def Load_TRIPOS(force_field):
ff_file1 = "./DataBase/ForceFields/TRIPOS/tripos.dat" # In current directory
ff_file2 = "./DataBase/ForceFields/TRIPOS/tripos_bonds.dat" # In current directory
ff_file3 = "./DataBase/ForceFields/TRIPOS/tripos_angles.dat" # In current directory
ff_file4 = "./DataBase/ForceFields/TRIPOS/tripos_dihedrals.dat" # In current directory
#------- Here are some basic patterns -------------
INT = '([1-9]([0-9]*))'
NINT = '([0-9]+)'
SP = '\s+'
#DOUBLE = '([-+]?(\d*\.\d*)([eE][-+]?\d+)?)'
DOUBLE = '([-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?)'
WORD = '([a-zA-Z]+)'
ID = '(([a-zA-Z]+)([a-zA-Z]+|\d+|\.|\*)*)'
PHRASE = '"((\w|\W)+)"'
CONNECTOR = '\s*[-]\s*'
#------- Here we define a format of file ----------
# p - means 'Pattern'
pAtom_type_keyword = '(?P<Atom_type_keyword>' + 'TYPE' + ')' + SP
pAtom_ff_int_type = '(?P<Atom_ff_int_type>' + DOUBLE + ')' + SP
pAtom_ff_type = '(?P<Atom_ff_type>' + ID + ')' + SP
pAtom_val = '(?P<Atom_val>' + INT + ')' + SP
pAtom_geom = '(?P<Atom_geom>' + WORD + ')' + SP
pAtom_Hbd = '(?P<Atom_Hbd>' + NINT + ')' + SP
pAtom_Hba = '(?P<Atom_Hba>' + NINT + ')' + SP
pAtom_LP = '(?P<Atom_LP>' + NINT + ')' + SP
pAtom1_ff_type = '(?P<Atom1_ff_type>' + ID + ')' + SP
pAtom2_ff_type = '(?P<Atom2_ff_type>' + ID + ')' + SP
pAtom3_ff_type = '(?P<Atom3_ff_type>' + ID + ')' + SP
pAtom4_ff_type = '(?P<Atom4_ff_type>' + ID + ')' + SP
pBond_r_eq = '(?P<Bond_r_eq>' + DOUBLE + ')' + SP
pBond_k_bond = '(?P<Bond_k_bond>' + DOUBLE + ')' + SP
pBond_bo = '(?P<Bond_bo>' + WORD + ')' + SP
pAngle_theta_eq = '(?P<Angle_theta_eq>' + DOUBLE + ')' + SP
pAngle_k_angle = '(?P<Angle_k_angle>' + DOUBLE + ')' + SP
pDihedral_mult = '(?P<Dihedral_mult>' + INT + ')' + SP
pDihedral_vphi = '(?P<Dihedral_vphi>' + DOUBLE + ')' + SP
pDihedral_phase = '(?P<Dihedral_phase>' + DOUBLE + ')' + SP
pAtom_sigma = '(?P<Atom_sigma>' + DOUBLE + ')' + SP
pAtom_epsilon = '(?P<Atom_epsilon>' + DOUBLE + ')' + SP
pAtom_C_star = '(?P<Atom_C_star>' + DOUBLE + ')' + SP
pAtom_Z_star = '(?P<Atom_Z_star>' + DOUBLE + ')' + SP
pAtom_scale = '(?P<Atom_scale>' + DOUBLE + ')' + SP
pAtom_GMP = '(?P<Atom_GMP>' + DOUBLE + ')' + SP
pFF_name_keyword = '(?P<FF_name_keyword>' + 'FORCE_FIELD' + ')' + SP
pFF_sigma_rule_keyword = '(?P<FF_sigma_rule_keyword>' + 'SIGMA_COMB_RULE' + ')' + SP
pFF_epsil_rule_keyword = '(?P<FF_epsil_rule_keyword>' + 'EPSILON_COMB_RULE' + ')' + SP
pFF_vdw_scale13_keyword = '(?P<FF_vdw_scale13_keyword>' + 'VDW_SCALE13' + ')' + SP
pFF_vdw_scale14_keyword = '(?P<FF_vdw_scale14_keyword>' + 'VDW_SCALE14' + ')' + SP
pFF_elec_scale12_keyword = '(?P<FF_elec_scale12_keyword>' + 'ELEC_SCALE12' + ')' + SP
pFF_elec_scale13_keyword = '(?P<FF_elec_scale13_keyword>' + 'ELEC_SCALE13' + ')' + SP
pFF_elec_scale14_keyword = '(?P<FF_elec_scale14_keyword>' + 'ELEC_SCALE14' + ')' + SP
pFF_name_value = '(?P<FF_name_value>' + WORD + ')' + SP
pFF_sigma_rule_value = '(?P<FF_sigma_rule_value>' + WORD + ')' + SP
pFF_epsil_rule_value = '(?P<FF_epsil_rule_value>' + WORD + ')' + SP
pFF_vdw_scale13_value = '(?P<FF_vdw_scale13_value>' + DOUBLE + ')' + SP
pFF_vdw_scale14_value = '(?P<FF_vdw_scale14_value>' + DOUBLE + ')' + SP
pFF_elec_scale12_value = '(?P<FF_elec_scale12_value>' + DOUBLE + ')' + SP
pFF_elec_scale13_value = '(?P<FF_elec_scale13_value>' + DOUBLE + ')' + SP
pFF_elec_scale14_value = '(?P<FF_elec_scale14_value>' + DOUBLE + ')' + SP
FF_name_record = pFF_name_keyword + pFF_name_value
FF_sigma_rule_record = pFF_sigma_rule_keyword + pFF_sigma_rule_value
FF_epsil_rule_record = pFF_epsil_rule_keyword + pFF_epsil_rule_value
FF_vdw_scale13_record = pFF_vdw_scale13_keyword + pFF_vdw_scale13_value
FF_vdw_scale14_record = pFF_vdw_scale14_keyword + pFF_vdw_scale14_value
FF_elec_scale12_record = pFF_elec_scale12_keyword + pFF_elec_scale12_value
FF_elec_scale13_record = pFF_elec_scale13_keyword + pFF_elec_scale13_value
FF_elec_scale14_record = pFF_elec_scale14_keyword + pFF_elec_scale14_value
TRIPOS_Atom_Type_Record = pAtom_ff_type + pAtom_val + pAtom_geom + pAtom_Hbd + pAtom_Hba + pAtom_LP + pAtom_sigma + pAtom_epsilon
TRIPOS_Bond_Type_Record = pAtom1_ff_type + pAtom2_ff_type + pBond_bo + pBond_r_eq + pBond_k_bond
TRIPOS_Angle_Type_Record = pAtom1_ff_type + pAtom2_ff_type + pAtom3_ff_type + pAngle_theta_eq + pAngle_k_angle
TRIPOS_Dihedral_Type_Record = pAtom1_ff_type + pAtom2_ff_type + pAtom3_ff_type + pAtom4_ff_type + pBond_bo + pDihedral_vphi + pDihedral_mult
#-------------- Atoms ------------------------------------
print "Loading atom types...\n"
f = open(ff_file1, 'r')
A = f.readlines()
f.close()
class atomrecord:
pass
ff_par = {}
for a in A:
m1 = re.search(TRIPOS_Atom_Type_Record, a)
m2 = re.search(FF_sigma_rule_record, a)
m3 = re.search(FF_epsil_rule_record, a)
m4 = re.search(FF_vdw_scale13_record, a)
m5 = re.search(FF_vdw_scale14_record, a)
m6 = re.search(FF_elec_scale13_record, a)
m7 = re.search(FF_elec_scale14_record, a)
m8 = re.search(FF_name_record, a)
if m1 != None:
ff = atomrecord()
ff.Atom_ff_type = (
a[m1.start('Atom_ff_type'):m1.end('Atom_ff_type')])
ff.Atom_sigma = float(
a[m1.start('Atom_sigma'):m1.end('Atom_sigma')])
ff.Atom_epsilon = float(
a[m1.start('Atom_epsilon'):m1.end('Atom_epsilon')])
atom_record = lcccsObjects.Atom_Record()
atom_record.set(ff)
res = force_field.Add_Atom_Record(atom_record)
print "load type", ff.Atom_ff_type
if m2 != None:
ff_par["sigma_comb_rule"] = a[m2.start('FF_sigma_rule_value'):m2.
