def Get_Add_Int(mol_icords, Z_BONDS, Z_ANGLES, Z_TORSIONS):
all_bonds_mol, all_angles_mol, all_torsions_mol = mol_icords[
'BONDS'], mol_icords['ANGLES'], mol_icords['TORSIONS']
Z_B = {
pairing_func(i[0] - 3, i[1] - 3): [i[0] - 3, i[1] - 3]
for i in Z_BONDS.values()
}
Z_A = {
ang_id([i[0] - 3, i[1] - 3, i[2] - 3]): [i[0] - 3, i[1] - 3, i[2] - 3]
for i in Z_ANGLES.values()
}
Z_T = {
tor_id([i[0] - 3, i[1] - 3, i[2] - 3, i[3] - 3], False,
list(Z_B.keys())): [i[0] - 3, i[1] - 3, i[2] - 3, i[3] - 3]
for i in Z_TORSIONS.values()
}
Z_Ad_B, Z_Ad_A, Z_Ad_T = collections.OrderedDict(
), collections.OrderedDict(), collections.OrderedDict()
Z_Ad_I = collections.OrderedDict()
for b_ij in all_bonds_mol.values():
uid_b_ij = pairing_func(b_ij[0], b_ij[1])
if uid_b_ij not in list(Z_B.keys()):
Z_Ad_B[uid_b_ij] = [b_ij[0], b_ij[1]]
for a_ij in all_angles_mol.keys():
if a_ij not in list(Z_A.keys()):
Z_Ad_A[a_ij] = [i for i in all_angles_mol[a_ij]]
for t_ij in all_torsions_mol.keys():
if t_ij not in list(Z_T.keys()):
Z_Ad_T[t_ij] = [i + 3 for i in all_torsions_mol[t_ij]]
for c in mol_icords['IMPROPERS'].values():
Z_Ad_I[impr_id([c[0], c[2], c[3]])] = [i for i in c]
return (Z_Ad_B, Z_Ad_A, Z_Ad_T, Z_Ad_I)
def tor_id(a, isImp, bndlist):
bond = pairing_func(a[1], a[2])
ends = pairing_func(a[0], a[3])
if isImp:
ndata = tor_cent(a, bndlist)
aimp = np.sort(ndata[1:])
return (ang_id(aimp))
else:
return (pairing_func(bond, ends))
def PrintPairs(tordf_A, tordf_B, itp):
'''
tordf_A: DF with proper and improper torsions of State A
tordf_B: DF with proper and improper torsions of State B
itp : File object to write
'''
pA = tordf_A[tordf_A.ADIH_TYP == False][['AI', 'AL']]
pB = tordf_B[tordf_B.BDIH_TYP == False][['BI', 'BL']]
pA['UID'] = [pairing_func(i, j) for i, j in zip(pA.AI, pA.AL)]
pB['UID'] = [pairing_func(i, j) for i, j in zip(pB.BI, pB.BL)]
a_dict = pA.set_index('UID')[['AI', 'AL']].to_dict()
b_dict = pB.set_index('UID')[['BI', 'BL']].to_dict()
# pALL_I = {**a_dict['AI'], **b_dict['BI']}
# pALL_L = {**a_dict['AL'], **b_dict['BL']}
pALL_I = merge_two_dicts(a_dict['AI'], b_dict['BI'])
pALL_L = merge_two_dicts(a_dict['AL'], b_dict['BL'])
itp.write('''[ pairs ]\n; ai aj funct\n''')
for k in list(pALL_I.keys()):
itp.write('%5d %5d %5d\n' % (pALL_I[k], pALL_L[k], 1))
return None
def make_graphs(atoms, coos, bonds):
G = nx.DiGraph()
# ADD NODES USING ATOM TYPES AND COORDINATES
for i in coos.keys():
G.add_node(i,
XYZ=coos[i],
elem=atoms[i],
atno=bossElement2Num(atoms[i]))
for (i, j, rij) in zip(bonds['BI'], bonds['BJ'], bonds['RIJ']):
G.add_edge(i, j, distance=rij)
G.add_edge(j, i, distance=rij)
