wwood-bioruby 1.2.11
Sign up to get free protection for your applications and to get access to all the features.
- data/README.rdoc +205 -0
- data/README_DEV.rdoc +285 -0
- data/VERSION.yml +4 -0
- data/bin/bioruby +44 -0
- data/bin/br_biofetch.rb +47 -0
- data/bin/br_bioflat.rb +293 -0
- data/bin/br_biogetseq.rb +45 -0
- data/bin/br_pmfetch.rb +421 -0
- data/lib/bio.rb +306 -0
- data/lib/bio/alignment.rb +2518 -0
- data/lib/bio/appl/bl2seq/report.rb +334 -0
- data/lib/bio/appl/blast.rb +505 -0
- data/lib/bio/appl/blast/ddbj.rb +142 -0
- data/lib/bio/appl/blast/format0.rb +1438 -0
- data/lib/bio/appl/blast/format8.rb +83 -0
- data/lib/bio/appl/blast/genomenet.rb +263 -0
- data/lib/bio/appl/blast/ncbioptions.rb +220 -0
- data/lib/bio/appl/blast/remote.rb +105 -0
- data/lib/bio/appl/blast/report.rb +767 -0
- data/lib/bio/appl/blast/rexml.rb +144 -0
- data/lib/bio/appl/blast/rpsblast.rb +277 -0
- data/lib/bio/appl/blast/wublast.rb +635 -0
- data/lib/bio/appl/blast/xmlparser.rb +236 -0
- data/lib/bio/appl/blat/report.rb +530 -0
- data/lib/bio/appl/clustalw.rb +219 -0
- data/lib/bio/appl/clustalw/report.rb +152 -0
- data/lib/bio/appl/emboss.rb +203 -0
- data/lib/bio/appl/fasta.rb +235 -0
- data/lib/bio/appl/fasta/format10.rb +325 -0
- data/lib/bio/appl/gcg/msf.rb +212 -0
- data/lib/bio/appl/gcg/seq.rb +195 -0
- data/lib/bio/appl/genscan/report.rb +552 -0
- data/lib/bio/appl/hmmer.rb +126 -0
- data/lib/bio/appl/hmmer/report.rb +683 -0
- data/lib/bio/appl/iprscan/report.rb +374 -0
- data/lib/bio/appl/mafft.rb +259 -0
- data/lib/bio/appl/mafft/report.rb +226 -0
- data/lib/bio/appl/muscle.rb +52 -0
- data/lib/bio/appl/paml/baseml.rb +95 -0
- data/lib/bio/appl/paml/baseml/report.rb +32 -0
- data/lib/bio/appl/paml/codeml.rb +242 -0
- data/lib/bio/appl/paml/codeml/rates.rb +67 -0
- data/lib/bio/appl/paml/codeml/report.rb +67 -0
- data/lib/bio/appl/paml/common.rb +348 -0
- data/lib/bio/appl/paml/common_report.rb +38 -0
- data/lib/bio/appl/paml/yn00.rb +103 -0
- data/lib/bio/appl/paml/yn00/report.rb +32 -0
- data/lib/bio/appl/phylip/alignment.rb +133 -0
- data/lib/bio/appl/phylip/distance_matrix.rb +96 -0
- data/lib/bio/appl/probcons.rb +41 -0
- data/lib/bio/appl/psort.rb +548 -0
- data/lib/bio/appl/psort/report.rb +542 -0
- data/lib/bio/appl/pts1.rb +263 -0
- data/lib/bio/appl/sim4.rb +124 -0
- data/lib/bio/appl/sim4/report.rb +485 -0
- data/lib/bio/appl/sosui/report.rb +151 -0
- data/lib/bio/appl/spidey/report.rb +593 -0
- data/lib/bio/appl/targetp/report.rb +267 -0
- data/lib/bio/appl/tcoffee.rb +55 -0
- data/lib/bio/appl/tmhmm/report.rb +231 -0
- data/lib/bio/command.rb +593 -0
- data/lib/bio/compat/features.rb +157 -0
- data/lib/bio/compat/references.rb +128 -0
- data/lib/bio/data/aa.rb +353 -0
- data/lib/bio/data/codontable.rb +722 -0
- data/lib/bio/data/na.rb +223 -0
- data/lib/bio/db.rb +329 -0
- data/lib/bio/db/aaindex.rb +357 -0
- data/lib/bio/db/biosql/biosql_to_biosequence.rb +67 -0
- data/lib/bio/db/biosql/sequence.rb +508 -0
- data/lib/bio/db/embl/common.rb +352 -0
- data/lib/bio/db/embl/embl.rb +500 -0
- data/lib/bio/db/embl/embl_to_biosequence.rb +85 -0
- data/lib/bio/db/embl/format_embl.rb +190 -0
- data/lib/bio/db/embl/sptr.rb +1283 -0
- data/lib/bio/db/embl/swissprot.rb +42 -0
- data/lib/bio/db/embl/trembl.rb +41 -0
- data/lib/bio/db/embl/uniprot.rb +42 -0
- data/lib/bio/db/fantom.rb +597 -0
- data/lib/bio/db/fasta.rb +410 -0
- data/lib/bio/db/fasta/defline.rb +532 -0
- data/lib/bio/db/fasta/fasta_to_biosequence.rb +63 -0
- data/lib/bio/db/fasta/format_fasta.rb +97 -0
- data/lib/bio/db/genbank/common.rb +307 -0
- data/lib/bio/db/genbank/ddbj.rb +22 -0
- data/lib/bio/db/genbank/format_genbank.rb +187 -0
- data/lib/bio/db/genbank/genbank.rb +250 -0
- data/lib/bio/db/genbank/genbank_to_biosequence.rb +86 -0
- data/lib/bio/db/genbank/genpept.rb +60 -0
- data/lib/bio/db/genbank/refseq.rb +18 -0
- data/lib/bio/db/gff.rb +1846 -0
- data/lib/bio/db/go.rb +481 -0
- data/lib/bio/db/kegg/brite.rb +41 -0
- data/lib/bio/db/kegg/compound.rb +131 -0
- data/lib/bio/db/kegg/drug.rb +98 -0
- data/lib/bio/db/kegg/enzyme.rb +148 -0
- data/lib/bio/db/kegg/expression.rb +155 -0
- data/lib/bio/db/kegg/genes.rb +263 -0
- data/lib/bio/db/kegg/genome.rb +241 -0
- data/lib/bio/db/kegg/glycan.rb +166 -0
- data/lib/bio/db/kegg/keggtab.rb +357 -0
- data/lib/bio/db/kegg/kgml.rb +256 -0
- data/lib/bio/db/kegg/orthology.rb +136 -0
- data/lib/bio/db/kegg/reaction.rb +82 -0
- data/lib/bio/db/kegg/taxonomy.rb +331 -0
- data/lib/bio/db/lasergene.rb +209 -0
- data/lib/bio/db/litdb.rb +107 -0
- data/lib/bio/db/medline.rb +326 -0
- data/lib/bio/db/nbrf.rb +191 -0
- data/lib/bio/db/newick.rb +658 -0
- data/lib/bio/db/nexus.rb +1854 -0
- data/lib/bio/db/pdb.rb +29 -0
