NetworkBuilder.h

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#ifndef KINETX_NETWORKBUILDER_H_
#define KINETX_NETWORKBUILDER_H_

#include <Eigen/Dense>
#include <Eigen/Sparse>

namespace Scine {
namespace Kinetx {

class Network;

class NetworkBuilder {
 public:
  NetworkBuilder() = default;
  Network generate();
  void reserve(unsigned int nCompounds, unsigned int nReactions, unsigned int nChannelsPerReaction);
  void addReaction(std::vector<double> rfs, std::vector<double> rbs, std::vector<std::pair<unsigned int, int>> lhs,
                   std::vector<std::pair<unsigned int, int>> rhs);
  void addReactionChannel(unsigned int reaction, double rf, double rb);
  void addCompound(double mass, std::string label = "");

 private:
  unsigned int _nCompounds = 0;
  unsigned int _nReactions = 0;
  unsigned int _nChannels = 0;
  Eigen::VectorXi _channelCounts;
  Eigen::VectorXd _masses;
  std::vector<std::string> _labels;
  Eigen::SparseMatrix<double> _ratesForward;
  Eigen::SparseMatrix<double> _ratesBackward;
  Eigen::SparseMatrix<int> _stoichiometryForward;
  Eigen::SparseMatrix<int> _stoichiometryBackward;
};

} /* namespace Kinetx */
} /* namespace Scine */

#endif // KINETX_NETWORKBUILDER_H_