end('FF_sigma_rule_value')]
if m3 != None:
ff_par["epsilon_comb_rule"] = a[m3.start('FF_epsil_rule_value'):m3.
end('FF_epsil_rule_value')]
if m4 != None:
ff_par["vdw_scale13"] = float(
a[m4.start('FF_vdw_scale13_value'):m4.
end('FF_vdw_scale13_value')])
if m5 != None:
ff_par["vdw_scale14"] = float(
a[m5.start('FF_vdw_scale14_value'):m5.
end('FF_vdw_scale14_value')])
if m6 != None:
ff_par["elec_scale13"] = float(
a[m6.start('FF_elec_scale13_value'):m6.
end('FF_elec_scale13_value')])
if m7 != None:
ff_par["elec_scale14"] = float(
a[m7.start('FF_elec_scale14_value'):m7.
end('FF_elec_scale14_value')])
if m8 != None:
ff_par["ForceField_Name"] = a[m8.start('FF_name_value'):m8.
end('FF_name_value')]
force_field.set(ff_par)
#-------------- Bonds ------------------------------------
print "Loading bonds...\n"
f = open(ff_file2, 'r')
A = f.readlines()
f.close()
class bondrecord:
pass
for a in A:
m1 = re.search(TRIPOS_Bond_Type_Record, a)
if m1 != None:
ff = bondrecord()
ff.Atom1_ff_type = a[m1.start('Atom1_ff_type'):m1.
end('Atom1_ff_type')]
ff.Atom2_ff_type = a[m1.start('Atom2_ff_type'):m1.
end('Atom2_ff_type')]
ff.Bond_k_bond = float(
a[m1.start('Bond_k_bond'):m1.end('Bond_k_bond')])
ff.Bond_r_eq = float(a[m1.start('Bond_r_eq'):m1.end('Bond_r_eq')])
bond_record = lcccsObjects.Bond_Record()
bond_record.set(ff)
#bond_record.show_info()
res = force_field.Add_Bond_Record(bond_record)
#----------------- Angles -------------------------------------
print "Loading angles...\n"
f = open(ff_file3, 'r')
A = f.readlines()
f.close()
class anglerecord:
pass
for a in A:
m1 = re.search(TRIPOS_Angle_Type_Record, a)
if m1 != None:
ff = anglerecord()
ff.Atom1_ff_type = a[m1.start('Atom1_ff_type'):m1.
end('Atom1_ff_type')]
ff.Atom2_ff_type = a[m1.start('Atom2_ff_type'):m1.
end('Atom2_ff_type')]
ff.Atom3_ff_type = a[m1.start('Atom3_ff_type'):m1.
end('Atom3_ff_type')]
ff.Angle_k_angle = float(
a[m1.start('Angle_k_angle'):m1.end('Angle_k_angle')])
ff.Angle_theta_eq = float(
a[m1.start('Angle_theta_eq'):m1.end('Angle_theta_eq')])
angle_record = lcccsObjects.Angle_Record()
angle_record.set(ff)
#angle_record.show_info()
res = force_field.Add_Angle_Record(angle_record)
#----------------- Dihedrals -------------------------------------
print "Loading dihedral...\n"
f = open(ff_file4, 'r')
A = f.readlines()
f.close()
class dihedralrecord:
pass
for a in A:
m1 = re.search(TRIPOS_Dihedral_Type_Record, a)
if m1 != None:
ff = dihedralrecord()
ff.Atom1_ff_type = a[m1.start('Atom1_ff_type'):m1.
end('Atom1_ff_type')]
ff.Atom2_ff_type = a[m1.start('Atom2_ff_type'):m1.
end('Atom2_ff_type')]
ff.Atom3_ff_type = a[m1.start('Atom3_ff_type'):m1.
end('Atom3_ff_type')]
ff.Atom4_ff_type = a[m1.start('Atom4_ff_type'):m1.
end('Atom4_ff_type')]
ff.Dihedral_mult = int(
float(a[m1.start('Dihedral_mult'):m1.end('Dihedral_mult')]))
ff.Dihedral_vphi = float(
a[m1.start('Dihedral_vphi'):m1.end('Dihedral_vphi')])
dihedral_record = lcccsObjects.Dihedral_Record()
dihedral_record.set(ff)
#dihedral_record.show_info()
res = force_field.Add_Dihedral_Record(dihedral_record)
def Load_MMFF94(force_field):
ff_file11 = "./DataBase/ForceFields/MMFF94/mmff94_types1.dat" # In current directory
ff_file12 = "./DataBase/ForceFields/MMFF94/mmff94_types2.dat" # In current directory
ff_file21 = "./DataBase/ForceFields/MMFF94/mmff94_bonds1.dat" # In current directory
ff_file22 = "./DataBase/ForceFields/MMFF94/mmff94_bonds2.dat" # In current directory
ff_file23 = "./DataBase/ForceFields/MMFF94/mmff94_bonds3.dat" # In current directory
ff_file31 = "./DataBase/ForceFields/MMFF94/mmff94_angles1.dat" # In current directory
ff_file32 = "./DataBase/ForceFields/MMFF94/mmff94_angles2.dat" # In current directory
ff_file33 = "./DataBase/ForceFields/MMFF94/mmff94_angles3.dat" # In current directory
ff_file4 = "./DataBase/ForceFields/MMFF94/mmff94_torsions.dat" # In current directory
ff_file5 = "./DataBase/ForceFields/MMFF94/mmff94_oop.dat" # In current directory
#------- Here are some basic patterns -------------
INT = '([1-9]([0-9]*))'
NINT = '([0-9]+)'
SP = '\s+'
#DOUBLE = '([-+]?(\d*\.\d*)([eE][-+]?\d+)?)'
DOUBLE = '([-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?)'
