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67b4555611
* parse templates as smarts * accept ring templates in SMARTS format * undo CLAUDE mistake * rename files
111 lines
3.7 KiB
C++
111 lines
3.7 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 "Templates.h"
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#include "RDDepictor.h"
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namespace RDDepict {
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void CoordinateTemplates::assertValidTemplate(RDKit::ROMol &mol,
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const std::string &smiles) {
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// template must have 2D coordinates
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if (mol.getNumConformers() == 0) {
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std::string msg = "Template missing coordinates: " + smiles;
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throw RDDepict::DepictException(msg);
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}
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if (mol.getConformer().is3D()) {
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std::string msg =
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"Template has 3D coordinates, 2D coordinates required: " + smiles;
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throw RDDepict::DepictException(msg);
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}
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// Make sure this template is a single ring system (spiro'd ring systems are
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// OK). We can check this by ensuring that every bond is in a ring and that
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// there is only one connected component in the molecular graph.
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if (RDKit::MolOps::getMolFrags(mol).size() != 1) {
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std::string msg =
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"Template consists of multiple fragments, single fragment required: " +
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smiles;
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throw RDDepict::DepictException(msg);
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}
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if (mol.getNumAtoms() == 1) {
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std::string msg = "Template is not a ring system: " + smiles;
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throw RDDepict::DepictException(msg);
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}
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auto ri = mol.getRingInfo();
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for (unsigned int i = 0; i < mol.getNumBonds(); ++i) {
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if (!ri->numBondRings(i)) {
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std::string msg = "Template is not a ring system: " + smiles;
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throw RDDepict::DepictException(msg);
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}
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}
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}
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void CoordinateTemplates::loadTemplatesFromPath(
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const std::string &templatePath,
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std::unordered_map<unsigned int, std::vector<std::shared_ptr<RDKit::ROMol>>>
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&templates) {
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std::ifstream cxsmiles(templatePath);
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if (!cxsmiles) {
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std::string msg = "Could not open file " + templatePath;
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throw RDDepict::DepictException(msg);
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}
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// Try loading templates in from this directory, if unsuccessful, keep current
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// templates
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std::string line;
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while (std::getline(cxsmiles, line)) {
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RDKit::ROMol *mol_ptr = RDKit::SmartsToMol(line);
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if (!mol_ptr) {
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std::string msg =
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"Could not load templates from " + templatePath + ": Invalid smarts";
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cxsmiles.close();
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throw RDDepict::DepictException(msg);
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}
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std::shared_ptr<RDKit::ROMol> mol(mol_ptr);
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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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try {
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assertValidTemplate(*mol, line);
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} catch (RDDepict::DepictException &e) {
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cxsmiles.close();
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throw e;
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}
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templates[mol->getNumAtoms()].push_back(mol);
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}
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cxsmiles.close();
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}
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void CoordinateTemplates::setRingSystemTemplates(
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const std::string &templatePath) {
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// Try loading templates in from this directory, if unsuccessful, keep current
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// templates
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std::unordered_map<unsigned int, std::vector<std::shared_ptr<RDKit::ROMol>>>
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templates;
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loadTemplatesFromPath(templatePath, templates);
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clearTemplates();
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m_templates = std::move(templates);
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}
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void CoordinateTemplates::addRingSystemTemplates(
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const std::string &templatePath) {
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// Try loading templates in from this directory, if unsuccessful, keep current
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// templates
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std::unordered_map<unsigned int, std::vector<std::shared_ptr<RDKit::ROMol>>>
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templates;
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loadTemplatesFromPath(templatePath, templates);
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for (auto &kv : templates) {
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m_templates[kv.first].insert(m_templates[kv.first].begin(),
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kv.second.begin(), kv.second.end());
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}
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}
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} // namespace RDDepict
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