Affinity Chromatography

backend/api/affinity_chromatography_routes.py

@@ -0,0 +1,43 @@
+from typing import Any, Dict
+
+from fastapi import APIRouter
+from pydantic import BaseModel, Field
+
+from backend.logic.affinity_chromatography import AffinityChromatography
+
+
+router = APIRouter(
+    prefix="/affinity_chromatography",
+    tags=["Affinity Chromatography"],
+)
+
+class AffinityChromatographyRequest(BaseModel):
+    """
+    Request body schema for running Affinity Chromatography.
+    """
+    fasta_content: str = Field(..., description="FASTA content as raw text")
+    prosite_strong: str = Field(..., description="PROSITE motif matching strongly bound proteins")
+    prosite_weak: str = Field(..., description="PROSITE motif matching weakly bound proteins")
+
+    # Fractionation and simulation controls
+    fraction_count: int = Field(80, ge=1, le=500)
+    noise: float = Field(0.10, ge=0.0, le=1.0, description="Overlap between fractions")
+
+@router.post("/process", response_model=Dict[str, Any])
+async def process_affinity(body: AffinityChromatographyRequest) -> Any:
+    """
+    Run affinity chromatography and return the simulated result.
+    """
+    if not body.fasta_content.strip():
+        return {"error": "No FASTA content provided."}
+
+    try:
+        return AffinityChromatography.process(
+            fasta_content=body.fasta_content,
+            fraction_count=body.fraction_count,
+            prosite_strong=body.prosite_strong,
+            prosite_weak=body.prosite_weak
+        )
+    except ValueError as exc:
+        return {"error": str(exc)}  
+

backend/logic/affinity_chromatography.py

@@ -0,0 +1,76 @@
+from __future__ import annotations
+from backend.utility.protein import Protein
+
+from typing import Any, Dict
+
+from backend.logic.fractionation.fractionation import Fractionation
+
+class AffinityChromatography:
+    """
+    Simulates affinity chromatography.
+
+    Main idea:
+    - Each different ligand in affinity chromatography bonds to different "motifs" at different strengths
+    - Divide all proteins into either strongly binded, weakly binded, or unbinded
+    - Wash comes out in first 1/2 fractions
+    - Weakly binded comes out in next 1/4 fractions
+    - Strongly bound comes out in next 1/4 fractions
+    """
+
+    @staticmethod
+    def process (fasta_content: str, prosite_strong: str, prosite_weak: str, fraction_count: int = 80, noise: float = 0.10) -> Dict[str, Any]:
+        """
+        Main affinity chromatography simulation function.
+
+        Parameters:
+        - prosite_strong: the PROSITE motif that matches strongly bound proteins
+        - prosite_weak: the PROSITE motif that matches weakly bound proteins
+        - fraction_count: number of output fractions
+        - noise: overlap between fractions
+        """
+
+        if fraction_count < 4:
+            raise ValueError("fraction_count must be at least 4")
+        if noise < 0:
+            raise ValueError("noise must be >= 0")
+
+        # Parse all input FASTA records
+        entries, skipped = Fractionation.convert_fasta_to_protein_entries(fasta_content)
+
+        # 1. "extract" (filter and remove) all strongly bound proteins
+        strongly_bound = [entry for entry in entries if Protein.matches_prosite(entry.sequence, prosite_strong)]
+        unbound =  [entry for entry in entries if not Protein.matches_prosite(entry.sequence, prosite_strong)]
+
+        # 2. "extract" (filter and remove) all weakly bound proteins
+        weakly_bound = [entry for entry in entries if Protein.matches_prosite(entry.sequence, prosite_weak)]
+        unbound =  [entry for entry in unbound if not Protein.matches_prosite(entry.sequence, prosite_weak)]
+
+        # now we have 3 our 3 lists! divide them cool-ly into the fractions
+        # this is a very convoluted way to get the following ratios: 1/2 1/4 1/4
+        wash_fractions = fraction_count // 2
+        weak_fractions = (fraction_count - wash_fractions) // 2
+        strong_fractions = fraction_count - (wash_fractions + weak_fractions)
+
+        fractions = list(Fractionation.fractionate_with_overlap(unbound, wash_fractions, noise))
+        fractions.extend(Fractionation.fractionate_with_overlap(weakly_bound, weak_fractions, noise))
+        fractions.extend(Fractionation.fractionate_with_overlap(strongly_bound, strong_fractions, noise))
+
+        return {
+            "ok": True,
+            "params": {
+                "fractions": fraction_count,
+            },
+            "counts": {
+                "total": len(entries),
+                "strongly_bound": len(strongly_bound),
+                "weakly_bound": len(weakly_bound),
+                "unbound": len(unbound),
+                "skipped": skipped,
+            },
+            "fraction_counts": {
+                "wash_fractions": wash_fractions,
+                "weak_fractions": weak_fractions,
+                "strong_fractions": strong_fractions
+            },
+            "fractions": Fractionation.process_fractions(fractions)
+        }

