Update for colab

scratch/checkContentTST.py

@@ -0,0 +1,137 @@
+def getTotalNlipids(system):
+    NLIPIDS = 0
+    for molecule in system['COMPOSITION']:
+        if molecule in lipids_dict:
+            NLIPIDS += np.sum(system['COMPOSITION'][molecule]['COUNT'])
+    return NLIPIDS
+
+def getTotalNsolvent(system):
+    NMOLECULES = 0
+    for molecule in system['COMPOSITION']:
+        if molecule not in lipids_dict:
+            NMOLECULES += np.sum(system['COMPOSITION'][molecule]['COUNT'])
+    return NMOLECULES
+
+def checkAvailabilitySIM(system,lipid,counterion):
+    status = {}
+    TotalNlipids = getTotalNlipids(system)
+    TotalNsolvent = getTotalNsolvent(system)
+    Nwater = system['COMPOSITION']['SOL']['COUNT']
+    if counterion != 'no':
+        try:
+            Ncounterion = system['COMPOSITION'][counterion]['COUNT']
+        except:
+            Ncounterion = 0
+
+    try:
+        Nlipid = np.sum(system['COMPOSITION'][lipid]['COUNT'])
+    except:
+        Nlipid = 0
+
+    path = system['path']
+
+    QualityEvaluated = False
+    TotalQualityFilePath = path + '/SYSTEM_quality.json'
+    if (os.path.isfile(TotalQualityFilePath)):
+        with open(TotalQualityFilePath) as json_file:
+            Quality = json.load(json_file)
+        json_file.close()
+        if all(value > 0 for value in Quality.values()):
+            #print(Quality)
+            QualityEvaluated = True
+
+    xrayQualityEvaluated = False
+    xrayQualityFilePath = path + '/FormFactorQuality.json'
+    if (os.path.isfile(xrayQualityFilePath)):
+        with open(xrayQualityFilePath) as json_file:
+            xrayQuality = json.load(json_file)
+        json_file.close()
+        if len(xrayQuality) > 0 and xrayQuality[0] > 0:
+            xrayQualityEvaluated = True
+
+    SingleComponentSystem = False
+    if Nlipid == TotalNlipids:
+        if counterion == 'no' and Nwater == TotalNsolvent:
+            SingleComponentSystem = True
+        if counterion != 'no'and  Nwater == TotalNsolvent-Ncounterion and Nlipid == Ncounterion:    
+            SingleComponentSystem = True
+
+    if SingleComponentSystem:
+        status['Simulation'] = 'yes'
+        status['FF'] = system['FF']
+        if QualityEvaluated:
+            status['Experiment'] = 'yes'
+            status['Quality'] = Quality['total']
+
+        if not QualityEvaluated:
+            status['Experiment'] = 'no'
+            status['Quality'] = 0 
+
+        if xrayQualityEvaluated:
+            status['xrayExperiment'] = 'yes'
+            status['xrayQuality'] = xrayQuality[0]
+
+        if not xrayQualityEvaluated:
+            status['xrayExperiment'] = 'no'
+            status['xrayQuality'] = 0 
+
+    return status 
+
+
+def giveStatus(systems,lipid,counterion):  
+    status = {'Simulation': 'no', 'Experiment': 'no', 'Quality': 0, 'xrayExperiment': 'no', 'xrayQuality': 0}
+    QualityEvaluatedFound = False
+    for system in systems:
+        TMPstatus = checkAvailabilitySIM(system,lipid,counterion)
+        if TMPstatus and TMPstatus['Quality'] > status['Quality']:
+            QualityEvaluatedFound = True
+            status = TMPstatus 
+        if TMPstatus and not QualityEvaluatedFound and TMPstatus['Simulation'] == 'yes':
+            status = TMPstatus
+    return status
+
+def giveExpStatus(lipids,counterion,status):
+
+
+
+    return status
+
+
+
+HGs = {'PC', 'PE', 'PG', 'PS'}
+tails = {'PO', 'DO', 'DP'}
+table = {}
+
+for tail in tails:
+    table[tail] = {}
+    for HG in HGs:
+        lipid = tail + HG
+
+        if lipid == 'POPS' or lipid == 'POPG' or lipid == 'DPPG':
+            counterion = 'SOD'
+        else:
+            counterion = 'no'
+
+        status = giveStatus(systems,lipid,counterion)
+        statusString = ''
+
+        if status['Quality'] > 0:
+            if 'ECC-lipids' in status['FF']:
+                FF = 'ECClipids'
+            else:
+                FF = status['FF']
+            #print(status['xrayQuality'])
+            statusString = FF + '(' + str(round(status['Quality'],2)) + ',' + str(round(status['xrayQuality'])) + ')'
+        else:
+            if status['Simulation'] == 'no':
+                statusString = statusString + 'MD,'
+            if status['Experiment'] == 'no':
+                statusString = statusString + 'NMR,'
+            if status['xrayExperiment'] == 'no':
+                statusString = statusString + 'x-ray'
+
+        table[tail][HG] = statusString
+
+
+print(pd.DataFrame(table))
+display(pd.DataFrame(table))