wwood-bioruby 1.2.11
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- 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
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +4 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +368 -0
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- 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
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- 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
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- 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
@@ -0,0 +1,148 @@
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#
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# = bio/db/pdb/model.rb - model class for PDB
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#
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# Copyright:: Copyright (C) 2004, 2006
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# Alex Gutteridge <alexg@ebi.ac.uk>
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# Naohisa Goto <ng@bioruby.org>
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# License:: The Ruby License
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#
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# $Id: model.rb,v 1.10 2007/12/18 13:48:42 ngoto Exp $
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#
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# = Bio::PDB::Model
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#
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# Please refer Bio::PDB::Model.
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#
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require 'bio/db/pdb'
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module Bio
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class PDB
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# Bio::PDB::Model is a class to store a model.
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#
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# The object would contain some chains (Bio::PDB::Chain objects).
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class Model
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include Utils
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include AtomFinder
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include ResidueFinder
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include ChainFinder
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include HetatmFinder
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include HeterogenFinder
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include Enumerable
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include Comparable
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# Creates a new Model object
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def initialize(serial = nil, structure = nil)
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@serial = serial
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@structure = structure
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@chains = []
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@chains_hash = {}
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@solvents = Chain.new('', self)
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end
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# chains in this model
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attr_reader :chains
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# (OBSOLETE) solvents (water, HOH) in this model
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attr_reader :solvents
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# serial number of this model. (Integer or nil)
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attr_accessor :serial
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# for backward compatibility
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alias model_serial serial
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# (reserved for future extension)
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attr_reader :structure
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# Adds a chain to this model
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def addChain(chain)
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raise "Expecting a Bio::PDB::Chain" unless chain.is_a? Bio::PDB::Chain
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@chains.push(chain)
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if @chains_hash[chain.chain_id] then
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$stderr.puts "Warning: chain_id #{chain.chain_id.inspect} is already used" if $VERBOSE
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else
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@chains_hash[chain.chain_id] = chain
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end
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self
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end
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# rehash chains hash
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def rehash
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begin
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chains_bak = @chains
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chains_hash_bak = @chains_hash
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@chains = []
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@chains_hash = {}
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chains_bak.each do |chain|
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self.addChain(chain)
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end
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rescue RuntimeError
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@chains = chains_bak
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@chains_hash = chains_hash_bak
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raise
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end
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self
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end
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# (OBSOLETE) Adds a solvent molecule to this model
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def addSolvent(solvent)
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raise "Expecting a Bio::PDB::Residue" unless solvent.is_a? Bio::PDB::Residue
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@solvents.addResidue(solvent)
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end
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# (OBSOLETE) not recommended to use this method
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def removeSolvent
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@solvents = nil
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end
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# Iterates over each chain
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def each(&x) #:yields: chain
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@chains.each(&x)
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end
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# Alias to override ChainFinder#each_chain
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alias each_chain each
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# Operator aimed to sort models based on serial number
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def <=>(other)
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return @serial <=> other.model_serial
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end
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# Keyed access to chains
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def [](key)
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#chain = @chains.find{ |chain| key == chain.id }
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@chains_hash[key]
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end
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# stringifies to chains
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def to_s
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string = ""
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if model_serial
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string = "MODEL #{model_serial}\n" #Should use proper formatting
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end
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@chains.each{ |chain| string << chain.to_s }
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#if solvent
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# string << @solvent.to_s
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#end
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if model_serial
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string << "ENDMDL\n"
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end
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return string
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end
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# returns a string containing human-readable representation
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# of this object.
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def inspect
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"#<#{self.class.to_s} serial=#{serial.inspect} chains.size=#{chains.size}>"
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end
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end #class Model
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end #class PDB
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end #module Bio
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#
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# = bio/db/pdb/pdb.rb - PDB database class for PDB file format
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#
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# Copyright:: Copyright (C) 2003-2006
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# GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>
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# Alex Gutteridge <alexg@ebi.ac.uk>
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# License:: The Ruby License
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#
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# $Id: pdb.rb,v 1.28 2008/04/01 10:36:44 ngoto Exp $
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#
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# = About Bio::PDB
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#
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# Please refer document of Bio::PDB class.
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#
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# = References
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#
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# * ((<URL:http://www.rcsb.org/pdb/>))
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# * PDB File Format Contents Guide Version 2.2 (20 December 1996)
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# ((<URL:http://www.rcsb.org/pdb/file_formats/pdb/pdbguide2.2/guide2.2_frame.html>))
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#
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# = *** CAUTION ***
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# This is beta version. Specs shall be changed frequently.
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#
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require 'bio/db/pdb'
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require 'bio/data/aa'
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module Bio
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# This is the main PDB class which takes care of parsing, annotations
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# and is the entry way to the co-ordinate data held in models.
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#
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# There are many related classes.
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#
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# Bio::PDB::Model
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# Bio::PDB::Chain
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# Bio::PDB::Residue
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# Bio::PDB::Heterogen
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# Bio::PDB::Record::ATOM
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# Bio::PDB::Record::HETATM
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# Bio::PDB::Record::*
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# Bio::PDB::Coordinate
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#
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class PDB
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include Utils
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include AtomFinder
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include ResidueFinder
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include ChainFinder
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include ModelFinder
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include HetatmFinder
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include HeterogenFinder
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include Enumerable
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# delimiter for reading via Bio::FlatFile
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DELIMITER = RS = nil # 1 file 1 entry
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# Modules required by the field definitions
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module DataType
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Pdb_Continuation = nil
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module Pdb_Integer
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def self.new(str)
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str.to_i
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end
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end
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module Pdb_SList
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def self.new(str)
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str.to_s.strip.split(/\;\s*/)
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end
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end
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module Pdb_List
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def self.new(str)
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str.to_s.strip.split(/\,\s*/)
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end
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end
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module Pdb_Specification_list
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def self.new(str)
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a = str.to_s.strip.split(/\;\s*/)
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a.collect! { |x| x.split(/\:\s*/, 2) }
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a
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end
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end
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module Pdb_String
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def self.new(str)
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str.to_s.gsub(/\s+\z/, '')
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end
|
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|
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#Creates a new module with a string left justified to the
|
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#length given in nn
|
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def self.[](nn)
|
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m = Module.new
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m.module_eval %Q{
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@@nn = nn
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def self.new(str)
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str.to_s.gsub(/\s+\z/, '').ljust(@@nn)[0, @@nn]
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end
|
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}
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m
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end
|
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end #module Pdb_String
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module Pdb_LString
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def self.[](nn)
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m = Module.new
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m.module_eval %Q{
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@@nn = nn
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def self.new(str)
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str.to_s.ljust(@@nn)[0, @@nn]
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end
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}
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m
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end
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def self.new(str)
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String.new(str.to_s)
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end
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end
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module Pdb_Real
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def self.[](fmt)
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m = Module.new
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m.module_eval %Q{
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@@format = fmt
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def self.new(str)
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str.to_f
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end
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}
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m
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end
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def self.new(str)
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str.to_f
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end
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end
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module Pdb_StringRJ
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def self.new(str)
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str.to_s.gsub(/\A\s+/, '')
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end
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end
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Pdb_Date = Pdb_String
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Pdb_IDcode = Pdb_String
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Pdb_Residue_name = Pdb_String
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Pdb_SymOP = Pdb_String
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Pdb_Atom = Pdb_String
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Pdb_AChar = Pdb_String
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Pdb_Character = Pdb_LString
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module ConstLikeMethod
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def Pdb_LString(nn)
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Pdb_LString[nn]
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end
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|
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def Pdb_String(nn)
|
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Pdb_String[nn]
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end
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|
165
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def Pdb_Real(fmt)
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Pdb_Real[fmt]
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end
|
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end #module ConstLikeMethod
|
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end #module DataType
|
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|
171
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# The ancestor of every single PDB record class.
|
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# It inherits <code>Struct</code> class.
|
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# Basically, each line of a PDB file corresponds to
|
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# an instance of each corresponding child class.
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175
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# If continuation exists, multiple lines may correspond to
|
176
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# single instance.
|
177
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#
|
178
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class Record < Struct
|
179
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include DataType
|
180
|
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extend DataType::ConstLikeMethod
|
181
|
+
|
182
|
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# Internal use only.
|
183
|
+
#
|
184
|
+
# parse filed definitions.
|
185
|
+
def self.parse_field_definitions(ary)
|
186
|
+
symbolhash = {}
|
187
|
+
symbolary = []
|
188
|
+
cont = false
|
189
|
+
|
190
|
+
# For each field definition (range(start, end), type,symbol)
|
191
|
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ary.each do |x|
|
192
|
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range = (x[0] - 1)..(x[1] - 1)
|
193
|
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# If type is nil (Pdb_Continuation) then set 'cont' to the range
|
194
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# (other wise it is false to indicate no continuation
|
195
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unless x[2] then
|
196
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cont = range
|
197
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+
else
|
198
|
+
klass = x[2]
|
199
|
+
sym = x[3]
|
200
|
+
# If the symbol is a proper symbol then...
|
201
|
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if sym.is_a?(Symbol) then
|
202
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# ..if we have the symbol already in the symbol hash
|
203
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# then add the range onto the range array
|
204
|
+
if symbolhash.has_key?(sym) then
|
205
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+
symbolhash[sym][1] << range
|
206
|
+
else
|
207
|
+
# Other wise put a new symbol in with its type and range
|
208
|
+
# range is given its own array. You can have
|
209
|
+
# anumber of ranges.
|
210
|
+
symbolhash[sym] = [ klass, [ range ] ]
|
211
|
+
symbolary << sym
|
212
|
+
end
|
213
|
+
end
|
214
|
+
end
|
215
|
+
end #each
|
216
|
+
[ symbolhash, symbolary, cont ]
|
217
|
+
end
|
218
|
+
private_class_method :parse_field_definitions
|
219
|
+
|
220
|
+
# Creates new class by given field definition
|
221
|
+
# The difference from new_direct() is the class
|
222
|
+
# created by the method does lazy evaluation.
|
223
|
+
#
|
224
|
+
# Internal use only.
|
225
|
+
def self.def_rec(*ary)
|
226
|
+
symbolhash, symbolary, cont = parse_field_definitions(ary)
|
227
|
+
|
228
|
+
klass = Class.new(self.new(*symbolary))
|
229
|
+
klass.module_eval {
|
230
|
+
@definition = ary
|
231
|
+
@symbols = symbolhash
|
232
|
+
@cont = cont
|
233
|
+
}
|
234
|
+
klass.module_eval {
|
235
|
+
symbolary.each do |x|
|
236
|
+
define_method(x) { do_parse; super() }
|
237
|
+
end
|
238
|
+
}
|
239
|
+
klass
|
240
|
+
end #def self.def_rec
|
241
|
+
|
242
|
+
# creates new class which inherits given class.
|
243
|
+
def self.new_inherit(klass)
|
244
|
+
newklass = Class.new(klass)
|
245
|
+
newklass.module_eval {
|
246
|
+
@definition = klass.module_eval { @definition }
|
247
|
+
@symbols = klass.module_eval { @symbols }
|
248
|
+
@cont = klass.module_eval { @cont }
|
249
|
+
}
|
250
|
+
newklass
|
251
|
+
end
|
252
|
+
|
253
|
+
# Creates new class by given field definition.
|
254
|
+
#
|
255
|
+
# Internal use only.
|
256
|
+
def self.new_direct(*ary)
|
257
|
+
symbolhash, symbolary, cont = parse_field_definitions(ary)
|
258
|
+
if cont
|
259
|
+
raise 'continuation not allowed. please use def_rec instead'
|
260
|
+
end
|
261
|
+
|
262
|
+
klass = Class.new(self.new(*symbolary))
|
263
|
+
klass.module_eval {
|
264
|
+
@definition = ary
|
265
|
+
@symbols = symbolhash
|
266
|
+
@cont = cont
|
267
|
+
}
|
268
|
+
klass.module_eval {
|
269
|
+
define_method(:initialize_from_string) { |str|
|
270
|
+
r = super(str)
|
271
|
+
do_parse
|
272
|
+
r
|
273
|
+
}
|
274
|
+
}
|
275
|
+
klass
|
276
|
+
end #def self.new_direct
|
277
|
+
|
278
|
+
# symbols
|
279
|
+
def self.symbols
|
280
|
+
#p self
|
281
|
+
@symbols
|
282
|
+
end
|
283
|
+
|
284
|
+
# Returns true if this record has a field type which allows
|
285
|
+
# continuations.
|
286
|
+
def self.continue?
|
287
|
+
@cont
|
288
|
+
end
|
289
|
+
|
290
|
+
# Returns true if this record has a field type which allows
|
291
|
+
# continuations.
|
292
|
+
def continue?
