#Nd += len(X)
#Nt += Nu
Nt += 1
if len(X) > 0:
Nd += 1
X = np.stack(X)
x = X[0].reshape(1, X.shape[1], 3) # keep only the first guy
print(' -kept', len(x), 'of', Nu)
if len(X) > 0:
S = gdb.get_symbols_rdkitmol(m)
hdn.write_rcdb_input(x[0],
S,
int(id),
wdir,
fpf,
100,
LOT,
'500.0',
fill=4,
comment='smiles: ' + Chem.MolToSmiles(m) +
' GDB-ID: ' + str(ridx))
hdn.writexyzfile(wdir + fpf + '-' + str(id).zfill(4) + '.xyz',
x.reshape(1, x.shape[1], x.shape[2]), S)
#print(str(id).zfill(8))
molnfo.close()
print('Total mols:', Nd, 'of', Nt, 'percent:',
"{:.2f}".format(100.0 * Nd / float(Nt)))
for i, f in enumerate(files):
data = hdn.read_rcdb_coordsandnm(idir + f)
X = data['coordinates']
S = data['species']
mol = Atoms(positions=X, symbols=S)
mol.set_calculator(ANI(False))
mol.calc.setnc(nc)
dyn = LBFGS(mol, logfile='optimization.log')
dyn.run(fmax=0.00001, steps=1000)
X = mol.get_positions()
Nc = int(f.split(".")[0].split("-")[1])
Fp = f.split("-")[0]
smiles = get_smiles(idir + f)
print(i, 'of', len(files), ':', f, dyn.get_number_of_steps(), Nc)
hdn.write_rcdb_input(X,
S,
Nc,
sdir,
Fp,
50,
'wb97x/6-31g*',
'800.0',
fill=4,
comment='Smiles: ' + smiles)
storedir = '/home/jujuman/Research/extensibility_test_sets/drugbank/'
suppl = Chem.SDMolSupplier(
'/home/jujuman/Dropbox/ChemSciencePaper.AER/Benchmark_Datasets/drugbank/drugbank_3d_1564.sdf',
removeHs=False)
for id, m in enumerate(suppl):
if m is None: continue
name = m.GetProp('_Name')
xyz, spc = pya.__convert_rdkitconfs_to_nparr__(m)
print(xyz.shape)
print(name, id, spc)
hdt.writexyzfile(storedir + 'xyz/drugbank_' + str(id).zfill(4) + '.xyz',
xyz, spc)
hdt.write_rcdb_input(xyz[0],
spc,
id,
storedir,
'drugbank',
10,
'wb97x/6-31g*',
'300.0',
fill=4,
comment='Name: ' + name)
# Print size
#print(m.GetNumAtoms(), m.GetNumHeavyAtoms())
energies = np.vstack(energies)
modl_std = np.std(energies[::-1],axis=0) / float(len(spc))
bad_cnt = 0
bad_xyz = []
bad_idx = []
for i,(X,s) in enumerate(zip(xyz,modl_std)):
if s > 0.05:
if bad_cnt%3 == 0:
bad_xyz.append(X)
bad_idx.append(i)
bad_cnt = bad_cnt + 1
for j,(X,i) in enumerate(zip(bad_xyz,bad_idx)):
idx = s_idx + str(j).zfill(3)
hdt.write_rcdb_input(X, spc, int(idx), r, fp, 5, 'wb97x/6-31g*', '500.0', freq='1', opt='0', fill=6, comment=' index: '+ str(i))
print(s_idx,' ',bad_cnt,'of',modl_std.shape[0],' Bad kept: ', len(bad_xyz))
#print("CV1:", modl_std)
#plt.plot(Rc[:, 1], np.abs(hdt.hatokcal*Eact[::-1] - energies[0,:][::-1]), color='red',label='Delta')
#plt.plot(Rc[:, 1], energies[0,:][::-1]-energies[0,:][::-1].min(),color='green',label='ANI-0')
#plt.plot(Rc[:, 1], energies[1,:][::-1]-energies[1,:][::-1].min(),color='green',label='ANI-1')
