render_molecule.h

// -*-c++-*-
#ifndef STORMM_RENDER_MOLECULE_H
#define STORMM_RENDER_MOLECULE_H
 
#include <fstream>
#include <iostream>
#include <string>
#include <vector>
#include "copyright.h"
#include "Chemistry/periodic_table.h"
#include "Math/rounding.h"
#include "Math/vector_ops.h"
#include "Parsing/parse.h"
#include "Parsing/parsing_enumerators.h"
#include "Topology/atomgraph.h"
#include "Topology/atomgraph_abstracts.h"
#include "Trajectory/coordinateframe.h"
#include "Trajectory/coordinate_series.h"
#include "render_options.h"
 
namespace stormm {
namespace review {
 
using chemistry::element_maximum_count;
using chemistry::elemental_symbols;
using parse::char2ToString;
using parse::char4ToString;
using parse::intToString;
using parse::NumberFormat;
using parse::realToString;
using parse::removeTailingWhiteSpace;
using stmath::accumulateBitmask;
using stmath::readBitFromMask;
using stmath::roundUp;
using topology::AtomGraph;
using topology::ChemicalDetailsKit;
using topology::NonbondedKit;
using trajectory::CoordinateFrame;
using trajectory::CoordinateFrameReader;
using trajectory::CoordinateSeries;
using trajectory::CoordinateSeriesReader;

std::vector<int> traceBondLines(const NonbondedKit<double> &nbk, const ChemicalDetailsKit &cdk,
                                const int mol_index, std::vector<uint> *atom_coverage,
                                std::vector<uint> *bond_coverage);
  
template <typename T>
void renderMolecule(std::ofstream *foutp, const T* atom_x, const T* atom_y, const T* atom_z,
                    const NonbondedKit<double> &nbk, const ChemicalDetailsKit &cdk,
                    const RenderOptions &ropt, GridFileSyntax syntax, size_t nframe = 1);
 
void renderMolecule(std::ofstream *foutp, const CoordinateFrame *cf, const AtomGraph *ag,
                    const RenderOptions *ropt, GridFileSyntax syntax);
 
void renderMolecule(std::ofstream *foutp, const CoordinateFrame &cf, const AtomGraph &ag,
                    const RenderOptions &ropt, GridFileSyntax syntax);
 
template <typename T>
void renderMolecule(std::ofstream *foutp, const CoordinateSeries<T> *cs, const AtomGraph *ag,
                    const RenderOptions *ropt, GridFileSyntax syntax);
 
template <typename T>
void renderMolecule(std::ofstream *foutp, const CoordinateSeries<T> &cs, const AtomGraph &ag,
                    const RenderOptions &ropt, GridFileSyntax syntax);
 
} // namespace review
} // namespace stormm
 
#include "render_molecule.tpp"
 
#endif