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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;
RDKIT_RGROUPDECOMPOSITION_EXPORT extern const std::string RLABEL_TYPE;
RDKIT_RGROUPDECOMPOSITION_EXPORT extern const std::string RLABEL_CORE_INDEX;
RDKIT_RGROUPDECOMPOSITION_EXPORT extern const std::string SIDECHAIN_RLABELS;
RDKIT_RGROUPDECOMPOSITION_EXPORT extern const std::string done;
RDKIT_RGROUPDECOMPOSITION_EXPORT extern const std::string
UNLABELED_CORE_ATTACHMENT;
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 isAtomWithMultipleNeighborsOrNotDummyRGroupAttachment(const Atom &atom);
//! Return true if the atom has a user-defined R group label
bool isUserRLabel(const Atom &atom);
// ! Return true if the atom is a terminal dummy R group (user labelled or
// unlabelled)
bool isDummyRGroupAttachment(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 isAtomWithMultipleNeighborsOrNotDummyRGroupAttachment(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 = "");
//! Relabel dummy atoms bearing an R-group mapping (as
/// atom map number, isotope or MDLRGroup label) such that
/// they will be displayed by the rendering code as R# rather
/// than #*, *:#, #*:#, etc. By default, only the MDLRGroup label
/// is retained on output; this may be configured through the
/// outputLabels parameter.
/// In case there are multiple potential R-group mappings,
/// the priority on input is Atom map number > Isotope > MDLRGroup.
/// The inputLabels parameter allows to configure which mappings
/// are taken into consideration.
RDKIT_RGROUPDECOMPOSITION_EXPORT void relabelMappedDummies(
ROMol &mol, unsigned int inputLabels = AtomMap | Isotope | MDLRGroup,
unsigned int outputLabels = MDLRGroup);
} // 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:126
RDKit::ROMol
Definition ROMol.h:199
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:417
RDKit
Std stuff.
Definition Abbreviations.h:19
RDKit::RLABEL_CORE_INDEX
RDKIT_RGROUPDECOMPOSITION_EXPORT const std::string RLABEL_CORE_INDEX
RDKit::labellingToString
std::string labellingToString(Labelling type)
return the user friendly name for the given labelling
RDKit::done
RDKIT_RGROUPDECOMPOSITION_EXPORT const std::string done
RDKit::UNLABELED_CORE_ATTACHMENT
RDKIT_RGROUPDECOMPOSITION_EXPORT const std::string UNLABELED_CORE_ATTACHMENT
RDKit::rdvalue_is
bool rdvalue_is(const RDValue_cast_t)
Definition RDValue-doublemagic.h:372
RDKit::RGroupRow
std::map< std::string, ROMOL_SPTR > RGroupRow
Definition RGroupDecomp.h:31
RDKit::RGroupColumn
std::vector< ROMOL_SPTR > RGroupColumn
Definition RGroupDecomp.h:32
RDKit::relabelMappedDummies
RDKIT_RGROUPDECOMPOSITION_EXPORT void relabelMappedDummies(ROMol &mol, unsigned int inputLabels=AtomMap|Isotope|MDLRGroup, unsigned int outputLabels=MDLRGroup)
RDKit::isDummyRGroupAttachment
bool isDummyRGroupAttachment(const Atom &atom)
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::RGroupColumns
std::map< std::string, RGroupColumn > RGroupColumns
Definition RGroupDecomp.h:35
RDKit::isAtomWithMultipleNeighborsOrNotDummyRGroupAttachment
bool isAtomWithMultipleNeighborsOrNotDummyRGroupAttachment(const Atom &atom)
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::SIDECHAIN_RLABELS
RDKIT_RGROUPDECOMPOSITION_EXPORT const std::string SIDECHAIN_RLABELS
RDKit::MDLRGroup
@ MDLRGroup
Definition RGroupDecompParams.h:41
RDKit::AtomMap
@ AtomMap
Definition RGroupDecompParams.h:39
RDKit::Isotope
@ Isotope
Definition RGroupDecompParams.h:40
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:72
RDKit::RLABEL_TYPE
RDKIT_RGROUPDECOMPOSITION_EXPORT const std::string RLABEL_TYPE
RDKit::EMPTY_CORE_LABEL
const unsigned int EMPTY_CORE_LABEL
Definition RGroupUtils.h:27
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:34
RDKit::getRlabels
std::map< int, Atom * > getRlabels(const RWMol &mol)
Get the RLabels,atom mapping for the current molecule.
RDKit::Labelling
Labelling
Definition RGroupUtils.h:31
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