|
293
|
+
self.class.continue?
|
294
|
+
end
|
295
|
+
|
296
|
+
# yields the symbol(k), type(x[0]) and array of ranges
|
297
|
+
# of each symbol.
|
298
|
+
def each_symbol
|
299
|
+
self.class.symbols.each do |k, x|
|
300
|
+
yield k, x[0], x[1]
|
301
|
+
end
|
302
|
+
end
|
303
|
+
|
304
|
+
# Return original string (except that "\n" are truncated)
|
305
|
+
# for this record (usually just @str, but
|
306
|
+
# sometimes add on the continuation data from other lines.
|
307
|
+
# Returns an array of string.
|
308
|
+
#
|
309
|
+
def original_data
|
310
|
+
if defined?(@cont_data) then
|
311
|
+
[ @str, *@cont_data ]
|
312
|
+
else
|
313
|
+
[ @str ]
|
314
|
+
end
|
315
|
+
end
|
316
|
+
|
317
|
+
# initialize this record from the given string.
|
318
|
+
# <em>str</em> must be a line (in PDB format).
|
319
|
+
#
|
320
|
+
# You can add continuation lines later using
|
321
|
+
# <code>add_continuation</code> method.
|
322
|
+
def initialize_from_string(str)
|
323
|
+
@str = str
|
324
|
+
@record_name = fetch_record_name(str)
|
325
|
+
@parsed = false
|
326
|
+
self
|
327
|
+
end
|
328
|
+
|
329
|
+
#--
|
330
|
+
# Called when we need to access the data, takes the string
|
331
|
+
# and the array of FieldDefs and parses it out.
|
332
|
+
#++
|
333
|
+
|
334
|
+
# In order to speeding up processing of PDB file format,
|
335
|
+
# fields have not been parsed before calling this method.
|
336
|
+
#
|
337
|
+
# Normally, it is automatically called and you don't explicitly
|
338
|
+
# need to call it .
|
339
|
+
#
|
340
|
+
def do_parse
|
341
|
+
return self if @parsed or !@str
|
342
|
+
str = @str
|
343
|
+
each_symbol do |key, klass, ranges|
|
344
|
+
#If we only have one range then pull that out
|
345
|
+
#and store it in the hash
|
346
|
+
if ranges.size <= 1 then
|
347
|
+
self[key] = klass.new(str[ranges.first])
|
348
|
+
else
|
349
|
+
#Go through each range and add the string to an array
|
350
|
+
#set the hash key to point to that array
|
351
|
+
ary = []
|
352
|
+
ranges.each do |r|
|
353
|
+
ary << klass.new(str[r]) unless str[r].to_s.strip.empty?
|
354
|
+
end
|
355
|
+
self[key] = ary
|
356
|
+
end
|
357
|
+
end #each_symbol
|
358
|
+
#If we have continuations then for each line of extra data...
|
359
|
+
if defined?(@cont_data) then
|
360
|
+
@cont_data.each do |str|
|
361
|
+
#Get the symbol, type and range array
|
362
|
+
each_symbol do |key, klass, ranges|
|
363
|
+
#If there's one range then grab that range
|
364
|
+
if ranges.size <= 1 then
|
365
|
+
r = ranges.first
|
366
|
+
unless str[r].to_s.strip.empty?
|
367
|
+
#and concatenate the new data onto the old
|
368
|
+
v = klass.new(str[r])
|
369
|
+
self[key].concat(v) if self[key] != v
|
370
|
+
end
|
371
|
+
else
|
372
|
+
#If there's more than one range then add to the array
|
373
|
+
ary = self[key]
|
374
|
+
ranges.each do |r|
|
375
|
+
ary << klass.new(str[r]) unless str[r].to_s.strip.empty?
|
376
|
+
end
|
377
|
+
end
|
378
|
+
end
|
379
|
+
end
|
380
|
+
end
|
381
|
+
@parsed = true
|
382
|
+
self
|
383
|
+
end
|
384
|
+
|
385
|
+
# fetches record name
|
386
|
+
def fetch_record_name(str)
|
387
|
+
str[0..5].strip
|
388
|
+
end
|
389
|
+
private :fetch_record_name
|
390
|
+
|
391
|
+
# fetches record name
|
392
|
+
def self.fetch_record_name(str)
|
393
|
+
str[0..5].strip
|
394
|
+
end
|
395
|
+
private_class_method :fetch_record_name
|
396
|
+
|
397
|
+
# If given <em>str</em> can be the continuation of the current record,
|
398
|
+
# then return the order number of the continuation associated with
|
399
|
+
# the Pdb_Continuation field definition.
|
400
|
+
# Otherwise, returns -1.
|
401
|
+
def fetch_cont(str)
|
402
|
+
(c = continue?) ? str[c].to_i : -1
|
403
|
+
end
|
404
|
+
private :fetch_cont
|
405
|
+
|
406
|
+
# Record name of this record, e.g. "HEADER", "ATOM".
|
407
|
+
def record_name
|
408
|
+
@record_name or self.class.to_s.split(/\:\:/)[-1].to_s.upcase
|
409
|
+
end
|
410
|
+
# keeping compatibility with old version
|
411
|
+
alias record_type record_name
|
412
|
+
|
413
|
+
# Internal use only.
|
414
|
+
#
|
415
|
+
# Adds continuation data to the record from str if str is
|
416
|
+
# really the continuation of current record.
|
417
|
+
# Returns self (= not nil) if str is the continuation.
|
418
|
+
# Otherwaise, returns false.
|
419
|
+
#
|
420
|
+
def add_continuation(str)
|
421
|
+
#Check that this record can continue
|
422
|
+
#and that str has the same type and definition
|
423
|
+
return false unless self.continue?
|
424
|
+
return false unless fetch_record_name(str) == @record_name
|
425
|
+
return false unless self.class.get_record_class(str) == self.class
|
426
|
+
return false unless fetch_cont(str) >= 2
|
427
|
+
#If all this is OK then add onto @cont_data
|
428
|
+
unless defined?(@cont_data)
|
429
|
+
@cont_data = []
|
430
|
+
end
|
431
|
+
@cont_data << str
|
432
|
+
# Returns self (= not nil) if succeeded.
|
433
|
+
self
|
434
|
+
end
|
435
|
+
|
436
|
+
# creates definition hash from current classes constants
|
437
|
+
def self.create_definition_hash
|
438
|
+
hash = {}
|
439
|
+
constants.each do |x|
|
440
|
+
x = x.intern # keep compatibility both Ruby 1.8 and 1.9
|
441
|
+
hash[x] = const_get(x) if /\A[A-Z][A-Z0-9]+\z/ =~ x.to_s
|
442
|
+
end
|
443
|
+
if x = const_get(:Default) then
|
444
|
+
hash.default = x
|
445
|
+
end
|
446
|
+
hash
|
447
|
+
end
|
448
|
+
|
449
|
+
# same as Struct#inspect.
|
450
|
+
#
|
451
|
+
# Note that <code>do_parse</code> is automatically called
|
452
|
+
# before <code>inspect</code>.
|
453
|
+
#
|
454
|
+
# (Warning: The do_parse might sweep hidden bugs in PDB classes.)
|
455
|
+
def inspect
|
456
|
+
do_parse
|
457
|
+
super
|
458
|
+
end
|
459
|
+
|
460
|
+
#--
|
461
|
+
#
|
462
|
+
# definitions
|
463
|
+
# contains all the rules for parsing each field
|
464
|
+
# based on format V 2.2, 16-DEC-1996
|
465
|
+
#
|
466
|
+
# http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html
|
467
|
+
# http://www.rcsb.org/pdb/docs/format/pdbguide2.2/Contents_Guide_21.html
|
468
|
+
#
|
469
|
+
# Details of following data are taken from these documents.
|
470
|
+
|
471
|
+
# [ 1..6, :Record_name, nil ],
|
472
|
+
|
473
|
+
# XXXXXX =
|
474
|
+
# new([ start, end, type of data, symbol to access ], ...)
|
475
|
+
#
|
476
|
+
#++
|
477
|
+
|
478
|
+
# HEADER record class
|
479
|
+
HEADER =
|
480
|
+
def_rec([ 11, 50, Pdb_String, :classification ], #Pdb_String(40)
|
481
|
+
[ 51, 59, Pdb_Date, :depDate ],
|
482
|
+
[ 63, 66, Pdb_IDcode, :idCode ]
|
483
|
+
)
|
484
|
+
|
485
|
+
# OBSLTE record class
|
486
|
+
OBSLTE =
|
487
|
+
def_rec([ 9, 10, Pdb_Continuation, nil ],
|
488
|
+
[ 12, 20, Pdb_Date, :repDate ],
|
489
|
+
[ 22, 25, Pdb_IDcode, :idCode ],
|
490
|
+
[ 32, 35, Pdb_IDcode, :rIdCode ],
|
491
|
+
[ 37, 40, Pdb_IDcode, :rIdCode ],
|
492
|
+
[ 42, 45, Pdb_IDcode, :rIdCode ],
|
493
|
+
[ 47, 50, Pdb_IDcode, :rIdCode ],
|
494
|
+
[ 52, 55, Pdb_IDcode, :rIdCode ],
|
495
|
+
[ 57, 60, Pdb_IDcode, :rIdCode ],
|
496
|
+
[ 62, 65, Pdb_IDcode, :rIdCode ],
|
497
|
+
[ 67, 70, Pdb_IDcode, :rIdCode ]
|
498
|
+
)
|
499
|
+
|
500
|
+
# TITLE record class
|
501
|
+
TITLE =
|
502
|
+
def_rec([ 9, 10, Pdb_Continuation, nil ],
|
503
|
+
[ 11, 70, Pdb_String, :title ]
|
504
|
+
)
|
505
|
+
|
506
|
+
# CAVEAT record class
|
507
|
+
CAVEAT =
|
508
|
+
def_rec([ 9, 10, Pdb_Continuation, nil ],
|
509
|
+
[ 12, 15, Pdb_IDcode, :idcode ],
|
510
|
+
[ 20, 70, Pdb_String, :comment ]
|
511
|
+
)
|
512
|
+
|
513
|
+
# COMPND record class
|
514
|
+
COMPND =
|
515
|
+
def_rec([ 9, 10, Pdb_Continuation, nil ],
|
516
|
+
[ 11, 70, Pdb_Specification_list, :compound ]
|
517
|
+
)
|
518
|
+
|
519
|
+
# SOURCE record class
|
520
|
+
SOURCE =
|
521
|
+
def_rec([ 9, 10, Pdb_Continuation, nil ],
|
522
|
+
