00001 /*************************************************************************** 00002 *cr 00003 *cr (C) Copyright 1995-2019 The Board of Trustees of the 00004 *cr University of Illinois 00005 *cr All Rights Reserved 00006 *cr 00007 ***************************************************************************/ 00008 00009 /*************************************************************************** 00010 * RCS INFORMATION: 00011 * 00012 * $RCSfile: Molecule.h,v $ 00013 * $Author: johns $ $Locker: $ $State: Exp $ 00014 * $Revision: 1.67 $ $Date: 2020年10月28日 17:26:39 $ 00015 * 00016 *************************************************************************** 00017 * DESCRIPTION: 00018 * 00019 * Main Molecule objects, which contains all the capabilities necessary to 00020 * store, draw, and manipulate a molecule. This adds to the functions of 00021 * DrawMolecule and BaseMolecule by adding file I/O interfaces 00022 * 00023 ***************************************************************************/ 00024 #ifndef MOLECULE_H 00025 #define MOLECULE_H 00026 00027 #include "DrawMolecule.h" 00028 #include "ResizeArray.h" 00029 #include "utilities.h" 00030 00031 class VMDApp; 00032 class CoorData; 00033 00037 class Molecule : public DrawMolecule { 00038 00039 private: 00040 ResizeArray<char *> fileList; 00041 ResizeArray<char *> fileSpecList; 00042 ResizeArray<char *> typeList; 00043 ResizeArray<char *> dbList; 00044 ResizeArray<char *> accessionList; 00045 ResizeArray<char *> remarksList; 00046 00047 public: 00051 Molecule(const char *, VMDApp *, Displayable *); 00052 00054 virtual ~Molecule(void); 00055 00058 int rename(const char *newname); 00059 00061 int num_files() const { return int(fileList.num()); } 00062 00064 const char *get_type(int i) const { 00065 if (i < 0 || i >= typeList.num()) return NULL; 00066 return typeList[i]; 00067 } 00068 00070 const char *get_file(int i) const { 00071 if (i < 0 || i >= fileList.num()) return NULL; 00072 return fileList[i]; 00073 } 00074 00076 const char *get_file_specs(int i) const { 00077 if (i < 0 || i >= fileSpecList.num()) return NULL; 00078 return fileSpecList[i]; 00079 } 00080 00082 const char *get_database(int i) const { 00083 if (i < 0 || i >= dbList.num()) return NULL; 00084 return dbList[i]; 00085 } 00086 00088 const char *get_accession(int i) const { 00089 if (i < 0 || i >= accessionList.num()) return NULL; 00090 return accessionList[i]; 00091 } 00092 00094 const char *get_remarks(int i) const { 00095 if (i < 0 || i >= remarksList.num()) return NULL; 00096 return remarksList[i]; 00097 } 00098 00100 void record_file(const char *filename, const char *filetype, const char *filespecs) { 00101 fileList.append(stringdup(filename)); 00102 typeList.append(stringdup(filetype)); 00103 fileSpecList.append(stringdup(filespecs)); 00104 } 00105 00108 void record_database(const char *dbname, const char *dbcode) { 00109 dbList.append(stringdup(dbname)); 00110 accessionList.append(stringdup(dbcode)); 00111 } 00112 00114 void record_remarks(const char *remarks) { 00115 remarksList.append(stringdup(remarks)); 00116 } 00117 00121 void add_coor_file(CoorData *); 00122 00125 void close_coor_file(CoorData *); 00126 00128 int get_new_frames(); 00129 00132 int next_frame(); 00133 00136 int cancel(); 00137 00139 int file_in_progress() { return int(coorIOFiles.num()); } 00140 00143 virtual void prepare(); 00144 00145 // Forces: Various UIObjects add forces to the molecule during the 00146 // check_event stage. In prepare, Molecule sums all the forces, sets 00147 // the forces in Timestep, and calls app->imd_sendforces() if there's 00148 // anything to send. Only Molecule should modify the forces in Timestep 00149 // directly. 00150 00152 void addForce(int theatom, const float * f); 00153 00157 void addPersistentForce(int theatom, const float * f); 00158 00159 private: 00162 ResizeArray<int> force_indices; 00163 ResizeArray<float> force_vectors; 00164 00165 ResizeArray<int> persistent_force_indices; 00166 ResizeArray<float> persistent_force_vectors; 00167 00169 ResizeArray<int> last_force_indices; 00170 00173 ResizeArray<CoorData *> coorIOFiles; 00174 }; 00175 00176 #endif 00177