@mstone6969/graph 0.1.0 → 0.2.0

package/dist/charts/lifescience/RamachandranRegions.js

@@ -0,0 +1,2712 @@
+import { RamachandranClass, RamachandranVerdict } from "./ramachandranEnums.js";
+// src/charts/lifescience/RamachandranRegions.ts
+var FAVOURED_LEVEL = .02;
+/** Fraction of good-quality residues outside each class's allowed contour, as `mmtbx.validation.ramalyze` scores them. */
+var ALLOWED_LEVEL = {
+	[RamachandranClass.General]: 5e-4,
+	[RamachandranClass.Glycine]: .001,
+	[RamachandranClass.TransProline]: .001,
+	[RamachandranClass.CisProline]: .002,
+	[RamachandranClass.PreProline]: .001,
+	[RamachandranClass.IleVal]: .001
+};
+var percent = (level) => `${+((1 - level) * 100).toFixed(2)}%`;
+/**
+* Published reference regions: the MolProbity Top8000 Ramachandran contours, `rama8000-*.data` from
+* github.com/rlabduke/reference_data (Richardson Lab, Duke University, CC BY 4.0), described in
+* Williams et al. (2018) Protein Science 27:293-315, doi:10.1002/pro.3330.
+*
+* Adapted, not verbatim: the 2 degree percentile grids were contoured at the levels `ramalyze` uses
+* and simplified to within 0.5 degrees. Against the grids, the polygons disagree on at most 0.24%
+* of cells, all at a contour's edge, so use MolProbity itself for a formal validation report.
+*/
+var RamachandranRegions = class RamachandranRegions {
+	static source = "MolProbity Top8000 contours (Williams et al. 2018, CC BY 4.0)";
+	static favouredLabel() {
+		return `Favoured ${percent(FAVOURED_LEVEL)}`;
+	}
+	static allowedLabel(kind) {
+		return `Allowed ${percent(ALLOWED_LEVEL[kind])}`;
+	}
+	/** Rings in degrees. Nested rings are holes, so fill them with the even-odd rule. */
+	static rings(kind, level) {
+		return MAPS[kind][level].map((ring) => Array.from({ length: ring.length / 2 }, (_, i) => [ring[i * 2] / 2, ring[i * 2 + 1] / 2]));
+	}
+	static classify(kind, phi, psi) {
+		const map = MAPS[kind];
+		if (RamachandranRegions.#inside(map.favoured, phi, psi)) return RamachandranVerdict.Favoured;
+		return RamachandranRegions.#inside(map.allowed, phi, psi) ? RamachandranVerdict.Allowed : RamachandranVerdict.Outlier;
+	}
+	/** Even-odd crossing test, which handles holes because a ring inside another flips the answer back. */
+	static #inside(rings, phi, psi) {
+		let inside = false;
+		for (const ring of rings) for (let i = 0, j = ring.length - 2; i < ring.length; j = i, i += 2) {
+			const xi = ring[i] / 2, yi = ring[i + 1] / 2, xj = ring[j] / 2, yj = ring[j + 1] / 2;
+			if (yi > psi !== yj > psi && phi < (xj - xi) * (psi - yi) / (yj - yi) + xi) inside = !inside;
+		}
+		return inside;
+	}
+};
+var MAPS = {
+	[RamachandranClass.General]: {
+		favoured: [
+			[
+				-288,
+				-330,
+				-258,
+				-338,
+				-222,
+				-345,
+				-202,
+				-343,
+				-182,
+				-336,
+				-170,
+				-336,
+				-162,
+				-338,
+				-155,
+				-342,
+				-141,
+				-358,
+				-142,
+				-360,
+				-342,
+				-360,
+				-346,
+				-358,
+				-339,
+				-350,
+				-330,
+				-341,
+				-322,
+				-336,
+				-306,
+				-329,
+				-298,
+				-329
+			],
+			[
+				110,
+				-246,
+				112,
+				-250,
+				112,
+				-258,
+				110,
+				-262,
+				106,
+				-265,
+				102,
+				-264,
+				98,
+				-258,
+				98,
+				-250,
+				102,
+				-245,
+				106,
+				-244
+			],
+			[
+				-262,
+				106,
+				-246,
+				95,
+				-238,
+				92,
+				-222,
+				81,
+				-198,
+				70,
+				-175,
+				46,
+				-158,
+				26,
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+			],
+			[
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+			],
+			[
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+			]
+		],
+		allowed: [
+			[
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+				346,
