NameFinder.hpp

/*
 * Copyright (c) 2004-present, The University of Notre Dame. All rights
 * reserved.
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright notice,
 *    this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright notice,
 *    this list of conditions and the following disclaimer in the documentation
 *    and/or other materials provided with the distribution.
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 * 3. Neither the name of the copyright holder nor the names of its
 *    contributors may be used to endorse or promote products derived from
 *    this software without specific prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
 * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 * POSSIBILITY OF SUCH DAMAGE.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the following paper when you publish your work:
 *
 * [1] Drisko et al., J. Open Source Softw. 9, 7004 (2024).
 *
 * Good starting points for code and simulation methodology are:
 *
 * [2] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [3] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [4] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
 * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [7] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 * [9] Drisko & Gezelter, J. Chem. Theory Comput. 20, 4986-4997 (2024).
 */
 
#ifndef SELECTION_NAMEFINDER_HPP
#define SELECTION_NAMEFINDER_HPP
 
#include <map>
#include <memory>
#include <set>
#include <string>
 
#include "brains/SimInfo.hpp"
#include "selection/SelectionSet.hpp"
 
namespace OpenMD {
 
  class TreeNode {
  public:
    std::string name;
    SelectionSet bs;
    std::map<std::string, std::shared_ptr<TreeNode>> children;
  };
 
  using TreeNodePtr = std::shared_ptr<TreeNode>;
 
  class NameFinder {
  public:
    NameFinder(SimInfo* info);
    SelectionSet match(const std::string& name);
 
  private:
    void loadNames();
    void matchMolecule(const std::string& molName, SelectionSet& bs);
    void matchStuntDouble(const std::string& molName, const std::string& sdName,
                          SelectionSet& bs);
    void matchRigidAtoms(const std::string& molName, const std::string& rbName,
                         const std::string& rbAtomName, SelectionSet& bs);
    void matchBond(const std::string& molName, const std::string& bondName,
                   SelectionSet& bs);
    void matchBend(const std::string& molName, const std::string& bendName,
                   SelectionSet& bs);
    void matchTorsion(const std::string& molName,
                      const std::string& torsionName, SelectionSet& bs);
    void matchInversion(const std::string& molName,
                        const std::string& inversionName, SelectionSet& bs);
 
    void matchInternalIndex(const std::string& name, int internalIndex,
                            SelectionSet& bs);
 
    TreeNodePtr createNode(TreeNodePtr parent, const std::string& name);
    std::vector<TreeNodePtr> getAllChildren(TreeNodePtr node);
    std::vector<TreeNodePtr> getMatchedChildren(TreeNodePtr node,
                                                const std::string& name);
    bool isMatched(const std::string& str, const std::string& wildcard);
 
    bool isInteger(const std::string& str);
 
    SimInfo* info_ {nullptr};
    vector<int> nObjects_;
    TreeNodePtr root_ {nullptr};
  };
}  // namespace OpenMD
 
#endif