Difference between revisions of "Pdb to movie.py"
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import>Mp466 |
import>Mp466 |
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| (7 intermediate revisions by the same user not shown) | |||
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| + | #! /usr/bin/env python |
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| + | |||
| + | """ |
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| + | Calculates the movieseg or a OPTIM coord file from a given PDB file |
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| + | |||
| + | arguments: |
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| + | |||
| + | |||
| + | 50 format('CA: ',3(f8.3,1x),'CB: ',3(f8.3,1x),'Ox: ', 3(f8.3,1x)) |
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| + | 334 format(4(i8,1x),' nmres nmcrd numpro nmsnap') |
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| + | |||
| + | """ |
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| + | |||
| + | import sys |
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| + | import string |
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| + | from Bio.PDB.PDBParser import PDBParser |
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| + | |||
| + | PDBfile='1uzc' |
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| + | pars = PDBParser(PERMISSIVE = 1) |
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| + | struct = pars.get_structure(PDBfile.rstrip('.pdb'), PDBfile) |
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| + | model = struct.child_list[0] |
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| + | chain = model.child_list[0] |
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| + | |||
| + | print " 69 3 1 1 nmres nmcrd numpro nmsnap" |
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| + | |||
| + | for residue in chain: |
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| + | cx=0.0 |
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| + | cy=0.0 |
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| + | cz=0.0 |
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| + | cbx=0.0 |
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| + | cby=0.0 |
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| + | cbz=0.0 |
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| + | ox=0.0 |
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| + | oy=0.0 |
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| + | oz=0.0 |
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| + | |||
| + | if residue.has_id("CA"): |
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| + | ca=residue["CA"] |
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| + | cx=ca.get_coord()[0] |
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| + | cy=ca.get_coord()[1] |
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| + | cz=ca.get_coord()[2] |
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| + | |||
if residue.has_id("CB"): |
if residue.has_id("CB"): |
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cb=residue["CB"] |
cb=residue["CB"] |
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| − | # print "CB" |
+ | # print "CB" |
| − | # print cb.get_coord() |
+ | # print cb.get_coord() |
cbx=cb.get_coord()[0] |
cbx=cb.get_coord()[0] |
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cby=cb.get_coord()[1] |
cby=cb.get_coord()[1] |
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| Line 11: | Line 53: | ||
cby=cy |
cby=cy |
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cbz=cz |
cbz=cz |
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| + | |||
| − | |||
if residue.has_id("O"): |
if residue.has_id("O"): |
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o=residue["O"] |
o=residue["O"] |
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| − | # print " O" |
+ | # print " O" |
| − | # print o.get_coord() |
+ | # print o.get_coord() |
ox=o.get_coord()[0] |
ox=o.get_coord()[0] |
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oy=o.get_coord()[1] |
oy=o.get_coord()[1] |
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oz=o.get_coord()[2] |
oz=o.get_coord()[2] |
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| + | |||
| ⚫ | |||
| + | # Uncomment for lowest or OPTIM coord files |
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| ⚫ | |||
| + | # print " %8.3f %8.3f %8.3f " % (cx,cy,cz) |
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| + | # print " %8.3f %8.3f %8.3f " % (cbx,cby,cbz) |
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| + | # print " %8.3f %8.3f %8.3f " % (ox,oy,oz) |
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Latest revision as of 19:48, 8 May 2009
#! /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)