- data/lib/bio/db/pdb/atom.rb +77 -0
- data/lib/bio/db/pdb/chain.rb +210 -0
- data/lib/bio/db/pdb/chemicalcomponent.rb +224 -0
- data/lib/bio/db/pdb/model.rb +148 -0
- data/lib/bio/db/pdb/pdb.rb +1911 -0
- data/lib/bio/db/pdb/residue.rb +176 -0
- data/lib/bio/db/pdb/utils.rb +399 -0
- data/lib/bio/db/prosite.rb +597 -0
- data/lib/bio/db/rebase.rb +456 -0
- data/lib/bio/db/soft.rb +404 -0
- data/lib/bio/db/transfac.rb +375 -0
- data/lib/bio/db/url.rb +42 -0
- data/lib/bio/feature.rb +139 -0
- data/lib/bio/io/biosql/biodatabase.rb +64 -0
- data/lib/bio/io/biosql/bioentry.rb +29 -0
- data/lib/bio/io/biosql/bioentry_dbxref.rb +11 -0
- data/lib/bio/io/biosql/bioentry_path.rb +12 -0
- data/lib/bio/io/biosql/bioentry_qualifier_value.rb +10 -0
- data/lib/bio/io/biosql/bioentry_reference.rb +10 -0
- data/lib/bio/io/biosql/bioentry_relationship.rb +10 -0
- data/lib/bio/io/biosql/biosequence.rb +11 -0
- data/lib/bio/io/biosql/comment.rb +7 -0
- data/lib/bio/io/biosql/config/database.yml +20 -0
- data/lib/bio/io/biosql/dbxref.rb +13 -0
- data/lib/bio/io/biosql/dbxref_qualifier_value.rb +12 -0
- data/lib/bio/io/biosql/location.rb +32 -0
- data/lib/bio/io/biosql/location_qualifier_value.rb +11 -0
- data/lib/bio/io/biosql/ontology.rb +10 -0
- data/lib/bio/io/biosql/reference.rb +9 -0
- data/lib/bio/io/biosql/seqfeature.rb +32 -0
- data/lib/bio/io/biosql/seqfeature_dbxref.rb +11 -0
- data/lib/bio/io/biosql/seqfeature_path.rb +11 -0
- data/lib/bio/io/biosql/seqfeature_qualifier_value.rb +20 -0
- data/lib/bio/io/biosql/seqfeature_relationship.rb +11 -0
- data/lib/bio/io/biosql/taxon.rb +12 -0
- data/lib/bio/io/biosql/taxon_name.rb +9 -0
- data/lib/bio/io/biosql/term.rb +27 -0
- data/lib/bio/io/biosql/term_dbxref.rb +11 -0
- data/lib/bio/io/biosql/term_path.rb +12 -0
- data/lib/bio/io/biosql/term_relationship.rb +13 -0
- data/lib/bio/io/biosql/term_relationship_term.rb +11 -0
- data/lib/bio/io/biosql/term_synonym.rb +10 -0
- data/lib/bio/io/das.rb +461 -0
- data/lib/bio/io/dbget.rb +194 -0
- data/lib/bio/io/ddbjxml.rb +638 -0
- data/lib/bio/io/ebisoap.rb +158 -0
- data/lib/bio/io/ensembl.rb +229 -0
- data/lib/bio/io/fastacmd.rb +163 -0
- data/lib/bio/io/fetch.rb +195 -0
- data/lib/bio/io/flatfile.rb +482 -0
- data/lib/bio/io/flatfile/autodetection.rb +545 -0
- data/lib/bio/io/flatfile/bdb.rb +253 -0
- data/lib/bio/io/flatfile/buffer.rb +237 -0
- data/lib/bio/io/flatfile/index.rb +1381 -0
- data/lib/bio/io/flatfile/indexer.rb +805 -0
- data/lib/bio/io/flatfile/splitter.rb +297 -0
- data/lib/bio/io/higet.rb +73 -0
- data/lib/bio/io/hinv.rb +442 -0
- data/lib/bio/io/keggapi.rb +805 -0
- data/lib/bio/io/ncbirest.rb +733 -0
- data/lib/bio/io/ncbisoap.rb +155 -0
- data/lib/bio/io/pubmed.rb +307 -0
- data/lib/bio/io/registry.rb +292 -0
- data/lib/bio/io/soapwsdl.rb +119 -0
- data/lib/bio/io/sql.rb +186 -0
- data/lib/bio/location.rb +867 -0
- data/lib/bio/map.rb +410 -0
- data/lib/bio/pathway.rb +960 -0
- data/lib/bio/reference.rb +602 -0
- data/lib/bio/sequence.rb +456 -0
- data/lib/bio/sequence/aa.rb +152 -0
- data/lib/bio/sequence/adapter.rb +108 -0
- data/lib/bio/sequence/common.rb +310 -0
- data/lib/bio/sequence/compat.rb +123 -0
- data/lib/bio/sequence/dblink.rb +54 -0
- data/lib/bio/sequence/format.rb +358 -0
- data/lib/bio/sequence/format_raw.rb +23 -0
- data/lib/bio/sequence/generic.rb +24 -0
- data/lib/bio/sequence/na.rb +491 -0
- data/lib/bio/shell.rb +44 -0
- data/lib/bio/shell/core.rb +578 -0
- data/lib/bio/shell/demo.rb +146 -0
- data/lib/bio/shell/interface.rb +218 -0
- data/lib/bio/shell/irb.rb +95 -0
- data/lib/bio/shell/object.rb +71 -0
- data/lib/bio/shell/plugin/blast.rb +42 -0
- data/lib/bio/shell/plugin/codon.rb +218 -0
- data/lib/bio/shell/plugin/das.rb +58 -0
- data/lib/bio/shell/plugin/emboss.rb +23 -0
- data/lib/bio/shell/plugin/entry.rb +105 -0
- data/lib/bio/shell/plugin/flatfile.rb +101 -0
- data/lib/bio/shell/plugin/keggapi.rb +181 -0
- data/lib/bio/shell/plugin/midi.rb +430 -0
- data/lib/bio/shell/plugin/obda.rb +45 -0
- data/lib/bio/shell/plugin/psort.rb +56 -0
- data/lib/bio/shell/plugin/seq.rb +247 -0
- data/lib/bio/shell/plugin/soap.rb +87 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb +29 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml +4 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml +27 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml +11 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +4 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml +7 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +368 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml +47 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb +144 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb +47 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml +8 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml +10 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml +26 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif +0 -0
