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67b4555611
* parse templates as smarts * accept ring templates in SMARTS format * undo CLAUDE mistake * rename files
105 lines
3.0 KiB
C++
105 lines
3.0 KiB
C++
//
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// Copyright (C) 2023 Schrödinger, LLC
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <GraphMol/ROMol.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/MolOps.h>
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#include "TemplateSmarts.h"
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#include <fstream>
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#include <unordered_map>
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namespace RDDepict {
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class RDKIT_DEPICTOR_EXPORT CoordinateTemplates {
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public:
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//! returns a reference to the singleton CoordinateTemplates
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/*
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\return a reference to the singleton CoordinateTemplates
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<b>Notes:</b>
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- if the singleton CoordinateTemplates has already been instantiated
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the singleton will be returned, otherwise the singleton will
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be constructed.
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*/
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static CoordinateTemplates &getRingSystemTemplates() {
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static CoordinateTemplates template_mols;
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return template_mols;
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}
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bool hasTemplateOfSize(unsigned int atomCount) {
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if (m_templates.find(atomCount) != m_templates.end()) {
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return true;
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}
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return false;
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}
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const std::vector<std::shared_ptr<RDKit::ROMol>> &getMatchingTemplates(
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unsigned int atomCount) {
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return m_templates[atomCount];
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}
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void setRingSystemTemplates(const std::string &templatePath);
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void addRingSystemTemplates(const std::string &templatePath);
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//! check if a template is considered valid
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/*
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\param template mol
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\param smiles for logging
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\return whether the template is valid
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<b>A template is considered valid if it:</b>
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- has 2D coordinates
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- is a ring system (spiro'd ring systems are OK)
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- consists of only 1 fragment
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*/
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static void assertValidTemplate(RDKit::ROMol &mol, const std::string &smiles);
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void loadDefaultTemplates() {
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clearTemplates();
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// load default templates into m_templates map by atom count
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for (const auto &smarts : TEMPLATE_SMARTS) {
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std::shared_ptr<RDKit::ROMol> mol(RDKit::SmartsToMol(smarts));
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if (!mol) {
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continue;
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}
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// Initialize ring info using symmetrizeSSSR to match depictor ring counting
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RDKit::VECT_INT_VECT arings;
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RDKit::MolOps::symmetrizeSSSR(*mol, arings);
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m_templates[mol->getNumAtoms()].push_back(mol);
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}
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}
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private:
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CoordinateTemplates() { loadDefaultTemplates(); }
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CoordinateTemplates(const CoordinateTemplates &) = delete;
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CoordinateTemplates &operator=(const CoordinateTemplates &) = delete;
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void clearTemplates() {
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for (auto &[atom_cout, romols] : m_templates) {
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romols.clear();
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}
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m_templates.clear();
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}
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~CoordinateTemplates() { clearTemplates(); }
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void loadTemplatesFromPath(
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const std::string &templatePath,
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std::unordered_map<
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unsigned int, std::vector<std::shared_ptr<RDKit::ROMol>>> &templates);
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std::unordered_map<unsigned int, std::vector<std::shared_ptr<RDKit::ROMol>>>
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m_templates;
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};
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} // namespace RDDepict
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