# all_ps = dict(nx.algorithms.all_pairs_shortest_path_length(G))
all_ps = dict(nx.algorithms.all_pairs_shortest_path_length(G, cutoff=3))
all_paths = []
for s in all_ps.keys():
for e in all_ps[s].keys():
if all_ps[s][e] == 1:
all_paths += list(
nx.algorithms.all_simple_paths(G, s, e, cutoff=1))
# all_paths += list(nx.algorithms.shortest_simple_paths(G, s, e))
elif all_ps[s][e] == 2:
all_paths += list(
nx.algorithms.all_simple_paths(G, s, e, cutoff=2))
# all_paths += list(nx.algorithms.shortest_simple_paths(G, s, e))
elif all_ps[s][e] == 3:
all_paths += list(
nx.algorithms.all_simple_paths(G, s, e, cutoff=3))
# all_paths += list(nx.algorithms.shortest_simple_paths(G, s, e))
all_bonds = [p for p in all_paths if len(set(p)) == 2]
new_angs = [p for p in all_paths if len(set(p)) == 3]
new_tors = [p for p in all_paths if len(set(p)) == 4]
bndlist = [pairing_func(a[0], a[1]) for a in all_bonds]
dict_new_tors = {tor_id(t, False, bndlist): t for t in new_tors}
dict_new_angs = {ang_id(t): t for t in new_angs}
imp_keys = [n for n in G.nodes() if G.degree(n) / 2 == 3]
all_imps = {}
for i in imp_keys:
nei = np.sort(list(G.neighbors(i)))
if G.node[i]['atno'] == 6:
all_imps[impr_id([nei[0], nei[1],
nei[2]])] = [nei[0], i, nei[1], nei[2]]
# print(all_imps)
MOL_ICOORDS = {
'BONDS': all_bonds,
'ANGLES': dict_new_angs,
'TORSIONS': dict_new_tors,
'IMPROPERS': all_imps
}
return (G, MOL_ICOORDS)
def GetGeomVars(ALL_BNDS, A_UID, B_UID, A_UID_RIJ, B_UID_RIJ, FEP_ITY,
FEP_FTY):
geom_var = pd.DataFrame(ALL_BNDS).T
geom_var.columns = ['BI', 'BJ']
geom_var['UID'] = [
pairing_func(i, j) for i, j in zip(geom_var.BI, geom_var.BJ)
]
geom_var['INI_BT'] = [
'%s-%s' % (FEP_ITY[i], FEP_ITY[j])
for i, j in zip(geom_var.BI, geom_var.BJ)
]
geom_var['FIN_BT'] = [
'%s-%s' % (FEP_FTY[i], FEP_FTY[j])
for i, j in zip(geom_var.BI, geom_var.BJ)
]
test_A = []
test_B = []
BL_A = []
BL_B = []
# print(geom_var)
for rb in geom_var.iterrows():
i, r = rb
if r.UID in A_UID:
test_A.append(1)
BL_A.append(A_UID_RIJ[r.UID])
if r.UID in B_UID:
test_B.append(1)
BL_B.append(B_UID_RIJ[r.UID])
if (r.UID not in A_UID):
test_A.append(0)
if ('100' in r.INI_BT) or ('4894' in r.INI_BT):
BL_A.append(0.300)
else:
BL_A.append(B_UID_RIJ[i])
if (r.UID not in B_UID):
test_B.append(0)
if ('100' in r.FIN_BT) or ('4894' in r.FIN_BT):
BL_B.append(0.300)
else:
BL_B.append(A_UID_RIJ[i])
geom_var['INIT'] = test_A
geom_var['FINAL'] = test_B
geom_var['IB'] = BL_A
geom_var['FB'] = BL_B
return (geom_var)
def impr_id(a):
a = np.sort(np.array(a))
bond_a = pairing_func(a[0], a[1])
bond_b = pairing_func(a[1], a[2])
return (pairing_func(bond_a, bond_b))
