RDKit
Open-source cheminformatics and machine learning.
RDKit::StructureCheck::StructChecker Class Reference

Class for performing structure validation and cleanup. More...

#include <StructChecker.h>

Public Types

enum  StructureFlags {
  NO_CHANGE = 0, BAD_MOLECULE = 0x0001, ALIAS_CONVERSION_FAILED = 0x0002, STEREO_ERROR = 0x0004,
  STEREO_FORCED_BAD = 0x0008, ATOM_CLASH = 0x0010, ATOM_CHECK_FAILED = 0x0020, SIZE_CHECK_FAILED = 0x0040,
  TRANSFORMED = 0x0100, FRAGMENTS_FOUND = 0x0200, EITHER_WARNING = 0x0400, DUBIOUS_STEREO_REMOVED = 0x0800,
  RECHARGED = 0x1000, STEREO_TRANSFORMED = 0x2000, TEMPLATE_TRANSFORMED = 0x4000, TAUTOMER_TRANSFORMED = 0x8000,
  BAD_SET, TRANSFORMED_SET
}
 
typedef enum RDKit::StructureCheck::StructChecker::StructureFlags StructureFlags
 

Public Member Functions

 StructChecker ()
 
 StructChecker (const StructCheckerOptions &options)
 
const StructCheckerOptionsGetOptions () const
 
void SetOptions (const StructCheckerOptions &options)
 
unsigned checkMolStructure (RWMol &mol) const
 

Static Public Member Functions

static std::string StructureFlagsToString (unsigned flags)
 
static unsigned StringToStructureFlags (const std::string &str)
 

Detailed Description

Class for performing structure validation and cleanup.

NOTE: This class should be considered beta. The API may change in future releases.

Examples of Usage

int flags = StructureCheck::checkMolStructure( mol ); // use defaults

or

StructureCheck::StructCheckerOptions options; // use defaults
// To use external data
StructureCheck::loadOptionsFromFiles(options, file1, file2);
StructChecker chk(options);
for( mol in mols ) {
int flags = StructureCheck::checkMolStructure( mol, &options);
if (0!=(flags & StructureCheck::StructureFlags::BAD_SET)) {
// write to error file
} else if (0!=(flags & StructureCheck::StructureFlags::TRANSFORMED_SET))
{
// input molecule was transformed
} else { // flag == NO_CHANGE
// no change
}
}

Definition at line 243 of file StructChecker.h.

Member Typedef Documentation

Member Enumeration Documentation

Enumerator
NO_CHANGE 
BAD_MOLECULE 
ALIAS_CONVERSION_FAILED 
STEREO_ERROR 
STEREO_FORCED_BAD 
ATOM_CLASH 
ATOM_CHECK_FAILED 
SIZE_CHECK_FAILED 
TRANSFORMED 
FRAGMENTS_FOUND 
EITHER_WARNING 
DUBIOUS_STEREO_REMOVED 
RECHARGED 
STEREO_TRANSFORMED 
TEMPLATE_TRANSFORMED 
TAUTOMER_TRANSFORMED 
BAD_SET 
TRANSFORMED_SET 

Definition at line 245 of file StructChecker.h.

Constructor & Destructor Documentation

RDKit::StructureCheck::StructChecker::StructChecker ( )
inline

Definition at line 277 of file StructChecker.h.

RDKit::StructureCheck::StructChecker::StructChecker ( const StructCheckerOptions options)
inline

Definition at line 278 of file StructChecker.h.

Member Function Documentation

unsigned RDKit::StructureCheck::StructChecker::checkMolStructure ( RWMol mol) const
const StructCheckerOptions& RDKit::StructureCheck::StructChecker::GetOptions ( ) const
inline

Definition at line 281 of file StructChecker.h.

void RDKit::StructureCheck::StructChecker::SetOptions ( const StructCheckerOptions options)
inline

Definition at line 282 of file StructChecker.h.

static unsigned RDKit::StructureCheck::StructChecker::StringToStructureFlags ( const std::string &  str)
static
static std::string RDKit::StructureCheck::StructChecker::StructureFlagsToString ( unsigned  flags)
static

The documentation for this class was generated from the following file: