Example #1
0
	print '    to each point in the Mout reparametrized string'
	print '(4) saves: (a) the coordinates of the center of mass (COM) of the new Mout points (CVs), '
	print '           (b) the indices of the pdb files between Nit1 and Nit2 used to create the new starting pdb files' 
	print '           (c) starting pdb files (Pi.pdb, 1<=i<=Mout) '
	print 'a new run will move the ligand from their initial positions in (c) to the positions specified in (a)     ' 
	print '########################################################'

	#Initial conditions
	pdb_tmp='temp.pdb'
	DIM=3

	#Put all strings in a single variable
	allstrings=[]
	existingF=[]
	for i in range(args.Nit1,args.Nit2):
		filea=getPdbFilename(1,i)
		string=[]
		if os.path.isfile(filea):
			#existingF.append(i) #existing files
			for j in range(1,args.Nimages+1):
				pdb_A=getPdbFilename(j,i)
				shutil.copy2(pdb_A, pdb_tmp)
				df=pdb2df(pdb_tmp)
				xc,yc,zc=ligCOM(df,args.ligand)
				string.append([xc,yc,zc])
		else:
			a=1
		if (not string):
			a=1
		else:
			allstrings.append(string)
Example #2
0
	print '(4) prefix of the pdb input files'
	print '(5) saves: (a) the coordinates of the center of mass (COM) of the new Mout points (CVs), '
	print '           (b) the indices of the pdb files between Nit1 and Nit2 used to create the new starting pdb files' 
	print '           (c) starting pdb files (Pi.pdb, 1<=i<=Mout) '
	print 'a new run will move the ligand from their initial positions in (c) to the positions specified in (a)     ' 
	print '########################################################'

	#Initial conditions
	pdb_tmp='temp.pdb'
	DIM=3

	#Put all strings in a single variable
	allstrings=[]
	existingF=[]
	for i in range(args.Nit1,args.Nit2):
		filea=getPdbFilename(1,i,args.prefix)
		string=[]
		if os.path.isfile(filea):
			#existingF.append(i) #existing files
			for j in range(1,args.Nimages+1):
				pdb_A=getPdbFilename(j,i,args.prefix)
				shutil.copy2(pdb_A, pdb_tmp)
				df=pdb2df(pdb_tmp)
				xc,yc,zc=ligCOM(df,args.ligand)
				string.append([xc,yc,zc])
		else:
			a=1
		if (not string):
			a=1
		else:
			allstrings.append(string)