WORD = '([a-zA-Z]+)'
WORD1 = '(([a-zA-Z]|[-])+)'
ID = '(([a-zA-Z]+)([a-zA-Z]+|\d+)*)'
PHRASE = '"((\w|\W)+)"'
CONNECTOR = '\s*[-]\s*'
#------- Here we define a format of file ----------
# p - means 'Pattern'
pAtom_type_keyword = '(?P<Atom_type_keyword>' + 'TYPE' + ')' + SP
pAtom_ff_int_type = '(?P<Atom_ff_int_type>' + DOUBLE + ')' + SP
pAtom_ff_type = '(?P<Atom_ff_type>' + PHRASE + ')' + SP
pAtom_ff_type_H = '(?P<Atom_ff_type_H>' + PHRASE + ')' + SP
pAtom_atomic_number = '(?P<Atom_atomic_number>' + DOUBLE + ')' + SP
pAtom1_ff_type = '(?P<Atom1_ff_type>' + ID + ')' + SP
pAtom2_ff_type = '(?P<Atom2_ff_type>' + ID + ')' + SP
pAtom3_ff_type = '(?P<Atom3_ff_type>' + ID + ')' + SP
pAtom4_ff_type = '(?P<Atom4_ff_type>' + ID + ')' + SP
pAtom1_ff_int_type = '(?P<Atom1_ff_int_type>' + DOUBLE + ')' + SP
pAtom2_ff_int_type = '(?P<Atom2_ff_int_type>' + DOUBLE + ')' + SP
pAtom3_ff_int_type = '(?P<Atom3_ff_int_type>' + DOUBLE + ')' + SP
pAtom4_ff_int_type = '(?P<Atom4_ff_int_type>' + DOUBLE + ')' + SP
pX_type_index = '(?P<X_type_index>' + DOUBLE + ')' + SP
pBond_r_eq = '(?P<Bond_r_eq>' + DOUBLE + ')' + SP
pBond_k_bond = '(?P<Bond_k_bond>' + DOUBLE + ')' + SP
pBond_bci = '(?P<Bond_bci>' + DOUBLE + ')' + SP
pAngle_theta_eq = '(?P<Angle_theta_eq>' + DOUBLE + ')' + SP
pAngle_k_angle = '(?P<Angle_k_angle>' + DOUBLE + ')' + SP
pAngle_k_ijk = '(?P<Angle_k_ijk>' + DOUBLE + ')' + SP
pAngle_k_kji = '(?P<Angle_k_kji>' + DOUBLE + ')' + SP
pDihedral_mult = '(?P<Dihedral_mult>' + INT + ')' + SP
pDihedral_vphi = '(?P<Dihedral_vphi>' + DOUBLE + ')' + SP
pDihedral_phase = '(?P<Dihedral_phase>' + DOUBLE + ')' + SP
pTors_V1 = '(?P<Tors_V1>' + DOUBLE + ')' + SP
pTors_V2 = '(?P<Tors_V2>' + DOUBLE + ')' + SP
pTors_V3 = '(?P<Tors_V3>' + DOUBLE + ')' + SP
pAtom_crd = '(?P<Atom_crd>' + DOUBLE + ')' + SP
pAtom_val = '(?P<Atom_val>' + DOUBLE + ')' + SP
pAtom_pilp = '(?P<Atom_pilp>' + DOUBLE + ')' + SP
pAtom_mltb = '(?P<Atom_mltb>' + DOUBLE + ')' + SP
pAtom_arom = '(?P<Atom_arom>' + DOUBLE + ')' + SP
pAtom_lin = '(?P<Atom_lin>' + DOUBLE + ')' + SP
pAtom_sbmb = '(?P<Atom_sbmb>' + DOUBLE + ')' + SP
pAtom_alpha = '(?P<Atom_alpha>' + DOUBLE + ')' + SP
pAtom_N_eff = '(?P<Atom_N_eff>' + DOUBLE + ')' + SP
pAtom_A_scale = '(?P<Atom_A_scale>' + DOUBLE + ')' + SP
pAtom_G_scale = '(?P<Atom_G_scale>' + DOUBLE + ')' + SP
pAtom_DAN = '(?P<Atom_DAN>' + WORD + ')' + SP
pAtom_pbci = '(?P<Atom_pbci>' + DOUBLE + ')' + SP
pAtom_fcadj = '(?P<Atom_fcadj>' + DOUBLE + ')' + SP
pAtom_sigma = '(?P<Atom_sigma>' + DOUBLE + ')' + SP
pAtom_epsilon = '(?P<Atom_epsilon>' + DOUBLE + ')' + SP
pAtom_C_star = '(?P<Atom_C_star>' + DOUBLE + ')' + SP
pAtom_Z_star = '(?P<Atom_Z_star>' + DOUBLE + ')' + SP
pAtom_scale = '(?P<Atom_scale>' + DOUBLE + ')' + SP
pAtom_GMP = '(?P<Atom_GMP>' + DOUBLE + ')' + SP
pFF_name_keyword = '(?P<FF_name_keyword>' + 'FORCE_FIELD' + ')' + SP
pFF_sigma_rule_keyword = '(?P<FF_sigma_rule_keyword>' + 'SIGMA_COMB_RULE' + ')' + SP
pFF_epsil_rule_keyword = '(?P<FF_epsil_rule_keyword>' + 'EPSILON_COMB_RULE' + ')' + SP
pFF_vdw_scale13_keyword = '(?P<FF_vdw_scale13_keyword>' + 'VDW_SCALE13' + ')' + SP
pFF_vdw_scale14_keyword = '(?P<FF_vdw_scale14_keyword>' + 'VDW_SCALE14' + ')' + SP
pFF_elec_scale13_keyword = '(?P<FF_elec_scale13_keyword>' + 'ELEC_SCALE13' + ')' + SP
pFF_elec_scale14_keyword = '(?P<FF_elec_scale14_keyword>' + 'ELEC_SCALE14' + ')' + SP
pFF_name_value = '(?P<FF_name_value>' + ID + ')' + SP
pFF_sigma_rule_value = '(?P<FF_sigma_rule_value>' + WORD1 + ')' + SP
pFF_epsil_rule_value = '(?P<FF_epsil_rule_value>' + WORD1 + ')' + SP
pFF_vdw_scale13_value = '(?P<FF_vdw_scale13_value>' + DOUBLE + ')' + SP
pFF_vdw_scale14_value = '(?P<FF_vdw_scale14_value>' + DOUBLE + ')' + SP
pFF_elec_scale13_value = '(?P<FF_elec_scale13_value>' + DOUBLE + ')' + SP
pFF_elec_scale14_value = '(?P<FF_elec_scale14_value>' + DOUBLE + ')' + SP
FF_name_record = pFF_name_keyword + pFF_name_value
FF_sigma_rule_record = pFF_sigma_rule_keyword + pFF_sigma_rule_value
FF_epsil_rule_record = pFF_epsil_rule_keyword + pFF_epsil_rule_value
FF_vdw_scale13_record = pFF_vdw_scale13_keyword + pFF_vdw_scale13_value
FF_vdw_scale14_record = pFF_vdw_scale14_keyword + pFF_vdw_scale14_value
FF_elec_scale13_record = pFF_elec_scale13_keyword + pFF_elec_scale13_value
FF_elec_scale14_record = pFF_elec_scale14_keyword + pFF_elec_scale14_value
MMFF94_Atom_Type_Record1 = pAtom_type_keyword + \
pAtom_ff_type + \
pAtom_ff_type_H + \
pAtom_ff_int_type + \
pAtom_atomic_number + \
pAtom_crd + \
pAtom_val + \
pAtom_pilp + \
pAtom_mltb + \
pAtom_arom + \
pAtom_lin + \
pAtom_sbmb + \
pAtom_alpha + \
pAtom_N_eff + \
pAtom_A_scale + \
pAtom_G_scale + \
pAtom_DAN + \
pAtom_pbci + \
pAtom_fcadj
MMFF94_Atom_Type_Record2 = pAtom_type_keyword + \
pAtom_ff_type + \
pAtom_ff_int_type + \
pAtom1_ff_int_type + \
pAtom2_ff_int_type + \
pAtom3_ff_int_type + \
pAtom4_ff_int_type
MMFF94_Bond_Type_Record1 = pX_type_index + pAtom1_ff_int_type + pAtom2_ff_int_type + pBond_k_bond + pBond_r_eq
MMFF94_Bond_Type_Record2 = pX_type_index + pAtom1_ff_int_type + pAtom2_ff_int_type + pBond_bci
MMFF94_Bond_Type_Record3 = pAtom1_ff_int_type + pAtom2_ff_int_type + pBond_r_eq + pBond_k_bond
MMFF94_Angle_Type_Record1 = pX_type_index + pAtom1_ff_int_type + pAtom2_ff_int_type + pAtom3_ff_int_type + pAngle_k_angle + pAngle_theta_eq
MMFF94_Angle_Type_Record2 = pX_type_index + pAtom1_ff_int_type + pAtom2_ff_int_type + pAtom3_ff_int_type + pAngle_k_ijk + pAngle_k_kji
MMFF94_Dihedral_Type_Record = pX_type_index + pAtom1_ff_int_type + pAtom2_ff_int_type + pAtom3_ff_int_type + pAtom4_ff_int_type + pTors_V1 + pTors_V2 + pTors_V3
MMFF94_OOP_Type_Record = pAtom1_ff_int_type + pAtom2_ff_int_type + pAtom3_ff_int_type + pAtom4_ff_int_type + pDihedral_vphi
#-------------- Atoms ------------------------------------
print "Loading atom types...\n"
f = open(ff_file11, 'r')
A1 = f.readlines()
f.close()
f = open(ff_file12, 'r')
A2 = f.readlines()
f.close()
class atomrecord:
pass
ff_par = {}
for a in A1:
m1 = re.search(MMFF94_Atom_Type_Record1, a)
m2 = re.search(FF_sigma_rule_record, a)
m3 = re.search(FF_epsil_rule_record, a)
m4 = re.search(FF_vdw_scale13_record, a)
m5 = re.search(FF_vdw_scale14_record, a)
m6 = re.search(FF_elec_scale13_record, a)
m7 = re.search(FF_elec_scale14_record, a)
m8 = re.search(FF_name_record, a)
if m1 != None:
ff = atomrecord()
vAtom_ff_type = (
a[m1.start('Atom_ff_type'):m1.end('Atom_ff_type')])
# Remove "" from atom type
sz = len(vAtom_ff_type)
ff.Atom_ff_type = vAtom_ff_type[1:sz - 1]
vAtom_ff_type_H = (
a[m1.start('Atom_ff_type_H'):m1.end('Atom_ff_type_H')])
# Remove "" from atom type H
sz = len(vAtom_ff_type_H)
ff.Atom_ff_type_H = vAtom_ff_type_H[1:sz - 1]
ff.Atom_ff_int_type = int(
float(a[m1.start('Atom_ff_int_type'):m1.end('Atom_ff_int_type'
)]))
ff.Atom_atomic_number = int(
float(a[m1.start('Atom_atomic_number'):m1.
