ambigator: Add --start-assignments

2 files changed, 56 insertions, 13 deletions

diff --git a/doc/man/ambigator.1 b/doc/man/ambigator.1
index 89dea842..2dd8c0c9 100644
--- a/doc/man/ambigator.1
+++ b/doc/man/ambigator.1
@@ -68,6 +68,10 @@ High resolution cutoff in Angstroms.
 Low resolution cutoff in Angstroms.
 
 .PD 0
+.IP \fB--start-assignments=\fR\fIfilename\fR
+Read the starting assignments to \fIfilename\fR.  The file must be a list of 0 or 1, one value per line, in the same order as the crystals appear in the input stream.  1 means that the pattern should be reindexed according to the ambiguity operator.  The length of the file must be at least equal to the number of crystals in the input stream.
+
+.PD 0
 .IP \fB--end-assignments=\fR\fIfilename\fR
 Write the end assignments to \fIfilename\fR.  The file will be a list of 0 or 1, one value per line, in the same order as the crystals appear in the input stream.  1 means that the pattern should be reindexed according to the ambiguity operator.
 
diff --git a/src/ambigator.c b/src/ambigator.c
index bf9db16a..ba154cd5 100644
--- a/src/ambigator.c
+++ b/src/ambigator.c
@@ -61,19 +61,20 @@ static void show_help(const char *s)
 	printf(
 "Resolve indexing ambiguities.\n"
 "\n"
-"  -h, --help                 Display this help message.\n"
+"  -h, --help                  Display this help message.\n"
 "\n"
-"  -o, --output=<filename>    Output stream.\n"
-"  -y, --symmetry=<sym>       Actual (\"target\") symmetry.\n"
-"  -w <sym>                   Apparent (\"source\" or \"twinned\") symmetry.\n"
-"  -n, --iterations=<n>       Iterate <n> times.\n"
-"      --highres=<n>          High resolution cutoff in A.\n"
-"      --lowres=<n>           Low resolution cutoff in A.\n"
-"      --end-assignments=<fn> Save end assignments to file <fn>.\n"
-"      --fg-graph=<fn>        Save f and g correlation values to file <fn>.\n"
-"      --ncorr=<n>            Use <n> correlations per crystal.  Default 1000\n"
-"  -j <n>                     Use <n> threads for CC calculation.\n"
-"      --really-random        Be non-deterministic.\n"
+"  -o, --output=<filename>     Output stream.\n"
+"  -y, --symmetry=<sym>        Actual (\"target\") symmetry.\n"
+"  -w <sym>                    Apparent (\"source\" or \"twinned\") symmetry.\n"
+"  -n, --iterations=<n>        Iterate <n> times.\n"
+"      --highres=<n>           High resolution cutoff in A.\n"
+"      --lowres=<n>            Low resolution cutoff in A.\n"
+"      --start-assignments=<f> Read starting assignments from file.\n"
+"      --end-assignments=<f>   Save end assignments to file.\n"
+"      --fg-graph=<f>          Save f and g correlation values to file.\n"
+"      --ncorr=<n>             Use <n> correlations per crystal.  Default 1000\n"
+"  -j <n>                      Use <n> threads for CC calculation.\n"
+"      --really-random         Be non-deterministic.\n"
 );
 }
 
@@ -697,6 +698,7 @@ int main(int argc, char *argv[])
 	int c;
 	const char *infile;
 	char *outfile = NULL;
+	char *start_ass_fn = NULL;
 	char *end_ass_fn = NULL;
 	char *fg_graph_fn = NULL;
 	char *s_sym_str = NULL;
@@ -736,6 +738,7 @@ int main(int argc, char *argv[])
 		{"end-assignments",    1, NULL,                4},
 		{"fg-graph",           1, NULL,                5},
 		{"ncorr",              1, NULL,                6},
+		{"start-assignments",  1, NULL,                7},
 
 		{"really-random",      0, &config_random,      1},
 
@@ -809,6 +812,10 @@ int main(int argc, char *argv[])
 			}
 			break;
 
+			case 7 :
+			start_ass_fn = strdup(optarg);
+			break;
+
 			case 0 :
 			break;
 
@@ -965,8 +972,40 @@ int main(int argc, char *argv[])
 		fclose(fh);
 	}
 
+	if ( start_ass_fn != NULL ) {
+
+		FILE *fh;
+		fh = fopen(start_ass_fn, "r");
+		if ( fh == NULL ) {
+			ERROR("Failed to open '%s'\n", start_ass_fn);
+			return 1;
+		}
+
+		for ( i=0; i<n_crystals; i++ ) {
+			int ass;
+			if ( fscanf(fh, "%i", &ass) != 1 ) {
+				ERROR("Invalid value at line %i of %s\n",
+				      i, start_ass_fn);
+				return 1;
+			}
+			if ( (ass != 0) && (ass != 1) ) {
+				ERROR("Invalid value at line %i of %s\n",
+				      i, start_ass_fn);
+				return 1;
+			}
+			assignments[i] = ass;
+		}
+
+		fclose(fh);
+		free(start_ass_fn);
+
+	} else {
+		for ( i=0; i<n_crystals; i++ ) {
+			assignments[i] = (random_flat(rng, 1.0) > 0.5);
+		}
+	}
+
 	for ( i=0; i<n_crystals; i++ ) {
-		assignments[i] = (random_flat(rng, 1.0) > 0.5);
 		orig_assignments[i] = assignments[i];
 	}