NMR shift calculation and experimental NMR description reading works

NMR.py

@@ -73,8 +73,8 @@ def ExpNMRFromDesc(self):
 
         ExpNMR_file.close()
 
-        self.Clabels, self.Cshifts = self.ParseExp(self, Cexp)
-        self.Hlabels, self.Hshifts = self.ParseExp(self, Hexp)
+        self.Clabels, self.Cshifts = self.ParseExp(Cexp)
+        self.Hlabels, self.Hshifts = self.ParseExp(Hexp)
         self.Equivalents = equivalents
         self.Omits = omits
 
@@ -95,18 +95,19 @@ def ParseExp(self, exp):
         return expLabels, expShifts
 
 
-def CalcBoltzmannWeightedShifts(Isomers):
+def CalcBoltzmannWeightedShieldings(Isomers):
 
     energies = []
 
     for i, iso in enumerate(Isomers):
 
         # Calculate rel. energies in kJ/mol
         minE = min(iso.DFTEnergies)
+
         relEs = []
 
-        for e in energies:
-            relEs.append(((e - minE) * hartreeEnergy))
+        for e in iso.DFTEnergies:
+            relEs.append((e - minE) * hartreeEnergy)
 
         Isomers[i].Energies = relEs
 
@@ -118,16 +119,18 @@ def CalcBoltzmannWeightedShifts(Isomers):
 
         q = sum(populations)
 
-        for i in range(0, len(populations)):
-            populations[i] = populations[i] / q
+        for p in range(0, len(populations)):
+            populations[p] = populations[p] / q
 
         Isomers[i].Populations = populations
 
+        print(Isomers[i].Populations)
+
         # Calculate Boltzmann weighed shielding constants
         # by summing the shifts multiplied by the isomers population
         BoltzmannShieldings = []
 
-        for atom in range(iso.Atoms):
+        for atom in range(len(iso.Atoms)):
             shielding = 0
             for population, shieldings in zip(iso.Populations, iso.ConformerShieldings):
                 shielding = shielding + shieldings[atom] * population
@@ -181,12 +184,12 @@ def NMRDataValid(Isomers):
     return True
 
 
-def GetCalcShifts(Isomers, settings):
+def CalcNMRShifts(Isomers, settings):
 
     print('WARNING: NMR shift calculation currently ignores the instruction to exclude atoms from analysis')
     for i, iso in enumerate(Isomers):
 
-        BShieldings = iso.IsomerShieldings
+        BShieldings = iso.BoltzmannShieldings
         Cvalues = []
         Hvalues = []
 
@@ -203,6 +206,12 @@ def GetCalcShifts(Isomers, settings):
         Isomers[i].Cshifts = Cvalues
         Isomers[i].Hshifts = Hvalues
 
+        print('C shifts for isomer ' + str(i) + ": ")
+        print(', '.join(['{0:.3f}'.format(x) for x in Isomers[i].Cshifts]))
+
+        print('H shifts for isomer ' + str(i) + ": ")
+        print(', '.join(['{0:.3f}'.format(x) for x in Isomers[i].Hshifts]))
+
     return Isomers
 
 

PyDP4.py

@@ -158,7 +158,7 @@ def __init__(self, InputFile, Charge=-100):
         self.NMROutputFiles = []    # list of DFT NMR output file names
         self.ShieldingLabels = []   # A list of atom labels corresponding to the shielding values
         self.ConformerShieldings = [] # list of calculated NMR shielding constant lists for every conformer
-        self.IsomerShieldings = []  # Boltzmann weighted NMR shielding constant list for the isomer
+        self.BolztmannShieldings = []  # Boltzmann weighted NMR shielding constant list for the isomer
         self.Cshifts = []           # Calculated C NMR shifts
         self.Hshifts = []           # Calculated H NMR shifts
 
@@ -324,6 +324,17 @@ def main(settings):
         print('\nReading experimental NMR data...')
         NMRData = NMR.NMRData(settings.NMRsource)
 
+        print('Clabels: ' + str(NMRData.Clabels))
+        print('Cshifts: ' + str(NMRData.Cshifts))
+
+        print('Hlabels: ' + str(NMRData.Hlabels))
+        print('Hshifts: ' + str(NMRData.Hshifts))
+
+        print('Equivalents: ' + str(NMRData.Equivalents))
+        print('Omits: ' + str(NMRData.Omits))
+
+        quit()
+
         print("Conformation data:")
         NMR.PrintConformationData(Isomers)