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-rw-r--r--libcrystfel/src/cell-utils.c262
1 files changed, 235 insertions, 27 deletions
diff --git a/libcrystfel/src/cell-utils.c b/libcrystfel/src/cell-utils.c
index 32e3bbe7..1bc937f9 100644
--- a/libcrystfel/src/cell-utils.c
+++ b/libcrystfel/src/cell-utils.c
@@ -3,13 +3,13 @@
*
* Unit Cell utility functions
*
- * Copyright © 2012 Deutsches Elektronen-Synchrotron DESY,
- * a research centre of the Helmholtz Association.
+ * Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY,
+ * a research centre of the Helmholtz Association.
* Copyright © 2012 Lorenzo Galli
*
* Authors:
- * 2009-2012 Thomas White <taw@physics.org>
- * 2012 Lorenzo Galli
+ * 2009-2012,2014 Thomas White <taw@physics.org>
+ * 2012 Lorenzo Galli
*
* This file is part of CrystFEL.
*
@@ -128,6 +128,27 @@ LatticeType lattice_from_str(const char *s)
}
+static int check_centering(char cen)
+{
+ switch ( cen ) {
+
+ case 'P' :
+ case 'A' :
+ case 'B' :
+ case 'C' :
+ case 'I' :
+ case 'F' :
+ case 'R' :
+ case 'H' :
+ return 0;
+
+ default:
+ return 1;
+
+ }
+}
+
+
int right_handed(UnitCell *cell)
{
double asx, asy, asz;
@@ -201,39 +222,46 @@ void cell_print(UnitCell *cell)
STATUS(", unique axis %c", cell_get_unique_axis(cell));
}
- if ( right_handed(cell) ) {
- STATUS(", right handed");
- } else {
- STATUS(", left handed");
+ if ( cell_has_parameters(cell) ) {
+ if ( right_handed(cell) ) {
+ STATUS(", right handed");
+ } else {
+ STATUS(", left handed");
+ }
}
STATUS(", point group '%s'.\n", cell_get_pointgroup(cell));
- cell_get_parameters(cell, &a, &b, &c, &alpha, &beta, &gamma);
+ if ( cell_has_parameters(cell) ) {
+ cell_get_parameters(cell, &a, &b, &c, &alpha, &beta, &gamma);
+
+ STATUS("a b c alpha beta gamma\n");
+ STATUS("%6.2f %6.2f %6.2f A %6.2f %6.2f %6.2f deg\n",
+ a*1e10, b*1e10, c*1e10,
+ rad2deg(alpha), rad2deg(beta), rad2deg(gamma));
- STATUS("a b c alpha beta gamma\n");
- STATUS("%6.2f %6.2f %6.2f A %6.2f %6.2f %6.2f deg\n",
- a*1e10, b*1e10, c*1e10,
- rad2deg(alpha), rad2deg(beta), rad2deg(gamma));
+ cell_get_cartesian(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
- cell_get_cartesian(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
+ STATUS("a = %10.3e %10.3e %10.3e m\n", ax, ay, az);
+ STATUS("b = %10.3e %10.3e %10.3e m\n", bx, by, bz);
+ STATUS("c = %10.3e %10.3e %10.3e m\n", cx, cy, cz);
- STATUS("a = %10.3e %10.3e %10.3e m\n", ax, ay, az);
- STATUS("b = %10.3e %10.3e %10.3e m\n", bx, by, bz);
- STATUS("c = %10.3e %10.3e %10.3e m\n", cx, cy, cz);
+ cell_get_reciprocal(cell, &asx, &asy, &asz,
+ &bsx, &bsy, &bsz,
+ &csx, &csy, &csz);
- cell_get_reciprocal(cell, &asx, &asy, &asz,
- &bsx, &bsy, &bsz,
- &csx, &csy, &csz);
+ STATUS("a* = %10.3e %10.3e %10.3e m^-1 (modulus %10.3e m^-1)\n",
+ asx, asy, asz, modulus(asx, asy, asz));
+ STATUS("b* = %10.3e %10.3e %10.3e m^-1 (modulus %10.3e m^-1)\n",
+ bsx, bsy, bsz, modulus(bsx, bsy, bsz));
+ STATUS("c* = %10.3e %10.3e %10.3e m^-1 (modulus %10.3e m^-1)\n",
+ csx, csy, csz, modulus(csx, csy, csz));
- STATUS("astar = %10.3e %10.3e %10.3e m^-1 (modulus = %10.3e m^-1)\n",
- asx, asy, asz, modulus(asx, asy, asz));
- STATUS("bstar = %10.3e %10.3e %10.3e m^-1 (modulus = %10.3e m^-1)\n",
- bsx, bsy, bsz, modulus(bsx, bsy, bsz));
- STATUS("cstar = %10.3e %10.3e %10.3e m^-1 (modulus = %10.3e m^-1)\n",
- csx, csy, csz, modulus(csx, csy, csz));
+ STATUS("Cell representation is %s.\n", cell_rep(cell));
- STATUS("Cell representation is %s.\n", cell_rep(cell));
+ } else {
+ STATUS("Unit cell parameters are not specified.\n");
+ }
}
@@ -1044,6 +1072,14 @@ static void determine_lattice(UnitCell *cell,
}
+/**
+ * load_cell_from_pdb:
+ *
+ * Loads a unit cell from a PDB file.
+ *
+ * Returns: a newly allocated %UnitCell.
