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Templates.h
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//
// Copyright (C) 2023 Schrödinger, LLC
//
// @@ 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 <GraphMol/ROMol.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/MolOps.h>
#include "TemplateSmiles.h"
#include <iostream>
#include <fstream>
#include <unordered_map>
namespace RDDepict {
class RDKIT_DEPICTOR_EXPORT CoordinateTemplates {
public:
//! returns a reference to the singleton CoordinateTemplates
/*
\return a reference to the singleton CoordinateTemplates
<b>Notes:</b>
- if the singleton CoordinateTemplates has already been instantiated
the singleton will be returned, otherwise the singleton will
be constructed.
*/
static CoordinateTemplates &getRingSystemTemplates() {
static CoordinateTemplates template_mols;
return template_mols;
}
bool hasTemplateOfSize(unsigned int atomCount) {
if (m_templates.find(atomCount) != m_templates.end()) {
return true;
}
return false;
}
const std::vector<std::shared_ptr<RDKit::ROMol>> &getMatchingTemplates(
unsigned int atomCount) {
return m_templates[atomCount];
}
void setRingSystemTemplates(const std::string &templatePath);
void addRingSystemTemplates(const std::string &templatePath);
//! check if a template is considered valid
/*
\param template mol
\param smiles for logging
\return whether the template is valid
<b>A template is considered valid if it:</b>
- has 2D coordinates
- is a ring system (spiro'd ring systems are OK)
- consists of only 1 fragment
*/
static void assertValidTemplate(RDKit::ROMol &mol, const std::string &smiles);
void loadDefaultTemplates() {
clearTemplates();
// load default templates into m_templates map by atom count
for (const auto &smiles : TEMPLATE_SMILES) {
std::shared_ptr<RDKit::ROMol> mol(RDKit::SmilesToMol(smiles));
m_templates[mol->getNumAtoms()].push_back(mol);
}
}
private:
CoordinateTemplates() { loadDefaultTemplates(); }
CoordinateTemplates(const CoordinateTemplates &) = delete;
CoordinateTemplates &operator=(const CoordinateTemplates &) = delete;
void clearTemplates() {
for (auto &[atom_cout, romols] : m_templates) {
romols.clear();
}
m_templates.clear();
}
~CoordinateTemplates() { clearTemplates(); }
void loadTemplatesFromPath(
const std::string &templatePath,
std::unordered_map<
unsigned int, std::vector<std::shared_ptr<RDKit::ROMol>>> &templates);
std::unordered_map<unsigned int, std::vector<std::shared_ptr<RDKit::ROMol>>>
m_templates;
};
} // namespace RDDepict
MolOps.h
ROMol.h
Defines the primary molecule class ROMol as well as associated typedefs.
SmilesParse.h
TemplateSmiles.h
TEMPLATE_SMILES
const std::vector< std::string > TEMPLATE_SMILES
Definition TemplateSmiles.h:20
RDDepict::CoordinateTemplates
Definition Templates.h:22
RDDepict::CoordinateTemplates::getMatchingTemplates
const std::vector< std::shared_ptr< RDKit::ROMol > > & getMatchingTemplates(unsigned int atomCount)
Definition Templates.h:46
RDDepict::CoordinateTemplates::hasTemplateOfSize
bool hasTemplateOfSize(unsigned int atomCount)
Definition Templates.h:39
RDDepict::CoordinateTemplates::addRingSystemTemplates
void addRingSystemTemplates(const std::string &templatePath)
RDDepict::CoordinateTemplates::assertValidTemplate
static void assertValidTemplate(RDKit::ROMol &mol, const std::string &smiles)
check if a template is considered valid
RDDepict::CoordinateTemplates::loadDefaultTemplates
void loadDefaultTemplates()
Definition Templates.h:68
RDDepict::CoordinateTemplates::setRingSystemTemplates
void setRingSystemTemplates(const std::string &templatePath)
RDDepict::CoordinateTemplates::getRingSystemTemplates
static CoordinateTemplates & getRingSystemTemplates()
returns a reference to the singleton CoordinateTemplates
Definition Templates.h:34
RDKit::ROMol
Definition ROMol.h:199
RDKIT_DEPICTOR_EXPORT
#define RDKIT_DEPICTOR_EXPORT
Definition export.h:97
RDDepict
Definition Reaction.h:477
RDKit::v1::SmilesToMol
RDKit::RWMol * SmilesToMol(const std::string &smi, const SmilesParserParams &ps)
Definition SmilesParse.h:118