Add proteome system, along with genome component and proteome component

CMakeLists.txt

@@ -1,6 +1,5 @@
 cmake_minimum_required(VERSION 3.7)
 
-
 option(VERSION_STRING "Project version string" "0.0.0")
 
 project(antkeeper VERSION ${VERSION_STRING} LANGUAGES CXX)

src/entity/components/genome.hpp

@@ -0,0 +1,50 @@
+/*
+ * Copyright (C) 2021  Christopher J. Howard
+ *
+ * This file is part of Antkeeper source code.
+ *
+ * Antkeeper source code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Antkeeper source code is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Antkeeper source code.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef ANTKEEPER_ENTITY_COMPONENT_GENOME_HPP
+#define ANTKEEPER_ENTITY_COMPONENT_GENOME_HPP
+
+#include <string>
+#include <vector>
+
+namespace entity {
+namespace component {
+
+/// Complete set of genetic material in an organism.
+struct genome
+{
+	/**
+	 * Number of complete sets of chromosomes in a cell.
+	 *
+	 * A value of `1` indicates the organism is haploid, `2` is diploid, `3` is triploid, etc.
+	 */
+	unsigned int ploidy;
+	
+	/**
+	 * Set of DNA base sequences for every chromosomes in the genome.
+	 *
+	 * A DNA base sequence is a string of IUPAC DNA base symbols. Homologous chromosomes should be stored consecutively, such that in a diploid organism, a chromosome with an even index is homologous to the following chromosome.
+	 */
+	std::vector<std::string> chromosomes;
+};
+
+} // namespace component
+} // namespace entity
+
+#endif // ANTKEEPER_ENTITY_COMPONENT_GENOME_HPP

src/entity/components/proteome.hpp

@@ -0,0 +1,39 @@
+/*
+ * Copyright (C) 2021  Christopher J. Howard
+ *
+ * This file is part of Antkeeper source code.
+ *
+ * Antkeeper source code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Antkeeper source code is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Antkeeper source code.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef ANTKEEPER_ENTITY_COMPONENT_PROTEOME_HPP
+#define ANTKEEPER_ENTITY_COMPONENT_PROTEOME_HPP
+
+#include <string>
+#include <vector>
+
+namespace entity {
+namespace component {
+
+/// Set of all proteins that can be expressed by an organism.
+struct proteome
+{
+	/// Set of amino acid sequences of every protein in the proteome.
+	std::vector<std::string> proteins;
+};
+
+} // namespace component
+} // namespace entity
+
+#endif // ANTKEEPER_ENTITY_COMPONENT_PROTEOME_HPP

src/entity/systems/morphogenesis.cpp

@@ -0,0 +1,34 @@
+/*
+ * Copyright (C) 2021  Christopher J. Howard
+ *
+ * This file is part of Antkeeper source code.
+ *
+ * Antkeeper source code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Antkeeper source code is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Antkeeper source code.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include "entity/systems/morphogenesis.hpp"
+#include "entity/id.hpp"
+
+namespace entity {
+namespace system {
+
+morphogenesis::morphogenesis(entity::registry& registry):
+	updatable(registry)
+{}
+
+void morphogenesis::update(double t, double dt)
+{}
+
+} // namespace system
+} // namespace entity

src/entity/systems/morphogenesis.hpp

@@ -0,0 +1,60 @@
+/*
+ * Copyright (C) 2021  Christopher J. Howard
+ *
+ * This file is part of Antkeeper source code.
+ *
+ * Antkeeper source code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Antkeeper source code is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Antkeeper source code.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef ANTKEEPER_ENTITY_SYSTEM_MORPHOGENESIS_HPP
+#define ANTKEEPER_ENTITY_SYSTEM_MORPHOGENESIS_HPP
+
+#include "entity/systems/updatable.hpp"
+
+namespace entity {
+namespace system {
+
+/**
+ * Constructs the forms of organisms from their genetic codes.
+ *
+ * Algorithm:
+ *
+ * 1. Consider inital egg cell as a sphere at the origin.
+ * 2. Use the marching cubes algorithm to generate a mesh from the isosurface formed by the sum of all cells.
+ * 3. Generate evenly-distributed points across surface area of the mesh (Poisson sample?).
+ * 4. For each point, evaluate morphogenic genes to determine type, direction, and color of the next cell.
+ * 5. Create new cells given the output of step 4.
+ * 6. Go to step 2 and repeat.
+ */
+class morphogenesis:
+	public updatable
+{
+public:
+	morphogenesis(entity::registry& registry);
+	
+	/**
+	 * Scales then adds the timestep `dt` to the current time, then recalculates the positions of morphogenesising bodies.
+	 *
+	 * @param t Time, in seconds.
+	 * @param dt Delta time, in seconds.
+	 */
+	virtual void update(double t, double dt);
+	
+private:
+};
+
+} // namespace system
+} // namespace entity
+
+#endif // ANTKEEPER_ENTITY_SYSTEM_MORPHOGENESIS_HPP

