mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-03 21:44:30 +08:00
693796d7af
* Fix zipping of rgroup decomps with broken rings * Add utility to molzip rgroup rows * Add RGroupRow molzip * Fix typo in example and test * Fix warning on integer size * Don't use ssize_t * a couple of suggestions * Update Code/GraphMol/ChemTransforms/MolFragmenter.cpp Co-authored-by: Greg Landrum <greg.landrum@gmail.com> * Update Code/GraphMol/ChemTransforms/MolFragmenter.cpp Co-authored-by: Greg Landrum <greg.landrum@gmail.com> * Move molzip rgroup row from RGroupDecomp to ChemTransforms * Fix exports --------- Co-authored-by: Brian Kelley <bkelley@relaytx.com> Co-authored-by: greg landrum <greg.landrum@gmail.com>
114 lines
4.1 KiB
C++
114 lines
4.1 KiB
C++
//
|
|
// 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 <GraphMol/ChemTransforms/MolFragmenter.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
|