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Addition for boolean flag inputs #200

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9d8db9e
Update openmmdlanalysis.py
talagayev Apr 6, 2026
a6a42a3
Update openmmdlsetup.py
talagayev Apr 7, 2026
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47 changes: 35 additions & 12 deletions openmmdl/openmmdl_analysis/openmmdlanalysis.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -65,6 +65,24 @@ def pushd(path: str):

_FLOAT_RE = re.compile(r"[-+]?\d*\.?\d+(?:[eE][-+]?\d+)?")

_TRUE_BOOL_VALUES = {"1", "true", "t", "yes", "y", "on"}
_FALSE_BOOL_VALUES = {"0", "false", "f", "no", "n", "off"}


def parse_bool_flag(value):
"""Parse flexible CLI boolean values like true/false, yes/no, y/n, 1/0."""
if isinstance(value, bool):
return value

normalized_value = str(value).strip().lower()
if normalized_value in _TRUE_BOOL_VALUES:
return True
if normalized_value in _FALSE_BOOL_VALUES:
return False

raise argparse.ArgumentTypeError(
"Boolean value expected. Use one of: true/false, yes/no, y/n, 1/0, on/off."
)

def parse_xyz(val):
"""
Expand Down Expand Up @@ -148,20 +166,23 @@ def main():
parser.add_argument(
"-p",
dest="generate_pml",
help="Generate .pml files for pharmacophore visualization",
help="Generate .pml files for pharmacophore visualization (accepts true/false, yes/no, y/n)",
default=False,
type=parse_bool_flag,
)
parser.add_argument(
"-r",
dest="frame_rmsd",
help='RMSD Difference between frames calculation type "True" to use it default is False,',
default="No",
help="Calculate RMSD differences between frames (accepts true/false, yes/no, y/n)",
default=False,
type=parse_bool_flag,
)
parser.add_argument(
"-nuc",
dest="receptor_nucleic",
help="Treat nucleic acids as receptor",
help="Treat nucleic acids as receptor (accepts true/false, yes/no, y/n)",
default=False,
type=parse_bool_flag,
)
parser.add_argument(
"-s",
Expand All @@ -184,14 +205,16 @@ def main():
parser.add_argument(
"-w",
dest="stable_water_analysis",
help="Should stable water analysis be performed? True or False",
help="Should stable water analysis be performed? (accepts true/false, yes/no, y/n)",
default=False,
type=parse_bool_flag,
)
parser.add_argument(
"-rep",
dest="representative_frame",
help="Calculate the representative frame for each binding mode. Defaults to False",
help="Calculate the representative frame for each binding mode (accepts true/false, yes/no, y/n)",
default=False,
type=parse_bool_flag,
)
parser.add_argument(
"--watereps",
Expand Down Expand Up @@ -270,7 +293,7 @@ def main():
W.write(u.atoms)
pdb_md = mda.Universe(topology, trajectory)
water_eps = float(args.water_eps)
stable_water_analysis = bool(args.stable_water_analysis)
stable_water_analysis = args.stable_water_analysis
if stable_water_analysis:
stable_water_analyser = StableWaters(trajectory, topology, water_eps)

Expand All @@ -290,8 +313,8 @@ def main():
dataframe = args.dataframe
min_transition = int(args.min_transition)
cpu_count = int(args.cpu_count)
generate_pml = bool(args.generate_pml)
receptor_nucleic = bool(args.receptor_nucleic)
generate_pml = args.generate_pml
receptor_nucleic = args.receptor_nucleic
special_ligand = args.special_ligand
reference = args.reference
peptide = args.peptide
Expand Down Expand Up @@ -380,7 +403,7 @@ def main():
selection1="nucleicbackbone",
selection2=["nucleic", f"resname {ligand}"],
)
if frame_rmsd != "No":
if frame_rmsd:
pairwise_rmsd_prot, pairwise_rmsd_lig = rmsd_analyzer.rmsd_dist_frames(
fig_type, lig=f"{ligand}", nucleic=True
)
Expand All @@ -391,7 +414,7 @@ def main():
selection1="backbone",
selection2=["protein", f"chainID {peptide}"],
)
if frame_rmsd != "No":
if frame_rmsd:
pairwise_rmsd_prot, pairwise_rmsd_lig = rmsd_analyzer.rmsd_dist_frames(fig_type, lig=f"chainID {peptide}")
logger.info("\033[1mRMSD calculated\033[0m")
else:
Expand All @@ -400,7 +423,7 @@ def main():
selection1="backbone",
selection2=["protein", f"resname {ligand}"],
)
if frame_rmsd != "No":
if frame_rmsd:
pairwise_rmsd_prot, pairwise_rmsd_lig = rmsd_analyzer.rmsd_dist_frames(fig_type, lig=f"{ligand}")
logger.info("\033[1mRMSD calculated\033[0m")

