320 lines
8.9 KiB
C++
320 lines
8.9 KiB
C++
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/* MACHINE GENERATED FILE, DO NOT EDIT! */
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#define VMDPLUGIN molfile_brixplugin
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#define STATIC_PLUGIN 1
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/***************************************************************************
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*cr
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*cr (C) Copyright 1995-2016 The Board of Trustees of the
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*cr University of Illinois
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*cr All Rights Reserved
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*cr
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***************************************************************************/
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/***************************************************************************
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* RCS INFORMATION:
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*
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* $RCSfile: brixplugin.C,v $
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* $Author: johns $ $Locker: $ $State: Exp $
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* $Revision: 1.20 $ $Date: 2016/11/28 05:01:53 $
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*
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***************************************************************************/
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/*
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* BRIX format electron density maps.
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*
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* More info for format can be found at
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* <http://zombie.imsb.au.dk/~mok/brix/brix-1.html#ss1.2>
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*
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* TODO: Speed up inner loop of read_data, perhaps reading one full brick
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* from the file at a time.
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*/
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#include <stdlib.h>
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#include <stdio.h>
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#include <ctype.h>
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#include <math.h>
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#include <string.h>
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#if defined(_AIX)
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#include <strings.h>
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#endif
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#if defined(WIN32) || defined(WIN64)
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#define strcasecmp stricmp
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#endif
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#ifndef M_PI
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#define M_PI 3.14159265358979323846
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#endif
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#include "molfile_plugin.h"
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typedef struct {
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FILE *fd;
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int nsets;
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float prod, plus;
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molfile_volumetric_t *vol;
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} brix_t;
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static void *open_brix_read(const char *filepath, const char *filetype,
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int *natoms) {
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FILE *fd;
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brix_t *brix;
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char keyWord[81];
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// File header data:
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int org_x, org_y, org_z, ext_x, ext_y, ext_z;
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float grid_x, grid_y, grid_z, cell_x, cell_y, cell_z,
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cell_alpha, cell_beta, cell_gamma, prod, plus, sigma,
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xaxis[3], yaxis[3], zaxis[3], z1, z2, z3;
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fd = fopen(filepath, "rb");
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if (!fd) {
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fprintf(stderr, "brixplugin) Error opening file.\n");
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return NULL;
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}
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// read in BRIX file header information -- stored as a 512-element char array
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fscanf(fd, "%3s", keyWord);
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if (strcmp(keyWord, ":-)") != 0) {
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fprintf(stderr, "brixplugin) Error improperly formatted header.\n");
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return NULL;
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}
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// "Origin: the origin of the map in grid units, along X, Y, Z."
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fscanf(fd, " %s %d %d %d", keyWord, &org_x, &org_y, &org_z);
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if (strcasecmp(keyWord, "origin") != 0) {
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fprintf(stderr, "brixplugin) Error reading origin.\n");
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return NULL;
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}
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// "Extent: the extent (size) of the map, along X, Y, Z, in grid units"
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fscanf(fd, " %s %d %d %d", keyWord, &ext_x, &ext_y, &ext_z);
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if (strcasecmp(keyWord, "extent") != 0) {
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fprintf(stderr, "brixplugin) Error reading extent.\n");
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return NULL;
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}
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// "Grid: number of grid points along the whole unit cell, along X, Y, Z."
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fscanf(fd, " %s %f %f %f", keyWord, &grid_x, &grid_y, &grid_z);
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if (strcasecmp(keyWord, "grid") != 0) {
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fprintf(stderr, "brixplugin) Error reading grid.\n");
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return NULL;
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}
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// "Cell: Unit cell parameters"
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// cell x, y, and z are the length of the unit cell along each axis,
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// cell alpha, beta, and cell_gamma are the angles between axes.