- data/lib/bio/shell/script.rb +25 -0
- data/lib/bio/shell/setup.rb +109 -0
- data/lib/bio/shell/web.rb +102 -0
- data/lib/bio/tree.rb +852 -0
- data/lib/bio/util/color_scheme.rb +191 -0
- data/lib/bio/util/color_scheme/buried.rb +59 -0
- data/lib/bio/util/color_scheme/helix.rb +59 -0
- data/lib/bio/util/color_scheme/hydropathy.rb +64 -0
- data/lib/bio/util/color_scheme/nucleotide.rb +31 -0
- data/lib/bio/util/color_scheme/strand.rb +59 -0
- data/lib/bio/util/color_scheme/taylor.rb +50 -0
- data/lib/bio/util/color_scheme/turn.rb +59 -0
- data/lib/bio/util/color_scheme/zappo.rb +50 -0
- data/lib/bio/util/contingency_table.rb +370 -0
- data/lib/bio/util/restriction_enzyme.rb +228 -0
- data/lib/bio/util/restriction_enzyme/analysis.rb +249 -0
- data/lib/bio/util/restriction_enzyme/analysis_basic.rb +217 -0
- data/lib/bio/util/restriction_enzyme/cut_symbol.rb +107 -0
- data/lib/bio/util/restriction_enzyme/double_stranded.rb +321 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb +130 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb +103 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb +38 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb +76 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb +107 -0
- data/lib/bio/util/restriction_enzyme/enzymes.yaml +7061 -0
- data/lib/bio/util/restriction_enzyme/range/cut_range.rb +24 -0
- data/lib/bio/util/restriction_enzyme/range/cut_ranges.rb +47 -0
- data/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb +67 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +257 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +242 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb +51 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb +41 -0
- data/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb +77 -0
- data/lib/bio/util/restriction_enzyme/single_strand.rb +200 -0
- data/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb +135 -0
- data/lib/bio/util/restriction_enzyme/single_strand_complement.rb +23 -0
- data/lib/bio/util/restriction_enzyme/string_formatting.rb +111 -0
- data/lib/bio/util/sirna.rb +288 -0
- data/test/data/HMMER/hmmpfam.out +64 -0
- data/test/data/HMMER/hmmsearch.out +88 -0
- data/test/data/SOSUI/sample.report +11 -0
- data/test/data/TMHMM/sample.report +21 -0
- data/test/data/aaindex/DAYM780301 +30 -0
- data/test/data/aaindex/PRAM900102 +20 -0
- data/test/data/bl2seq/cd8a_cd8b_blastp.bl2seq +53 -0
- data/test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq +37 -0
- data/test/data/blast/2.2.15.blastp.m7 +876 -0
- data/test/data/blast/b0002.faa +15 -0
- data/test/data/blast/b0002.faa.m0 +128 -0
- data/test/data/blast/b0002.faa.m7 +65 -0
- data/test/data/blast/b0002.faa.m8 +1 -0
- data/test/data/blast/blastp-multi.m7 +188 -0
- data/test/data/command/echoarg2.bat +1 -0
- data/test/data/embl/AB090716.embl +65 -0
- data/test/data/embl/AB090716.embl.rel89 +63 -0
- data/test/data/fasta/example1.txt +75 -0
- data/test/data/fasta/example2.txt +21 -0
- data/test/data/genscan/sample.report +63 -0
- data/test/data/iprscan/merged.raw +32 -0
- data/test/data/iprscan/merged.txt +74 -0
- data/test/data/paml/codeml/control_file.txt +30 -0
- data/test/data/paml/codeml/output.txt +78 -0
- data/test/data/paml/codeml/rates +217 -0
- data/test/data/prosite/prosite.dat +2233 -0
- data/test/data/refseq/nm_126355.entret +64 -0
- data/test/data/rpsblast/misc.rpsblast +193 -0
- data/test/data/soft/GDS100_partial.soft +92 -0
- data/test/data/soft/GSE3457_family_partial.soft +874 -0
- data/test/data/uniprot/p53_human.uniprot +1456 -0
- data/test/functional/bio/appl/test_pts1.rb +115 -0
- data/test/functional/bio/io/test_ensembl.rb +229 -0
- data/test/functional/bio/io/test_soapwsdl.rb +52 -0
- data/test/functional/bio/sequence/test_output_embl.rb +51 -0
- data/test/functional/bio/test_command.rb +301 -0
- data/test/runner.rb +14 -0
- data/test/unit/bio/appl/bl2seq/test_report.rb +134 -0
- data/test/unit/bio/appl/blast/test_ncbioptions.rb +112 -0
- data/test/unit/bio/appl/blast/test_report.rb +1135 -0
- data/test/unit/bio/appl/blast/test_rpsblast.rb +398 -0
- data/test/unit/bio/appl/genscan/test_report.rb +182 -0
- data/test/unit/bio/appl/hmmer/test_report.rb +342 -0
- data/test/unit/bio/appl/iprscan/test_report.rb +338 -0
- data/test/unit/bio/appl/mafft/test_report.rb +63 -0
- data/test/unit/bio/appl/paml/codeml/test_rates.rb +45 -0
- data/test/unit/bio/appl/paml/codeml/test_report.rb +45 -0
- data/test/unit/bio/appl/paml/test_codeml.rb +174 -0
- data/test/unit/bio/appl/sosui/test_report.rb +81 -0