end('Atom_atomic_number')]))
ff.Atom_crd = int(float(
a[m1.start('Atom_crd'):m1.end('Atom_crd')]))
ff.Atom_val = int(float(
a[m1.start('Atom_val'):m1.end('Atom_val')]))
ff.Atom_pilp = int(
float(a[m1.start('Atom_pilp'):m1.end('Atom_pilp')]))
ff.Atom_mltb = int(
float(a[m1.start('Atom_mltb'):m1.end('Atom_mltb')]))
ff.Atom_arom = int(
float(a[m1.start('Atom_arom'):m1.end('Atom_arom')]))
ff.Atom_lin = int(float(
a[m1.start('Atom_lin'):m1.end('Atom_lin')]))
ff.Atom_sbmb = int(
float(a[m1.start('Atom_sbmb'):m1.end('Atom_sbmb')]))
ff.Atom_alpha = float(
a[m1.start('Atom_alpha'):m1.end('Atom_alpha')])
ff.Atom_N_eff = float(
a[m1.start('Atom_N_eff'):m1.end('Atom_N_eff')])
ff.Atom_A_scale = float(
a[m1.start('Atom_A_scale'):m1.end('Atom_A_scale')])
ff.Atom_G_scale = float(
a[m1.start('Atom_G_scale'):m1.end('Atom_G_scale')])
ff.Atom_DAN = a[m1.start('Atom_DAN'):m1.end('Atom_DAN')]
ff.Atom_pbci = float(a[m1.start('Atom_pbci'):m1.end('Atom_pbci')])
ff.Atom_fcadj = float(
a[m1.start('Atom_fcadj'):m1.end('Atom_fcadj')])
atom_record = lcccsObjects.Atom_Record()
atom_record.set(ff)
res = force_field.Add_Atom_Record(atom_record)
print "load type", ff.Atom_ff_type
if m2 != None:
ff_par["sigma_comb_rule"] = a[m2.start('FF_sigma_rule_value'):m2.
end('FF_sigma_rule_value')]
if m3 != None:
ff_par["epsilon_comb_rule"] = a[m3.start('FF_epsil_rule_value'):m3.
end('FF_epsil_rule_value')]
if m4 != None:
ff_par["vdw_scale13"] = float(
a[m4.start('FF_vdw_scale13_value'):m4.
end('FF_vdw_scale13_value')])
if m5 != None:
ff_par["vdw_scale14"] = float(
a[m5.start('FF_vdw_scale14_value'):m5.
end('FF_vdw_scale14_value')])
if m6 != None:
ff_par["elec_scale13"] = float(
a[m6.start('FF_elec_scale13_value'):m6.
end('FF_elec_scale13_value')])
if m7 != None:
ff_par["elec_scale14"] = float(
a[m7.start('FF_elec_scale14_value'):m7.
end('FF_elec_scale14_value')])
if m8 != None:
ff_par["ForceField_Name"] = a[m8.start('FF_name_value'):m8.
end('FF_name_value')]
force_field.set(ff_par)
for a in A2:
m1 = re.search(MMFF94_Atom_Type_Record2, a)
if m1 != None:
ff = atomrecord()
vAtom_ff_type = (
a[m1.start('Atom_ff_type'):m1.end('Atom_ff_type')])
# Remove "" from atom type
sz = len(vAtom_ff_type)
ff.Atom_ff_type = vAtom_ff_type[1:sz - 1]
ff.Atom_ff_int_type = int(
float(a[m1.start('Atom_ff_int_type'):m1.end('Atom_ff_int_type'
)]))
ff.Atom_ff_eq_int_type2 = int(
float(a[m1.start('Atom1_ff_int_type'):m1.
end('Atom1_ff_int_type')]))
ff.Atom_ff_eq_int_type3 = int(
float(a[m1.start('Atom2_ff_int_type'):m1.
end('Atom2_ff_int_type')]))
ff.Atom_ff_eq_int_type4 = int(
float(a[m1.start('Atom3_ff_int_type'):m1.
end('Atom3_ff_int_type')]))
ff.Atom_ff_eq_int_type5 = int(
float(a[m1.start('Atom4_ff_int_type'):m1.
end('Atom4_ff_int_type')]))
atom_record = lcccsObjects.Atom_Record()
atom_record.set(ff)
res = force_field.Add_Atom_Record(atom_record)
# force_field.show_atom_records()
# force_field.show_info()
#-------------- Bonds ------------------------------------
print "Loading bonds...\n"
f = open(ff_file21, 'r')
A1 = f.readlines()
f.close()
f = open(ff_file22, 'r')
A2 = f.readlines()
f.close()
f = open(ff_file23, 'r')
A3 = f.readlines()
f.close()
class bondrecord:
pass
for a in A1:
m1 = re.search(MMFF94_Bond_Type_Record1, a)
if m1 != None:
ff = bondrecord()
ff.Atom1_ff_int_type = int(
float(a[m1.start('Atom1_ff_int_type'):m1.
end('Atom1_ff_int_type')]))
ff.Atom2_ff_int_type = int(
float(a[m1.start('Atom2_ff_int_type'):m1.
end('Atom2_ff_int_type')]))
ff.Bond_type_index = int(
float(a[m1.start('X_type_index'):m1.end('X_type_index')]))
ff.Bond_k_bond = float(
a[m1.start('Bond_k_bond'):m1.end('Bond_k_bond')])
ff.Bond_r_eq = float(a[m1.start('Bond_r_eq'):m1.end('Bond_r_eq')])
bond_record = lcccsObjects.Bond_Record()
bond_record.set(ff)
res = force_field.Add_Bond_Record(bond_record)
for a in A2:
m1 = re.search(MMFF94_Bond_Type_Record2, a)
if m1 != None:
# print a
ff = bondrecord()
ff.Atom1_ff_int_type = int(
float(a[m1.start('Atom1_ff_int_type'):m1.
end('Atom1_ff_int_type')]))
ff.Atom2_ff_int_type = int(
float(a[m1.start('Atom2_ff_int_type'):m1.
end('Atom2_ff_int_type')]))
ff.Bond_type_index = int(
float(a[m1.start('X_type_index'):m1.end('X_type_index')]))
ff.Bond_bci = float(a[m1.start('Bond_bci'):m1.end('Bond_bci')])
bond_record = lcccsObjects.Bond_Record()
bond_record.set(ff)
res = force_field.Add_Bond_Record(bond_record)
print "Setting parameters for rule-based calculations"
for a in A3:
m1 = re.search(MMFF94_Bond_Type_Record3, a)
# Note that the meaning of patterns is different from that of variables!!!
if m1 != None:
ff = bondrecord()
ff.Atom1_atomic_number = int(
float(a[m1.start('Atom1_ff_int_type'):m1.
end('Atom1_ff_int_type')]))
ff.Atom2_atomic_number = int(
float(a[m1.start('Atom2_ff_int_type'):m1.
