1 / 9

Bio::Structure

Bio::Structure. Why. Ad hoc scripts Code is not reusable Nothing available for structure work in Bioperl (Biopython, Biojava). It’s fun. Protein Data Bank (PDB). ~18000 structures column based format entries created by user, validated when submitting

edith
Télécharger la présentation

Bio::Structure

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Bio::Structure

  2. Why • Ad hoc scripts • Code is not reusable • Nothing available for structure work in Bioperl • (Biopython, Biojava) • It’s fun Bio::Structure

  3. Protein Data Bank (PDB) • ~18000 structures • column based format • entries created by user, validated when submitting • multiple versions of PDB format • not all entries in same format • a lot of info squeezed into format • entry / model / chain / residue / atom • ‘lingua franca’ • mmCIF (successor, but who uses it) Bio::Structure

  4. Example code • my $structio = Bio::Structure::IO->new(-file => $bpti_file, -format => 'pdb'); • # read the structure • my $struc = $structio->next_structure; • # loop over whole structure and store CYS SG atoms • for my $res ($struc->residue) { # we only look at CYS residues • next unless($res->id =~ /^CYS/); # and we only take SG atoms • for my $atom ($struc->get_atoms($res)) { • next unless( $atom->id eq "SG"); • push @sgatoms, $atom; • } • } • # • # loop over all SG atoms and calculate the distance between them • # • [ … ] • # get $atom1 and $atom2 • my $dist = calculate_distance($atom1,$atom2); • printf("%-6s %s - %-6s %s %-.2f\n", • $struc->parent($atom1)->id, $atom1->id, • $struc->parent($atom2)->id, $atom2->id, $dist); Bio::Structure

  5. Example code (cont) • # now have a look what the annotation was in the PDB file • print "\nThe annotation in the PDB file\n"; • my ($ann) = $struc->annotation->get_Annotations("ssbond"); • my $txt = $ann->as_text; # this text starts with "Value: " • $txt =~ s/^Value: //; # it contains lines of 65 chars long each • for (my $t = 0; $t <= length($txt); $t += 65) { • my $line = substr ($txt,$t, 65); • print "$line\n"; • } • Complete code can be found in the bioperl distribution in • examples/structure/struct_example2.pl Bio::Structure

  6. Output • The measured SG-SG distances are • CYS-5 SG - CYS-14 SG 24.10 • CYS-5 SG - CYS-30 SG 8.36 • … • CYS-5 SG - CYS-55 SG 2.00 • … • CYS-14 SG - CYS-38 SG 2.05 • … • CYS-30 SG - CYS-51 SG 2.05 • The annotation in the PDB file • 1 CYS 5 CYS 55 • 2 CYS 14 CYS 38 • 3 CYS 30 CYS 51 Bio::Structure

  7. What’s not perfect – the future • “ CA “ “CA “ (*) • MTRIXn • segID (*) • altloc (biopython) • Writing ‘old format’ PDB files • BOF ideas • (*) fixed in CVS Bio::Structure

  8. Thanks • Bioperl mailing list for help in designing objects • Yan-Yuan Tseng • Ethan Merritt • Joe Krahn • AlgoNomics Bio::Structure

  9. kris.boulez@algonomics.comAlgoNomics NVTechnologiepark 4B-9052 Gent-Belgiumhttp://www.algonomics.com/

More Related