Add mmcif tests to api

Currently just one stub of a test - but the point of this commit
was to make something that can be build as a stand-alone executable
and as a chapi function.

CMakeLists.txt

@@ -183,6 +183,7 @@ add_library(cootapi SHARED
             ${coot_src}/api/molecules-container-superpose.cc
             ${coot_src}/api/molecules-container-modelling.cc
             ${coot_src}/api/molecules-container-ligand-fitting.cc
+            ${coot_src}/api/mmcif-tests.cc
             ${coot_src}/api/phi-psi-prob.cc
             ${coot_src}/api/moorhen-h-bonds.cc
             ${coot_src}/api/add-terminal-residue.cc
@@ -482,6 +483,8 @@ add_executable(res-tracer-libcootapi ${coot_src}/ligand/res-tracer.cc)
 
 add_executable(test-molecules-container ${coot_src}/api/test-molecules-container.cc ${coot_src}/api/filo-tests.cc ${coot_src}/api/lucrezia-tests.cc)
 
+add_executable(mmcif-tests ${coot_src}/api/mmcif-tests-main.cc)
+
 target_compile_features(coot-mini-rsr PRIVATE cxx_std_17)
 
 target_compile_features(res-tracer-libcootapi PRIVATE cxx_std_17)
@@ -508,6 +511,10 @@ target_include_directories(test-molecules-container PRIVATE ${coot_src} ${coot_s
 
 target_link_libraries(test-molecules-container PUBLIC cootapi ${SSM_LIBRARY} ${CLIPPER-MINIMOL_LIBRARY} ${CLIPPER-MMDB_LIBRARY} ${CLIPPER-CIF_LIBRARY} ${CLIPPER-CORE_LIBRARY} ${CLIPPER-CCP4_LIBRARY} ${CLIPPER-CONTRIB_LIBRARY} ${FFTW2_LIBRARY} ${RFFTW2_LIBRARY} ${MMDB2_LIBRARY} ${CCP4C_LIBRARY} ${ZLIB_LIBRARIES} ${GSL_LIBRARIES} ${RDKit_libs_for_libcootapi} ${PNG_LIBRARY} gemmi::gemmi_cpp ${libdwarf} ${libelf} Threads::Threads)
 
+target_include_directories(mmcif-tests PRIVATE ${MMDB2_INCLUDE_DIR}/include)
+
+target_link_libraries(mmcif-tests PUBLIC cootapi ${MMDB2_LIBRARY})
+
 set_target_properties(cootapi PROPERTIES INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
 
 set_target_properties(cootapi PROPERTIES INSTALL_RPATH_USE_LINK_PATH TRUE)

api/mmcif-tests-main.cc

@@ -0,0 +1,14 @@
+#include <string>
+#include <iostream>
+
+namespace mmcif_tests {
+   int run_tests(bool last_test_only);
+}
+
+int main(int argc, char **argv) {
+
+   std::cout << "------------- main() --- start ---" << std::endl;
+   int status = 0;
+   std::cout << "------------- main() --- end ---" << std::endl;
+   return status;
+}

