RGroupUtils.h
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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.
//
#ifndef RGROUP_UTILS
#define RGROUP_UTILS
#include <GraphMol/RDKitBase.h>
#include "RGroupDecomp.h"
#include <map>
namespace RDKit {
RDKIT_RGROUPDECOMPOSITION_EXPORT extern const std::string RLABEL;
extern const std::string RLABEL_TYPE;
extern const std::string RLABEL_CORE_INDEX;
extern const std::string SIDECHAIN_RLABELS;
extern const std::string done;
const unsigned int EMPTY_CORE_LABEL = -100000;
// Various places where rgroups can be labeled
// the order of precedence
enum class Labelling {
RGROUP_LABELS,
ISOTOPE_LABELS,
ATOMMAP_LABELS,
INDEX_LABELS,
DUMMY_LABELS,
INTERNAL_LABELS
};
//! return the user friendly name for the given labelling
std::string labellingToString(Labelling type);
//! Get the RLabels,atom mapping for the current molecule
std::map<int, Atom *> getRlabels(const RWMol &mol);
//! Remove the user labels from the atom
void clearInputLabels(Atom *atom);
//! Set the rgroup label for the current atom, this also sets the
/// appropriate MDL or other label
bool setLabel(Atom *atom, int label, std::set<int> &labels, int &maxLabel,
bool relabel, Labelling type);
//! Returns true if the core has a dummy atom
bool hasDummy(const RWMol &core);
//! Returns true if the core atom is either an atom with multiple
/// connections or an atom with a single connection that has no user
/// defined rgroup label
bool isAtomWithMultipleNeighborsOrNotUserRLabel(const Atom &atom);
//! Return true if the atom has a user-defined R group label
bool isUserRLabel(const Atom &atom);
//! Returns true if the core atom is either a dummy atom with multiple
/// connections or a dummy atom with a single connection that has no user
/// defined rgroup label
inline bool isAnyAtomWithMultipleNeighborsOrNotUserRLabel(const Atom &atom) {
if (atom.getAtomicNum()) {
return false;
}
return isAtomWithMultipleNeighborsOrNotUserRLabel(atom);
}
//! Returns a JSON form
/// The prefix argument is added to each line in the output
RDKIT_RGROUPDECOMPOSITION_EXPORT std::string toJSON(
const RGroupRow &rgr, const std::string &prefix = "");
//! Returns a JSON form
/// The prefix argument is added to each line in the output
RDKIT_RGROUPDECOMPOSITION_EXPORT std::string toJSON(
const RGroupRows &rgr, const std::string &prefix = "");
//! Returns a JSON form
/// The prefix argument is added to each line in the output
RDKIT_RGROUPDECOMPOSITION_EXPORT std::string toJSON(
const RGroupColumn &rgr, const std::string &prefix = "");
//! Returns a JSON form
/// The prefix argument is added to each line in the output
RDKIT_RGROUPDECOMPOSITION_EXPORT std::string toJSON(
const RGroupColumns &rgr, const std::string &prefix = "");
} // namespace RDKit
#endif
RDKitBase.h
pulls in the core RDKit functionality
RGroupDecomp.h
RDKit::Atom
The class for representing atoms.
Definition: Atom.h:68
RDKit::Atom::getAtomicNum
int getAtomicNum() const
returns our atomic number
Definition: Atom.h:115
RDKit::RWMol
RWMol is a molecule class that is intended to be edited.
Definition: RWMol.h:32
RDKIT_RGROUPDECOMPOSITION_EXPORT
#define RDKIT_RGROUPDECOMPOSITION_EXPORT
Definition: export.h:385
RDKit
Std stuff.
Definition: Abbreviations.h:18
RDKit::getRlabels
std::map< int, Atom * > getRlabels(const RWMol &mol)
Get the RLabels,atom mapping for the current molecule.
RDKit::labellingToString
std::string labellingToString(Labelling type)
return the user friendly name for the given labelling
RDKit::RLABEL_TYPE
const std::string RLABEL_TYPE
RDKit::RLABEL_CORE_INDEX
const std::string RLABEL_CORE_INDEX
RDKit::RGroupRow
std::map< std::string, ROMOL_SPTR > RGroupRow
Definition: RGroupDecomp.h:132
RDKit::RGroupColumn
std::vector< ROMOL_SPTR > RGroupColumn
Definition: RGroupDecomp.h:133
RDKit::setLabel
bool setLabel(Atom *atom, int label, std::set< int > &labels, int &maxLabel, bool relabel, Labelling type)
RDKit::clearInputLabels
void clearInputLabels(Atom *atom)
Remove the user labels from the atom.
RDKit::done
const std::string done
RDKit::RGroupColumns
std::map< std::string, RGroupColumn > RGroupColumns
Definition: RGroupDecomp.h:136
RDKit::RLABEL
RDKIT_RGROUPDECOMPOSITION_EXPORT const std::string RLABEL
RDKit::hasDummy
bool hasDummy(const RWMol &core)
Returns true if the core has a dummy atom.
RDKit::toJSON
RDKIT_RGROUPDECOMPOSITION_EXPORT std::string toJSON(const RGroupRow &rgr, const std::string &prefix="")
RDKit::isAnyAtomWithMultipleNeighborsOrNotUserRLabel
bool isAnyAtomWithMultipleNeighborsOrNotUserRLabel(const Atom &atom)
Definition: RGroupUtils.h:66
RDKit::isAtomWithMultipleNeighborsOrNotUserRLabel
bool isAtomWithMultipleNeighborsOrNotUserRLabel(const Atom &atom)
RDKit::SIDECHAIN_RLABELS
const std::string SIDECHAIN_RLABELS
RDKit::EMPTY_CORE_LABEL
const unsigned int EMPTY_CORE_LABEL
Definition: RGroupUtils.h:25
RDKit::isUserRLabel
bool isUserRLabel(const Atom &atom)
Return true if the atom has a user-defined R group label.
RDKit::RGroupRows
std::vector< RGroupRow > RGroupRows
Definition: RGroupDecomp.h:135
RDKit::Labelling
Labelling
Definition: RGroupUtils.h:29
RDKit::Labelling::DUMMY_LABELS
@ DUMMY_LABELS
RDKit::Labelling::INDEX_LABELS
@ INDEX_LABELS
RDKit::Labelling::ISOTOPE_LABELS
@ ISOTOPE_LABELS
RDKit::Labelling::RGROUP_LABELS
@ RGROUP_LABELS
RDKit::Labelling::ATOMMAP_LABELS
@ ATOMMAP_LABELS
RDKit::Labelling::INTERNAL_LABELS
@ INTERNAL_LABELS