Expand Down
44 changes: 22 additions & 22 deletions openmmdl/openmmdl_setup/openmmdlsetup.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -423,7 +423,7 @@ def createAmberBashScript():
)
elif nmLigFile[-4:] == ".pdb":
a_script.append(
"obabel ${nmLigFile}.pdb -O ${nmLigFile}.sdf -p # convert to sdf file for openmmdl_analysis, -p: add hydrogens appropriate for pH7.4"
"obabel ${nmLigFile}.pdb -O ${nmLigFile}.sdf -p # convert to sdf file for openmmdl analysis, -p: add hydrogens appropriate for pH7.4"
)

a_script.append(
Expand Down Expand Up @@ -691,7 +691,7 @@ def createAmberBashScript():
def extractLigName(lig_file_name):
"""
Extract the ligand name from the pdb file as a string, which is the fourth column of the first line in the pdb file.
This string can be used for openmmdl_analysis in later function `createScript`.
This string can be used for openmmdl analysis in later function `createScript`.

Params:
-------
Expand Down Expand Up @@ -1873,11 +1873,11 @@ def _xml_script_segment(to_serialize, target_file):
if fileType == "pdb":
if has_pdb_ligands:
script.append(
f"analysis_jobs.append(('Final_Output/All_Atoms', f'openmmdl_analysis -t centered_top{top_ext} -d centered_traj{traj_ext} -l {{ligands[0]}} -n {{ligand_names[0]}}{{analysis_special_flags}} -b {session['binding_mode']} -m {session['min_transition']} -r {session['rmsd_diff']} -p {session['pml_generation']} -w {session['stable_water']} --watereps {session['wc_distance']}'))"
f"analysis_jobs.append(('Final_Output/All_Atoms', f'openmmdl analysis -t centered_top{top_ext} -d centered_traj{traj_ext} -l {{ligands[0]}} -n {{ligand_names[0]}}{{analysis_special_flags}} -b {session['binding_mode']} -m {session['min_transition']} -r {session['rmsd_diff']} -p {session['pml_generation']} -w {session['stable_water']} --watereps {session['wc_distance']}'))"
)
elif not has_pdb_ligands:
script.append(
"analysis_jobs.append(('Final_Output/All_Atoms', 'openmmdl_analysis -t centered_top%s -d centered_traj%s -b %s -m %s -r %s -p %s -w %s --watereps %s'))"
"analysis_jobs.append(('Final_Output/All_Atoms', 'openmmdl analysis -t centered_top%s -d centered_traj%s -b %s -m %s -r %s -p %s -w %s --watereps %s'))"
% (
top_ext,
traj_ext,
Expand All @@ -1892,7 +1892,7 @@ def _xml_script_segment(to_serialize, target_file):
elif fileType == "amber":
if not session["nmLig"] and not session["spLig"]:
script.append(
"analysis_jobs.append(('Final_Output/All_Atoms', 'openmmdl_analysis -t centered_top%s -d centered_traj%s -b %s -m %s -r %s -p %s -w %s --watereps %s'))"
"analysis_jobs.append(('Final_Output/All_Atoms', 'openmmdl analysis -t centered_top%s -d centered_traj%s -b %s -m %s -r %s -p %s -w %s --watereps %s'))"
% (
top_ext,
traj_ext,
Expand All @@ -1906,7 +1906,7 @@ def _xml_script_segment(to_serialize, target_file):
)
elif session["nmLig"] and not session["spLig"]:
script.append(
"analysis_jobs.append(('Final_Output/All_Atoms', 'openmmdl_analysis -t centered_top%s -d centered_traj%s -n %s -b %s -m %s -r %s -p %s -w %s --watereps %s'))"