src/entity/systems/proteome.cpp

@@ -0,0 +1,74 @@
+/*
+ * Copyright (C) 2021  Christopher J. Howard
+ *
+ * This file is part of Antkeeper source code.
+ *
+ * Antkeeper source code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Antkeeper source code is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Antkeeper source code.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include "entity/systems/proteome.hpp"
+#include "entity/components/proteome.hpp"
+#include "genetics/sequence.hpp"
+#include "genetics/standard-code.hpp"
+
+namespace entity {
+namespace system {
+
+proteome::proteome(entity::registry& registry):
+	updatable(registry)
+{
+	registry.on_construct<entity::component::genome>().connect<&proteome::on_genome_construct>(this);
+	registry.on_replace<entity::component::genome>().connect<&proteome::on_genome_replace>(this);
+}
+
+void proteome::update(double t, double dt)
+{}
+
+void proteome::on_genome_construct(entity::registry& registry, entity::id entity_id, entity::component::genome& genome)
+{
+	on_genome_replace(registry, entity_id, genome);
+}
+
+void proteome::on_genome_replace(entity::registry& registry, entity::id entity_id, entity::component::genome& genome)
+{
+	// Allocate a proteome component
+	entity::component::proteome proteome_component;
+	
+	// For each chromosome in the genome
+	for (const std::string& chromosome: genome.chromosomes)
+	{
+		// Find the first ORF in the chromosome
+		auto orf = genetics::sequence::find_orf(chromosome.begin(), chromosome.end(), genetics::standard_code);
+		
+		// While the ORF is valid
+		while (orf.start != chromosome.end())
+		{
+			// Translate the base sequence into an amino acid sequence (protein)
+			std::string protein;
+			genetics::sequence::translate(orf.start, orf.stop, std::back_inserter(protein), genetics::standard_code);
+			
+			// Append protein to the proteome
+			proteome_component.proteins.push_back(protein);
+			
+			// Find the next ORF
+			orf = genetics::sequence::find_orf(orf.stop, chromosome.end(), genetics::standard_code);
+		}
+	}
+	
+	// Assign or replace the entity's proteome component
+	registry.assign_or_replace<entity::component::proteome>(entity_id, proteome_component);
+}
+
+} // namespace system
+} // namespace entity

src/entity/systems/proteome.hpp

@@ -0,0 +1,55 @@
+/*
+ * Copyright (C) 2021  Christopher J. Howard
+ *
+ * This file is part of Antkeeper source code.
+ *
+ * Antkeeper source code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Antkeeper source code is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Antkeeper source code.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef ANTKEEPER_ENTITY_SYSTEM_PROTEOME_HPP
+#define ANTKEEPER_ENTITY_SYSTEM_PROTEOME_HPP
+
+#include "entity/systems/updatable.hpp"
+#include "entity/components/genome.hpp"
+#include "entity/id.hpp"
+
+namespace entity {
+namespace system {
+
+/**
+ * Generates proteomes for every genome.
+ */
+class proteome:
+	public updatable
+{
+public:
+	proteome(entity::registry& registry);
+	
+	/**
+	 * Scales then adds the timestep `dt` to the current time, then recalculates the positions of proteomeing bodies.
+	 *
+	 * @param t Time, in seconds.
+	 * @param dt Delta time, in seconds.
+	 */
+	virtual void update(double t, double dt);
+	
+private:
+	void on_genome_construct(entity::registry& registry, entity::id entity_id, entity::component::genome& genome);
+	void on_genome_replace(entity::registry& registry, entity::id entity_id, entity::component::genome& genome);
+};
+
+} // namespace system
+} // namespace entity
+
+#endif // ANTKEEPER_ENTITY_SYSTEM_PROTEOME_HPP

src/game/bootloader.cpp

@@ -77,6 +77,7 @@
 #include "entity/systems/blackbody.hpp"
 #include "entity/systems/atmosphere.hpp"
 #include "entity/systems/orbit.hpp"
+#include "entity/systems/proteome.hpp"
 #include "entity/components/marker.hpp"
 #include "entity/commands.hpp"
 #include "utility/paths.hpp"
@@ -878,6 +879,9 @@ void setup_systems(game_context* ctx)
 	// Setup astronomy system
 	ctx->astronomy_system = new entity::system::astronomy(*ctx->entity_registry);
 	
