SYMBOL INDEX (120 symbols across 7 files)

FILE: Example_scripts_and_sequences/ImmunoPDB.py
  class PDBNumber (line 94) | class PDBNumber(object):
    method __init__ (line 101) | def __init__(self,scheme,allowed_domains, region_definition=None, warn...
    method numberChain (line 107) | def numberChain(self, chain, sequence=''):
    method annotateChainRegions (line 173) | def annotateChainRegions(self, chain, scheme, definition=None, domain_...
    method numberSequence (line 190) | def numberSequence(self,sequenceName, sequence):
  class AntigenReceptorPDBParser (line 205) | class AntigenReceptorPDBParser(PDBParser):
    method __init__ (line 214) | def __init__( self, PERMISSIVE=True, get_header=False,
    method get_structure (line 225) | def get_structure(self, id, file):
    method read_seqres (line 280) | def read_seqres(self, file):
    method number_receptor_chains (line 291) | def number_receptor_chains(self, structure, sequences={}):
    method find_pairs (line 302) | def find_pairs(self,structure):
  class TcrPDBParser (line 328) | class TcrPDBParser(AntigenReceptorPDBParser):
  class AntibodyPDBParser (line 334) | class AntibodyPDBParser(AntigenReceptorPDBParser):
  class SelectFv (line 340) | class SelectFv(Select):
    method accept_residue (line 341) | def accept_residue(self, residue):
  class SelectFvScFv (line 347) | class SelectFvScFv(Select):
    method accept_residue (line 348) | def accept_residue(self, residue):
  function Entity_switch_numbering_scheme (line 357) | def Entity_switch_numbering_scheme(self, scheme, domain_index=0): # Stru...
  function Chain_switch_numbering_scheme (line 363) | def Chain_switch_numbering_scheme(self, scheme, domain_index=0):
  function Residue_switch_numbering_scheme (line 387) | def Residue_switch_numbering_scheme(self, scheme, domain_index=0):
  function Chain_interface_cys_CA (line 393) | def Chain_interface_cys_CA(self, scheme, domain_index=0 ):
  function Entity_save (line 402) | def Entity_save(self,filename, select=Select(), write_end=True):
  function compile_remarks (line 417) | def compile_remarks( chain, rtype, only_loaded=False ):
  function compile_seqres (line 447) | def compile_seqres( chain ):
  function rename_chains (line 455) | def rename_chains( structure ):
  function split_scfv (line 483) | def split_scfv( structure ):
  function extract_sequence (line 521) | def extract_sequence(chain):
  function convert_3_to_1 (line 536) | def convert_3_to_1(r):
  function pairwise_muscle (line 548) | def pairwise_muscle(seq1, seq2,exact=True):
  function easy_alignment (line 595) | def easy_alignment(seq1, seq2):
  function which (line 614) | def which(name, flags=os.X_OK):
  function uniq (line 651) | def uniq(seq, idfun=None):
  function get_alignment_dict (line 674) | def get_alignment_dict(ali1,ali2):
  function fix_deletions (line 709) | def fix_deletions(chain):
  function analyse_continuity (line 731) | def analyse_continuity( chain ):
  function PdbSeqresIterator (line 756) | def PdbSeqresIterator(handle):
  function get_region (line 924) | def get_region( position, chain, numbering_scheme="chothia", definition=...
  function annotate_regions (line 976) | def annotate_regions(numbered_sequence, chain,numbering_scheme="chothia"...
  class Accept (line 1118) | class Accept:
    method __init__ (line 1137) | def __init__(self, numbering_scheme="chothia", definition="chothia", N...
    method set_regions (line 1145) | def set_regions( self, regions=[] ):
    method add_regions (line 1155) | def add_regions(self, regions):
    method add_positions (line 1176) | def add_positions( self, positions, chain ):
    method exclude_positions (line 1181) | def exclude_positions( self, positions, chain ):
    method accept (line 1186) | def accept(self, position, chain):

FILE: build_pipeline/FastaIO.py
  function chunkify (line 9) | def chunkify(fh):
  class FASTARecord (line 45) | class FASTARecord(object):
    method __init__ (line 46) | def __init__(self, description, seq):

FILE: build_pipeline/FormatAlignments.py
  function read_alignment (line 62) | def read_alignment(input_file, read_all=False, region_name=""):
  function read_fasta (line 123) | def read_fasta(filename):
  function write_fasta (line 132) | def write_fasta( sequences ):
  function format_c_genes (line 145) | def format_c_genes(calignments, gene_name=""):
  function format_j_genes (line 170) | def format_j_genes(jalignments):
  function format_v_genes (line 208) | def format_v_genes(valignments):
  function mouse_delta (line 232) | def mouse_delta(sequence):
  function rhesus_lambda (line 245) | def rhesus_lambda(sequence):
  function mouse_alpha (line 252) | def mouse_alpha(sequence):
  function combine_sequences (line 259) | def combine_sequences(vsequences, jsequences):
  function make_putative_alignments (line 272) | def make_putative_alignments( vsequences, jsequences, calignments = None ):
  function write_germlines (line 288) | def write_germlines(vsequences, jsequences):
  function output_python_lookup (line 324) | def output_python_lookup(all_gene_alignments, path=None):
  function write_stockholm (line 335) | def write_stockholm( sequences, ID, outfile):
  function output_C_alignments (line 346) | def output_C_alignments(alignments, c_name):
  function output_stockholm_all_and_C (line 353) | def output_stockholm_all_and_C(all_sequences, all_C_alignments, path=None):
  function output_stockholm_all (line 374) | def output_stockholm_all(all_sequences, path=None):
  function output_stockholm (line 391) | def output_stockholm(sequences, name, path=None):
  function main (line 409) | def main():

