From 8c1060b312e34ad16079065ed8e421ce33a394fb Mon Sep 17 00:00:00 2001 From: Erik Poppleton Date: Wed, 11 Dec 2024 22:51:45 +0100 Subject: [PATCH] update all forces converters to use the word 'forces' instead some using 'force' --- analysis/oat-completion.sh | 2 +- .../src/oxDNA_analysis_tools/{db_to_force.py => db2forces.py} | 2 +- .../{generate_force.py => generate_forces.py} | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) rename analysis/src/oxDNA_analysis_tools/{db_to_force.py => db2forces.py} (99%) rename analysis/src/oxDNA_analysis_tools/{generate_force.py => generate_forces.py} (98%) diff --git a/analysis/oat-completion.sh b/analysis/oat-completion.sh index 371baa65a..7dfb6f683 100755 --- a/analysis/oat-completion.sh +++ b/analysis/oat-completion.sh @@ -8,7 +8,7 @@ _oat_completions(){ fi - COMPREPLY=($(compgen -W "align anm_parameterize backbone_flexibility bond_analysis centroid clustering config contact_map db_to_force decimate deviations distance duplex_angle_plotter duplex_finder file_info forces2pairs generate_force mean minify multidimensional_scaling_mean output_bonds oxDNA_PDB pca persistence_length plot_energy subset_trajectory superimpose" "${COMP_WORDS[COMP_CWORD]}")) + COMPREPLY=($(compgen -W "align anm_parameterize backbone_flexibility bond_analysis centroid clustering config contact_map db2forces decimate deviations distance duplex_angle_plotter duplex_finder file_info forces2pairs generate_forces mean minify multidimensional_scaling_mean output_bonds oxDNA_PDB pca persistence_length plot_energy subset_trajectory superimpose" "${COMP_WORDS[COMP_CWORD]}")) } complete -F _oat_completions oat diff --git a/analysis/src/oxDNA_analysis_tools/db_to_force.py b/analysis/src/oxDNA_analysis_tools/db2forces.py similarity index 99% rename from analysis/src/oxDNA_analysis_tools/db_to_force.py rename to analysis/src/oxDNA_analysis_tools/db2forces.py index d8d292d3d..c2e12d7bc 100755 --- a/analysis/src/oxDNA_analysis_tools/db_to_force.py +++ b/analysis/src/oxDNA_analysis_tools/db2forces.py @@ -83,7 +83,7 @@ def db_to_forcelist(db_str:str, stiff:float, reverse:bool, r0:float=1.2, PBC:boo return force_list -def cli_parser(prog="db_to_force.py"): +def cli_parser(prog="db2forces.py"): parser = argparse.ArgumentParser(prog = prog, description="Create an external forces file enforcing the current base-pairing arrangement") parser.add_argument('db_file', type=str, nargs=1, help="A text file containing dot-bracket notation of the base-pairing arrangement") parser.add_argument('-o', '--output', type=str, nargs=1, help='Name of the file to write the force list to') diff --git a/analysis/src/oxDNA_analysis_tools/generate_force.py b/analysis/src/oxDNA_analysis_tools/generate_forces.py similarity index 98% rename from analysis/src/oxDNA_analysis_tools/generate_force.py rename to analysis/src/oxDNA_analysis_tools/generate_forces.py index 9740b3194..8aa0a5646 100755 --- a/analysis/src/oxDNA_analysis_tools/generate_force.py +++ b/analysis/src/oxDNA_analysis_tools/generate_forces.py @@ -3,7 +3,7 @@ from oxDNA_analysis_tools.UTILS.logger import log, logger_settings import oxpy -def cli_parser(prog="generate_force.py"): +def cli_parser(prog="generate_forces.py"): parser = argparse.ArgumentParser(prog = prog, description="Create an external forces file enforcing the current base-pairing arrangement") parser.add_argument('inputfile', type=str, nargs=1, help="The inputfile used to run the simulation") parser.add_argument('configuration', type=str, nargs=1, help="The configuration to generate the forces from")