Adk44: Created page with " #! /usr/bin/env python """ Calculates the movieseg or a OPTIM coord file from a given PDB file arguments: 50 format('CA: ',3(f8.3,1x),'CB: ',3(f8..."

2019-05-13T12:17:24Z

Created page with " #! /usr/bin/env python """ Calculates the movieseg or a OPTIM coord file from a given PDB file arguments: 50 format('CA: ',3(f8.3,1x),'CB: ',3(f8..."

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#! /usr/bin/env python

"""
Calculates the movieseg or a OPTIM coord file from a given PDB file

arguments:

50 format('CA: ',3(f8.3,1x),'CB: ',3(f8.3,1x),'Ox: ', 3(f8.3,1x))
334 format(4(i8,1x),' nmres nmcrd numpro nmsnap')

"""

import sys
import string
from Bio.PDB.PDBParser import PDBParser

PDBfile='1uzc'
pars = PDBParser(PERMISSIVE = 1)
struct = pars.get_structure(PDBfile.rstrip('.pdb'), PDBfile)
model = struct.child_list[0]
chain = model.child_list[0]

print " 69 3 1 1 nmres nmcrd numpro nmsnap"

for residue in chain:
cx=0.0
cy=0.0
cz=0.0
cbx=0.0
cby=0.0
cbz=0.0
ox=0.0
oy=0.0
oz=0.0

if residue.has_id("CA"):
ca=residue["CA"]
cx=ca.get_coord()[0]
cy=ca.get_coord()[1]
cz=ca.get_coord()[2]

if residue.has_id("CB"):
cb=residue["CB"]
# print "CB"
# print cb.get_coord()
cbx=cb.get_coord()[0]
cby=cb.get_coord()[1]
cbz=cb.get_coord()[2]
else:
cbx=cx
cby=cy
cbz=cz

if residue.has_id("O"):
o=residue["O"]
# print " O"
# print o.get_coord()
ox=o.get_coord()[0]
oy=o.get_coord()[1]
oz=o.get_coord()[2]

print "CA: %8.3f %8.3f %8.3f CB: %8.3f %8.3f %8.3f OX: %8.3f %8.3f %8.3f" % (cx,cy,cz,cbx,cby,cbz,ox,oy,oz)

# Uncomment for lowest or OPTIM coord files
# print " %8.3f %8.3f %8.3f " % (cx,cy,cz)
# print " %8.3f %8.3f %8.3f " % (cbx,cby,cbz)
# print " %8.3f %8.3f %8.3f " % (ox,oy,oz)

Pdb to movie.py - Revision history

Adk44: Created page with " #! /usr/bin/env python """ Calculates the movieseg or a OPTIM coord file from a given PDB file arguments: 50 format('CA: ',3(f8.3,1x),'CB: ',3(f8..."