Re: [Rdkit-discuss] problem using RDKit c++ class to read sdf file

Wong, Sergio E. Tue, 14 Jul 2015 12:55:10 -0700

Dear Greg;

   Thank you for the file and the suggestion.  I tried following the examples 
and your suggestion and yet, I am still getting some errors.  Here is my code 
and below are the errors:



#include <GraphMol/RDKitBase.h>
#include <string>
#include <iostream>
#include <fstream>
#include <map>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/FileParsers/MolWriters.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <RDGeneral/FileParseException.h>
#include <RDGeneral/BadFileException.h>
#include <RDGeneral/RDLog.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/Depictor/RDDepictor.h>

using namespace RDKit;

int main()
{
SDMolSupplier supplier("Pubchem_info_dat.sdf");

int i = 0;

while (!supplier.atEnd())
   {
   ROMol *nmol = supplier.next();
   i++;
   }

return 0;

}

Compilation line:

g++ -I${RDBASE}/Code -L/${RDBASE}/lib test.c


Error:

In file included from 
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/hash_set:60,
                 from /usr/include/boost/graph/adjacency_list.hpp:25,
                 from /usr/gapps/bbs/rdkit-master//Code/GraphMol/ROMol.h:24,
                 from /usr/gapps/bbs/rdkit-master//Code/GraphMol/GraphMol.h:19,
                 from /usr/gapps/bbs/rdkit-master//Code/GraphMol/RDKitBase.h:25,
                 from test.c:1:
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/backward_warning.h:28:2:
 warning: #warning This file includes at least one deprecated or antiquated 
header which may be removed without further notice at a future date. Please use 
a non-deprecated interface with equivalent functionality instead. For a listing 
of replacement headers and interfaces, consult the file backward_warning.h. To 
disable this warning use -Wno-deprecated.
/var/tmp/swong/ccJYjg6o.o: In function `main':
test.c:(.text+0x4b): undefined reference to 
`RDKit::SDMolSupplier::SDMolSupplier(std::basic_string<char, 
std::char_traits<char>, std::allocator<char> > const&, bool, bool, bool)'
test.c:(.text+0xcd): undefined reference to `RDKit::SDMolSupplier::next()'
test.c:(.text+0xe1): undefined reference to `RDKit::SDMolSupplier::atEnd()'
/var/tmp/swong/ccJYjg6o.o: In function 
`RDKit::ForwardSDMolSupplier::~ForwardSDMolSupplier()':
test.c:(.text._ZN5RDKit20ForwardSDMolSupplierD2Ev[_ZN5RDKit20ForwardSDMolSupplierD5Ev]+0x16):
 undefined reference to `vtable for RDKit::ForwardSDMolSupplier'
/var/tmp/swong/ccJYjg6o.o: In function `RDKit::SDMolSupplier::~SDMolSupplier()':
test.c:(.text._ZN5RDKit13SDMolSupplierD2Ev[_ZN5RDKit13SDMolSupplierD5Ev]+0x16): 
undefined reference to `vtable for RDKit::SDMolSupplier'
collect2: ld returned 1 exit status

Do you think I need to re-install rdkit?  The python wrapper works fine.

Thanks again;
-Sergio


________________________________
From: Greg Landrum [greg.land...@gmail.com]
Sent: Monday, July 13, 2015 10:16 PM
To: Wong, Sergio E.
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] problem using RDKit c++ class to read sdf file

Hi Sergio,

You need to provide the filename when you construct the SDMolSupplier.
Here's some sample code from one of the RDKit tests that demonstrates how to 
use the supplier:
https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/FileParsers/testMolSupplier.cpp#L42

(that file contains other examples of using the suppliers too)

-greg


On Tue, Jul 14, 2015 at 7:10 AM, Wong, Sergio E. 
<wong...@llnl.gov<mailto:wong...@llnl.gov>> wrote:
Dear RDKit users;

    I am trying to read a sdf file using the following code:

#include<stdlib.h>
#include<GraphMol/FileParsers/MolSupplier.h>
#include<RDGeneral/FileParseException.h>
#include<RDGeneral/BadFileException.h>
#include<RDGeneral/RDLog.h>
#include<GraphMol/RDKitBase.h>

int main()
{
RDKit::SDMolSupplier supplier;

supplier.init();
supplier.SDMolSupplier("PubChem_info_dat.sdf");

return 0;

}

When I try to compile it, I get the following error:

test.c: In function ‘int main()’:
test.c:19:10: error: invalid use of ‘RDKit::SDMolSupplier::SDMolSupplier’
 supplier.SDMolSupplier("PubChem_info_dat.sdf");
          ^

Can anyone suggest anything?

Thanks!
-Sergio



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