[ 11, 70, Pdb_Specification_list, :srcName ]
|
523
|
+
)
|
524
|
+
|
525
|
+
# KEYWDS record class
|
526
|
+
KEYWDS =
|
527
|
+
def_rec([ 9, 10, Pdb_Continuation, nil ],
|
528
|
+
[ 11, 70, Pdb_List, :keywds ]
|
529
|
+
)
|
530
|
+
|
531
|
+
# EXPDTA record class
|
532
|
+
EXPDTA =
|
533
|
+
def_rec([ 9, 10, Pdb_Continuation, nil ],
|
534
|
+
[ 11, 70, Pdb_SList, :technique ]
|
535
|
+
)
|
536
|
+
|
537
|
+
# AUTHOR record class
|
538
|
+
AUTHOR =
|
539
|
+
def_rec([ 9, 10, Pdb_Continuation, nil ],
|
540
|
+
[ 11, 70, Pdb_List, :authorList ]
|
541
|
+
)
|
542
|
+
|
543
|
+
# REVDAT record class
|
544
|
+
REVDAT =
|
545
|
+
def_rec([ 8, 10, Pdb_Integer, :modNum ],
|
546
|
+
[ 11, 12, Pdb_Continuation, nil ],
|
547
|
+
[ 14, 22, Pdb_Date, :modDate ],
|
548
|
+
[ 24, 28, Pdb_String, :modId ], # Pdb_String(5)
|
549
|
+
[ 32, 32, Pdb_Integer, :modType ],
|
550
|
+
[ 40, 45, Pdb_LString(6), :record ],
|
551
|
+
[ 47, 52, Pdb_LString(6), :record ],
|
552
|
+
[ 54, 59, Pdb_LString(6), :record ],
|
553
|
+
[ 61, 66, Pdb_LString(6), :record ]
|
554
|
+
)
|
555
|
+
|
556
|
+
# SPRSDE record class
|
557
|
+
SPRSDE =
|
558
|
+
def_rec([ 9, 10, Pdb_Continuation, nil ],
|
559
|
+
[ 12, 20, Pdb_Date, :sprsdeDate ],
|
560
|
+
[ 22, 25, Pdb_IDcode, :idCode ],
|
561
|
+
[ 32, 35, Pdb_IDcode, :sIdCode ],
|
562
|
+
[ 37, 40, Pdb_IDcode, :sIdCode ],
|
563
|
+
[ 42, 45, Pdb_IDcode, :sIdCode ],
|
564
|
+
[ 47, 50, Pdb_IDcode, :sIdCode ],
|
565
|
+
[ 52, 55, Pdb_IDcode, :sIdCode ],
|
566
|
+
[ 57, 60, Pdb_IDcode, :sIdCode ],
|
567
|
+
[ 62, 65, Pdb_IDcode, :sIdCode ],
|
568
|
+
[ 67, 70, Pdb_IDcode, :sIdCode ]
|
569
|
+
)
|
570
|
+
|
571
|
+
# 'JRNL' is defined below
|
572
|
+
JRNL = nil
|
573
|
+
|
574
|
+
# 'REMARK' is defined below
|
575
|
+
REMARK = nil
|
576
|
+
|
577
|
+
# DBREF record class
|
578
|
+
DBREF =
|
579
|
+
def_rec([ 8, 11, Pdb_IDcode, :idCode ],
|
580
|
+
[ 13, 13, Pdb_Character, :chainID ],
|
581
|
+
[ 15, 18, Pdb_Integer, :seqBegin ],
|
582
|
+
[ 19, 19, Pdb_AChar, :insertBegin ],
|
583
|
+
[ 21, 24, Pdb_Integer, :seqEnd ],
|
584
|
+
[ 25, 25, Pdb_AChar, :insertEnd ],
|
585
|
+
[ 27, 32, Pdb_String, :database ], #Pdb_LString
|
586
|
+
[ 34, 41, Pdb_String, :dbAccession ], #Pdb_LString
|
587
|
+
[ 43, 54, Pdb_String, :dbIdCode ], #Pdb_LString
|
588
|
+
[ 56, 60, Pdb_Integer, :dbseqBegin ],
|
589
|
+
[ 61, 61, Pdb_AChar, :idbnsBeg ],
|
590
|
+
[ 63, 67, Pdb_Integer, :dbseqEnd ],
|
591
|
+
[ 68, 68, Pdb_AChar, :dbinsEnd ]
|
592
|
+
)
|
593
|
+
|
594
|
+
# SEQADV record class
|
595
|
+
SEQADV =
|
596
|
+
def_rec([ 8, 11, Pdb_IDcode, :idCode ],
|
597
|
+
[ 13, 15, Pdb_Residue_name, :resName ],
|
598
|
+
[ 17, 17, Pdb_Character, :chainID ],
|
599
|
+
[ 19, 22, Pdb_Integer, :seqNum ],
|
600
|
+
[ 23, 23, Pdb_AChar, :iCode ],
|
601
|
+
[ 25, 28, Pdb_String, :database ], #Pdb_LString
|
602
|
+
[ 30, 38, Pdb_String, :dbIdCode ], #Pdb_LString
|
603
|
+
[ 40, 42, Pdb_Residue_name, :dbRes ],
|
604
|
+
[ 44, 48, Pdb_Integer, :dbSeq ],
|
605
|
+
[ 50, 70, Pdb_LString, :conflict ]
|
606
|
+
)
|
607
|
+
|
608
|
+
# SEQRES record class
|
609
|
+
SEQRES =
|
610
|
+
def_rec(#[ 9, 10, Pdb_Integer, :serNum ],
|
611
|
+
[ 9, 10, Pdb_Continuation, nil ],
|
612
|
+
[ 12, 12, Pdb_Character, :chainID ],
|
613
|
+
[ 14, 17, Pdb_Integer, :numRes ],
|
614
|
+
[ 20, 22, Pdb_Residue_name, :resName ],
|
615
|
+
[ 24, 26, Pdb_Residue_name, :resName ],
|
616
|
+
[ 28, 30, Pdb_Residue_name, :resName ],
|
617
|
+
[ 32, 34, Pdb_Residue_name, :resName ],
|
618
|
+
[ 36, 38, Pdb_Residue_name, :resName ],
|
619
|
+
[ 40, 42, Pdb_Residue_name, :resName ],
|
620
|
+
[ 44, 46, Pdb_Residue_name, :resName ],
|
621
|
+
[ 48, 50, Pdb_Residue_name, :resName ],
|
622
|
+
[ 52, 54, Pdb_Residue_name, :resName ],
|
623
|
+
[ 56, 58, Pdb_Residue_name, :resName ],
|
624
|
+
[ 60, 62, Pdb_Residue_name, :resName ],
|
625
|
+
[ 64, 66, Pdb_Residue_name, :resName ],
|
626
|
+
[ 68, 70, Pdb_Residue_name, :resName ]
|
627
|
+
)
|
628
|
+
|
629
|
+
# MODRS record class
|
630
|
+
MODRES =
|
631
|
+
def_rec([ 8, 11, Pdb_IDcode, :idCode ],
|
632
|
+
[ 13, 15, Pdb_Residue_name, :resName ],
|
633
|
+
[ 17, 17, Pdb_Character, :chainID ],
|
634
|
+
[ 19, 22, Pdb_Integer, :seqNum ],
|
635
|
+
[ 23, 23, Pdb_AChar, :iCode ],
|
636
|
+
[ 25, 27, Pdb_Residue_name, :stdRes ],
|
637
|
+
[ 30, 70, Pdb_String, :comment ]
|
638
|
+
)
|
639
|
+
|
640
|
+
# HET record class
|
641
|
+
HET =
|
642
|
+
def_rec([ 8, 10, Pdb_LString(3), :hetID ],
|
643
|
+
[ 13, 13, Pdb_Character, :ChainID ],
|
644
|
+
[ 14, 17, Pdb_Integer, :seqNum ],
|
645
|
+
[ 18, 18, Pdb_AChar, :iCode ],
|
646
|
+
[ 21, 25, Pdb_Integer, :numHetAtoms ],
|
647
|
+
[ 31, 70, Pdb_String, :text ]
|
648
|
+
)
|
649
|
+
|
650
|
+
# HETNAM record class
|
651
|
+
HETNAM =
|
652
|
+
def_rec([ 9, 10, Pdb_Continuation, nil ],
|
653
|
+
[ 12, 14, Pdb_LString(3), :hetID ],
|
654
|
+
[ 16, 70, Pdb_String, :text ]
|
655
|
+
)
|
656
|
+
|
657
|
+
# HETSYN record class
|
658
|
+
HETSYN =
|
659
|
+
def_rec([ 9, 10, Pdb_Continuation, nil ],
|
660
|
+
[ 12, 14, Pdb_LString(3), :hetID ],
|
661
|
+
[ 16, 70, Pdb_SList, :hetSynonyms ]
|
662
|
+
)
|
663
|
+
|
664
|
+
# FORMUL record class
|
665
|
+
FORMUL =
|
666
|
+
def_rec([ 9, 10, Pdb_Integer, :compNum ],
|
667
|
+
[ 13, 15, Pdb_LString(3), :hetID ],
|
668
|
+
[ 17, 18, Pdb_Integer, :continuation ],
|
669
|
+
[ 19, 19, Pdb_Character, :asterisk ],
|
670
|
+
[ 20, 70, Pdb_String, :text ]
|
671
|
+
)
|
672
|
+
|
673
|
+
# HELIX record class
|
674
|
+
HELIX =
|
675
|
+
def_rec([ 8, 10, Pdb_Integer, :serNum ],
|
676
|
+
#[ 12, 14, Pdb_LString(3), :helixID ],
|
677
|
+
[ 12, 14, Pdb_StringRJ, :helixID ],
|
678
|
+
[ 16, 18, Pdb_Residue_name, :initResName ],
|
679
|
+
[ 20, 20, Pdb_Character, :initChainID ],
|
680
|
+
[ 22, 25, Pdb_Integer, :initSeqNum ],
|
681
|
+
[ 26, 26, Pdb_AChar, :initICode ],
|
682
|
+
[ 28, 30, Pdb_Residue_name, :endResName ],
|
683
|
+
[ 32, 32, Pdb_Character, :endChainID ],
|
684
|
+
[ 34, 37, Pdb_Integer, :endSeqNum ],
|
685
|
+
[ 38, 38, Pdb_AChar, :endICode ],
|
686
|
+
[ 39, 40, Pdb_Integer, :helixClass ],
|
687
|
+
[ 41, 70, Pdb_String, :comment ],
|
688
|
+
[ 72, 76, Pdb_Integer, :length ]
|
689
|
+
)
|
690
|
+
|
691
|
+
# SHEET record class
|
692
|
+
SHEET =
|
693
|
+
def_rec([ 8, 10, Pdb_Integer, :strand ],
|
694
|
+
#[ 12, 14, Pdb_LString(3), :sheetID ],
|
695
|
+
[ 12, 14, Pdb_StringRJ, :sheetID ],
|
696
|
+
[ 15, 16, Pdb_Integer, :numStrands ],
|
697
|
+
[ 18, 20, Pdb_Residue_name, :initResName ],
|
698
|
+
[ 22, 22, Pdb_Character, :initChainID ],
|
699
|
+
[ 23, 26, Pdb_Integer, :initSeqNum ],
|
700
|
+
[ 27, 27, Pdb_AChar, :initICode ],
|
701
|
+
[ 29, 31, Pdb_Residue_name, :endResName ],
|
702
|
+
[ 33, 33, Pdb_Character, :endChainID ],
|
703
|
+
[ 34, 37, Pdb_Integer, :endSeqNum ],
|
704
|
+
[ 38, 38, Pdb_AChar, :endICode ],
|
705
|
+
[ 39, 40, Pdb_Integer, :sense ],
|
706
|
+
[ 42, 45, Pdb_Atom, :curAtom ],
|
707
|
+
[ 46, 48, Pdb_Residue_name, :curResName ],
|
708
|
+
[ 50, 50, Pdb_Character, :curChainId ],
|
709
|
+
[ 51, 54, Pdb_Integer, :curResSeq ],
|
710
|
+
[ 55, 55, Pdb_AChar, :curICode ],
|
711
|
+
[ 57, 60, Pdb_Atom, :prevAtom ],
|
712
|
+
[ 61, 63, Pdb_Residue_name, :prevResName ],
|
713
|
+
[ 65, 65, Pdb_Character, :prevChainId ],
|
714
|
+
[ 66, 69, Pdb_Integer, :prevResSeq ],
|
715
|
+
[ 70, 70, Pdb_AChar, :prevICode ]
|
716
|
+
)
|
717
|
+
|
718
|
+
# TURN record class
|
719
|
+
TURN =
|
720
|
+
def_rec([ 8, 10, Pdb_Integer, :seq ],
|
721
|
+
#[ 12, 14, Pdb_LString(3), :turnId ],
|
722
|
+
[ 12, 14, Pdb_StringRJ, :turnId ],
|
723
|
+
[ 16, 18, Pdb_Residue_name, :initResName ],
|
724
|
+
[ 20, 20, Pdb_Character, :initChainId ],
|
725
|
+
[ 21, 24, Pdb_Integer, :initSeqNum ],
|
726
|
+
[ 25, 25, Pdb_AChar, :initICode ],
|
727
|
+
[ 27, 29, Pdb_Residue_name, :endResName ],
