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//
// Copyright (C) 2023 Novartis Biomedical Research
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#ifndef RD_MOLSTANDARDIZE_PIPELINE_H
#define RD_MOLSTANDARDIZE_PIPELINE_H
#include <RDGeneral/export.h>
#include <GraphMol/RWMol.h>
#include <memory>
#include <string>
#include <utility>
#include <vector>
namespace RDKit {
namespace MolStandardize {
struct RDKIT_MOLSTANDARDIZE_EXPORT PipelineOptions {
// parsing
bool strictParsing{false};
// validation
bool reportAllFailures{true};
bool allowEmptyMolecules{false};
bool allowEnhancedStereo{false};
bool allowAromaticBondType{false};
bool allowDativeBondType{false};
double is2DZeroThreshold{1e-3};
double atomClashLimit{0.03};
double minMedianBondLength{1e-3};
double bondLengthLimit{100.};
bool allowLongBondsInRings{true};
bool allowAtomBondClashExemption{true};
// cleanup/standardization
// metal disconnector options
std::string metalNof{"[Li,Na,K,Rb,Cs,Fr]~[#7,#8,F]"};
std::string metalNon{};
// normalizer options
std::string normalizerData{
"// Name\tSMIRKS\n"
"Nitro to N+(O-)=O\t[N,P,As,Sb;X3:1](=[O,S,Se,Te:2])=[O,S,Se,Te:3]>>[*+1:1]([*-1:2])=[*:3]\n"
"Sulfone to S(=O)(=O)\t[S+2:1]([O-:2])([O-:3])>>[S+0:1](=[O-0:2])(=[O-0:3])\n"
"Pyridine oxide to n+O-\t[nH0+0:1]=[OH0+0:2]>>[n+:1][O-:2]\n"
"Azide to N=N+=N-\t[*:1][N:2]=[N:3]#[N:4]>>[*:1][N:2]=[N+:3]=[N-:4]\n"
"Diazo/azo to =N+=N-\t[*:1]=[N:2]#[N:3]>>[*:1]=[N+:2]=[N-:3]\n"
// Note: the sulfoxide transformation by default included in the
// Normalizer configuration was removed Note: the transformation below was
// ported from STRUCHK and it's not part of the default Normalizer
// configuration
"[SH](=O)(=O) to S(=O)O\t[c,C,N,O,F,Cl,Br,I:1][SH+0:2](=[O:3])=[O:4]>>[*:1][*:2]([*:3])=[*:4]\n"
// Note: the two transformations below replace the default Phosphate
// normalization in order to ensure that, if an O is available, the double
// bond is placed between P and O
"Phosphate to P(O-)=O\t[O-:1][P+;D4:2][O,S,Se,Te;-1:3]>>[O+0:1]=[P+0;D5:2][*-1:3]\n"
"Generalized phosphate to P(X-)=Y\t[S,Se,Te;-1:1][P+;D4:2][S,Se,Te;-1:3]>>[*+0:1]=[P+0;D5:2][*-1:3]\n"
"C/S+N to C/S=N+\t[C,S&!$([S+]-[O-]);X3+1:1]([NX3:2])[NX3!H0:3]>>[*+0:1]([N:2])=[N+:3]\n"
"P+N to P=N+\t[P;X4+1:1]([NX3:2])[NX3!H0:3]>>[*+0:1]([N:2])=[N+:3]\n"
"Recombine 1,3-separated charges\t[N,P,As,Sb,O,S,Se,Te;-1:1]-[A+0:2]=[N,P,As,Sb,O,S,Se,Te;+1:3]>>[*-0:1]=[*:2]-[*+0:3]\n"
"Recombine 1,3-separated charges\t[n,o,p,s;-1:1]:[a:2]=[N,O,P,S;+1:3]>>[*-0:1]:[*:2]-[*+0:3]\n"
"Recombine 1,3-separated charges\t[N,O,P,S;-1:1]-[a+0:2]:[n,o,p,s;+1:3]>>[*-0:1]=[*:2]:[*+0:3]\n"
"Recombine 1,5-separated charges\t[N,P,As,Sb,O,S,Se,Te;-1:1]-[A+0:2]=[A:3]-[A:4]=[N,P,As,Sb,O,S,Se,Te;+1:5]>>[*-0:1]=[*:2]-[*:3]=[*:4]-[*+0:5]\n"
"Recombine 1,5-separated charges\t[n,o,p,s;-1:1]:[a:2]:[a:3]:[c:4]=[N,O,P,S;+1:5]>>[*-0:1]:[*:2]:[*:3]:[c:4]-[*+0:5]\n"
"Recombine 1,5-separated charges\t[N,O,P,S;-1:1]-[c:2]:[a:3]:[a:4]:[n,o,p,s;+1:5]>>[*-0:1]=[c:2]:[*:3]:[*:4]:[*+0:5]\n"
// Note: four transformations were added to the normalization of aliphatic
