Pipeline.h File Reference

#include <RDGeneral/export.h>
#include <GraphMol/RWMol.h>
#include <memory>
#include <string>
#include <utility>
#include <vector>

Go to the source code of this file.

Classes
struct	RDKit::MolStandardize::PipelineOptions
struct	RDKit::MolStandardize::PipelineLogEntry
struct	RDKit::MolStandardize::PipelineResult
class	RDKit::MolStandardize::Pipeline

Namespaces
namespace	RDKit
	Std stuff.
namespace	RDKit::MolStandardize
namespace	RDKit::MolStandardize::Operations

Typedefs
using	RDKit::MolStandardize::PipelineLog = std::vector< PipelineLogEntry >
using	RDKit::MolStandardize::RWMOL_SPTR_PAIR = std::pair< RWMOL_SPTR, RWMOL_SPTR >
using	RDKit::MolStandardize::Operations::ParseOperation = decltype(&parse)
using	RDKit::MolStandardize::Operations::SerializeOperation = decltype(&serialize)
using	RDKit::MolStandardize::Operations::Operation = decltype(&prepareForValidation)
using	RDKit::MolStandardize::Operations::ParentOperation = decltype(&makeParent)
using	RDKit::MolStandardize::Operations::PipelineVector = std::vector< std::pair< std::uint32_t, Operation > >

Functions
RDKIT_MOLSTANDARDIZE_EXPORT RWMOL_SPTR	RDKit::MolStandardize::Operations::prepareForValidation (RWMOL_SPTR mol, PipelineResult &result, const PipelineOptions &options)
RDKIT_MOLSTANDARDIZE_EXPORT RWMOL_SPTR	RDKit::MolStandardize::Operations::validate (RWMOL_SPTR mol, PipelineResult &result, const PipelineOptions &options)
RDKIT_MOLSTANDARDIZE_EXPORT RWMOL_SPTR	RDKit::MolStandardize::Operations::prepareForStandardization (RWMOL_SPTR mol, PipelineResult &result, const PipelineOptions &options)
RDKIT_MOLSTANDARDIZE_EXPORT RWMOL_SPTR	RDKit::MolStandardize::Operations::standardize (RWMOL_SPTR mol, PipelineResult &result, const PipelineOptions &options)
RDKIT_MOLSTANDARDIZE_EXPORT RWMOL_SPTR	RDKit::MolStandardize::Operations::reapplyWedging (RWMOL_SPTR mol, PipelineResult &result, const PipelineOptions &options)
RDKIT_MOLSTANDARDIZE_EXPORT RWMOL_SPTR	RDKit::MolStandardize::Operations::cleanup2D (RWMOL_SPTR mol, PipelineResult &result, const PipelineOptions &options)
RDKIT_MOLSTANDARDIZE_EXPORT RWMOL_SPTR_PAIR	RDKit::MolStandardize::Operations::makeParent (RWMOL_SPTR mol, PipelineResult &result, const PipelineOptions &options)
RDKIT_MOLSTANDARDIZE_EXPORT RWMOL_SPTR	RDKit::MolStandardize::Operations::parse (const std::string &molblock, PipelineResult &result, const PipelineOptions &options)
RDKIT_MOLSTANDARDIZE_EXPORT void	RDKit::MolStandardize::Operations::serialize (RWMOL_SPTR_PAIR output, PipelineResult &result, const PipelineOptions &options)

Variables
	NO_EVENT = 0
	INPUT_ERROR = (1 << 0)
	PREPARE_FOR_VALIDATION_ERROR = (1 << 1)
	FEATURES_VALIDATION_ERROR = (1 << 2)
	BASIC_VALIDATION_ERROR = (1 << 3)
	IS2D_VALIDATION_ERROR = (1 << 4)
	LAYOUT2D_VALIDATION_ERROR = (1 << 5)
	STEREO_VALIDATION_ERROR = (1 << 6)
	VALIDATION_ERROR
	PREPARE_FOR_STANDARDIZATION_ERROR = (1 << 7)
	METAL_STANDARDIZATION_ERROR = (1 << 8)
	NORMALIZER_STANDARDIZATION_ERROR = (1 << 9)
	FRAGMENT_STANDARDIZATION_ERROR = (1 << 10)
	CHARGE_STANDARDIZATION_ERROR = (1 << 11)
	STANDARDIZATION_ERROR
	OUTPUT_ERROR = (1 << 12)
	PIPELINE_ERROR
	METALS_DISCONNECTED = (1 << 23)
	NORMALIZATION_APPLIED = (1 << 24)
	FRAGMENTS_REMOVED = (1 << 25)
	PROTONATION_CHANGED = (1 << 26)
enum RDKIT_MOLSTANDARDIZE_EXPORT	RDKit::MolStandardize::PipelineStage
enum RDKIT_MOLSTANDARDIZE_EXPORT	RDKit::MolStandardize::PARSING_INPUT
enum RDKIT_MOLSTANDARDIZE_EXPORT	RDKit::MolStandardize::PREPARE_FOR_VALIDATION
enum RDKIT_MOLSTANDARDIZE_EXPORT	RDKit::MolStandardize::VALIDATION
enum RDKIT_MOLSTANDARDIZE_EXPORT	RDKit::MolStandardize::PREPARE_FOR_STANDARDIZATION
enum RDKIT_MOLSTANDARDIZE_EXPORT	RDKit::MolStandardize::STANDARDIZATION
enum RDKIT_MOLSTANDARDIZE_EXPORT	RDKit::MolStandardize::REAPPLY_WEDGING
enum RDKIT_MOLSTANDARDIZE_EXPORT	RDKit::MolStandardize::CLEANUP_2D
enum RDKIT_MOLSTANDARDIZE_EXPORT	RDKit::MolStandardize::MAKE_PARENT
enum RDKIT_MOLSTANDARDIZE_EXPORT	RDKit::MolStandardize::SERIALIZING_OUTPUT
enum RDKIT_MOLSTANDARDIZE_EXPORT	RDKit::MolStandardize::COMPLETED
const PipelineVector	RDKit::MolStandardize::Operations::validationSteps
const PipelineVector	RDKit::MolStandardize::Operations::standardizationSteps

