wasm: work in progress

wasm/Makefile

@@ -1,4 +1,4 @@
-# currently using Emscripten 3.1.53
+# currently using Emscripten 3.1.56
 CXX = em++
 
 INCLUDE = -I../include
@@ -14,7 +14,7 @@ LINK_FLAGS = \
   --post-js post.js \
   --no-entry \
   -lembind \
-  -s EXPORTED_RUNTIME_METHODS=ccall,writeArrayToMemory,getValue,UTF8ToString \
+  -s EXPORTED_RUNTIME_METHODS=writeArrayToMemory,HEAPU8 \
   -s EXPORTED_FUNCTIONS=_malloc \
   -s INCOMING_MODULE_JS_API=print,printErr,setStatus,onRuntimeInitialized \
   -s ALLOW_MEMORY_GROWTH=1 \
@@ -25,19 +25,19 @@ LINK_FLAGS = \
 
 GEMMI_OBJS = mmcif.o polyheur.o resinfo.o sprintf.o json.o
 
-BINDING_OBJS = gemmi.o mol.o mtz_fft.o
+BINDING_OBJS = gemmi.o cell.o mol.o mtz_fft.o
 
 gemmi.js: $(GEMMI_OBJS) $(BINDING_OBJS)
 	$(CXX) $(FLAGS) $(LINK_FLAGS) $(GEMMI_OBJS) $(BINDING_OBJS) -o $@
 
 # old mtz module (not built by default)
-mtz.js: mtz_fft.cpp
+mtz.js: mtz_fft.cpp cell.o
 	$(CXX) -DSTANDALONE_MTZ=1 $(INCLUDE) $(FLAGS) \
 	-lembind --no-entry --pre-js=pre.js \
 	-s MODULARIZE=1 -s ALLOW_MEMORY_GROWTH=1 \
 	-s EXPORTED_FUNCTIONS=_malloc \
 	-s EXPORTED_RUNTIME_METHODS=writeArrayToMemory \
-	-s EXPORT_NAME=GemmiMtz $< -o $@
+	-s EXPORT_NAME=GemmiMtz $^ -o $@
 
 $(GEMMI_OBJS): %.o: ../src/%.cpp
 	$(CXX) $(INCLUDE) $(FLAGS) -c $< -o $@
@@ -49,6 +49,6 @@ $(BINDING_OBJS): %.o: %.cpp
 	$(CXX) $(INCLUDE) $(FLAGS) -c $<
 
 clean:
-	rm -f *.o gemmi.js *.wasm
+	rm -f *.o gemmi.js mtz.js *.wasm
 
 .PHONY: clean

wasm/README.md

@@ -1,3 +1,7 @@
+Work in progress...
+
+here is old documentation for reading MTZ only
+
 # MTZ reader in WebAssembly
 
 The MTZ file format is used for the storage of reflection data --

wasm/cell.cpp

@@ -0,0 +1,15 @@
+// Copyright Global Phasing Ltd.
+
+#include "common.h"
+#include <gemmi/unitcell.hpp>
+
+void add_cell() {
+  em::class_<gemmi::UnitCell>("UnitCell")
+    .property("a", &gemmi::UnitCell::a)
+    .property("b", &gemmi::UnitCell::b)
+    .property("c", &gemmi::UnitCell::c)
+    .property("alpha", &gemmi::UnitCell::alpha)
+    .property("beta", &gemmi::UnitCell::beta)
+    .property("gamma", &gemmi::UnitCell::gamma)
+    ;
+}

wasm/common.h

@@ -4,5 +4,6 @@
 #include <emscripten/bind.h>
 namespace em = emscripten;
 
-void add_mol();
-void add_mtz_fft();
+void add_cell();    // cell.cpp
+void add_mol();     // mol.cpp
+void add_mtz_fft(); // mtz_fft.cpp

wasm/gemmi.cpp

@@ -4,6 +4,7 @@
 #include <emscripten/em_asm.h>
 
 EMSCRIPTEN_BINDINGS(Gemmi) {
+  add_cell();
   add_mol();
   add_mtz_fft();
   EM_ASM( finalize_gemmi(); );

wasm/mol.cpp

@@ -48,15 +48,6 @@ em::class_<T> wrap_children() {
 }
 
 void add_mol() {
-  em::class_<gemmi::UnitCell>("UnitCell")
-    .property("a", &gemmi::UnitCell::a)
-    .property("b", &gemmi::UnitCell::b)
-    .property("c", &gemmi::UnitCell::c)
-    .property("alpha", &gemmi::UnitCell::alpha)
-    .property("beta", &gemmi::UnitCell::beta)
-    .property("gamma", &gemmi::UnitCell::gamma)
-    ;
-
   wrap_children<gemmi::Structure>()
     .property("name", &gemmi::Structure::name)
     .property("cell", &gemmi::Structure::cell)

wasm/mtz.d.ts

@@ -0,0 +1,28 @@
+// interface for mtz.js that can be built with "make mtz.js"
+
+export interface UnitCell {
+  a: number;
+  b: number;
+  c: number;
+  alpha: number;
+  beta: number;
+  gamma: number;
+  delete(): void;
+}
+
+export interface Mtz {
+  readonly cell: UnitCell;
+  readonly nx: number;
+  readonly ny: number;
+  readonly nz: number;
+  readonly rmsd: number;
+  readonly last_error: string;
+  read(_0: number, _1: number): boolean;
+  calculate_map(_0: boolean): any;
+  calculate_map_from_labels(_0: string, _1: string): any;
+  delete(): void;
+}
+
+export interface Module {
+  readMtz(mtz_buf: string|ArrayBuffer): Mtz;
+}

wasm/mtz_fft.cpp

@@ -118,6 +118,7 @@ void add_mtz_fft() {
 
 #ifdef STANDALONE_MTZ
 EMSCRIPTEN_BINDINGS(GemmiMtz) {
+  add_cell();
   add_mtz_fft();
 }
 #endif

wasm/mtz_fft.test.js

@@ -0,0 +1,16 @@
+const fs = require('node:fs');
+const zlib = require('node:zlib');
+const Gemmi = require('./gemmi.js')
+
+
+test('counts atom occupancies', () => {
+  Gemmi().then((gemmi) => {
+    const path = '../tests/5wkd_phases.mtz.gz';
+    const buffer_gz = fs.readFileSync(path);
+    const buffer = zlib.gunzipSync(new Buffer.from(buffer_gz));
+    const mtz = gemmi.readMtz(buffer);
+    expect(mtz.cell.a).toBe(50.347);
+    expect(mtz.cell.gamma).toBe(90.);
+    mtz.delete();
+  });
+});