- data/test/unit/bio/appl/targetp/test_report.rb +146 -0
- data/test/unit/bio/appl/test_blast.rb +277 -0
- data/test/unit/bio/appl/test_fasta.rb +130 -0
- data/test/unit/bio/appl/test_psort.rb +57 -0
- data/test/unit/bio/appl/test_pts1.rb +77 -0
- data/test/unit/bio/appl/tmhmm/test_report.rb +126 -0
- data/test/unit/bio/data/test_aa.rb +90 -0
- data/test/unit/bio/data/test_codontable.rb +107 -0
- data/test/unit/bio/data/test_na.rb +80 -0
- data/test/unit/bio/db/embl/test_common.rb +117 -0
- data/test/unit/bio/db/embl/test_embl.rb +214 -0
- data/test/unit/bio/db/embl/test_embl_rel89.rb +219 -0
- data/test/unit/bio/db/embl/test_embl_to_bioseq.rb +203 -0
- data/test/unit/bio/db/embl/test_sptr.rb +1812 -0
- data/test/unit/bio/db/embl/test_uniprot.rb +31 -0
- data/test/unit/bio/db/kegg/test_genes.rb +45 -0
- data/test/unit/bio/db/pdb/test_pdb.rb +152 -0
- data/test/unit/bio/db/test_aaindex.rb +197 -0
- data/test/unit/bio/db/test_fasta.rb +250 -0
- data/test/unit/bio/db/test_gff.rb +1190 -0
- data/test/unit/bio/db/test_lasergene.rb +95 -0
- data/test/unit/bio/db/test_medline.rb +127 -0
- data/test/unit/bio/db/test_newick.rb +293 -0
- data/test/unit/bio/db/test_nexus.rb +364 -0
- data/test/unit/bio/db/test_prosite.rb +1437 -0
- data/test/unit/bio/db/test_rebase.rb +101 -0
- data/test/unit/bio/db/test_soft.rb +138 -0
- data/test/unit/bio/db/test_url.rb +36 -0
- data/test/unit/bio/io/flatfile/test_autodetection.rb +375 -0
- data/test/unit/bio/io/flatfile/test_buffer.rb +251 -0
- data/test/unit/bio/io/flatfile/test_splitter.rb +369 -0
- data/test/unit/bio/io/test_ddbjxml.rb +80 -0
- data/test/unit/bio/io/test_ensembl.rb +109 -0
- data/test/unit/bio/io/test_fastacmd.rb +42 -0
- data/test/unit/bio/io/test_flatfile.rb +505 -0
- data/test/unit/bio/io/test_soapwsdl.rb +32 -0
- data/test/unit/bio/sequence/test_aa.rb +115 -0
- data/test/unit/bio/sequence/test_common.rb +373 -0
- data/test/unit/bio/sequence/test_compat.rb +69 -0
- data/test/unit/bio/sequence/test_dblink.rb +58 -0
- data/test/unit/bio/sequence/test_na.rb +330 -0
- data/test/unit/bio/shell/plugin/test_seq.rb +185 -0
- data/test/unit/bio/test_alignment.rb +1025 -0
- data/test/unit/bio/test_command.rb +349 -0
- data/test/unit/bio/test_db.rb +96 -0
- data/test/unit/bio/test_feature.rb +144 -0
- data/test/unit/bio/test_location.rb +599 -0
- data/test/unit/bio/test_map.rb +230 -0
- data/test/unit/bio/test_pathway.rb +499 -0
- data/test/unit/bio/test_reference.rb +252 -0
- data/test/unit/bio/test_sequence.rb +329 -0
- data/test/unit/bio/test_shell.rb +18 -0
- data/test/unit/bio/test_tree.rb +593 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb +299 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb +103 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb +240 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb +101 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb +75 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb +73 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb +53 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb +104 -0
- data/test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb +83 -0
- data/test/unit/bio/util/restriction_enzyme/test_analysis.rb +246 -0
- data/test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb +44 -0
- data/test/unit/bio/util/restriction_enzyme/test_double_stranded.rb +115 -0
- data/test/unit/bio/util/restriction_enzyme/test_single_strand.rb +147 -0
- data/test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb +147 -0
- data/test/unit/bio/util/restriction_enzyme/test_string_formatting.rb +60 -0
- data/test/unit/bio/util/test_color_scheme.rb +33 -0
- data/test/unit/bio/util/test_contingency_table.rb +94 -0
- data/test/unit/bio/util/test_restriction_enzyme.rb +42 -0
- data/test/unit/bio/util/test_sirna.rb +245 -0
- metadata +543 -0
data/lib/bio/db/pdb.rb
ADDED
@@ -0,0 +1,29 @@
|
|
1
|
+
#
|
2
|
+
# = bio/db/pdb.rb - PDB database classes
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2004
|
5
|
+
# GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>
|
6
|
+
# License:: The Ruby License
|
7
|
+
#
|
8
|
+
# $Id: pdb.rb,v 1.8 2007/04/05 23:35:40 trevor Exp $
|
9
|
+
#
|
10
|
+
|
11
|
+
require 'bio/db'
|
12
|
+
|
13
|
+
# definition of the PDB class
|
14
|
+
module Bio
|
15
|
+
class PDB #< DB
|
16
|
+
|
17
|
+
autoload :ChemicalComponent, 'bio/db/pdb/chemicalcomponent'
|
18
|
+
|
19
|
+
end #class PDB
|
20
|
+
end #module Bio
|
21
|
+
|
22
|
+
# require other files under pdb directory
|
23
|
+
require 'bio/db/pdb/utils'
|
24
|
+
require 'bio/db/pdb/atom'
|
25
|
+
require 'bio/db/pdb/residue'
|
26
|
+
require 'bio/db/pdb/chain'
|
27
|
+
require 'bio/db/pdb/model'
|
28
|
+
require 'bio/db/pdb/pdb'
