nmr_cnstr.py

'''
See more here: http://www.pymolwiki.org/index.php/nmr_cnstr
##############################################################################################################
# Pymol Script: For visualizing the NMR constrains (DYANA & CNS format), on top of the calculated structure. #
#               Author: Evangelos Papadopoulos.                                                              #
#  previous affiliation: Dept. of Biochemistry and Biophysics,                                               #
#                       Arrhenius Laboratories,                                                              #
#                       Stockholm University                                                                 #
#                       SE-106 91 Stockholm, Sweden                                                          #
#                email:evangelos.papadopoulos@gmail.com                                                      #
#                NOTES: This is a preliminary version.                                                       #
#                                                                                                            #
#     Reference: please if you find this script usefull add the following reference:                   #
#     NMR Solution Structure of the Peptide Fragment 1-30, Derived from Unprocessed Mouse Doppel             #
#     Protein, in DHPC Micelles. Biochemistry. 2006 Jan 10;45(1):159-166. PMID: 16388591                     #
#                                                                                                            #
##############################################################################################################
'''
 
 
def upl(fname):
 
	f=open(fname,'r')
	i=1
	upl=f.readline()
#
	while upl!='':
 
		print upl,i
		cns=string.split(upl)
		cmd.dist('upl'+str(i),'i. '+cns[0]+' & n. '+cns[2],'i. '+cns[3]+' & n. '+cns[5])
		upl=f.readline()
		i+=1
#
	f.close()
	cmd.hide('labels')
	cmd.set ('dash_gap', 0.05)
	cmd.do ("orient")
	cmd.set ('movie_delay', 1500)
 
def cns(fname):
 
	f=open(fname,'r')
	i=1
	upl=f.readline()
	print upl,i
	while upl!='':
		if upl=='\n': 
			upl=f.readline()
			continue
		cns=string.split(upl)
		print cns,i
		if cns[0]=='assign' : 
			print 'CNS'
			if cns[5]=='HB*': print 'CNS***'
			cmd.dist('upl'+str(i),'i. '+cns[2]+' & n. '+cns[5],'i. '+cns[7]+' & n. '+cns[10])
		i+=1
		upl=f.readline()
		print '*'+upl+'*',i
 
	f.close()
	cmd.set ('dash_gap', 0.05)
	cmd.hide('labels')
	cmd.do ("orient")
	cmd.set ('movie_delay', 1500)