Re: [Rdkit-discuss] sdf reading error between osx and windows

2016-04-27 Thread Steven Combs 
and that fixed it. Thanks again Paolo!

Steven Combs

On Wed, Apr 27, 2016 at 12:28 PM, Steven Combs 
wrote:

> I will give that a try and let you know!
>
> On Wed, Apr 27, 2016 at 12:20 PM, Paolo Tosco 
> wrote:
>
>> Dear Steven,
>>
>> did you try to open the file in binary mode on the Windows build ans see
>> if it makes a difference? It does not make any difference on Linux and OS
>> X, but it will change how newlines are handled on Windows. I suspect that's
>> where the problem might be. Please get back to me, later I'll try and
>> reproduce the problem.
>>
>> Cheers,
>> p.
>>
>>
>> On 04/27/16 17:04, Steven Combs wrote:
>>
>> Hi!
>>
>> I am writing in c++ and loading an sdf file. This works perfectly for an
>> osx build, but when I try to load the same file with the windows build of
>> the program, I get errors and crashing (note: no errors in either the osx
>> or linux build). I have attached the sdf file as well.
>>
>> The errors I get are:
>> [11:57:17] ERROR: Cannot convert to int on line 24
>> [11:57:17] ERROR: moving to the begining of the next molecule
>> [11:57:17] ERROR: Cannot convert to int on line 51
>> [11:57:17] ERROR: moving to the begining of the next molecule
>> [11:57:17] ERROR: Cannot convert to int on line 71
>> [11:57:17] ERROR: moving to the begining of the next molecule
>> [11:57:17] ERROR: Cannot convert to int on line 100
>> [11:57:17] ERROR: moving to the begining of the next molecule
>> [11:57:17] ERROR: Cannot convert to int on line 138
>> [11:57:17] ERROR: moving to the begining of the next molecule
>> [11:57:17] ERROR: Cannot convert 1 8 to int on line 171
>> [11:57:17] ERROR: moving to the begining of the next molecule
>> [11:57:17] ERROR: Counts line too short: '' on line231
>> [11:57:17] ERROR: moving to the begining of the next molecule
>>
>>
>> Here is the relevant code snippet:
>>
>> void load_sdf( std::string const & filename, utility::vector1< 
>> ::RDKit::ROMolOP > & mol_vector, bool removeHs) {
>>  utility::io::izstream data( filename );
>>  if ( ! data.good() ) {
>>  TR.Error << "ERROR: Cannot open fragment file '" << filename << 
>> "'" << std::endl;
>>  utility_exit_with_message("Cannot open fragment file 
>> "+filename);
>>  }
>>  ::RDKit::SDMolSupplier supplier( (), /*takeOwnership=*/ false, 
>> /*sanitize=*/ true, removeHs); // Yes, pointer to std::istream - that's what 
>> RDKit wants
>>  while( ! supplier.atEnd() ) {
>>  ::RDKit::ROMolOP mol( supplier.next() );
>>  if( mol ) {
>>  mol_vector.push_back( mol );
>>  }
>>  }
>>
>> }
>>
>>  Regards,
>>
>> Steven Combs
>>
>>
>>
>> --
>> Find and fix application performance issues faster with Applications Manager
>> Applications Manager provides deep performance insights into multiple tiers 
>> of
>> your business applications. It resolves application problems quickly and
>> reduces your MTTR. Get your free 
>> trial!https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
>>
>>
>>
>> ___
>> Rdkit-discuss mailing 
>> listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>>
>
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Re: [Rdkit-discuss] sdf reading error between osx and windows

2016-04-27 Thread Paolo Tosco 

Dear Steven,

did you try to open the file in binary mode on the Windows build ans see 
if it makes a difference? It does not make any difference on Linux and 
OS X, but it will change how newlines are handled on Windows. I suspect 
that's where the problem might be. Please get back to me, later I'll try 
and reproduce the problem.


Cheers,
p.

On 04/27/16 17:04, Steven Combs wrote:

Hi!