"analysis_jobs.append(('Final_Output/All_Atoms', 'openmmdl analysis -t centered_top%s -d centered_traj%s -n %s -b %s -m %s -r %s -p %s -w %s --watereps %s'))"
% (
top_ext,
traj_ext,
Expand All @@ -1921,7 +1921,7 @@ def _xml_script_segment(to_serialize, target_file):
)
elif session["nmLig"] and session["spLig"]:
script.append(
"analysis_jobs.append(('Final_Output/All_Atoms', 'openmmdl_analysis -t centered_top%s -d centered_traj%s -n %s -s %s -b %s -m %s -r %s -p %s -w %s --watereps %s'))"
"analysis_jobs.append(('Final_Output/All_Atoms', 'openmmdl analysis -t centered_top%s -d centered_traj%s -n %s -s %s -b %s -m %s -r %s -p %s -w %s --watereps %s'))"
% (
top_ext,
traj_ext,
Expand All @@ -1940,11 +1940,11 @@ def _xml_script_segment(to_serialize, target_file):
if fileType == "pdb":
if has_pdb_ligands:
script.append(
f"analysis_jobs.append(('Final_Output/Prot_Lig', f'openmmdl_analysis -t prot_lig_top{top_ext} -d prot_lig_traj{traj_ext} -l {{ligands[0]}} -n {{ligand_names[0]}}{{analysis_special_flags}} -b {session['binding_mode']} -m {session['min_transition']} -r {session['rmsd_diff']} -p {session['pml_generation']} -w {session['stable_water']} --watereps {session['wc_distance']}'))"
f"analysis_jobs.append(('Final_Output/Prot_Lig', f'openmmdl analysis -t prot_lig_top{top_ext} -d prot_lig_traj{traj_ext} -l {{ligands[0]}} -n {{ligand_names[0]}}{{analysis_special_flags}} -b {session['binding_mode']} -m {session['min_transition']} -r {session['rmsd_diff']} -p {session['pml_generation']} -w {session['stable_water']} --watereps {session['wc_distance']}'))"
)
elif not has_pdb_ligands:
script.append(
"analysis_jobs.append(('Final_Output/Prot_Lig', 'openmmdl_analysis -t prot_lig_top%s -d prot_lig_traj%s -b %s -m %s -r %s -p %s -w %s --watereps %s'))"
"analysis_jobs.append(('Final_Output/Prot_Lig', 'openmmdl analysis -t prot_lig_top%s -d prot_lig_traj%s -b %s -m %s -r %s -p %s -w %s --watereps %s'))"
% (
top_ext,
traj_ext,
Expand All @@ -1959,7 +1959,7 @@ def _xml_script_segment(to_serialize, target_file):
elif fileType == "amber":
if not session["nmLig"] and not session["spLig"]:
script.append(
"analysis_jobs.append(('Final_Output/Prot_Lig', 'openmmdl_analysis -t prot_lig_top%s -d prot_lig_traj%s -b %s -m %s -r %s -p %s -w %s --watereps %s'))"
"analysis_jobs.append(('Final_Output/Prot_Lig', 'openmmdl analysis -t prot_lig_top%s -d prot_lig_traj%s -b %s -m %s -r %s -p %s -w %s --watereps %s'))"
% (
top_ext,
traj_ext,
Expand All @@ -1973,7 +1973,7 @@ def _xml_script_segment(to_serialize, target_file):
)
elif session["nmLig"] and not session["spLig"]:
script.append(
"analysis_jobs.append(('Final_Output/Prot_Lig', 'openmmdl_analysis -t prot_lig_top%s -d prot_lig_traj%s -n %s -b %s -m %s -r %s -p %s -w %s --watereps %s'))"
"analysis_jobs.append(('Final_Output/Prot_Lig', 'openmmdl analysis -t prot_lig_top%s -d prot_lig_traj%s -n %s -b %s -m %s -r %s -p %s -w %s --watereps %s'))"