|
728
|
+
[ 31, 31, Pdb_Character, :endChainId ],
|
729
|
+
[ 32, 35, Pdb_Integer, :endSeqNum ],
|
730
|
+
[ 36, 36, Pdb_AChar, :endICode ],
|
731
|
+
[ 41, 70, Pdb_String, :comment ]
|
732
|
+
)
|
733
|
+
|
734
|
+
# SSBOND record class
|
735
|
+
SSBOND =
|
736
|
+
def_rec([ 8, 10, Pdb_Integer, :serNum ],
|
737
|
+
[ 12, 14, Pdb_LString(3), :pep1 ], # "CYS"
|
738
|
+
[ 16, 16, Pdb_Character, :chainID1 ],
|
739
|
+
[ 18, 21, Pdb_Integer, :seqNum1 ],
|
740
|
+
[ 22, 22, Pdb_AChar, :icode1 ],
|
741
|
+
[ 26, 28, Pdb_LString(3), :pep2 ], # "CYS"
|
742
|
+
[ 30, 30, Pdb_Character, :chainID2 ],
|
743
|
+
[ 32, 35, Pdb_Integer, :seqNum2 ],
|
744
|
+
[ 36, 36, Pdb_AChar, :icode2 ],
|
745
|
+
[ 60, 65, Pdb_SymOP, :sym1 ],
|
746
|
+
[ 67, 72, Pdb_SymOP, :sym2 ]
|
747
|
+
)
|
748
|
+
|
749
|
+
# LINK record class
|
750
|
+
LINK =
|
751
|
+
def_rec([ 13, 16, Pdb_Atom, :name1 ],
|
752
|
+
[ 17, 17, Pdb_Character, :altLoc1 ],
|
753
|
+
[ 18, 20, Pdb_Residue_name, :resName1 ],
|
754
|
+
[ 22, 22, Pdb_Character, :chainID1 ],
|
755
|
+
[ 23, 26, Pdb_Integer, :resSeq1 ],
|
756
|
+
[ 27, 27, Pdb_AChar, :iCode1 ],
|
757
|
+
[ 43, 46, Pdb_Atom, :name2 ],
|
758
|
+
[ 47, 47, Pdb_Character, :altLoc2 ],
|
759
|
+
[ 48, 50, Pdb_Residue_name, :resName2 ],
|
760
|
+
[ 52, 52, Pdb_Character, :chainID2 ],
|
761
|
+
[ 53, 56, Pdb_Integer, :resSeq2 ],
|
762
|
+
[ 57, 57, Pdb_AChar, :iCode2 ],
|
763
|
+
[ 60, 65, Pdb_SymOP, :sym1 ],
|
764
|
+
[ 67, 72, Pdb_SymOP, :sym2 ]
|
765
|
+
)
|
766
|
+
|
767
|
+
# HYDBND record class
|
768
|
+
HYDBND =
|
769
|
+
def_rec([ 13, 16, Pdb_Atom, :name1 ],
|
770
|
+
[ 17, 17, Pdb_Character, :altLoc1 ],
|
771
|
+
[ 18, 20, Pdb_Residue_name, :resName1 ],
|
772
|
+
[ 22, 22, Pdb_Character, :Chain1 ],
|
773
|
+
[ 23, 27, Pdb_Integer, :resSeq1 ],
|
774
|
+
[ 28, 28, Pdb_AChar, :ICode1 ],
|
775
|
+
[ 30, 33, Pdb_Atom, :nameH ],
|
776
|
+
[ 34, 34, Pdb_Character, :altLocH ],
|
777
|
+
[ 36, 36, Pdb_Character, :ChainH ],
|
778
|
+
[ 37, 41, Pdb_Integer, :resSeqH ],
|
779
|
+
[ 42, 42, Pdb_AChar, :iCodeH ],
|
780
|
+
[ 44, 47, Pdb_Atom, :name2 ],
|
781
|
+
[ 48, 48, Pdb_Character, :altLoc2 ],
|
782
|
+
[ 49, 51, Pdb_Residue_name, :resName2 ],
|
783
|
+
[ 53, 53, Pdb_Character, :chainID2 ],
|
784
|
+
[ 54, 58, Pdb_Integer, :resSeq2 ],
|
785
|
+
[ 59, 59, Pdb_AChar, :iCode2 ],
|
786
|
+
[ 60, 65, Pdb_SymOP, :sym1 ],
|
787
|
+
[ 67, 72, Pdb_SymOP, :sym2 ]
|
788
|
+
)
|
789
|
+
|
790
|
+
# SLTBRG record class
|
791
|
+
SLTBRG =
|
792
|
+
def_rec([ 13, 16, Pdb_Atom, :atom1 ],
|
793
|
+
[ 17, 17, Pdb_Character, :altLoc1 ],
|
794
|
+
[ 18, 20, Pdb_Residue_name, :resName1 ],
|
795
|
+
[ 22, 22, Pdb_Character, :chainID1 ],
|
796
|
+
[ 23, 26, Pdb_Integer, :resSeq1 ],
|
797
|
+
[ 27, 27, Pdb_AChar, :iCode1 ],
|
798
|
+
[ 43, 46, Pdb_Atom, :atom2 ],
|
799
|
+
[ 47, 47, Pdb_Character, :altLoc2 ],
|
800
|
+
[ 48, 50, Pdb_Residue_name, :resName2 ],
|
801
|
+
[ 52, 52, Pdb_Character, :chainID2 ],
|
802
|
+
[ 53, 56, Pdb_Integer, :resSeq2 ],
|
803
|
+
[ 57, 57, Pdb_AChar, :iCode2 ],
|
804
|
+
[ 60, 65, Pdb_SymOP, :sym1 ],
|
805
|
+
[ 67, 72, Pdb_SymOP, :sym2 ]
|
806
|
+
)
|
807
|
+
|
808
|
+
# CISPEP record class
|
809
|
+
CISPEP =
|
810
|
+
def_rec([ 8, 10, Pdb_Integer, :serNum ],
|
811
|
+
[ 12, 14, Pdb_LString(3), :pep1 ],
|
812
|
+
[ 16, 16, Pdb_Character, :chainID1 ],
|
813
|
+
[ 18, 21, Pdb_Integer, :seqNum1 ],
|
814
|
+
[ 22, 22, Pdb_AChar, :icode1 ],
|
815
|
+
[ 26, 28, Pdb_LString(3), :pep2 ],
|
816
|
+
[ 30, 30, Pdb_Character, :chainID2 ],
|
817
|
+
[ 32, 35, Pdb_Integer, :seqNum2 ],
|
818
|
+
[ 36, 36, Pdb_AChar, :icode2 ],
|
819
|
+
[ 44, 46, Pdb_Integer, :modNum ],
|
820
|
+
[ 54, 59, Pdb_Real('6.2'), :measure ]
|
821
|
+
)
|
822
|
+
|
823
|
+
# SITE record class
|
824
|
+
SITE =
|
825
|
+
def_rec([ 8, 10, Pdb_Integer, :seqNum ],
|
826
|
+
[ 12, 14, Pdb_LString(3), :siteID ],
|
827
|
+
[ 16, 17, Pdb_Integer, :numRes ],
|
828
|
+
[ 19, 21, Pdb_Residue_name, :resName1 ],
|
829
|
+
[ 23, 23, Pdb_Character, :chainID1 ],
|
830
|
+
[ 24, 27, Pdb_Integer, :seq1 ],
|
831
|
+
[ 28, 28, Pdb_AChar, :iCode1 ],
|
832
|
+
[ 30, 32, Pdb_Residue_name, :resName2 ],
|
833
|
+
[ 34, 34, Pdb_Character, :chainID2 ],
|
834
|
+
[ 35, 38, Pdb_Integer, :seq2 ],
|
835
|
+
[ 39, 39, Pdb_AChar, :iCode2 ],
|
836
|
+
[ 41, 43, Pdb_Residue_name, :resName3 ],
|
837
|
+
[ 45, 45, Pdb_Character, :chainID3 ],
|
838
|
+
[ 46, 49, Pdb_Integer, :seq3 ],
|
839
|
+
[ 50, 50, Pdb_AChar, :iCode3 ],
|
840
|
+
[ 52, 54, Pdb_Residue_name, :resName4 ],
|
841
|
+
[ 56, 56, Pdb_Character, :chainID4 ],
|
842
|
+
[ 57, 60, Pdb_Integer, :seq4 ],
|
843
|
+
[ 61, 61, Pdb_AChar, :iCode4 ]
|
844
|
+
)
|
845
|
+
|
846
|
+
# CRYST1 record class
|
847
|
+
CRYST1 =
|
848
|
+
def_rec([ 7, 15, Pdb_Real('9.3'), :a ],
|
849
|
+
[ 16, 24, Pdb_Real('9.3'), :b ],
|
850
|
+
[ 25, 33, Pdb_Real('9.3'), :c ],
|
851
|
+
[ 34, 40, Pdb_Real('7.2'), :alpha ],
|
852
|
+
[ 41, 47, Pdb_Real('7.2'), :beta ],
|
853
|
+
[ 48, 54, Pdb_Real('7.2'), :gamma ],
|
854
|
+
[ 56, 66, Pdb_LString, :sGroup ],
|
855
|
+
[ 67, 70, Pdb_Integer, :z ]
|
856
|
+
)
|
857
|
+
|
858
|
+
# ORIGX1 record class
|
859
|
+
#
|
860
|
+
# ORIGXn n=1, 2, or 3
|
861
|
+
ORIGX1 =
|
862
|
+
def_rec([ 11, 20, Pdb_Real('10.6'), :On1 ],
|
863
|
+
[ 21, 30, Pdb_Real('10.6'), :On2 ],
|
864
|
+
[ 31, 40, Pdb_Real('10.6'), :On3 ],
|
865
|
+
[ 46, 55, Pdb_Real('10.5'), :Tn ]
|
866
|
+
)
|
867
|
+
|
868
|
+
# ORIGX2 record class
|
869
|
+
ORIGX2 = new_inherit(ORIGX1)
|
870
|
+
# ORIGX3 record class
|
871
|
+
ORIGX3 = new_inherit(ORIGX1)
|
872
|
+
|
873
|
+
# SCALE1 record class
|
874
|
+
#
|
875
|
+
# SCALEn n=1, 2, or 3
|
876
|
+
SCALE1 =
|
877
|
+
def_rec([ 11, 20, Pdb_Real('10.6'), :Sn1 ],
|
878
|
+
[ 21, 30, Pdb_Real('10.6'), :Sn2 ],
|
879
|
+
[ 31, 40, Pdb_Real('10.6'), :Sn3 ],
|
880
|
+
[ 46, 55, Pdb_Real('10.5'), :Un ]
|
881
|
+
)
|
882
|
+
|
883
|
+
# SCALE2 record class
|
884
|
+
SCALE2 = new_inherit(SCALE1)
|
885
|
+
# SCALE3 record class
|
886
|
+
SCALE3 = new_inherit(SCALE1)
|
887
|
+
|
888
|
+
# MTRIX1 record class
|
889
|
+
#
|
890
|
+
# MTRIXn n=1,2, or 3
|
891
|
+
MTRIX1 =
|
892
|
+
def_rec([ 8, 10, Pdb_Integer, :serial ],
|
893
|
+
[ 11, 20, Pdb_Real('10.6'), :Mn1 ],
|
894
|
+
[ 21, 30, Pdb_Real('10.6'), :Mn2 ],
|
895
|
+
[ 31, 40, Pdb_Real('10.6'), :Mn3 ],
|
896
|
+
[ 46, 55, Pdb_Real('10.5'), :Vn ],
|
897
|
+
[ 60, 60, Pdb_Integer, :iGiven ]
|
898
|
+
)
|
899
|
+
|
900
|
+
# MTRIX2 record class
|
901
|
+
MTRIX2 = new_inherit(MTRIX1)
|
902
|
+
# MTRIX3 record class
|
903
|
+
MTRIX3 = new_inherit(MTRIX1)
|
904
|
+
|
905
|
+
# TVECT record class
|
906
|
+
TVECT =
|
907
|
+
def_rec([ 8, 10, Pdb_Integer, :serial ],
|
908
|
+
[ 11, 20, Pdb_Real('10.5'), :t1 ],
|
909
|
+
[ 21, 30, Pdb_Real('10.5'), :t2 ],
|
910
|
+
[ 31, 40, Pdb_Real('10.5'), :t3 ],
|
911
|
+
[ 41, 70, Pdb_String, :text ]
|
912
|
+
)
|
913
|
+
|
914
|
+
# MODEL record class
|
915
|
+
MODEL =
|
916
|
+
def_rec([ 11, 14, Pdb_Integer, :serial ]
|
917
|
+
)
|
918
|
+
# ChangeLog: model_serial are changed to serial
|
919
|
+
|
920
|
+
# ATOM record class
|
921
|
+
ATOM =
|
922
|
+
new_direct([ 7, 11, Pdb_Integer, :serial ],
|
923
|
+
[ 13, 16, Pdb_Atom, :name ],
|
924
|
+
[ 17, 17, Pdb_Character, :altLoc ],
|
925
|
+
[ 18, 20, Pdb_Residue_name, :resName ],
|
926
|
+
[ 22, 22, Pdb_Character, :chainID ],
|
927
|
+
[ 23, 26, Pdb_Integer, :resSeq ],
|
928
|
+
[ 27, 27, Pdb_AChar, :iCode ],
|
929
|
+
[ 31, 38, Pdb_Real('8.3'), :x ],
|
930
|
+
[ 39, 46, Pdb_Real('8.3'), :y ],
|
931
|
+
[ 47, 54, Pdb_Real('8.3'), :z ],
|
932
|
+
[ 55, 60, Pdb_Real('6.2'), :occupancy ],
|
933
|
+
[ 61, 66, Pdb_Real('6.2'), :tempFactor ],
|
934
|
+
[ 73, 76, Pdb_LString(4), :segID ],
|
935
|
+
[ 77, 78, Pdb_LString(2), :element ],
|
936
|
+
[ 79, 80, Pdb_LString(2), :charge ]
|
937
|
+
)