I am writing in c++ and loading an sdf file. This works perfectly for 
an osx build, but when I try to load the same file with the windows 
build of the program, I get errors and crashing (note: no errors in 
either the osx or linux build). I have attached the sdf file as well.


The errors I get are:
[11:57:17] ERROR: Cannot convert to int on line 24
[11:57:17] ERROR: moving to the begining of the next molecule
[11:57:17] ERROR: Cannot convert to int on line 51
[11:57:17] ERROR: moving to the begining of the next molecule
[11:57:17] ERROR: Cannot convert to int on line 71
[11:57:17] ERROR: moving to the begining of the next molecule
[11:57:17] ERROR: Cannot convert to int on line 100
[11:57:17] ERROR: moving to the begining of the next molecule
[11:57:17] ERROR: Cannot convert to int on line 138
[11:57:17] ERROR: moving to the begining of the next molecule
[11:57:17] ERROR: Cannot convert 1 8 to int on line 171
[11:57:17] ERROR: moving to the begining of the next molecule
[11:57:17] ERROR: Counts line too short: '' on line231
[11:57:17] ERROR: moving to the begining of the next molecule


Here is the relevant code snippet:

void  load_sdf(  std::string  const  &  filename,  utility::vector1<  
::RDKit::ROMolOP>  &  mol_vector,  bool  removeHs)  {
utility::io::izstream data(  filename);
if  (  !  data.good()  )  {
TR.Error<<  "ERROR: Cannot open fragment file '"  <<  filename<<  "'" 
 <<  std::endl;
utility_exit_with_message("Cannot open fragment file 
"+filename);
}
::RDKit::SDMolSupplier supplier(  (),  /*takeOwnership=*/  false,  
/*sanitize=*/  true,  removeHs);  // Yes, pointer to std::istream - that's what 
RDKit wants
while(  !  supplier.atEnd()  )  {
::RDKit::ROMolOP mol(  supplier.next()  );
if(  mol)  {
mol_vector.push_back(  mol);
}
}
}
Regards,
Steven Combs


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[Rdkit-discuss] sdf reading error between osx and windows

2016-04-27 Thread Steven Combs 
Hi!

I am writing in c++ and loading an sdf file. This works perfectly for an
osx build, but when I try to load the same file with the windows build of
the program, I get errors and crashing (note: no errors in either the osx
or linux build). I have attached the sdf file as well.

The errors I get are:
[11:57:17] ERROR: Cannot convert to int on line 24
[11:57:17] ERROR: moving to the begining of the next molecule
[11:57:17] ERROR: Cannot convert to int on line 51
[11:57:17] ERROR: moving to the begining of the next molecule
[11:57:17] ERROR: Cannot convert to int on line 71
[11:57:17] ERROR: moving to the begining of the next molecule
[11:57:17] ERROR: Cannot convert to int on line 100
[11:57:17] ERROR: moving to the begining of the next molecule
[11:57:17] ERROR: Cannot convert to int on line 138
[11:57:17] ERROR: moving to the begining of the next molecule
[11:57:17] ERROR: Cannot convert 1 8 to int on line 171
[11:57:17] ERROR: moving to the begining of the next molecule
[11:57:17] ERROR: Counts line too short: '' on line231
[11:57:17] ERROR: moving to the begining of the next molecule


Here is the relevant code snippet:

void load_sdf( std::string const & filename, utility::vector1<
::RDKit::ROMolOP > & mol_vector, bool removeHs) {
utility::io::izstream data( filename );
if ( ! data.good() ) {
TR.Error << "ERROR: Cannot open fragment file '" << filename << 
"'"
<< std::endl;
utility_exit_with_message("Cannot open fragment file 
"+filename);
}
::RDKit::SDMolSupplier supplier( (), /*takeOwnership=*/ false,
/*sanitize=*/ true, removeHs); // Yes, pointer to std::istream -
that's what RDKit wants
while( ! supplier.atEnd() ) {
::RDKit::ROMolOP mol( supplier.next() );
if( mol ) {
mol_vector.push_back( mol );
}
}

}


Regards,

Steven Combs


basic_fragments.sdf
Description: Binary data
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