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_prmtop.py
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import sys
import numpy as np
def print_solvent_pointers (data, fout):
key_words = 'SOLVENT_POINTERS'
str_flag = '%-80s'%('%FLAG '+key_words)+'\n'
str_format = '%-80s'%('%FORMAT(3I8)')+'\n'
fout.write (str_flag)
fout.write (str_format)
line = '%8d%8d%8d'%(data[0], data[1], data[2]) + '\n'
fout.write (line)
def print_string_radius_set (fout):
key_words = 'RADIUS_SET'
str_flag = '%-80s'%('%FLAG '+key_words)+'\n'
str_format = '%-80s'%('%FORMAT(1a80)')+'\n'
fout.write (str_flag)
fout.write (str_format)
line = '%-80s'%('H(N)-modified Bondi radii (mbondi2)') + '\n'
fout.write (line)
def print_string_data (key_words, data, fout):
str_flag = '%-80s'%('%FLAG '+key_words)+'\n'
str_format = '%-80s'%('%FORMAT(20a4)')+'\n'
fout.write (str_flag)
fout.write (str_format)
num = len(data)
for ii in range (0, num, 20):
if ii + 20 < num:
str = ''
for jj in range(20):
val = data[ii+jj]
str += '%-4s'%val
line = str + '\n'
fout.write(line)
else:
str = ''
len0 = num - ii
for jj in range (len0):
val = data[ii+jj]
str += '%-4s'%val
line='%-80s'%str+'\n'
fout.write(line)
def print_integer_data (key_words, data, fout):
str_flag = '%-80s'%('%FLAG '+key_words)+'\n'
str_format = '%-80s'%('%FORMAT(10I8)')+'\n'
fout.write (str_flag)
fout.write (str_format)
num = len(data)
for ii in range (0, num, 10):
if ii + 10 < num:
str = ''
for jj in range(10):
val = data[ii+jj]
str += '%8d'%val
line = str+'\n'
fout.write(line)
else:
str = ''
len0 = num - ii
for jj in range (len0):
val = data[ii+jj]
str += '%8d'%val
line = '%-80s'%str+'\n'
fout.write(line)
def print_double_data (key_words, data, fout):
str_flag = '%-80s'%('%FLAG '+key_words)+'\n'
str_format = '%-80s'%('%FORMAT(5E16.8)')+'\n'
fout.write (str_flag)
fout.write (str_format)
num = len(data)
if num == 0:
line = '\n'
fout.write(line)
else:
for ii in range (0, num, 5):
if ii + 5 < num:
str = ''
for jj in range(5):
val = data[ii+jj]
str += '%16.8E'%val
line = str+'\n'
fout.write(line)
else:
str = ''
len0 = num - ii
for jj in range (len0):
val = data[ii+jj]
str += '%16.8E'%val
line = '%-80s'%str+'\n'
fout.write(line)
class PrmTop (object):
def __init__ (self):
self.atom_name_list = []
self.atom_type_list = []
self.atomic_number_list = []
self.atom_type_index_list = []
self.amber_atom_type_list = []
self.res_name_list = []
self.res_ptr_list = []
self.chg_list = []
self.mass_list = []
self.radii_list = []
self.bond_k_list = []
self.bond_length_list = []
self.bond_wH_list = []
self.bond_nH_list = []
self.angle_k_list = []
self.angle_length_list = []
self.angle_wH_list = []
self.angle_nH_list = []
self.proper_wH_list = []
self.proper_nH_list = []
self.proper_periodicity_list = []
self.proper_phase_list = []
self.proper_k_list = []
# self.scee_list = []
# self.scnb_list = []
self.solty_list = [0.0, 0.0]
self.lj_acoef_list = []
self.lj_bcoef_list = []
self.nb_idx_list = []
self.num_excluded_atoms = []
self.excluded_atoms_list = []
self.is_box = 0
self.box_info = []
self.sol_ptr = [0, 1, 2] # The last residue number of the solute, total number of molecules, the first solvent "molecule"
self.atoms_per_molecule = []
self.max_res_natom = 100
def write_pointers(self, key_words, fout):
str_flag = '%-80s'%('%FLAG '+key_words)+'\n'
str_format = '%-80s'%('%FORMAT(10I8)')+'\n'
fout.write(str_flag)
fout.write(str_format)
data = []
data.append(len(self.atom_name_list))
data.append(len(self.atom_type_list))
data.append(len(self.bond_wH_list)/3)
data.append(len(self.bond_nH_list)/3)
data.append(len(self.angle_wH_list)/4)
data.append(len(self.angle_nH_list)/4)
data.append(len(self.proper_wH_list)/5)
data.append(len(self.proper_nH_list)/5)
data.append(0) # NHPARM: NOT USED
data.append(0) # NPARM: NOT USED
nnb = sum(self.num_excluded_atoms)
data.append(nnb)
data.append(len(self.res_name_list))
data.append(len(self.bond_nH_list)/3)
data.append(len(self.angle_nH_list)/4)
data.append(len(self.proper_nH_list)/5)
data.append(len(self.bond_k_list))
data.append(len(self.angle_k_list))
data.append(len(self.proper_k_list))
data.append(len(self.solty_list)) # NATYP: NOT USED
data.append(0) # NPHB: number of distinct 10-12 HB pair types
data.append(0) # IFPERT: set to 1 if perturbation info is to be read in
data.append(0) # NBPER
data.append(0) # NGPER
