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kravcoff_1w39.py
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kravcoff_1w39.py
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import re
import csv
import numpy
name_of_file = '6rrs.pdb'
ln10 = 2.30258509299
pH = 7
pKa = {
'ASP': 3.71,
'GLU': 4.15,
'TYR': 10.10,
'ARG': 12.10,
'HIS': 6.04,
'LYS': 10.67,
'CYS': 8.14,
}
m_atom = {
'N': 14.0067,
'C': 12.011,
'O': 15.999,
'H': 1.00784,
'S': 32.065,
}
keys_of_m_atom = ['N', 'C', 'O', 'H', 'S']
data_chem_elem = []
data_amino_acid = []
x_i = 0
y_i = 0
z_i = 0
x_i_q = 0
y_i_q = 0
z_i_q = 0
q_i_o = 0
m_i = 0
a = 0
b = 0
x=[]
y=[]
z=[]
def main_A(name_file: str):
slice_file(name_file)
for line in csv.DictReader(open(name_file[:4] + '_sliced.csv')):
global x_i, y_i, z_i, m_i, x_i_q, y_i_q, z_i_q, q_i_o, a, b
if line['chem_elem'] not in data_chem_elem:
data_chem_elem.append(line['chem_elem'])
if line['amino_acid'] not in data_amino_acid:
data_amino_acid.append(line['amino_acid'])
if line['name_protein'] == 'A':
try:
x.append(float(line['X']))
y.append(float(line['Y']))
z.append(float(line['Z']))
x_i += float(line['X']) * m_atom[line['chem_elem']]
y_i += float(line['Y']) * m_atom[line['chem_elem']]
z_i += float(line['Z']) * m_atom[line['chem_elem']]
q_i_o += q_i(line['amino_acid'])
if line['chem_elem'] in keys_of_m_atom:
m_i += m_atom[line['chem_elem']]
else:
m_i += 0
x_i_q += float(line['X']) * q_i(line['amino_acid'])
y_i_q += float(line['Y']) * q_i(line['amino_acid'])
z_i_q += float(line['Z']) * q_i(line['amino_acid'])
'''print('Mass gravity:{} {} {} Charge center: X = {} Y = {} Z = \
{} qi: {} name of acid: {}'.format(line['X'], line['Y'], \
line['Z'], x_i_q, y_i_q, z_i_q, q_i(line['amino_acid']), \
line['amino_acid']))'''
except KeyError:
continue
a = (x_i/m_i, y_i/m_i, z_i/m_i)
b = (x_i_q/q_i_o, y_i_q/q_i_o, z_i_q/q_i_o)
#return {'mass_gravity': a, 'charge_center': b, 'all_acid': data_amino_acid}
return {'mass_gravity': a, 'charge_center': b}
def main_B(name_file: str):
slice_file(name_file)
for line in csv.DictReader(open(name_file[:4] + '_sliced.csv')):
global x_i, y_i, z_i, m_i, x_i_q, y_i_q, z_i_q, q_i_o, a, b
if line['chem_elem'] not in data_chem_elem:
data_chem_elem.append(line['chem_elem'])
if line['amino_acid'] not in data_amino_acid:
data_amino_acid.append(line['amino_acid'])
if line['name_protein'] == 'B':
try:
x_i += float(line['X']) * m_atom[line['chem_elem']]
y_i += float(line['Y']) * m_atom[line['chem_elem']]
z_i += float(line['Z']) * m_atom[line['chem_elem']]
q_i_o += q_i(line['amino_acid'])
if line['chem_elem'] in keys_of_m_atom:
m_i += m_atom[line['chem_elem']]
else:
m_i += 0
x_i_q += float(line['X']) * q_i(line['amino_acid'])
y_i_q += float(line['Y']) * q_i(line['amino_acid'])
z_i_q += float(line['Z']) * q_i(line['amino_acid'])
'''print('Mass gravity:{} {} {} Charge center: X = {} Y = {} Z = \
{} qi: {} name of acid: {}'.format(line['X'], line['Y'], \
line['Z'], x_i_q, y_i_q, z_i_q, q_i(line['amino_acid']), \
line['amino_acid']))'''
except KeyError:
continue
a = (x_i/m_i, y_i/m_i, z_i/m_i)
b = (x_i_q/q_i_o, y_i_q/q_i_o, z_i_q/q_i_o)
#return {'mass_gravity': a, 'charge_center': b, 'all_acid': data_amino_acid}
return {'mass_gravity': a, 'charge_center': b}
def main_C(name_file: str):
slice_file(name_file)
for line in csv.DictReader(open(name_file[:4] + '_sliced.csv')):
global x_i, y_i, z_i, m_i, x_i_q, y_i_q, z_i_q, q_i_o, a, b
if line['chem_elem'] not in data_chem_elem:
data_chem_elem.append(line['chem_elem'])
if line['amino_acid'] not in data_amino_acid:
data_amino_acid.append(line['amino_acid'])
if line['name_protein'] == 'C':
try:
x_i += float(line['X']) * m_atom[line['chem_elem']]
y_i += float(line['Y']) * m_atom[line['chem_elem']]
z_i += float(line['Z']) * m_atom[line['chem_elem']]
q_i_o += q_i(line['amino_acid'])
if line['chem_elem'] in keys_of_m_atom:
m_i += m_atom[line['chem_elem']]
else:
m_i += 0
x_i_q += float(line['X']) * q_i(line['amino_acid'])
y_i_q += float(line['Y']) * q_i(line['amino_acid'])
z_i_q += float(line['Z']) * q_i(line['amino_acid'])
'''print('Mass gravity:{} {} {} Charge center: X = {} Y = {} Z = \
{} qi: {} name of acid: {}'.format(line['X'], line['Y'], \
line['Z'], x_i_q, y_i_q, z_i_q, q_i(line['amino_acid']), \
line['amino_acid']))'''
except KeyError:
continue
a = (x_i/m_i, y_i/m_i, z_i/m_i)
b = (x_i_q/q_i_o, y_i_q/q_i_o, z_i_q/q_i_o)
#return {'mass_gravity': a, 'charge_center': b, 'all_acid': data_amino_acid}
return {'mass_gravity': a, 'charge_center': b}
def slice_file(name_file: str):
f = open(name_file)
f_new = open(name_file[:4] + '_sliced.csv', 'w')
f_new.write('ATOM/HETATM,number,atom_type,amino_acid,name_protein,' +
'residue_number,X,Y,Z,occupancy,B-factor,chem_elem\n')
for i in f:
if re.match(r'ATOM ', i):
f_new.write(repl_spac_to_comma(i))
f.close()
f_new.close()
def repl_spac_to_comma(stroke: str):
return stroke.replace(' ', ' ').replace(' ', ' ')\
.replace(' ', ' ').replace(' ', ' ')\
.replace(' ', ' ').replace(' ', ',').replace('-', ',-') \
.replace(',,', ',')
def q_i(amino_acid: str):
if amino_acid in ['ARG', 'HIS', "LYS"]:
return 1/(1 + numpy.exp(ln10*(pH - pKa[amino_acid])))
elif amino_acid in ['ASP', 'GLU', 'TYR']:
return (-1)/(1 + numpy.exp(ln10*(-(pH - pKa[amino_acid]))))
else:
return (-1)/(1 + numpy.exp(ln10*(pH)))
print('Name of virus ' + name_of_file[:-4])
print('For protein A: ', end='')
print(main_A(name_of_file))
print('For protein B:', end='')
print(main_B(name_of_file))
print('For protein C:', end='')
print(main_C(name_of_file))
if '__init__' == '__main__':
pass