Rosetta 3.3
Functions | Variables
get_pdb Namespace Reference

Functions

def download_pdb
def check_and_print_pdb

Variables

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

Function Documentation

def get_pdb::check_and_print_pdb (   count,
  residue_buffer,
  residue_letter 
)
def get_pdb::download_pdb (   pdb_id,
  dest_dir 
)

Variable Documentation

list get_pdb::altpos = line[16]
string get_pdb::chainid = argv[2]
get_pdb::fastaid = stdout
string get_pdb::fastaseq = ""
string get_pdb::fixed_pdb = "/work/robetta/src/rosetta_server/fixed_pdbs/"
string get_pdb::flag_altpos = "---"
string get_pdb::flag_insres = "---"
string get_pdb::flag_misdns = "---"
string get_pdb::flag_modres = "---"
string get_pdb::flag_successful = "OK"
list get_pdb::insres = line[26]
list get_pdb::line = lines[i]

Is it a modified residue ?

What does this do ?

other substitution (of atoms mainly)

if so replace it with its canonical equivalent !

tuple get_pdb::lines = popen( 'zcat '+netpdbname,'r')
tuple get_pdb::netpdbname = '/net/wwpdb/'
tuple get_pdb::nres = len(fastaseq)
get_pdb::ok = False
tuple get_pdb::outfile = string.lower(pdbname[0:4])
tuple get_pdb::outid = open( outfile, 'w')
string get_pdb::pdbfile = ""
list get_pdb::pdbname = argv[1]
string get_pdb::remote_host = 'ws0.nrb'
list get_pdb::resnum = line_edit[22:27]

if line_edit[13:14]=='P': #Nucleic acid? Skip.

resnum = line_edit[23:26] oldresnum = resnum while (resnum == oldresnum): print "HERE" i += 1 line = lines[i] resnum = line_edit[23:26]

Referenced by main(), read_in_mutations(), and RunPepSpec().

Is thresidue_letter.

if unsuccessful

is there a residue in the buffer ? if unsuccessful

dont count MSEs as modiied residues (cos they're so common and get_pdb deal with them previosuly)

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