|
938
|
+
|
939
|
+
# ATOM record class
|
940
|
+
class ATOM
|
941
|
+
|
942
|
+
include Utils
|
943
|
+
include Comparable
|
944
|
+
|
945
|
+
# for backward compatibility
|
946
|
+
alias occ occupancy
|
947
|
+
# for backward compatibility
|
948
|
+
alias bfac tempFactor
|
949
|
+
|
950
|
+
# residue the atom belongs to.
|
951
|
+
attr_accessor :residue
|
952
|
+
|
953
|
+
# SIGATM record
|
954
|
+
attr_accessor :sigatm
|
955
|
+
|
956
|
+
# ANISOU record
|
957
|
+
attr_accessor :anisou
|
958
|
+
|
959
|
+
# TER record
|
960
|
+
attr_accessor :ter
|
961
|
+
|
962
|
+
#Returns a Coordinate class instance of the xyz positions
|
963
|
+
def xyz
|
964
|
+
Coordinate[ x, y, z ]
|
965
|
+
end
|
966
|
+
|
967
|
+
#Returns an array of the xyz positions
|
968
|
+
def to_a
|
969
|
+
[ x, y, z ]
|
970
|
+
end
|
971
|
+
|
972
|
+
#Sorts based on serial numbers
|
973
|
+
def <=>(other)
|
974
|
+
return serial <=> other.serial
|
975
|
+
end
|
976
|
+
|
977
|
+
def do_parse
|
978
|
+
return self if @parsed or !@str
|
979
|
+
self.serial = @str[6..10].to_i
|
980
|
+
self.name = @str[12..15].strip
|
981
|
+
self.altLoc = @str[16..16]
|
982
|
+
self.resName = @str[17..19].strip
|
983
|
+
self.chainID = @str[21..21]
|
984
|
+
self.resSeq = @str[22..25].to_i
|
985
|
+
self.iCode = @str[26..26].strip
|
986
|
+
self.x = @str[30..37].to_f
|
987
|
+
self.y = @str[38..45].to_f
|
988
|
+
self.z = @str[46..53].to_f
|
989
|
+
self.occupancy = @str[54..59].to_f
|
990
|
+
self.tempFactor = @str[60..65].to_f
|
991
|
+
self.segID = @str[72..75].to_s.rstrip
|
992
|
+
self.element = @str[76..77].to_s.lstrip
|
993
|
+
self.charge = @str[78..79].to_s.strip
|
994
|
+
@parsed = true
|
995
|
+
self
|
996
|
+
end
|
997
|
+
|
998
|
+
def justify_atomname
|
999
|
+
atomname = self.name.to_s
|
1000
|
+
return atomname[0, 4] if atomname.length >= 4
|
1001
|
+
case atomname.length
|
1002
|
+
when 0
|
1003
|
+
return ' '
|
1004
|
+
when 1
|
1005
|
+
return ' ' + atomname + ' '
|
1006
|
+
when 2
|
1007
|
+
if /\A[0-9]/ =~ atomname then
|
1008
|
+
return sprintf('%-4s', atomname)
|
1009
|
+
elsif /[0-9]\z/ =~ atomname then
|
1010
|
+
return sprintf(' %-3s', atomname)
|
1011
|
+
end
|
1012
|
+
when 3
|
1013
|
+
if /\A[0-9]/ =~ atomname then
|
1014
|
+
return sprintf('%-4s', atomname)
|
1015
|
+
end
|
1016
|
+
end
|
1017
|
+
# ambiguous case for two- or three-letter name
|
1018
|
+
elem = self.element.to_s.strip
|
1019
|
+
if elem.size > 0 and i = atomname.index(elem) then
|
1020
|
+
if i == 0 and elem.size == 1 then
|
1021
|
+
return sprintf(' %-3s', atomname)
|
1022
|
+
else
|
1023
|
+
return sprintf('%-4s', atomname)
|
1024
|
+
end
|
1025
|
+
end
|
1026
|
+
if self.kind_of?(HETATM) then
|
1027
|
+
if /\A(B[^AEHIKR]|C[^ADEFLMORSU]|F[^EMR]|H[^EFGOS]|I[^NR]|K[^R]|N[^ABDEIOP]|O[^S]|P[^ABDMORTU]|S[^BCEGIMNR]|V|W|Y[^B])/ =~
|
1028
|
+
atomname then
|
1029
|
+
return sprintf(' %-3s', atomname)
|
1030
|
+
else
|
1031
|
+
return sprintf('%-4s', atomname)
|
1032
|
+
end
|
1033
|
+
else # ATOM
|
1034
|
+
if /\A[CHONSP]/ =~ atomname then
|
1035
|
+
return sprintf(' %-3s', atomname)
|
1036
|
+
else
|
1037
|
+
return sprintf('%-4s', atomname)
|
1038
|
+
end
|
1039
|
+
end
|
1040
|
+
# could not be reached here
|
1041
|
+
raise 'bug!'
|
1042
|
+
end
|
1043
|
+
private :justify_atomname
|
1044
|
+
|
1045
|
+
def to_s
|
1046
|
+
atomname = justify_atomname
|
1047
|
+
sprintf("%-6s%5d %-4s%-1s%3s %-1s%4d%-1s %8.3f%8.3f%8.3f%6.2f%6.2f %-4s%2s%-2s\n",
|
1048
|
+
self.record_name,
|
1049
|
+
self.serial,
|
1050
|
+
atomname,
|
1051
|
+
self.altLoc,
|
1052
|
+
self.resName,
|
1053
|
+
self.chainID,
|
1054
|
+
self.resSeq,
|
1055
|
+
self.iCode,
|
1056
|
+
self.x, self.y, self.z,
|
1057
|
+
self.occupancy,
|
1058
|
+
self.tempFactor,
|
1059
|
+
self.segID,
|
1060
|
+
self.element,
|
1061
|
+
self.charge)
|
1062
|
+
end
|
1063
|
+
end #class ATOM
|
1064
|
+
|
1065
|
+
# SIGATM record class
|
1066
|
+
SIGATM =
|
1067
|
+
def_rec([ 7, 11, Pdb_Integer, :serial ],
|
1068
|
+
[ 13, 16, Pdb_Atom, :name ],
|
1069
|
+
[ 17, 17, Pdb_Character, :altLoc ],
|
1070
|
+
[ 18, 20, Pdb_Residue_name, :resName ],
|
1071
|
+
[ 22, 22, Pdb_Character, :chainID ],
|
1072
|
+
[ 23, 26, Pdb_Integer, :resSeq ],
|
1073
|
+
[ 27, 27, Pdb_AChar, :iCode ],
|
1074
|
+
[ 31, 38, Pdb_Real('8.3'), :sigX ],
|
1075
|
+
[ 39, 46, Pdb_Real('8.3'), :sigY ],
|
1076
|
+
[ 47, 54, Pdb_Real('8.3'), :sigZ ],
|
1077
|
+
[ 55, 60, Pdb_Real('6.2'), :sigOcc ],
|
1078
|
+
[ 61, 66, Pdb_Real('6.2'), :sigTemp ],
|
1079
|
+
[ 73, 76, Pdb_LString(4), :segID ],
|
1080
|
+
[ 77, 78, Pdb_LString(2), :element ],
|
1081
|
+
[ 79, 80, Pdb_LString(2), :charge ]
|
1082
|
+
)
|
1083
|
+
|
1084
|
+
# ANISOU record class
|
1085
|
+
ANISOU =
|
1086
|
+
def_rec([ 7, 11, Pdb_Integer, :serial ],
|
1087
|
+
[ 13, 16, Pdb_Atom, :name ],
|
1088
|
+
[ 17, 17, Pdb_Character, :altLoc ],
|
1089
|
+
[ 18, 20, Pdb_Residue_name, :resName ],
|
1090
|
+
[ 22, 22, Pdb_Character, :chainID ],
|
1091
|
+
[ 23, 26, Pdb_Integer, :resSeq ],
|
1092
|
+
[ 27, 27, Pdb_AChar, :iCode ],
|
1093
|
+
[ 29, 35, Pdb_Integer, :U11 ],
|
1094
|
+
[ 36, 42, Pdb_Integer, :U22 ],
|
1095
|
+
[ 43, 49, Pdb_Integer, :U33 ],
|
1096
|
+
[ 50, 56, Pdb_Integer, :U12 ],
|
1097
|
+
[ 57, 63, Pdb_Integer, :U13 ],
|
1098
|
+
[ 64, 70, Pdb_Integer, :U23 ],
|
1099
|
+
[ 73, 76, Pdb_LString(4), :segID ],
|
1100
|
+
[ 77, 78, Pdb_LString(2), :element ],
|
1101
|
+
[ 79, 80, Pdb_LString(2), :charge ]
|
1102
|
+
)
|
1103
|
+
|
1104
|
+
# ANISOU record class
|
1105
|
+
class ANISOU
|
1106
|
+
# SIGUIJ record
|
1107
|
+
attr_accessor :siguij
|
1108
|
+
end #class ANISOU
|
1109
|
+
|
1110
|
+
# SIGUIJ record class
|
1111
|
+
SIGUIJ =
|
1112
|
+
def_rec([ 7, 11, Pdb_Integer, :serial ],
|
1113
|
+
[ 13, 16, Pdb_Atom, :name ],
|
1114
|
+
[ 17, 17, Pdb_Character, :altLoc ],
|
1115
|
+
[ 18, 20, Pdb_Residue_name, :resName ],
|
1116
|
+
[ 22, 22, Pdb_Character, :chainID ],
|
1117
|
+
[ 23, 26, Pdb_Integer, :resSeq ],
|
1118
|
+
[ 27, 27, Pdb_AChar, :iCode ],
|
1119
|
+
[ 29, 35, Pdb_Integer, :SigmaU11 ],
|
1120
|
+
[ 36, 42, Pdb_Integer, :SigmaU22 ],
|
1121
|
+
[ 43, 49, Pdb_Integer, :SigmaU33 ],
|
1122
|
+
[ 50, 56, Pdb_Integer, :SigmaU12 ],
|
1123
|
+
[ 57, 63, Pdb_Integer, :SigmaU13 ],
|
1124
|
+
[ 64, 70, Pdb_Integer, :SigmaU23 ],
|
1125
|
+
[ 73, 76, Pdb_LString(4), :segID ],
|
1126
|
+
[ 77, 78, Pdb_LString(2), :element ],
|
1127
|
+
[ 79, 80, Pdb_LString(2), :charge ]
|
1128
|
+
)
|
1129
|
+
|
1130
|
+
# TER record class
|
1131
|
+
TER =
|
1132
|
+
def_rec([ 7, 11, Pdb_Integer, :serial ],
|
1133
|
+
[ 18, 20, Pdb_Residue_name, :resName ],
|
1134
|
+
[ 22, 22, Pdb_Character, :chainID ],
|
1135
|
+
[ 23, 26, Pdb_Integer, :resSeq ],
|
1136
|
+
[ 27, 27, Pdb_AChar, :iCode ]
|
1137
|
+
)
|
1138
|
+
|
1139
|
+
#HETATM =
|
1140
|
+
# new_direct([ 7, 11, Pdb_Integer, :serial ],
|
1141
|
+
# [ 13, 16, Pdb_Atom, :name ],
|
1142
|
+
# [ 17, 17, Pdb_Character, :altLoc ],
|
1143
|
+
# [ 18, 20, Pdb_Residue_name, :resName ],
|
1144
|
+
# [ 22, 22, Pdb_Character, :chainID ],
|
1145
|
+
# [ 23, 26, Pdb_Integer, :resSeq ],
|
1146
|
+
# [ 27, 27, Pdb_AChar, :iCode ],
|
1147
|
+
# [ 31, 38, Pdb_Real('8.3'), :x ],
|
1148
|
+
# [ 39, 46, Pdb_Real('8.3'), :y ],
|
1149
|
+
# [ 47, 54, Pdb_Real('8.3'), :z ],
|
1150
|
+
# [ 55, 60, Pdb_Real('6.2'), :occupancy ],
|
1151
|
+
# [ 61, 66, Pdb_Real('6.2'), :tempFactor ],
|
1152
|
+
# [ 73, 76, Pdb_LString(4), :segID ],
|
1153
|
+
# [ 77, 78, Pdb_LString(2), :element ],
|
1154
|
+
# [ 79, 80, Pdb_LString(2), :charge ]
|
1155
|
+
# )
|
1156
|
+
|
1157
|
+
# HETATM record class
|
1158
|
+
HETATM = new_inherit(ATOM)