+ *
+ */
UnitCell *load_cell_from_pdb(const char *filename)
{
FILE *fh;
@@ -1116,6 +1152,178 @@ UnitCell *load_cell_from_pdb(const char *filename)
}
+static int get_length_m(char **bits, int nbits, double *pl)
+{
+ char *rval;
+
+ if ( nbits < 4 ) {
+ ERROR("No units specified for '%s'\n", bits[0]);
+ return 1;
+ }
+
+ *pl = strtod(bits[2], &rval);
+ if ( *rval != '\0' ) {
+ ERROR("Invalid value '%s'.\n", bits[2]);
+ return 1;
+ }
+
+ if ( strcmp(bits[3], "nm") == 0 ) {
+ *pl *= 1e-9;
+ } else if ( strcmp(bits[3], "A") == 0 ) {
+ *pl *= 1e-10;
+ } else {
+ ERROR("Unrecognised length units '%s'\n", bits[3]);
+ return 1;
+ }
+
+ return 0;
+}
+
+
+static int get_angle_rad(char **bits, int nbits, double *pl)
+{
+ char *rval;
+
+ if ( nbits < 4 ) {
+ ERROR("No units specified for '%s'\n", bits[0]);
+ return 1;
+ }
+
+ *pl = strtod(bits[2], &rval);
+ if ( *rval != '\0' ) {
+ ERROR("Invalid value '%s'.\n", bits[2]);
+ return 1;
+ }
+
+ if ( strcmp(bits[3], "rad") == 0 ) {
+ /* Do nothing, already in rad */
+ } else if ( strcmp(bits[3], "deg") == 0 ) {
+ *pl = deg2rad(*pl);
+ } else {
+ ERROR("Unrecognised angle units '%s'\n", bits[3]);
+ return 1;
+ }
+
+ return 0;
+}
+
+
+/**
+ * load_cell_from_file:
+ *
+ * Loads a unit cell from a file of any type (PDB or CrystFEL format)
+ *
+ * Returns: a newly allocated %UnitCell.
+ *
+ */
+UnitCell *load_cell_from_file(const char *filename)
+{
+ FILE *fh;
+ char *rval;
+ char line[1024];
+ UnitCell *cell;
+ int have_a = 0, have_b = 0, have_c = 0;
+ int have_al = 0, have_be = 0, have_ga = 0;
+ double a, b, c, al, be, ga;
+
+ fh = fopen(filename, "r");
+ if ( fh == NULL ) {
+ ERROR("Couldn't open '%s'\n", filename);
+ return NULL;
+ }
+
+ rval = fgets(line, 1023, fh);
+ chomp(line);
+
+ if ( strcmp(line, "CrystFEL unit cell file version 1.0") != 0 ) {
+ fclose(fh);
+ return load_cell_from_pdb(filename);
+ }
+
+ cell = cell_new();
+
+ do {
+
+ char line[1024];
+ int n1;
+ int i;
+ char **bits;
+
+ rval = fgets(line, 1023, fh);
+ chomp(line);
+
+ n1 = assplode(line, " \t", &bits, ASSPLODE_NONE);
+ if ( n1 < 3 ) {
+ for ( i=0; i<n1; i++ ) free(bits[i]);
+ free(bits);
+ continue;
+ }
+
+ if ( bits[0][0] == ';' ) {
+ for ( i=0; i<n1; i++ ) free(bits[i]);
+ free(bits);
+ continue;
+ }
+
+ if ( strcmp(bits[0], "lattice_type") == 0 ) {
+ LatticeType lt = lattice_from_str(bits[2]);
+ cell_set_lattice_type(cell, lt);
+
+ } else if ( strcmp(bits[0], "centering") == 0 ) {
+ char cen = bits[2][0];
+ if ( !check_centering(cen) ) {
+ cell_set_centering(cell, cen);
+ } else {
+ ERROR("Unrecognised centering '%c'\n", cen);
+ }
+
+ } else if ( strcmp(bits[0], "a") == 0 ) {
+ if ( !get_length_m(bits, n1, &a) ) {
+ have_a = 1;
+ }
+
+ } else if ( strcmp(bits[0], "b") == 0 ) {
+ if ( !get_length_m(bits, n1, &b) ) {
+ have_b = 1;
+ }
+
+ } else if ( strcmp(bits[0], "c") == 0 ) {
+ if ( !get_length_m(bits, n1, &c) ) {
+ have_c = 1;
+ }
+
+ } else if ( strcmp(bits[0], "al") == 0 ) {
+ if ( !get_angle_rad(bits, n1, &al) ) {
+ have_al = 1;
+ }
+
+ } else if ( strcmp(bits[0], "be") == 0 ) {
+ if ( !get_angle_rad(bits, n1, &be) ) {
+ have_be = 1;
+ }
+
+ } else if ( strcmp(bits[0], "ga") == 0 ) {
+ if ( !get_angle_rad(bits, n1, &ga) ) {
+ have_ga = 1;
+ }
+
+ } else {
+ ERROR("Unrecognised field '%s'\n", bits[0]);
+ }
+
+ for ( i=0; i<n1; i++ ) free(bits[i]);
+ free(bits);
+
+ } while ( rval != NULL );
+
+ if ( have_a && have_b && have_c && have_al && have_be && have_ga ) {
+ cell_set_parameters(cell, a, b, c, al, be, ga);
+ }
+
+ return cell;
+}
+
+
/* Force the linker to bring in CBLAS to make GSL happy */
void cell_fudge_gslcblas()
{
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