#plt.plot(Rc[:, 1], energies[2,:][::-1]-energies[2,:][::-1].min(),color='green',label='ANI-2')
#plt.plot(Rc[:, 1], energies[3,:][::-1]-energies[3,:][::-1].min(),color='green',label='ANI-3')
#plt.plot(Rc[:, 1], energies[4,:][::-1]-energies[4,:][::-1].min(),color='green',label='ANI-4')
#plt.plot(Rc[:, 1], float(len(spc))*modl_std[::-1],color='blue', label='std')
#plt.plot([Rc[:, 1].min(),Rc[:, 1].max()],[float(len(spc))*0.05,float(len(spc))*0.05],r'--')
#plt.plot(Rc[:, 1], hdt.hatokcal*(Rc[:, 0]-Rc[:, 0].min()),color='Black', label='Act')
#plt.legend(bbox_to_anchor=(0.01, 0.99), loc=2, borderaxespad=0., fontsize=14)
X = np.stack(X)
#X = X[0].reshape(1, X.shape[1], 3) # keep only the first guy
print(' -kept', len(X), 'of', Nu)
if len(X) > 0:
S = gdb.get_symbols_rdkitmol(m)
P = np.random.binomial(1, Pr, Ns)
for i, (x, p) in enumerate(zip(X, P)):
#print(' -Keep:', p)
if p:
id = int(str(n) + str(i))
hdn.write_rcdb_input(x,
S,
id,
wdir,
fpf,
LOT,
charge=str(chg),
fill=8,
comment='smiles: ' +
Chem.MolToSmiles(m))
hdn.writexyzfile(
wdir + fpf + '-' + str(id).zfill(8) + '.xyz',
x.reshape(1, x.shape[0], x.shape[1]), S)
#print(str(id).zfill(8))
print('Total mols:', Nd, 'of', Nt, 'percent:',
"{:.2f}".format(100.0 * Nd / float(Nt)))
if len(X) > 0:
Nd += 1
X = np.stack(X)
#X = X[0].reshape(1, X.shape[1], 3) # keep only the first guy
print(' -kept', len(X),'of',Nu)
if len(X) > 0:
S = gdb.get_symbols_rdkitmol(m)
P = np.random.binomial(1, Pr, Ns)
for i,(x,p) in enumerate(zip(X,P)):
print(' -Keep:', p)
if p:
id = int(str(n)+str(i))
hdn.write_rcdb_input(x,S,id,wdir,fpf,100,LOT,'500.0',fill=8,comment='smiles: '+Chem.MolToSmiles(m))
hdn.writexyzfile(wdir+fpf+'-'+str(id).zfill(8)+'.xyz',x.reshape(1,x.shape[0],x.shape[1]),S)
#print(str(id).zfill(8))
=======
chg = 0
for a in m.GetAtoms():
chg += a.GetFormalCharge()
print(' -Total Charge:',chg)
if chg == 0:
# generate Nc conformers
cids = AllChem.EmbedMultipleConfs(m, Nc, useRandomCoords=True)
# Classical Optimization
for cid in cids:
_ = AllChem.MMFFOptimizeMolecule(m, confId=cid, maxIters=1000)
import pygau09tools as g09
import hdnntools as hdn
import numpy as np
wkdir = '/home/jujuman/Research/GDB-11-wB97X-6-31gd/dnnts_rxns/scans_double_bond_migration_1/'
filef = '/home/jujuman/Research/GDB-11-wB97X-6-31gd/dnnts_rxns/scans_double_bond_migration_1/IRC_fwd.log'
#fileb = '/home/jujuman/Research/GDB-11-wB97X-6-31gd/dnnts_rxns/scans_double_bond_migration/IRC_bck.log'
dataf = g09.read_irc(filef)
#datab = g09.read_irc(fileb)
#xyz = np.concatenate([np.flipud(datab[1]),dataf[1]])
xyz = dataf[1]
for i,x in enumerate(xyz):
hdn.write_rcdb_input(x,dataf[2],i,wkdir,'double_B_mig',50,'wb97x/6-31g*','1000.0',opt='0')