|
29
|
+
|
@@ -0,0 +1,77 @@
|
|
1
|
+
#
|
2
|
+
# = bio/db/pdb/atom.rb - Coordinate class for PDB
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2004, 2006
|
5
|
+
# Alex Gutteridge <alexg@ebi.ac.uk>
|
6
|
+
# Naohisa Goto <ng@bioruby.org>
|
7
|
+
# License:: The Ruby License
|
8
|
+
#
|
9
|
+
# $Id: atom.rb,v 1.8 2007/04/05 23:35:41 trevor Exp $
|
10
|
+
#
|
11
|
+
# = Bio::PDB::Coordinate
|
12
|
+
#
|
13
|
+
# Coordinate class for PDB.
|
14
|
+
#
|
15
|
+
# = Compatibility Note
|
16
|
+
#
|
17
|
+
# From bioruby 0.7.0, the Bio::PDB::Atom class is no longer available.
|
18
|
+
# Please use Bio::PDB::Record::ATOM and Bio::PDB::Record::HETATM instead.
|
19
|
+
#
|
20
|
+
|
21
|
+
require 'matrix'
|
22
|
+
require 'bio/db/pdb'
|
23
|
+
|
24
|
+
module Bio
|
25
|
+
class PDB
|
26
|
+
|
27
|
+
# Bio::PDB::Coordinate is a class to store a 3D coordinate.
|
28
|
+
# It inherits Vector (in bundled library in Ruby).
|
29
|
+
#
|
30
|
+
class Coordinate < Vector
|
31
|
+
# same as Vector.[x,y,z]
|
32
|
+
def self.[](x,y,z)
|
33
|
+
super
|
34
|
+
end
|
35
|
+
|
36
|
+
# same as Vector.elements
|
37
|
+
def self.elements(array, *a)
|
38
|
+
raise 'Size of given array must be 3' if array.size != 3
|
39
|
+
super
|
40
|
+
end
|
41
|
+
|
42
|
+
# x
|
43
|
+
def x; self[0]; end
|
44
|
+
# y
|
45
|
+
def y; self[1]; end
|
46
|
+
# z
|
47
|
+
def z; self[2]; end
|
48
|
+
# x=(n)
|
49
|
+
def x=(n); self[0]=n; end
|
50
|
+
# y=(n)
|
51
|
+
def y=(n); self[1]=n; end
|
52
|
+
# z=(n)
|
53
|
+
def z=(n); self[2]=n; end
|
54
|
+
|
55
|
+
# Implicit conversion to an array.
|
56
|
+
#
|
57
|
+
# Note that this method would be deprecated in the future.
|
58
|
+
#
|
59
|
+
#--
|
60
|
+
# Definition of 'to_ary' means objects of the class is
|
61
|
+
# implicitly regarded as an array.
|
62
|
+
#++
|
63
|
+
def to_ary; self.to_a; end
|
64
|
+
|
65
|
+
# returns self.
|
66
|
+
def xyz; self; end
|
67
|
+
|
68
|
+
# distance between <em>object2</em>.
|
69
|
+
def distance(object2)
|
70
|
+
Utils::convert_to_xyz(object2)
|
71
|
+
(self - object2).r
|
72
|
+
end
|
73
|
+
end #class Coordinate
|
74
|
+
|
75
|
+
end #class PDB
|
76
|
+
end #class Bio
|
77
|
+
|
@@ -0,0 +1,210 @@
|
|
1
|
+
#
|
2
|
+
# = bio/db/pdb/chain.rb - chain class for PDB
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2004, 2006
|
5
|
+
# Alex Gutteridge <alexg@ebi.ac.uk>
|
6
|
+
# Naohisa Goto <ng@bioruby.org>
|
7
|
+
# License:: The Ruby License
|
8
|
+
#
|
9
|
+
# $Id: chain.rb,v 1.10 2008/04/01 10:36:44 ngoto Exp $
|
10
|
+
#
|
11
|
+
# = Bio::PDB::Chain
|
12
|
+
#
|
13
|
+
# Please refer Bio::PDB::Chain.
|
14
|
+
#
|
15
|
+
|
16
|
+
require 'bio/db/pdb'
