Implement interface-adaptive binding energy calculator

2025-03-06 12:51:36 -08:00
parent 2cfbf64e92
commit 83525663c9
4 changed files with 654 additions and 60 deletions
--- a/test.nf
+++ b/test.nf
@@ -0,0 +1,140 @@
+#!/usr/bin/env nextflow
+nextflow.enable.dsl=2
+
+// Define parameters
+params.complex_name = "mhc_tcr"
+params.protein1_fasta = "/mnt/OmicNAS/private/old/olamide/bioemu/input/complexes/mhc_peptide.fasta"
+params.protein2_fasta = "/mnt/OmicNAS/private/old/olamide/bioemu/input/complexes/tcr_jm22.fasta"
+params.exp_dG = -7.21  // kcal/mol from experimental database
+params.outdir = "/mnt/OmicNAS/private/old/olamide/bioemu/output"
+params.cache_dir = "/mnt/OmicNAS/private/old/olamide/bioemu/cache"
+params.num_samples = 20
+params.batch_size = 5
+params.temperature = 300
+params.n_clusters = 5
+
+// First process: Generate structure for protein1
+process GENERATE_PROTEIN1 {
+    container 'bioemu:latest'
+    containerOptions '--rm --gpus all -v /mnt:/mnt'
+    publishDir "${params.outdir}/${params.complex_name}/protein1", mode: 'copy'
+
+    output:
+        path "protein1_topology.pdb", emit: topology
+        path "protein1_samples.xtc", emit: samples
+
+    script:
+    """
+    # Extract sequence from FASTA
+    SEQUENCE=\$(grep -v ">" ${params.protein1_fasta} | tr -d '\\n')
+
+    # Run BioEmu
+    python3 -m bioemu.sample \\
+        --sequence "\${SEQUENCE}" \\
+        --num_samples ${params.num_samples} \\
+        --batch_size_100 ${params.batch_size} \\
+        --output_dir . \\
+        --cache_embeds_dir ${params.cache_dir}
+
+    # Rename output files
+    mv topology.pdb protein1_topology.pdb
+    mv samples.xtc protein1_samples.xtc
+    """
+}
+
+// Second process: Generate structure for protein2
+process GENERATE_PROTEIN2 {
+    container 'bioemu:latest'
+    containerOptions '--rm --gpus all -v /mnt:/mnt'
+    publishDir "${params.outdir}/${params.complex_name}/protein2", mode: 'copy'
+
+    output:
+        path "protein2_topology.pdb", emit: topology
+        path "protein2_samples.xtc", emit: samples
+
+    script:
+    """
+    # Extract sequence from FASTA
+    SEQUENCE=\$(grep -v ">" ${params.protein2_fasta} | tr -d '\\n')
+
+    # Run BioEmu
+    python3 -m bioemu.sample \\
+        --sequence "\${SEQUENCE}" \\
+        --num_samples ${params.num_samples} \\
+        --batch_size_100 ${params.batch_size} \\
+        --output_dir . \\
+        --cache_embeds_dir ${params.cache_dir}
+
+    # Rename output files
+    mv topology.pdb protein2_topology.pdb
+    mv samples.xtc protein2_samples.xtc
+    """
+}
+
+// Third process: Calculate binding energy
+process CALCULATE_BINDING {
+    container 'bioemu:latest'
+    containerOptions '--rm --gpus all -v /mnt:/mnt -v /data:/data'
+    publishDir "${params.outdir}/${params.complex_name}/analysis", mode: 'copy'
+
+    input:
+        path protein1_topology
+        path protein1_samples
+        path protein2_topology
+        path protein2_samples
+
+    output:
+        path "binding_energy.csv"
+        path "binding_energy_report.txt"
+        path "energy_comparison.png"
+
+    script:
+    """
+    # Run binding energy calculation
+    python3 /data/olamide/fresh-bioemu2/scripts/calculate_binding.py \\
+        --protein1_topology ${protein1_topology} \\
+        --protein1_samples ${protein1_samples} \\
+        --protein2_topology ${protein2_topology} \\
+        --protein2_samples ${protein2_samples} \\
+        --temperature ${params.temperature} \\
+        --n_clusters ${params.n_clusters} \\
+        --output binding_energy.csv \\
+        --plot energy_comparison.png
+
+    # Generate report
+    echo "# Binding Free Energy Analysis: ${params.complex_name}" > binding_energy_report.txt
+    echo "======================================================" >> binding_energy_report.txt
+    echo "## Experimental Value (Database)" >> binding_energy_report.txt
+    echo "ΔG = ${params.exp_dG} kcal/mol" >> binding_energy_report.txt
+    echo "" >> binding_energy_report.txt
+
+    # Extract predicted value
+    PREDICTED_DG=\$(grep -A1 "binding_free_energy" binding_energy.csv | tail -n1 | cut -d',' -f2)
+
+    echo "## BioEmu Prediction" >> binding_energy_report.txt
+    echo "ΔG = \${PREDICTED_DG} kcal/mol" >> binding_energy_report.txt
+    echo "" >> binding_energy_report.txt
+
+    # Calculate comparison metrics
+    echo "## Comparison" >> binding_energy_report.txt
+    ABS_DIFF=\$(python3 -c "print('%.2f' % abs(float('\${PREDICTED_DG}') - (${params.exp_dG})))")
+    REL_ERROR=\$(python3 -c "print('%.2f' % (((float('\${PREDICTED_DG}') - (${params.exp_dG}))/(${params.exp_dG}))*100))")
+
+    echo "Absolute Difference: \${ABS_DIFF} kcal/mol" >> binding_energy_report.txt
+    echo "Relative Error: \${REL_ERROR}%" >> binding_energy_report.txt
+    """
+}
+
+workflow {
+    // Generate structures for both proteins
+    protein1_results = GENERATE_PROTEIN1()
+    protein2_results = GENERATE_PROTEIN2()
+
+    // Calculate binding energy
+    CALCULATE_BINDING(
+        protein1_results.topology,
+        protein1_results.samples,
+        protein2_results.topology,
+        protein2_results.samples
+    )
+}