diff options
Diffstat (limited to 'libcrystfel/src/xds.c')
| -rw-r--r-- | libcrystfel/src/xds.c | 132 |
1 files changed, 74 insertions, 58 deletions
diff --git a/libcrystfel/src/xds.c b/libcrystfel/src/xds.c index cc8d48d2..b5bed29e 100644 --- a/libcrystfel/src/xds.c +++ b/libcrystfel/src/xds.c @@ -73,18 +73,42 @@ struct xds_private }; +/* Essentially the reverse of spacegroup_for_lattice(), below */ +static int convert_spacegroup_number(int spg, LatticeType *lt, char *cen) +{ + switch ( spg ) { + + case 1: *lt = L_TRICLINIC; *cen = 'P'; return 0; + case 3: *lt = L_MONOCLINIC; *cen = 'P'; return 0; + case 5: *lt = L_MONOCLINIC; *cen = 'C'; return 0; + case 16: *lt = L_ORTHORHOMBIC; *cen = 'P'; return 0; + case 21: *lt = L_ORTHORHOMBIC; *cen = 'C'; return 0; + case 22: *lt = L_ORTHORHOMBIC; *cen = 'F'; return 0; + case 23: *lt = L_ORTHORHOMBIC; *cen = 'I'; return 0; + case 75: *lt = L_TETRAGONAL; *cen = 'P'; return 0; + case 79: *lt = L_TETRAGONAL; *cen = 'I'; return 0; + case 143: *lt = L_HEXAGONAL; *cen = 'P'; return 0; + case 146: *lt = L_HEXAGONAL; *cen = 'H'; return 0; + case 195: *lt = L_CUBIC; *cen = 'P'; return 0; + case 196: *lt = L_CUBIC; *cen = 'F'; return 0; + case 197: *lt = L_CUBIC; *cen = 'I'; return 0; + default: return 1; + + } +} + + static int read_cell(struct image *image) { FILE * fh; - float axstar, aystar, azstar; - float bxstar, bystar, bzstar; - float cxstar, cystar, czstar; - char asx[11], asy[11], asz[11]; - char bsx[11], bsy[11], bsz[11]; - char csx[11], csy[11], csz[11]; + float ax, ay, az; + float bx, by, bz; + float cx, cy, cz; + int spg; char *rval, line[1024]; - int r; UnitCell *cell; + LatticeType latticetype; + char centering; Crystal *cr; fh = fopen("IDXREF.LP", "r"); @@ -97,74 +121,65 @@ static int read_cell(struct image *image) return 0; } - } while ( strcmp(line, " # COORDINATES OF REC. BASIS VECTOR" - " LENGTH 1/LENGTH\n") != 0 ); + } while ( strcmp(line, " ***** DIFFRACTION PARAMETERS USED AT START OF " + "INTEGRATION *****\n") != 0 ); - /* Free line after chunk */ - rval = fgets(line, 1023, fh); - if ( rval == NULL ) { + /* Find and read space group number */ + do { + rval = fgets(line, 1023, fh); + if ( rval == NULL ) { + fclose(fh); + return 0; + } + } while ( strncmp(line, " SPACE GROUP NUMBER ", 20) != 0 ); + sscanf(line+20, "%i\n", &spg); + + /* Find and read a */ + do { + rval = fgets(line, 1023, fh); + if ( rval == NULL ) { + fclose(fh); + return 0; + } + } while ( strncmp(line, " COORDINATES OF UNIT CELL A-AXIS ", 33) != 0 ); + if ( sscanf(line+33, "%f %f %f\n", &ax, &ay, &az) < 3 ) { fclose(fh); return 0; } - /* Get first vector */ + /* Read b */ rval = fgets(line, 1023, fh); if ( rval == NULL ) { fclose(fh); return 0; } - if ( line[4] != '1' ) { - ERROR("No first vector from XDS.\n"); + if ( sscanf(line+33, "%f %f %f\n", &bx, &by, &bz) < 3 ) { + fclose(fh); return 0; } - memcpy(asx, line+7, 10); asx[10] = '\0'; - memcpy(asy, line+17, 10); asy[10] = '\0'; - memcpy(asz, line+27, 10); asz[10] = '\0'; - /* Get second vector */ + /* Read c */ rval = fgets(line, 1023, fh); if ( rval == NULL ) { fclose(fh); return 0; } - if ( line[4] != '2' ) { - ERROR("No second vector from XDS.\n"); + if ( sscanf(line+33, "%f %f %f\n", &cx, &cy, &cz) < 3 ) { + fclose(fh); return 0; } - memcpy(bsx, line+7, 10); bsx[10] = '\0'; - memcpy(bsy, line+17, 10); bsy[10] = '\0'; - memcpy(bsz, line+27, 10); bsz[10] = '\0'; - /* Get third vector */ - rval = fgets(line, 1023, fh); - fclose(fh); - if ( rval == NULL ) return 0; - if ( line[4] != '3' ) return 0; /* No error message this time - * - happens a lot */ - memcpy(csx, line+7, 10); csx[10] = '\0'; - memcpy(csy, line+17, 10); csy[10] = '\0'; - memcpy(csz, line+27, 10); csz[10] = '\0'; - - r = sscanf(asx, "%f", &cxstar); - r += sscanf(asy, "%f", &cystar); - r += sscanf(asz, "%f", &czstar); - r += sscanf(bsx, "%f", &bxstar); - r += sscanf(bsy, "%f", &bystar); - r += sscanf(bsz, "%f", &bzstar); - r += sscanf(csx, "%f", &axstar); - r += sscanf(csy, "%f", &aystar); - r += sscanf(csz, "%f", &azstar); - - if ( r != 9 ) { - STATUS("Fewer than 9 parameters found in NEWMAT file.\n"); + cell = cell_new(); + cell_set_cartesian(cell, + ax*1e-10, ay*1e-10, az*1e-10, + bx*1e-10, by*1e-10, bz*1e-10, + -cx*1e-10, -cy*1e-10, -cz*1e-10); + if ( convert_spacegroup_number(spg, &latticetype, ¢ering) ) { + ERROR("Failed to convert XDS space group number (%i)\n", spg); return 0; } - - cell = cell_new(); - cell_set_reciprocal(cell, - axstar*10e9, aystar*10e9, azstar*10e9, - bxstar*10e9, bystar*10e9, bzstar*10e9, - -cxstar*10e9, -cystar*10e9, -czstar*10e9); + cell_set_lattice_type(cell, latticetype); + cell_set_centering(cell, centering); cr = crystal_new(); if ( cr == NULL ) { @@ -252,7 +267,7 @@ static const char *spacegroup_for_lattice(UnitCell *cell) if ( centering == 'P' ) { g = "16"; } else if ( centering == 'C' ) { - g = "20"; + g = "21"; } else if ( centering == 'F' ) { g = "22"; } else if ( centering == 'I' ) { @@ -268,15 +283,16 @@ static const char *spacegroup_for_lattice(UnitCell *cell) } break; + /* Unfortunately, XDS only does "hexagonal H" */ case L_RHOMBOHEDRAL : - if ( centering == 'R' ) { - g = "146"; - } - break; + return NULL; case L_HEXAGONAL : if ( centering == 'P' ) { - g = "168"; + g = "143"; + } + if ( centering == 'H' ) { + g = "146"; } break; |