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 StructCheckerOptions &	GetOptions () 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

StructChecker chk;
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 245 of file StructChecker.h.

Member Typedef Documentation

StructureFlags

typedef enum RDKit::StructureCheck::StructChecker::StructureFlags RDKit::StructureCheck::StructChecker::StructureFlags

Member Enumeration Documentation

StructureFlags

enum RDKit::StructureCheck::StructChecker::StructureFlags

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 247 of file StructChecker.h.

Constructor & Destructor Documentation

StructChecker() [1/2]

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

inline

Definition at line 279 of file StructChecker.h.

StructChecker() [2/2]

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

inline

Definition at line 280 of file StructChecker.h.

Member Function Documentation

checkMolStructure()

unsigned RDKit::StructureCheck::StructChecker::checkMolStructure

(

RWMol &

mol

)

const

GetOptions()

const StructCheckerOptions & RDKit::StructureCheck::StructChecker::GetOptions ( ) const

inline

Definition at line 283 of file StructChecker.h.

SetOptions()

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

inline

Definition at line 284 of file StructChecker.h.

StringToStructureFlags()

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

static

StructureFlagsToString()

static std::string RDKit::StructureCheck::StructChecker::StructureFlagsToString ( unsigned flags )

static

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

• StructChecker.h