def set_representative_structure(self, seq_outdir=None, struct_outdir=None, pdb_file_type=None,
engine='needle', always_use_homology=False, rez_cutoff=0.0,
seq_ident_cutoff=0.5, allow_missing_on_termini=0.2,
allow_mutants=True, allow_deletions=False,
allow_insertions=False, allow_unresolved=True,
clean=True, force_rerun=False):
"""Set all representative structure for proteins from a structure in the structures attribute.
Each gene can have a combination of the following, which will be analyzed to set a representative structure.
* Homology model(s)
* Ranked PDBs
* BLASTed PDBs
If the ``always_use_homology`` flag is true, homology models are always set as representative when they exist.
If there are multiple homology models, we rank by the percent sequence coverage.
Args:
seq_outdir (str): Path to output directory of sequence alignment files, must be set if GEM-PRO directories
were not created initially
struct_outdir (str): Path to output directory of structure files, must be set if GEM-PRO directories
were not created initially
pdb_file_type (str): ``pdb``, ``pdb.gz``, ``mmcif``, ``cif``, ``cif.gz``, ``xml.gz``, ``mmtf``, ``mmtf.gz`` -
choose a file type for files downloaded from the PDB
engine (str): ``biopython`` or ``needle`` - which pairwise alignment program to use.
``needle`` is the standard EMBOSS tool to run pairwise alignments.
``biopython`` is Biopython's implementation of needle. Results can differ!
always_use_homology (bool): If homology models should always be set as the representative structure
rez_cutoff (float): Resolution cutoff, in Angstroms (only if experimental structure)
seq_ident_cutoff (float): Percent sequence identity cutoff, in decimal form
allow_missing_on_termini (float): Percentage of the total length of the reference sequence which will be ignored
when checking for modifications. Example: if 0.1, and reference sequence is 100 AA, then only residues
5 to 95 will be checked for modifications.
allow_mutants (bool): If mutations should be allowed or checked for
allow_deletions (bool): If deletions should be allowed or checked for
allow_insertions (bool): If insertions should be allowed or checked for
allow_unresolved (bool): If unresolved residues should be allowed or checked for
clean (bool): If structures should be cleaned
force_rerun (bool): If sequence to structure alignment should be rerun
"""
for g in tqdm(self.genes):
repstruct = g.protein.set_representative_structure(seq_outdir=seq_outdir,
struct_outdir=struct_outdir,
pdb_file_type=pdb_file_type,
engine=engine,
rez_cutoff=rez_cutoff,
seq_ident_cutoff=seq_ident_cutoff,
always_use_homology=always_use_homology,
allow_missing_on_termini=allow_missing_on_termini,
allow_mutants=allow_mutants,
allow_deletions=allow_deletions,
allow_insertions=allow_insertions,
allow_unresolved=allow_unresolved,
clean=clean,
force_rerun=force_rerun)
log.info('{}/{}: number of genes with a representative structure'.format(len(self.genes_with_a_representative_structure),
len(self.genes)))
log.info('See the "df_representative_structures" attribute for a summary dataframe.')
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