CODEWITHSUNDEEP
bioinformatics
user2372158
user2372158

Reputation: 27

compute the distance between coordinates

I would like to compute the distances between atoms from PDB files. How can I do this calculation for PDB files ?

ATOM      1  N   GLY A  23     -10.507   5.621  25.325  1.00 60.45           N  
ATOM      2  CA  GLY A  23      -9.475   4.636  25.745  1.00 56.55           C
ATOM      3  C   GLY A  23      -8.714   4.045  24.571  1.00 58.66           C
ATOM      4  O   GLY A  23      -8.526   2.829  24.498  1.00 60.74           O 
ATOM      5  N   GLN A  24      -8.275   4.899  23.651  1.00 52.00           N 
ATOM      6  CA  GLN A  24      -7.532   4.446  22.482  1.00 45.40           C 
ATOM      7  C   GLN A  24      -6.089   4.139  22.865  1.00 39.62           C  
ATOM      8  O   GLN A  24      -5.617   4.536  23.928  1.00 35.50           O  
ATOM     14  N   ARG A  25      -5.391   3.428  21.991  1.00 37.97           N 
ATOM     15  CA  ARG A  25      -4.003   3.065  22.237  1.00 37.23           C
ATOM     16  C   ARG A  25      -3.133   4.276  22.555  1.00 36.13           C 
ATOM     17  O   ARG A  25      -2.441   4.293  23.571  1.00 31.46           O

distance = sqrt((x1-x2)^2+(y1-y2)^2+(z1-z2)^2)

Upvotes: 1

Views: 2023

Answers (1)

David Cain
David Cain

Reputation: 17333

You should refrain from parsing the PDB files yourself. PDB files have a lot of irregularities that tools like awk aren't well suited for. Instead, you should parse the structure into a meaningful object using an already implemented parser.

I like Biopython. You should look into the tutorial for more on how to interact with structures, but this is a really basic way to get distance between two atoms. Note that the - operator is overridden to return atom distance (no need to deal with coordinates or the distance formula!).

from Bio import PDB

parser = PDB.PDBParser()

# Parse the PDB file into a meaningful structure object
pdb_path = "/path/to/files/1abc.pdb"
pdb_id = "1abc"
struct = parser.get_struct(pdb_id, pdb_path)

# Get two atoms to compare by navigating the SMRCA structure
chain_a = struct[0]["A"]
res1 = chain_a[26]
res2 = chain_a[23]
atom1 = res1["C"] 
atom2 = res2["C"]

print "Distance: %d" % (atom1 - atom2)

It's slightly unclear to me which atoms you wish to calculate distance for, but you can look at the resname field of a PDB.Residue object (e.g. res1) if you want to compare based on residue name.

You may also want to look Bio.PDB.NeighborSearch to look for nearby atoms (it's an implementation of a k-d tree).

Upvotes: 3

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