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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)
PREPARE_FOR_STANDARDIZATION_ERROR
PREPARE_FOR_STANDARDIZATION_ERROR
Definition Pipeline.h:102
PREPARE_FOR_VALIDATION_ERROR
PREPARE_FOR_VALIDATION_ERROR
Definition Pipeline.h:93
STANDARDIZATION_ERROR
STANDARDIZATION_ERROR
Definition Pipeline.h:107
OUTPUT_ERROR
OUTPUT_ERROR
Definition Pipeline.h:110
INPUT_ERROR
INPUT_ERROR
Definition Pipeline.h:92
VALIDATION_ERROR
VALIDATION_ERROR
Definition Pipeline.h:99

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)
FRAGMENT_STANDARDIZATION_ERROR
FRAGMENT_STANDARDIZATION_ERROR
Definition Pipeline.h:105
NORMALIZER_STANDARDIZATION_ERROR
NORMALIZER_STANDARDIZATION_ERROR
Definition Pipeline.h:104
CHARGE_STANDARDIZATION_ERROR
CHARGE_STANDARDIZATION_ERROR
Definition Pipeline.h:106
METAL_STANDARDIZATION_ERROR
METAL_STANDARDIZATION_ERROR
Definition Pipeline.h:103

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)
FEATURES_VALIDATION_ERROR
FEATURES_VALIDATION_ERROR
Definition Pipeline.h:94
LAYOUT2D_VALIDATION_ERROR
LAYOUT2D_VALIDATION_ERROR
Definition Pipeline.h:97
STEREO_VALIDATION_ERROR
STEREO_VALIDATION_ERROR
Definition Pipeline.h:98
IS2D_VALIDATION_ERROR
IS2D_VALIDATION_ERROR
Definition Pipeline.h:96
BASIC_VALIDATION_ERROR
BASIC_VALIDATION_ERROR
Definition Pipeline.h:95

Definition at line 99 of file Pipeline.h.