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-rw-r--r--libcrystfel/src/dirax.c6
-rw-r--r--libcrystfel/src/grainspotter.c6
-rw-r--r--libcrystfel/src/index.c25
-rw-r--r--libcrystfel/src/index.h4
-rw-r--r--libcrystfel/src/mosflm.c7
-rw-r--r--libcrystfel/src/xds.c2
6 files changed, 41 insertions, 9 deletions
diff --git a/libcrystfel/src/dirax.c b/libcrystfel/src/dirax.c
index e6ff36b1..fb60656a 100644
--- a/libcrystfel/src/dirax.c
+++ b/libcrystfel/src/dirax.c
@@ -637,8 +637,10 @@ IndexingPrivate *dirax_prepare(IndexingMethod *indm, UnitCell *cell,
if ( *indm & INDEXING_CHECK_CELL_AXES ) need_cell = 1;
if ( need_cell && (cell == NULL) ) {
- ERROR("DirAx needs a unit cell for this set of flags.\n");
- return NULL;
+ ERROR("Altering your DirAx flags because no PDB file was"
+ " provided.\n");
+ *indm &= ~INDEXING_CHECK_CELL_COMBINATIONS;
+ *indm &= ~INDEXING_CHECK_CELL_AXES;
}
/* Flags that DirAx knows about */
diff --git a/libcrystfel/src/grainspotter.c b/libcrystfel/src/grainspotter.c
index 8bdb03aa..8def8091 100644
--- a/libcrystfel/src/grainspotter.c
+++ b/libcrystfel/src/grainspotter.c
@@ -482,10 +482,8 @@ IndexingPrivate *grainspotter_prepare(IndexingMethod *indm, UnitCell *cell,
if ( gp == NULL ) return NULL;
/* Flags that GrainSpotter knows about */
- *indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_PEAKS;
-
- /* Flags that GrainSpotter requires */
- *indm |= INDEXING_USE_LATTICE_TYPE;
+ *indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_PEAKS
+ | INDEXING_USE_LATTICE_TYPE | INDEXING_USE_CELL_PARAMETERS;
gp->cell = cell;
gp->indm = *indm;
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 0ab467a6..311dc2ce 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -316,6 +316,19 @@ static IndexingMethod set_lattice(IndexingMethod a)
}
+/* Set the indexer flags for "use no unit cell parameters" */
+static IndexingMethod set_nocellparams(IndexingMethod a)
+{
+ return a & ~INDEXING_USE_CELL_PARAMETERS;
+}
+
+
+/* Set the indexer flags for "use unit cell parameters" */
+static IndexingMethod set_cellparams(IndexingMethod a)
+{
+ return a | INDEXING_USE_CELL_PARAMETERS;
+}
+
char *indexer_str(IndexingMethod indm)
{
char *str;
@@ -379,6 +392,12 @@ char *indexer_str(IndexingMethod indm)
strcat(str, "-nolatt");
}
+ if ( indm & INDEXING_USE_CELL_PARAMETERS ) {
+ strcat(str, "-cell");
+ } else {
+ strcat(str, "-nocell");
+ }
+
return str;
}
@@ -433,6 +452,12 @@ IndexingMethod *build_indexer_list(const char *str)
} else if ( strcmp(methods[i], "nolatt") == 0) {
list[nmeth] = set_nolattice(list[nmeth]);
+ } else if ( strcmp(methods[i], "cell") == 0) {
+ list[nmeth] = set_cellparams(list[nmeth]);
+
+ } else if ( strcmp(methods[i], "nocell") == 0) {
+ list[nmeth] = set_nocellparams(list[nmeth]);
+
} else {
ERROR("Bad list of indexing methods: '%s'\n", str);
return NULL;
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index 94b0d457..f60bb18f 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -52,13 +52,16 @@
| INDEXING_USE_LATTICE_TYPE)
#define INDEXING_DEFAULTS_REAX (INDEXING_REAX | INDEXING_USE_LATTICE_TYPE \
+ | INDEXING_USE_CELL_PARAMETERS \
| INDEXING_CHECK_PEAKS)
#define INDEXING_DEFAULTS_GRAINSPOTTER (INDEXING_GRAINSPOTTER \
| INDEXING_USE_LATTICE_TYPE \
+ | INDEXING_USE_CELL_PARAMETERS \
| INDEXING_CHECK_PEAKS)
#define INDEXING_DEFAULTS_XDS (INDEXING_XDS | INDEXING_USE_LATTICE_TYPE \
+ | INDEXING_USE_CELL_PARAMETERS \
| INDEXING_CHECK_PEAKS)
/**
@@ -87,6 +90,7 @@ typedef enum {
INDEXING_CHECK_CELL_AXES = 512,
INDEXING_CHECK_PEAKS = 1024,
INDEXING_USE_LATTICE_TYPE = 2048,
+ INDEXING_USE_CELL_PARAMETERS = 4096,
} IndexingMethod;
diff --git a/libcrystfel/src/mosflm.c b/libcrystfel/src/mosflm.c
index a03e621d..187d0c9b 100644
--- a/libcrystfel/src/mosflm.c
+++ b/libcrystfel/src/mosflm.c
@@ -817,8 +817,11 @@ IndexingPrivate *mosflm_prepare(IndexingMethod *indm, UnitCell *cell,
if ( *indm & INDEXING_USE_LATTICE_TYPE ) need_cell = 1;
if ( need_cell && (cell == NULL) ) {
- ERROR("MOSFLM needs a unit cell for this set of flags.\n");
- return NULL;
+ ERROR("Altering your MOSFLM flags because no PDB file was"
+ " provided.\n");
+ *indm &= ~INDEXING_CHECK_CELL_COMBINATIONS;
+ *indm &= ~INDEXING_CHECK_CELL_AXES;
+ *indm &= ~INDEXING_USE_LATTICE_TYPE;
}
/* Flags that MOSFLM knows about */
diff --git a/libcrystfel/src/xds.c b/libcrystfel/src/xds.c
index 098de504..92619d65 100644
--- a/libcrystfel/src/xds.c
+++ b/libcrystfel/src/xds.c
@@ -648,7 +648,7 @@ IndexingPrivate *xds_prepare(IndexingMethod *indm, UnitCell *cell,
/* Flags that XDS knows about */
*indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_CELL_COMBINATIONS
| INDEXING_CHECK_CELL_AXES | INDEXING_USE_LATTICE_TYPE
- | INDEXING_CHECK_PEAKS;
+ | INDEXING_CHECK_PEAKS | INDEXING_USE_CELL_PARAMETERS;
xp->ltl = ltl;
xp->cell = cell;