def ang_id(a):
bond_a = pairing_func(a[0], a[1])
bond_b = pairing_func(a[1], a[2])
return (pairing_func(bond_a, bond_b))
def print_FEPZMAT(atoms,
G_mol,
mol_icords,
coos,
umatchA,
umatchB,
extra,
G_vars,
num2typ,
zmat_name='TEST_A2B.z',
resid='A2B'):
Z_ATOMS = {1: 'X', 2: 'X'}
Z_INI = {1: -1, 2: -1}
Z_FIN = {1: -1, 2: -1}
Z_BONDS = {1: (1, 0, 0.000), 2: (2, 1, 1.00), 3: (3, 2, 1.00)}
Z_ANGLES = {
1: (1, 0, 0, 0.000),
2: (2, 1, 0, 0.000),
3: (3, 2, 1, 90.00),
4: (4, 3, 2, 90.0)
}
Z_TORSIONS = {
1: (1, 0, 0, 0, 0.00),
2: (2, 1, 0, 0, 0.00),
3: (3, 2, 1, 0, 0.00),
4: (4, 3, 2, 1, 0.00),
5: (5, 4, 3, 2, 90.0)
}
for i in range(len(atoms)):
Z_ATOMS[i + 3] = atoms[i]
for i in range(len(atoms)):
Z_INI[i + 3] = G_mol.node[i]['init_no']
Z_FIN[i + 3] = G_mol.node[i]['finl_no']
#print(i,Z_INI[i + 3],Z_FIN[i + 3])
######## collect all the bonds ######################
n_ats = 0
B_LINK = {}
for i in range(1, len(G_mol.nodes())):
# if n_ats > 0:
neigs = np.sort(list(G_mol.neighbors(i)))
B_LINK[i] = neigs[0]
Z_BONDS[i + 3] = (i + 3, neigs[0] + 3,
Distance(coos[i], coos[neigs[0]]))
n_ats += 1
######## Collect all the angles #####################
n_ats = 0
A_LINK = {}
for i in G_mol.nodes():
if n_ats > 1:
neigs = np.sort(list(G_mol.neighbors(B_LINK[i])))
neigs = neigs[neigs < i]
if i > (len(coos) - len(umatchB) - 1):
neigs = np.array([j for j in neigs if j not in umatchA])
A_LINK[i] = neigs[0]
ang = angle(coos[i], coos[B_LINK[i]], coos[neigs[0]])
Z_ANGLES[i + 3] = (i + 3, B_LINK[i] + 3, neigs[0] + 3, ang)
n_ats += 1
######## Collect all the IC torsions/impropers ######
n_ats = 0
for i in G_mol.nodes():
if n_ats > 2:
neigs = list(G_mol.neighbors(A_LINK[i]))
neigs = np.array(
[j for j in neigs if j not in [i, B_LINK[i], A_LINK[i]]])
neigs = np.sort(neigs)
neigs = neigs[neigs < i]
if len(neigs) < 1:
neigs = [
j for j in list(G_mol.neighbors(B_LINK[i]))
if j not in [i, A_LINK[i]]
]
if impr_id([i, A_LINK[i],
neigs[0]]) in mol_icords['IMPROPERS'].keys():
del mol_icords['IMPROPERS'][impr_id(
[i, A_LINK[i], neigs[0]])]
[ti, tj, tk, tl] = [i, B_LINK[i], A_LINK[i], neigs[0]]
dihed = dihedral(coos[ti], coos[tj], coos[tk], coos[tl])
Z_TORSIONS[i + 3] = (ti + 3, tj + 3, tk + 3, tl + 3, dihed)
n_ats += 1
######## Removing the repeated IC using Additional ICs ##############
UID_2_IB = G_vars.set_index('UID')['IB'].to_dict()
UID_2_FB = G_vars.set_index('UID')['FB'].to_dict()
GG_V = {
i: [
UID_2_IB[pairing_func(Z_BONDS[i][0] - 3, Z_BONDS[i][1] - 3)],
UID_2_FB[pairing_func(Z_BONDS[i][0] - 3, Z_BONDS[i][1] - 3)]
]
for i in range(4,
len(G_mol.nodes()) + 3)
}
Z_Ad_B, Z_Ad_A, Z_Ad_T, Z_Ad_I = Get_Add_Int(mol_icords, Z_BONDS, Z_ANGLES,
