Add wip PDB parsers for ATOM, HETATM, TER, DBREF records

CSBiology · May 11, 2022 · 426dee6 · 426dee6
1 parent c925318
commit 426dee6
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Showing 6 changed files with 2,270 additions and 1 deletion.
diff --git a/src/BioFSharp.IO/BioFSharp.IO.fsproj b/src/BioFSharp.IO/BioFSharp.IO.fsproj
@@ -37,6 +37,7 @@
       <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
     </None>
     <None Include="GenerateSOFTTypes.fsx" />
+    <Compile Include="PDB.fs" />
     <Compile Include="GAF.fs" />
     <Compile Include="AgilentRaw.fs" />
     <Compile Include="BlastWrapper.fs" />

diff --git a/src/BioFSharp.IO/PDB.fs b/src/BioFSharp.IO/PDB.fs
diff --git a/src/BioFSharp.Interactive/test.ipynb b/src/BioFSharp.Interactive/test.ipynb
@@ -48,6 +48,97 @@
     "#r \"nuget: BioFSharp.Interactive, 0.0.0-dev\""
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "dotnet_interactive": {
+     "language": "fsharp"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "\n",
+    "open BioFSharp\n",
+    "\n",
+    "open BioFSharp\n",
+    "open BioFSharp.Algorithm\n",
+    "open BioFSharp.Algorithm.PairwiseAlignment\n",
+    "\n",
+    "let aaScoring = ScoringMatrix.getScoringMatrixAminoAcid ScoringMatrix.ScoringMatrixAminoAcid.BLOSUM62\n",
+    "let nucScoring = ScoringMatrix.getScoringMatrixNucleotide  ScoringMatrix.ScoringMatrixNucleotide.EDNA\n",
+    "\n",
+    "//For aminoacids\n",
+    "let costAA = {\n",
+    "    Open = -5\n",
+    "    Continuation = -1\n",
+    "    Similarity = aaScoring \n",
+    "    }\n",
+    "\n",
+    "//For nucleotides\n",
+    "let costN = {\n",
+    "    Open = -5\n",
+    "    Continuation = -1\n",
+    "    Similarity = nucScoring \n",
+    "    }\n",
+    "\n",
+    "let query1AA = \"NLFVAAAAQTKNGQGWVPSNYITPVNSAAA\" |> BioArray.ofAminoAcidSymbolString\n",
+    "let query2AA = \"NLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPVNS\" |> BioArray.ofAminoAcidSymbolString\n",
+    "\n",
+    "let localAA = \n",
+    "    PairwiseAlignment.Local.SmithWaterman.align(query1AA,query2AA,costAA)\n",
+    "\n",
+    "let globalAA =\n",
+    "    PairwiseAlignment.Global.NeedlemanWunsch.align(query1AA,query2AA,costAA)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "dotnet_interactive": {
+     "language": "fsharp"
+    }
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<table><thead><tr><th>Score</th><th>GapPenalty</th><th>ExtendGapPenalty</th><th>Length</th><th>Identity</th><th>IdentityFraction</th><th>Seq1AlignmentStartIndex</th><th>Seq2AlignmentStartIndex</th></tr></thead><tbody><tr><td><div class=\"dni-plaintext\">104</div></td><td><div class=\"dni-plaintext\">-5</div></td><td><div class=\"dni-plaintext\">-1</div></td><td><div class=\"dni-plaintext\">41</div></td><td><div class=\"dni-plaintext\">22</div></td><td><div class=\"dni-plaintext\">0.5365853658536586</div></td><td><div class=\"dni-plaintext\">27</div></td><td><div class=\"dni-plaintext\">58</div></td></tr></tbody></table>"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "localAA.MetaData"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "dotnet_interactive": {
+     "language": "fsharp"
+    }
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<table><thead><tr><th><i>index</i></th></tr></thead><tbody><tr><td>0</td></tr><tr><td>1</td></tr><tr><td>2</td></tr><tr><td>3</td></tr><tr><td>4</td></tr><tr><td>5</td></tr><tr><td>6</td></tr><tr><td>7</td></tr><tr><td>8</td></tr><tr><td>9</td></tr><tr><td>10</td></tr><tr><td>11</td></tr><tr><td>12</td></tr><tr><td>13</td></tr><tr><td>14</td></tr><tr><td>15</td></tr><tr><td>16</td></tr><tr><td>17</td></tr><tr><td>18</td></tr><tr><td>19</td></tr><tr><td colspan=\"1\"><i>... (more)</i></td></tr></tbody></table>"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "let a = localAA.Sequences |> Seq.item 0\n",
+    "a\n"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,

diff --git a/src/BioFSharp/Playground.fsx b/src/BioFSharp/Playground.fsx
@@ -39,4 +39,36 @@ open FSharpAux
 open FSharpAux.IO
 open FSharp.Stats
 
-open BioFSharp
+open BioFSharp
+
+open BioFSharp
+open BioFSharp.Algorithm
+open BioFSharp.Algorithm.PairwiseAlignment
+
+let aaScoring = ScoringMatrix.getScoringMatrixAminoAcid ScoringMatrix.ScoringMatrixAminoAcid.BLOSUM62
+let nucScoring = ScoringMatrix.getScoringMatrixNucleotide  ScoringMatrix.ScoringMatrixNucleotide.EDNA
+
+//For aminoacids
+let costAA = {
+    Open = 5
+    Continuation = -1
+    Similarity = aaScoring 
+    }
+
+//For nucleotides
+let costN = {
+    Open = -5
+    Continuation = -1
+    Similarity = nucScoring 
+    }
+
+let query1AA = "NLFVAAAAQTKNGQGWVPSNYITPVNSAAA" |> BioArray.ofAminoAcidSymbolString
+let query2AA = "NLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPVNS" |> BioArray.ofAminoAcidSymbolString
+
+let localAA = 
+    PairwiseAlignment.Local.SmithWaterman.align(query1AA,query2AA,costAA)
+
+let globalAA =
+    PairwiseAlignment.Global.NeedlemanWunsch.align(query1AA,query2AA,costAA)
+
+localAA.MetaData.Score
diff --git a/tests/BioFSharp.IO.Tests/BioFSharp.IO.Tests.fsproj b/tests/BioFSharp.IO.Tests/BioFSharp.IO.Tests.fsproj
@@ -7,6 +7,7 @@
   </PropertyGroup>
 
   <ItemGroup>
+    <Compile Include="ParserTests\PDB.fs" />
     <Compile Include="ParserTests\Stride.fs" />
     <Compile Include="ParserTests\DSSP.fs" />
     <Compile Include="Main.fs" />