get_pdb.py File Reference

Namespaces
	get_pdb

Functions
def	get_pdb.download_pdb
def	get_pdb.check_and_print_pdb

Variables
string	get_pdb.remote_host = 'ws0.nrb'
	get_pdb.shit_stat_insres = False
	get_pdb.shit_stat_altpos = False
	get_pdb.shit_stat_modres = False
	dont count MSEs as modiied residues (cos they're so common and get_pdb deal with them previosuly) More...
	get_pdb.shit_stat_misdns = False
	Is thresidue_letter. More...
string	get_pdb.fastaseq = ""
string	get_pdb.pdbfile = ""
list	get_pdb.files_to_unlink = []
list	get_pdb.pdbname = argv[1]
list	get_pdb.chainid = argv[2]
tuple	get_pdb.outfile = string.lower(pdbname[0:4])
int	get_pdb.nopdbout = 0
int	get_pdb.removechain = 0
int	get_pdb.ignorechain = 0
string	get_pdb.netpdbname = '/net/wwpdb/'
string	get_pdb.fixed_pdb = "/work/robetta/src/rosetta_server/fixed_pdbs/"
tuple	get_pdb.f = gzip.open( netpdbname , 'r' )
tuple	get_pdb.lines = f.readlines()
string	get_pdb.oldresnum = ' '
int	get_pdb.count = 1
string	get_pdb.modifiedres = ''
list	get_pdb.residue_buffer = []
string	get_pdb.residue_letter = ''
	get_pdb.residue_invalid = False
list	get_pdb.line = lines[i]
	get_pdb.line_edit = line
	Is it a modified residue ? More...
	get_pdb.ok = False
list	get_pdb.resnum = line_edit[22:27]
	if line_edit[13:14]=='P': #Nucleic acid? Skip. More...
list	get_pdb.insres = line[26]
list	get_pdb.altpos = line[16]
list	get_pdb.longname = line_edit[17:20]
string	get_pdb.flag_altpos = "---"
string	get_pdb.flag_insres = "---"
string	get_pdb.flag_modres = "---"
string	get_pdb.flag_misdns = "---"
tuple	get_pdb.nres = len(fastaseq)
string	get_pdb.flag_successful = "OK"
tuple	get_pdb.outid = open( outfile, 'w')
	get_pdb.fastaid = stdout