Skip to content

Commit

Permalink
Added ESP compatibility with point charges from MM calculation
Browse files Browse the repository at this point in the history
  • Loading branch information
@mane292
mane292 committed May 14, 2024
1 parent 351e829 commit 8c69a10
Showing 1 changed file with 71 additions and 14 deletions.
85 changes: 71 additions & 14 deletions pyef/analysis.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -32,13 +32,14 @@ class Electrostatics:
hasECP: boolean
indicates if an effective core potential was used... in this case, molden file will need to be re-formatted to be compatible multiwfn!
'''
def __init__(self, lst_of_folders, lst_of_tmcm_idx, folder_to_file_path, inGaCage, hasECP=False):
def __init__(self, lst_of_folders, lst_of_tmcm_idx, folder_to_file_path, inGaCage, hasECP=False, includePtChgs=False):
self.lst_of_folders = lst_of_folders
self.lst_of_tmcm_idx = lst_of_tmcm_idx
self.folder_to_file_path = folder_to_file_path
self.dict_of_calcs = {'Hirshfeld': '1', 'Voronoi':'2', 'Mulliken': '5', 'Lowdin': '6', 'SCPA': '7', 'Becke': '10', 'ADCH': '11', 'CHELPG': '12', 'MK':'13', 'AIM': '14', 'Hirshfeld_I': '15', 'CM5':'16', 'EEM': '17', 'RESP': '18', 'PEOE': '19'}
self.inGaCageBool = inGaCage
self.dielectric = 1
self.ptChgs = includePtChgs

#To avoid over-estimating screening from bound atoms, set dielectric to 1 for primary bound atoms in ESP calv
self.changeDielectBoundBool = False
Expand Down Expand Up @@ -82,6 +83,9 @@ def __init__(self, lst_of_folders, lst_of_tmcm_idx, folder_to_file_path, inGaCag
'Cm': (247.07, 96, 1.69, 10), 'Bk': (247.07, 97, 1.68, 11), 'Cf': (251.08, 98, 1.68, 12)}
self.prepData()

def includePtChgs(self):
self.ptChgs = True

def minDielecBonds(self, bool_bonds):
self.changeDielectBoundBool = bool_bonds

Expand Down Expand Up @@ -159,9 +163,8 @@ def prepData(self):


os.chdir(owd)


# Accepts path to the xyz file and returns a dataframe containing the atoms names and the coordinates
#Accepts path to the xyz file and returns a dataframe containing the atoms names and the coordinates
def getGeomInfo(self, filepathtoxyz):
data = []
counter_idx = 0
Expand All @@ -174,6 +177,9 @@ def getGeomInfo(self, filepathtoxyz):
tokens = line.split()
if len(tokens) == 4: # Assuming atom name and x, y, z coordinates are present
atom_name = tokens[0]
#for xyz in QMMM simulation, pnt charges at end of file, skip them!
if atom_name == 'pnt':
break
x, y, z = map(float, tokens[1:])
rad = self.amassdict[atom_name][2]
data.append([counter_idx, atom_name, x, y, z, rad])
Expand Down Expand Up @@ -262,7 +268,13 @@ def getmultipoles(multipole_name):
atomDict = {"Index": index, "Element": element, "Atom_Charge": atomic_charge, 'Dipole_Moment': dipole_moment, 'Quadrupole_Moment': quadrupole_moment}
atomicDicts.append(atomDict)
return atomicDicts

#Function will process a point charge file (as generated by amber) and return a dataframe with partial charges and coordinates for use in ESP calculation
def getPtChgs(self, filename_pt):
chg_df = pd.read_table(filename_pt, skiprows=2, delim_whitespace=True, names=['charge', 'x', 'y', 'z'])
atm_name = ['pnt']
atoms = atm_name*len(chg_df['charge'])
chg_df['Atom'] = atoms
return chg_df