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+				342,
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+			],
+			[
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+			],
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+			],
+			[
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+				222,
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+				358,
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+				360
+			],
+			[
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+				170,
+				270,
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+			],
+			[
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+				342,
+				360,
+				358,
+				360
+			]
+		]
+	},
+	[RamachandranClass.Glycine]: {
+		favoured: [
+			[
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+				202,
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+			],
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+			]
+		],
+		allowed: [[
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+				-106,
+				-45,
+				-114,
+				-46,
+				-122,
+				-50,
+				-130,
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+				-138,
+				-70,
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+				-134,
+				-153,
+				-150,
+				-151,
+				-162,
+				-147,
+				-181,
+				-138,
+				-193,
+				-130,
+				-204,
+				-118,
+				-225,
+				-78,
+				-231,
+				-62,
+				-232,
+				-50,
+				-232,
+				-30,
+				-230,
+				-26,
+				-228,
+				-14,
+				-225,
+				-10,
+				-224,
+				-6,
+				-214,
+				0,
+				-210,
+				0
+			],
+			[
+				136,
+				178,
+				150,
+				171,
+				158,
+				164,
+				165,
+				150,
+				167,
+				138,
+				166,
+				122,
+				155,
+				90,
+				148,
+				78,
+				138,
+				69,
+				118,
+				61,
+				106,
+				60,
+				94,
+				62,
+				86,
+				66,
+				54,
+				90,
+				33,
+				110,
+				26,
+				126,
+				24,
+				142,
+				30,
+				157,
+				34,
+				163,
+				42,
+				169,
+				62,
+				176,
+				110,
+				179,
+				126,
+				180
+			],
+			[
+				157,
+				342,
+				162,
+				340,
+				168,
+				334,
+				172,
+				326,
+				174,
+				314,
+				171,
+				302,
+				164,
+				294,
+				154,
+				288,
+				142,
+				288,
+				136,
+				290,
+				122,
+				304,
+				119,
+				318,
+				120,
+				326,
+				124,
+				334,
+				130,
+				340,
+				138,
+				344,
+				146,
+				345
+			],
+			[
+				-111,
+				358,
+				-82,
+				326,
+				-72,
+				302,
+				-56,
+				278,
+				-44,
+				254,
+				-40,
+				242,
+				-39,
+				230,
+				-41,
+				218,
+				-47,
+				206,
+				-58,
+				197,
+				-70,
+				192,
+				-90,
+				191,
+				-122,
+				195,
+				-146,
+				193,
+				-154,
+				189,
+				-193,
+				158,
+				-202,
+				147,
+				-207,
+				134,
+				-210,
+				98,
+				-217,
+				74,
+				-230,
+				52,
+				-242,
+				44,
+				-262,
+				47,
+				-277,
+				54,
+				-314,
+				80,
+				-333,
+				90,
+				-344,
+				98,
+				-352,
+				106,
+				-360,
+				118,
+				-360,
+				358,
+				-358,
+				360,
+				-114,
+				360
+			],
+			[
+				360,
+				358,
+				360,
+				126,
+				358,
+				125,
+				353,
+				162,
+				352,
+				214,
+				346,
+				262,
+				344,
+				278,
+				333,
+				310,
+				332,
+				326,
+				337,
+				346,
+				344,
+				358,
+				346,
+				360,
+				358,
+				360
+			]
+		]
+	},
+	[RamachandranClass.IleVal]: {
+		favoured: [
+			[
+				-248,
+				-358,
+				-250,
+				-360,
+				-278,
+				-360,
+				-279,
+				-358,
+				-274,
+				-356,
+				-266,
+				-354,
+				-258,
+				-355
+			],
+			[
+				-234,
+				62,
+				-226,
+				59,
+				-214,
+				52,
+				-198,
+				40,
+				-165,
+				10,
+				-134,
+				-7,
+				-126,
+				-13,
+				-115,
+				-26,
+				-100,
+				-50,