end('Atom2_ff_int_type')]))
ff.Bond_r_eq_ref = float(
a[m1.start('Bond_r_eq'):m1.end('Bond_r_eq')])
ff.Bond_k_bond_ref = float(
a[m1.start('Bond_k_bond'):m1.end('Bond_k_bond')])
bond_record = lcccsObjects.Bond_Record()
bond_record.set(ff)
# bond_record.show_info()
res = force_field.Add_Bond_Record(bond_record)
print res
# print "Printing all bond records in this force field"
# force_field.show_bond_records();
#----------------- Angles -------------------------------------
print "Loading angles and stretch-bending...\n"
f = open(ff_file31, 'r')
A1 = f.readlines()
f.close()
f = open(ff_file32, 'r')
A2 = f.readlines()
f.close()
f = open(ff_file33, 'r')
A3 = f.readlines()
f.close()
class anglerecord:
pass
for a in A1:
m1 = re.search(MMFF94_Angle_Type_Record1, a)
if m1 != None:
ff = anglerecord()
ff.Atom1_ff_int_type = int(
float(a[m1.start('Atom1_ff_int_type'):m1.
end('Atom1_ff_int_type')]))
ff.Atom2_ff_int_type = int(
float(a[m1.start('Atom2_ff_int_type'):m1.
end('Atom2_ff_int_type')]))
ff.Atom3_ff_int_type = int(
float(a[m1.start('Atom3_ff_int_type'):m1.
end('Atom3_ff_int_type')]))
ff.Angle_type_index = int(
float(a[m1.start('X_type_index'):m1.end('X_type_index')]))
ff.Angle_k_angle = float(
a[m1.start('Angle_k_angle'):m1.end('Angle_k_angle')])
ff.Angle_theta_eq = float(
a[m1.start('Angle_theta_eq'):m1.end('Angle_theta_eq')])
angle_record = lcccsObjects.Angle_Record()
angle_record.set(ff)
res = force_field.Add_Angle_Record(angle_record, 0)
for a in A2:
m1 = re.search(MMFF94_Angle_Type_Record2, a)
if m1 != None:
ff = anglerecord()
ff.Atom1_ff_int_type = int(
float(a[m1.start('Atom1_ff_int_type'):m1.
end('Atom1_ff_int_type')]))
ff.Atom2_ff_int_type = int(
float(a[m1.start('Atom2_ff_int_type'):m1.
end('Atom2_ff_int_type')]))
ff.Atom3_ff_int_type = int(
float(a[m1.start('Atom3_ff_int_type'):m1.
end('Atom3_ff_int_type')]))
ff.Angle_type_index = int(
float(a[m1.start('X_type_index'):m1.end('X_type_index')]))
ff.Angle_kijk_sb = float(
a[m1.start('Angle_k_ijk'):m1.end('Angle_k_ijk')])
ff.Angle_kkji_sb = float(
a[m1.start('Angle_k_kji'):m1.end('Angle_k_kji')])
angle_record = lcccsObjects.Angle_Record()
angle_record.set(ff)
res = force_field.Add_Angle_Record(angle_record, 1)
# print "Printing all angle records in this force field"
# force_field.show_angle_records();
#----------------- Dihedrals -------------------------------------
print "Loading dihedral...\n"
f = open(ff_file4, 'r')
A = f.readlines()
f.close()
class dihedralrecord:
pass
for a in A:
m1 = re.search(MMFF94_Dihedral_Type_Record, a)
if m1 != None:
ff = dihedralrecord()
ff.Atom1_ff_int_type = int(
float(a[m1.start('Atom1_ff_int_type'):m1.
end('Atom1_ff_int_type')]))
ff.Atom2_ff_int_type = int(
float(a[m1.start('Atom2_ff_int_type'):m1.
end('Atom2_ff_int_type')]))
ff.Atom3_ff_int_type = int(
float(a[m1.start('Atom3_ff_int_type'):m1.
end('Atom3_ff_int_type')]))
ff.Atom4_ff_int_type = int(
float(a[m1.start('Atom4_ff_int_type'):m1.
end('Atom4_ff_int_type')]))
ff.Dihedral_type_index = int(
float(a[m1.start('X_type_index'):m1.end('X_type_index')]))
ff.Dihedral_vphi1 = float(a[m1.start('Tors_V1'):m1.end('Tors_V1')])
ff.Dihedral_vphi2 = float(a[m1.start('Tors_V2'):m1.end('Tors_V2')])
ff.Dihedral_vphi3 = float(a[m1.start('Tors_V3'):m1.end('Tors_V3')])
ff.Dihedral_vphi = float(a[m1.start('Tors_V1'):m1.end('Tors_V1')])
dihedral_record = lcccsObjects.Dihedral_Record()
dihedral_record.set(ff)
res = force_field.Add_Dihedral_Record(dihedral_record, 0)
# print "Printing all dihedral(torsion) records in this force field"
# force_field.show_dihedral_records();
#----------------- Out-of-plane -------------------------------------
print "Loading oop...\n"
f = open(ff_file5, 'r')
A = f.readlines()
f.close()
class dihedralrecord:
pass
for a in A:
m1 = re.search(MMFF94_OOP_Type_Record, a)
if m1 != None:
ff = dihedralrecord()
ff.Atom1_ff_int_type = int(
float(a[m1.start('Atom1_ff_int_type'):m1.
end('Atom1_ff_int_type')]))
ff.Atom2_ff_int_type = int(
float(a[m1.start('Atom2_ff_int_type'):m1.
end('Atom2_ff_int_type')]))
ff.Atom3_ff_int_type = int(
float(a[m1.start('Atom3_ff_int_type'):m1.
end('Atom3_ff_int_type')]))
ff.Atom4_ff_int_type = int(
float(a[m1.start('Atom4_ff_int_type'):m1.
end('Atom4_ff_int_type')]))
ff.Dihedral_vphi = float(
a[m1.start('Dihedral_vphi'):m1.end('Dihedral_vphi')])
dihedral_record = lcccsObjects.Dihedral_Record()
dihedral_record.set(ff)
res = force_field.Add_Improper_Record(dihedral_record)
def Load_DREIDING(force_field):
ff_file = "./DataBase/ForceFields/DREIDING/dreiding.dat" # In current directory
#------- Here are some basic patterns -------------
INT = '([1-9]([0-9]*))'
NINT = '([0-9]+)'
SP = '\s+'
#DOUBLE = '([-+]?(\d*\.\d*)([eE][-+]?\d+)?)'
DOUBLE = '([-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?)'