# Define the functions to calculate the ESP:
def mapcount(filename):
Expand Down Expand Up @@ -383,6 +395,17 @@ def calcesp(self, path_to_xyz, espatom_idx, charge_range, charge_file):
ys = df['y']
zs = df['z']

#For QMMM calculation, include point charges in ESP calculation
if self.ptChgs:
ptchg_filename = 'ptchrg.xyz'
init_file_path = path_to_xyz[0:-len('final_optim.xyz')]
full_ptchg_fp = init_file_path + ptchg_filename
df_ptchg = self.getPtChgs(full_ptchg_fp)
xs = xs + df_ptchg['x']
ys = ys + df_ptchg['y']
zs = zs + df_ptchg['z']
charges = charges + df_ptchg['charge']
atoms = atoms + df_ptchg['Atom']
# Pick the index of the atom at which the esp should be calculated
idx_atom = espatom_idx

Expand Down Expand Up @@ -453,8 +476,6 @@ def calc_firstTermE(espatom_idx, charge_range, charge_file):
C_e = 1.6023*(10**-19)
one_mol = 6.02*(10**23)

print('This is the charge range...')
print(charge_range)
for idx in charge_range:
if idx == idx_atom:
continue
Expand Down Expand Up @@ -633,7 +654,7 @@ def ESP_all_calcs(self, path_to_xyz, filename, atom_idx, cageTrue):
print('ESP just cage: ' + str(ESP_just_cage) + ' kJ/(mol*e)')
return [ESP_all, ESP_just_ligand, ESP_just_cage, atom_type]
else:
# print('ESP for all atoms: ' + str(ESP_all) + ' kJ/(mol*e)')
print('ESP for all atoms: ' + str(ESP_all) + ' kJ/(mol*e)')
return [ESP_all, atom_type]


Expand Down Expand Up @@ -666,6 +687,19 @@ def esp_bydistance(self, path_to_xyz, espatom_idx, charge_file):
yo = ys[idx_atom]
zo = zs[idx_atom]
chargeo = charges[idx_atom]

#For QMMM calculation, include point charges in ESP calculation
if self.ptChgs:
ptchg_filename = 'ptchrg.xyz'
init_file_path = path_to_xyz[0:-len('final_optim.xyz')]
full_ptchg_fp = init_file_path + ptchg_filename
df_ptchg = self.getPtChgs(full_ptchg_fp)
xs = xs + df_ptchg['x']
ys = ys + df_ptchg['y']
zs = zs + df_ptchg['z']
charges = charges + df_ptchg['charge']
atoms = atoms + df_ptchg['Atom']

total_esp = 0
# Create an ordering of the atoms based on distance from the central atom
total_atoms = len(xs)
Expand All @@ -686,14 +720,33 @@ def esp_bydistance(self, path_to_xyz, espatom_idx, charge_file):
distances.append(r)
esps.append(k*(1/dielectric)*C_e*cal_J*faraday*charges[idx]/r)
# Now we sort the distance list, and use sorted indices to sort the
atm_lst = list(atoms)
atm_lst.pop(idx_atom)

chg_lst = list(charges)
chg_lst.pop(idx_atom)
chg_arr = np.array(chg_lst)

dist_arr = np.array(distances)
sorted_idx = np.argsort(dist_arr)
init_sorted_idx = np.argsort(dist_arr)
lst_sorted_idx = list(init_sorted_idx)
lst_sorted_idx.append(len(lst_sorted_idx))
lst_sorted_idx.remove(idx_atom)
sorted_idx = np.array(lst_sorted_idx)

esp_arr = np.array(esps)
sorted_esps = esp_arr.take(sorted_idx)
sorted_esps = esp_arr.take(init_sorted_idx)
cumulative_esps = np.cumsum(sorted_esps)
sorted_dist = dist_arr.take(sorted_idx)

return [sorted_dist, sorted_esps, cumulative_esps]
sorted_dist = dist_arr.take(init_sorted_idx)
sorted_partial_charges = chg_arr.take(init_sorted_idx)
sorted_atomTypes = [atm_lst[i] for i in init_sorted_idx]

print('Here is idx_atom: ' + str(idx_atom))
new_bool_still = idx_atom in sorted_idx
print(new_bool_still)
#final_sorted_idx = np.delete(init_sorted_idx, init_sorted_idx[idx_atom])
return [sorted_dist, sorted_esps, cumulative_esps, sorted_idx, sorted_partial_charges, sorted_atomTypes]

