PeriodicVmdReporter.h

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/* -------------------------------------------------------------------------- *
 *                      SimTK Core: SimTK Molmodel                            *
 * -------------------------------------------------------------------------- *
 * This is part of the SimTK Core biosimulation toolkit originating from      *
 * Simbios, the NIH National Center for Physics-Based Simulation of           *
 * Biological Structures at Stanford, funded under the NIH Roadmap for        *
 * Medical Research, grant U54 GM072970. See https://simtk.org.               *
 *                                                                            *
 * Portions copyright (c) 2008 Stanford University and the Authors.           *
 * Authors: Christopher Bruns                                                 *
 * Contributors:                                                              *
 *                                                                            *
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#ifndef SimTK_MOLMODEL_PERIODICVMDREPORTER_H_
#define SimTK_MOLMODEL_PERIODICVMDREPORTER_H_

#include "SimTKsimbody.h"
#include "molmodel/internal/Compound.h"
#include "molmodel/internal/VmdConnection.h"
#include <iostream>
#include <iomanip>
#include <vector>

namespace SimTK {

class PeriodicVmdReporter : public PeriodicEventReporter {
public:
    PeriodicVmdReporter(
        const CompoundSystem& system, 
        Real interval,
        int localSocketNumber,
        bool blockWaitingForVmdConnection = false
        ) 
        : PeriodicEventReporter(interval), 
          system(system), 
          vmdConnection(localSocketNumber),
          blockWaitingForVmdConnection(blockWaitingForVmdConnection)
    {}

    void handleEvent(const State& state) const 
    {
        // checkForConnection() can be slow when there is none
        // so only check every so often
        static int timeStepNumber = 0;
        int checkFrequency = 20;
        
        // Try our best to connect to vmd
        if (! vmdConnection.clientIsConnected() )
        {
            if (blockWaitingForVmdConnection)
            {
                while ( ! vmdConnection.clientIsConnected() ) 
                {
                    std::cerr << "Waiting for vmd IMD connection on port " << vmdConnection.getSocketNumber() << "..." << std::endl;

                    vmdConnection.checkForConnection();

                    sleep(1);

                }  
            }
            else
            {
                if ( 0 == (timeStepNumber % checkFrequency) )
                vmdConnection.checkForConnection();
            } 
        }

        // Write the coordinates, if we are connected to vmd
        if ( vmdConnection.clientIsConnected() )
        {
            system.realize(state, Stage::Position);
            
            // To ensure that the atom coordinates are in the same order as PDB output,
            // create PDB output, and parse that to generate the coordinates
            std::stringstream pdbString;
            
            // 1) Write pdb coordinates into the string
            int nextAtomSerialNumber = 1; // atom serial number for each compound picks up where previous compound left off
            for (SimTK::Compound::Index c(0); c < system.getNumCompounds(); ++c)
                system.getCompound(c).writePdb(state, pdbString, nextAtomSerialNumber);
            
            // 2) Read pdb coordinates from the string
            std::vector<VmdFloat3> vmdCoordinates;
            char lineBuffer[102];
            while ( ! pdbString.eof() )
            {
                pdbString.getline(lineBuffer, 100);
                std::string line(lineBuffer);
                
                if ( (line.length() > 55) && ((line.substr(0, 6) == "ATOM  ") || (line.substr(0, 6) == "HETATM")) )
                {
                    float x, y, z;
                    std::istringstream(line.substr(30, 8)) >> x;
                    std::istringstream(line.substr(38, 8)) >> y;
                    std::istringstream(line.substr(46, 8)) >> z;
                    vmdCoordinates.push_back(VmdFloat3(x, y, z));
                }
            }
            
            vmdConnection.sendCoordinates(vmdCoordinates);
        }

        ++timeStepNumber;
        
    }

private:
    const CompoundSystem& system;
    mutable VmdConnection vmdConnection;
    bool blockWaitingForVmdConnection;
};

} // namespace SimTK

#endif // SimTK_MOLMODEL_PERIODICVMDREPORTER_H_