diff options
| -rw-r--r-- | doc/reference/CrystFEL-sections.txt | 3 | ||||
| -rw-r--r-- | src/reflist.c | 2 | ||||
| -rw-r--r-- | src/reflist.h | 4 | ||||
| -rw-r--r-- | src/symmetry.c | 57 | ||||
| -rw-r--r-- | src/symmetry.h | 9 |
5 files changed, 53 insertions, 22 deletions
diff --git a/doc/reference/CrystFEL-sections.txt b/doc/reference/CrystFEL-sections.txt index d46646bf..62acf0d8 100644 --- a/doc/reference/CrystFEL-sections.txt +++ b/doc/reference/CrystFEL-sections.txt @@ -205,13 +205,14 @@ get_equiv special_position get_asymm get_ambiguities -is_centrosymmetric +is_subgroup <SUBSECTION> new_symopmask free_symopmask <SUBSECTION> describe_symmetry symmetry_name +is_centrosymmetric </SECTION> <SECTION> diff --git a/src/reflist.c b/src/reflist.c index 5b594d76..aefbf4e2 100644 --- a/src/reflist.c +++ b/src/reflist.c @@ -570,7 +570,7 @@ void set_scalable(Reflection *refl, int scalable) /** * set_refinable: * @refl: A %Reflection - * @scalable: Non-zero if this reflection can be used for post refinement. + * @refinable: Non-zero if this reflection can be used for post refinement. * **/ void set_refinable(Reflection *refl, int refinable) diff --git a/src/reflist.h b/src/reflist.h index 6c0285f1..a49d4a61 100644 --- a/src/reflist.h +++ b/src/reflist.h @@ -85,8 +85,8 @@ extern void set_int(Reflection *refl, double intensity); extern void set_scalable(Reflection *refl, int scalable); extern void set_refinable(Reflection *refl, int refinable); extern void set_redundancy(Reflection *refl, int red); -extern void set_temp1(Reflection *refl, double dev); -extern void set_temp2(Reflection *refl, double dev); +extern void set_temp1(Reflection *refl, double temp); +extern void set_temp2(Reflection *refl, double temp); extern void set_esd_intensity(Reflection *refl, double esd); extern void set_ph(Reflection *refl, double phase); extern void set_symmetric_indices(Reflection *refl, diff --git a/src/symmetry.c b/src/symmetry.c index 87088c80..a978eff1 100644 --- a/src/symmetry.c +++ b/src/symmetry.c @@ -46,20 +46,6 @@ struct sym_op }; -/** - * SECTION:symoplist - * @short_description: A list of point symmetry operations - * @title: SymOpList - * @section_id: - * @see_also: - * @include: "symmetry.h" - * @Image: - * - * The SymOpList is an opaque data structure containing a list of point symmetry - * operations. It could represent an point group or a list of indexing - * ambiguities (twin laws), or similar. - */ - struct _symoplist { struct sym_op *ops; @@ -797,6 +783,20 @@ static SymOpList *make_m3barm() } +/** + * get_pointgroup: + * @sym: A string representation of a point group + * + * This function parses @sym and returns the corresponding %SymOpList. + * In the string representation of the point group, use a preceding minus sign + * for any character which would have a "bar". Trigonal groups must be suffixed + * with either "_H" or "_R" for a hexagonal or rhombohedral lattice + * respectively. + * + * Examples: -1 1 2/m 2 m mmm 222 mm2 4/m 4 -4 4/mmm 422 -42m -4m2 4mm + * 3_R -3_R 32_R 3m_R -3m_R 3_H -3_H 321_H 312_H 3m1_H 31m_H -3m1_H -31m_H + * 6/m 6 -6 6/mmm 622 -62m -6m2 6mm 23 m-3 432 -43m m-3m. + **/ SymOpList *get_pointgroup(const char *sym) { /* Triclinic */ @@ -999,6 +999,20 @@ void special_position(const SymOpList *ops, SymOpMask *m, } +/** + * get_asymm: + * @ops: A %SymOpList, usually corresponding to a point group + * @h: index of a reflection + * @k: index of a reflection + * @l: index of a reflection + * @hp: location for asymmetric index of reflection + * @kp: location for asymmetric index of reflection + * @lp: location for asymmetric index of reflection + * + * This function determines the asymmetric version of the reflection @h, @k, @l + * in symmetry group @ops, and puts the result in @hp, @kp, @lp. + * + **/ void get_asymm(const SymOpList *ops, signed int h, signed int k, signed int l, signed int *hp, signed int *kp, signed int *lp) @@ -1103,7 +1117,6 @@ static int struct_ops_equal(const struct sym_op *op1, const struct sym_op *op2) } - /* Return true if a*b = ans */ static int check_mult(const struct sym_op *ans, const struct sym_op *a, const struct sym_op *b) @@ -1126,7 +1139,13 @@ static int check_mult(const struct sym_op *ans, } -/* Check that every operation in "target" is also in "source" */ +/** + * is_subgroup: + * @source: A %SymOpList + * @target: Another %SymOpList, which might be a subgroup of @source. + * + * Returns: non-zero if every operation in @target is also in @source. + **/ int is_subgroup(const SymOpList *source, const SymOpList *target) { int n_src, n_tgt; @@ -1423,6 +1442,12 @@ void describe_symmetry(const SymOpList *s) } +/** + * symmetry_name: + * @ops: A %SymOpList + * + * Returns: a text description of @ops. + */ const char *symmetry_name(const SymOpList *ops) { return ops->name; diff --git a/src/symmetry.h b/src/symmetry.h index c91864bb..071ebbde 100644 --- a/src/symmetry.h +++ b/src/symmetry.h @@ -20,14 +20,19 @@ /** * SymOpList * - * Opaque type. + * The SymOpList is an opaque data structure containing a list of point symmetry + * operations. It could represent an point group or a list of indexing + * ambiguities (twin laws), or similar. **/ typedef struct _symoplist SymOpList; /** * SymOpMask * - * Opaque type. + * The SymOpMask is an opaque data structure containing a list of flags + * associated with point symmetry operations in a specific %SymOpList. It is + * used to filter the operations in the %SymOpList to avoid duplicating + * equivalent reflections when the reflection is somehow special (e.g. 'hk0'). **/ typedef struct _symopmask SymOpMask; |