Hi Jason,
Correct. You'd probably better use std::unique_ptr unless you are
planning to reference the original pointer from multiple std::shared_ptr's.
Cheers,
p.
On 11/01/2018 14:42, Jason Biggs wrote:
On Thu, Jan 11, 2018 at 8:03 AM, Paolo Tosco <[email protected]
<mailto:[email protected]>> wrote:
Hi Jason,
I believe the problem here is that if you are building outside
CMake the WIN32 preprocessor macro is not defined (_WIN32 is). So,
when ROMol.h is parsed, the ROMol class definition includes a
"private" directive that should not be there, hence the error. To
fix the issue, you need to add to your cl command line a /DWIN32.
Thank you! This did the trick. I should learn to use CMake instead
of compiling everything in Mathematica (when all you have is a hammer,
everything looks like a nail)
As a side note, I am not sure you really want to do:
RDKit::ROMol mol = *(RDKit::SmilesToMol(smi));
std::string res = RDKit::MolToSmiles(mol);
In fact, this makes a copy of the molecule that the pointer
returned by SmilesToMol() points to, while leaking the memory
pointed to.
If you are not interested in making a copy of the returned
molecule, you should probably rather do:
RDKit::RWMol *mol = RDKit::SmilesToMol(smi);
std::string res = RDKit::MolToSmiles(*mol);
delete mol;
You are definitely correct here, I was trying to make the simplest
failing example and the example without the copy compiled fine -
declaring a pointer to an ROMol is fine but declaring an actual object
triggered the error.
I'm very new to c++, will keep in mind to always delete my pointers.
If I understand correctly, if I always wrap my ROMol objects in a
std::shared_ptr (or the boost equivalent), then the memory will not be
leaked. Is that right?
Best,
Jason
If you actually meant to make a copy, you'd better do:
RDKit::RWMol *mol = RDKit::SmilesToMol(smi);
RDKit::ROMol molCopy(*mol);
delete mol;
std::string res = RDKit::MolToSmiles(molCopy);
Cheers,
p.
On 11/01/2018 02:33, Jason Biggs wrote:
I'm trying to use the rdkit as a library in another project, and
am having trouble getting it to build on windows. I can get the
code to compile on mac and linux, but it fails for windows, both
32-big and 64-bit varieties. I don't know how specific this is
to the rdkit, but I have zero experience compiling with visual
studio (and very little C++ coding background) and I am very
confused here. The following is just a toy example showing the
minimum necessary for me to get the error. I get the same error
using the full code.
If I create a test class using this code, I can compile it just
fine in windows:
#include <GraphMol/GraphMol.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
classtestClass{
testClass();
~testClass();
std::string testFunc() {
std::string smi = "CCC";
RDKit::ROMol mol = *(RDKit::SmilesToMol(smi));
std::string res = RDKit::MolToSmiles(mol);
returnres;
};
};
testClass::testClass() {
}
testClass::~testClass() {
}
But if I move the definition of the testFunc() function outside
of the class declaration (which is the normal case, where the
definitions are in separate files), like this
#include <GraphMol/GraphMol.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
classtestClass{
testClass();
~testClass();
std::string testFunc();
};
testClass::testClass() {
}
testClass::~testClass() {
}
std::string testClass::testFunc() {
std::string smi = "CCC";
RDKit::ROMol mol = *(RDKit::SmilesToMol(smi));
std::string res = RDKit::MolToSmiles(mol);
returnres;
};
then I get the following linker errors:
error LNK2019: unresolved external symbol "private: virtual void
__thiscall RDKit::ROMol::destroy(void)"
(?destroy@ROMol@RDKit@@EAEXXZ) referenced in function "public:
virtual __thiscall RDKit::ROMol::~ROMol(void)"
(??1ROMol@RDKit@@UAE@XZ)
failing.obj : error LNK2019: unresolved external symbol "private:
void __thiscall RDKit::ROMol::initFromOther(class RDKit::ROMol
const &,bool,int)" (?initFromOther@ROMol@RDKit@@AAEXABV12@_NH@Z)
referenced in function "public: __thiscall
RDKit::ROMol::ROMol(class RDKit::ROMol const &,bool,int)"
(??0ROMol@RDKit@@QAE@ABV01@_NH@Z)
C:\Users\IEUser\Documents\rdkitlink_windows_compile_issue\Working-ie11win7-3268-3284-12\RDKitLink.dll
: fatal error LNK1120: 2 unresolved externals
I can't understand why moving the definition of testFunc() causes
this error.
Any help would be most appreciated. Clearly I can use the
workaround of making all definitions for testClass in the header
file, but I would rather not do that.
Thank you,
Jason
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