Python parse_atom_line Examples

Example #1

File: identify_residues_in_pdb.py Project: Jinke233/Biopython

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()

Example #2

File: identify_residues_in_pdb.py Project: HunterAllman/ipython

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()

Example #3

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

Example #4

File: calc_all_calpha_distance.py Project: HunterAllman/ipython

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

Example #5

'''

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]))

Example #6

File: calc_atom_atom_distance.py Project: HunterAllman/ipython

'''

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])