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00018 #include <string.h>
00019 #include "molfile_plugin.h"
00020 #include "ReadPARM7.h"
00021
00022 typedef struct {
00023 parmstruct *prm;
00024 int popn;
00025 FILE *fd;
00026 int nbonds;
00027 int *from, *to;
00028 } parmdata;
00029
00030 static void *open_parm7_read(const char *filename, const char *,int *natoms) {
00031 FILE *fd;
00032 int popn = 0;
00033 if(!(fd = open_parm7_file(filename, &popn))) {
00034 fprintf(stderr, "Cannot open parm file '%s'\n", filename);
00035 return NULL;
00036 }
00037 parmstruct *prm = read_parm7_header(fd);
00038 if (!prm) {
00039 close_parm7_file(fd, popn);
00040 return NULL;
00041 }
00042
00043 *natoms = prm->Natom;
00044 parmdata *p = new parmdata;
00045 memset(p, 0, sizeof(parmdata));
00046 p->prm = prm;
00047 p->popn = popn;
00048 p->fd = fd;
00049 p->from = new int[prm->Nbonh + prm->Nbona];
00050 p->to = new int[prm->Nbonh + prm->Nbona];
00051 return p;
00052 }
00053
00054 static int read_parm7_structure(void *mydata, int *optflags, molfile_atom_t *atoms) {
00055 parmdata *p = (parmdata *)mydata;
00056 const parmstruct *prm = p->prm;
00057 FILE *file = p->fd;
00058 char buf[85];
00059 char field[85];
00060 char *resnames = NULL;
00061 *optflags = 0;
00062
00063 while (fgets(buf, 85, file)) {
00064
00065 if (strncmp(buf, "%FLAG ", 6)) continue;
00066
00067 sscanf(buf+6, "%s\n", field);
00068 fscanf(file, "%s\n", buf);
00069 if (!strcmp(field, "ATOM_NAME")) {
00070 if (!parse_parm7_atoms(buf, prm->Natom, atoms, file)) break;
00071 } else if (!strcmp(field, "CHARGE")) {
00072 *optflags |= MOLFILE_CHARGE;
00073 if (!parse_parm7_charge(buf, prm->Natom, atoms, file)) break;
00074 } else if (!strcmp(field, "MASS")) {
00075 *optflags |= MOLFILE_MASS;
00076 if (!parse_parm7_mass(buf, prm->Natom, atoms, file)) break;
00077 } else if (!strcmp(field, "AMBER_ATOM_TYPE")) {
00078 if (!parse_parm7_atype(buf, prm->Natom, atoms, file)) break;
00079 } else if (!strcmp(field, "RESIDUE_LABEL")) {
00080 resnames = new char[4*prm->Nres];
00081 if (!parse_parm7_resnames(buf, prm->Nres, resnames, file)) break;
00082 } else if (!strcmp(field, "RESIDUE_POINTER")) {
00083 if (!resnames) {
00084 fprintf(stderr,
00085 "PARM7: cannot parse RESIDUE_POINTER before RESIDUE_LABEL\n");
00086 continue;
00087 }
00088 if (!parse_parm7_respointers(buf, prm->Natom, atoms,
00089 prm->Nres, resnames, file))
00090 break;
00091 } else if (!strcmp(field, "BONDS_WITHOUT_HYDROGEN")) {
00092 if (!parse_parm7_bonds(buf, prm->Nbona, p->from+p->nbonds,
00093 p->to+p->nbonds, file)) break;
00094 p->nbonds += prm->Nbona;
00095 } else if (!strcmp(field, "BONDS_INC_HYDROGEN")) {
00096 if (!parse_parm7_bonds(buf, prm->Nbonh, p->from+p->nbonds,
00097 p->to+p->nbonds, file)) break;
00098 p->nbonds += prm->Nbonh;
00099 }
00100 }
00101
00102
00103 for (int i=0; i<prm->Natom; i++) {
00104 atoms[i].chain[0] = '\0';
00105 atoms[i].segid[0] = '\0';
00106 }
00107
00108 delete [] resnames;
00109 return MOLFILE_SUCCESS;
00110 }
00111
00112 static int read_parm7_bonds(void *v, int *nbonds, int **fromptr, int **toptr, float **bondorderptr){
00113 parmdata *p = (parmdata *)v;
00114 *nbonds = p->nbonds;
00115 *fromptr = p->from;
00116 *toptr = p->to;
00117 *bondorderptr = NULL;
00118 return MOLFILE_SUCCESS;
00119 }
00120
00121 static void close_parm7_read(void *mydata) {
00122 parmdata *p = (parmdata *)mydata;
00123 close_parm7_file(p->fd, p->popn);
00124 delete p->prm;
00125 delete [] p->from;
00126 delete [] p->to;
00127 delete p;
00128 }
00129
00130
00131
00132
00133
00134 static molfile_plugin_t parm7plugin = {
00135 vmdplugin_ABIVERSION,
00136 MOLFILE_PLUGIN_TYPE,
00137 "parm7",
00138 "AMBER7 Parm",
00139 "Brian Bennion, Justin Gullingsrud, John E. Stone",
00140 0,
00141 7,
00142 VMDPLUGIN_THREADUNSAFE,
00143 "prmtop,parm7",
00144 open_parm7_read,
00145 read_parm7_structure,
00146 read_parm7_bonds,
00147 0,
00148 close_parm7_read,
00149 0,
00150 0,
00151 0,
00152 0,
00153 };
00154
00155 VMDPLUGIN_API int VMDPLUGIN_init(){
00156 return VMDPLUGIN_SUCCESS;
00157 }
00158 VMDPLUGIN_API int VMDPLUGIN_fini(){
00159 return VMDPLUGIN_SUCCESS;
00160 }
00161 VMDPLUGIN_API int VMDPLUGIN_register(void *v, vmdplugin_register_cb cb) {
00162 (*cb)(v,(vmdplugin_t *)&parm7plugin);
00163 return VMDPLUGIN_SUCCESS;
00164 }