export_helpers.hpp

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// *************************************************************************
//
// Licensed under the MIT License (see accompanying LICENSE file).
//
// The authors of this code are: Thomas Holder
//
// *************************************************************************
//
// Helper functions and classes for exporting MMTF data.
// See "examples/tableexport.cpp" for example usage.
//
// *************************************************************************
 
#ifndef MMTF_EXPORT_HELPERS_H
#define MMTF_EXPORT_HELPERS_H
 
#include "errors.hpp"
#include "structure_data.hpp"
 
#include <vector>
 
namespace mmtf
{

class BondAdder {
  StructureData* m_data;
  std::vector<int32_t> m_atom2groupType;
  std::vector<int32_t> m_atomOffsets;
 
public:
  BondAdder(StructureData& data)
      : m_data(&data), m_atomOffsets(data.groupTypeList.size(), -1)
  {
    m_atom2groupType.reserve(data.numAtoms);
 
    for (size_t i = 0; i < data.groupTypeList.size(); ++i) {
      int32_t groupType = data.groupTypeList[i];
 
      // sanity check
      if (m_atomOffsets[groupType] != -1) {
        throw EncodeError("groupTypeList has duplicates");
      }
 
      size_t atomOffset = m_atom2groupType.size();
      size_t groupSize = data.groupList[groupType].atomNameList.size();
 
      m_atomOffsets[groupType] = atomOffset;
      m_atom2groupType.resize(atomOffset + groupSize, groupType);
    }
  }

  bool operator()(int32_t atom1, int32_t atom2, int8_t order)
  {
    if (atom1 >= m_atom2groupType.size() ||
        atom2 >= m_atom2groupType.size())
      return false;
 
    if (m_atom2groupType[atom1] == m_atom2groupType[atom2]) {
      int32_t groupType = m_atom2groupType[atom1];
      GroupType& group = m_data->groupList[groupType];
      group.bondAtomList.push_back(atom1 - m_atomOffsets[groupType]);
      group.bondAtomList.push_back(atom2 - m_atomOffsets[groupType]);
      group.bondOrderList.push_back(order);
    } else {
      m_data->bondAtomList.push_back(atom1);
      m_data->bondAtomList.push_back(atom2);
      m_data->bondOrderList.push_back(order);
    }
 
    ++m_data->numBonds;
    return true;
  }
};

inline void compressGroupList(StructureData& data)
{
  size_t n_old = data.groupList.size();
  size_t i_free = 0;
  std::vector<size_t> idremap(n_old, 0);
 
  for (size_t i = 1; i < n_old; ++i) {
    size_t i_found = 0;
 
    while (i_found < i && !(data.groupList[i] == data.groupList[i_found])) {
      ++i_found;
    }
 
    if (i_found == i) {
      if (i_free != 0) {
        data.groupList[i_free] = data.groupList[i]; // std::move possible with C++11
        i_found = i_free;
        ++i_free;
      }
    } else if (i_free == 0) {
      i_free = i;
    }
 
    idremap[i] = i_found;
  }
 
  if (i_free != 0) {
    data.groupList.resize(i_free);
 
    for (size_t i = 0; i < data.groupTypeList.size(); ++i) {
      data.groupTypeList[i] = idremap[data.groupTypeList[i]];
    }
  }
}
 
} // namespace mmtf
 
#endif
 
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