Variable Documentation

BASIC_VALIDATION_ERROR

BASIC_VALIDATION_ERROR = (1 << 3)

Definition at line 95 of file Pipeline.h.

CHARGE_STANDARDIZATION_ERROR

CHARGE_STANDARDIZATION_ERROR = (1 << 11)

Definition at line 106 of file Pipeline.h.

FEATURES_VALIDATION_ERROR

FEATURES_VALIDATION_ERROR = (1 << 2)

Definition at line 94 of file Pipeline.h.

FRAGMENT_STANDARDIZATION_ERROR

FRAGMENT_STANDARDIZATION_ERROR = (1 << 10)

Definition at line 105 of file Pipeline.h.

FRAGMENTS_REMOVED

FRAGMENTS_REMOVED = (1 << 25)

Definition at line 116 of file Pipeline.h.

INPUT_ERROR

INPUT_ERROR = (1 << 0)

Definition at line 92 of file Pipeline.h.

IS2D_VALIDATION_ERROR

IS2D_VALIDATION_ERROR = (1 << 4)

Definition at line 96 of file Pipeline.h.

LAYOUT2D_VALIDATION_ERROR

LAYOUT2D_VALIDATION_ERROR = (1 << 5)

Definition at line 97 of file Pipeline.h.

METAL_STANDARDIZATION_ERROR

METAL_STANDARDIZATION_ERROR = (1 << 8)

Definition at line 103 of file Pipeline.h.

METALS_DISCONNECTED

METALS_DISCONNECTED = (1 << 23)

Definition at line 114 of file Pipeline.h.

NO_EVENT

NO_EVENT = 0

Definition at line 91 of file Pipeline.h.

NORMALIZATION_APPLIED

NORMALIZATION_APPLIED = (1 << 24)

Definition at line 115 of file Pipeline.h.

NORMALIZER_STANDARDIZATION_ERROR

NORMALIZER_STANDARDIZATION_ERROR = (1 << 9)

Definition at line 104 of file Pipeline.h.

OUTPUT_ERROR

OUTPUT_ERROR = (1 << 12)

Definition at line 110 of file Pipeline.h.

PIPELINE_ERROR

PIPELINE_ERROR

Initial value:

= (INPUT_ERROR | PREPARE_FOR_VALIDATION_ERROR |
                    VALIDATION_ERROR | PREPARE_FOR_STANDARDIZATION_ERROR |
                    STANDARDIZATION_ERROR | OUTPUT_ERROR)

Definition at line 111 of file Pipeline.h.

PREPARE_FOR_STANDARDIZATION_ERROR

PREPARE_FOR_STANDARDIZATION_ERROR = (1 << 7)

Definition at line 102 of file Pipeline.h.

PREPARE_FOR_VALIDATION_ERROR

PREPARE_FOR_VALIDATION_ERROR = (1 << 1)

Definition at line 93 of file Pipeline.h.

PROTONATION_CHANGED

PROTONATION_CHANGED = (1 << 26)

Definition at line 117 of file Pipeline.h.

STANDARDIZATION_ERROR

STANDARDIZATION_ERROR

Initial value:

=
      (METAL_STANDARDIZATION_ERROR | NORMALIZER_STANDARDIZATION_ERROR |
       FRAGMENT_STANDARDIZATION_ERROR | CHARGE_STANDARDIZATION_ERROR)

Definition at line 107 of file Pipeline.h.

STEREO_VALIDATION_ERROR

STEREO_VALIDATION_ERROR = (1 << 6)

Definition at line 98 of file Pipeline.h.

VALIDATION_ERROR

VALIDATION_ERROR

Initial value:

= (FEATURES_VALIDATION_ERROR | BASIC_VALIDATION_ERROR |
                      IS2D_VALIDATION_ERROR | LAYOUT2D_VALIDATION_ERROR |
                      STEREO_VALIDATION_ERROR)

Definition at line 99 of file Pipeline.h.