From 12ca06fe9103d2a769b5c1b42515f7b0d62653b1 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Sat, 12 Mar 2022 11:44:27 -0800
Subject: [PATCH] fix handling of empty symmetry cell data
---
CHANGELOG.md | 1 +
.../structure/property/symmetry.ts | 15 +++++++++++++--
2 files changed, 14 insertions(+), 2 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8df9ea307..1f329d45d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,6 +12,7 @@ Note that since we don't clearly distinguish between a public and private interf
- Add Zenodo import extension (load structures, trajectories, volumes, and zip files)
- Fix loading of some compressed files within sessions
- Fix wrong element assignment for atoms with Charmm ion names
+- Fix handling of empty symmetry cell data
## [v3.3.1] - 2022-02-27
diff --git a/src/mol-model-formats/structure/property/symmetry.ts b/src/mol-model-formats/structure/property/symmetry.ts
index 299cf5c8f..316358e30 100644
--- a/src/mol-model-formats/structure/property/symmetry.ts
+++ b/src/mol-model-formats/structure/property/symmetry.ts
@@ -63,10 +63,21 @@ function getSpacegroupNameOrNumber(symmetry: Table<mmCIF_Schema['symmetry']>) {
function getSpacegroup(symmetry: Table<mmCIF_Schema['symmetry']>, cell: Table<mmCIF_Schema['cell']>): Spacegroup {
if (symmetry._rowCount === 0 || cell._rowCount === 0) return Spacegroup.ZeroP1;
+
+ const a = cell.length_a.value(0);
+ const b = cell.length_b.value(0);
+ const c = cell.length_c.value(0);
+ if (a === 0 || b === 0 || c === 0) return Spacegroup.ZeroP1;
+
+ const alpha = cell.angle_alpha.value(0);
+ const beta = cell.angle_beta.value(0);
+ const gamma = cell.angle_gamma.value(0);
+ if (alpha === 0 || beta === 0 || gamma === 0) return Spacegroup.ZeroP1;
+
const nameOrNumber = getSpacegroupNameOrNumber(symmetry);
const spaceCell = SpacegroupCell.create(nameOrNumber,
- Vec3.create(cell.length_a.value(0), cell.length_b.value(0), cell.length_c.value(0)),
- Vec3.scale(Vec3.zero(), Vec3.create(cell.angle_alpha.value(0), cell.angle_beta.value(0), cell.angle_gamma.value(0)), Math.PI / 180));
+ Vec3.create(a, b, c),
+ Vec3.scale(Vec3(), Vec3.create(alpha, beta, gamma), Math.PI / 180));
return Spacegroup.create(spaceCell);
}
--
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