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Functions | Variables
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 auto-DRRAFTER_setup.auto_setup_helices(), calc_dihedral_rms(), calculate_percent_disorder(), correct_dunbrack(), correct_rama(), fmt::internal.count_digits(), count_numerically(), basic::resource_manager::ResourceManager.deallocate_resource(), utility::io::icstream.get(), utility::io::izstream.get(), basic::citation_manager::CitationCollection.get_citations_formatted(), numeric::MathNTensor< double, 2 >.get_mathmatrix(), utility.get_resnum_and_chain_from_one_tag(), 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::linear_algebra.minimum_bounding_ellipse(), 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(), 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')
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)
clean_pdb_keep_ligand.ok = False
clean_pdb_keep_ligand.oldresnum = ' '

residue_invalid = True

tuple clean_pdb_keep_ligand.outfile = pdbname
tuple clean_pdb_keep_ligand.outid = open( outfile, 'w')
list clean_pdb_keep_ligand.pdbcode = argv[1]
string clean_pdb_keep_ligand.pdbfile = ""
list clean_pdb_keep_ligand.pdbname = argv[1]
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]
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)