From c10d9db3111c62a614502a482e30de27f2423a09 Mon Sep 17 00:00:00 2001
From: Sebastian Bittrich <bittrich@hs-mittweida.de>
Date: Fri, 22 Mar 2019 16:44:43 -0700
Subject: [PATCH] moves dihedral calc to Vec3, decreases allocation inside
function
---
src/mol-math/linear-algebra/3d/vec3.ts | 22 +++++++++++++++
.../properties/utils/secondary-structure.ts | 28 ++-----------------
2 files changed, 24 insertions(+), 26 deletions(-)
diff --git a/src/mol-math/linear-algebra/3d/vec3.ts b/src/mol-math/linear-algebra/3d/vec3.ts
index 59308ddf0..bb16cc353 100644
--- a/src/mol-math/linear-algebra/3d/vec3.ts
+++ b/src/mol-math/linear-algebra/3d/vec3.ts
@@ -434,6 +434,28 @@ namespace Vec3 {
}
}
+ const tmp_dh_ab = Vec3.zero();
+ const tmp_dh_cb = Vec3.zero();
+ const tmp_dh_bc = Vec3.zero();
+ const tmp_dh_dc = Vec3.zero();
+ const tmp_dh_abc = Vec3.zero();
+ const tmp_dh_bcd = Vec3.zero();
+ const tmp_dh_cross = Vec3.zero();
+ /** Computes the dihedral angles of 4 related atoms. phi: C, N+1, CA+1, C+1 - psi: N, CA, C, N+1 - omega: CA, C, N+1, CA+1 */
+ export function dihedralAngle(a: Vec3, b: Vec3, c: Vec3, d: Vec3) {
+ Vec3.sub(tmp_dh_ab, a, b);
+ Vec3.sub(tmp_dh_cb, c, b);
+ Vec3.sub(tmp_dh_bc, b, c);
+ Vec3.sub(tmp_dh_dc, d, c);
+
+ Vec3.cross(tmp_dh_abc, tmp_dh_ab, tmp_dh_cb);
+ Vec3.cross(tmp_dh_bcd, tmp_dh_bc, tmp_dh_dc);
+
+ const angle = Vec3.angle(tmp_dh_abc, tmp_dh_bcd) * 360.0 / (2 * Math.PI);
+ Vec3.cross(tmp_dh_cross, tmp_dh_abc, tmp_dh_bcd);
+ return Vec3.dot(tmp_dh_cb, tmp_dh_cross) > 0 ? angle : -angle;
+ }
+
/**
* Returns whether or not the vectors have exactly the same elements in the same position (when compared with ===)
*/
diff --git a/src/mol-model/structure/model/properties/utils/secondary-structure.ts b/src/mol-model/structure/model/properties/utils/secondary-structure.ts
index 5192456d5..cbc23b4db 100644
--- a/src/mol-model/structure/model/properties/utils/secondary-structure.ts
+++ b/src/mol-model/structure/model/properties/utils/secondary-structure.ts
@@ -407,11 +407,11 @@ function calculateDihedralAngles(hierarchy: AtomicHierarchy, conformation: Atomi
// angle calculations return NaN upon missing atoms
// TODO would be nice to be provided elsewhere, omega is related but not needed here
function calculatePhi(c: Vec3, nNext: Vec3, caNext: Vec3, cNext: Vec3) {
- return angle(c, nNext, caNext, cNext);
+ return Vec3.dihedralAngle(c, nNext, caNext, cNext);
}
function calculatePsi(n: Vec3, ca: Vec3, c: Vec3, nNext: Vec3) {
- return angle(n, ca, c, nNext);
+ return Vec3.dihedralAngle(n, ca, c, nNext);
}
// function calculateOmega(ca: Vec3, c: Vec3, nNext: Vec3, caNext: Vec3) {
@@ -800,30 +800,6 @@ function assignHelices(ctx: DSSPContext) {
// console.log(`${ count[3] + count[4] + count[5] } helix elements - ${ count[3] } 3-10, ${ count[4] } alpha, ${ count[5] } pi`)
}
-function angle(a: Vec3, b: Vec3, c: Vec3, d: Vec3) {
- const ab = Vec3.zero();
- const cb = Vec3.zero();
- const bc = Vec3.zero();
- const dc = Vec3.zero();
-
- Vec3.sub(ab, a, b);
- Vec3.sub(cb, c, b);
- Vec3.sub(bc, b, c);
- Vec3.sub(dc, d, c);
-
- const abc = Vec3.zero();
- const bcd = Vec3.zero();
-
- Vec3.cross(abc, ab, cb);
- Vec3.cross(bcd, bc, dc);
-
- const angle = Vec3.angle(abc, bcd) * 360.0 / (2 * Math.PI);
- const cross = Vec3.zero();
- Vec3.cross(cross, abc, bcd);
-
- return Vec3.dot(cb, cross) > 0 ? angle : -angle;
-}
-
/**
* ladder=: set of one or more consecutive bridges of identical type
*
--
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