clean_pdb_keep_ligand.py File Reference

Namespaces
	clean_pdb_keep_ligand

Functions
def	clean_pdb_keep_ligand.check_and_print_pdb

Variables
string	clean_pdb_keep_ligand.local_pdb_database = "/lab/shared/scaffolds/"
	set your scaffold source here ################################# More...
	clean_pdb_keep_ligand.keep_ligand = True
	clean_pdb_keep_ligand.shit_stat_insres = False
	clean_pdb_keep_ligand.shit_stat_altpos = False
	clean_pdb_keep_ligand.shit_stat_modres = False
	dont count MSEs as modiied residues (cos they're so common and get_pdb deal with them previosuly) More...
	clean_pdb_keep_ligand.shit_stat_misdns = False
	Print out the residue when the new line is for a new residue. More...
list	clean_pdb_keep_ligand.hetatm_list = []
	clean_pdb_keep_ligand.CA_MODEL = True
	keep a record of the hetatms observed so far that are not in the amino acid dictionary More...
	clean_pdb_keep_ligand.NO_OCCUPANCY = True
string	clean_pdb_keep_ligand.fastaseq = ""
string	clean_pdb_keep_ligand.pdbfile = ""
list	clean_pdb_keep_ligand.pdbname = argv[1]
list	clean_pdb_keep_ligand.pdbcode = argv[1]
list	clean_pdb_keep_ligand.chainid = argv[2]
	clean_pdb_keep_ligand.outfile = pdbname
int	clean_pdb_keep_ligand.nopdbout = 0
int	clean_pdb_keep_ligand.removechain = 0
int	clean_pdb_keep_ligand.ignorechain = 0
list	clean_pdb_keep_ligand.netpdbname = local_pdb_database+pdbname[1:3]
tuple	clean_pdb_keep_ligand.lines = popen( 'zcat '+netpdbname,'r')
string	clean_pdb_keep_ligand.oldresnum = ' '
	residue_invalid = True More...
int	clean_pdb_keep_ligand.count = 1
string	clean_pdb_keep_ligand.modifiedres = ''
list	clean_pdb_keep_ligand.residue_buffer = []
string	clean_pdb_keep_ligand.residue_letter = ''
	clean_pdb_keep_ligand.residue_invalid = False
list	clean_pdb_keep_ligand.line = lines[i]
	clean_pdb_keep_ligand.line_edit = line
	Is it a modified residue ? More...
	clean_pdb_keep_ligand.ok = False
list	clean_pdb_keep_ligand.resnum = line_edit[22:27]
	if line_edit[13:14]=='P': #Nucleic acid? Skip. More...
list	clean_pdb_keep_ligand.insres = line[26]
list	clean_pdb_keep_ligand.altpos = line[16]
list	clean_pdb_keep_ligand.longname = line_edit[17:20]
string	clean_pdb_keep_ligand.flag_altpos = "---"
string	clean_pdb_keep_ligand.flag_insres = "---"
string	clean_pdb_keep_ligand.flag_modres = "---"
string	clean_pdb_keep_ligand.flag_misdns = "---"
tuple	clean_pdb_keep_ligand.nres = len(fastaseq)
string	clean_pdb_keep_ligand.flag_successful = "OK"
tuple	clean_pdb_keep_ligand.outid = open( outfile, 'w')
	clean_pdb_keep_ligand.fastaid = stderr