|
17
|
+
|
18
|
+
module Bio
|
19
|
+
|
20
|
+
class PDB
|
21
|
+
|
22
|
+
# Bio::PDB::Chain is a class to store a chain.
|
23
|
+
#
|
24
|
+
# The object would contain some residues (Bio::PDB::Residue objects)
|
25
|
+
# and some heterogens (Bio::PDB::Heterogen objects).
|
26
|
+
#
|
27
|
+
class Chain
|
28
|
+
|
29
|
+
include Utils
|
30
|
+
include AtomFinder
|
31
|
+
include ResidueFinder
|
32
|
+
|
33
|
+
include HetatmFinder
|
34
|
+
include HeterogenFinder
|
35
|
+
|
36
|
+
include Enumerable
|
37
|
+
include Comparable
|
38
|
+
|
39
|
+
# Creates a new chain object.
|
40
|
+
def initialize(id = nil, model = nil)
|
41
|
+
|
42
|
+
@chain_id = id
|
43
|
+
|
44
|
+
@model = model
|
45
|
+
|
46
|
+
@residues = []
|
47
|
+
@residues_hash = {}
|
48
|
+
@heterogens = []
|
49
|
+
@heterogens_hash = {}
|
50
|
+
end
|
51
|
+
|
52
|
+
# Identifier of this chain
|
53
|
+
attr_accessor :chain_id
|
54
|
+
# alias
|
55
|
+
alias id chain_id
|
56
|
+
|
57
|
+
# the model to which this chain belongs.
|
58
|
+
attr_reader :model
|
59
|
+
|
60
|
+
# residues in this chain
|
61
|
+
attr_reader :residues
|
62
|
+
|
63
|
+
# heterogens in this chain
|
64
|
+
attr_reader :heterogens
|
65
|
+
|
66
|
+
# get the residue by id
|
67
|
+
def get_residue_by_id(key)
|
68
|
+
#@residues.find { |r| r.residue_id == key }
|
69
|
+
@residues_hash[key]
|
70
|
+
end
|
71
|
+
|
72
|
+
# get the residue by id.
|
73
|
+
#
|
74
|
+
# Compatibility Note: Now, you cannot find HETATMS in this method.
|
75
|
+
# To add "LIGAND" to the id is no longer available.
|
76
|
+
# To get heterogens, you must use <code>get_heterogen_by_id</code>.
|
77
|
+
def [](key)
|
78
|
+
get_residue_by_id(key)
|
79
|
+
end
|
80
|
+
|
81
|
+
# get the heterogen (ligand) by id
|
82
|
+
def get_heterogen_by_id(key)
|
83
|
+
#@heterogens.find { |r| r.residue_id == key }
|
84
|
+
@heterogens_hash[key]
|
85
|
+
end
|
86
|
+
|
87
|
+
#Add a residue to this chain
|
88
|
+
def addResidue(residue)
|
89
|
+
raise "Expecting a Bio::PDB::Residue" unless residue.is_a? Bio::PDB::Residue
|
90
|
+
@residues.push(residue)
|
91
|
+
if @residues_hash[residue.residue_id] then
|
92
|
+
$stderr.puts "Warning: residue_id #{residue.residue_id.inspect} is already used" if $VERBOSE
|
93
|
+
else
|
94
|
+
@residues_hash[residue.residue_id] = residue
|
95
|
+
end
|
96
|
+
self
|
97
|
+
end
|
98
|
+
|
99
|
+
#Add a heterogen (ligand) to this chain
|
100
|
+
def addLigand(ligand)
|
101
|
+
raise "Expecting a Bio::PDB::Residue" unless ligand.is_a? Bio::PDB::Residue
|
102
|
+
@heterogens.push(ligand)
|
103
|
+
if @heterogens_hash[ligand.residue_id] then
|
104
|
+
$stderr.puts "Warning: heterogen_id (residue_id) #{ligand.residue_id.inspect} is already used" if $VERBOSE
|
105
|
+
else
|
106
|
+
@heterogens_hash[ligand.residue_id] = ligand
|
107
|
+
end
|
108
|
+
self
|
109
|
+
end
|
110
|
+
|
111
|
+
# rehash residues hash
|
112
|
+
def rehash_residues
|
113
|
+
begin
|
114
|
+
residues_bak = @residues
|
115
|
+
residues_hash_bak = @residues_hash
|
116
|
+
@residues = []
|
117
|
+
@residues_hash = {}
|
118
|
+
residues_bak.each do |residue|
|
119
|
+
self.addResidue(residue)
|
120
|
+
end
|
121
|
+
rescue RuntimeError
|
122
|
+
@residues = residues_bak
|
123
|
+
@residues_hash = residues_hash_bak
|
124
|
+
raise
|
125
|
+
end
|
126
|
+
self
|
127
|
+
end
|
128
|
+
|
129
|
+
# rehash heterogens hash
|
130
|
+
def rehash_heterogens
|
131
|
+
begin
|
132
|
+
heterogens_bak = @heterogens
|
133
|
+
heterogens_hash_bak = @heterogens_hash
|
134
|
+
@heterogens = []
|
135
|
+
@heterogens_hash = {}
|
136
|
+
heterogens_bak.each do |heterogen|
|
137
|
+
self.addLigand(heterogen)
|
138
|
+
end
|
139
|
+
rescue RuntimeError
|
140
|
+
@heterogens = heterogens_bak
|
141
|
+
@heterogens_hash = heterogens_hash_bak
|
142
|
+
raise
|
143
|
+
end
|
144
|
+
self
|
145
|
+
end
|
146
|
+
|
147
|
+
# rehash residues hash and heterogens hash
|
148
|
+
def rehash
|
149
|
+
rehash_residues
|
150
|
+
rehash_heterogens
|
151
|
+
end
|
152
|
+
|
153
|
+
# Iterates over each residue
|
154
|
+
def each(&x) #:yields: residue
|
155
|
+
@residues.each(&x)
|
156
|
+
end
|
157
|
+
#Alias to override ResidueFinder#each_residue
|
158
|
+
alias each_residue each
|
159
|
+
|
160
|
+
# Iterates over each hetero-compound
|
161
|
+
def each_heterogen(&x) #:yields: heterogen
|
162
|
+
@heterogens.each(&x)
|
163
|
+
end
|
164
|
+
|
165
|
+
# Operator aimed to sort based on chain id
|
166
|
+
def <=>(other)
|
167
|
+
return @chain_id <=> other.chain_id
|
168
|
+
end
|
169
|
+
|
170
|
+
# Stringifies each residue
|
171
|
+
def to_s
|
172
|
+
@residues.join('') + "TER\n" + @heterogens.join('')