data.append(0) # NDPER
data.append(0) # MBPER
data.append(0) # MGPER
data.append(0) # MDPER
data.append(self.is_box) # IFBXO: 1 if standard periodic box
data.append(self.max_res_natom) #
data.append(0) # ifcap : CAP option
data.append(0) # numextra
data.append(0) # ncopy
num = len(data)
for ii in range (0, num, 10):
if ii + 10 < num:
str = ''
for jj in range(10):
val = data[ii+jj]
str += '%8d'%val
line = str+'\n'
fout.write(line)
else:
str = ''
len0 = num - ii
for jj in range (len0):
val = data[ii+jj]
str += '%8d'%val
line = '%-80s'%str+'\n'
fout.write(line)
def write (self, fname):
fout = open (fname, 'w')
head = '%-80s'%'%VERSION VERSION_STAMP = V0001.000 DATE = 02/26/19 15:36:56'+'\n'
head += '%-80s'%'%FLAG TITLE' + '\n'
head += '%-80s'%'%FORMAT(20a4)' + '\n'
head += '%-80s'%'default_name' + '\n'
fout.write(head)
self.write_pointers('POINTERS', fout)
#f_C.write('%FLAG POINTERS\n')
#f_C.write('%FORMAT(10I8) \n')
print_string_data ('ATOM_NAME', self.atom_name_list, fout)
print_double_data ('CHARGE', self.chg_list, fout)
tot_chg = 0.0
for chg in self.chg_list:
tot_chg += chg
print ('tot_chg ', tot_chg/18.2223)
print_integer_data ('ATOMIC_NUMBER', self.atomic_number_list, fout)
print_double_data ('MASS', self.mass_list, fout)
print_integer_data ('ATOM_TYPE_INDEX', self.atom_type_index_list, fout)
print_integer_data ('NUMBER_EXCLUDED_ATOMS', self.num_excluded_atoms, fout)
print_integer_data ('NONBONDED_PARM_INDEX', self.nb_idx_list, fout)
print_string_data ('RESIDUE_LABEL', self.res_name_list, fout)
print_integer_data('RESIDUE_POINTER', self.res_ptr_list, fout)
print_double_data ('BOND_FORCE_CONSTANT', self.bond_k_list, fout)
print_double_data ('BOND_EQUIL_VALUE', self.bond_length_list, fout)
print_double_data ('ANGLE_FORCE_CONSTANT', self.angle_k_list, fout)
print_double_data ('ANGLE_EQUIL_VALUE', self.angle_length_list, fout)
print_double_data ('DIHEDRAL_FORCE_CONSTANT', self.proper_k_list, fout)
print_double_data ('DIHEDRAL_PERIODICITY', self.proper_periodicity_list, fout)
print_double_data ('DIHEDRAL_PHASE', self.proper_phase_list, fout)
scee_list = np.ones ( (len(self.proper_phase_list)) )*1.2
print_double_data ('SCEE_SCALE_FACTOR', scee_list, fout)
scnb_list = np.ones ( (len(self.proper_phase_list)) )*2.0
print_double_data ('SCNB_SCALE_FACTOR', scnb_list, fout)
print_double_data ('SOLTY', self.solty_list, fout)
print_double_data ('LENNARD_JONES_ACOEF', self.lj_acoef_list, fout)
print_double_data ('LENNARD_JONES_BCOEF', self.lj_bcoef_list, fout)
print_integer_data('BONDS_INC_HYDROGEN', self.bond_wH_list, fout)
print_integer_data('BONDS_WITHOUT_HYDROGEN', self.bond_nH_list, fout)
print_integer_data('ANGLES_INC_HYDROGEN', self.angle_wH_list, fout)
print_integer_data('ANGLES_WITHOUT_HYDROGEN', self.angle_nH_list, fout)
print_integer_data('DIHEDRALS_INC_HYDROGEN', self.proper_wH_list, fout)
print_integer_data('DIHEDRALS_WITHOUT_HYDROGEN', self.proper_nH_list, fout)
print_integer_data('EXCLUDED_ATOMS_LIST', self.excluded_atoms_list, fout)
data = []
print_double_data ('HBOND_ACOEF', data, fout)
print_double_data ('HBOND_BCOEF', data, fout)
print_double_data ('HBCUT', data, fout)
print_string_data ('AMBER_ATOM_TYPE', self.amber_atom_type_list, fout)
data = []
for ii in range(len(self.atomic_number_list)):
data.append('BLA')
print_string_data('TREE_CHAIN_CLASSIFICATION', data, fout)
data = []
for ii in range(len(self.atomic_number_list)):
data.append(0)
print_integer_data('JOIN_ARRAY', data, fout)
print_integer_data('IROTAT', data, fout)
if self.is_box == 1:
print_solvent_pointers (self.sol_ptr, fout)
if len (self.atoms_per_molecule) == 0:
self.atoms_per_molecule.append (len (self.atom_name_list))
print_integer_data('ATOMS_PER_MOLECULE', self.atoms_per_molecule, fout)
print_double_data('BOX_DIMENSIONS', self.box_info, fout)
print_string_radius_set(fout)
print_double_data('RADII', self.radii_list, fout)
data = []
for znum in self.atomic_number_list:
if znum == 1:
data.append(0.85)
elif znum == 6:
data.append(0.72)
elif znum == 7:
data.append(0.79)
elif znum == 8:
data.append(0.85)
elif znum == 9:
data.append(0.88)
elif znum == 15:
data.append(0.86)
elif znum == 16:
data.append(0.96)
elif znum == 26:
data.append(0.88)
else:
data.append(0.80)
print_double_data('SCREEN', data, fout)
data = [0]
print_integer_data('IPOL', data, fout)
fout.close()