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authorThomas White <taw@physics.org>2012-06-01 18:15:17 +0200
committerThomas White <taw@physics.org>2012-10-02 15:02:11 +0200
commit766d90e7d92ee0e10877e90466829ff3f4925269 (patch)
tree12a5997bb01d5d8383302aeaf1af4dba667e07d8 /libcrystfel/src
parentea8e5c457b96184bd152eb20b72fb15682b18474 (diff)
Handle lattice type, centering and unique axis information
Diffstat (limited to 'libcrystfel/src')
-rw-r--r--libcrystfel/src/cell.c280
-rw-r--r--libcrystfel/src/cell.h22
2 files changed, 281 insertions, 21 deletions
diff --git a/libcrystfel/src/cell.c b/libcrystfel/src/cell.c
index 3d2a28bf..1cd6fb88 100644
--- a/libcrystfel/src/cell.c
+++ b/libcrystfel/src/cell.c
@@ -92,8 +92,11 @@ struct _unitcell {
double ays; double bys; double cys;
double azs; double bzs; double czs;
- char *pointgroup;
- char *spacegroup;
+ char *pointgroup;
+ char *spacegroup;
+ LatticeType lattice_type;
+ char centering;
+ char unique_axis;
};
@@ -126,6 +129,9 @@ UnitCell *cell_new()
cell->pointgroup = strdup("1");
cell->spacegroup = strdup("P 1");
+ cell->lattice_type = L_TRICLINIC;
+ cell->centering = 'P';
+ cell->unique_axis = 'c';
return cell;
}
@@ -296,6 +302,24 @@ void cell_set_pointgroup(UnitCell *cell, const char *sym)
}
+void cell_set_centering(UnitCell *cell, char centering)
+{
+ cell->centering = centering;
+}
+
+
+void cell_set_lattice_type(UnitCell *cell, LatticeType lattice_type)
+{
+ cell->lattice_type = lattice_type;
+}
+
+
+void cell_set_unique_axis(UnitCell *cell, char unique_axis)
+{
+ cell->unique_axis = unique_axis;
+}
+
+
/************************* Getter helper functions ****************************/
static int cell_crystallographic_to_cartesian(UnitCell *cell,
@@ -561,6 +585,23 @@ const char *cell_get_spacegroup(UnitCell *cell)
}
+char cell_get_centering(UnitCell *cell)
+{
+ return cell->centering;
+}
+
+
+LatticeType cell_get_lattice_type(UnitCell *cell)
+{
+ return cell->lattice_type;
+}
+
+
+char cell_get_unique_axis(UnitCell *cell)
+{
+ return cell->unique_axis;
+}
+
@@ -617,6 +658,23 @@ UnitCell *cell_rotate(UnitCell *in, struct quaternion quat)
}
+static const char *str_lattice(LatticeType l)
+{
+ switch ( l )
+ {
+ case L_TRICLINIC : return "triclinic";
+ case L_MONOCLINIC : return "monoclinic";
+ case L_ORTHORHOMBIC : return "orthorhombic";
+ case L_TETRAGONAL : return "tetragonal";
+ case L_RHOMBOHEDRAL : return "rhombohedral";
+ case L_HEXAGONAL : return "hexagonal";
+ case L_CUBIC : return "cubic";
+ }
+
+ return "unknown lattice";
+}
+
+
void cell_print(UnitCell *cell)
{
double asx, asy, asz;
@@ -625,6 +683,9 @@ void cell_print(UnitCell *cell)
double a, b, c, alpha, beta, gamma;
double ax, ay, az, bx, by, bz, cx, cy, cz;
+ STATUS("%s %c\n", str_lattice(cell_get_lattice_type(cell)),
+ cell_get_centering(cell));
+
cell_get_parameters(cell, &a, &b, &c, &alpha, &beta, &gamma);
STATUS(" a b c alpha beta gamma\n");
@@ -1019,21 +1080,122 @@ double resolution(UnitCell *cell, signed int h, signed int k, signed int l)
}
-static void cell_set_pointgroup_from_pdb(UnitCell *cell, const char *sym)
+static void determine_lattice(UnitCell *cell,
+ const char *as, const char *bs, const char *cs,
+ const char *als, const char *bes, const char *gas)
{
- char *new = NULL;
+ int n_right;
- if ( strcmp(sym, "P 1") == 0 ) new = "1";