% (
top_ext,
traj_ext,
Expand All @@ -1988,7 +1988,7 @@ def _xml_script_segment(to_serialize, target_file):
)
elif session["nmLig"] and session["spLig"]:
script.append(
"analysis_jobs.append(('Final_Output/Prot_Lig', 'openmmdl_analysis -t prot_lig_top%s -d prot_lig_traj%s -n %s -s %s -b %s -m %s -r %s -p %s -w %s --watereps %s'))"
"analysis_jobs.append(('Final_Output/Prot_Lig', 'openmmdl analysis -t prot_lig_top%s -d prot_lig_traj%s -n %s -s %s -b %s -m %s -r %s -p %s -w %s --watereps %s'))"
% (
top_ext,
traj_ext,
Expand All @@ -2007,14 +2007,14 @@ def _xml_script_segment(to_serialize, target_file):
if fileType == "pdb":
if has_pdb_ligands:
script.append(
f"analysis_jobs.append(('Final_Output/All_Atoms', f'openmmdl_analysis -t centered_top{top_ext} -d centered_traj{traj_ext} -l {{ligands[0]}} -n {{ligand_names[0]}}{{analysis_special_flags}} -b {session['binding_mode']} -m {session['min_transition']} -r {session['rmsd_diff']} -p {session['pml_generation']} -w {session['stable_water']} --watereps {session['wc_distance']}'))"
f"analysis_jobs.append(('Final_Output/All_Atoms', f'openmmdl analysis -t centered_top{top_ext} -d centered_traj{traj_ext} -l {{ligands[0]}} -n {{ligand_names[0]}}{{analysis_special_flags}} -b {session['binding_mode']} -m {session['min_transition']} -r {session['rmsd_diff']} -p {session['pml_generation']} -w {session['stable_water']} --watereps {session['wc_distance']}'))"
)
script.append(
f"analysis_jobs.append(('Final_Output/Prot_Lig', f'openmmdl_analysis -t prot_lig_top{top_ext} -d prot_lig_traj{traj_ext} -l {{ligands[0]}} -n {{ligand_names[0]}}{{analysis_special_flags}} -b {session['binding_mode']} -m {session['min_transition']} -r {session['rmsd_diff']} -p {session['pml_generation']} -w {session['stable_water']} --watereps {session['wc_distance']}'))"
f"analysis_jobs.append(('Final_Output/Prot_Lig', f'openmmdl analysis -t prot_lig_top{top_ext} -d prot_lig_traj{traj_ext} -l {{ligands[0]}} -n {{ligand_names[0]}}{{analysis_special_flags}} -b {session['binding_mode']} -m {session['min_transition']} -r {session['rmsd_diff']} -p {session['pml_generation']} -w {session['stable_water']} --watereps {session['wc_distance']}'))"
)
elif not has_pdb_ligands:
script.append(
"analysis_jobs.append(('Final_Output/All_Atoms', 'openmmdl_analysis -t centered_top%s -d centered_traj%s -b %s -m %s -r %s -p %s -w %s --watereps %s'))"
"analysis_jobs.append(('Final_Output/All_Atoms', 'openmmdl analysis -t centered_top%s -d centered_traj%s -b %s -m %s -r %s -p %s -w %s --watereps %s'))"
% (
top_ext,
traj_ext,
Expand All @@ -2027,7 +2027,7 @@ def _xml_script_segment(to_serialize, target_file):
)
)
script.append(
"analysis_jobs.append(('Final_Output/Prot_Lig', 'openmmdl_analysis -t prot_lig_top%s -d prot_lig_traj%s -b %s -m %s -r %s -p %s -w %s --watereps %s'))"
"analysis_jobs.append(('Final_Output/Prot_Lig', 'openmmdl analysis -t prot_lig_top%s -d prot_lig_traj%s -b %s -m %s -r %s -p %s -w %s --watereps %s'))"
