Read symmetry from PDB and store in unit cell structure

6 files changed, 50 insertions, 10 deletions

diff --git a/src/Makefile.am b/src/Makefile.am
index 81089265..b7108918 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -22,7 +22,7 @@ process_hkl_LDADD = @LIBS@
 
 indexamajig_SOURCES = indexamajig.c hdf5-file.c utils.c cell.c image.c \
                       peaks.c index.c filters.c diffraction.c detector.c \
-                      sfac.c dirax.c reflections.c templates.c
+                      sfac.c dirax.c reflections.c templates.c symmetry.c
 indexamajig_LDADD = @LIBS@
 if HAVE_OPENCL
 indexamajig_SOURCES += diffraction-gpu.c cl-utils.c
diff --git a/src/Makefile.in b/src/Makefile.in
index 23079835..9355ef39 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -88,7 +88,7 @@ hdfsee_OBJECTS = $(am_hdfsee_OBJECTS)
 hdfsee_DEPENDENCIES =
 am__indexamajig_SOURCES_DIST = indexamajig.c hdf5-file.c utils.c \
 	cell.c image.c peaks.c index.c filters.c diffraction.c \
-	detector.c sfac.c dirax.c reflections.c templates.c \
+	detector.c sfac.c dirax.c reflections.c templates.c symmetry.c \
 	diffraction-gpu.c cl-utils.c
 @HAVE_OPENCL_TRUE@am__objects_1 = diffraction-gpu.$(OBJEXT) \
 @HAVE_OPENCL_TRUE@	cl-utils.$(OBJEXT)
@@ -96,7 +96,8 @@ am_indexamajig_OBJECTS = indexamajig.$(OBJEXT) hdf5-file.$(OBJEXT) \
 	utils.$(OBJEXT) cell.$(OBJEXT) image.$(OBJEXT) peaks.$(OBJEXT) \
 	index.$(OBJEXT) filters.$(OBJEXT) diffraction.$(OBJEXT) \
 	detector.$(OBJEXT) sfac.$(OBJEXT) dirax.$(OBJEXT) \
-	reflections.$(OBJEXT) templates.$(OBJEXT) $(am__objects_1)
+	reflections.$(OBJEXT) templates.$(OBJEXT) symmetry.$(OBJEXT) \
+	$(am__objects_1)
 indexamajig_OBJECTS = $(am_indexamajig_OBJECTS)
 indexamajig_DEPENDENCIES =
 am__pattern_sim_SOURCES_DIST = pattern_sim.c diffraction.c utils.c \
@@ -259,7 +260,7 @@ process_hkl_SOURCES = process_hkl.c sfac.c statistics.c cell.c utils.c \
 process_hkl_LDADD = @LIBS@
 indexamajig_SOURCES = indexamajig.c hdf5-file.c utils.c cell.c image.c \
 	peaks.c index.c filters.c diffraction.c detector.c sfac.c \
-	dirax.c reflections.c templates.c $(am__append_3)
+	dirax.c reflections.c templates.c symmetry.c $(am__append_3)
 indexamajig_LDADD = @LIBS@
 @HAVE_GTK_TRUE@hdfsee_SOURCES = hdfsee.c displaywindow.c render.c hdf5-file.c utils.c image.c \
 @HAVE_GTK_TRUE@                 filters.c
diff --git a/src/cell.c b/src/cell.c
index cc252b70..d6464a71 100644
--- a/src/cell.c
+++ b/src/cell.c
@@ -56,6 +56,8 @@ struct _unitcell {
 	double ays;	double bys;	double cys;
 	double azs;	double bzs;	double czs;
 
+	char *pointgroup;
+
 };
 
 
@@ -77,6 +79,8 @@ UnitCell *cell_new()
 
 	cell->rep = CELL_REP_CRYST;
 
+	cell->pointgroup = strdup("1");
+
 	return cell;
 }
 
@@ -447,6 +451,12 @@ int cell_get_reciprocal(UnitCell *cell,
 }
 
 
+const char *cell_get_pointgroup(UnitCell *cell)
+{
+	return cell->pointgroup;
+}
+
+
 /********************************* Utilities **********************************/
 
 void cell_print(UnitCell *cell)
@@ -731,6 +741,21 @@ 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)
+{
+	char *new = NULL;
+
+	if ( strcmp(sym, "P 63") == 0 ) new = "6";
+
+	if ( new != NULL ) {
+		free(cell->pointgroup);
+		cell->pointgroup = strdup(new);
+	} else {
+		ERROR("Can't determine point group for space group %s\n", sym);
+	}
+}
+
+
 UnitCell *load_cell_from_pdb(const char *filename)
 {
 	FILE *fh;
@@ -753,8 +778,9 @@ UnitCell *load_cell_from_pdb(const char *filename)
 
 			float a, b, c, al, be, ga;
 			int r;
+			char *sym;
 
-			r = sscanf(line+7, "%f %f %f %f %f %f",
+			r = sscanf(line+7, "%f %f %f %f %f %f\n",
 			           &a, &b, &c, &al, &be, &ga);
 			if ( r != 6 ) {
 				ERROR("Couldn't understand CRYST1 line\n");
@@ -767,6 +793,11 @@ UnitCell *load_cell_from_pdb(const char *filename)
 	                                                deg2rad(be),
 	                                                deg2rad(ga));
 
+			sym = strndup(line+55, 11);
+			notrail(sym);
+			cell_set_pointgroup_from_pdb(cell, sym);
+			free(sym);
+
 		}
 
 	} while ( rval != NULL );
diff --git a/src/cell.h b/src/cell.h
index 42ef2eb6..f44de74f 100644
--- a/src/cell.h
+++ b/src/cell.h
@@ -67,6 +67,8 @@ extern void cell_set_reciprocal(UnitCell *cell,
                                double bsx, double bsy, double bsz,
                                double csx, double csy, double csz);
 
+extern const char *cell_get_pointgroup(UnitCell *cell);
+
 extern double resolution(UnitCell *cell,
                          signed int h, signed int k, signed int l);
 
diff --git a/src/utils.c b/src/utils.c
index 0f20435e..a47f234f 100644
--- a/src/utils.c
+++ b/src/utils.c
@@ -18,15 +18,21 @@
 #include "image.h"
 
 
-size_t skipspace(const char *s)
+size_t notrail(char *s)
 {
 	size_t i;
+	size_t munched = 0;
 
-	for ( i=0; i<strlen(s); i++ ) {
-		if ( (s[i] != ' ') && (s[i] != '\t') ) return i;
+	for ( i=strlen(s)-1; i>=0; i-- ) {
+		if ( (s[i] == ' ') || (s[i] == '\t') ) {
+			s[i] = '\0';
+			munched++;
+		} else {
+			return munched;
+		}
 	}
 
-	return strlen(s);
+	return munched;
 }
 
 
diff --git a/src/utils.h b/src/utils.h
index f7e98469..a8d7aa2d 100644
--- a/src/utils.h
+++ b/src/utils.h
@@ -65,7 +65,7 @@ extern struct rvec quat_rot(struct rvec q, struct quaternion z);
 
 /* --------------------------- Useful functions ----------------------------- */
 
-extern size_t skipspace(const char *s);
+extern size_t notrail(char *s);
 extern void chomp(char *s);
 
 typedef enum {