int main(int argc, char *argv[])
{
#ifdef ENABLE_LOGGING
setupDebug();
#endif
// ncurses stuff
initscr(); // Initialize ncurses
noecho(); // Don't echo keypresses
cbreak(); // C-style breaks (e.g. ^C to SIGINT)
keypad(stdscr, true); // Numpad is numbers
init_colors(); // See color.cpp
curs_set(0); // Invisible cursor
std::srand(time(NULL));
bool quit_game = false;
bool delete_world = false;
game *g = new game;
MAPBUFFER = mapbuffer(g);
MAPBUFFER.load();
load_options();
do {
g->setup();
while (!g->do_turn()) ;
if (g->uquit == QUIT_DELETE_WORLD)
delete_world = true;
if (g->game_quit())
quit_game = true;
} while (!quit_game);
MAPBUFFER.save();
if (delete_world && (remove("save/") != 0))
{
#if (defined _WIN32 || defined __WIN32__)
system("rmdir /s /q save");
#else
system("rm -rf save/*");
#endif
}
erase(); // Clear screen
endwin(); // End ncurses
#if (defined _WIN32 || defined WINDOWS)
system("cls"); // Tell the terminal to clear itself
system("color 07");
#else
system("clear"); // Tell the terminal to clear itself
#endif
return 0;
}
int main(int argc, char *argv[])
{
#ifdef ENABLE_LOGGING
setupDebug();
#endif
srand(time(NULL));
// ncurses stuff
initscr(); // Initialize ncurses
noecho(); // Don't echo keypresses
cbreak(); // C-style breaks (e.g. ^C to SIGINT)
keypad(stdscr, true); // Numpad is numbers
init_colors(); // See color.cpp
curs_set(0); // Invisible cursor
rand(); // For some reason a call to rand() seems to be necessary to avoid
// repetion.
bool quit_game = false;
game *g = new game;
MAPBUFFER = mapbuffer(g);
MAPBUFFER.load();
load_options();
do {
g->setup();
while (!g->do_turn());
if (g->game_quit())
quit_game = true;
} while (!quit_game);
MAPBUFFER.save();
erase(); // Clear screen
endwin(); // End ncurses
#if (defined _WIN32 || defined WINDOWS)
system("cls"); // Tell the terminal to clear itself
system("color 07");
#else
system("clear"); // Tell the terminal to clear itself
#endif
return 0;
}
/** Header is 256 4-byte words. Integer unless otherwise noted. First 56 words are:
* 0-2: columns, rows, sections (fastest changing to slowest)
* 3: mode: 0 = envelope stored as signed bytes (from -128 lowest to 127 highest)
* 1 = Image stored as Integer*2
* 2 = Image stored as Reals
* 3 = Transform stored as Complex Integer*2
* 4 = Transform stored as Complex Reals
* 5 == 0
* 4-6: Column, row, and section offsets
* 7-9: Intervals along X, Y, Z
* 10-15: float; 3x cell lengths (Ang) and 3x cell angles (deg)
* 16-18: Map of which axes correspond to cols, rows, sections (1,2,3 = x,y,z)
* 19-21: float; Min, max, and mean density
* 22-24: Space group, bytes used for storing symm ops, flag for skew transform
* If skew flag != 0, skew transformation is from standard orthogonal
* coordinate frame (as used for atoms) to orthogonal map frame, as:
* Xo(map) = S * (Xo(atoms) - t)
* 25-33: Skew matrix 'S' (in order S11, S12, S13, S21 etc)
* 34-36: Skew translation 't'
* 37-51: For future use and can be skipped.