// conjug cations in order to favor the positioning of new double bonds
// within rings
"Normalize 1,3 conjugated cation\t[N;+0!H0:1]@-[A:2]=[N!$(*~[N,O,P,S;-1]),O;+1H0:3]>>[*+1:1]=[*:2]-[*+0:3]\n"
"Normalize 1,5 conjugated cation\t[N;+0!H0:1]@-[A:2]=[A:3]@-[A:4]=[N!$(*~[N,O,P,S;-1]),O;+1H0:5]>>[*+1:1]=[*:2]-[*:3]=[*:4]-[*+0:5]\n"
"Normalize 1,3 conjugated cation\t[N,O!$(*N);+0!H0:1]-[A:2]=[N!$(*~[N,O,P,S;-1]),O;+1H0:3]>>[*+1:1]=[*:2]-[*+0:3]\n"
"Normalize 1,3 conjugated cation\t[n;+0!H0:1]:[c:2]=[N!$(*~[N,O,P,S;-1]),O;+1H0:3]>>[*+1:1]:[*:2]-[*+0:3]\n"
"Normalize 1,5 conjugated cation\t[N;+0!H0:1]@-[A:2]=[A:3]-[A:4]=[N!$(*~[N,O,P,S;-1]),O;+1H0:5]>>[*+1:1]=[*:2]-[*:3]=[*:4]-[*+0:5]\n"
"Normalize 1,5 conjugated cation\t[N,O!$(*N);+0!H0:1]-[A:2]=[A:3]@-[A:4]=[N!$(*~[N,O,P,S;-1]),O;+1H0:5]>>[*+1:1]=[*:2]-[*:3]=[*:4]-[*+0:5]\n"
"Normalize 1,5 conjugated cation\t[N,O!$(*N);+0!H0:1]-[A:2]=[A:3]-[A:4]=[N!$(*~[N,O,P,S;-1]),O;+1H0:5]>>[*+1:1]=[*:2]-[*:3]=[*:4]-[*+0:5]\n"
"Normalize 1,5 conjugated cation\t[n;+0!H0:1]:[a:2]:[a:3]:[c:4]=[N!$(*~[N,O,P,S;-1]),O;+1H0:5]>>[n+1:1]:[*:2]:[*:3]:[*:4]-[*+0:5]\n"
"Charge normalization\t[F,Cl,Br,I,At;-1:1]=[O:2]>>[*-0:1][O-:2]\n"
"Charge recombination\t[N,P,As,Sb;-1:1]=[C+;v3:2]>>[*+0:1]#[C+0:2]\n"};
unsigned int normalizerMaxRestarts{200};
double scaledMedianBondLength{1.};
// serialization
bool outputV2000{false};
};
enum RDKIT_MOLSTANDARDIZE_EXPORT PipelineStatus {
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 = (FEATURES_VALIDATION_ERROR | BASIC_VALIDATION_ERROR |
IS2D_VALIDATION_ERROR | LAYOUT2D_VALIDATION_ERROR |
STEREO_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 =
(METAL_STANDARDIZATION_ERROR | NORMALIZER_STANDARDIZATION_ERROR |
FRAGMENT_STANDARDIZATION_ERROR | CHARGE_STANDARDIZATION_ERROR),
OUTPUT_ERROR = (1 << 12),
PIPELINE_ERROR = (INPUT_ERROR | PREPARE_FOR_VALIDATION_ERROR |
VALIDATION_ERROR | PREPARE_FOR_STANDARDIZATION_ERROR |
STANDARDIZATION_ERROR | OUTPUT_ERROR),
METALS_DISCONNECTED = (1 << 23),
NORMALIZATION_APPLIED = (1 << 24),
FRAGMENTS_REMOVED = (1 << 25),
PROTONATION_CHANGED = (1 << 26),
STRUCTURE_MODIFICATION = (METALS_DISCONNECTED | NORMALIZATION_APPLIED |
FRAGMENTS_REMOVED | PROTONATION_CHANGED)
};
enum class RDKIT_MOLSTANDARDIZE_EXPORT PipelineStage : std::uint32_t {
NOT_STARTED = 0,
PARSING_INPUT,
PREPARE_FOR_VALIDATION,
VALIDATION,
PREPARE_FOR_STANDARDIZATION,
STANDARDIZATION,
REAPPLY_WEDGING,
CLEANUP_2D,
MAKE_PARENT,
SERIALIZING_OUTPUT,
COMPLETED
};
struct RDKIT_MOLSTANDARDIZE_EXPORT PipelineLogEntry {
PipelineStatus status;
std::string detail;
};
using PipelineLog = std::vector<PipelineLogEntry>;
struct RDKIT_MOLSTANDARDIZE_EXPORT PipelineResult {
PipelineStatus status;
std::uint32_t stage;
PipelineLog log;
std::string inputMolData;
std::string outputMolData;
std::string parentMolData;
void append(PipelineStatus newStatus, const std::string &info);
};
using RWMOL_SPTR_PAIR = std::pair<RWMOL_SPTR, RWMOL_SPTR>;
namespace Operations {
RDKIT_MOLSTANDARDIZE_EXPORT RWMOL_SPTR prepareForValidation(
