From f05e2baeefd645727211f66a27fba7e9d324dab8 Mon Sep 17 00:00:00 2001
From: Mark Driver <mdd31@alumni.cam.ac.uk>
Date: Tue, 16 Jun 2020 19:14:58 +0100
Subject: [PATCH] update CLI to allow option of polarised or unpolarised
solvent descriptions.
---
phasecalculator/phasecalculatorcli.py | 15 +++++++++++----
1 file changed, 11 insertions(+), 4 deletions(-)
diff --git a/phasecalculator/phasecalculatorcli.py b/phasecalculator/phasecalculatorcli.py
index 59921aa..259a0f8 100755
--- a/phasecalculator/phasecalculatorcli.py
+++ b/phasecalculator/phasecalculatorcli.py
@@ -135,7 +135,7 @@ def create_system_collection(args):
SystemCollection.
"""
- phases = read_phasecsv(args.phases)
+ phases = read_phasecsv(args.phases, args.unpolarised_ssips)
jar_path = args.jar
scratch_dir = args.scratch
output_dir = args.out_dir
@@ -216,13 +216,15 @@ def read_calculator_xml(xml_filename):
return sysproc.read_system_collection_file(xml_filename)
-def read_phasecsv(csv_filename):
+def read_phasecsv(csv_filename, unpolarised_ssips):
"""Read CSV file containing phase infomration and create Phases object.
Parameters
----------
csv_filename : str
phase information CSV file.
+ unpolarised_ssips : boolean
+ True if unpolarised SSIP descriptions are to be used.
Returns
-------
@@ -230,7 +232,7 @@ def read_phasecsv(csv_filename):
Phases representation of information.
"""
- return csvconv.convert_csv_file_to_phases(csv_filename)
+ return csvconv.convert_csv_file_to_phases(csv_filename, unpolarised_ssips)
def run_system_collection(system_collection, **kwargs):
@@ -372,7 +374,12 @@ Where systemcollection.xml was generated with inpgen. For large phase sets you n
"--filename", type=str, default="systemcollection.xml",
help="filename for XML file.",
)
- inpgen_argparser.set_defaults(func=process_inputgen)
+ ssip_desc = inpgen_argparser.add_mutually_exclusive_group(required=False)
+ ssip_desc.add_argument("--polarised", action="store_false", dest="unpolarised_ssips",
+ help="Use unpolarised SSIP descriptions in calculations")
+ ssip_desc.add_argument("--unpolarised", action="store_true", dest="unpolarised_ssips",
+ help="Use polarised SSIP descriptions in calculations")
+ inpgen_argparser.set_defaults(func=process_inputgen, unpolarised_ssips=False)
solvname_description = """Display acceptable solvent molecule names for inclusion in a phases csv file."""
solvnames_epilog = "Solvent molecule names:\n" + get_acceptable_solvent_names() + "\n"
solvent_nameparser = subparsers.add_parser(
--
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