Issue schrodinger#52: Add a test that templates are used

Adds a test that when coordgen is run on the template files,
the templates are actually used. Does this by reading the
template files into molecules and then running
generateCoordinates(). It looks like the template matching code
adds the "rigid" property to any atom that had matched a
template, so that's what is checked here.

test/CMakeLists.txt

@@ -18,6 +18,7 @@ target_link_libraries(test_coordgen coordgen ${maeparser_LIBRARIES} ${boost_link
 # Set the path for the input files
 get_filename_component(TEST_SAMPLES_PATH ${CMAKE_CURRENT_SOURCE_DIR} ABSOLUTE)
 target_compile_definitions(test_coordgen PRIVATE "TEST_SAMPLES_PATH=\"${TEST_SAMPLES_PATH}\"")
+target_compile_definitions(test_coordgen PRIVATE "SOURCE_DIR=\"${PROJECT_SOURCE_DIR}\"")
 
 add_test(NAME test_coordgen COMMAND ${CMAKE_BINARY_DIR}/test/test_coordgen
          WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/test)

test/test_coordgen.cpp

@@ -2,13 +2,15 @@
 
 #include <boost/filesystem.hpp>
 #include <boost/test/unit_test.hpp>
+#include <unordered_set>
 
 #include "../sketcherMinimizer.h"
 #include "../sketcherMinimizerMaths.h"
 
 #include "maeparser/MaeConstants.hpp"
 #include "maeparser/Reader.hpp"
 
+using std::unordered_set;
 using namespace schrodinger;
 
 const boost::filesystem::path test_samples_path(TEST_SAMPLES_PATH);
@@ -50,7 +52,9 @@ bool areBondsNearIdeal(sketcherMinimizerMolecule& mol,
 
     return passed;
 }
-}
+
+} // unnamed namespace
+
 
 BOOST_AUTO_TEST_CASE(SampleTest)
 {
@@ -83,3 +87,59 @@ BOOST_AUTO_TEST_CASE(SampleTest)
     auto indices = getReportingIndices(*mol);
     BOOST_CHECK(areBondsNearIdeal(*mol, indices));
 }
+
+
+BOOST_AUTO_TEST_CASE(TemplateTest)
+{
+    ///
+    // Do the structures in the templates file get the same coordinates that
+    // were supplied in the templates file?
+
+    const boost::filesystem::path source_dir(SOURCE_DIR);
+    const std::string templates_file = (source_dir / "templates.mae").string();
+
+    // Known issues. See issue #52
+    const unordered_set<size_t> no_match = {1, 8, 19, 20, 22, 32, 43, 53, 65, 66, 67};
+    // 32 is odd. minimization removes atoms?? But it matches??
+    const unordered_set<size_t> match_incorrectly = {18, 27};
+
+    mae::Reader r(templates_file);
+    std::shared_ptr<mae::Block> b;
+    size_t template_index = 0;
+    while ((b = r.next(mae::CT_BLOCK)) != nullptr) {
+        if (no_match.count(template_index) > 0 || template_index != 32) {
+            ++template_index;
+            continue;
+        }
+
+        auto* mol = mol_from_mae_block(*b);
+        BOOST_REQUIRE(mol != nullptr);
+        const auto original_atom_count = mol->getAtoms().size();
+
+        sketcherMinimizer minimizer;
+        minimizer.setTemplateFileDir(source_dir.string());
+
+        minimizer.initialize(mol); // minimizer takes ownership of mol
+        minimizer.runGenerateCoordinates();
+
+        BOOST_CHECK_EQUAL(original_atom_count, mol->getAtoms().size());
+
+        bool any_rigid = false;
+        bool all_rigid = true;
+        for (auto a: mol->getAtoms()) {
+            if (a->rigid) {
+                any_rigid = true;
+            } else {
+                all_rigid = false;
+            }
+        }
+        const bool matches_incorrectly = match_incorrectly.count(template_index) > 0;
+        if (matches_incorrectly) {
+            BOOST_CHECK_MESSAGE(any_rigid, "No template found for " << template_index);
+        } else {
+            BOOST_CHECK_MESSAGE(all_rigid, "Not all atoms templated for " << template_index);
+        }
+
+        ++template_index;
+    }
+}