backend/server.py

@@ -12,6 +12,7 @@
 import backend.api.ion_exchange_fractionation_routes as ion_exchange_fractionation_routes
 import backend.api.size_exclusion as size_exclusion_routes
 import backend.api.hydrophobic_interaction_fractionation_routes as hydrophobic_interaction_fractionation_routes
+import backend.api.affinity_chromatography_routes as affinity_chromatography_routes
 
 
 """
@@ -67,6 +68,7 @@
 app.include_router(ion_exchange_fractionation_routes.router)
 app.include_router(size_exclusion_routes.router)
 app.include_router(hydrophobic_interaction_fractionation_routes.router)
+app.include_router(affinity_chromatography_routes.router)
 
 """ 
 NOTE FOR FUTURE DEVELOPERS:

frontend/jbio-app/src/App.tsx

@@ -22,6 +22,7 @@ import PeptideRetention from "./pages/PeptideRetention";
 import IonExchangeFractionation from "./pages/IonExchangeFractionation";
 import HydrophobicInteractionFractionation from "./pages/HydrophobicInteractionFractionation";
 import SizeExclusionPage from './pages/SizeExclusion';
+import AffinityChromatography from './pages/AffinityChromatography';
 
 function App() {
   const pages = [
@@ -76,6 +77,12 @@ function App() {
     },
     {
       id: 8,
+      icon: <SwapVertIcon />,
+      component: <AffinityChromatography />,
+      label: "Affinity Chromatography",
+    },
+    {
+      id: 9,
       icon: <GitHubIcon />,
       link: "https://github.com/paulcraig/ProSep",
       label: "GitHub Repository",

frontend/jbio-app/src/components/chromatography/graphs/Chromatogram.tsx

@@ -16,10 +16,12 @@ export type ChromatogramProps = {
     fractionRows: ChromatogramFractionDto[]
     data: FractionationResponse
     afterWash?: ProteinDto[]
-    saltGradient?: Array<{ x: number; y: number }>
+    elutionPoints?: Array<{ x: number; y: number }>
+    elutionLabel?: string,
+    elutionAxisLabel?: string
 }
 
-export function Chromatogram({ showLineGraph, useLogScale, showWash, washLabel = 'Wash', afterWashLabel = 'After Wash', fractionRows, data, afterWash, saltGradient }: ChromatogramProps) {
+export function Chromatogram({ showLineGraph, useLogScale, showWash, washLabel = 'Wash', afterWashLabel = 'After Wash', fractionRows, data, afterWash, elutionPoints, elutionLabel = "Salt Gradient", elutionAxisLabel = "Salt Concentration"}: ChromatogramProps) {
     const lineChartRef = useRef<ChartJS<'line'> | null>(null)
     const scatterChartRef = useRef<ChartJS<'scatter'> | null>(null)
     const chartTheme = useChartTheme()
@@ -47,6 +49,7 @@ export function Chromatogram({ showLineGraph, useLogScale, showWash, washLabel =
         const maxY = Math.max(...points.map(p => p.y), 1)
         for (const point of points) {
             point.y = Math.round((point.y / maxY) * 100) / 100
+            if(point.y === 0) point.y = 0.001 
         }
         return points
     }, [data, fractionRows, showWash, showAfterWash, afterWash, lastFractionX])
@@ -90,10 +93,10 @@ export function Chromatogram({ showLineGraph, useLogScale, showWash, washLabel =
             },
         ]
 