WORD = '([a-zA-Z]+)'
ID = '(([a-zA-Z]+)([a-zA-Z]+|\d+)*)'
PHRASE = '"((\w|\W)+)"'
#------- Here we define a format of file ----------
# p - means 'Pattern'
pAtom_ff_int_type = '(?P<Atom_ff_int_type>' + DOUBLE + ')' + SP
pAtom_ff_type = '(?P<Atom_ff_type>' + PHRASE + ')' + SP
pAtom_radius = '(?P<Atom_radius>' + DOUBLE + ')' + SP
pAtom_theta = '(?P<Atom_theta>' + DOUBLE + ')' + SP
pAtom_sigma = '(?P<Atom_sigma>' + DOUBLE + ')' + SP
pAtom_epsilon = '(?P<Atom_epsilon>' + DOUBLE + ')' + SP
pAtom_scale = '(?P<Atom_scale>' + DOUBLE + ')' + SP
pAtom_GMP = '(?P<Atom_GMP>' + DOUBLE + ')' + SP
pFF_name_keyword = '(?P<FF_name_keyword>' + 'FORCE_FIELD' + ')' + SP
pFF_sigma_rule_keyword = '(?P<FF_sigma_rule_keyword>' + 'SIGMA_COMB_RULE' + ')' + SP
pFF_epsil_rule_keyword = '(?P<FF_epsil_rule_keyword>' + 'EPSILON_COMB_RULE' + ')' + SP
pFF_vdw_scale12_keyword = '(?P<FF_vdw_scale12_keyword>' + 'VDW_SCALE12' + ')' + SP
pFF_vdw_scale13_keyword = '(?P<FF_vdw_scale13_keyword>' + 'VDW_SCALE13' + ')' + SP
pFF_vdw_scale14_keyword = '(?P<FF_vdw_scale14_keyword>' + 'VDW_SCALE14' + ')' + SP
pFF_elec_scale12_keyword = '(?P<FF_elec_scale12_keyword>' + 'ELEC_SCALE12' + ')' + SP
pFF_elec_scale13_keyword = '(?P<FF_elec_scale13_keyword>' + 'ELEC_SCALE13' + ')' + SP
pFF_elec_scale14_keyword = '(?P<FF_elec_scale14_keyword>' + 'ELEC_SCALE14' + ')' + SP
pFF_name_value = '(?P<FF_name_value>' + WORD + ')' + SP
pFF_sigma_rule_value = '(?P<FF_sigma_rule_value>' + WORD + ')' + SP
pFF_epsil_rule_value = '(?P<FF_epsil_rule_value>' + WORD + ')' + SP
pFF_vdw_scale12_value = '(?P<FF_vdw_scale12_value>' + DOUBLE + ')' + SP
pFF_vdw_scale13_value = '(?P<FF_vdw_scale13_value>' + DOUBLE + ')' + SP
pFF_vdw_scale14_value = '(?P<FF_vdw_scale14_value>' + DOUBLE + ')' + SP
pFF_elec_scale12_value = '(?P<FF_elec_scale12_value>' + DOUBLE + ')' + SP
pFF_elec_scale13_value = '(?P<FF_elec_scale13_value>' + DOUBLE + ')' + SP
pFF_elec_scale14_value = '(?P<FF_elec_scale14_value>' + DOUBLE + ')' + SP
FF_name_record = pFF_name_keyword + pFF_name_value
FF_sigma_rule_record = pFF_sigma_rule_keyword + pFF_sigma_rule_value
FF_epsil_rule_record = pFF_epsil_rule_keyword + pFF_epsil_rule_value
FF_vdw_scale12_record = pFF_vdw_scale12_keyword + pFF_vdw_scale12_value
FF_vdw_scale13_record = pFF_vdw_scale13_keyword + pFF_vdw_scale13_value
FF_vdw_scale14_record = pFF_vdw_scale14_keyword + pFF_vdw_scale14_value
FF_elec_scale12_record = pFF_elec_scale12_keyword + pFF_elec_scale12_value
FF_elec_scale13_record = pFF_elec_scale13_keyword + pFF_elec_scale13_value
FF_elec_scale14_record = pFF_elec_scale14_keyword + pFF_elec_scale14_value
DREIDING_Atom_Type_Record = pAtom_ff_int_type + \
pAtom_ff_type + \
pAtom_radius + \
pAtom_theta + \
pAtom_sigma + \
pAtom_epsilon + \
pAtom_scale + \
pAtom_GMP
f = open(ff_file, 'r')
A = f.readlines()
f.close()
class atomrecord:
pass
ff_par = {}
for a in A:
m1 = re.search(DREIDING_Atom_Type_Record, a)
m2 = re.search(FF_sigma_rule_record, a)
m3 = re.search(FF_epsil_rule_record, a)
m4 = re.search(FF_vdw_scale13_record, a)
m5 = re.search(FF_vdw_scale14_record, a)
m6 = re.search(FF_elec_scale13_record, a)
m7 = re.search(FF_elec_scale14_record, a)
m8 = re.search(FF_name_record, a)
m9 = re.search(FF_vdw_scale12_record, a)
m10 = re.search(FF_elec_scale12_record, a)
if m1 != None:
ff = atomrecord()
ff.Atom_ff_int_type = int(
float(a[m1.start('Atom_ff_int_type'):m1.end('Atom_ff_int_type'
)]))
vAtom_ff_type = (
a[m1.start('Atom_ff_type'):m1.end('Atom_ff_type')])
ff.Atom_radius = float(
a[m1.start('Atom_radius'):m1.end('Atom_radius')])
ff.Atom_theta = float(
a[m1.start('Atom_theta'):m1.end('Atom_theta')])
ff.Atom_sigma = float(
a[m1.start('Atom_sigma'):m1.end('Atom_sigma')])
ff.Atom_epsilon = float(
a[m1.start('Atom_epsilon'):m1.end('Atom_epsilon')])
ff.Atom_scale = float(
a[m1.start('Atom_scale'):m1.end('Atom_scale')])
ff.Atom_GMP = float(a[m1.start('Atom_GMP'):m1.end('Atom_GMP')])
# Remove "" from atom type
sz = len(vAtom_ff_type)
ff.Atom_ff_type = vAtom_ff_type[1:sz - 1]
atom_record = lcccsObjects.Atom_Record()
atom_record.set(ff)
res = force_field.Add_Atom_Record(atom_record)
print "load type", ff.Atom_ff_type
if m2 != None:
ff_par["sigma_comb_rule"] = a[m2.start('FF_sigma_rule_value'):m2.
end('FF_sigma_rule_value')]
if m3 != None:
ff_par["epsilon_comb_rule"] = a[m3.start('FF_epsil_rule_value'):m3.
end('FF_epsil_rule_value')]
if m4 != None:
ff_par["vdw_scale13"] = float(
a[m4.start('FF_vdw_scale13_value'):m4.
end('FF_vdw_scale13_value')])
if m5 != None:
ff_par["vdw_scale14"] = float(
a[m5.start('FF_vdw_scale14_value'):m5.
end('FF_vdw_scale14_value')])
if m6 != None:
ff_par["elec_scale13"] = float(
a[m6.start('FF_elec_scale13_value'):m6.
end('FF_elec_scale13_value')])
if m7 != None:
ff_par["elec_scale14"] = float(
a[m7.start('FF_elec_scale14_value'):m7.
end('FF_elec_scale14_value')])
if m8 != None:
ff_par["ForceField_Name"] = a[m8.start('FF_name_value'):m8.
end('FF_name_value')]
if m9 != None:
ff_par["vdw_scale12"] = float(
a[m9.start('FF_vdw_scale12_value'):m9.
end('FF_vdw_scale12_value')])
if m10 != None:
ff_par["elec_scale12"] = float(
a[m10.start('FF_elec_scale12_value'):m10.
end('FF_elec_scale12_value')])
force_field.set(ff_par)
def Load_MALINA(force_field):
ff_file1 = "./DataBase/ForceFields/MALINA/malina_types.dat" # In current directory
ff_file2 = "./DataBase/ForceFields/MALINA/malina_bonds1.dat" # In current directory
#------- Here are some basic patterns -------------
INT = '([1-9]([0-9]*))'
NINT = '([0-9]+)'
SP = '\s+'
#DOUBLE = '([-+]?(\d*\.\d*)([eE][-+]?\d+)?)'
DOUBLE = '([-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?)'