Z_TORSIONS)
#Z_BONDS = {1: (1, 0, 0.000), 2: (2, 1, 1.00), 3: (3, 2, 1.00)}
GG_V[1] = [0.0, 0.0]
GG_V[2] = [1.0, 1.0]
GG_V[3] = [1.0, 1.0]
# PRINTING ACTUAL Z-MATRIX
ofile = open(zmat_name, 'w+')
ofile.write('MCPRO/BOSS FEP Z-Matrix by LSD\n')
for i in range(1, len(atoms) + 3):
ofile.write('%4d %-3s%5d%5d%5d%12.6f%4d%12.6f%4d%12.6f%4s%5d\n' %
(i, Z_ATOMS[i], Z_INI[i], Z_FIN[i], Z_BONDS[i][1],
GG_V[i][0], Z_ANGLES[i][-2], Z_ANGLES[i][-1],
Z_TORSIONS[i][-2], Z_TORSIONS[i][-1], resid[0:3], 1))
ofile.write(
' Geometry Variations follow (2I4,F12.6)\n')
for k in range(4, len(G_mol.nodes()) + 3):
ofile.write('%4d%4d%12.6f\n' % (k, 1, GG_V[k][1]))
ofile.write(' Variable Bonds follow (I4)\n')
for i in range(4, len(atoms) + 3):
ofile.write('%4d\n' % i)
ofile.write(' Additional Bonds follow (2I4)\n')
if len(Z_Ad_B) > 0:
for i in Z_Ad_B.values():
ofile.write('%4d%4d\n' % (i[0] + 3, i[1] + 3))
# CREATE A FUNCTION TO DEFINE ADDITIONAL BONDS IN CASE OF RINGS
ofile.write(
''' Harmonic Constraints follow (2I4,4F10.4)
Variable Bond Angles follow (I4)\n''')
for i in range(5, len(atoms) + 3):
ofile.write('%4d\n' % i)
ofile.write(' Additional Bond Angles follow (3I4)\n')
if len(Z_Ad_A) > 0:
for i in Z_Ad_A.values():
ofile.write('%4d%4d%4d\n' % (i[0] + 3, i[1] + 3, i[2] + 3))
# CREATE A FUNCTION TO DEFINE ADDITIONAL BONDS IN CASE OF RINGS
ofile.write(
' Variable Dihedrals follow (3I4,F12.6)\n')
for i in range(6, len(atoms) + 3):
ofile.write('%4d%4d%4d%12.6f\n' % (i, -1, -1, 0.000))
ofile.write(' Additional Dihedrals follow (6I4)\n')
if len(Z_Ad_T) > 0:
for k in Z_Ad_T.keys():
torsion = Z_Ad_T[k]
ofile.write(
'%4d%4d%4d%4d%4d%4d\n' %
(torsion[0], torsion[1], torsion[2], torsion[3], -1, -1))
add_imp_lines = []
if len(Z_Ad_I) > 0:
for k in Z_Ad_I.keys():
imp = Z_Ad_I[k]
ui = Z_INI[imp[1] + 3]
uf = Z_FIN[imp[1] + 3]
imp_ity = CENT2IMPty(num2typ[ui])
imp_fty = CENT2IMPty(num2typ[uf])
#print(num2typ[ui],num2typ[uf],imp_ity,imp_fty)
#print(ui,uf,imp_ity,imp_fty)
add_imp_lines.append('%4d%4d%4d%4d%4d%4d\n' %
(imp[0] + 3, imp[1] + 3, imp[2] + 3,
imp[3] + 3, imp_ity, imp_fty))
# ofile.write('%4d%4d%4d%4d%4d%4d\n'%(imp[0]+3,imp[1]+3,imp[2]+3,imp[3]+3,imp_ity,imp_fty))
ofile.write(' Domain Definitions follow (4I4)\n')
for i in umatchA:
for j in umatchB:
ofile.write('%4d%4d%4d%4d\n' % (i + 3, i + 3, j + 3, j + 3))
ofile.write(''' Conformational Search (2I4,2F12.6)
Local Heating Residues follow (I4 or I4-I4)
Final blank line\n
Final Non-Bonded Parameters for QM (AM1 CM1Ax1.14) Atoms:\n
''')
for i in extra:
ofile.write('%s' % i)
ofile.close()
return add_imp_lines