* 52: char; 'MAP '
* 53: char; machine stamp for determining endianness
* 54: float; RMS deviation of map from mean
* 55: Number of labels
*/
int DataIO_CCP4::ReadData(FileName const& fname,
DataSetList& datasetlist, std::string const& dsname)
{
CpptrajFile infile;
if (infile.OpenRead( fname )) return 1;
// Read first 56 words of the header into a buffer.
headerbyte buffer;
if (infile.Read(buffer.i, 224*sizeof(unsigned char)) < 1) {
mprinterr("Error: Could not buffer CCP4 header.\n");
return 1;
}
if (debug_ > 0)
mprintf("DEBUG: MAP= '%c %c %c %c' MACHST= '%x %x %x %x'\n",
buffer.c[208], buffer.c[209], buffer.c[210], buffer.c[211],
buffer.c[212], buffer.c[213], buffer.c[214], buffer.c[215]);
// SANITY CHECK
if (!MapCharsValid(buffer.c + 208)) {
mprinterr("Error: CCP4 file missing 'MAP ' string at word 53\n");
return 1;
}
// Check endianess
bool isBigEndian = (buffer.c[212] == 0x11 && buffer.c[213] == 0x11 &&
buffer.c[214] == 0x00 && buffer.c[215] == 0x00);
if (!isBigEndian) {
if (debug_ > 0) mprintf("DEBUG: Little endian.\n");
// SANITY CHECK
if ( !(buffer.c[212] == 0x44 && buffer.c[213] == 0x41 &&
buffer.c[214] == 0x00 && buffer.c[215] == 0x00) )
mprintf("Warning: Invalid machine stamp: %x %x %x %x : assuming little endian.\n",
buffer.c[212], buffer.c[213], buffer.c[214], buffer.c[215]);
} else {
if (debug_ > 0) mprintf("DEBUG: Big endian.\n");
// Perform endian swapping on header if necessary
endian_swap(buffer.i, 56);
}
// Print DEBUG info
if (debug_ > 0) {
mprintf("DEBUG: Columns=%i Rows=%i Sections=%i\n", buffer.i[0], buffer.i[1], buffer.i[2]);
mprintf("DEBUG: Mode=%i\n", buffer.i[3]);
mprintf("DEBUG: Offsets: C=%i R=%i S=%i\n", buffer.i[4], buffer.i[5], buffer.i[6]);
mprintf("DEBUG: NXYZ={ %i %i %i }\n", buffer.i[7], buffer.i[8], buffer.i[9]);
mprintf("DEBUG: Box XYZ={ %f %f %f } ABG={ %f %f %f }\n",
buffer.f[10], buffer.f[11], buffer.f[12],
buffer.f[13], buffer.f[14], buffer.f[15]);
mprintf("DEBUG: Map: ColAxis=%i RowAxis=%i SecAxis=%i\n",
buffer.i[16], buffer.i[17], buffer.i[18]);
mprintf("DEBUG: SpaceGroup#=%i SymmOpBytes=%i SkewFlag=%i\n",
buffer.i[22], buffer.i[23], buffer.i[24]);
const int* MSKEW = buffer.i + 25;
mprintf("DEBUG: Skew matrix: %i %i %i\n"
" %i %i %i\n"
" %i %i %i\n", MSKEW[0], MSKEW[1], MSKEW[2], MSKEW[3],
MSKEW[4], MSKEW[5], MSKEW[6], MSKEW[7], MSKEW[8]);
const int* TSKEW = buffer.i + 34;
mprintf("DEBUG: Skew translation: %i %i %i\n", TSKEW[0], TSKEW[1], TSKEW[2]);
mprintf("DEBUG: Nlabels=%i\n", buffer.i[55]);
}
// Check input data. Only support mode 2 for now.
if (buffer.i[3] != 2) {
mprinterr("Error: Mode %i; currently only mode 2 for CCP4 files is supported.\n", buffer.i[3]);
return 1;
}
// Check offsets.
if (buffer.i[4] != 0 || buffer.i[5] != 0 || buffer.i[6] != 0)
mprintf("Warning: Non-zero offsets present. This is not yet supported and will be ignored.\n");
// Check that mapping is col=x row=y section=z
if (buffer.i[16] != 1 || buffer.i[17] != 2 || buffer.i[18] != 3) {
mprinterr("Error: Currently only support cols=X, rows=Y, sections=Z\n");
return 1;
}
if (buffer.i[24] != 0) {
mprintf("Warning: Skew information present but not yet supported and will be ignored.\n");
return 1;
}
// Read 10 80 character text labels
char Labels[801];
Labels[800] = '\0';
infile.Read( Labels, 200*wSize );
mprintf("\t%s\n", Labels);
// Symmetry records: operators separated by * and grouped into 'lines' of 80 characters
int NsymmRecords = buffer.i[23] / 80;
if (NsymmRecords > 0) {
char symBuffer[81];
mprintf("\t%i symmetry records.\n", NsymmRecords);
for (int ib = 0; ib != NsymmRecords; ib++) {
infile.Gets( symBuffer, 80 );
mprintf("\t%s\n", symBuffer);
}
}
// Add grid data set. Default to float for now.
