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<h1 id="index">Index</h1> |
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<div class="genindex-jumpbox"> |
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<a href="#A"><strong>A</strong></a> |
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| <a href="#B"><strong>B</strong></a> |
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| <a href="#C"><strong>C</strong></a> |
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| <a href="#D"><strong>D</strong></a> |
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| <a href="#E"><strong>E</strong></a> |
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| <a href="#F"><strong>F</strong></a> |
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| <a href="#G"><strong>G</strong></a> |
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| <a href="#I"><strong>I</strong></a> |
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| <a href="#L"><strong>L</strong></a> |
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| <a href="#M"><strong>M</strong></a> |
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| <a href="#P"><strong>P</strong></a> |
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| <a href="#R"><strong>R</strong></a> |
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| <a href="#S"><strong>S</strong></a> |
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| <a href="#T"><strong>T</strong></a> |
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| <a href="#U"><strong>U</strong></a> |
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| <a href="#W"><strong>W</strong></a> |
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</div> |
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<h2 id="A">A</h2> |
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<table style="width: 100%" class="indextable genindextable"><tr> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="api/index.html#dscript.alphabets.Alphabet">Alphabet (class in dscript.alphabets)</a> |
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</li> |
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</ul></td> |
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</tr></table> |
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<h2 id="B">B</h2> |
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<table style="width: 100%" class="indextable genindextable"><tr> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="api/dscript.models.html#dscript.models.contact.ContactCNN.broadcast">broadcast() (dscript.models.contact.ContactCNN method)</a> |
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</li> |
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</ul></td> |
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</tr></table> |
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<h2 id="C">C</h2> |
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<table style="width: 100%" class="indextable genindextable"><tr> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="api/index.html#dscript.utils.collate_paired_sequences">collate_paired_sequences() (in module dscript.utils)</a> |
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</li> |
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</ul></td> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="api/dscript.models.html#dscript.models.contact.ContactCNN">ContactCNN (class in dscript.models.contact)</a> |
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</li> |
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<li><a href="api/dscript.models.html#dscript.models.interaction.ModelInteraction.cpred">cpred() (dscript.models.interaction.ModelInteraction method)</a> |
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</li> |
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</ul></td> |
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</tr></table> |
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<h2 id="D">D</h2> |
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<table style="width: 100%" class="indextable genindextable"><tr> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="api/index.html#dscript.alphabets.Alphabet.decode">decode() (dscript.alphabets.Alphabet method)</a> |
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</li> |
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<li> |
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dscript.alphabets |
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<ul> |
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<li><a href="api/index.html#module-dscript.alphabets">module</a> |
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</li> |
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</ul></li> |
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<li> |
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dscript.commands.embed |
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<ul> |
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<li><a href="api/dscript.commands.html#module-dscript.commands.embed">module</a> |
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</li> |
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</ul></li> |
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<li> |
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dscript.commands.eval |
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<ul> |
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<li><a href="api/dscript.commands.html#module-dscript.commands.eval">module</a> |
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</li> |
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</ul></li> |
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<li> |
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dscript.commands.predict |
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<ul> |
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<li><a href="api/dscript.commands.html#module-dscript.commands.predict">module</a> |
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</li> |
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</ul></li> |
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<li> |
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dscript.commands.train |
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<ul> |
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<li><a href="api/dscript.commands.html#module-dscript.commands.train">module</a> |
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</li> |
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</ul></li> |
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<li> |
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dscript.fasta |
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<ul> |
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<li><a href="api/index.html#module-dscript.fasta">module</a> |
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</li> |
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</ul></li> |
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</ul></td> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li> |
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dscript.language_model |
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<ul> |
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<li><a href="api/index.html#module-dscript.language_model">module</a> |
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</li> |
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</ul></li> |
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<li> |
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dscript.models.contact |
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<ul> |
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<li><a href="api/dscript.models.html#module-dscript.models.contact">module</a> |
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</li> |
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</ul></li> |
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<li> |
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dscript.models.embedding |
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<ul> |
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<li><a href="api/dscript.models.html#module-dscript.models.embedding">module</a> |
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</li> |
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</ul></li> |
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<li> |
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dscript.models.interaction |
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<ul> |
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<li><a href="api/dscript.models.html#module-dscript.models.interaction">module</a> |