- if ( strcmp(sym, "P 63") == 0 ) new = "6";
- if ( strcmp(sym, "P 21 21 21") == 0 ) new = "222";
- if ( strcmp(sym, "P 2 2 2") == 0 ) new = "222";
- if ( strcmp(sym, "P 43 21 2") == 0 ) new = "422";
+ /* Rhombohedral or cubic? */
+ if ( (strcmp(as, bs) == 0) && (strcmp(as, cs) == 0) ) {
- if ( new != NULL ) {
- cell_set_pointgroup(cell, new);
- } else {
- ERROR("Can't determine point group for '%s'\n", sym);
+ if ( (strcmp(als, " 90.00") == 0)
+ && (strcmp(bes, " 90.00") == 0)
+ && (strcmp(gas, " 90.00") == 0) )
+ {
+ /* Cubic. Unique axis irrelevant. */
+ cell_set_lattice_type(cell, L_CUBIC);
+ return;
+ }
+
+ if ( (strcmp(als, bes) == 0) && (strcmp(als, gas) == 0) ) {
+ /* Rhombohedral. Unique axis irrelevant. */
+ cell_set_lattice_type(cell, L_RHOMBOHEDRAL);
+ return;
+ }
+
+ }
+
+ if ( (strcmp(als, " 90.00") == 0)
+ && (strcmp(bes, " 90.00") == 0)
+ && (strcmp(gas, " 90.00") == 0) )
+ {
+ if ( strcmp(bs, cs) == 0 ) {
+ /* Tetragonal, unique axis a */
+ cell_set_lattice_type(cell, L_TETRAGONAL);
+ cell_set_unique_axis(cell, 'a');
+ return;
+ }
+
+ if ( strcmp(as, cs) == 0 ) {
+ /* Tetragonal, unique axis b */
+ cell_set_lattice_type(cell, L_TETRAGONAL);
+ cell_set_unique_axis(cell, 'b');
+ return;
+ }
+
+ if ( strcmp(as, bs) == 0 ) {
+ /* Tetragonal, unique axis c */
+ cell_set_lattice_type(cell, L_TETRAGONAL);
+ cell_set_unique_axis(cell, 'c');
+ return;
+ }
+
+ /* Orthorhombic. Unique axis irrelevant, but point group
+ * can have different orientations. */
+ cell_set_lattice_type(cell, L_ORTHORHOMBIC);
+ return;
}
+
+ n_right = 0;
+ if ( strcmp(als, " 90.00") == 0 ) n_right++;
+ if ( strcmp(bes, " 90.00") == 0 ) n_right++;
+ if ( strcmp(gas, " 90.00") == 0 ) n_right++;
+
+ /* Hexgonal or monoclinic? */
+ if ( n_right == 2 ) {
+
+ if ( (strcmp(als, " 120.00") == 0)
+ && (strcmp(bs, cs) == 0) )
+ {
+ /* Hexagonal, unique axis a */
+ cell_set_lattice_type(cell, L_HEXAGONAL);
+ cell_set_unique_axis(cell, 'a');
+ return;
+ }
+
+ if ( (strcmp(bes, " 120.00") == 0)
+ && (strcmp(as, cs) == 0) )
+ {
+ /* Hexagonal, unique axis b */
+ cell_set_lattice_type(cell, L_HEXAGONAL);
+ cell_set_unique_axis(cell, 'b');
+ return;
+ }
+
+ if ( (strcmp(gas, " 120.00") == 0)
+ && (strcmp(as, bs) == 0) )
+ {
+ /* Hexagonal, unique axis c */
+ cell_set_lattice_type(cell, L_HEXAGONAL);
+ cell_set_unique_axis(cell, 'c');
+ return;
+ }
+
+ if ( strcmp(als, " 90.00") != 0 ) {
+ /* Monoclinic, unique axis a */
+ cell_set_lattice_type(cell, L_MONOCLINIC);
+ cell_set_unique_axis(cell, 'a');
+ return;
+ }
+
+ if ( strcmp(bes, " 90.00") != 0 ) {
+ /* Monoclinic, unique axis b */
+ cell_set_lattice_type(cell, L_MONOCLINIC);
+ cell_set_unique_axis(cell, 'b');
+ return;
+ }
+
+ if ( strcmp(gas, " 90.00") != 0 ) {
+ /* Monoclinic, unique axis c */
+ cell_set_lattice_type(cell, L_MONOCLINIC);
+ cell_set_unique_axis(cell, 'c');
+ return;
+ }
+ }
+
+ /* Triclinic, unique axis irrelevant. */
+ cell_set_lattice_type(cell, L_TRICLINIC);
}
@@ -1060,7 +1222,6 @@ UnitCell *load_cell_from_pdb(const char *filename)
float a, b, c, al, be, ga;
char as[10], bs[10], cs[10];
char als[8], bes[8], gas[8];
- char *sym;
int r;
memcpy(as, line+6, 9); as[9] = '\0';
@@ -1088,16 +1249,14 @@ UnitCell *load_cell_from_pdb(const char *filename)
deg2rad(be),
deg2rad(ga));
