scfix behaviour change

bin/martinize2

@@ -53,6 +53,7 @@ from vermouth.rcsu.contact_map import read_go_map
 from vermouth.rcsu.go_pipeline import GoPipeline
 from vermouth.citation_parser import citation_formatter
 from vermouth.gmx.topology import write_gmx_topology
+from operator import not_
 
 # TODO Since vermouth's __init__.py does some logging (KDTree), this may or may
 # not work as intended. Investigation required.
@@ -625,12 +626,19 @@ def entry():
 
 
     prot_group = parser.add_argument_group("Protein description")
+    prot_group.add_argument(
+        "-noscfix",
+        dest="noscfix",
+        action="store_true",
+        default=False,
+        help="Don't apply side chain corrections. Please note the change in behaviour from martinize v0.11.0",
+    )
     prot_group.add_argument(
         "-scfix",
         dest="scfix",
-        action="store_false",
-        default=True,
-        help="[don't] apply side chain corrections.",
+        action="store_true",
+        help="Old -scfix argument. Side chain fixes are now assumed by default, and the flag does not need"
+             " to be specified. Will be depreciated in future."
     )
     prot_group.add_argument(
         "-cys",
@@ -923,14 +931,23 @@ def entry():
             type="missing-feature",
         )
     vermouth.SetMoleculeMeta(extdih=args.extdih).run_system(system)
-    if args.scfix and not target_ff.has_feature("scfix"):
+    if args.scfix:
+        LOGGER.warning(
+            "The scfix argument has been depreciated and will be removed in future. "
+            "Side chain fixing is now assumed by default, so no flag needs to be "
+            "passed. If you do not want side chain fixes to be applied, the -noscfix "
+            "flag can be used."
+        )
+    scfix = not_(args.noscfix)
+    if scfix and not target_ff.has_feature("scfix"):
         LOGGER.warning(
             'The force field "{}" does not define angle and '
-            "torsion for the side chain corrections (-scfix).",
+            "torsion for the side chain corrections."
+            " If intended, please specify -noscfix explicitly",
             target_ff.name,
             type="missing-feature",
         )
-    vermouth.SetMoleculeMeta(scfix=args.scfix).run_system(system)
+    vermouth.SetMoleculeMeta(scfix=scfix).run_system(system)
 
     vermouth.SetMoleculeMeta(idr=args.idr_tune).run_system(system)
     if args.idr_tune:

vermouth/tests/data/integration_tests/tier-0/dipro-termini/martinize2/command

@@ -4,4 +4,4 @@ martinize2
 -o topol.top
 -ff martini3001
 -nt
--scfix
+-noscfix

vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/martinize2/command

@@ -5,4 +5,4 @@ martinize2
 -ff martini22
 -dssp
 -cys auto
--scfix
+-noscfix

vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/martinize2/command

@@ -7,4 +7,4 @@ martinize2
 -nter NH2-ter
 -cter COOH-ter
 -ef 500
--scfix
+-noscfix

vermouth/tests/data/integration_tests/tier-0/mini-protein3_trp-cage/martinize2/command

@@ -6,4 +6,4 @@ martinize2
 -dssp 
 -eu 0.7
 -ef 800.0
--scfix
+-noscfix

vermouth/tests/data/integration_tests/tier-1/bpti/martinize2/command

@@ -9,5 +9,5 @@ martinize2
 -ep 2
 -modify A-ASP50:ASP-HD2
 -ignore HOH
--scfix
+-noscfix
 -ef 500

vermouth/tests/data/integration_tests/tier-1/hst5/martinize2/command

@@ -8,4 +8,4 @@ martinize2
 -water-bias-eps idr:0.5
 -id-regions 1:24
 -idr-tune
--scfix
+-noscfix

vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/command

@@ -10,5 +10,5 @@ martinize2
 -eu 0.85
 -water-bias
 -water-bias-eps E:-.5 C:1.0 H:-1.0
--scfix
+-noscfix
 -cys none

vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/command

@@ -6,5 +6,5 @@ martinize2
 -ignore HOH 
 -ss CBCCHHHHHHHHHHTTCTTBTTBCHHHHHHHHHHHHTTBTTCEEECTTSCEEETTTTEETTTTCBCSCCTTCCCTTCSBGGGGGSSSCHHHHHHHHHHHHTSSGGGGSHHHHHHTTTSCGGGGGTTCCC 
 -go ../map.map 
--scfix
+-noscfix
 -cys none

vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/command

@@ -8,5 +8,5 @@ martinize2
 -go ../map.map 
 -water-bias
 -water-bias-eps E:-.5 C:1.0 H:-1.0
--scfix
+-noscfix
 -cys none

vermouth/tests/data/integration_tests/tier-1/villin/martinize2/command

@@ -5,4 +5,4 @@ martinize2
 -ff martini22p
 -mutate A-MET53:VAL
 -resid input
--scfix
+-noscfix

vermouth/tests/test_name_moltype.py

@@ -150,7 +150,7 @@ def test_martinize2_moltypes(tmp_path, deduplicate):
         '-f', str(PDB_HB),
         '-o', 'topol.top',
         '-x', 'out.pdb',
-        '-ignore', 'HOH', '-ignore', 'HEME', '-scfix',
+        '-ignore', 'HOH', '-ignore', 'HEME', '-noscfix',
     ]
     if deduplicate:
         expected = ['molecule_{}.itp'.format(i) for i in range(2)]