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</li> |
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</ul></li> |
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<li> |
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dscript.pretrained |
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<ul> |
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<li><a href="api/index.html#module-dscript.pretrained">module</a> |
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</li> |
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</ul></li> |
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<li> |
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dscript.utils |
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<ul> |
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<li><a href="api/index.html#module-dscript.utils">module</a> |
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</li> |
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</ul></li> |
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</ul></td> |
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</tr></table> |
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<h2 id="E">E</h2> |
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<table style="width: 100%" class="indextable genindextable"><tr> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="api/dscript.models.html#dscript.models.interaction.ModelInteraction.embed">embed() (dscript.models.interaction.ModelInteraction method)</a> |
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</li> |
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<li><a href="api/index.html#dscript.language_model.embed_from_directory">embed_from_directory() (in module dscript.language_model)</a> |
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</li> |
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</ul></td> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="api/index.html#dscript.language_model.embed_from_fasta">embed_from_fasta() (in module dscript.language_model)</a> |
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</li> |
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<li><a href="api/index.html#dscript.alphabets.Alphabet.encode">encode() (dscript.alphabets.Alphabet method)</a> |
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</li> |
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</ul></td> |
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</tr></table> |
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<h2 id="F">F</h2> |
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<table style="width: 100%" class="indextable genindextable"><tr> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="api/dscript.models.html#dscript.models.contact.ContactCNN.forward">forward() (dscript.models.contact.ContactCNN method)</a> |
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<ul> |
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<li><a href="api/dscript.models.html#dscript.models.contact.FullyConnected.forward">(dscript.models.contact.FullyConnected method)</a> |
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</li> |
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<li><a href="api/dscript.models.html#dscript.models.embedding.FullyConnectedEmbed.forward">(dscript.models.embedding.FullyConnectedEmbed method)</a> |
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</li> |
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<li><a href="api/dscript.models.html#dscript.models.embedding.IdentityEmbed.forward">(dscript.models.embedding.IdentityEmbed method)</a> |
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</li> |
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<li><a href="api/dscript.models.html#dscript.models.interaction.LogisticActivation.forward">(dscript.models.interaction.LogisticActivation method)</a> |
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</li> |
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</ul></li> |
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</ul></td> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="api/dscript.models.html#dscript.models.contact.FullyConnected">FullyConnected (class in dscript.models.contact)</a> |
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</li> |
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<li><a href="api/dscript.models.html#dscript.models.embedding.FullyConnectedEmbed">FullyConnectedEmbed (class in dscript.models.embedding)</a> |
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</li> |
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</ul></td> |
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</tr></table> |
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<h2 id="G">G</h2> |
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<table style="width: 100%" class="indextable genindextable"><tr> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="api/index.html#dscript.pretrained.get_pretrained">get_pretrained() (in module dscript.pretrained)</a> |
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</li> |
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</ul></td> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="api/index.html#dscript.pretrained.get_state_dict">get_state_dict() (in module dscript.pretrained)</a> |
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</li> |
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<li><a href="api/index.html#dscript.utils.gpu_mem">gpu_mem() (in module dscript.utils)</a> |
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</li> |
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</ul></td> |
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</tr></table> |
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|
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<h2 id="I">I</h2> |
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<table style="width: 100%" class="indextable genindextable"><tr> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="api/dscript.models.html#dscript.models.embedding.IdentityEmbed">IdentityEmbed (class in dscript.models.embedding)</a> |
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</li> |
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</ul></td> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="api/dscript.commands.html#dscript.commands.train.interaction_eval">interaction_eval() (in module dscript.commands.train)</a> |
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</li> |
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<li><a href="api/dscript.commands.html#dscript.commands.train.interaction_grad">interaction_grad() (in module dscript.commands.train)</a> |
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</li> |
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</ul></td> |
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</tr></table> |
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|
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<h2 id="L">L</h2> |
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<table style="width: 100%" class="indextable genindextable"><tr> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="api/index.html#dscript.language_model.lm_embed">lm_embed() (in module dscript.language_model)</a> |
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</li> |
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</ul></td> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="api/index.html#dscript.utils.log">log() (in module dscript.utils)</a> |
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</li> |
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<li><a href="api/dscript.models.html#dscript.models.interaction.LogisticActivation">LogisticActivation (class in dscript.models.interaction)</a> |
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</li> |
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</ul></td> |
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</tr></table> |
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<h2 id="M">M</h2> |
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<table style="width: 100%" class="indextable genindextable"><tr> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="api/dscript.models.html#dscript.models.interaction.ModelInteraction.map_predict">map_predict() (dscript.models.interaction.ModelInteraction method)</a> |
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</li> |
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<li><a href="api/dscript.models.html#dscript.models.interaction.ModelInteraction">ModelInteraction (class in dscript.models.interaction)</a> |
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</li> |
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<li> |
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module |