DataSet* gridDS = datasetlist.AddSet( DataSet::GRID_FLT, dsname, "GRID" );
if (gridDS == 0) return 1;
DataSet_GridFlt& grid = static_cast<DataSet_GridFlt&>( *gridDS );
// Allocate grid from dims and spacing. FIXME OK to assume zero origin?
if (grid.Allocate_N_O_Box( buffer.i[7], buffer.i[8], buffer.i[9],
Vec3(0.0), Box(buffer.f + 10) ) != 0)
{
mprinterr("Error: Could not allocate grid.\n");
return 1;
}
// FIXME: Grids are currently indexed so Z is fastest changing.
// Should be able to change indexing in grid DataSet.
size_t mapSize = buffer.i[7] * buffer.i[8] * buffer.i[9];
mprintf("\tCCP4 map has %zu elements\n", mapSize);
mprintf("\tDensity: Min=%f Max=%f Mean=%f RMS=%f\n",
buffer.f[19], buffer.f[20], buffer.f[21], buffer.f[54]);
std::vector<float> mapbuffer( mapSize );
int mapBytes = mapSize * wSize;
int numRead = infile.Read( &mapbuffer[0], mapBytes );
if (numRead < 1) {
mprinterr("Error: Could not read CCP4 map data.\n");
return 1;
} else if (numRead < mapBytes)
mprintf("Warning: Expected %i bytes, read only %i bytes\n", mapBytes, numRead);
if (isBigEndian) endian_swap(&mapbuffer[0], mapSize);
// FIXME: Place data into grid DataSet with correct ordering.
int gidx = 0;
int NXY = buffer.i[7] * buffer.i[8];
for (int ix = 0; ix != buffer.i[7]; ix++)
for (int iy = 0; iy != buffer.i[8]; iy++)
for (int iz = 0; iz != buffer.i[9]; iz++) {
int midx = (iz * NXY) + (iy * buffer.i[7]) + ix;
grid[gidx++] = mapbuffer[midx];
}
infile.CloseFile();
return 0;
}
// DataIO_CCP4::WriteSet3D()
int DataIO_CCP4::WriteSet3D( DataSetList::const_iterator const& setIn, CpptrajFile& outfile ) {
if ((*setIn)->Size() < 1) return 1; // SANITY CHECK: No empty grid allowed
if ((*setIn)->Ndim() != 3) {
mprinterr("Internal Error: DataSet %s in DataFile %s has %zu dimensions, expected 3.\n",
(*setIn)->legend(), outfile.Filename().full(), (*setIn)->Ndim());
return 1;
}
DataSet_3D const& grid = static_cast<DataSet_3D const&>( *(*setIn) );
// Check input grid
Vec3 OXYZ = grid.GridOrigin();
if (OXYZ[0] < 0.0 || OXYZ[1] < 0.0 || OXYZ[2] < 0.0 ||
OXYZ[0] > 0.0 || OXYZ[1] > 0.0 || OXYZ[2] > 0.0)
mprintf("Warning: Grid '%s' origin is not 0.0, 0.0, 0.0\n"
"Warning: Origin other than 0.0 not yet supported for CCP4 write.\n");
// Set default title if none set
if (title_.empty())
title_.assign("CPPTRAJ CCP4 map volumetric data, set '" + grid.Meta().Legend() +
"'. Format revision A.");
// Check that title is not too big
if (title_.size() > 800) {
mprintf("Warning: CCP4 title is too large, truncating.\n");
title_.resize( 800 );
}
// Set up and write header
headerbyte buffer;
buffer.i[0] = (int)grid.NX();
buffer.i[1] = (int)grid.NY();
buffer.i[2] = (int)grid.NZ();
buffer.i[3] = 2; // Only mode 2 supported
buffer.i[4] = 0; // No offsets
buffer.i[5] = 0;