% (
top_ext,
traj_ext,
Expand All @@ -2042,7 +2042,7 @@ def _xml_script_segment(to_serialize, target_file):
elif fileType == "amber":
if not session["nmLig"] and not session["spLig"]:
script.append(
"analysis_jobs.append(('Final_Output/All_Atoms', 'openmmdl_analysis -t centered_top%s -d centered_traj%s -b %s -m %s -r %s -p %s -w %s --watereps %s'))"
"analysis_jobs.append(('Final_Output/All_Atoms', 'openmmdl analysis -t centered_top%s -d centered_traj%s -b %s -m %s -r %s -p %s -w %s --watereps %s'))"
% (
top_ext,
traj_ext,
Expand All @@ -2055,7 +2055,7 @@ def _xml_script_segment(to_serialize, target_file):
)
)
script.append(
"analysis_jobs.append(('Final_Output/Prot_Lig', 'openmmdl_analysis -t prot_lig_top%s -d prot_lig_traj%s -b %s -m %s -r %s -p %s -w %s --watereps %s'))"
"analysis_jobs.append(('Final_Output/Prot_Lig', 'openmmdl analysis -t prot_lig_top%s -d prot_lig_traj%s -b %s -m %s -r %s -p %s -w %s --watereps %s'))"
% (
top_ext,
traj_ext,
Expand All @@ -2069,7 +2069,7 @@ def _xml_script_segment(to_serialize, target_file):
)
elif session["nmLig"] and not session["spLig"]:
script.append(
"analysis_jobs.append(('Final_Output/All_Atoms', 'openmmdl_analysis -t centered_top%s -d centered_traj%s -n %s -b %s -m %s -r %s -p %s -w %s --watereps %s'))"
"analysis_jobs.append(('Final_Output/All_Atoms', 'openmmdl analysis -t centered_top%s -d centered_traj%s -n %s -b %s -m %s -r %s -p %s -w %s --watereps %s'))"
% (
top_ext,
traj_ext,
Expand All @@ -2083,7 +2083,7 @@ def _xml_script_segment(to_serialize, target_file):
)
)
script.append(
"analysis_jobs.append(('Final_Output/Prot_Lig', 'openmmdl_analysis -t prot_lig_top%s -d prot_lig_traj%s -n %s -b %s -m %s -r %s -p %s -w %s --watereps %s'))"
"analysis_jobs.append(('Final_Output/Prot_Lig', 'openmmdl analysis -t prot_lig_top%s -d prot_lig_traj%s -n %s -b %s -m %s -r %s -p %s -w %s --watereps %s'))"
% (
top_ext,
traj_ext,
Expand All @@ -2098,7 +2098,7 @@ def _xml_script_segment(to_serialize, target_file):
)
elif session["nmLig"] and session["spLig"]:
script.append(
"analysis_jobs.append(('Final_Output/All_Atoms', 'openmmdl_analysis -t centered_top%s -d centered_traj%s -n %s -s %s -b %s -m %s -r %s -p %s -w %s --watereps %s'))"
"analysis_jobs.append(('Final_Output/All_Atoms', 'openmmdl analysis -t centered_top%s -d centered_traj%s -n %s -s %s -b %s -m %s -r %s -p %s -w %s --watereps %s'))"
% (
top_ext,
traj_ext,
Expand All @@ -2113,7 +2113,7 @@ def _xml_script_segment(to_serialize, target_file):
)
)
script.append(
"analysis_jobs.append(('Final_Output/Prot_Lig', 'openmmdl_analysis -t prot_lig_top%s -d prot_lig_traj%s -n %s -s %s -b %s -m %s -r %s -p %s -w %s --watereps %s'))"
"analysis_jobs.append(('Final_Output/Prot_Lig', 'openmmdl analysis -t prot_lig_top%s -d prot_lig_traj%s -n %s -s %s -b %s -m %s -r %s -p %s -w %s --watereps %s'))"
% (
top_ext,
traj_ext,
Expand Down
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