From 1fa9872ad4683de387b2594ed25677cf3fd99309 Mon Sep 17 00:00:00 2001
From: sanine <sanine.not@pm.me>
Date: Sun, 25 Jun 2023 00:06:43 -0500
Subject: add protein

---
 src/mind/topology.test.js   | 28 ++++++++++++++--------------
 src/protein/protein.js      | 10 ++++++++++
 src/protein/protein.test.js | 29 +++++++++++++++++++++++++++++
 3 files changed, 53 insertions(+), 14 deletions(-)
 create mode 100644 src/protein/protein.js
 create mode 100644 src/protein/protein.test.js

diff --git a/src/mind/topology.test.js b/src/mind/topology.test.js
index 9776132..52c196f 100644
--- a/src/mind/topology.test.js
+++ b/src/mind/topology.test.js
@@ -175,20 +175,20 @@ test('arbitrary hidden neurons', () => {
 		.connect(1, 2, -1)
 		.connect(2, 3, 2)
 
-  const [output, state] = n.compute([1], [0, 0]);
-
-  expect(output).toEqual([
-    Math.tanh(
-      2*Math.tanh(
-        -1*Math.tanh(1)
-      )
-    )
-  ]);
-
-  expect(state).toEqual([
-    Math.tanh(1),
-    Math.tanh( -Math.tanh(1) ),
-  ]);
+	const [output, state] = n.compute([1], [0, 0]);
+
+	expect(output).toEqual([
+		Math.tanh(
+			2*Math.tanh(
+				-1*Math.tanh(1)
+			)
+		)
+	]);
+
+	expect(state).toEqual([
+		Math.tanh(1),
+		Math.tanh( -Math.tanh(1) ),
+	]);
 });
 
 
diff --git a/src/protein/protein.js b/src/protein/protein.js
new file mode 100644
index 0000000..0223203
--- /dev/null
+++ b/src/protein/protein.js
@@ -0,0 +1,10 @@
+const xnor = (a, b) => a === b ? 1 : 0;
+
+export function compare(pa, pb) {
+	if (pa.length !== pb.length) {
+		throw new Error(`attempted to compare proteins with different lengths: ${pa.length} vs ${pb.length}`);
+	}
+	return (1/pa.length) * pa
+		.map((_, i) => xnor(pa[i], pb[i]))
+		.reduce((acc, val) => acc + val, 0)
+}
diff --git a/src/protein/protein.test.js b/src/protein/protein.test.js
new file mode 100644
index 0000000..61c4896
--- /dev/null
+++ b/src/protein/protein.test.js
@@ -0,0 +1,29 @@
+'use strict';
+
+import { compare } from './protein';
+
+test('compare size-1 proteins', () => {
+	expect(compare([0], [0])).toBe(1);
+	expect(compare([0], [1])).toBe(0);
+	expect(compare([1], [0])).toBe(0);
+	expect(compare([1], [1])).toBe(1);
+});
+
+
+test('compare larger proteins', () => {
+	expect(compare([0,0], [0,0])).toBe(1);
+	expect(compare([1,1], [1,1])).toBe(1);
+	expect(compare([0,1], [1,1])).toBeCloseTo(0.5);
+	expect(compare([0,1,0], [1,1,1])).toBeCloseTo(1/3);
+	expect(compare([0,1,0,1], [1,1,1,1])).toBeCloseTo(0.5);
+	expect(compare([0,1,0,1], [0,1,1,1])).toBeCloseTo(0.75);
+	expect(compare([0,1,0,1], [0,1,1,0])).toBeCloseTo(0.5);
+	expect(compare([0,1,0,0], [0,1,1,0])).toBeCloseTo(0.75);
+	expect(compare([0,1,1,0], [0,1,1,0])).toBeCloseTo(1);
+});
+
+
+test('comparisons between differently-sized proteins throw', () => {
+	expect(() => compare([0], [0, 0])).toThrow();
+	expect(() => compare([0, 0], [0])).toThrow();
+});
-- 
cgit v1.2.1