FILE: build_pipeline/RipIMGT.py
  class GENEDBParser (line 71) | class GENEDBParser(HTMLParser):
    method handle_starttag (line 75) | def handle_starttag(self, tag, attrs):
    method handle_endtag (line 77) | def handle_endtag(self, tag):
    method handle_data (line 79) | def handle_data(self, data):
    method handle_entityref (line 107) | def handle_entityref(self, name):
    method handle_charref (line 109) | def handle_charref(self, name):
    method rip_sequences (line 115) | def rip_sequences(self,htmlstring):
  function get_html (line 130) | def get_html(species, gene_type, force = True):
  function write_fasta (line 143) | def write_fasta( sequences, species, gene_type ):
  function ripfasta (line 153) | def ripfasta(species, gene_type, force = True):
  function main (line 170) | def main():

FILE: lib/python/anarci/anarci.py
  class HMMscanError (line 78) | class HMMscanError(Exception):
    method __init__ (line 79) | def __init__(self, message):
  function read_fasta (line 84) | def read_fasta(filename):
  function fasta_iter (line 94) | def fasta_iter(fasta_name):
  function write_fasta (line 114) | def write_fasta(sequences, f):
  function validate_sequence (line 127) | def validate_sequence(sequence):
  function validate_numbering (line 135) | def validate_numbering(xxx_todo_changeme, name_seq=[]):
  function grouper (line 155) | def grouper(n, iterable):
  function anarci_output (line 165) | def anarci_output(numbered, sequences, alignment_details, outfile, seque...
  function csv_output (line 214) | def csv_output(sequences, numbered, details, outfileroot):
  function _domains_are_same (line 300) | def _domains_are_same(dom1, dom2):
  function _parse_hmmer_query (line 314) | def _parse_hmmer_query(query, bit_score_threshold=80, hmmer_species=None):
  function _hmm_alignment_to_states (line 380) | def _hmm_alignment_to_states(hsp, n, seq_length):
  function parse_hmmer_output (line 463) | def parse_hmmer_output(filedescriptor="", bit_score_threshold=80, hmmer_...
  function run_hmmer (line 481) | def run_hmmer(sequence_list,hmm_database="ALL",hmmerpath="", ncpu=None, ...
  function get_hmm_length (line 536) | def get_hmm_length( species, ctype ):
  function number_sequence_from_alignment (line 547) | def number_sequence_from_alignment(state_vector, sequence, scheme="imgt"...
  function number_sequences_from_alignment (line 594) | def number_sequences_from_alignment(sequences, alignments, scheme="imgt"...
  function get_identity (line 645) | def get_identity( state_sequence, germline_sequence ):
  function run_germline_assignment (line 663) | def run_germline_assignment(state_vector, sequence, chain_type, allowed_...
  function check_for_j (line 706) | def check_for_j( sequences, alignments, scheme ):
  function anarci (line 766) | def anarci(sequences, scheme="imgt", database="ALL", output=False, outfi...
  function run_anarci (line 857) | def run_anarci( seq, ncpu=1, **kwargs):
  function number (line 956) | def number(sequence, scheme="imgt", database="ALL", allow=set(["H","K","...

FILE: lib/python/anarci/schemes.py
  function smooth_insertions (line 81) | def smooth_insertions(state_vector):
  function _number_regions (line 202) | def _number_regions(sequence, state_vector, state_string , region_string...
  function number_imgt (line 306) | def number_imgt(state_vector, sequence):
  function get_imgt_cdr (line 434) | def get_imgt_cdr(length, maxlength, start, end):
  function number_aho (line 493) | def number_aho(state_vector, sequence, chain_type):
  function number_chothia_heavy (line 747) | def number_chothia_heavy(state_vector, sequence):
  function number_chothia_light (line 864) | def number_chothia_light(state_vector, sequence):
  function number_kabat_heavy (line 979) | def number_kabat_heavy(state_vector, sequence):
  function number_kabat_light (line 1094) | def number_kabat_light(state_vector, sequence):
  function number_martin_heavy (line 1198) | def number_martin_heavy(state_vector, sequence):
  function number_martin_light (line 1325) | def number_martin_light(state_vector, sequence):
  function number_wolfguy_heavy (line 1372) | def number_wolfguy_heavy(state_vector, sequence):
  function number_wolfguy_light (line 1464) | def number_wolfguy_light(state_vector, sequence):
  function _get_wolfguy_L1 (line 1569) | def _get_wolfguy_L1(seq, length):
  function gap_missing (line 1617) | def gap_missing( numbering ):
  function get_cdr3_annotations (line 1635) | def get_cdr3_annotations(length, scheme="imgt", chain_type=""):

FILE: setup.py
  class CustomInstallCommand (line 7) | class CustomInstallCommand(install):
    method run (line 8) | def run(self):