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<ul> |
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<li><a href="api/index.html#module-dscript.alphabets">dscript.alphabets</a> |
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</li> |
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<li><a href="api/dscript.commands.html#module-dscript.commands.embed">dscript.commands.embed</a> |
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</li> |
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<li><a href="api/dscript.commands.html#module-dscript.commands.eval">dscript.commands.eval</a> |
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</li> |
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<li><a href="api/dscript.commands.html#module-dscript.commands.predict">dscript.commands.predict</a> |
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</li> |
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<li><a href="api/dscript.commands.html#module-dscript.commands.train">dscript.commands.train</a> |
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</li> |
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<li><a href="api/index.html#module-dscript.fasta">dscript.fasta</a> |
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</li> |
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<li><a href="api/index.html#module-dscript.language_model">dscript.language_model</a> |
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</li> |
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<li><a href="api/dscript.models.html#module-dscript.models.contact">dscript.models.contact</a> |
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</li> |
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<li><a href="api/dscript.models.html#module-dscript.models.embedding">dscript.models.embedding</a> |
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</li> |
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<li><a href="api/dscript.models.html#module-dscript.models.interaction">dscript.models.interaction</a> |
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</li> |
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<li><a href="api/index.html#module-dscript.pretrained">dscript.pretrained</a> |
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</li> |
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<li><a href="api/index.html#module-dscript.utils">dscript.utils</a> |
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</li> |
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</ul></li> |
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</ul></td> |
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</tr></table> |
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|
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<h2 id="P">P</h2> |
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<table style="width: 100%" class="indextable genindextable"><tr> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="api/index.html#dscript.utils.PairedDataset">PairedDataset (class in dscript.utils)</a> |
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</li> |
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<li><a href="api/index.html#dscript.fasta.parse">parse() (in module dscript.fasta)</a> |
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</li> |
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<li><a href="api/index.html#dscript.fasta.parse_directory">parse_directory() (in module dscript.fasta)</a> |
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</li> |
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<li><a href="api/dscript.commands.html#dscript.commands.eval.plot_eval_predictions">plot_eval_predictions() (in module dscript.commands.eval)</a> |
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</li> |
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<li><a href="api/index.html#dscript.utils.plot_PR_curve">plot_PR_curve() (in module dscript.utils)</a> |
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</li> |
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</ul></td> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="api/index.html#dscript.utils.plot_ROC_curve">plot_ROC_curve() (in module dscript.utils)</a> |
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</li> |
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<li><a href="api/dscript.models.html#dscript.models.contact.ContactCNN.predict">predict() (dscript.models.contact.ContactCNN method)</a> |
|
|
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<ul> |
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<li><a href="api/dscript.models.html#dscript.models.interaction.ModelInteraction.predict">(dscript.models.interaction.ModelInteraction method)</a> |
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</li> |
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</ul></li> |
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<li><a href="api/dscript.commands.html#dscript.commands.train.predict_cmap_interaction">predict_cmap_interaction() (in module dscript.commands.train)</a> |
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</li> |
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<li><a href="api/dscript.commands.html#dscript.commands.train.predict_interaction">predict_interaction() (in module dscript.commands.train)</a> |
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</li> |
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</ul></td> |
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</tr></table> |
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<h2 id="R">R</h2> |
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<table style="width: 100%" class="indextable genindextable"><tr> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="api/index.html#dscript.utils.RBF">RBF() (in module dscript.utils)</a> |
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</li> |
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</ul></td> |
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</tr></table> |
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<h2 id="S">S</h2> |
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<table style="width: 100%" class="indextable genindextable"><tr> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="api/dscript.models.html#dscript.models.embedding.SkipLSTM">SkipLSTM (class in dscript.models.embedding)</a> |
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</li> |
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</ul></td> |
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</tr></table> |
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<h2 id="T">T</h2> |
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<table style="width: 100%" class="indextable genindextable"><tr> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="api/dscript.models.html#dscript.models.embedding.SkipLSTM.to_one_hot">to_one_hot() (dscript.models.embedding.SkipLSTM method)</a> |
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</li> |
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</ul></td> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="api/dscript.models.html#dscript.models.embedding.SkipLSTM.transform">transform() (dscript.models.embedding.SkipLSTM method)</a> |
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</li> |
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</ul></td> |
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</tr></table> |
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|
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<h2 id="U">U</h2> |
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<table style="width: 100%" class="indextable genindextable"><tr> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="api/index.html#dscript.alphabets.Uniprot21">Uniprot21 (class in dscript.alphabets)</a> |
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</li> |
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</ul></td> |
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</tr></table> |
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<h2 id="W">W</h2> |
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<table style="width: 100%" class="indextable genindextable"><tr> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="api/index.html#dscript.fasta.write">write() (in module dscript.fasta)</a> |
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</li> |
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</ul></td> |
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</tr></table> |
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</div> |
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</div> |
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