Merge branch 'develop' into staging_protocol

config/sample_config_monomer.txt

@@ -140,7 +140,9 @@ align:
 
 # Inference of evolutionary couplings from sequence alignment
 couplings:
-    # current options: standard (model inference using plmc)
+    # current options: 
+    # - standard (model inference using plmc)
+    # - mean_field (mean field direct coupling analysis, see below)
     protocol: standard
 
     # number of plmc iterations
@@ -163,13 +165,22 @@ couplings:
     lambda_h: 0.01
     lambda_group:
     scale_clusters:
-
+    
     # reuse ECs and model parameters, if this stage has been run before
     reuse_ecs: True
 
     # Sequence separation filter for generation of CouplingScores_longrange.csv table (i.e. to take out short-range
     # ECs from table, only pairs with abs(i-j)>=min_sequence_distance will be kept.
     min_sequence_distance: 6
+
+# Alternative protocol: compute couplings with mean field direct coupling analysis
+# Uncomment, and comment all values in align section above to enable the mean_field protocol
+    # protocol: mean_field
+    # pseudo_count: 0.5
+    # alphabet:
+    # ignore_gaps: False
+    # reuse_ecs: True
+    # min_sequence_distance: 6
 
     # Following input parameters will usually be overriden by "global" and outputs of "align" stage
     # prefix:

evcouplings/couplings/protocol.py

@@ -625,6 +625,9 @@ def mean_field(**kwargs):
         ascending=False
     )
 
+    # Add dummy probability value for compatibility with downstream code
+    ecs.loc[:, "probability"] = np.nan
+
     is_single_segment = segments is None or len(segments) == 1
     outcfg = {
         **outcfg,

evcouplings/utils/update_database.py

@@ -177,8 +177,8 @@ def run(**kwargs):
 
 @click.command(context_settings=CONTEXT_SETTINGS)
 # run settings
-@click.option("-s", "--sifts", default="/groups/marks/databases/SIFTS/", help="SIFTS output directory")
-@click.option("-d", "--db", default="/groups/marks/databases/jackhmmer/", help="Uniprot output directory")
+@click.option("-s", "--sifts", default="/n/groups/marks/databases/SIFTS/", help="SIFTS output directory")
+@click.option("-d", "--db", default="/n/groups/marks/databases/jackhmmer/", help="Uniprot output directory")
 @click.option("-l", "--symlink", default=False, is_flag=True,
               help="Creates symlink with ending '_current.' pointing to the newly created db files")
 @click.option("-v", "--verbose", default=False, is_flag=True, help="Enables verbose output")