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update plddt
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@minh-biocommons
minh-biocommons committed Sep 26, 2024
1 parent 11cdda4 commit 5251c21
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Showing 2 changed files with 50 additions and 15 deletions.
17 changes: 11 additions & 6 deletions assets/proteinfold_template.html
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Original file line number Diff line number Diff line change
Expand Up @@ -315,12 +315,12 @@ <h1 class="text-4xl md:text-5xl font-bold tracking-tight text-white">Structure p
<div>
<div class="text-2xl font-bold tracking-tight text-gray-900">Information</div>
<!-- Structure information -->
<div
id="structure-info"
class="mt-2 mb-6 shadow-md p-6 bg-white rounded border flex justify-between font-semibold"
>
<div>Program: <span class="font-normal">*prog_name*</span></div>
<div>ID: <span class="font-normal">*sample_name*</span></div>
<div id="structure-info" class="mt-2 mb-6 shadow-md p-6 bg-white rounded border font-semibold">
<div class="flex justify-between">
<div>Program: <span class="font-normal">*prog_name*</span></div>
<div>ID: <span class="font-normal">*sample_name*</span></div>
</div>
<div>Average: <span id="lddt-average" class="font-normal"></span></div>
</div>

<div>
Expand Down Expand Up @@ -602,6 +602,8 @@ <h1 class="text-4xl md:text-5xl font-bold tracking-tight text-white">Structure p
"coverage_LDDT_4.png",
];

const LDDT_AVERAGES = [];

const REPRESENTATIONS = ["cartoon", "ball+stick", "surface", "backbone"];

const DEFAULT_REPRESENTATION = REPRESENTATIONS[0];
Expand Down Expand Up @@ -634,6 +636,8 @@ <h1 class="text-4xl md:text-5xl font-bold tracking-tight text-white">Structure p
// Handle window resizing
window.addEventListener("resize", () => stage.handleResize());

document.getElementById("lddt-average").textContent = LDDT_AVERAGES[0];

loadModel();
loadModelImage();
generateButtons();
Expand All @@ -654,6 +658,7 @@ <h1 class="text-4xl md:text-5xl font-bold tracking-tight text-white">Structure p
const setModel = (ix) => {
state.model = ix;
//document.getElementById("lddt_img").src = LDDT_IMGS[ix];
document.getElementById("lddt-average").textContent = LDDT_AVERAGES[ix];
stage.removeComponent(state.modelObject);
setLoading(1);

Expand Down
48 changes: 39 additions & 9 deletions bin/generat_plots.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,6 @@
import plotly.graph_objects as go
from plotly.subplots import make_subplots
import re

#from Bio import PDB

def generate_output_images(msa_path, plddt_paths, name, out_dir, in_type):
Expand Down Expand Up @@ -110,7 +109,7 @@ def generate_output_images(msa_path, plddt_paths, name, out_dir, in_type):
y=value_plddt,
mode='lines',
name=rank_label,
text=[f"Position {i}: {value:.2f}" for i, value in enumerate(value_plddt)],
text=[f"({i}, {value:.2f})" for i, value in enumerate(value_plddt)],
hoverinfo='text'
))
fig.update_layout(
Expand Down Expand Up @@ -168,7 +167,6 @@ def generate_output_images(msa_path, plddt_paths, name, out_dir, in_type):
plt.savefig(f"{out_dir}/{name+('_' if name else '')}PAE.png")
"""
##################################################################


def generate_plots(msa_path, plddt_paths, name, out_dir):
msa = []
Expand Down Expand Up @@ -263,11 +261,42 @@ def align_structures(structures):
return aligned_structures
"""

def pdb_to_lddt(pdb_files):
output_files = []
averages = []

for pdb_file in pdb_files:
output_file = f"{pdb_file.replace('.pdb', '')}_plddt.tsv"
output_files.append(output_file)

plddt_values = []
seen_lines = set()

with open(pdb_file, 'r') as infile:
for line in infile:
columns = line.split()
if len(columns) >= 11:
key = f"{columns[5]}\t{columns[10]}"
if key not in seen_lines:
seen_lines.add(key)
plddt_values.append(float(columns[10]))

# Calculate the average PLDDT value for the current file
if plddt_values:
avg_plddt = sum(plddt_values) / len(plddt_values)
averages.append(avg_plddt)
else:
averages.append(0.0)

with open(output_file, 'w') as outfile:
outfile.write("\t".join(map(str, plddt_values)) + "\n")

return output_files, averages

print("Starting..")
parser = argparse.ArgumentParser()
parser.add_argument('--type', dest='in_type')
parser.add_argument('--msa', dest='msa',required=True)
parser.add_argument('--plddt', dest='plddt',required=True, nargs="+")
parser.add_argument('--pdb', dest='pdb',required=True, nargs="+")
parser.add_argument('--name', dest='name')
parser.add_argument('--output_dir',dest='output_dir')
Expand All @@ -277,9 +306,9 @@ def align_structures(structures):
parser.set_defaults(name='')
args = parser.parse_args()

lddt_files, lddt_averages = pdb_to_lddt(args.pdb)

generate_output_images(args.msa, args.plddt, args.name, args.output_dir, args.in_type)

generate_output_images(args.msa, lddt_files, args.name, args.output_dir, args.in_type)
#generate_plots(args.msa, args.plddt, args.name, args.output_dir)

print("generating html report...")
Expand All @@ -299,17 +328,17 @@ def align_structures(structures):
alphafold_template = alphafold_template.replace(f"*sample_name*", args.name)
alphafold_template = alphafold_template.replace(f"*prog_name*", args.in_type)

# Convert the Python pdb args list to a JavaScript array format
args_pdb_array_js = ",\n".join([f'"{model}"' for model in structures])

# Use regex to find and replace the MODELS array in the HTML file
alphafold_template = re.sub(
r'const MODELS = \[.*?\];', # Match the existing MODELS array in HTML template
f'const MODELS = [\n {args_pdb_array_js}\n];', # Replace with the new array
alphafold_template,
flags=re.DOTALL,
)

averages_js_array = f"const LDDT_AVERAGES = {lddt_averages};"
alphafold_template = alphafold_template.replace("const LDDT_AVERAGES = [];", averages_js_array)

i = 0
for structure in aligned_structures:
alphafold_template = alphafold_template.replace(f"*_data_ranked_{i}.pdb*", open(structure, "r").read().replace("\n", "\\n"))
Expand Down Expand Up @@ -352,5 +381,6 @@ def align_structures(structures):
alphafold_template = alphafold_template.replace(f"coverage_LDDT_{i}.png", f"{in_file.read()}")
"""

with open(f"{args.output_dir}/{args.name}_{args.in_type}_report.html", "w") as out_file:
out_file.write(alphafold_template)

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