From 6f42f355135fc90183028743f5df87d5294eaeef Mon Sep 17 00:00:00 2001
From: James Graham <j.graham@soton.ac.uk>
Date: Wed, 17 Mar 2021 21:15:00 +0000
Subject: [PATCH] refactor: add warning that backmap is experimental
Also remove unused --map-only CLI option
---
docs/source/index.rst | 1 -
pycgtool/__main__.py | 17 ++++++++++-------
2 files changed, 10 insertions(+), 8 deletions(-)
diff --git a/docs/source/index.rst b/docs/source/index.rst
index fc11bdb..9050812 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -165,7 +165,6 @@ Option Description Values
output_name Base name of output files **out**, any string
output Coordinate output format **gro**
output_xtc Should a pseudo-CG XTC be created **False**, True
-map_only Run in mapping-only mode **False**, True
map_center Mapping method **geom**, mass
virtual_map_center Virtual site mapping method **geom**, mass
constr_threshold Convert stiff bonds to constraints over **100000**, any number
diff --git a/pycgtool/__main__.py b/pycgtool/__main__.py
index b2b589c..77f770a 100755
--- a/pycgtool/__main__.py
+++ b/pycgtool/__main__.py
@@ -168,8 +168,6 @@ def parse_arguments(arg_list):
# Mapping options
mapping_options = parser.add_argument_group("mapping options")
- mapping_options.add_argument("--map-only", '--no-map-only', default=False, action=BooleanAction,
- help="Run in mapping-only mode?")
mapping_options.add_argument("--map-center", default="geom",
choices=["geom", "mass", "first"],
help="Mapping method")
@@ -182,7 +180,7 @@ def parse_arguments(arg_list):
# Bond options
bond_options = parser.add_argument_group("bond options")
- bond_options.add_argument("--constr_threshold", type=float, default=100000,
+ bond_options.add_argument("--constr-threshold", type=float, default=100000,
help="Convert bonds with force constants over [value] to constraints")
bond_options.add_argument("--temperature", type=float, default=310,
help="Temperature of reference simulation")
@@ -227,12 +225,17 @@ def validate_arguments(args):
"""
if not args.dump_measurements:
args.dump_measurements = bool(args.bondset) and not bool(args.mapping)
-
- if not args.map_only:
- args.map_only = not bool(args.bondset)
+ logger.info(
+ 'Argument --dump-measurements has been set because you have provided a bondset but no mapping'
+ )
if not args.mapping and not args.bondset:
- raise ArgumentValidationError("One or both of -m and -b is required.")
+ raise ArgumentValidationError('One or both of -m and -b is required')
+
+ if args.backmapper_resname:
+ logger.warning(
+ 'Backmapping is an experimental feature and has not yet been fully validated'
+ )
return args
--
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