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fscanf(fd, " %s %f %f %f %f %f %f", keyWord,
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&cell_x, &cell_y, &cell_z, &cell_alpha, &cell_beta, &cell_gamma);
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if (strcasecmp(keyWord, "cell") != 0) {
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fprintf(stderr, "brixplugin) Error reading cell.\n");
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return NULL;
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}
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// Convert angles to radians
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cell_alpha *= M_PI / 180.0;
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cell_beta *= M_PI / 180.0;
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cell_gamma *= M_PI / 180.0;
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// "Prod, plus: Constants that bring the electron density from byte to
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// normal scale."
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fscanf(fd, " %s %f", keyWord, &prod);
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if (strcasecmp(keyWord, "prod") != 0) {
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fprintf(stderr, "brixplugin) Error reading prod.\n");
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return NULL;
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}
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fscanf(fd, " %s %f", keyWord, &plus);
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if (strcasecmp(keyWord, "plus") != 0) {
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fprintf(stderr, "brixplugin) Error reading plus.\n");
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return NULL;
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}
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// "Sigma: Rms deviation of electron density map."
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fscanf(fd, " %s %f", keyWord, &sigma);
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if (strcasecmp(keyWord, "sigma") != 0) {
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fprintf(stderr, "brixplugin) Error reading sigma.\n");
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return NULL;
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}
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// Allocate and initialize the brix structure
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brix = new brix_t;
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brix->fd = fd;
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brix->vol = NULL;
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*natoms = MOLFILE_NUMATOMS_NONE;
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brix->nsets = 1; // this file contains only one data set
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brix->prod = prod;
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brix->plus = plus;
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brix->vol = new molfile_volumetric_t[1];
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strcpy(brix->vol[0].dataname, "BRIX Electron Density Map");
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// Calculate non-orthogonal unit cell coordinates
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xaxis[0] = cell_x / grid_x;
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xaxis[1] = 0;
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xaxis[2] = 0;
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yaxis[0] = cos(cell_gamma) * cell_y / grid_y;
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yaxis[1] = sin(cell_gamma) * cell_y / grid_y;
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yaxis[2] = 0;
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z1 = cos(cell_beta);
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z2 = (cos(cell_alpha) - cos(cell_beta)*cos(cell_gamma)) / sin(cell_gamma);
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z3 = sqrt(1.0 - z1*z1 - z2*z2);
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zaxis[0] = z1 * cell_z / grid_z;
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zaxis[1] = z2 * cell_z / grid_z;
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zaxis[2] = z3 * cell_z / grid_z;
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brix->vol[0].origin[0] = xaxis[0] * org_x + yaxis[0] * org_y +
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zaxis[0] * org_z;
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brix->vol[0].origin[1] = yaxis[1] * org_y + zaxis[1] * org_z;
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brix->vol[0].origin[2] = zaxis[2] * org_z;
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brix->vol[0].xaxis[0] = xaxis[0] * (ext_x - 1);
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brix->vol[0].xaxis[1] = 0;
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brix->vol[0].xaxis[2] = 0;
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brix->vol[0].yaxis[0] = yaxis[0] * (ext_y - 1);
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brix->vol[0].yaxis[1] = yaxis[1] * (ext_y - 1);
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brix->vol[0].yaxis[2] = 0;
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brix->vol[0].zaxis[0] = zaxis[0] * (ext_z - 1);
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brix->vol[0].zaxis[1] = zaxis[1] * (ext_z - 1);
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brix->vol[0].zaxis[2] = zaxis[2] * (ext_z - 1);
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brix->vol[0].xsize = ext_x;
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brix->vol[0].ysize = ext_y;
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brix->vol[0].zsize = ext_z;
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brix->vol[0].has_color = 0;
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return brix;
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}
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static int read_brix_metadata(void *v, int *nsets,
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molfile_volumetric_t **metadata) {
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brix_t *brix = (brix_t *)v;
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*nsets = brix->nsets;
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*metadata = brix->vol;
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return MOLFILE_SUCCESS;
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}
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static int read_brix_data(void *v, int set, float *datablock,
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float *colorblock) {
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brix_t *brix = (brix_t *)v;
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float * cell = datablock;
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int xsize, ysize, zsize, xysize, xbrix, ybrix, zbrix, cellIndex;
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int x, y, z, xbrik, ybrik, zbrik;
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unsigned char brick[512];
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FILE * fd = brix->fd;
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float div, plus;
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// Read 512-byte "bricks" of data. Each brick contains data for 8*8*8
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// gridpoints.
