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) More...
	shit_stat_misdns = False
	Is thresidue_letter. More...
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	f = gzip.open( netpdbname , 'r' )
tuple	lines = f.readlines()
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 ? More...
	ok = False
list	resnum = line_edit[22:27]
	if line_edit[13:14]=='P': #Nucleic acid? Skip. More...
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
	)

References extract_scores_and_constraints.join.

Variable Documentation

list get_pdb.altpos = line[16]

string get_pdb.chainid = argv[2]

int get_pdb.count = 1

tuple get_pdb.f = gzip.open( netpdbname , 'r' )

Referenced by numeric::interpolation::periodic_range::full.bilinearly_interpolated(), numeric::interpolation::periodic_range::half.bilinearly_interpolated(), numeric::kinematic_closure.bridgeObjects(), numeric::kinematic_closure.buildsturm(), close_loops(), numeric::deriv.dihedral_p1_cosine_deriv_first(), numeric::deriv.dihedral_p2_cosine_deriv_first(), numeric::kinematic_closure.evalpoly(), ObjexxFCL::format.F(), figure_out_fold_tree(), utility.filename(), utility::signals::SignalHub< ReturnType, Signal >.find_connection(), Wrapper_PosePyObserver.generalEvent(), numeric.hsv_to_rgb(), numeric::geometry::hashing::xyzStripeHash.init(), basic.interpolate_bilinear_by_value(), basic.interpolate_trilinear_by_value(), numeric::interpolation::periodic_range::half.interpolated(), numeric::interpolation::periodic_range::full.interpolated(), numeric::fourier.kf_work(), ObjexxFCL.left_Fstring_of(), ObjexxFCL.left_string_of(), utility::options::OptionCollection.load_options_from_stream(), main(), molfile_to_params.memoize(), ObjexxFCL.mod(), nucleobase_probe_score_test(), numeric::kinematic_closure.numchanges(), numeric::kinematic_closure.numroots(), numeric::deriv.p1_theta_deriv(), ObjexxFCL.right_Fstring_of(), ObjexxFCL.right_string_of(), run_pep_prep(), RunPepSpec(), setup_fold_tree(), setup_fold_tree_sample_res(), DougsDockDesignMinimizeMagicMover.setup_pert_foldtree(), basic.subtract_radian_angles(), basic::Tracer.super_mute(), basic::svd::SVD_Solver.svdcmp(), svm_train(), svm_train_one(), numeric::kinematic_closure.test_triaxialCoefficients(), numeric::kinematic_closure.torsion(), numeric::kinematic_closure::radians.torsion(), and basic::Emitter.write_raw().

get_pdb.fastaid = stdout

string get_pdb.fastaseq = ""

list get_pdb.files_to_unlink = []

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"

int get_pdb.ignorechain = 0

list get_pdb.insres = line[26]

list get_pdb.line = lines[i]

list get_pdb.line_edit = line

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 = f.readlines()

list get_pdb.longname = line_edit[17:20]

list get_pdb.modifiedres = ''

tuple get_pdb.netpdbname = '/net/wwpdb/'

int get_pdb.nopdbout = 0

tuple get_pdb.nres = len(fastaseq)

Referenced by add_rosetta_options_15().

get_pdb.ok = False

get_pdb.oldresnum = ' '

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'

int get_pdb.removechain = 0

list get_pdb.residue_buffer = []

get_pdb.residue_invalid = False

string get_pdb.residue_letter = ''

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]

get_pdb.shit_stat_altpos = False

get_pdb.shit_stat_insres = False

get_pdb.shit_stat_misdns = False

Is thresidue_letter.

if unsuccessful

is there a residue in the buffer ? if unsuccessful

get_pdb.shit_stat_modres = False

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