symmetry.cpp

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/*-
 * SPDX-License-Identifier: BSD-2-Clause
 * 
 * Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
 * 
 * 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.
 * 
 * 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 OWNER 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 INTERRUPTION) HOWEVER CAUSED AND
 * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */

#include "cif++/symmetry.hpp"

#include <stdexcept>

#include "symop_table_data.hpp"

namespace cif
{

// --------------------------------------------------------------------
// Unfortunately, clipper has a different numbering scheme than PDB
// for rotation numbers. So we created a table to map those.
// Perhaps a bit over the top, but hey....

// --------------------------------------------------------------------

int get_space_group_number(std::string spacegroup)
{
    if (spacegroup == "P 21 21 2 A")
        spacegroup = "P 21 21 2 (a)";
    else if (spacegroup.empty())
        throw std::runtime_error("No spacegroup, cannot continue");

    int result = 0;

    const size_t N = kNrOfSpaceGroups;
    int32_t L = 0, R = static_cast<int32_t>(N - 1);
    while (L <= R)
    {
        int32_t i = (L + R) / 2;

        int d = spacegroup.compare(kSpaceGroups[i].name);

        if (d > 0)
            L = i + 1;
        else if (d < 0)
            R = i - 1;
        else
        {
            result = kSpaceGroups[i].nr;
            break;
        }
    }

    // not found, see if we can find a match based on xHM name
    if (result == 0)
    {
        for (size_t i = 0; i < kNrOfSpaceGroups; ++i)
        {
            auto& sp = kSpaceGroups[i];
            if (sp.xHM == spacegroup)
            {
                result = sp.nr;
                break;
            }
        }
    }

    if (result == 0)
        throw std::runtime_error("Spacegroup name " + spacegroup + " was not found in table");
    
    return result;
}

// --------------------------------------------------------------------

int get_space_group_number(std::string spacegroup, space_group_name type)
{
    if (spacegroup == "P 21 21 2 A")
        spacegroup = "P 21 21 2 (a)";
    else if (spacegroup.empty())
        throw std::runtime_error("No spacegroup, cannot continue");

    int result = 0;

    if (type == space_group_name::full)
    {
        const size_t N = kNrOfSpaceGroups;
        int32_t L = 0, R = static_cast<int32_t>(N - 1);
        while (L <= R)
        {
            int32_t i = (L + R) / 2;

            int d = spacegroup.compare(kSpaceGroups[i].name);

            if (d > 0)
                L = i + 1;
            else if (d < 0)
                R = i - 1;
            else
            {
                result = kSpaceGroups[i].nr;
                break;
            }
        }
    }
    else if (type == space_group_name::xHM)
    {
        for (auto &sg : kSpaceGroups)
        {
            if (sg.xHM == spacegroup)
            {
                result = sg.nr;
                break;
            }
        }
    }
    else
    {
        for (auto &sg : kSpaceGroups)
        {
            if (sg.Hall == spacegroup)
            {
                result = sg.nr;
                break;
            }
        }
    }

    // not found, see if we can find a match based on xHM name
    if (result == 0)
        throw std::runtime_error("Spacegroup name " + spacegroup + " was not found in table");
    
    return result;
}

}