+				-92,
+				-70,
+				-88,
+				-86,
+				-88,
+				-94,
+				-89,
+				-102,
+				-91,
+				-106,
+				-98,
+				-114,
+				-110,
+				-120,
+				-118,
+				-121,
+				-174,
+				-122,
+				-230,
+				-127,
+				-242,
+				-125,
+				-249,
+				-118,
+				-252,
+				-110,
+				-249,
+				-98,
+				-229,
+				-66,
+				-230,
+				-62,
+				-250,
+				-48,
+				-257,
+				-38,
+				-260,
+				-30,
+				-263,
+				-10,
+				-261,
+				38,
+				-259,
+				50,
+				-254,
+				58,
+				-246,
+				63
+			],
+			[
+				-238,
+				358,
+				-198,
+				333,
+				-190,
+				330,
+				-182,
+				330,
+				-154,
+				337,
+				-146,
+				336,
+				-138,
+				333,
+				-121,
+				318,
+				-92,
+				274,
+				-90,
+				262,
+				-91,
+				258,
+				-96,
+				250,
+				-102,
+				245,
+				-127,
+				230,
+				-135,
+				222,
+				-158,
+				192,
+				-168,
+				170,
+				-174,
+				164,
+				-178,
+				164,
+				-182,
+				166,
+				-193,
+				178,
+				-202,
+				182,
+				-214,
+				184,
+				-250,
+				184,
+				-258,
+				186,
+				-266,
+				191,
+				-280,
+				210,
+				-301,
+				254,
+				-321,
+				274,
+				-330,
+				290,
+				-331,
+				302,
+				-329,
+				310,
+				-322,
+				318,
+				-306,
+				327,
+				-296,
+				346,
+				-286,
+				357,
+				-282,
+				360,
+				-238,
+				360
+			]
+		],
+		allowed: [
+			[
+				-239,
+				-302,
+				-234,
+				-303,
+				-170,
+				-334,
+				-138,
+				-347,
+				-123,
+				-358,
+				-126,
+				-360,
+				-318,
+				-360,
+				-321,
+				-358,
+				-310,
+				-346,
+				-296,
+				-326,
+				-278,
+				-308,
+				-270,
+				-303,
+				-258,
+				-300,
+				-246,
+				-300
+			],
+			[
+				156,
+				-86,
+				166,
+				-94,
+				173,
+				-106,
+				173,
+				-118,
+				172,
+				-126,
+				168,
+				-134,
+				158,
+				-144,
+				146,
+				-148,
+				138,
+				-148,
+				126,
+				-141,
+				117,
+				-130,
+				114,
+				-118,
+				116,
+				-102,
+				122,
+				-93,
+				134,
+				-84,
+				146,
+				-83
+			],
+			[
+				125,
+				142,
+				130,
+				139,
+				136,
+				130,
+				139,
+				118,
+				140,
+				98,
+				136,
+				78,
+				132,
+				66,
+				122,
+				51,
+				114,
+				47,
+				98,
+				47,
+				78,
+				59,
+				63,
+				74,
+				56,
+				90,
+				56,
+				106,
+				59,
+				114,
+				66,
+				123,
+				78,
+				133,
+				90,
+				140,
+				106,
+				145,
+				118,
+				145
+			],
+			[
+				-119,
+				358,
+				-108,
+				342,
+				-90,
+				310,
+				-77,
+				290,
+				-69,
+				270,
+				-68,
+				254,
+				-73,
+				242,
+				-79,
+				234,
+				-86,
+				227,
+				-114,
+				207,
+				-126,
+				190,
+				-134,
+				172,
+				-140,
+				142,
+				-145,
+				130,
+				-150,
+				122,
+				-158,
+				113,
+				-166,
+				108,
+				-188,
+				98,
+				-194,
+				91,
+				-195,
+				86,
+				-187,
+				74,
+				-161,
+				46,
+				-134,
+				22,
+				-113,
+				-2,
+				-95,
+				-30,
+				-75,
+				-66,
+				-67,
+				-90,
+				-66,
+				-102,
+				-67,
+				-110,
+				-75,
+				-126,
+				-82,
+				-132,
+				-90,
+				-137,
+				-146,
+				-149,
+				-155,
+				-154,
+				-178,
+				-173,
+				-202,
+				-185,
+				-210,
+				-188,
+				-222,
+				-190,
+				-234,
+				-189,
+				-238,
+				-188,
+				-250,
+				-181,
+				-272,
+				-158,
+				-284,
+				-142,
+				-292,
+				-122,
+				-296,
+				-82,
+				-298,
+				30,
+				-301,
+				50,
+				-297,
+				90,
+				-293,
+				118,
+				-296,
+				162,
+				-298,
+				170,
+				-308,
+				190,
+				-318,
+				218,
+				-322,
+				226,
+				-340,
+				250,
+				-360,
+				282,
+				-360,
+				322,
+				-356,
+				330,
+				-348,
+				342,
+				-322,
+				360,
+				-122,
+				360
+			]
+		]
+	}
+};
+export { RamachandranRegions };