+	// Setup proteome system
+	ctx->proteome_system = new entity::system::proteome(*ctx->entity_registry);
+	
 	// Set time scale
 	float time_scale = 60.0f;
 	if (ctx->config->has("time_scale"))
@@ -1277,7 +1281,7 @@ void setup_callbacks(game_context* ctx)
 			ctx->constraint_system->update(t, dt);
 			ctx->tracking_system->update(t, dt);
 			ctx->painting_system->update(t, dt);
-
+			ctx->proteome_system->update(t, dt);
 			
 			//(*ctx->focal_point_tween)[1] = ctx->orbit_cam->get_focal_point();
 			
@@ -1295,8 +1299,6 @@ void setup_callbacks(game_context* ctx)
 			ctx->application_controls->update();
 			ctx->menu_controls->update();
 			ctx->camera_controls->update();
-			
-
 		}
 	);
 	

src/game/game-context.hpp

@@ -99,6 +99,7 @@ namespace entity
 		class nest;
 		class render;
 		class samara;
+		class proteome;
 	}
 }
 
@@ -255,6 +256,7 @@ struct game_context
 	entity::system::atmosphere* atmosphere_system;
 	entity::system::astronomy* astronomy_system;
 	entity::system::orbit* orbit_system;
+	entity::system::proteome* proteome_system;
 	
 	// Game
 	biome* biome;

src/game/states/play-state.cpp

@@ -26,6 +26,7 @@
 #include "entity/components/copy-transform.hpp"
 #include "entity/components/copy-translation.hpp"
 #include "entity/components/model.hpp"
+#include "entity/components/genome.hpp"
 #include "entity/components/snap.hpp"
 #include "entity/components/terrain.hpp"
 #include "entity/components/tool.hpp"
@@ -362,13 +363,20 @@ void play_state_enter(game_context* ctx)
 	
 	// Place larva in chamber
 	{
-		auto larva = larva_archetype->create(entity_registry);
-		entity::command::assign_render_layers(entity_registry, larva, 1);
-		entity::command::warp_to(entity_registry, larva, {50, 0.1935f, 0});
+		auto larva_eid = larva_archetype->create(entity_registry);
+		entity::command::assign_render_layers(entity_registry, larva_eid, 1);
+		entity::command::warp_to(entity_registry, larva_eid, {50, 0.1935f, 0});
 		//auto& transform = entity_registry.get<entity::component::transform>(larva_entity);
 		//transform.transform = math::identity_transform<float>;
 		//transform.transform.translation = nest->get_shaft_position(*central_shaft, central_shaft->depth[1]);
 		//transform.transform.translation.y -= 1.0f;
+		
+		// Construct larva genome
+		entity::component::genome genome;
+		genome.ploidy = 2;
+		const std::string antp = "ATGACCATGAGCACCAACAACTGCGAAAGCATGACCAGCTATTTTACCAACAGCTATATGGGCGCGGATATGCATCATGGCCATTATCCGGGCAACGGCGTGACCGATCTGGATGCGCAGCAGATGCATCATTATAGCCAGAACGCGAACCATCAGGGCAACATGCCGTATCCGCGCTTTCCGCCGTATGATCGCATGCCGTATTATAACGGCCAGGGCATGGATCAGCAGCAGCAGCATCAGGTGTATAGCCGCCCGGATAGCCCGAGCAGCCAGGTGGGCGGCGTGATGCCGCAGGCGCAGACCAACGGCCAGCTGGGCGTGCCGCAGCAGCAGCAGCAGCAGCAGCAGCAGCCGAGCCAGAACCAGCAGCAGCAGCAGGCGCAGCAGGCGCCGCAGCAGCTGCAGCAGCAGCTGCCGCAGGTGACCCAGCAGGTGACCCATCCGCAGCAGCAGCAGCAGCAGCCGGTGGTGTATGCGAGCTGCAAACTGCAGGCGGCGGTGGGCGGCCTGGGCATGGTGCCGGAAGGCGGCAGCCCGCCGCTGGTGGATCAGATGAGCGGCCATCATATGAACGCGCAGATGACCCTGCCGCATCATATGGGCCATCCGCAGGCGCAGGTGCATCAGAACCATCATAACATGGGCATGTATCAGCAGCAGAGCGGCGTGCCGCCGGTGGGCGCGCCGCCGCAGGGCATGATGCATCAGGGCCAGGGCCCGCCGCAGATGCATCAGGGCCATCCGGGCCAGCATACCCCGCCGAGCCAGAACCCGAACAGCCAGAGCAGCGGCATGCCGAGCCCGCTGTATCCGTGGATGCGCAGCCAGTTTGAACGCAAACGCGGCCGCCAGACCTATACCCGCTATCAGACCCTGGAACTGGAAAAAGAATTTCATTTTAACCGCTATCTGACCCGCCGCCGCCGCATTGAAATTGCGCATGCGCTGTGCCTGACCGAACGCCAGATTAAAATTTGGTTTCAGAACCGCCGCATGAAATGGAAAAAAGAAAACAAAACCAAAGGCGAACCGGGCAGCGGCGGCGAAGGCGATGAAATTACCCCGCCGAACAGCCCGCAGTAG";
+		genome.chromosomes.push_back(antp);
+		entity_registry.assign<entity::component::genome>(larva_eid, genome);
 	}
 	
