starting work on WebAssembly bindings (based on Embind)

wasm/Makefile

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+CXX = em++
+
+INCLUDE = -I../include
+
+FLAGS = \
+  -O3 -flto -Wall -Wextra -std=c++20 \
+  -DEMSCRIPTEN_HAS_UNBOUND_TYPE_NAMES=0 -fno-rtti \
+  -s STRICT=1 \
+  -s DISABLE_EXCEPTION_CATCHING=0
+
+LINK_FLAGS = \
+  --pre-js pre.js \
+  -s EXPORTED_RUNTIME_METHODS=ccall,writeArrayToMemory,getValue,UTF8ToString \
+  -s EXPORTED_FUNCTIONS=_malloc \
+  -s INCOMING_MODULE_JS_API=print,printErr,setStatus,onRuntimeInitialized \
+  -s ALLOW_MEMORY_GROWTH=1 -s MODULARIZE=1
+
+#  -s ASSERTIONS=1 -s SAFE_HEAP=1 \
+
+GEMMI_OBJS = mmcif.o polyheur.o resinfo.o sprintf.o json.o
+
+BINDING_OBJS = mol.o
+
+gemmi.js: $(GEMMI_OBJS) $(BINDING_OBJS)
+	$(CXX) --bind $(FLAGS) $(LINK_FLAGS) $(GEMMI_OBJS) $(BINDING_OBJS) -o $@
+
+$(GEMMI_OBJS): %.o: ../src/%.cpp
+	$(CXX) $(INCLUDE) $(FLAGS) -c $< -o $@
+
+$(BINDING_OBJS): %.o: %.cpp
+	$(CXX) $(INCLUDE) $(FLAGS) -c $< -o $@
+
+%.o: %.cpp
+	$(CXX) $(INCLUDE) $(FLAGS) -c $<
+
+clean:
+	rm -f *.o gemmi.js *.wasm
+
+.PHONY: clean

wasm/mol.cpp

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+// Copyright Global Phasing Ltd.
+
+#include <gemmi/model.hpp>
+#include <gemmi/select.hpp>   // for Selection
+#include <gemmi/mmread.hpp>   // for read_structure_from_memory
+#include <emscripten/bind.h>
+#include <emscripten/val.h>
+
+namespace em = emscripten;
+
+gemmi::CoorFormat format_to_enum(const std::string& format) {
+  using gemmi::CoorFormat;
+  if (format == "unknown")
+    return CoorFormat::Unknown;
+  if (format == "detect")
+    return CoorFormat::Detect;
+  if (format == "pdb")
+    return CoorFormat::Pdb;
+  if (format == "mmcif")
+    return CoorFormat::Mmcif;
+  if (format == "mmjson")
+    return CoorFormat::Mmjson;
+  if (format == "chemcomp")
+    return CoorFormat::ChemComp;
+  gemmi::fail("unknown file format: " + format);
+}
+
+// IIUC passing string by value is OK here, it's copied the JS side anyway
+gemmi::Structure read_structure(std::string buf, std::string name, std::string format) {
+  return gemmi::read_structure_from_memory(buf.data(), buf.size(), name,
+                                           format_to_enum(format));
+}
+
+template <typename T>
+size_t get_children_length(const T& t) { return t.children().size(); }
+
+template <typename T>
+typename T::child_type* get_child(T& t, size_t n) { return &t.children().at(n); }
+
+template <typename T>
+em::class_<T> wrap_children() {
+  return em::class_<T>(T::what())
+    .template constructor<>()
+    .property("length", &get_children_length<T>)
+    .function("get", &get_child<T>, em::allow_raw_pointers())
+    ;
+}
+
+EMSCRIPTEN_BINDINGS(Gemmi) {
+  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)
+    ;
+
+  wrap_children<gemmi::Model>()
+    .property("name", &gemmi::Model::name)
+    .function("count_occupancies", &gemmi::count_occupancies<gemmi::Model>,
+              em::allow_raw_pointers())
+    ;
+
+  wrap_children<gemmi::Chain>()
+    .property("name", &gemmi::Chain::name)
+    ;
+
+  wrap_children<gemmi::Residue>()
+    .property("subchain", &gemmi::Residue::subchain)
+    ;
+
+  em::class_<gemmi::Atom>("Atom")
+    .constructor<>()
+    .property("name", &gemmi::Atom::name)
+    .property("altloc", &gemmi::Atom::altloc)
+    .property("charge", &gemmi::Atom::charge)
+    .property("serial", &gemmi::Atom::serial)
+    .property("occ", &gemmi::Atom::occ)
+    .property("b_iso", &gemmi::Atom::b_iso)
+    ;
+
+  em::class_<gemmi::Selection>("Selection")
+    .constructor<>()
+    ;
+
+  // wrapped in pre.js to add default value
+  em::function("_read_structure", &read_structure);
+}

wasm/pre.js

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+
+Module['read_structure'] = function (buf, name, format) {
+  return Module._read_structure(buf, name, format || 'unknown');
+};