WORD = '([a-zA-Z]+)'
WORD1 = '(([a-zA-Z]|[-])+)'
ID = '(([a-zA-Z]+)([a-zA-Z]+|\d+)*)'
PHRASE = '"((\w|\W)+)"'
CONNECTOR = '\s*[-]\s*'
#------- Here we define a format of file ----------
# p - means 'Pattern'
pAtom_type_keyword = '(?P<Atom_type_keyword>' + 'TYPE' + ')' + SP
pAtom_ff_int_type = '(?P<Atom_ff_int_type>' + DOUBLE + ')' + SP
pAtom_ff_type = '(?P<Atom_ff_type>' + PHRASE + ')' + SP
pAtom_ff_type_H = '(?P<Atom_ff_type_H>' + PHRASE + ')' + SP
pAtom_atomic_number = '(?P<Atom_atomic_number>' + DOUBLE + ')' + SP
pAtom_charge = '(?P<Atom_charge>' + DOUBLE + ')' + SP
pAtom1_ff_type = '(?P<Atom1_ff_type>' + ID + ')' + SP
pAtom2_ff_type = '(?P<Atom2_ff_type>' + ID + ')' + SP
pAtom3_ff_type = '(?P<Atom3_ff_type>' + ID + ')' + SP
pAtom4_ff_type = '(?P<Atom4_ff_type>' + ID + ')' + SP
pAtom1_ff_int_type = '(?P<Atom1_ff_int_type>' + DOUBLE + ')' + SP
pAtom2_ff_int_type = '(?P<Atom2_ff_int_type>' + DOUBLE + ')' + SP
pAtom3_ff_int_type = '(?P<Atom3_ff_int_type>' + DOUBLE + ')' + SP
pAtom4_ff_int_type = '(?P<Atom4_ff_int_type>' + DOUBLE + ')' + SP
pBond_r_eq = '(?P<Bond_r_eq>' + DOUBLE + ')' + SP
pBond_D_bond = '(?P<Bond_D_bond>' + DOUBLE + ')' + SP
pBond_alpha = '(?P<Bond_alpha>' + DOUBLE + ')' + SP
pBond_delta = '(?P<Bond_delta>' + DOUBLE + ')' + SP
pBond_bci = '(?P<Bond_bci>' + DOUBLE + ')' + SP
pBond_wij = '(?P<Bond_wij>' + DOUBLE + ')' + SP
pBond_wij_1 = '(?P<Bond_wij_1>' + DOUBLE + ')' + SP
pBond_wij_2 = '(?P<Bond_wij_2>' + DOUBLE + ')' + SP
pBond_alpij = '(?P<Bond_alpij>' + DOUBLE + ')' + SP
pBond_alpij_1 = '(?P<Bond_alpij_1>' + DOUBLE + ')' + SP
pBond_alpij_2 = '(?P<Bond_alpij_2>' + DOUBLE + ')' + SP
pBond_rij_1 = '(?P<Bond_rij_1>' + DOUBLE + ')' + SP
pBond_rij_2 = '(?P<Bond_rij_2>' + DOUBLE + ')' + SP
pFF_sigma_rule_keyword = '(?P<FF_sigma_rule_keyword>' + 'SIGMA_COMB_RULE' + ')' + SP
pFF_epsil_rule_keyword = '(?P<FF_epsil_rule_keyword>' + 'EPSILON_COMB_RULE' + ')' + SP
pFF_vdw_scale13_keyword = '(?P<FF_vdw_scale13_keyword>' + 'VDW_SCALE13' + ')' + SP
pFF_vdw_scale14_keyword = '(?P<FF_vdw_scale14_keyword>' + 'VDW_SCALE14' + ')' + SP
pFF_elec_scale13_keyword = '(?P<FF_elec_scale13_keyword>' + 'ELEC_SCALE13' + ')' + SP
pFF_elec_scale14_keyword = '(?P<FF_elec_scale14_keyword>' + 'ELEC_SCALE14' + ')' + SP
pFF_sigma_rule_value = '(?P<FF_sigma_rule_value>' + WORD1 + ')' + SP
pFF_epsil_rule_value = '(?P<FF_epsil_rule_value>' + WORD1 + ')' + SP
pFF_vdw_scale13_value = '(?P<FF_vdw_scale13_value>' + DOUBLE + ')' + SP
pFF_vdw_scale14_value = '(?P<FF_vdw_scale14_value>' + DOUBLE + ')' + SP
pFF_elec_scale13_value = '(?P<FF_elec_scale13_value>' + DOUBLE + ')' + SP
pFF_elec_scale14_value = '(?P<FF_elec_scale14_value>' + DOUBLE + ')' + SP
FF_sigma_rule_record = pFF_sigma_rule_keyword + pFF_sigma_rule_value
FF_epsil_rule_record = pFF_epsil_rule_keyword + pFF_epsil_rule_value
FF_vdw_scale13_record = pFF_vdw_scale13_keyword + pFF_vdw_scale13_value
FF_vdw_scale14_record = pFF_vdw_scale14_keyword + pFF_vdw_scale14_value
FF_elec_scale13_record = pFF_elec_scale13_keyword + pFF_elec_scale13_value
FF_elec_scale14_record = pFF_elec_scale14_keyword + pFF_elec_scale14_value
MALINA_Atom_Type_Record = pAtom_type_keyword + \
pAtom_ff_type + \
pAtom_ff_int_type + \
pAtom_atomic_number + \
pAtom_charge
MALINA_Bond_Type_Record = pAtom1_ff_int_type + \
pAtom2_ff_int_type + \
pBond_D_bond + \
pBond_r_eq + \
pBond_alpha + \
pBond_delta + \
pBond_bci + \
pBond_wij_1 + \
pBond_wij_2 + \
pBond_alpij_1 + \
pBond_alpij_2 + \
pBond_rij_1 + \
pBond_rij_2 + \
pBond_wij + \
pBond_alpij
#-------------- Atoms ------------------------------------
print "Loading atom types...\n"
f = open(ff_file1, 'r')
A = f.readlines()
f.close()
class atomrecord:
pass
for a in A:
m1 = re.search(MALINA_Atom_Type_Record, a)
m2 = re.search(FF_sigma_rule_record, a)
m3 = re.search(FF_epsil_rule_record, a)
m4 = re.search(FF_vdw_scale13_record, a)
m5 = re.search(FF_vdw_scale14_record, a)
m6 = re.search(FF_elec_scale13_record, a)
m7 = re.search(FF_elec_scale14_record, a)
if m1 != None:
ff = atomrecord()
vAtom_ff_type = (
a[m1.start('Atom_ff_type'):m1.end('Atom_ff_type')])
# Remove "" from atom type
sz = len(vAtom_ff_type)
ff.Atom_ff_type = vAtom_ff_type[1:sz - 1]
ff.Atom_ff_int_type = int(
float(a[m1.start('Atom_ff_int_type'):m1.end('Atom_ff_int_type'
)]))
ff.Atom_atomic_number = int(
float(a[m1.start('Atom_atomic_number'):m1.
end('Atom_atomic_number')]))
ff.Atom_Z_star = float(
a[m1.start('Atom_charge'):m1.end('Atom_charge')])
atom_record = lcccsObjects.Atom_Record()
atom_record.set(ff)
# atom_record.show_info()
res = force_field.Add_Atom_Record(atom_record)
print "load type", ff.Atom_ff_type
# print res
if m2 != None:
ff = atomrecord()
ff.ForceField_sigma_comb_rule = a[
m2.start('FF_sigma_rule_value'):m2.end('FF_sigma_rule_value')]
force_field.set(ff)
if m3 != None:
ff = atomrecord()
ff.ForceField_epsilon_comb_rule = a[
m3.start('FF_epsil_rule_value'):m3.end('FF_epsil_rule_value')]
force_field.set(ff)
if m4 != None:
ff = atomrecord()
ff.ForceField_vdw_scale13 = float(
a[m4.start('FF_vdw_scale13_value'):m4.
end('FF_vdw_scale13_value')])
force_field.set(ff)
if m5 != None:
ff = atomrecord()
ff.ForceField_vdw_scale14 = float(
a[m5.start('FF_vdw_scale14_value'):m5.
end('FF_vdw_scale14_value')])
force_field.set(ff)
if m6 != None:
ff = atomrecord()
ff.ForceField_elec_scale13 = float(
a[m6.start('FF_elec_scale13_value'):m6.
end('FF_elec_scale13_value')])
force_field.set(ff)
if m7 != None:
ff = atomrecord()
ff.ForceField_elec_scale14 = float(
a[m7.start('FF_elec_scale14_value'):m7.
end('FF_elec_scale14_value')])
force_field.set(ff)
force_field.show_atom_records()
force_field.show_info()
#-------------- Bonds ------------------------------------
print "Loading bonds...\n"
f = open(ff_file2, 'r')
A1 = f.readlines()
f.close()
class bondrecord:
pass
for a in A1:
m1 = re.search(MALINA_Bond_Type_Record, a)
if m1 != None:
ff = bondrecord()
ff.Atom1_ff_int_type = int(
float(a[m1.start('Atom1_ff_int_type'):m1.