+ determine_lattice(cell, as, bs, cs, als, bes, gas);
+
if ( strlen(line) > 65 ) {
- sym = strndup(line+55, 10);
- notrail(sym);
- cell_set_pointgroup_from_pdb(cell, sym);
- cell_set_spacegroup(cell, sym);
- free(sym);
+ cell_set_centering(cell, line[55]);
} else {
- cell_set_pointgroup_from_pdb(cell, "P 1");
+ cell_set_pointgroup(cell, "1");
cell_set_spacegroup(cell, "P 1");
- ERROR("CRYST1 line without space group.\n");
+ ERROR("CRYST1 line without centering.\n");
}
break; /* Done */
@@ -1107,6 +1266,8 @@ UnitCell *load_cell_from_pdb(const char *filename)
fclose(fh);
+ validate_cell(cell);
+
return cell;
}
@@ -1196,3 +1357,80 @@ int cell_is_sensible(UnitCell *cell)
if ( isnan(ga) ) return 0;
return 1;
}
+
+
+static int bravais_lattice(UnitCell *cell)
+{
+ LatticeType lattice = cell_get_lattice_type(cell);
+ char centering = cell_get_centering(cell);
+ char ua = cell_get_unique_axis(cell);
+
+ switch ( centering )
+ {
+ case 'P' :
+ return 1;
+
+ case 'A' :
+ case 'B' :
+ case 'C' :
+ if ( (lattice != L_MONOCLINIC)
+ && (lattice != L_ORTHORHOMBIC) )
+ {
+ return 0;
+ }
+ if ( (ua=='a') && (centering=='A') ) return 1;
+ if ( (ua=='b') && (centering=='B') ) return 1;
+ if ( (ua=='c') && (centering=='C') ) return 1;
+ return 0;
+
+ case 'I' :
+ if ( (lattice == L_ORTHORHOMBIC)
+ || (lattice == L_TETRAGONAL)
+ || (lattice == L_CUBIC) )
+ {
+ return 1;
+ }
+ return 0;
+
+ case 'F' :
+ if ( (lattice == L_ORTHORHOMBIC) || (lattice == L_CUBIC) ) {
+ return 1;
+ }
+ return 0;
+
+ case 'H' :
+ if ( lattice == L_HEXAGONAL ) return 1;
+ return 0;
+
+ default :
+ return 0;
+ }
+}
+
+
+/**
+ * validate_cell:
+ * @cell: A %UnitCell to validate
+ *
+ * Perform some checks for crystallographic validity @cell, such as that the
+ * lattice is a conventional Bravais lattice.
+ * Warnings are printied if any of the checks are failed.
+ *
+ */
+void validate_cell(UnitCell *cell)
+{
+ int err = 0;
+
+ if ( !cell_is_sensible(cell) ) {
+ ERROR("Warning: Unit cell parameters are not sensible.\n");
+ err = 1;
+ }
+
+ if ( !bravais_lattice(cell) ) {
+ ERROR("Warning: Unit cell is not a conventional Bravais"
+ " lattice.\n");
+ err = 1;
+ }
+
+ if ( err ) cell_print(cell);
+}
diff --git a/libcrystfel/src/cell.h b/libcrystfel/src/cell.h
index bd2719dd..851237cf 100644
--- a/libcrystfel/src/cell.h
+++ b/libcrystfel/src/cell.h
@@ -48,6 +48,17 @@ struct rvec
double w;
};
+typedef enum
+{
+ L_TRICLINIC,
+ L_MONOCLINIC,
+ L_ORTHORHOMBIC,
+ L_TETRAGONAL,
+ L_RHOMBOHEDRAL,
+ L_HEXAGONAL,
+ L_CUBIC
+} LatticeType;
+
/**
* UnitCell:
@@ -108,6 +119,15 @@ extern const char *cell_get_pointgroup(UnitCell *cell);
extern const char *cell_get_spacegroup(UnitCell *cell);
+extern LatticeType cell_get_lattice_type(UnitCell *cell);
+extern void cell_set_lattice_type(UnitCell *cell, LatticeType lattice_type);
+
+extern char cell_get_centering(UnitCell *cell);
+extern void cell_set_centering(UnitCell *cell, char centering);
+
+extern char cell_get_unique_axis(UnitCell *cell);
+extern void cell_set_unique_axis(UnitCell *cell, char unique_axis);
+
extern double resolution(UnitCell *cell,
signed int h, signed int k, signed int l);
@@ -126,4 +146,6 @@ extern UnitCell *load_cell_from_pdb(const char *filename);
extern int cell_is_sensible(UnitCell *cell);
+extern void validate_cell(UnitCell *cell);
+
#endif /* CELL_H */