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phiplugin.C

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00001 /***************************************************************************
00002  *cr
00003  *cr            (C) Copyright 1995-2016 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: phiplugin.C,v $
00013  *      $Author: johns $       $Locker:  $             $State: Exp $
00014  *      $Revision: 1.28 $       $Date: 2016/11/28 05:01:54 $
00015  *
00016  ***************************************************************************/
00017 
00018 /* 
00019  * "Formatted ASCII '.big'" potential maps from Delphi
00020  *   This format is created by the 'ASCIIPHI' program which was available with
00021  *   Delphi V3:
00022  *     http://www.csb.yale.edu/userguides/datamanip/delphi/manual.html#ASCIIPHI
00023  *
00024  *   More info for this format can be found at:
00025  *     http://www.msg.ucsf.edu/local/programs/insightII/doc/life/insight2000.1/delphi/B_Utilities.html
00026  * 
00027  */
00028 
00029 #include <stdlib.h>
00030 #include <stdio.h>
00031 #include <ctype.h>
00032 #include <math.h>
00033 #include <string.h>
00034 
00035 #if defined(_AIX)
00036 #include <strings.h>
00037 #endif
00038 
00039 #if defined(WIN32) || defined(WIN64)
00040 #define strcasecmp  stricmp
00041 #define strncasecmp strnicmp
00042 #endif
00043 
00044 #include "molfile_plugin.h"
00045 
00046 #define LINESIZE 85
00047 
00048 typedef struct {
00049   FILE *fd;
00050   int nsets;
00051   int ndata;
00052   molfile_volumetric_t *vol;
00053 } phi_t;
00054 
00055 
00056 // Get a string from a stream, printing any errors that occur
00057 static char *phigets(char *s, int n, FILE *stream) {
00058   char *returnVal;
00059 
00060   if (feof(stream)) {
00061     fprintf(stderr, "phiplugin) Unexpected end-of-file.\n");
00062     returnVal = NULL; 
00063   }
00064   else if (ferror(stream)) {
00065     fprintf(stderr, "phiplugin) Error reading file.\n");
00066     return NULL;
00067   }
00068   else {
00069     returnVal = fgets(s, n, stream);
00070     if (returnVal == NULL) {
00071       fprintf(stderr, "phiplugin) Error reading line.\n");
00072     }
00073   }
00074 
00075   return returnVal;
00076 }
00077 
00078 
00079 static void *open_phi_read(const char *filepath, const char *filetype,
00080     int *natoms) {
00081   FILE *fd;
00082   phi_t *phi;
00083   char inbuf[LINESIZE];
00084 
00085   float scale, midX, midY, midZ;
00086   float cellSize, iGrid = 0.0;
00087   
00088   fd = fopen(filepath, "rb");
00089   if (!fd) {
00090     fprintf(stderr, "phiplugin) Error opening file.\n");
00091     return NULL;
00092   }
00093 
00094   /* Skip the header */
00095   if (phigets(inbuf, LINESIZE, fd) == NULL) {
00096     return NULL;
00097   }
00098   if (phigets(inbuf, LINESIZE, fd) == NULL) {
00099     return NULL;
00100   }
00101   if (phigets(inbuf, LINESIZE, fd) == NULL) {
00102     return NULL;
00103   }
00104 
00105   /* Unit cell information is located at the *end* of the file. */
00106   if (phigets(inbuf, LINESIZE, fd) == NULL) {
00107     return NULL;
00108   }
00109   while (strncasecmp(inbuf, " end of phimap", 14) != 0) {
00110     /* use integer division so trailing whitespace isn't included in the
00111      * count */
00112     iGrid += strlen(inbuf) / 4; 
00113 
00114     if (phigets(inbuf, LINESIZE, fd) == NULL) {
00115       return NULL;
00116     }
00117   } 
00118 
00119   /* Find the cube-root of the number of datapoints (this will give the
00120    * number of datapoints in each direction) and make sure it's an integer
00121    */
00122   cellSize = pow((double) iGrid, (double) 1.0/3.0);
00123   if (fabs((double)(cellSize - floor(cellSize))) > 1e-8) {
00124     return NULL;
00125   }
00126 
00127   /* Read the unit cell information */
00128   if (phigets(inbuf, LINESIZE, fd) == NULL) {
00129     return NULL;
00130   }
00131   sscanf(inbuf, " %f %f %f %f", &scale, &midX, &midY, &midZ);
00132 
00133   /* Allocate and initialize the phi structure */
00134   phi = new phi_t;
00135   phi->fd = fd;
00136   phi->vol = NULL;
00137   phi->ndata = (int) iGrid;
