init

.gitignore

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+data

.gitmodules

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+[submodule "modules/proscope"]
+	path = modules/proscope
+	url = [email protected]:fuxialexander/proscope.git

Dockerfile

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+# Use an official miniconda3 as a parent image
+FROM mambaorg/micromamba
+
+# Set the working directory in the container to /app
+WORKDIR /app
+
+
+# Create a new environment using mamba with specified packages
+RUN micromamba install -n base -c conda-forge -c bioconda -y python=3.10 git pip biopython nglview tqdm matplotlib pandas xmlschema seaborn numpy py3Dmol 
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+# Activate the environment and install additional packages via pip
+RUN pip3 install gradio 
+
+USER root
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    git \
+    ssh \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+USER $MAMBA_USER
+
+# copy modules from local to container
+COPY --chown=$MAMBA_USER:$MAMBA_USER modules /app/modules
+
+# copy modules from local to container
+COPY --chown=$MAMBA_USER:$MAMBA_USER app /app/app
+
+# copy modules from local to container
+# COPY --chown=$MAMBA_USER:$MAMBA_USER data /app/data
+
+# Clone a specific git repository and install it as an editable package
+RUN cd modules/proscope && \
+    pip3 install .
+
+WORKDIR /app
+
+# Make port 80 available to the world outside this container
+EXPOSE 7681
+# Set the working directory where your app resides
+
+# Command to run the Gradio app automatically
+CMD ["python", "app/main.py", "-p", "7681", "-s", "-d", "/data"]

app/main.py

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+import glob
+import os
+
+import argparse
+import gradio as gr
+import matplotlib.pyplot as plt
+from proscope.data import get_seq, get_genename_to_uniprot, get_lddt
+seq = get_seq()
+genename_to_uniprot = get_genename_to_uniprot()
+lddt = get_lddt()
+from proscope.af2 import AFPairseg
+from proscope.protein import Protein
+from proscope.viewer import view_pdb_html
+
+
+args = argparse.ArgumentParser()
+args.add_argument("-p", "--port", type=int, default=7860, help="Port number")
+args.add_argument("-s", "--share", action="store_true", help="Share on network")
+args.add_argument("-d", "--data", type=str, default="/data", help="Data directory")
+args = args.parse_args()
+gene_pairs = glob.glob(f"{args.data}/structures/causal/*")
+gene_pairs = [os.path.basename(pair) for pair in gene_pairs]
+
+# set plot ppi to 100
+plt.rcParams['figure.dpi'] = 100
+
+def visualize_AF2(tf_pair, a):
+    strcture_dir = f"{args.data}/structures/causal/{tf_pair}"
+    fasta_dir = f"{args.data}/sequences/causal/{tf_pair}"
+    if not os.path.exists(strcture_dir):
+        gr.ErrorText("No such gene pair")
+
+    a = AFPairseg(strcture_dir, fasta_dir)
+    segpair.choices = list(a.pairs_data.keys())
+    fig1, ax1 = a.plot_plddt_gene1()
+    fig2, ax2 = a.plot_plddt_gene2()
+    fig3, ax3 = a.protein1.plot_plddt()
+    fig4, ax4 = a.protein2.plot_plddt()
+    fig5, ax5 = a.plot_score_heatmap()
+    plt.tight_layout()
+    new_dropdown = update_dropdown(list(a.pairs_data.keys()), 'Segment pair')
+    return fig1, fig2, fig3, fig4, fig5, new_dropdown, a
+
+def view_pdb(seg_pair, a):
+    pdb_path = a.pairs_data[seg_pair].pdb
+    return view_pdb_html(pdb_path), a, pdb_path
+
+
+def update_dropdown(x, label):
+    return gr.Dropdown.update(choices=x, label=label)
+
+
+# main
+if __name__ == '__main__':
+    with gr.Blocks(theme='sudeepshouche/minimalist') as demo:
+
+        seg_pairs = gr.State([''])
+        af = gr.State(None)
+        with gr.Row() as row:
+            with gr.Column():
+                tf_pairs = gr.Dropdown(label='TF pair', choices=gene_pairs)
+                tf_pairs_btn = gr.Button(value='Load & Plot')
+                interact_plddt1 = gr.Plot(label='Interact pLDDT 1')
+                interact_plddt2 = gr.Plot(label='Interact pLDDT 2')
+                protein1_plddt = gr.Plot(label='Protein 1 pLDDT')
+                protein2_plddt = gr.Plot(label='Protein 2 pLDDT')
+
+                heatmap = gr.Plot(label='Heatmap')
+            
+            with gr.Column():
+                segpair = gr.Dropdown(label='Seg pair', choices=seg_pairs.value)
+                segpair_btn = gr.Button(value='Get PDB')
+                pdb_html = gr.HTML(label="PDB HTML")
+                pdb_file = gr.File(label='Download PDB')
+
+        tf_pairs_btn.click(visualize_AF2, inputs = [tf_pairs, af], outputs = [ interact_plddt1, interact_plddt2, protein1_plddt, protein2_plddt, heatmap, segpair, af])
+        segpair_btn.click(view_pdb, inputs=[segpair, af], outputs=[pdb_html, af, pdb_file])
+
+    demo.launch(share=args.share, server_port=args.port)
+

modules/proscope

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+Subproject commit 3dd461a01e95eb9bb5a2b3e41f0dbe24fb9f3c76