def main(pdb_filename, residues, output_filename):
'''writes residues from a PDB file to an output file.'''
pdb = open(pdb_filename)
outfile = open(output_filename, "w")
for line in pdb:
if line.startswith("ATOM"):
chain, res_type, res_num, atom, x, y, z = parse_atom_line(line)
for aa, num in residues:
if res_type == aa and res_num == num:
outfile.write(line)
outfile.close()
def main(pdb_filename, residues, output_filename):
'''writes residues from a PDB file to an output file.'''
pdb = open(pdb_filename)
outfile = open(output_filename, "w")
for line in pdb:
if line.startswith("ATOM"):
chain, res_type, res_num, atom, x, y, z = parse_atom_line(line)
for aa, num in residues:
if res_type == aa and res_num == num:
outfile.write(line)
outfile.close()
def get_ca_atoms(pdb_filename):
'''returns a list of all C-alpha atoms in chain A'''
pdb_file = open(pdb_filename, "r")
ca_list = []
for line in pdb_file:
if line.startswith('ATOM'):
data = parse_atom_line(line)
chain, res_type, res_num, atom, x, y, z = data
if atom == 'CA' and chain == 'A':
ca_list.append(data)
pdb_file.close()
return ca_list
def get_ca_atoms(pdb_filename):
'''returns a list of all C-alpha atoms in chain A'''
pdb_file = open(pdb_filename, "r")
ca_list = []
for line in pdb_file:
if line.startswith('ATOM'):
data = parse_atom_line(line)
chain, res_type, res_num, atom, x, y, z = data
if atom == 'CA' and chain == 'A':
ca_list.append(data)
pdb_file.close()
return ca_list
'''
Find two alpha-C atoms in a PDB structure and calculate their distance.
-----------------------------------------------------------
(c) 2013 Allegra Via and Kristian Rother
Licensed under the conditions of the Python License
This code appears in section 10.4.4 of the book
"Managing Biological Data with Python".
-----------------------------------------------------------
'''
from math import sqrt
from distance import calc_dist
from parse_pdb import parse_atom_line
pdb = open('3G5U.pdb')
points = []
while len(points) < 2:
line = pdb.readline()
if line.startswith("ATOM"):
chain, res_type, res_num, atom, x, y, z = parse_atom_line(line)
if res_num == '123' and chain == 'A' and atom == 'CA':
points.append((x, y, z))
if res_num == '209' and chain == 'A' and atom == 'CA':
points.append((x, y, z))
print(calc_dist(points[0], points[1]))
'''
Find two alpha-C atoms in a PDB structure and calculate their distance.
-----------------------------------------------------------
(c) 2013 Allegra Via and Kristian Rother
Licensed under the conditions of the Python License
This code appears in section 10.4.4 of the book
"Managing Biological Data with Python".
-----------------------------------------------------------
'''
from math import sqrt
from distance import calc_dist
from parse_pdb import parse_atom_line
pdb = open('3G5U.pdb')
points = []
while len(points) < 2:
line = pdb.readline()
if line.startswith("ATOM"):
chain, res_type, res_num, atom, x, y, z = parse_atom_line(line)
if res_num == '123' and chain == 'A' and atom == 'CA':
points.append((x, y, z))
if res_num == '209' and chain == 'A' and atom == 'CA':
points.append((x, y, z))
print calc_dist(points[0], points[1])