 	entity::system::control* control_system = ctx->control_system;
@@ -382,62 +390,6 @@ void play_state_enter(game_context* ctx)
 	
 	std::string biome_name = (*ctx->strings)[ctx->biome->name];
 	logger->log("Entered biome \"" + biome_name + "\"");
-	
-	
-	std::srand(std::time(nullptr));
-	//auto rng = [](){ return std::rand(); };
-	
-	std::random_device rd;
-	std::mt19937 rng(rd());
-	
-	
-	std::string sequence_a = "CCTTGCCCTTTGGGTCGCCCCCCTAG";
-	std::string sequence_b = "ATGTTTCCCGAAGGGTAG";
-	std::string sequence_c = "AAATGCCCCCCCCCCCCCCCCCCCCCCCCCCCTAGAAAAAAAAA";
-	std::string orf_a;
-	std::string protein_a;
-	std::string protein_b;
-	std::string protein_c;
-	
-	
-	std::cout << "sequence a: " << sequence_a << std::endl;
-	genetics::sequence::transcribe(sequence_a.begin(), sequence_a.end(), sequence_a.begin());
-	std::cout << "sequence a: " << sequence_a << std::endl;
-	
-	std::string complement;
-	genetics::sequence::rna::complement(sequence_a.begin(), sequence_a.end(), std::back_inserter(complement));
-	std::cout << "complement: "  << complement << std::endl;
-	
-	auto orf = genetics::sequence::find_orf(sequence_a.begin(), sequence_a.end(), genetics::standard_code);
-	if (orf.start != sequence_a.end())
-	{
-		std::copy(orf.start, orf.stop, std::back_inserter(orf_a));
-		std::cout << "orf      a: " << orf_a << std::endl;
-		
-		genetics::sequence::translate(orf.start, orf.stop, std::back_inserter(protein_a), genetics::standard_code);
-		std::cout << "protein  a: " << protein_a << std::endl;
-	}
-	
-	protein_b = "MFFFFP";
-	protein_c = "MFFFYP";
-	int score;
-
-	std::cout << std::endl;
-	std::cout << "protein_b: " << protein_b << std::endl;
-	std::cout << "protein_c: " << protein_c << std::endl;
-	
-	score = genetics::protein::score(protein_b.begin(), protein_b.end(), protein_c.begin(), genetics::matrix::blosum62<int>);
-	std::cout << "score blosum62: " << score << std::endl;
-	
-	score = genetics::protein::score(protein_b.begin(), protein_b.end(), protein_c.begin(), genetics::matrix::blosum80<int>);
-	std::cout << "score blosum80: " << score << std::endl;
-	
-	
-	std::cout << "identity  : " << genetics::protein::identity<float>(protein_b.begin(), protein_b.end(), protein_c.begin()) << std::endl;
-	std::cout << "similarity62: " << genetics::protein::similarity<float>(protein_b.begin(), protein_b.end(), protein_c.begin(), genetics::matrix::blosum62<int>) << std::endl;
-	std::cout << "similarity80: " << genetics::protein::similarity<float>(protein_b.begin(), protein_b.end(), protein_c.begin(), genetics::matrix::blosum80<int>) << std::endl;
-	
-	
 }
 
 void play_state_exit(game_context* ctx)