-        if (saltGradient && saltGradient.length > 0) {
+        if (elutionPoints && elutionPoints.length > 0) {
             datasets.push({
-                label: 'Salt Gradient',
-                data: saltGradient,
+                label: elutionLabel,
+                data: elutionPoints,
                 borderColor: 'rgba(255, 107, 107, 1)',
                 backgroundColor: 'rgba(255, 107, 107, 1)',
                 pointRadius: 0,
@@ -105,13 +108,13 @@ export function Chromatogram({ showLineGraph, useLogScale, showWash, washLabel =
                 yAxisID: 'y1',
             })
 
-            const saltGradientScale = {
+            const elutionScale = {
                 y1: {
                     type: 'linear',
                     position: 'right',
                     title: {
                         display: true,
-                        text: 'Salt Concentration',
+                        text: elutionAxisLabel,
                         color: chartTheme.text,
                     },
                     ticks: {
@@ -124,11 +127,11 @@ export function Chromatogram({ showLineGraph, useLogScale, showWash, washLabel =
                 },
             } as const
 
-            return { datasets, saltGradientScale }
+            return { datasets, elutionScale }
         }
 
         return { datasets }
-    }, [proteinSeriesPoints, saltGradient])
+    }, [proteinSeriesPoints, elutionPoints, elutionLabel, elutionAxisLabel, chartTheme.text, chartTheme.grid])
 
     const activeChart = showLineGraph ? lineChartRef.current : scatterChartRef.current
     const downloadChart = useDownloadChart()
@@ -162,6 +165,7 @@ export function Chromatogram({ showLineGraph, useLogScale, showWash, washLabel =
                                             text: 'Fractions',
                                             color: chartTheme.text,
                                         },
+                                        // TODO: this always shows zeroth (wash) fraction, either change how wash works or conditionally remove
                                         beginAtZero: true,
                                         ticks: {
                                             callback: fractionTickLabel,
@@ -186,7 +190,7 @@ export function Chromatogram({ showLineGraph, useLogScale, showWash, washLabel =
                                             color: chartTheme.grid,
                                         },
                                     },
-                                    ...(lineData.saltGradientScale ?? {})
+                                    ...(lineData.elutionScale ?? {})
                                 },
                             }}
                         />
@@ -213,6 +217,7 @@ export function Chromatogram({ showLineGraph, useLogScale, showWash, washLabel =
                                             text: 'Fractions',
                                             color: chartTheme.text,
                                         },
+                                        // TODO: this always shows zeroth (wash) fraction, either change how wash works or conditionally remove
                                         beginAtZero: true,
                                         ticks: {
                                             callback: fractionTickLabel,
@@ -237,7 +242,7 @@ export function Chromatogram({ showLineGraph, useLogScale, showWash, washLabel =
                                             color: chartTheme.grid,
                                         },
                                     },
-                                    ...(lineData.saltGradientScale ?? {})
+                                    ...(lineData.elutionScale ?? {})
                                 },
                             }}
                         />

frontend/jbio-app/src/components/chromatography/tables/ProteinTable.tsx

@@ -20,7 +20,7 @@
 import { Search } from '@mui/icons-material'
 import { SortDirection } from './Common'
 
-type ProteinTableProteinDto = Pick<ProteinDto, "id" | "name" | "description" | "sequence" | "molecularWeight" | "color">
+export type ProteinTableProteinDto = Pick<ProteinDto, "id" | "name" | "description" | "sequence" | "molecularWeight" | "color">
 
 export type ProteinTableMetricDto<P> = {
     label: string
@@ -94,7 +94,7 @@
         })
 
         return rows
     }, [filteredRetainedRows, proteinSort, metrics])
 
     const pagedProteins = useMemo(() => {
         const start = proteinPage * proteinRowsPerPage