RWMOL_SPTR mol, PipelineResult &result, const PipelineOptions &options);
RDKIT_MOLSTANDARDIZE_EXPORT RWMOL_SPTR validate(RWMOL_SPTR mol,
PipelineResult &result,
const PipelineOptions &options);
RDKIT_MOLSTANDARDIZE_EXPORT RWMOL_SPTR prepareForStandardization(
RWMOL_SPTR mol, PipelineResult &result, const PipelineOptions &options);
RDKIT_MOLSTANDARDIZE_EXPORT RWMOL_SPTR standardize(
RWMOL_SPTR mol, PipelineResult &result, const PipelineOptions &options);
RDKIT_MOLSTANDARDIZE_EXPORT RWMOL_SPTR reapplyWedging(
RWMOL_SPTR mol, PipelineResult &result, const PipelineOptions &options);
RDKIT_MOLSTANDARDIZE_EXPORT RWMOL_SPTR cleanup2D(
RWMOL_SPTR mol, PipelineResult &result, const PipelineOptions &options);
RDKIT_MOLSTANDARDIZE_EXPORT RWMOL_SPTR_PAIR makeParent(
RWMOL_SPTR mol, PipelineResult &result, const PipelineOptions &options);
RDKIT_MOLSTANDARDIZE_EXPORT RWMOL_SPTR parse(const std::string &molblock,
PipelineResult &result,
const PipelineOptions &options);
RDKIT_MOLSTANDARDIZE_EXPORT void serialize(RWMOL_SPTR_PAIR output,
PipelineResult &result,
const PipelineOptions &options);
using ParseOperation = decltype(&parse);
using SerializeOperation = decltype(&serialize);
using Operation = decltype(&prepareForValidation);
using ParentOperation = decltype(&makeParent);
using PipelineVector = std::vector<std::pair<std::uint32_t, Operation>>;
const PipelineVector validationSteps{
// input sanitization and cleanup
{static_cast<uint32_t>(PipelineStage::PREPARE_FOR_VALIDATION),
&prepareForValidation},
// validate the structure
{static_cast<uint32_t>(PipelineStage::VALIDATION), &validate}};
const PipelineVector standardizationSteps{
{static_cast<uint32_t>(PipelineStage::PREPARE_FOR_STANDARDIZATION),
&prepareForStandardization},
{static_cast<uint32_t>(PipelineStage::STANDARDIZATION), &standardize},
{static_cast<uint32_t>(PipelineStage::REAPPLY_WEDGING), &reapplyWedging},
{static_cast<uint32_t>(PipelineStage::CLEANUP_2D), &cleanup2D}};
} // namespace Operations
class RDKIT_MOLSTANDARDIZE_EXPORT Pipeline {
private:
PipelineOptions options;
Operations::ParseOperation parse = Operations::parse;
Operations::SerializeOperation serialize = Operations::serialize;
Operations::PipelineVector validationSteps = Operations::validationSteps;
Operations::PipelineVector standardizationSteps =
Operations::standardizationSteps;
Operations::ParentOperation makeParent = Operations::makeParent;
public:
Pipeline() = default;
explicit Pipeline(const PipelineOptions &o) : options(o) {};
~Pipeline() = default;
PipelineResult run(const std::string &molblock) const;
void setValidationSteps(const Operations::PipelineVector &steps) {
validationSteps = steps;
}
void setStandardizationSteps(const Operations::PipelineVector &steps) {
standardizationSteps = steps;
}
void setMakeParent(Operations::ParentOperation op) { makeParent = op; }
void setParse(Operations::ParseOperation op) { parse = op; }
void setSerialize(Operations::SerializeOperation op) { serialize = op; }
private:
};
} // namespace MolStandardize
} // namespace RDKit
#endif
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