|
173
|
+
end
|
174
|
+
|
175
|
+
# returns a string containing human-readable representation
|
176
|
+
# of this object.
|
177
|
+
def inspect
|
178
|
+
"#<#{self.class.to_s} id=#{chain_id.inspect} model.serial=#{(model ? model.serial : nil).inspect} residues.size=#{residues.size} heterogens.size=#{heterogens.size} aaseq=#{aaseq.inspect}>"
|
179
|
+
end
|
180
|
+
|
181
|
+
# gets an amino acid sequence of this chain from ATOM records
|
182
|
+
def aaseq
|
183
|
+
unless defined? @aaseq
|
184
|
+
string = ""
|
185
|
+
last_residue_num = nil
|
186
|
+
@residues.each do |residue|
|
187
|
+
if last_residue_num and
|
188
|
+
(x = (residue.resSeq.to_i - last_residue_num).abs) > 1 then
|
189
|
+
x.times { string << 'X' }
|
190
|
+
end
|
191
|
+
tlc = residue.resName.capitalize
|
192
|
+
olc = (begin
|
193
|
+
Bio::AminoAcid.three2one(tlc)
|
194
|
+
rescue ArgumentError
|
195
|
+
nil
|
196
|
+
end || 'X')
|
197
|
+
string << olc
|
198
|
+
end
|
199
|
+
@aaseq = Bio::Sequence::AA.new(string)
|
200
|
+
end
|
201
|
+
@aaseq
|
202
|
+
end
|
203
|
+
# for backward compatibility
|
204
|
+
alias atom_seq aaseq
|
205
|
+
|
206
|
+
end #class Chain
|
207
|
+
|
208
|
+
end #class PDB
|
209
|
+
|
210
|
+
end #module Bio
|
@@ -0,0 +1,224 @@
|
|
1
|
+
#
|
2
|
+
# = bio/db/pdb/chemicalcomponent.rb - PDB Chemical Component Dictionary parser
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2006
|
5
|
+
# GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>
|
6
|
+
# License:: The Ruby License
|
7
|
+
#
|
8
|
+
# $Id: chemicalcomponent.rb,v 1.3 2007/04/05 23:35:41 trevor Exp $
|
9
|
+
#
|
10
|
+
# = About Bio::PDB::ChemicalComponent
|
11
|
+
#
|
12
|
+
# Please refer Bio::PDB::ChemicalComponent.
|
13
|
+
#
|
14
|
+
# = References
|
15
|
+
#
|
16
|
+
# * ((<URL:http://deposit.pdb.org/cc_dict_tut.html>))
|
17
|
+
# * http://deposit.pdb.org/het_dictionary.txt
|
18
|
+
#
|
19
|
+
|
20
|
+
require 'bio/db/pdb/pdb'
|
21
|
+
|
22
|
+
module Bio
|
23
|
+
class PDB
|
24
|
+
|
25
|
+
# Bio::PDB::ChemicalComponet is a parser for a entry of
|
26
|
+
# the PDB Chemical Component Dictionary.
|
27
|
+
#
|
28
|
+
# The PDB Chemical Component Dictionary is available in
|
29
|
+
# http://deposit.pdb.org/het_dictionary.txt
|
30
|
+
class ChemicalComponent
|
31
|
+
|
32
|
+
# delimiter for reading via Bio::FlatFile
|
33
|
+
DELIMITER = RS = "\n\n"
|
34
|
+
|
35
|
+
# Single field (normally single line) of a entry
|
36
|
+
class Record < Bio::PDB::Record
|
37
|
+
|
38
|
+
# fetches record name
|
39
|
+
def fetch_record_name(str)
|
40
|
+
str[0..6].strip
|
41
|
+
end
|
42
|
+
private :fetch_record_name
|
43
|
+
|
44
|
+
# fetches record name
|
45
|
+
def self.fetch_record_name(str)
|
46
|
+
str[0..6].strip
|
47
|
+
end
|
48
|
+
private_class_method :fetch_record_name
|
49
|
+
|
50
|
+
# RESIDUE field.
|
51
|
+
# It would be wrong because the definition described in documents
|
52
|
+
# seems ambiguous.
|
53
|
+
RESIDUE =
|
54
|
+
def_rec([ 11, 13, Pdb_LString[3], :hetID ],
|
55
|
+
[ 16, 20, Pdb_Integer, :numHetAtoms ]
|
56
|
+
)
|
57
|
+
|
58
|
+
# CONECT field
|
59
|
+
# It would be wrong because the definition described in documents
|
60
|
+
# seems ambiguous.
|
61
|
+
CONECT =
|
62
|
+
def_rec([ 12, 15, Pdb_Atom, :name ],
|
63
|
+
[ 19, 20, Pdb_Integer, :num ],
|
64
|
+
[ 21, 24, Pdb_Atom, :other_atoms ],
|
65
|
+
[ 26, 29, Pdb_Atom, :other_atoms ],
|
66
|
+
[ 31, 34, Pdb_Atom, :other_atoms ],
|
67
|
+
[ 36, 39, Pdb_Atom, :other_atoms ],
|
68
|
+
[ 41, 44, Pdb_Atom, :other_atoms ],
|
69
|
+
[ 46, 49, Pdb_Atom, :other_atoms ],
|
70
|
+
[ 51, 54, Pdb_Atom, :other_atoms ],
|
71
|
+
[ 56, 59, Pdb_Atom, :other_atoms ],
|
72
|
+
[ 61, 64, Pdb_Atom, :other_atoms ],
|
73
|
+
[ 66, 69, Pdb_Atom, :other_atoms ],
|
74
|
+
[ 71, 74, Pdb_Atom, :other_atoms ],
|
75
|
+
[ 76, 79, Pdb_Atom, :other_atoms ]
|
76
|
+
)
