input_directory = 'C:\\development\\sources\\'
output_directory = 'C:\\development\\workdir\\'
processed_energies = cast_values('%s\\%s' %
(input_directory, '1KXP_energies.txt'))
input_file = open('%s\\1KXP_dockedPoses\\filelist.txt' %
input_directory).readlines()
file_list = []
for line in input_file:
file_list.append(line[:-1])
output_file = open('%s\\visualization_ligands.pdb' % output_directory, 'w')
counter = 0
for file_name in file_list:
atoms = read_pdb_file('%s\\afterSplit\\%s_lig.pdb' %
(output_directory, file_name[0:-4]))
s_tuple = []
for atom_line in atoms:
if atom_line[0:4] == 'ATOM':
coord_tuple = (float(atom_line[30:38].strip()),
float(atom_line[38:46].strip()),
float(atom_line[46:54].strip()))
s_tuple.append(coord_tuple)
cx, cy, cz = get_centroid(s_tuple)
counter += 1
output_file.write('HETATM%5s%5s VIS X%4i %8.3f%8.3f%8.3f 1.00%6.2f\n' %
(str(counter), file_name.replace('.pdb', ''), 0, cx, cy,
cz, processed_energies[file_name]))
output_file.close()
residue_id = ''
chain_id = ''
for line in atoms:
chain_id = line[21]
residue_id = line[22:26]
break
for line in atoms:
if line[21] != chain_id:
chain_id = line[21]
residue_id = line[22:26]
if int(line[22:26]) != int(residue_id) and int(line[22:26]) != (int(residue_id)+1):
distance_C_N = get_distance(coord_C['%s%s' % (chain_id, residue_id)], coord_N['%s%s' % (line[21], line[22:26])])
print('Suspicious %s%s: C-N %f' % (line[21], line[22:26], distance_C_N))
if distance_C_N > 1.40:
missing_residue = 'MISSING RESIDUE BEFORE: %s' % line[17:26]
break
residue_id = line[22:26]
return missing_residue
if __name__ == '__main__':
main_directory = 'C:\\development\\sources\\'
atoms = read_pdb_file('%s\\%s' % (main_directory, 'missing1.pdb'))
#atoms = read_pdb_file('%s\\%s' % (main_directory, 'missing2.pdb'))
#atoms = read_pdb_file('%s\\%s' % (main_directory, 'missing3.pdb'))
#atoms = read_pdb_file('%s\\%s' % (main_directory, 'missing4.pdb'))
#atoms = read_pdb_file('%s\\%s' % (main_directory, 'missing5.pdb'))
#atoms = read_pdb_file('%s\\%s' % (main_directory, 'missing6.pdb'))
print(find_missing_atoms(atoms))
print(find_missing_residues(atoms))
from task3_readPDB import read_pdb_file
from task9_findDistance import get_distance
def get_interface_residues(atoms1, atoms2):
"""
:param atoms1: ATOM records list for atom 1
:type atoms1: list
:param atoms2: ATOM records list for atom 2
:type atoms2: list
:return: interface residues as a list
"""
interface = []
for a1 in atoms1:
for a2 in atoms2:
distance = get_distance(a1, a2)
if distance <= 10.0:
interaction = '%s WITH %s' % (a1[17:26], a2[17:26])
if interaction not in interface:
interface.append(interaction)
return interface
if __name__ == '__main__':
main_directory = 'C:\\development\\workdir\\'
atoms_receptor = read_pdb_file('%s\\afterSplit\\%s' % (main_directory, '0a_rec.pdb'))
atoms_ligand = read_pdb_file('%s\\afterSplit\\%s' % (main_directory, '0a_lig.pdb'))
print(get_interface_residues(atoms_receptor, atoms_ligand))
from task3_readPDB import read_pdb_file
from task8_printSequence import get_sequence
import numpy as np
import matplotlib.pyplot as plt
if __name__ == '__main__':
main_directory = 'C:\\development\\sources'
atoms = read_pdb_file('%s\\1KXP_dockedPoses\\%s' %
(main_directory, '0a.pdb'))
sequence = get_sequence(atoms)
seqsplit = sequence.split('\n')
chains = []
position = 0
sequence = ''
while position < len(seqsplit):
if seqsplit[position] != '':
sequence += seqsplit[position]
else:
if len(sequence) > 0:
chains.append(sequence)
sequence = ''
position += 1
res1lett = [
'G', 'A', 'L', 'I', 'V', 'D', 'E', 'N', 'Q', 'R', 'K', 'S', 'T', 'C',
'M', 'F', 'Y', 'H', 'W', 'P'
]
res_dictionary = {'CHAIN A': {}, 'CHAIN B': {}}
for res in res1lett:
res_dictionary['CHAIN A'][res] = 0
for line in energies_file:
spline = line.split()
my_tuple = (spline[0], float(spline[1]))
energies.append(my_tuple)
energies.sort(key=lambda x: x[1])
output = open('%s\\clusters_reduced.txt' % output_directory, 'w')
for i in range(0, len(energies)):
structure1 = energies[i][0]
if structure1 in already_clustered:
continue
new_cluster = [structure1]
already_clustered.append(structure1)
atoms1 = read_pdb_file(
'%s\\afterSplit\\%s' %
(output_directory, '%s_lig.pdb' % structure1[0:-4]))
s1_tuple = []
for atom_line_1 in atoms1:
if atom_line_1[0:4] == 'ATOM':
coord_tuple = (float(atom_line_1[30:38].strip()),
float(atom_line_1[38:46].strip()),
float(atom_line_1[46:54].strip()))
s1_tuple.append(coord_tuple)
counter = 0
for j in range(i + 1, len(energies)):
structure2 = energies[j][0]
if structure2 in already_clustered:
continue
counter += 1
atoms2 = read_pdb_file(
:type s1: tuple
:param s2: x,y,z coordinates of structure 2
:type s2: tuple
:return: RMSD as float
"""
rmsd = 0.0
for i in range(0, len(s1)):
rmsd = rmsd + ((s2[i][0] - s1[i][0])**2) + (
(s2[i][1] - s1[i][1])**2) + ((s2[i][2] - s1[i][2])**2)
rmsd = sqrt(rmsd / len(s1))
return rmsd
if __name__ == '__main__':
main_directory = 'C:\\development\\workdir\\'
atoms1 = read_pdb_file('%s\\afterSplit\\%s' %
(main_directory, '100a_lig.pdb'))
atoms2 = read_pdb_file('%s\\afterSplit\\%s' %
(main_directory, '100d_lig.pdb'))
s1_tuple = []
s2_tuple = []
for atom_line in atoms1:
if atom_line[0:4] == 'ATOM':
coord_tuple = (float(atom_line[30:38].strip()),
float(atom_line[38:46].strip()),
float(atom_line[46:54].strip()))
s1_tuple.append(coord_tuple)
for atom_line in atoms2:
if atom_line[0:4] == 'ATOM':
coord_tuple = (float(atom_line[30:38].strip()),
float(atom_line[38:46].strip()),
float(atom_line[46:54].strip()))