Pdb to movie.py - Revision history

import>Mp466 at 19:48, 8 May 2009

2009-05-08T19:48:58Z

← Older revision		Revision as of 19:48, 8 May 2009
Line 1:		Line 1:


	#! /usr/bin/env python		#! /usr/bin/env python
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	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)		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 " % (cx,cy,cz)
	# print " %8.3f %8.3f %8.3f " % (cbx,cby,cbz)		# print " %8.3f %8.3f %8.3f " % (cbx,cby,cbz)

import>Mp466 at 19:41, 8 May 2009

2009-05-08T19:41:36Z

← Older revision		Revision as of 19:41, 8 May 2009
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	"""		"""
	Calculates the movieseg from a given PDB file		Calculates the movieseg or a OPTIM coord file from a given PDB file

	arguments:		arguments:
Line 65:		Line 64:

	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)		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)

			# 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)

import>Mp466 at 19:27, 8 May 2009

2009-05-08T19:27:08Z

← Older revision		Revision as of 19:27, 8 May 2009
Line 1:		Line 1:



	#! /usr/bin/env python		#! /usr/bin/env python

import>Mp466 at 19:25, 8 May 2009

2009-05-08T19:25:04Z

← Older revision		Revision as of 19:25, 8 May 2009
Line 6:		Line 6:
	arguments:		arguments:

	PDBfile - the PDB file to score

	50 format('CA: ',3(f8.3,1x),'CB: ',3(f8.3,1x),'Ox: ', 3(f8.3,1x))		50 format('CA: ',3(f8.3,1x),'CB: ',3(f8.3,1x),'Ox: ', 3(f8.3,1x))

import>Mp466 at 19:24, 8 May 2009

2009-05-08T19:24:17Z

← Older revision		Revision as of 19:24, 8 May 2009
Line 53:		Line 53:
	cby=cy		cby=cy
	cbz=cz		cbz=cz


	if residue.has_id("O"):		if residue.has_id("O"):
	o=residue["O"]		o=residue["O"]
Line 61:		Line 61:
	oy=o.get_coord()[1]		oy=o.get_coord()[1]
	oz=o.get_coord()[2]		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)		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)

import>Mp466 at 19:23, 8 May 2009

2009-05-08T19:23:40Z

← Older revision		Revision as of 19:23, 8 May 2009
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	import string		import string
	from Bio.PDB.PDBParser import PDBParser		from Bio.PDB.PDBParser import PDBParser


	PDBfile='1uzc'		PDBfile='1uzc'
	pars = PDBParser(PERMISSIVE = 1)		pars = PDBParser(PERMISSIVE = 1)
Line 24:		Line 24:

	print " 69 3 1 1 nmres nmcrd numpro nmsnap"		print " 69 3 1 1 nmres nmcrd numpro nmsnap"


	for residue in chain:		for residue in chain:
	cx=0.0		cx=0.0

import>Mp466 at 19:23, 8 May 2009

2009-05-08T19:23:13Z

← Older revision		Revision as of 19:23, 8 May 2009
Line 1:		Line 1:
	#! /usr/bin/env python		#! /usr/bin/env python


	"""		"""
	Calculates the movieseg from a given PDB file		Calculates the movieseg from a given PDB file


	arguments:		arguments:

	PDBfile - the PDB file to score		PDBfile - the PDB file to score

		⚫	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'
⚫	50 format('CA: ',3(f8.3,1x),'CB: ',3(f8.3,1x),'Ox: ', 3(f8.3,1x))
		⚫	pars = PDBParser(PERMISSIVE = 1)
⚫	334 format(4(i8,1x),' nmres nmcrd numpro nmsnap')
		⚫	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:
⚫	"""

⚫	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		cx=0.0
	cy=0.0		cy=0.0
Line 35:		Line 35:
	oy=0.0		oy=0.0
	oz=0.0		oz=0.0


	if residue.has_id("CA"):		if residue.has_id("CA"):
	ca=residue["CA"]		ca=residue["CA"]
Line 41:		Line 41:
	cy=ca.get_coord()[1]		cy=ca.get_coord()[1]
	cz=ca.get_coord()[2]		cz=ca.get_coord()[2]


	if residue.has_id("CB"):		if residue.has_id("CB"):
	cb=residue["CB"]		cb=residue["CB"]
	# print "CB"		# print "CB"
	# print cb.get_coord()		# print cb.get_coord()
	cbx=cb.get_coord()[0]		cbx=cb.get_coord()[0]
	cby=cb.get_coord()[1]		cby=cb.get_coord()[1]
Line 56:		Line 56:
	if residue.has_id("O"):		if residue.has_id("O"):
	o=residue["O"]		o=residue["O"]
	# print " O"		# print " O"
	# print o.get_coord()		# print o.get_coord()
	ox=o.get_coord()[0]		ox=o.get_coord()[0]
	oy=o.get_coord()[1]		oy=o.get_coord()[1]

import>Mp466 at 19:22, 8 May 2009

2009-05-08T19:22:14Z

← Older revision		Revision as of 19:22, 8 May 2009
Line 1:		Line 1:
			#! /usr/bin/env python

			"""
			Calculates the movieseg from a given PDB file

			arguments:

			PDBfile - the PDB file to score

			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"):		if residue.has_id("CB"):

import>Mp466 at 19:21, 8 May 2009

2009-05-08T19:21:12Z

New page

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)