00138   *natoms = MOLFILE_NUMATOMS_NONE;
00139   phi->nsets = 1; /* this file contains only one data set */
00140 
00141   phi->vol = new molfile_volumetric_t[1];
00142   strcpy(phi->vol[0].dataname, "PHIMAP Electron Density Map");
00143 
00144   /* <midX, midY, midZ> is the middle point of the grid. */
00145   phi->vol[0].origin[0] = -0.5*(cellSize+1.0) / scale + midX;
00146   phi->vol[0].origin[1] = -0.5*(cellSize+1.0) / scale + midY;
00147   phi->vol[0].origin[2] = -0.5*(cellSize+1.0) / scale + midZ;
00148 
00149   phi->vol[0].xaxis[0] = cellSize / scale;
00150   phi->vol[0].xaxis[1] = 0;
00151   phi->vol[0].xaxis[2] = 0;
00152 
00153   phi->vol[0].yaxis[0] = 0;
00154   phi->vol[0].yaxis[1] = cellSize / scale;
00155   phi->vol[0].yaxis[2] = 0;
00156   
00157   phi->vol[0].zaxis[0] = 0;
00158   phi->vol[0].zaxis[1] = 0;
00159   phi->vol[0].zaxis[2] = cellSize / scale;
00160 
00161   phi->vol[0].xsize = (int) cellSize;
00162   phi->vol[0].ysize = (int) cellSize;
00163   phi->vol[0].zsize = (int) cellSize;
00164 
00165   phi->vol[0].has_color = 0;
00166 
00167   return phi;
00168 }
00169 
00170 static int read_phi_metadata(void *v, int *nsets, 
00171   molfile_volumetric_t **metadata) {
00172   phi_t *phi = (phi_t *)v;
00173   *nsets = phi->nsets; 
00174   *metadata = phi->vol;  
00175 
00176   return MOLFILE_SUCCESS;
00177 }
00178 
00179 static int read_phi_data(void *v, int set, float *datablock,
00180                          float *colorblock) {
00181   phi_t *phi = (phi_t *)v;
00182   float *cellIndex;
00183   int value, ndata, count = 0;
00184   FILE *fd = phi->fd;
00185   char inbuf[LINESIZE], currNum[5], *currChar;
00186 
00187   cellIndex = datablock;
00188   ndata = phi->ndata;
00189   memset(currNum, 0, 5);
00190 
00191   /* Skip the header */
00192   rewind(fd);
00193   if (phigets(inbuf, LINESIZE, fd) == NULL) {
00194     return MOLFILE_ERROR;
00195   }
00196   if (phigets(inbuf, LINESIZE, fd) == NULL) {
00197     return MOLFILE_ERROR;
00198   }
00199   if (phigets(inbuf, LINESIZE, fd) == NULL) {
00200     return MOLFILE_ERROR;
00201   }
00202 
00203   /* Read the densities. Order for file is x fast, y medium, z slow */
00204   while (count < ndata) {
00205     if (phigets(inbuf, LINESIZE, fd) == NULL) {
00206       return MOLFILE_ERROR;
00207     }
00208 
00209     for (currChar = inbuf; (*currChar != '\n') && (*currChar != '\0'); 
00210          currChar += 4) {
00211       strncpy(currNum, currChar, 4);
00212       value = atoi(currNum);
00213       /* Scale -- units are in kT/e (25.6mV, 0.593 kcal/mole at 25C). */
00214       *cellIndex = 0.01 * (value - 5000);
00215       cellIndex++;
00216       count++;
00217     }
00218   }
00219 
00220   return MOLFILE_SUCCESS;
00221 }
00222 
00223 static void close_phi_read(void *v) {
00224   phi_t *phi = (phi_t *)v;
00225 
00226   fclose(phi->fd);
00227   if (phi->vol != NULL)
00228     delete [] phi->vol; 
00229   delete phi;
00230 }
00231 
00232 /*
00233  * Initialization stuff here
00234  */
00235 static molfile_plugin_t plugin;
00236 
00237 VMDPLUGIN_API int VMDPLUGIN_init(void) {
00238   memset(&plugin, 0, sizeof(molfile_plugin_t));
00239   plugin.abiversion = vmdplugin_ABIVERSION;
00240   plugin.type = MOLFILE_PLUGIN_TYPE;
00241   plugin.name = "delphibig";
00242   plugin.prettyname = "Delphi 'Big' Formatted Potential Map";
00243   plugin.author = "Eamon Caddigan";
00244   plugin.majorv = 0;
00245   plugin.minorv = 7;
00246   plugin.is_reentrant = VMDPLUGIN_THREADSAFE;
00247   plugin.filename_extension = "big";
00248   plugin.open_file_read = open_phi_read;
00249   plugin.read_volumetric_metadata = read_phi_metadata;
00250   plugin.read_volumetric_data = read_phi_data;
00251   plugin.close_file_read = close_phi_read;
00252   return VMDPLUGIN_SUCCESS; 
00253 }
00254 
00255 VMDPLUGIN_API int VMDPLUGIN_register(void *v, vmdplugin_register_cb cb) {
00256   (*cb)(v, (vmdplugin_t *)&plugin);
00257   return VMDPLUGIN_SUCCESS;
00258 }
00259 
00260 VMDPLUGIN_API int VMDPLUGIN_fini(void) { return VMDPLUGIN_SUCCESS; }
00261 

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