'''
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]))
from parse_pdb import parse_atom_line
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
ca_atoms = get_ca_atoms("1TLD.pdb")
for i, atom1 in enumerate(ca_atoms):
# save coordinates in a variable
name1 = atom1[1] + atom1[2]
coord1 = atom1[4:]
# compare atom1 with all other atoms
for j in range(i + 1, len(ca_atoms)):
atom2 = ca_atoms[j]
name2 = atom2[1] + atom2[2]
coord2 = atom2[4:]
# calculate the distance between atoms
dist = calc_dist(coord1, coord2)
print(name1, name2, dist)
from math import sqrt
from distance import calc_dist
from parse_pdb import parse_atom_line
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
ca_atoms = get_ca_atoms("1TLD.pdb")
for i, atom1 in enumerate(ca_atoms):
# save coordinates in a variable
name1 = atom1[1] + atom1[2]
coord1 = atom1[4:]
# compare atom1 with all other atoms
for j in range(i+1, len(ca_atoms)):
atom2 = ca_atoms[j]
name2 = atom2[1] + atom2[2]
coord2 = atom2[4:]
# calculate the distance between atoms
dist = calc_dist(coord1, coord2)
print name1, name2, dist
'''
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])
