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ljvmiranda921/gym-lattice: Major Release (v0.1.0)

Lester James Validad Miranda


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    <subfield code="x">Lau, K.F. and Dill, K.A., 1989. A lattice statistical mechanics model of the conformational and sequence spaces of proteins. Macromolecules, 22(10), pp.3986-3997.</subfield>
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    <subfield code="a">Lester James Validad Miranda</subfield>
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    <subfield code="a">&lt;p&gt;Major Release (v0.1.0)&lt;/p&gt;

&lt;p&gt;Gym-lattice is an HP 2D Lattice Environment with a Gym-like API for the protein folding problem.&lt;/p&gt;

&lt;p&gt;This is a Python library that formulates Lau and Dill&amp;#39;s (1989) hydrophobic-polar two-dimensional lattice model as a reinforcement learning problem. It follows OpenAI Gym&amp;#39;s API, easing integration for reinforcement learning solutions.&lt;/p&gt;

&lt;p&gt;Features&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;OpenAI Integration: uses Gym&amp;#39;s API to ease compatibility to reinforcement learning solutions.&lt;/li&gt;
	&lt;li&gt;Lattice 2D Environment: implements Dill and Lau&amp;#39;s two-dimensional lattice as an RL problem.&lt;/li&gt;
	&lt;li&gt;Command-line rendering environment: the method &lt;code&gt;render()&lt;/code&gt; draws the chain on the command-line.&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;Additionally, there is an option to set the penalty parameters for training the agent, this includes:&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;Collision penalty (&lt;code&gt;collision_penalty&lt;/code&gt;): accounts for the time whenever the agent decides to assign a molecule to an already-occupied space; and&lt;/li&gt;
	&lt;li&gt;Trap penalty (&lt;code&gt;trap_penalty&lt;/code&gt;): induces heavy deductions whenever the agent traps itself and cannot accomplish the task anymore.&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;Tests&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;Error-handling: all public-facing methods now use &lt;code&gt;Exceptions&lt;/code&gt; instead of &lt;code&gt;asserts&lt;/code&gt; when catching errors.&lt;/li&gt;
	&lt;li&gt;Testing with pytest and tox: unit-testing is being done with &lt;code&gt;pytest&lt;/code&gt; and &lt;code&gt;tox&lt;/code&gt;.&lt;/li&gt;
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