|
77
|
+
|
78
|
+
# HET field.
|
79
|
+
# It is the same as Bio::PDB::Record::HET.
|
80
|
+
HET = Bio::PDB::Record::HET
|
81
|
+
|
82
|
+
#--
|
83
|
+
#HETSYN = Bio::PDB::Record::HETSYN
|
84
|
+
#++
|
85
|
+
|
86
|
+
# HETSYN field.
|
87
|
+
# It is very similar to Bio::PDB::Record::HETSYN.
|
88
|
+
HETSYN =
|
89
|
+
def_rec([ 9, 10, Pdb_Continuation, nil ],
|
90
|
+
[ 12, 14, Pdb_LString(3), :hetID ],
|
91
|
+
[ 16, 70, Pdb_String, :hetSynonyms ]
|
92
|
+
)
|
93
|
+
|
94
|
+
# HETNAM field.
|
95
|
+
# It is the same as Bio::PDB::Record::HETNAM.
|
96
|
+
HETNAM = Bio::PDB::Record::HETNAM
|
97
|
+
|
98
|
+
# FORMUL field.
|
99
|
+
# It is the same as Bio::PDB::Record::FORMUL.
|
100
|
+
FORMUL = Bio::PDB::Record::FORMUL
|
101
|
+
|
102
|
+
# default definition for unknown fields.
|
103
|
+
Default = Bio::PDB::Record::Default
|
104
|
+
|
105
|
+
# Hash to store allowed definitions.
|
106
|
+
Definition = create_definition_hash
|
107
|
+
|
108
|
+
# END record class.
|
109
|
+
#
|
110
|
+
# Because END is a reserved word of Ruby, it is separately
|
111
|
+
# added to the hash
|
112
|
+
End = Bio::PDB::Record::End
|
113
|
+
Definition['END'] = End
|
114
|
+
|
115
|
+
# Look up the class in Definition hash
|
116
|
+
def self.get_record_class(str)
|
117
|
+
t = fetch_record_name(str)
|
118
|
+
return Definition[t]
|
119
|
+
end
|
120
|
+
end #class Record
|
121
|
+
|
122
|
+
# Creates a new object.
|
123
|
+
def initialize(str)
|
124
|
+
@data = str.split(/[\r\n]+/)
|
125
|
+
@hash = {}
|
126
|
+
|
127
|
+
#Flag to say whether the current line is part of a continuation
|
128
|
+
cont = false
|
129
|
+
|
130
|
+
#Goes through each line and replace that line with a PDB::Record
|
131
|
+
@data.collect! do |line|
|
132
|
+
#Go to next if the previous line was contiunation able, and
|
133
|
+
#add_continuation returns true. Line is added by add_continuation
|
134
|
+
next if cont and cont = cont.add_continuation(line)
|
135
|
+
|
136
|
+
#Make the new record
|
137
|
+
f = Record.get_record_class(line).new.initialize_from_string(line)
|
138
|
+
#p f
|
139
|
+
#Set cont
|
140
|
+
cont = f if f.continue?
|
141
|
+
#Set the hash to point to this record either by adding to an
|
142
|
+
#array, or on it's own
|
143
|
+
key = f.record_name
|
144
|
+
if a = @hash[key] then
|
145
|
+
a << f
|
146
|
+
else
|
147
|
+
@hash[key] = [ f ]
|
148
|
+
end
|
149
|
+
f
|
150
|
+
end #each
|
151
|
+
#At the end we need to add the final model
|
152
|
+
@data.compact!
|
153
|
+
end
|
154
|
+
|
155
|
+
# all records in this entry as an array.
|
156
|
+
attr_reader :data
|
157
|
+
|
158
|
+
# all records in this entry as an hash accessed by record names.
|
159
|
+
attr_reader :hash
|
160
|
+
|
161
|
+
# Identifier written in the first line "RESIDUE" record. (e.g. CMP)
|
162
|
+
def entry_id
|
163
|
+
@data[0].hetID
|
164
|
+
end
|
165
|
+
|
166
|
+
# Synonyms for the comical component. Returns an array of strings.
|
167
|
+
def hetsyn
|
168
|
+
unless defined? @hetsyn
|
169
|
+
if r = @hash["HETSYN"]
|
170
|
+
@hetsyn = r[0].hetSynonyms.to_s.split(/\;\s*/)
|
171
|
+
else
|
172
|
+
return []
|
173
|
+
end
|
174
|
+
end
|
175
|
+
@hetsyn
|
176
|
+
end
|
177
|
+
|
178
|
+
# The name of the chemical component.
|
179
|
+
# Returns a string (or nil, if the entry is something wrong).
|
180
|
+
def hetnam
|
181
|
+
@hash["HETNAM"][0].text
|
182
|
+
end
|
183
|
+
|
184
|
+
# The chemical formula of the chemical component.
|
185
|
+
# Returns a string (or nil, if the entry is something wrong).
|
186
|
+
def formul
|
187
|
+
@hash["FORMUL"][0].text
|
188
|
+
end
|
189
|
+
|
190
|
+
# Returns an hash of bindings of atoms.
|
191
|
+
# Note that each white spaces are stripped for atom symbols.
|
192
|
+
def conect
|
193
|
+
unless defined? @conect
|
194
|
+
c = {}
|
195
|
+
@hash["CONECT"].each do |e|
|
196
|
+
key = e.name.to_s.strip
|
197
|
+
unless key.empty?
|
198
|
+
val = e.other_atoms.collect { |x| x.strip }
|
199
|
+
#warn "Warning: #{key}: atom name conflict?" if c[key]
|
200
|
+
c[key] = val
|
201
|
+
end
|
202
|
+
end
|
203
|
+
@conect = c
|
204
|
+
end
|
205
|
+
@conect
|
206
|
+
end
|
207
|
+
|
208
|
+
# Gets all records whose record type is _name_.
|
209
|
+
# Returns an array of <code>Bio::PDB::Record::*</code> objects.
|
210
|
+
#
|
211
|
+
# if _name_ is nil, returns hash storing all record data.
|
212
|
+
#
|
213
|
+
# Example:
|
214
|
+
# p pdb.record('CONECT')
|
215
|
+
# p pdb.record['CONECT']
|
216
|
+
#
|
217
|
+
def record(name = nil)
|
218
|
+
name ? @hash[name] : @hash
|
219
|
+
end
|
220
|
+
|
221
|
+
end #class ChemicalComponent
|
222
|
+
end #class PDB
|
223
|
+
end #module Bio
|
224
|
+
|