|
1159
|
+
|
1160
|
+
# HETATM record class.
|
1161
|
+
# It inherits ATOM class.
|
1162
|
+
class HETATM; end
|
1163
|
+
|
1164
|
+
# ENDMDL record class
|
1165
|
+
ENDMDL =
|
1166
|
+
def_rec([ 2, 1, Pdb_Integer, :serial ] # dummy field (always 0)
|
1167
|
+
)
|
1168
|
+
|
1169
|
+
# CONECT record class
|
1170
|
+
CONECT =
|
1171
|
+
def_rec([ 7, 11, Pdb_Integer, :serial ],
|
1172
|
+
[ 12, 16, Pdb_Integer, :serial ],
|
1173
|
+
[ 17, 21, Pdb_Integer, :serial ],
|
1174
|
+
[ 22, 26, Pdb_Integer, :serial ],
|
1175
|
+
[ 27, 31, Pdb_Integer, :serial ],
|
1176
|
+
[ 32, 36, Pdb_Integer, :serial ],
|
1177
|
+
[ 37, 41, Pdb_Integer, :serial ],
|
1178
|
+
[ 42, 46, Pdb_Integer, :serial ],
|
1179
|
+
[ 47, 51, Pdb_Integer, :serial ],
|
1180
|
+
[ 52, 56, Pdb_Integer, :serial ],
|
1181
|
+
[ 57, 61, Pdb_Integer, :serial ]
|
1182
|
+
)
|
1183
|
+
|
1184
|
+
# MASTER record class
|
1185
|
+
MASTER =
|
1186
|
+
def_rec([ 11, 15, Pdb_Integer, :numRemark ],
|
1187
|
+
[ 16, 20, Pdb_Integer, "0" ],
|
1188
|
+
[ 21, 25, Pdb_Integer, :numHet ],
|
1189
|
+
[ 26, 30, Pdb_Integer, :numHelix ],
|
1190
|
+
[ 31, 35, Pdb_Integer, :numSheet ],
|
1191
|
+
[ 36, 40, Pdb_Integer, :numTurn ],
|
1192
|
+
[ 41, 45, Pdb_Integer, :numSite ],
|
1193
|
+
[ 46, 50, Pdb_Integer, :numXform ],
|
1194
|
+
[ 51, 55, Pdb_Integer, :numCoord ],
|
1195
|
+
[ 56, 60, Pdb_Integer, :numTer ],
|
1196
|
+
[ 61, 65, Pdb_Integer, :numConect ],
|
1197
|
+
[ 66, 70, Pdb_Integer, :numSeq ]
|
1198
|
+
)
|
1199
|
+
|
1200
|
+
# JRNL record classes
|
1201
|
+
class Jrnl < self
|
1202
|
+
# subrecord of JRNL
|
1203
|
+
# 13, 16
|
1204
|
+
# JRNL AUTH record class
|
1205
|
+
AUTH =
|
1206
|
+
def_rec([ 13, 16, Pdb_String, :sub_record ], # "AUTH"
|
1207
|
+
[ 17, 18, Pdb_Continuation, nil ],
|
1208
|
+
[ 20, 70, Pdb_List, :authorList ]
|
1209
|
+
)
|
1210
|
+
|
1211
|
+
# JRNL TITL record class
|
1212
|
+
TITL =
|
1213
|
+
def_rec([ 13, 16, Pdb_String, :sub_record ], # "TITL"
|
1214
|
+
[ 17, 18, Pdb_Continuation, nil ],
|
1215
|
+
[ 20, 70, Pdb_LString, :title ]
|
1216
|
+
)
|
1217
|
+
|
1218
|
+
# JRNL EDIT record class
|
1219
|
+
EDIT =
|
1220
|
+
def_rec([ 13, 16, Pdb_String, :sub_record ], # "EDIT"
|
1221
|
+
[ 17, 18, Pdb_Continuation, nil ],
|
1222
|
+
[ 20, 70, Pdb_List, :editorList ]
|
1223
|
+
)
|
1224
|
+
|
1225
|
+
# JRNL REF record class
|
1226
|
+
REF =
|
1227
|
+
def_rec([ 13, 16, Pdb_String, :sub_record ], # "REF"
|
1228
|
+
[ 17, 18, Pdb_Continuation, nil ],
|
1229
|
+
[ 20, 47, Pdb_LString, :pubName ],
|
1230
|
+
[ 50, 51, Pdb_LString(2), "V." ],
|
1231
|
+
[ 52, 55, Pdb_String, :volume ],
|
1232
|
+
[ 57, 61, Pdb_String, :page ],
|
1233
|
+
[ 63, 66, Pdb_Integer, :year ]
|
1234
|
+
)
|
1235
|
+
|
1236
|
+
# JRNL PUBL record class
|
1237
|
+
PUBL =
|
1238
|
+
def_rec([ 13, 16, Pdb_String, :sub_record ], # "PUBL"
|
1239
|
+
[ 17, 18, Pdb_Continuation, nil ],
|
1240
|
+
[ 20, 70, Pdb_LString, :pub ]
|
1241
|
+
)
|
1242
|
+
|
1243
|
+
# JRNL REFN record class
|
1244
|
+
REFN =
|
1245
|
+
def_rec([ 13, 16, Pdb_String, :sub_record ], # "REFN"
|
1246
|
+
[ 20, 23, Pdb_LString(4), "ASTM" ],
|
1247
|
+
[ 25, 30, Pdb_LString(6), :astm ],
|
1248
|
+
[ 33, 34, Pdb_LString(2), :country ],
|
1249
|
+
[ 36, 39, Pdb_LString(4), :BorS ], # "ISBN" or "ISSN"
|
1250
|
+
[ 41, 65, Pdb_LString, :isbn ],
|
1251
|
+
[ 67, 70, Pdb_LString(4), :coden ] # "0353" for unpublished
|
1252
|
+
)
|
1253
|
+
|
1254
|
+
# default or unknown record
|
1255
|
+
#
|
1256
|
+
Default =
|
1257
|
+
def_rec([ 13, 16, Pdb_String, :sub_record ]) # ""
|
1258
|
+
|
1259
|
+
# definitions (hash)
|
1260
|
+
Definition = create_definition_hash
|
1261
|
+
end #class JRNL
|
1262
|
+
|
1263
|
+
# REMARK record classes for REMARK 1
|
1264
|
+
class Remark1 < self
|
1265
|
+
# 13, 16
|
1266
|
+
# REMARK 1 REFERENCE record class
|
1267
|
+
EFER =
|
1268
|
+
def_rec([ 8, 10, Pdb_Integer, :remarkNum ], # "1"
|
1269
|
+
[ 12, 20, Pdb_String, :sub_record ], # "REFERENCE"
|
1270
|
+
[ 22, 70, Pdb_Integer, :refNum ]
|
1271
|
+
)
|
1272
|
+
|
1273
|
+
# REMARK 1 AUTH record class
|
1274
|
+
AUTH =
|
1275
|
+
def_rec([ 8, 10, Pdb_Integer, :remarkNum ], # "1"
|
1276
|
+
[ 13, 16, Pdb_String, :sub_record ], # "AUTH"
|
1277
|
+
[ 17, 18, Pdb_Continuation, nil ],
|
1278
|
+
[ 20, 70, Pdb_List, :authorList ]
|
1279
|
+
)
|
1280
|
+
|
1281
|
+
# REMARK 1 TITL record class
|
1282
|
+
TITL =
|
1283
|
+
def_rec([ 8, 10, Pdb_Integer, :remarkNum ], # "1"
|
1284
|
+
[ 13, 16, Pdb_String, :sub_record ], # "TITL"
|
1285
|
+
[ 17, 18, Pdb_Continuation, nil ],
|
1286
|
+
[ 20, 70, Pdb_LString, :title ]
|
1287
|
+
)
|
1288
|
+
|
1289
|
+
# REMARK 1 EDIT record class
|
1290
|
+
EDIT =
|
1291
|
+
def_rec([ 8, 10, Pdb_Integer, :remarkNum ], # "1"
|
1292
|
+
[ 13, 16, Pdb_String, :sub_record ], # "EDIT"
|
1293
|
+
[ 17, 18, Pdb_Continuation, nil ],
|
1294
|
+
[ 20, 70, Pdb_LString, :editorList ]
|
1295
|
+
)
|
1296
|
+
|
1297
|
+
# REMARK 1 REF record class
|
1298
|
+
REF =
|
1299
|
+
def_rec([ 8, 10, Pdb_Integer, :remarkNum ], # "1"
|
1300
|
+
[ 13, 16, Pdb_LString(3), :sub_record ], # "REF"
|
1301
|
+
[ 17, 18, Pdb_Continuation, nil ],
|
1302
|
+
[ 20, 47, Pdb_LString, :pubName ],
|
1303
|
+
[ 50, 51, Pdb_LString(2), "V." ],
|
1304
|
+
[ 52, 55, Pdb_String, :volume ],
|
1305
|
+
[ 57, 61, Pdb_String, :page ],
|
1306
|
+
[ 63, 66, Pdb_Integer, :year ]
|
1307
|
+
)
|
1308
|
+
|
1309
|
+
# REMARK 1 PUBL record class
|
1310
|
+
PUBL =
|
1311
|
+
def_rec([ 8, 10, Pdb_Integer, :remarkNum ], # "1"
|
1312
|
+
[ 13, 16, Pdb_String, :sub_record ], # "PUBL"
|
1313
|
+
[ 17, 18, Pdb_Continuation, nil ],
|
1314
|
+
[ 20, 70, Pdb_LString, :pub ]
|
1315
|
+
)
|
1316
|
+
|
1317
|
+
# REMARK 1 REFN record class
|
1318
|
+
REFN =
|
1319
|
+
def_rec([ 8, 10, Pdb_Integer, :remarkNum ], # "1"
|
1320
|
+
[ 13, 16, Pdb_String, :sub_record ], # "REFN"
|
1321
|
+
[ 20, 23, Pdb_LString(4), "ASTM" ],
|
1322
|
+
[ 25, 30, Pdb_LString, :astm ],
|
1323
|
+
[ 33, 34, Pdb_LString, :country ],
|
1324
|
+
[ 36, 39, Pdb_LString(4), :BorS ],
|
1325
|
+
[ 41, 65, Pdb_LString, :isbn ],
|
1326
|
+
[ 68, 70, Pdb_LString(4), :coden ]
|
1327
|
+
)
|
1328
|
+
|
1329
|
+
# default (or unknown) record class for REMARK 1
|
1330
|
+
Default =
|
1331
|
+
def_rec([ 8, 10, Pdb_Integer, :remarkNum ], # "1"
|
1332
|
+
[ 13, 16, Pdb_String, :sub_record ] # ""
|
1333
|
+
)
|
1334
|
+
|
1335
|
+
# definitions (hash)
|
1336
|
+
Definition = create_definition_hash
|
1337
|
+
end #class Remark1
|
1338
|
+
|
1339
|
+
# REMARK record classes for REMARK 2
|
1340
|
+
class Remark2 < self
|
1341
|
+
# 29, 38 == 'ANGSTROMS.'
|
1342
|
+
ANGSTROMS =
|
1343
|
+
def_rec([ 8, 10, Pdb_Integer, :remarkNum ], # "2"
|
1344
|
+
[ 12, 22, Pdb_LString(11), :sub_record ], # "RESOLUTION."
|
1345
|
+
[ 23, 27, Pdb_Real('5.2'), :resolution ],
|
1346
|
+
[ 29, 38, Pdb_LString(10), "ANGSTROMS." ]
|
1347
|
+
)
|
1348
|
+
|
1349
|
+
# 23, 38 == ' NOT APPLICABLE.'
|
1350
|
+
NOT_APPLICABLE =
|
1351
|
+
def_rec([ 8, 10, Pdb_Integer, :remarkNum ], # "2"
|
1352
|
+
[ 12, 22, Pdb_LString(11), :sub_record ], # "RESOLUTION."
|
1353
|
+
[ 23, 38, Pdb_LString(16), :resolution ], # " NOT APPLICABLE."
|
1354
|
+
[ 41, 70, Pdb_String, :comment ]
|
1355
|
+
)
|
1356
|
+
|
1357
|
+
# others
|
1358
|
+
Default =
|
1359
|
+
def_rec([ 8, 10, Pdb_Integer, :remarkNum ], # "2"
|
1360
|
+
[ 12, 22, Pdb_LString(11), :sub_record ], # "RESOLUTION."
