clean_pdb_keep_ligand Namespace Reference

Functions
def	check_and_print_pdb

Variables
string	local_pdb_database = "/lab/shared/scaffolds/"
	set your scaffold source here ################################# More...
	keep_ligand = True
	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
	Print out the residue when the new line is for a new residue. More...
list	hetatm_list = []
	CA_MODEL = True
	keep a record of the hetatms observed so far that are not in the amino acid dictionary More...
	NO_OCCUPANCY = True
string	fastaseq = ""
string	pdbfile = ""
list	pdbname = argv[1]
list	pdbcode = argv[1]
list	chainid = argv[2]
	outfile = pdbname
int	nopdbout = 0
int	removechain = 0
int	ignorechain = 0
list	netpdbname = local_pdb_database+pdbname[1:3]
tuple	lines = popen( 'zcat '+netpdbname,'r')
string	oldresnum = ' '
	residue_invalid = True More...
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 = stderr

Function Documentation

def clean_pdb_keep_ligand.check_and_print_pdb	(		count,
			residue_buffer,
			residue_letter
	)

References ObjexxFCL.len().

Variable Documentation

list clean_pdb_keep_ligand.altpos = line[16]

clean_pdb_keep_ligand.CA_MODEL = True

keep a record of the hetatms observed so far that are not in the amino acid dictionary

string clean_pdb_keep_ligand.chainid = argv[2]

int clean_pdb_keep_ligand.count = 1

Referenced by CoupledMovesProtocol.apply(), correct_dunbrack(), fmt::internal.count_digits(), exclude.filter_code_creators(), utility::io::icstream.get(), utility::io::izstream.get(), numeric::random::mt19937_RG.init_by_array(), load_loops_from_file(), main(), rosetta_binders::utility_vector_binder< Vector, L, T, Allocator >.maybe_default_constructible(), rosetta_binders::utility_vector_binder< Vector, L, T, Allocator >.maybe_has_equal_operator(), numeric::geometry::hashing::xyzStripeHash.nbcount(), numeric::geometry::hashing::xyzStripeHashWithMeta< float >.nbcount(), numeric::geometry::hashing::xyzStripeHash.nbcount_raw(), nucleobase_probe_score_test(), output_packstat_pdb(), predict_chem_map_test(), numeric::expression_parser::TokenSet.print_to_curr_pos(), utility::io::icstream.read(), utility::io::izstream.read(), utility::io::icstream.readsome(), utility::io::izstream.readsome(), recenter_with_missing(), rhiju_pdbstats(), setup_alignment_map(), setup_mask(), basic::datacache::ConstDataMap.size(), numeric::interpolation.spline_from_file(), svm_check_parameter(), svm_cross_validation(), svm_group_classes(), svm_svr_probability(), svm_train(), zlib_stream::basic_unzip_streambuf< Elem, Tr, ElemA, ByteT, ByteAT >.unzip_from_stream(), wrap_std_set(), utility::io::ocstream.write(), and utility::io::ozstream.write().

clean_pdb_keep_ligand.fastaid = stderr

string clean_pdb_keep_ligand.fastaseq = ""

string clean_pdb_keep_ligand.flag_altpos = "---"

string clean_pdb_keep_ligand.flag_insres = "---"

string clean_pdb_keep_ligand.flag_misdns = "---"

string clean_pdb_keep_ligand.flag_modres = "---"

string clean_pdb_keep_ligand.flag_successful = "OK"

list clean_pdb_keep_ligand.hetatm_list = []

int clean_pdb_keep_ligand.ignorechain = 0

list clean_pdb_keep_ligand.insres = line[26]

clean_pdb_keep_ligand.keep_ligand = True

list clean_pdb_keep_ligand.line = lines[i]

list clean_pdb_keep_ligand.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 clean_pdb_keep_ligand.lines = popen( 'zcat '+netpdbname,'r')

Referenced by utility::io.get_lines_from_file_data(), binder.indent(), and binder.split().

string clean_pdb_keep_ligand.local_pdb_database = "/lab/shared/scaffolds/"

set your scaffold source here #################################

list clean_pdb_keep_ligand.longname = line_edit[17:20]

list clean_pdb_keep_ligand.modifiedres = ''

clean_pdb_keep_ligand.netpdbname = local_pdb_database+pdbname[1:3]

clean_pdb_keep_ligand.NO_OCCUPANCY = True

int clean_pdb_keep_ligand.nopdbout = 0

tuple clean_pdb_keep_ligand.nres = len(fastaseq)

Referenced by add_rosetta_options_15(), AnchorFinderMover.apply(), densityTools(), figure_out_fold_tree(), main(), measure_sequence_recovery(), minimize_test(), process_for_motifs(), repack_test(), rna_features_from_pose(), rna_sequence_recovery_metrics(), DockFragmentsMover.run(), ScoreFragmentSetMover.run(), FragmentAssemblyMover.run(), ConsensusFragmentMover.run(), FragmentAssemblyMover.score(), setup_ca_constraints(), zinc1_homodimer_design.setup_metalsite_constraints(), statistics(), and src.PyMolLink.PyMOLMover.view_foldtree_diagram().

clean_pdb_keep_ligand.ok = False

clean_pdb_keep_ligand.oldresnum = ' '

residue_invalid = True

tuple clean_pdb_keep_ligand.outfile = pdbname

Referenced by correct_dunbrack(), create_bp_jump_database_test(), create_rna_vall_torsions_test(), filter_combine_long_loop(), graft_pdb(), main(), make_fragments(), mg_modeler_test(), output_superimposed_pdb(), rhiju_pdbstats(), rna_build_helix_test(), rna_design_test(), rna_thread_test(), FragmentAssemblyMover.run(), and swa_rna_cluster().

tuple clean_pdb_keep_ligand.outid = open( outfile, 'w')

list clean_pdb_keep_ligand.pdbcode = argv[1]

string clean_pdb_keep_ligand.pdbfile = ""

Referenced by densityTools(), and spanfile_from_pdb().

list clean_pdb_keep_ligand.pdbname = argv[1]

Referenced by AnchorFinderMover.apply(), main(), minimize_test(), repack_test(), and sequence_tolerance_main().

int clean_pdb_keep_ligand.removechain = 0

list clean_pdb_keep_ligand.residue_buffer = []

clean_pdb_keep_ligand.residue_invalid = False

string clean_pdb_keep_ligand.residue_letter = ''

list clean_pdb_keep_ligand.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 CoupledMovesProtocol.apply(), define_interface(), utility.get_resnum_and_chain(), utility.get_resnum_and_segid(), ligand_rmsd(), main(), output_packstat_pdb(), read_in_mutations(), utility::options::ResidueChainVectorOption.resnum_and_chain(), rna_score_test(), RunPepSpec(), utility::options::ResidueChainVectorOption.value_of(), and utility::options::ResidueChainVectorOption.values_of().

clean_pdb_keep_ligand.shit_stat_altpos = False

clean_pdb_keep_ligand.shit_stat_insres = False

clean_pdb_keep_ligand.shit_stat_misdns = False

Print out the residue when the new line is for a new residue.

if unsuccessful

is there a residue in the buffer ? If so print it out, then reinitialize print "call from the loop:\n" ## new if unsuccessful

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)