end('Atom1_ff_int_type')]))
ff.Atom2_ff_int_type = int(
float(a[m1.start('Atom2_ff_int_type'):m1.
end('Atom2_ff_int_type')]))
ff.Bond_D_bond = float(
a[m1.start('Bond_D_bond'):m1.end('Bond_D_bond')])
ff.Bond_r_eq = float(a[m1.start('Bond_r_eq'):m1.end('Bond_r_eq')])
ff.Bond_alpha = float(
a[m1.start('Bond_alpha'):m1.end('Bond_alpha')])
ff.Bond_shift_elec = float(
a[m1.start('Bond_delta'):m1.end('Bond_delta')])
ff.Bond_bci = float(a[m1.start('Bond_bci'):m1.end('Bond_bci')])
ff.Bond_wij = float(a[m1.start('Bond_wij'):m1.end('Bond_wij')])
ff.Bond_wij_1 = float(
a[m1.start('Bond_wij_1'):m1.end('Bond_wij_1')])
ff.Bond_wij_2 = float(
a[m1.start('Bond_wij_2'):m1.end('Bond_wij_2')])
ff.Bond_alpij = float(
a[m1.start('Bond_alpij'):m1.end('Bond_alpij')])
ff.Bond_alpij_1 = float(
a[m1.start('Bond_alpij_1'):m1.end('Bond_alpij_1')])
ff.Bond_alpij_2 = float(
a[m1.start('Bond_alpij_2'):m1.end('Bond_alpij_2')])
ff.Bond_rij_1 = float(
a[m1.start('Bond_rij_1'):m1.end('Bond_rij_1')])
ff.Bond_rij_2 = float(
a[m1.start('Bond_rij_2'):m1.end('Bond_rij_2')])
bond_record = lcccsObjects.Bond_Record()
bond_record.set(ff)
res = force_field.Add_Bond_Record(bond_record)
print "Printing all bond records in this force field"
force_field.show_bond_records()
def Load_ESFF(force_field):
ff_file = "./DataBase/ForceFields/ESFF/esff1.dat" # In current directory
#------- Here are some basic patterns -------------
INT = '([1-9]([0-9]*))'
NINT = '([0-9]+)'
SP = '\s+'
#DOUBLE = '([-+]?(\d*\.\d*)([eE][-+]?\d+)?)'
DOUBLE = '([-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?)'
WORD = '([a-zA-Z]+)'
ID = '(([a-zA-Z]+)([a-zA-Z]+|\d+)*)'
PHRASE = '((\w|[-+=*]|\')+)'
#------- Here we define a format of file ----------
# p - means 'Pattern'
pAtom_ff_int_type = '(?P<Atom_ff_int_type>' + DOUBLE + ')' + SP
pAtom_ff_type = '(?P<Atom_ff_type>' + PHRASE + ')' + SP
pAtom_dative = '(?P<Atom_dative>' + DOUBLE + ')' + SP
pAtom_brdr1 = '(?P<Atom_brdr1>' + DOUBLE + ')' + SP
pAtom_brdr2 = '(?P<Atom_brdr2>' + DOUBLE + ')' + SP
pAtom_brdr3 = '(?P<Atom_brdr3>' + DOUBLE + ')' + SP
pAtom_theta = '(?P<Atom_theta>' + DOUBLE + ')' + SP
pAtom_sigma = '(?P<Atom_sigma>' + DOUBLE + ')' + SP
pAtom_epsilon = '(?P<Atom_epsilon>' + DOUBLE + ')' + SP
pAtom_scale = '(?P<Atom_scale>' + DOUBLE + ')' + SP
pAtom_Z_star = '(?P<Atom_Z_star>' + DOUBLE + ')' + SP
pAtom_GMP = '(?P<Atom_GMP>' + DOUBLE + ')' + SP
ESFF_Bond_Ref_Value_Record3 = pAtom_ff_type + \
pAtom_dative + \
pAtom_brdr1 + \
pAtom_brdr2 + \
pAtom_brdr3
ESFF_Bond_Ref_Value_Record2 = pAtom_ff_type + \
pAtom_dative + \
pAtom_brdr1 + \
pAtom_brdr2
ESFF_Bond_Ref_Value_Record1 = pAtom_ff_type + \
pAtom_dative + \
pAtom_brdr1
f = open(ff_file, 'r')
A = f.readlines()
f.close()
class atomrecord:
pass
for a in A:
m1 = re.search(ESFF_Bond_Ref_Value_Record1, a)
m2 = re.search(ESFF_Bond_Ref_Value_Record2, a)
m3 = re.search(ESFF_Bond_Ref_Value_Record3, a)
if m1 != None:
ff = atomrecord()
ff.Atom_ff_type = (
a[m1.start('Atom_ff_type'):m1.end('Atom_ff_type')])
ff.Atom_dative = float(
a[m1.start('Atom_dative'):m1.end('Atom_dative')])
ff.Atom_brdr1 = float(
a[m1.start('Atom_brdr1'):m1.end('Atom_brdr1')])
if m2 != None:
ff.Atom_brdr2 = float(
a[m2.start('Atom_brdr2'):m2.end('Atom_brdr2')])
if m3 != None:
ff.Atom_brdr3 = float(
a[m3.start('Atom_brdr3'):m3.end('Atom_brdr3')])
atom_record = lcccsObjects.Atom_Record()
atom_record.set(ff)
res = force_field.Add_Atom_Record(atom_record)
print "load type", ff.Atom_ff_type
def Load_SuttonChen(force_field):
ff_file = "./DataBase/ForceFields/SuttonChen/suttonchen.dat"
#------- Here are some basic patterns -------------
INT = '([1-9]([0-9]*))'
NINT = '([0-9]+)'
SP = '\s+'
#DOUBLE = '([-+]?(\d*\.\d*)([eE][-+]?\d+)?)'
DOUBLE = '([-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?)'
WORD = '([a-zA-Z]+)'
ID = '(([a-zA-Z]+)([a-zA-Z]+|\d+)*)'
PHRASE = '"((\w|\W)+)"'
#------- Here we define a format of file ----------
# p - means 'Pattern'
pAtom_element = '(?P<Atom_element>' + WORD + ')' + SP
pAtom_such_n = '(?P<Atom_such_n>' + INT + ')' + SP
pAtom_such_m = '(?P<Atom_such_m>' + INT + ')' + SP
pAtom_such_a = '(?P<Atom_such_a>' + DOUBLE + ')' + SP
pAtom_such_D = '(?P<Atom_such_D>' + DOUBLE + ')' + SP
pAtom_such_c = '(?P<Atom_such_c>' + DOUBLE + ')' + SP
SUCH_Atom_Type_Record = pAtom_element + \
pAtom_such_n + \
pAtom_such_m + \
pAtom_such_D + \
pAtom_such_c + \
pAtom_such_a
f = open(ff_file, 'r')
A = f.readlines()
f.close()
class atomrecord:
pass
convert = 0.0964853 # convertion from meV to kcal/mol
for a in A:
m1 = re.search(SUCH_Atom_Type_Record, a)
if m1 != None:
ff = atomrecord()
ff.Atom_ff_type = a[m1.start('Atom_element'):m1.end('Atom_element'
)]
ff.Atom_element = a[m1.start('Atom_element'):m1.end('Atom_element'
)]
ff.Atom_such_n = float(
a[m1.start('Atom_such_n'):m1.end('Atom_such_n')])
ff.Atom_such_m = float(
a[m1.start('Atom_such_m'):m1.end('Atom_such_m')])
ff.Atom_such_a = float(
a[m1.start('Atom_such_a'):m1.end('Atom_such_a')])
ff.Atom_such_D = convert * float(
a[m1.start('Atom_such_D'):m1.end('Atom_such_D')])
ff.Atom_such_c = float(
a[m1.start('Atom_such_c'):m1.end('Atom_such_c')])
atom_record = lcccsObjects.Atom_Record()
atom_record.set(ff)
res = force_field.Add_Atom_Record(atom_record)
print "load element", ff.Atom_element
print ff.Atom_ff_type, ff.Atom_element, ff.Atom_such_n