|
1361
|
+
[ 24, 70, Pdb_String, :comment ]
|
1362
|
+
)
|
1363
|
+
end #class Remark2
|
1364
|
+
|
1365
|
+
# REMARK record class for REMARK n (n>=3)
|
1366
|
+
RemarkN =
|
1367
|
+
def_rec([ 8, 10, Pdb_Integer, :remarkNum ],
|
1368
|
+
[ 12, 70, Pdb_LString, :text ]
|
1369
|
+
)
|
1370
|
+
|
1371
|
+
# default (or unknown) record class
|
1372
|
+
Default = def_rec([ 8, 70, Pdb_LString, :text ])
|
1373
|
+
|
1374
|
+
# definitions (hash)
|
1375
|
+
Definition = create_definition_hash
|
1376
|
+
|
1377
|
+
# END record class.
|
1378
|
+
#
|
1379
|
+
# Because END is a reserved word of Ruby, it is separately
|
1380
|
+
# added to the hash
|
1381
|
+
End =
|
1382
|
+
def_rec([ 2, 1, Pdb_Integer, :serial ]) # dummy field (always 0)
|
1383
|
+
|
1384
|
+
Definition['END'.intern] = End
|
1385
|
+
|
1386
|
+
# Basically just look up the class in Definition hash
|
1387
|
+
# do some munging for JRNL and REMARK
|
1388
|
+
def self.get_record_class(str)
|
1389
|
+
t = fetch_record_name(str)
|
1390
|
+
t = t.intern unless t.empty?
|
1391
|
+
if d = Definition[t] then
|
1392
|
+
return d
|
1393
|
+
end
|
1394
|
+
case t
|
1395
|
+
when :JRNL
|
1396
|
+
ts = str[12..15].to_s.strip
|
1397
|
+
ts = ts.intern unless ts.empty?
|
1398
|
+
d = Jrnl::Definition[ts]
|
1399
|
+
when :REMARK
|
1400
|
+
case str[7..9].to_i
|
1401
|
+
when 1
|
1402
|
+
ts = str[12..15].to_s.strip
|
1403
|
+
ts = ts.intern unless ts.empty?
|
1404
|
+
d = Remark1::Definition[ts]
|
1405
|
+
when 2
|
1406
|
+
if str[28..37] == 'ANGSTROMS.' then
|
1407
|
+
d = Remark2::ANGSTROMS
|
1408
|
+
elsif str[22..37] == ' NOT APPLICABLE.' then
|
1409
|
+
d = Remark2::NOT_APPLICABLE
|
1410
|
+
else
|
1411
|
+
d = Remark2::Default
|
1412
|
+
end
|
1413
|
+
else
|
1414
|
+
d = RemarkN
|
1415
|
+
end
|
1416
|
+
else
|
1417
|
+
# unknown field
|
1418
|
+
d = Default
|
1419
|
+
end
|
1420
|
+
return d
|
1421
|
+
end
|
1422
|
+
end #class Record
|
1423
|
+
|
1424
|
+
Coordinate_fileds = {
|
1425
|
+
'MODEL' => true,
|
1426
|
+
:MODEL => true,
|
1427
|
+
'ENDMDL' => true,
|
1428
|
+
:ENDMDL => true,
|
1429
|
+
'ATOM' => true,
|
1430
|
+
:ATOM => true,
|
1431
|
+
'HETATM' => true,
|
1432
|
+
:HETATM => true,
|
1433
|
+
'SIGATM' => true,
|
1434
|
+
:SIGATM => true,
|
1435
|
+
'SIGUIJ' => true,
|
1436
|
+
:SIGUIJ => true,
|
1437
|
+
'ANISOU' => true,
|
1438
|
+
:ANISOU => true,
|
1439
|
+
'TER' => true,
|
1440
|
+
:TER => true,
|
1441
|
+
}
|
1442
|
+
|
1443
|
+
# Creates a new Bio::PDB object from given <em>str</em>.
|
1444
|
+
def initialize(str)
|
1445
|
+
#Aha! Our entry into the world of PDB parsing, we initialise a PDB
|
1446
|
+
#object with the whole PDB file as a string
|
1447
|
+
#each PDB has an array of the lines of the original file
|
1448
|
+
#a bit memory-tastic! A hash of records and an array of models
|
1449
|
+
#also has an id
|
1450
|
+
|
1451
|
+
@data = str.split(/[\r\n]+/)
|
1452
|
+
@hash = {}
|
1453
|
+
@models = []
|
1454
|
+
@id = nil
|
1455
|
+
|
1456
|
+
#Flag to say whether the current line is part of a continuation
|
1457
|
+
cont = false
|
1458
|
+
|
1459
|
+
#Empty current model
|
1460
|
+
cModel = Model.new
|
1461
|
+
cChain = nil #Chain.new
|
1462
|
+
cResidue = nil #Residue.new
|
1463
|
+
cLigand = nil #Heterogen.new
|
1464
|
+
c_atom = nil
|
1465
|
+
|
1466
|
+
#Goes through each line and replace that line with a PDB::Record
|
1467
|
+
@data.collect! do |line|
|
1468
|
+
#Go to next if the previous line was contiunation able, and
|
1469
|
+
#add_continuation returns true. Line is added by add_continuation
|
1470
|
+
next if cont and cont = cont.add_continuation(line)
|
1471
|
+
|
1472
|
+
#Make the new record
|
1473
|
+
f = Record.get_record_class(line).new.initialize_from_string(line)
|
1474
|
+
#p f
|
1475
|
+
#Set cont
|
1476
|
+
cont = f if f.continue?
|
1477
|
+
#Set the hash to point to this record either by adding to an
|
1478
|
+
#array, or on it's own
|
1479
|
+
key = f.record_name
|
1480
|
+
if a = @hash[key] then
|
1481
|
+
a << f
|
1482
|
+
else
|
1483
|
+
@hash[key] = [ f ]
|
1484
|
+
end
|
1485
|
+
|
1486
|
+
# Do something for ATOM and HETATM
|
1487
|
+
if key == 'ATOM' or key == 'HETATM' then
|
1488
|
+
if cChain and f.chainID == cChain.id
|
1489
|
+
chain = cChain
|
1490
|
+
else
|
1491
|
+
if chain = cModel[f.chainID]
|
1492
|
+
cChain = chain unless cChain
|
1493
|
+
else
|
1494
|
+
# If we don't have chain, add a new chain
|
1495
|
+
newChain = Chain.new(f.chainID, cModel)
|
1496
|
+
cModel.addChain(newChain)
|
1497
|
+
cChain = newChain
|
1498
|
+
chain = newChain
|
1499
|
+
end
|
1500
|
+
# chain might be changed, clearing cResidue and cLigand
|
1501
|
+
cResidue = nil
|
1502
|
+
cLigand = nil
|
1503
|
+
end
|
1504
|
+
end
|
1505
|
+
|
1506
|
+
case key
|
1507
|
+
when 'ATOM'
|
1508
|
+
c_atom = f
|
1509
|
+
residueID = Residue.get_residue_id_from_atom(f)
|
1510
|
+
|
1511
|
+
if cResidue and residueID == cResidue.id
|
1512
|
+
residue = cResidue
|
1513
|
+
else
|
1514
|
+
if residue = chain.get_residue_by_id(residueID)
|
1515
|
+
cResidue = residue unless cResidue
|
1516
|
+
else
|
1517
|
+
# add a new residue
|
1518
|
+
newResidue = Residue.new(f.resName, f.resSeq, f.iCode, chain)
|
1519
|
+
chain.addResidue(newResidue)
|
1520
|
+
cResidue = newResidue
|
1521
|
+
residue = newResidue
|
1522
|
+
end
|
1523
|
+
end
|
1524
|
+
|
1525
|
+
f.residue = residue
|
1526
|
+
residue.addAtom(f)
|
1527
|
+
|
1528
|
+
when 'HETATM'
|
1529
|
+
c_atom = f
|
1530
|
+
residueID = Heterogen.get_residue_id_from_atom(f)
|
1531
|
+
|
1532
|
+
if cLigand and residueID == cLigand.id
|
1533
|
+
ligand = cLigand
|
1534
|
+
else
|
1535
|
+
if ligand = chain.get_heterogen_by_id(residueID)
|
1536
|
+
cLigand = ligand unless cLigand
|
1537
|
+
else
|
1538
|
+
# add a new heterogen
|
1539
|
+
newLigand = Heterogen.new(f.resName, f.resSeq, f.iCode, chain)
|
1540
|
+
chain.addLigand(newLigand)
|
1541
|
+
cLigand = newLigand
|
1542
|
+
ligand = newLigand
|
1543
|
+
#Each model has a special solvent chain. (for compatibility)
|
1544
|
+
if f.resName == 'HOH'
|
1545
|
+
cModel.addSolvent(newLigand)
|
1546
|
+
end
|
1547
|
+
end
|
1548
|
+
end
|
1549
|
+
|
1550
|
+
f.residue = ligand
|
1551
|
+
ligand.addAtom(f)
|
1552
|
+
|
1553
|
+
when 'MODEL'
|
1554
|
+
c_atom = nil
|
1555
|
+
cChain = nil
|
1556
|
+
cResidue = nil
|
1557
|
+
cLigand = nil
|
1558
|
+
if cModel.model_serial or cModel.chains.size > 0 then
|
1559
|
+
self.addModel(cModel)
|
1560
|
+
end
|
1561
|
+
cModel = Model.new(f.serial)
|
1562
|
+
|
1563
|
+
when 'TER'
|
1564
|
+
if c_atom
|
1565
|
+
c_atom.ter = f
|
1566
|
+
else
|
1567
|
+
#$stderr.puts "Warning: stray TER?"
|
1568
|
+
end
|
1569
|
+
when 'SIGATM'
|
1570
|
+
if c_atom
|
1571
|
+
#$stderr.puts "Warning: duplicated SIGATM?" if c_atom.sigatm
|
1572
|
+
c_atom.sigatm = f
|
1573
|
+
else
|
1574
|
+
#$stderr.puts "Warning: stray SIGATM?"
|
1575
|
+
end
|
1576
|
+
when 'ANISOU'
|
1577
|
+
if c_atom
|
1578
|
+
#$stderr.puts "Warning: duplicated ANISOU?" if c_atom.anisou
|
1579
|
+
c_atom.anisou = f
|
1580
|
+
else
|
1581
|
+
#$stderr.puts "Warning: stray ANISOU?"
|
1582
|
+
end
|
1583
|
+
when 'SIGUIJ'
|
1584
|
+
if c_atom and c_atom.anisou
|
1585
|
+
#$stderr.puts "Warning: duplicated SIGUIJ?" if c_atom.anisou.siguij
|
1586
|
+
c_atom.anisou.siguij = f
|
1587
|
+
else
|
1588
|
+
#$stderr.puts "Warning: stray SIGUIJ?"
|
1589
|
+
end
|
1590
|
+
|
1591
|
+
else
|
1592
|
+
c_atom = nil
|
1593
|
+
|
1594
|
+
end
|
1595
|
+
f
|
1596
|
+
end #each
|
1597
|
+
#At the end we need to add the final model
|
1598
|
+
self.addModel(cModel)
|
1599
|
+
@data.compact!
|
1600
|
+
end #def initialize
|
1601
|
+
|
1602
|
+
# all records in this entry as an array.
|
1603
|
+
attr_reader :data
|
1604
|
+
|
1605
|
+
# all records in this entry as an hash accessed by record names.
|
1606
|
+
attr_reader :hash
|
1607
|
+
|
1608
|
+
# models in this entry (array).
|
1609
|
+
attr_reader :models
|
1610
|
+
|
1611
|
+
# Adds a <code>Bio::Model</code> object to the current strucutre.
|
1612
|
+
# Adds a model to the current structure.
|
1613
|
+
# Returns self.
|
1614
|
+
def addModel(model)
|
1615
|
+
raise "Expecting a Bio::PDB::Model" if not model.is_a? Bio::PDB::Model
|
1616
|
+
@models.push(model)
|
1617
|
+
self
|
1618
|
+
end
|
1619
|
+
|
1620
|
+
# Iterates over each model.
|
1621
|
+
# Iterates over each of the models in the structure.
|
1622
|
+
# Returns <code>self</code>.
|
1623
|
+
def each
|
1624
|
+
@models.each{ |model| yield model }
|
1625
|
+
self
|
1626
|
+
end
|
1627
|
+
# Alias needed for Bio::PDB::ModelFinder
|
1628
|
+
alias each_model each
|
1629
|
+
|
1630
|
+
# Provides keyed access to the models based on serial number
|
1631
|
+
# returns nil if it's not there
|
1632
|
+
def [](key)
|
1633
|
+
@models.find{ |model| key == model.model_serial }
|
1634
|
+
end
|
1635
|
+
#--
|
1636
|
+
# (should it raise an exception?)
|
1637
|
+
#++
|
1638
|
+
|
1639
|
+
#--
|
1640
|
+
#Stringifies to a list of atom records - we could add the annotation
|
1641
|
+
#as well if needed
|
1642
|
+
#++
|
1643
|
+
|
1644
|
+
# Returns a string of Bio::PDB::Models. This propogates down the heirarchy
|
1645
|
+
# till you get to Bio::PDB::Record::ATOM which are outputed in PDB format
|
1646
|
+
def to_s
|
1647
|
+
string = ""
|
1648
|
+
@models.each{ |model| string << model.to_s }
|
1649
|
+
string << "END\n"
|
1650
|
+
return string
|
1651
|
+
end
|
1652
|
+
|
1653
|
+
#Makes a hash out of an array of PDB::Records and some kind of symbol
|
1654
|
+
#.__send__ invokes the method specified by the symbol.
