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Update openmmdlanalysis.py
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Adjusted to the new functions
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@talagayev
talagayev authored Jul 31, 2024
1 parent b7a34d3 commit aeaa9c7
Showing 1 changed file with 32 additions and 33 deletions.
65 changes: 32 additions & 33 deletions openmmdl/openmmdl_analysis/openmmdlanalysis.py
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Original file line number Diff line number Diff line change
Expand Up @@ -57,13 +57,10 @@
from openmmdl.openmmdl_analysis.markov_state_figure_generation import MarkovChainAnalysis

from openmmdl.openmmdl_analysis.rdkit_figure_generation import (
split_interaction_data,
highlight_numbers,
generate_interaction_dict,
update_dict,
create_and_merge_images,
arranged_figure_generation,
generate_ligand_image,
InteractionProcessor,
LigandImageGenerator,
FigureArranger,
ImageMerger,
)
from openmmdl.openmmdl_analysis.barcode_generation import (
BarcodeGenerator,
Expand Down Expand Up @@ -577,6 +574,7 @@ def main():
# Generate an Figure for each of the binding modes with rdkit Drawer with the atoms interacting highlighted by colors
try:
if peptide is None:
interaction_processor = InteractionProcessor("complex.pdb", "lig_no_h.pdb")
matplotlib.use("Agg")
binding_site = {}
merged_image_paths = []
Expand All @@ -594,7 +592,7 @@ def main():
)
# Generate 2D coordinates for the molecule
AllChem.Compute2DCoords(prepared_ligand)
split_data = split_interaction_data(values)
split_data = interaction_processor.split_interaction_data(values)
# Get the highlighted atom indices based on interaction type
(
highlighted_hbond_donor,
Expand All @@ -608,47 +606,47 @@ def main():
highlighted_pi,
highlighted_pication,
highlighted_metal,
) = highlight_numbers(split_data, starting_idx=lig_index)
) = interaction_processor.highlight_numbers(split_data, starting_idx=lig_index)

# Generate a dictionary for hydrogen bond acceptors
hbond_acceptor_dict = generate_interaction_dict(
hbond_acceptor_dict = interaction_processor.generate_interaction_dict(
"hbond_acceptor", highlighted_hbond_acceptor
)
# Generate a dictionary for hydrogen bond acceptors and donors
hbond_both_dict = generate_interaction_dict(
hbond_both_dict = interaction_processor.generate_interaction_dict(
"hbond_both", highlighted_hbond_both
)
# Generate a dictionary for hydrogen bond donors
hbond_donor_dict = generate_interaction_dict(
hbond_donor_dict = interaction_processor.generate_interaction_dict(
"hbond_donor", highlighted_hbond_donor
)
# Generate a dictionary for hydrophobic features
hydrophobic_dict = generate_interaction_dict(
hydrophobic_dict = interaction_processor.generate_interaction_dict(
"hydrophobic", highlighted_hydrophobic
)
# Generate a dictionary for water bridge interactions
waterbridge_dict = generate_interaction_dict(
waterbridge_dict = interaction_processor.generate_interaction_dict(
"waterbridge", highlighted_waterbridge
)
# Generate a dictionary for pistacking
pistacking_dict = generate_interaction_dict(
pistacking_dict = interaction_processor.generate_interaction_dict(
"pistacking", highlighted_pistacking
)
# Generate a dictionary for halogen interactions
halogen_dict = generate_interaction_dict("halogen", highlighted_halogen)
halogen_dict = interaction_processor.generate_interaction_dict("halogen", highlighted_halogen)
# Generate a dictionary for negative ionizables
ni_dict = generate_interaction_dict("ni", highlighted_ni)
ni_dict = interaction_processor.generate_interaction_dict("ni", highlighted_ni)
# Generate a dictionary for negative ionizables
pi_dict = generate_interaction_dict("pi", highlighted_pi)
pi_dict = interaction_processor.generate_interaction_dict("pi", highlighted_pi)
# Generate a dictionary for pication
pication_dict = generate_interaction_dict(
pication_dict = interaction_processor.generate_interaction_dict(
"pication", highlighted_pication
)
# Generate a dictionary for metal interactions
metal_dict = generate_interaction_dict("metal", highlighted_metal)
metal_dict = interaction_processor.generate_interaction_dict("metal", highlighted_metal)

# Call the function to update hbond_donor_dict with values from other dictionaries
update_dict(
interaction_processor.update_dict(
hbond_donor_dict,
hbond_acceptor_dict,
ni_dict,
Expand Down Expand Up @@ -699,21 +697,22 @@ def main():
)

# Generate the interactions legend and combine it with the ligand png
merged_image_paths = create_and_merge_images(
binding_mode, occurrence_percent, split_data, merged_image_paths
)
image_merger = ImageMerger(binding_mode, occurrence_percent, split_data, merged_image_paths)
merged_image_paths = image_merger.create_and_merge_images()

# Create Figure with all Binding modes
arranged_figure_generation(
merged_image_paths, "all_binding_modes_arranged.png"
)
generate_ligand_image(
ligand, "complex.pdb", "lig_no_h.pdb", "lig.smi", f"ligand_numbering.svg"
figure_arranger = FigureArranger(merged_image_paths, "all_binding_modes_arranged.png")
figure_arranger.arranged_figure_generation()

generator = LigandImageGenerator(
ligand,
"complex.pdb",
"lig_no_h.pdb",
"lig.smi",
f"ligand_numbering.svg",
fig_type
)
if fig_type == "png":
cairosvg.svg2png(
url=f"ligand_numbering.svg", write_to=f"ligand_numbering.png"
)
generator.generate_image()
print("\033[1mBinding mode figure generated\033[0m")
except Exception as e:
print(f"Ligand could not be recognized, use the -l option")
Expand Down

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