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//
// Copyright (C) 2017 Novartis Institutes for 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.
//
#include <RDGeneral/export.h>
#ifndef RDKIT_RGROUPDECOMP_H
#define RDKIT_RGROUPDECOMP_H
#include "../RDKitBase.h"
#include <GraphMol/Substruct/SubstructMatch.h>
#include <chrono>
namespace RDKit {
//! Compute the isomorphic degenerative points in the
//! molecule. These are points that are symmetrically
//! equivalent.
/*!
\param mol Molecule to compute the degenerative points
\return the set of degenerative points (set<unsigned int>)
*/
typedef enum {
IsotopeLabels = 0x01,
AtomMapLabels = 0x02,
AtomIndexLabels = 0x04,
RelabelDuplicateLabels = 0x08,
MDLRGroupLabels = 0x10,
DummyAtomLabels = 0x20, // These are rgroups but will get relabelled
AutoDetect = 0xFF,
} RGroupLabels;
typedef enum {
Greedy = 0x01,
GreedyChunks = 0x02,
Exhaustive = 0x04, // not really useful for large sets
NoSymmetrization = 0x08,
} RGroupMatching;
typedef enum {
AtomMap = 0x01,
Isotope = 0x02,
MDLRGroup = 0x04,
} RGroupLabelling;
typedef enum {
// DEPRECATED, remove the folowing line in release 2021.03
None = 0x0,
NoAlignment = 0x0,
MCS = 0x01,
} RGroupCoreAlignment;
struct RDKIT_RGROUPDECOMPOSITION_EXPORT RGroupDecompositionParameters {
unsigned int labels = AutoDetect;
unsigned int matchingStrategy = GreedyChunks;
unsigned int rgroupLabelling = AtomMap | MDLRGroup;
unsigned int alignment = MCS;
unsigned int chunkSize = 5;
bool onlyMatchAtRGroups = false;
bool removeAllHydrogenRGroups = true;
bool removeHydrogensPostMatch = true;
double timeout = -1.0; ///< timeout in seconds. <=0 indicates no timeout
// Determine how to assign the rgroup labels from the given core
unsigned int autoGetLabels(const RWMol &);
// Prepare the core for substructure searching and rgroup assignment
bool prepareCore(RWMol &, const RWMol *alignCore);
private:
int indexOffset{-1};
};
typedef std::map<std::string, boost::shared_ptr<ROMol>> RGroupRow;
typedef std::vector<boost::shared_ptr<ROMol>> RGroupColumn;
typedef std::vector<RGroupRow> RGroupRows;
typedef std::map<std::string, RGroupColumn> RGroupColumns;
struct RGroupDecompData;
class RDKIT_RGROUPDECOMPOSITION_EXPORT RGroupDecomposition {
RGroupDecompData *data; // implementation details
RGroupDecomposition(const RGroupDecomposition &); // no copy construct
RGroupDecomposition &operator=(
const RGroupDecomposition &); // Prevent assignment
public:
RGroupDecomposition(const ROMol &core,
const RGroupDecompositionParameters ¶ms =
RGroupDecompositionParameters());
RGroupDecomposition(const std::vector<ROMOL_SPTR> &cores,
const RGroupDecompositionParameters ¶ms =
RGroupDecompositionParameters());
~RGroupDecomposition();
int add(const ROMol &mol);
bool process();
const RGroupDecompositionParameters ¶ms() const;
//! return the current group labels
std::vector<std::string> getRGroupLabels() const;
//! return rgroups in row order group[row][attachment_point] = ROMol
RGroupRows getRGroupsAsRows() const;
//! return rgroups in column order group[attachment_point][row] = ROMol
RGroupColumns getRGroupsAsColumns() const;
};
RDKIT_RGROUPDECOMPOSITION_EXPORT unsigned int RGroupDecompose(
const std::vector<ROMOL_SPTR> &cores, const std::vector<ROMOL_SPTR> &mols,
RGroupRows &rows, std::vector<unsigned int> *unmatched = nullptr,
const RGroupDecompositionParameters &options =
RGroupDecompositionParameters());
RDKIT_RGROUPDECOMPOSITION_EXPORT unsigned int RGroupDecompose(
const std::vector<ROMOL_SPTR> &cores, const std::vector<ROMOL_SPTR> &mols,
RGroupColumns &columns, std::vector<unsigned int> *unmatched = nullptr,
const RGroupDecompositionParameters &options =
RGroupDecompositionParameters());
inline bool checkForTimeout(const std::chrono::steady_clock::time_point &t0,
double timeout, bool throwOnTimeout = true) {
if (timeout <= 0) return false;
auto t1 = std::chrono::steady_clock::now();
std::chrono::duration<double> elapsed = t1 - t0;
if (elapsed.count() >= timeout) {
if (throwOnTimeout) {
throw std::runtime_error("operation timed out");
}
return true;
}
return false;
}
} // namespace RDKit
#endif
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