# Function that can be called on a class object to compute key error analysis metrics for a transition metal complex
def errorAnalysis(self, csvName):
Expand Down Expand Up @@ -747,6 +800,7 @@ def getESPData(self, charge_types, ESPdata_filename):
allspeciesdict = []
counter = 0 # Iterator to account for atomic indices of interest
for f in list_of_file:
print('-----------------' + str(f) + '------------------')
atom_idx = metal_idxs[counter]
counter = counter + 1
os.chdir(owd)
Expand All @@ -759,7 +813,7 @@ def getESPData(self, charge_types, ESPdata_filename):
results_dict['Name'] = f

for key in charge_types:
print('Current key:' + str(key))
print('Partial Charge Scheme:' + str(key))
try:
full_file_path = os.getcwd() +'/final_optim_' +key+'.txt'
path_to_xyz = os.getcwd() + '/final_optim.xyz'
Expand All @@ -774,7 +828,7 @@ def getESPData(self, charge_types, ESPdata_filename):
[ESP_all, atom_type] = self.ESP_all_calcs(path_to_xyz, full_file_path, atom_idx, self.inGaCageBool)

[total_charge,partial_charge_atom] = Electrostatics.charge_atom(full_file_path, atom_idx)
[sorted_distances, sorted_esps, cum_esps] = self.esp_bydistance(path_to_xyz, atom_idx, full_file_path)
[sorted_distances, sorted_esps, cum_esps, sorted_cum_idx, sorted_cum_chg, sorted_atomTypes] = self.esp_bydistance(path_to_xyz, atom_idx, full_file_path)
ESP_fcoord = self.esp_first_coord(atom_idx, full_file_path, path_to_xyz)
ESP_scoord = self.esp_second_coord(atom_idx, full_file_path, path_to_xyz)

Expand All @@ -800,7 +854,7 @@ def getESPData(self, charge_types, ESPdata_filename):
[ESP_all, atom_type] = self.ESP_all_calcs(full_file_path, atom_idx, self.inGaCageBool)

[total_charge,partial_charge_atom] = Electrostatics.charge_atom(full_file_path, atom_idx)
[sorted_distances, sorted_esps, cum_esps] = self.esp_bydistance(path_to_xyz, atom_idx, full_file_path)
[sorted_distances, sorted_esps, cum_esps, sorted_cum_idx, sorted_cum_chg, sorted_atomTypes] = self.esp_bydistance(path_to_xyz, atom_idx, full_file_path)
ESP_fcoord = self.esp_first_coord(atom_idx, full_file_path, path_to_xyz)
ESP_scoord = self.esp_second_coord(atom_idx, full_file_path, path_to_xyz)

Expand All @@ -819,6 +873,9 @@ def getESPData(self, charge_types, ESPdata_filename):
results_dict['Sorted Distances'] = sorted_distances
results_dict['Sorted ESP '+ str(key)] = sorted_esps
results_dict['Cumulative ESP ' + str(key)] = cum_esps
results_dict['Dist Sorted Idxs' + str(key)] = sorted_cum_idx
results_dict['Dist Sorted Partial Charges' + str(key)] = sorted_cum_chg
results_dict['Dist Sorted Atom Types' + str(key)] = sorted_atomTypes

# If .molden files deal with encapsulated TMCS, complete an additional set of analyses
if self.inGaCageBool:
Expand Down

0 comments on commit 8c69a10

Please sign in to comment.