID in items: if not ID in loaded_ids: entry=db.search_material(ID=ID)[0] m=db.select_material(entry) loaded_ids[ID]=m elements.append(number*loaded_ids[ID]) result=elements[0] for element in elements[1:]: # combine molecule matierials result+=element return result
def calculate_selection(ID): db=SLDDB(DB_FILE) res=db.search_material(ID=ID, filter_invalid=False) try: material=db.select_material(res[0]) except Exception as e: return render_template('base.html', error=repr(e)+'<br >'+"Raised when tried to parse material = %s"%res[0]) match_point=0. E, rho_x=material.rho_vs_E() _, delta=material.delta_vs_E() _, beta=material.beta_vs_E() script='' # get_graph(E, rho_x.real, rho_x.imag, res[0]['name']) if 'H' in material.formula or 'Hx' in material.formula: deuterated=material.deuterated if 'Hx' in material.formula: exchanged=material.exchanged match_point = 100.*material.match_exchange() else: exchanged=None else: deuterated=None exchanged=None if 'H' in material.formula or 'Hx' in material.formula or 'D' in material.formula \ or any([tag in res[0].get('tags', []) for tag in ['polymer', 'biology', 'membrane', 'lipid', 'small organic', 'surfactant', 'protein']]): contrast_matching = True else: contrast_matching = False return render_template('sldcalc.html', material=material, material_name=res[0]['name'], material_description=res[0]['description'], deuterated=deuterated, exchanged=exchanged, match_point=match_point, contrast_matching=contrast_matching, xray_E=E.tolist(), xray_rho_real=nan_to_num(rho_x.real).tolist(), xray_rho_imag=nan_to_num(rho_x.imag).tolist(), xray_delta=nan_to_num(delta).tolist(), xray_beta=nan_to_num(beta).tolist(), validated=res[0]['validated'], validated_by=res[0]['validated_by'], invalid=res[0]['invalid'], invalid_by=res[0]['invalid_by'], formula=res[0]['formula'], density=material.dens, mu=material.mu)
class SLDDBWindow(QtWidgets.QMainWindow): selected_material=None def __init__(self): super(SLDDBWindow, self).__init__() # Call the inherited classes __init__ method self.ui=uic.loadUi('qt_interface/slddb_window.ui', self) # Load the .ui file self.setColumns() self.show() # Show the GUI self.db=SLDDB(DB_FILE) def setColumns(self): tbl=self.ui.resultTable tbl.setColumnCount(len(DB_MATERIALS_FIELDS)-len(DB_MATERIALS_HIDDEN_DATA)) self.headers=[] for field in DB_MATERIALS_FIELDS: if field in DB_MATERIALS_HIDDEN_DATA: continue self.headers.append(field) tbl.setHorizontalHeaderLabels(self.headers) for i in range(len(self.headers)): tbl.setColumnHidden(i, True) tbl=self.ui.entryTable tbl.setRowCount(len(self.headers)) tbl.setVerticalHeaderLabels(self.headers) def searchDatabase(self): name=self.ui.nameEdit.text() description=self.ui.descriptionEdit.text() formula=self.ui.formulaEdit.text() search={'name': name, 'description': description, 'formula': formula} for key, value in list(search.items()): if value.strip()=='': del(search[key]) results=self.db.search_material(**search) hidden_columns=[True for field in self.headers] for row in results: for i, field in enumerate(self.headers): if row[field] is not None: hidden_columns[i]=False tbl=self.ui.resultTable tbl.sortByColumn(-1, QtCore.Qt.AscendingOrder) tbl.setRowCount(len(results)) for i, hidden in enumerate(hidden_columns): tbl.setColumnHidden(i, hidden) for i,result in enumerate(results): for j, field in enumerate(self.headers): item=result[field] if type(item) is datetime: item=str(item) titem=QtWidgets.QTableWidgetItem() titem.setData(QtCore.Qt.DisplayRole, item) tbl.setItem(i, j, titem) tbl.resizeColumnsToContents() self.results=results if len(results)==1: tbl.setRangeSelected(QtWidgets.QTableWidgetSelectionRange(0, -1, 1, -1), True) self.selectItem(0, 0) def selectItem(self, row, col): tbl=self.ui.resultTable ID=tbl.indexFromItem(tbl.item(row, 0)).data() orig_row=[res['ID'] for res in self.results].index(ID) result=self.results[orig_row] try: material=self.db.select_material(result) except Exception as e: return self.selected_material=material self.ui.resultName.setText(result['name']) self.updateResult() def updateResult(self): material=self.selected_material if material is None: return if self.ui.densityVolumeSelect.currentIndex()==0: self.ui.densityVolume.setText('%.4f'%material.dens) else: self.ui.densityVolume.setText('%.4g'%(1000./material.fu_dens)) self.ui.neutronSLD.setText("%.6f"%(1e6*material.rho_n.real)) self.ui.neutronSLDimag.setText("%.6f"%(1e6*material.rho_n.imag)) try: rhox=material.rho_of_E(float(self.ui.xrayEnergyEdit.currentText())) except ValueError: self.ui.xraySLD.setText("") self.ui.xraySLDimag.setText("") else: self.ui.xraySLD.setText("%.6f"%(1e6*rhox.real)) self.ui.xraySLDimag.setText("%.6f"%(1e6*rhox.imag))