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Add exception PDBQT_PARSE_ERROR for python #100

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merged 1 commit into from
Oct 28, 2022
Merged

Add exception PDBQT_PARSE_ERROR for python #100

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29 changes: 27 additions & 2 deletions build/python/vina/autodock_vina.i
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Original file line number Diff line number Diff line change
Expand Up @@ -64,6 +64,7 @@
#include "tree.h"
#include "triangular_matrix_index.h"
#include "utils.h"
SWIGRUNTIME PyObject* pPDBQT_PARSE_ERROR;
%}

// Set and reset dlopenflags so that plugin loading works fine for "import _openbabel"
Expand All @@ -75,17 +76,41 @@ if sys.platform.find("linux") != -1:
sys.setdlopenflags(dlflags | ctypes.RTLD_GLOBAL)
%}
%pythoncode %{
PDBQT_PARSE_ERROR = _vina_wrapper.PDBQT_PARSE_ERROR
if sys.platform.find("linux") != -1:
sys.setdlopenflags(dlflags)
%}

%init %{
pPDBQT_PARSE_ERROR = PyErr_NewException("_vina_wrapper.PDBQT_PARSE_ERROR", NULL, NULL);
Py_INCREF(pPDBQT_PARSE_ERROR);
PyModule_AddObject(m, "PDBQT_PARSE_ERROR", pPDBQT_PARSE_ERROR);
%}
// Add standard C++ library
%include "std_array.i"
%include "std_list.i"
%include "std_map.i"
%include "std_vector.i"
%include "std_string.i"

%include "stl.i"
%include "exception.i"
%exception set_ligand_from_string{
try {
$action
}
catch (const pdbqt_parse_error & e) {
PyErr_SetString(pPDBQT_PARSE_ERROR, e.what());
SWIG_fail;
}
}
%exception set_ligand_from_file{
try {
$action
}
catch (const pdbqt_parse_error & e) {
PyErr_SetString(pPDBQT_PARSE_ERROR, e.what());
SWIG_fail;
}
}
// Help SWIG to understand some special types, like list of strings
namespace std {
%template(IntVector) vector<int>;
Expand Down
24 changes: 12 additions & 12 deletions src/lib/parse_pdbqt.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -625,13 +625,13 @@ model parse_ligand_pdbqt_from_file(const std::string& name, atom_type::t atype)
non_rigid_parsed nrp;
context c;

try {
// try {
parse_pdbqt_ligand(make_path(name), nrp, c);
}
catch(pdbqt_parse_error& e) {
std::cerr << e.what();
exit(EXIT_FAILURE);
}
// }
// catch(pdbqt_parse_error& e) {
// std::cerr << e.what();
// exit(EXIT_FAILURE);
// }

pdbqt_initializer tmp(atype);
tmp.initialize_from_nrp(nrp, c, true);
Expand All @@ -643,14 +643,14 @@ model parse_ligand_pdbqt_from_string(const std::string& string_name, atom_type::
non_rigid_parsed nrp;
context c;

try {
// try {
std::stringstream molstream(string_name);
parse_pdbqt_ligand(molstream, nrp, c);
}
catch(pdbqt_parse_error& e) {
std::cerr << e.what() << '\n';
exit(EXIT_FAILURE);
}
// }
// catch(pdbqt_parse_error& e) {
// std::cerr << e.what() << '\n';
// exit(EXIT_FAILURE);
// }

pdbqt_initializer tmp(atype);
tmp.initialize_from_nrp(nrp, c, true);
Expand Down