buffer.i[6] = 0;
buffer.i[7] = (int)grid.NX();
buffer.i[8] = (int)grid.NY();
buffer.i[9] = (int)grid.NZ();
Box box( grid.Ucell() );
buffer.f[10] = (float)box[0];
buffer.f[11] = (float)box[1];
buffer.f[12] = (float)box[2];
buffer.f[13] = (float)box[3];
buffer.f[14] = (float)box[4];
buffer.f[15] = (float)box[5];
buffer.i[16] = 1; // Cols = X
buffer.i[17] = 2; // Rows = Y
buffer.i[18] = 3; // Secs = Z
// Determine min, max, and mean of data
double mean = grid[0];
double gmin = grid[0];
double gmax = grid[0];
double rmsd = grid[0] * grid[0];
for (unsigned int i = 1; i < grid.Size(); i++) {
gmin = std::min(grid[i], gmin);
gmax = std::max(grid[i], gmax);
mean += grid[i];
rmsd += grid[i] * grid[i];
}
mean /= (double)grid.Size();
rmsd /= (double)grid.Size();
rmsd = rmsd - (mean * mean);
if (rmsd > 0.0)
rmsd = sqrt(rmsd);
else
rmsd = 0.0;
mprintf("\t%s\n", title_.c_str());
mprintf("\tDensity: Min=%f Max=%f Mean=%f RMS=%f\n", gmin, gmax, mean, rmsd);
buffer.f[19] = (float)gmin;
buffer.f[20] = (float)gmax;
buffer.f[21] = (float)mean;
buffer.i[22] = 1; // Assume P1
buffer.i[23] = 0; // No bytes for symmetry ops
buffer.i[24] = 0; // No skew transform
// Skew matrix (S11, S12, S13, S21, ...) and translation; 12 total, followed
// by 15 'future use'; zero all.
std::fill( buffer.i+25, buffer.i+52, 0 );
// MAP and machine precision. FIXME determine endianness!
buffer.c[208] = 'M';
buffer.c[209] = 'A';
buffer.c[210] = 'P';
buffer.c[211] = ' ';
buffer.c[212] = 0x44; // little endian
buffer.c[213] = 0x41;
buffer.c[214] = 0x00;
buffer.c[215] = 0x00;
// Determine RMS deviation from mean.
buffer.f[54] = (float)rmsd;
// Determine number of labels being used
buffer.i[55] = (int)title_.size() / 80;
if ( ((int)title_.size() % 80) != 0)
buffer.i[55]++;
outfile.Write( buffer.c, 224*sizeof(unsigned char) );
// Write labels; 10 lines, 80 chars each
outfile.Write( title_.c_str(), title_.size() );
// FIXME this seems wasteful.
std::vector<char> remainder( 800 - title_.size(), 0 );
outfile.Write( &remainder[0], remainder.size() );
remainder.clear();
// No symmetry bytes
// Store data in buffer, then write. X changes fastest.
// SANITY CHECK; This will result in invalid files if size of float is not 4.
if (sizeof(float) != wSize)
mprintf("Warning: Size of float on this system is %zu, not 4.\n"
"Warning: Resulting CCP4 file data will not conform to standard.\n", sizeof(float));
std::vector<float> mapbuffer( grid.Size() );
std::vector<float>::iterator it = mapbuffer.begin();
for (unsigned int iz = 0; iz != grid.NZ(); iz++)
for (unsigned int iy = 0; iy != grid.NY(); iy++)
for (unsigned int ix = 0; ix != grid.NX(); ix++)
*(it++) = grid.GetElement( ix, iy, iz );
outfile.Write( &mapbuffer[0], mapbuffer.size() * sizeof(float) );
outfile.CloseFile();
return 0;
}
