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Molecule.h

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/***************************************************************************
 *cr                                                                       
 *cr            (C) Copyright 1995-2019 The Board of Trustees of the           
 *cr                        University of Illinois                       
 *cr                         All Rights Reserved                        
 *cr                                                                   
 ***************************************************************************/

/***************************************************************************
 * RCS INFORMATION:
 *
 *      $RCSfile: Molecule.h,v $
 *      $Author: johns $        $Locker:  $             $State: Exp $
 *      $Revision: 1.67 $       $Date: 2020/10/28 17:26:39 $
 *
 ***************************************************************************
 * DESCRIPTION:
 *
 * Main Molecule objects, which contains all the capabilities necessary to
 * store, draw, and manipulate a molecule.  This adds to the functions of
 * DrawMolecule and BaseMolecule by adding file I/O interfaces
 *
 ***************************************************************************/
#ifndef MOLECULE_H
#define MOLECULE_H

#include "DrawMolecule.h"
#include "ResizeArray.h"
#include "utilities.h"

class VMDApp;
class CoorData;

class Molecule : public DrawMolecule {

private:
  ResizeArray<char *> fileList;       
  ResizeArray<char *> fileSpecList;   
  ResizeArray<char *> typeList;       
  ResizeArray<char *> dbList;         
  ResizeArray<char *> accessionList;  
  ResizeArray<char *> remarksList;    
    
public:
  Molecule(const char *, VMDApp *, Displayable *);
  
  virtual ~Molecule(void);

  int rename(const char *newname);

  int num_files() const { return int(fileList.num()); }
 
  const char *get_type(int i) const {
    if (i < 0 || i >= typeList.num()) return NULL;
    return typeList[i];
  } 

  const char *get_file(int i) const {
    if (i < 0 || i >= fileList.num()) return NULL;
    return fileList[i];
  } 

  const char *get_file_specs(int i) const {
    if (i < 0 || i >= fileSpecList.num()) return NULL;
    return fileSpecList[i];
  } 

  const char *get_database(int i) const {
    if (i < 0 || i >= dbList.num()) return NULL;
    return dbList[i];
  }

  const char *get_accession(int i) const {
    if (i < 0 || i >= accessionList.num()) return NULL;
    return accessionList[i];
  }

  const char *get_remarks(int i) const {
    if (i < 0 || i >= remarksList.num()) return NULL;
    return remarksList[i];
  }

  void record_file(const char *filename, const char *filetype, const char *filespecs) {
    fileList.append(stringdup(filename));
    typeList.append(stringdup(filetype));
    fileSpecList.append(stringdup(filespecs));
  }

  void record_database(const char *dbname, const char *dbcode) {
    dbList.append(stringdup(dbname));
    accessionList.append(stringdup(dbcode));
  }

  void record_remarks(const char *remarks) {
    remarksList.append(stringdup(remarks));
  }
    
  void add_coor_file(CoorData *);

  void close_coor_file(CoorData *);

  int get_new_frames();

  int next_frame();
  
  int cancel();

  int file_in_progress() { return int(coorIOFiles.num()); }

  virtual void prepare();

  // Forces: Various UIObjects add forces to the molecule during the 
  // check_event stage.  In prepare, Molecule sums all the forces, sets
  // the forces in Timestep, and calls app->imd_sendforces() if there's
  // anything to send.  Only Molecule should modify the forces in Timestep
  // directly.

  void addForce(int theatom, const float * f);

  void addPersistentForce(int theatom, const float * f);
  
private:
  ResizeArray<int> force_indices;
  ResizeArray<float> force_vectors;

  ResizeArray<int> persistent_force_indices;
  ResizeArray<float> persistent_force_vectors;

  ResizeArray<int> last_force_indices;

  ResizeArray<CoorData *> coorIOFiles;
};

#endif

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