Add atom bonds cache and benchmark for SARS-CoV-2

README.md

@@ -62,6 +62,14 @@ cargo run --release
 
 (Bevy uses Metal; no Vulkan needed.)
 
+### Performance
+
+```bash
+just bench
+# or
+cargo bench -p vizmat-core --bench bond_cache
+```
+
 ## wasm
 
 It require rustc target `wasm32-unknown-unknown` installed.

justfile

@@ -1,22 +1,53 @@
 set shell := ["bash", "-eu", "-o", "pipefail", "-c"]
 
+check-pdb path:
+    @if rg -n -i "^[[:space:]]*<!doctype|^[[:space:]]*<html|^[[:space:]]*<head|^[[:space:]]*<body" {{path}} >/dev/null; then \
+        echo "ERROR: {{path}} looks like HTML, not PDB"; \
+        exit 1; \
+    fi
+    @if ! rg -n "^(ATOM  |HETATM)" {{path}} >/dev/null; then \
+        echo "ERROR: {{path}} has no ATOM/HETATM records"; \
+        exit 1; \
+    fi
+
+clean-broken-proteins:
+    rm -f vizmat-app/assets/proteins/4V6F.pdb vizmat-app/assets/proteins/4V6F.xyz
+    rm -f vizmat-app/assets/proteins/7K00.pdb vizmat-app/assets/proteins/7K00.xyz
+    ls -1 vizmat-app/assets/proteins
+
+verify-proteins:
+    @for f in vizmat-app/assets/proteins/*.pdb; do \
+        just check-pdb "$f"; \
+    done
+    @for f in vizmat-app/assets/proteins/*.xyz; do \
+        n="$(head -n 1 "$f" | tr -d '\r')"; \
+        if ! [[ "$n" =~ ^[0-9]+$ ]] || [ "$n" -eq 0 ]; then \
+            echo "ERROR: $f has invalid/zero atom count in line 1: '$n'"; \
+            exit 1; \
+        fi; \
+    done
+    echo "Protein files verify OK"
+
 protein-4hhb:
     mkdir -p vizmat-app/assets/proteins
-    curl -L "https://files.rcsb.org/download/4HHB.pdb" -o vizmat-app/assets/proteins/4HHB.pdb
+    curl -fL "https://files.rcsb.org/download/4HHB.pdb" -o vizmat-app/assets/proteins/4HHB.pdb
+    just check-pdb vizmat-app/assets/proteins/4HHB.pdb
     awk 'function trim(s){ gsub(/^ +| +$/, "", s); return s } BEGIN{ n=0 } /^(ATOM  |HETATM)/ { n++; x=substr($0,31,8)+0; y=substr($0,39,8)+0; z=substr($0,47,8)+0; el=trim(substr($0,77,2)); if (el=="") { name=trim(substr($0,13,4)); el=substr(name,1,1) } elem[n]=el; xs[n]=x; ys[n]=y; zs[n]=z } END{ out="vizmat-app/assets/proteins/4HHB.xyz"; print n > out; print "4HHB hemoglobin (from PDB ATOM/HETATM records)" >> out; for(i=1;i<=n;i++) printf "%s %.5f %.5f %.5f\n", elem[i], xs[i], ys[i], zs[i] >> out }' vizmat-app/assets/proteins/4HHB.pdb
     wc -l vizmat-app/assets/proteins/4HHB.xyz
     head -n 5 vizmat-app/assets/proteins/4HHB.xyz
 
 protein-6vxx:
     mkdir -p vizmat-app/assets/proteins
-    curl -L "https://files.rcsb.org/download/6VXX.pdb" -o vizmat-app/assets/proteins/6VXX.pdb
+    curl -fL "https://files.rcsb.org/download/6VXX.pdb" -o vizmat-app/assets/proteins/6VXX.pdb
+    just check-pdb vizmat-app/assets/proteins/6VXX.pdb
     awk 'function trim(s){ gsub(/^ +| +$/, "", s); return s } BEGIN{ n=0 } /^(ATOM  |HETATM)/ { n++; x=substr($0,31,8)+0; y=substr($0,39,8)+0; z=substr($0,47,8)+0; el=trim(substr($0,77,2)); if (el=="") { name=trim(substr($0,13,4)); el=substr(name,1,1) } elem[n]=el; xs[n]=x; ys[n]=y; zs[n]=z } END{ out="vizmat-app/assets/proteins/6VXX.xyz"; print n > out; print "6VXX structure (from PDB ATOM/HETATM records)" >> out; for(i=1;i<=n;i++) printf "%s %.5f %.5f %.5f\n", elem[i], xs[i], ys[i], zs[i] >> out }' vizmat-app/assets/proteins/6VXX.pdb
     wc -l vizmat-app/assets/proteins/6VXX.xyz
     head -n 5 vizmat-app/assets/proteins/6VXX.xyz
 
 protein-3j3a:
     mkdir -p vizmat-app/assets/proteins
-    curl -L "https://files.rcsb.org/download/3J3A.pdb" -o vizmat-app/assets/proteins/3J3A.pdb
+    curl -fL "https://files.rcsb.org/download/3J3A.pdb" -o vizmat-app/assets/proteins/3J3A.pdb
+    just check-pdb vizmat-app/assets/proteins/3J3A.pdb
     awk 'function trim(s){ gsub(/^ +| +$/, "", s); return s } BEGIN{ n=0 } /^(ATOM  |HETATM)/ { n++; x=substr($0,31,8)+0; y=substr($0,39,8)+0; z=substr($0,47,8)+0; el=trim(substr($0,77,2)); if (el=="") { name=trim(substr($0,13,4)); el=substr(name,1,1) } elem[n]=el; xs[n]=x; ys[n]=y; zs[n]=z } END{ out="vizmat-app/assets/proteins/3J3A.xyz"; print n > out; print "3J3A ribosome (from PDB ATOM/HETATM records)" >> out; for(i=1;i<=n;i++) printf "%s %.5f %.5f %.5f\n", elem[i], xs[i], ys[i], zs[i] >> out }' vizmat-app/assets/proteins/3J3A.pdb
     test "$(head -n 1 vizmat-app/assets/proteins/3J3A.xyz)" -gt 0
     test "$(wc -l < vizmat-app/assets/proteins/3J3A.xyz)" -eq "$(( $(head -n 1 vizmat-app/assets/proteins/3J3A.xyz) + 2 ))"
@@ -27,6 +58,9 @@ protein-3j3a:
 watch:
     cargo watch -x "run"
 
+bench:
+    cargo bench -p vizmat-core --bench bond_cache
+
 wasm:
     rustup target add wasm32-unknown-unknown --toolchain nightly-aarch64-apple-darwin
     cd vizmat-app && PATH="$HOME/.cargo/bin:$PATH" NO_COLOR=false trunk serve --port 8082