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fseek(fd, 512, SEEK_SET);
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div = 1.0 / brix->prod;
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plus = brix->plus;
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xsize = brix->vol[0].xsize;
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ysize = brix->vol[0].ysize;
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zsize = brix->vol[0].zsize;
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xysize = xsize * ysize;
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xbrix = (int) ceil((float) xsize / 8.0);
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ybrix = (int) ceil((float) ysize / 8.0);
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zbrix = (int) ceil((float) zsize / 8.0);
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// For every density value,
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// cellIndex = (x + xbrik*8) + (y + ybrik*8)*xsize + (z + zbrik*8) * xysize
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cellIndex = 0;
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for (zbrik = 0; zbrik < zbrix; zbrik++) {
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for (ybrik = 0; ybrik < ybrix; ybrik++) {
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for (xbrik = 0; xbrik < xbrix; xbrik++) {
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if (feof(fd)) {
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fprintf(stderr, "brixplugin) Unexpected end-of-file.\n");
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return MOLFILE_ERROR;
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}
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if (ferror(fd)) {
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fprintf(stderr, "brixplugin) Error reading file.\n");
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return MOLFILE_ERROR;
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}
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// Read a data brick into the buffer.
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fread(brick, sizeof(char), 512, fd);
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// Copy the brick values into the cell
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for (z = 0; z < 8; z++) {
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for (y = 0; y < 8; y++) {
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for (x = 0; x < 8; x++) {
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if ( ((x + xbrik*8) < xsize) && ((y + ybrik*8) < ysize) &&
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((z + zbrik*8) < zsize) )
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cell[cellIndex] =
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div * ((float) brick[x+y*8+z*64] - plus);
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cellIndex++;
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} // end for(x)
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cellIndex += xsize - 8;
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} // end for(y)
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cellIndex += xysize - 8*xsize;
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} // end for(z)
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cellIndex += 8 - 8*xysize;
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} // end for(xbrik)
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cellIndex += 8 * (xsize - xbrix);
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} // end for(ybrik)
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cellIndex += 8 * (xysize - xsize*ybrik);
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} // end for(zbrik)
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return MOLFILE_SUCCESS;
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}
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static void close_brix_read(void *v) {
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brix_t *brix = (brix_t *)v;
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fclose(brix->fd);
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if (brix->vol != NULL)
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delete [] brix->vol;
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delete brix;
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}
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/*
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* Initialization stuff here
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*/
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static molfile_plugin_t plugin;
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VMDPLUGIN_API int VMDPLUGIN_init(void) {
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memset(&plugin, 0, sizeof(molfile_plugin_t));
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plugin.abiversion = vmdplugin_ABIVERSION;
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plugin.type = MOLFILE_PLUGIN_TYPE;
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plugin.name = "brix";
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plugin.prettyname = "BRIX Density Map";
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plugin.author = "Eamon Caddigan";
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plugin.majorv = 0;
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plugin.minorv = 8;
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plugin.is_reentrant = VMDPLUGIN_THREADSAFE;
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plugin.filename_extension = "brix,brx";
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plugin.open_file_read = open_brix_read;
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plugin.read_volumetric_metadata = read_brix_metadata;
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plugin.read_volumetric_data = read_brix_data;
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plugin.close_file_read = close_brix_read;
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return VMDPLUGIN_SUCCESS;
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}
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VMDPLUGIN_API int VMDPLUGIN_register(void *v, vmdplugin_register_cb cb) {
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(*cb)(v, (vmdplugin_t *)&plugin);
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return VMDPLUGIN_SUCCESS;
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}
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VMDPLUGIN_API int VMDPLUGIN_fini(void) { return VMDPLUGIN_SUCCESS; }
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