|
1655
|
+
#Essentially it ends up with a hash with keys given in the sub_record
|
1656
|
+
#Not sure I fully understand this
|
1657
|
+
def make_hash(ary, meth)
|
1658
|
+
h = {}
|
1659
|
+
ary.each do |f|
|
1660
|
+
k = f.__send__(meth)
|
1661
|
+
h[k] = [] unless h.has_key?(k)
|
1662
|
+
h[k] << f
|
1663
|
+
end
|
1664
|
+
h
|
1665
|
+
end
|
1666
|
+
private :make_hash
|
1667
|
+
|
1668
|
+
#Takes an array and returns another array of PDB::Records
|
1669
|
+
def make_grouping(ary, meth)
|
1670
|
+
a = []
|
1671
|
+
k_prev = nil
|
1672
|
+
ary.each do |f|
|
1673
|
+
k = f.__send__(meth)
|
1674
|
+
if k_prev and k_prev == k then
|
1675
|
+
a.last << f
|
1676
|
+
else
|
1677
|
+
a << []
|
1678
|
+
a.last << f
|
1679
|
+
end
|
1680
|
+
k_prev = k
|
1681
|
+
end
|
1682
|
+
a
|
1683
|
+
end
|
1684
|
+
private :make_grouping
|
1685
|
+
|
1686
|
+
# Gets all records whose record type is _name_.
|
1687
|
+
# Returns an array of <code>Bio::PDB::Record::*</code> objects.
|
1688
|
+
#
|
1689
|
+
# if _name_ is nil, returns hash storing all record data.
|
1690
|
+
#
|
1691
|
+
# Example:
|
1692
|
+
# p pdb.record('HETATM')
|
1693
|
+
# p pdb.record['HETATM']
|
1694
|
+
#
|
1695
|
+
def record(name = nil)
|
1696
|
+
name ? (@hash[name] || []) : @hash
|
1697
|
+
end
|
1698
|
+
|
1699
|
+
#--
|
1700
|
+
# PDB original methods
|
1701
|
+
#Returns a hash of the REMARK records based on the remarkNum
|
1702
|
+
#++
|
1703
|
+
|
1704
|
+
# Gets REMARK records.
|
1705
|
+
# If no arguments, it returns all REMARK records as a hash.
|
1706
|
+
# If remark number is specified, returns only corresponding REMARK records.
|
1707
|
+
# If number == 1 or 2 ("REMARK 1" or "REMARK 2"), returns an array
|
1708
|
+
# of Bio::PDB::Record instances. Otherwise, returns an array of strings.
|
1709
|
+
#
|
1710
|
+
def remark(nn = nil)
|
1711
|
+
unless defined?(@remark)
|
1712
|
+
h = make_hash(self.record('REMARK'), :remarkNum)
|
1713
|
+
h.each do |i, a|
|
1714
|
+
a.shift # remove first record (= space only)
|
1715
|
+
if i != 1 and i != 2 then
|
1716
|
+
a.collect! { |f| f.text.gsub(/\s+\z/, '') }
|
1717
|
+
end
|
1718
|
+
end
|
1719
|
+
@remark = h
|
1720
|
+
end
|
1721
|
+
nn ? @remark[nn] : @remark
|
1722
|
+
end
|
1723
|
+
|
1724
|
+
# Gets JRNL records.
|
1725
|
+
# If no arguments, it returns all JRNL records as a hash.
|
1726
|
+
# If sub record name is specified, it returns only corresponding records
|
1727
|
+
# as an array of Bio::PDB::Record instances.
|
1728
|
+
#
|
1729
|
+
def jrnl(sub_record = nil)
|
1730
|
+
unless defined?(@jrnl)
|
1731
|
+
@jrnl = make_hash(self.record('JRNL'), :sub_record)
|
1732
|
+
end
|
1733
|
+
sub_record ? @jrnl[sub_record] : @jrnl
|
1734
|
+
end
|
1735
|
+
|
1736
|
+
#--
|
1737
|
+
#Finding methods - just grabs the record with the appropriate id
|
1738
|
+
#or returns and array of all of them
|
1739
|
+
#++
|
1740
|
+
|
1741
|
+
# Gets HELIX records.
|
1742
|
+
# If no arguments are given, it returns all HELIX records.
|
1743
|
+
# (Returns an array of <code>Bio::PDB::Record::HELIX</code> instances.)
|
1744
|
+
# If <em>helixID</em> is given, it only returns records
|
1745
|
+
# corresponding to given <em>helixID</em>.
|
1746
|
+
# (Returns an <code>Bio::PDB::Record::HELIX</code> instance.)
|
1747
|
+
#
|
1748
|
+
def helix(helixID = nil)
|
1749
|
+
if helixID then
|
1750
|
+
self.record('HELIX').find { |f| f.helixID == helixID }
|
1751
|
+
else
|
1752
|
+
self.record('HELIX')
|
1753
|
+
end
|
1754
|
+
end
|
1755
|
+
|
1756
|
+
# Gets TURN records.
|
1757
|
+
# If no arguments are given, it returns all TURN records.
|
1758
|
+
# (Returns an array of <code>Bio::PDB::Record::TURN</code> instances.)
|
1759
|
+
# If <em>turnId</em> is given, it only returns a record
|
1760
|
+
# corresponding to given <em>turnId</em>.
|
1761
|
+
# (Returns an <code>Bio::PDB::Record::TURN</code> instance.)
|
1762
|
+
#
|
1763
|
+
def turn(turnId = nil)
|
1764
|
+
if turnId then
|
1765
|
+
self.record('TURN').find { |f| f.turnId == turnId }
|
1766
|
+
else
|
1767
|
+
self.record('TURN')
|
1768
|
+
end
|
1769
|
+
end
|
1770
|
+
|
1771
|
+
# Gets SHEET records.
|
1772
|
+
# If no arguments are given, it returns all SHEET records
|
1773
|
+
# as an array of arrays of <code>Bio::PDB::Record::SHEET</code> instances.
|
1774
|
+
# If <em>sheetID</em> is given, it returns an array of
|
1775
|
+
# <code>Bio::PDB::Record::SHEET</code> instances.
|
1776
|
+
def sheet(sheetID = nil)
|
1777
|
+
unless defined?(@sheet)
|
1778
|
+
@sheet = make_grouping(self.record('SHEET'), :sheetID)
|
1779
|
+
end
|
1780
|
+
if sheetID then
|
1781
|
+
@sheet.find_all { |f| f.first.sheetID == sheetID }
|
1782
|
+
else
|
1783
|
+
@sheet
|
1784
|
+
end
|
1785
|
+
end
|
1786
|
+
|
1787
|
+
# Gets SSBOND records.
|
1788
|
+
def ssbond
|
1789
|
+
self.record('SSBOND')
|
1790
|
+
end
|
1791
|
+
|
1792
|
+
#--
|
1793
|
+
# Get seqres - we get this to return a nice Bio::Seq object
|
1794
|
+
#++
|
1795
|
+
|
1796
|
+
# Amino acid or nucleic acid sequence of backbone residues in "SEQRES".
|
1797
|
+
# If <em>chainID</em> is given, it returns corresponding sequence
|
1798
|
+
# as an array of string.
|
1799
|
+
# Otherwise, returns a hash which contains all sequences.
|
1800
|
+
#
|
1801
|
+
def seqres(chainID = nil)
|
1802
|
+
unless defined?(@seqres)
|
1803
|
+
h = make_hash(self.record('SEQRES'), :chainID)
|
1804
|
+
newHash = {}
|
1805
|
+
h.each do |k, a|
|
1806
|
+
a.collect! { |f| f.resName }
|
1807
|
+
a.flatten!
|
1808
|
+
# determine nuc or aa?
|
1809
|
+
tmp = Hash.new(0)
|
1810
|
+
a[0,13].each { |x| tmp[x.to_s.strip.size] += 1 }
|
1811
|
+
if tmp[3] >= tmp[1] then
|
1812
|
+
# amino acid sequence
|
1813
|
+
a.collect! do |aa|
|
1814
|
+
#aa is three letter code: i.e. ALA
|
1815
|
+
#need to look up with Ala
|
1816
|
+
aa = aa.capitalize
|
1817
|
+
(begin
|
1818
|
+
Bio::AminoAcid.three2one(aa)
|
1819
|
+
rescue ArgumentError
|
1820
|
+
nil
|
1821
|
+
end || 'X')
|
1822
|
+
end
|
1823
|
+
seq = Bio::Sequence::AA.new(a.to_s)
|
1824
|
+
else
|
1825
|
+
# nucleic acid sequence
|
1826
|
+
a.collect! do |na|
|
1827
|
+
na = na.delete('^a-zA-Z')
|
1828
|
+
na.size == 1 ? na : 'n'
|
1829
|
+
end
|
1830
|
+
seq = Bio::Sequence::NA.new(a.to_s)
|
1831
|
+
end
|
1832
|
+
newHash[k] = seq
|
1833
|
+
end
|
1834
|
+
@seqres = newHash
|
1835
|
+
end
|
1836
|
+
if chainID then
|
1837
|
+
@seqres[chainID]
|
1838
|
+
else
|
1839
|
+
@seqres
|
1840
|
+
end
|
1841
|
+
end
|
1842
|
+
|
1843
|
+
# Gets DBREF records.
|
1844
|
+
# Returns an array of Bio::PDB::Record::DBREF objects.
|
1845
|
+
#
|
1846
|
+
# If <em>chainID</em> is given, it returns corresponding DBREF records.
|
1847
|
+
def dbref(chainID = nil)
|
1848
|
+
if chainID then
|
1849
|
+
self.record('DBREF').find_all { |f| f.chainID == chainID }
|
1850
|
+
else
|
1851
|
+
self.record('DBREF')
|
1852
|
+
end
|
1853
|
+
end
|
1854
|
+
|
1855
|
+
# Keywords in "KEYWDS".
|
1856
|
+
# Returns an array of string.
|
1857
|
+
def keywords
|
1858
|
+
self.record('KEYWDS').collect { |f| f.keywds }.flatten
|
1859
|
+
end
|
1860
|
+
|
1861
|
+
# Classification in "HEADER".
|
1862
|
+
def classification
|
1863
|
+
f = self.record('HEADER').first
|
1864
|
+
f ? f.classification : nil
|
1865
|
+
end
|
1866
|
+
|
1867
|
+
# Get authors in "AUTHOR".
|
1868
|
+
def authors
|
1869
|
+
self.record('AUTHOR').collect { |f| f.authorList }.flatten
|
1870
|
+
end
|
1871
|
+
|
1872
|
+
#--
|
1873
|
+
# Bio::DB methods
|
1874
|
+
#++
|
1875
|
+
|
1876
|
+
# PDB identifier written in "HEADER". (e.g. 1A00)
|
1877
|
+
def entry_id
|
1878
|
+
unless @id
|
1879
|
+
f = self.record('HEADER').first
|
1880
|
+
@id = f ? f.idCode : nil
|
1881
|
+
end
|
1882
|
+
@id
|
1883
|
+
end
|
1884
|
+
|
1885
|
+
# Same as <tt>Bio::PDB#entry_id</tt>.
|
1886
|
+
def accession
|
1887
|
+
self.entry_id
|
1888
|
+
end
|
1889
|
+
|
1890
|
+
# Title of this entry in "TITLE".
|
1891
|
+
def definition
|
1892
|
+
f = self.record('TITLE').first
|
1893
|
+
f ? f.title : nil
|
1894
|
+
end
|
1895
|
+
|
1896
|
+
# Current modification number in "REVDAT".
|
1897
|
+
def version
|
1898
|
+
f = self.record('REVDAT').first
|
1899
|
+
f ? f.modNum : nil
|
1900
|
+
end
|
1901
|
+
|
1902
|
+
# returns a string containing human-readable representation
|
1903
|
+
# of this object.
|
1904
|
+
def inspect
|
1905
|
+
"#<#{self.class.to_s} entry_id=#{entry_id.inspect}>"
|
1906
|
+
end
|
1907
|
+
|
1908
|
+
end #class PDB
|
1909
|
+
|
1910
|
+
end #module Bio
|
1911
|
+
|