api/mmcif-tests.cc

@@ -0,0 +1,91 @@
+
+#include "mmdb2/mmdb_defs.h"
+#include "mmdb2/mmdb_model.h"
+#include <string>
+#include <iostream>
+#include <iomanip>
+#include <fstream>
+#include <vector>
+
+#include <mmdb2/mmdb_manager.h>
+
+int n_tests = 0;
+static std::vector<std::pair<std::string, int> > test_results;
+
+namespace mmcif_tests {
+
+   void write_test_name(const std::string &test_name);
+   int run_test(int (*test_func) (), const std::string &test_name);
+   int run_tests(bool last_test_only);
+   int read_pdb();
+   enum status_t { BAD, GOOD };
+}
+
+void
+mmcif_tests::write_test_name(const std::string &test_name) {
+
+   std::ofstream f(".current-test");
+   f << "\"" << test_name << "\"" << "\n";
+   f.close();
+}
+
+int
+mmcif_tests::run_test(int (*test_func) (), const std::string &test_name) {
+
+   n_tests++;
+   write_test_name(test_name);
+   int status = test_func();
+   std::string status_string = "FAIL: ";
+   std::string uncol = "";
+   std::string col = "";
+   if (status == 1) {
+      status_string = "PASS: ";
+      col = "";
+   }
+   std::cout << status_string << std::setw(40) << std::left << test_name << col << " ⬤ " << uncol << std::endl;
+   test_results.push_back(std::make_pair(test_name, status));
+
+   return status;
+}
+
+int mmcif_tests::read_pdb() {
+
+   int status = 0;
+   mmdb::Manager *mol = new mmdb::Manager;
+   // 6DGD for DNA bases
+   // https://files.rcsb.org/download/6GDG.cif
+   mmdb::ERROR_CODE read_status = mol->ReadCoorFile("6gdg.cif");
+   std::cout << "TEST read_pdb() with read_status " << read_status << std::endl;
+   if (read_status == mmdb::Error_NoError) {
+      for (int imod = 1; imod <= mol->GetNumberOfModels(); imod++) {
+        mmdb::Model *model_p = mol->GetModel(imod);
+        if (model_p) {
+          int n_links = model_p->GetNumberOfLinks();
+          std::cout << "n_links: " << n_links << std::endl;
+          for (int i_link = 0; i_link < n_links; i_link++) {
+            mmdb::Link *link_p = model_p->GetLink(i_link);
+            std::cout << "Link " << i_link << " " << link_p << std::endl;
+          }
+        }
+      }
+   }
+   return status;
+};
+
+// return "all pass" status (1 for true)
+int
+mmcif_tests::run_tests(bool last_test_only) {
+
+   std::cout << "--------------- run_tests() --- start --- " << std::endl;
+   if (! last_test_only) {
+      run_test(read_pdb, "read_pdb");
+   }
+   int status = 1;
+   for (const auto &t : test_results) {
+      if (t.second != 1)
+         status = 0;
+   }
+   std::cout << "--------------- run_tests() --- end --- " << std::endl;
+   return status;
+}
+

api/molecules-container-nanobind.cc

@@ -334,6 +334,7 @@ NB_MODULE(chapi, m) {
     .def("make_power_scaled_map", &molecules_container_t::make_power_scaled_map)
     .def("merge_molecules", nb::overload_cast<int,const std::string &>(&molecules_container_t::merge_molecules))
     .def("minimize_energy",&molecules_container_t::minimize_energy)
+    .def("mmcif_tests",&molecules_container_t::mmcif_tests)
     .def("mmrrcc",&molecules_container_t::mmrrcc)
     .def("move_molecule_to_new_centre",&molecules_container_t::move_molecule_to_new_centre)
     .def("multiply_residue_temperature_factors",&molecules_container_t::multiply_residue_temperature_factors)

api/molecules-container.cc

@@ -5367,6 +5367,20 @@ molecules_container_t::test_thread_pool_threads(unsigned int n_threads) {
 
 }
 
+namespace mmcif_tests {
+   int run_tests(bool last_test_only);
+}
+
+//! a test for mmdb/gemmi/mmcif functionality
+int
+molecules_container_t::mmcif_tests(bool last_test_only) {
+
+   int status = mmcif_tests::run_tests(last_test_only);
+   return status;
+
+}
+
+
 
 //! @return a vector of string pairs that were part of a gphl_chem_comp_info.
 //!  return an empty vector on failure to find any such info.

api/molecules-container.hh

@@ -2021,6 +2021,15 @@ public:
    //! @return time in microsections
    double test_thread_pool_threads(unsigned int n_threads);
 
+   //! a test for mmdb/gemmi/mmcif functionality
+   //
+   //! @param last_test_only is `true` to mean that only that last test should be run.
+   //! The default is `false`.
+   //! This is useful to set to `true` while a test is being developed.
+   //!
+   //! @return the success status: 1 means that all the tests passed.
+   int mmcif_tests(bool last_test_only);
+
    // get acces to protein geometry
    coot::protein_geometry & get_geometry() {
       return geom;