center_protein.py

Moves a given protein structure so its geometric center is located at (0,0,0)
USAGE:
python center_protein.py [which_model]

Keywords:

Categories:

  • core/data/io/find_pdb

Program source:

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import sys
sys.path.append('../../../../../bin/')
from pybioshell.core.data.io import find_pdb

if len(sys.argv) < 2 :
  print("""

    Moves a given protein structure so its geometric center is located at (0,0,0)
USAGE:
    python center_protein.py [which_model]

    CATEGORIES: core/data/io/find_pdb
    KEYWORDS: PDB input; center protein; coordinates

  """)
  sys.exit()

which_model = 0 if len(sys.argv) == 2 else int(sys.argv[2])

pdb_reader = find_pdb(sys.argv[1], "./")
structure = pdb_reader.create_structure(which_model)
cx, cy, cz, n = 0, 0, 0, 0
for ic in range(structure.count_chains()) :
    chain = structure[ic]
    for ir in range(chain.count_residues()) :
      resid = chain[ir]
      for ai in range(resid.count_atoms()) :
        cx += resid[ai].x
        cy += resid[ai].y
        cz += resid[ai].z
        n+=1.0
        
cx /= n
cy /= n
cz /= n
print("# Center was:",cx,cy,cz)

for ic in range(structure.count_chains()) :
    chain = structure[ic]
    for ir in range(chain.count_residues()) :
      resid = chain[ir]
      for ai in range(resid.count_atoms()) :
        resid[ai].x -= cx
        resid[ai].y -= cy
        resid[ai].z -= cz
        print(resid[ai].to_pdb_line())
../_images/file_icon.png