add pdb exporter

Remove NETStandard2.0
JensKrumsieck · Feb 19, 2024 · 355d3b0 · 355d3b0
1 parent 808002e
commit 355d3b0
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Showing 5 changed files with 76 additions and 4 deletions.
diff --git a/ChemSharp.Molecules/ChemSharp.Molecules.csproj b/ChemSharp.Molecules/ChemSharp.Molecules.csproj
@@ -3,7 +3,7 @@
   <PropertyGroup>
     <PackageId>ChemSharp.Molecules</PackageId>
     <Description>Chemsharp: Molecule IO (cif, xyz, ...) and Elemental Analysis</Description>
-    <TargetFrameworks>netstandard2.0;netstandard2.1;net6.0;net7.0</TargetFrameworks>
+    <TargetFrameworks>netstandard2.1;net6.0;net7.0</TargetFrameworks>
   </PropertyGroup>
 
   <ItemGroup>

diff --git a/ChemSharp.Molecules/Export/PDBExporter.cs b/ChemSharp.Molecules/Export/PDBExporter.cs
@@ -0,0 +1,72 @@
+using ChemSharp.Export;
+using ChemSharp.Extensions;
+
+namespace ChemSharp.Molecules.Export;
+
+public class PDBExporter : AbstractMoleculeExporter
+{
+	public static void Export(Molecule mol, string filename)
+	{
+		var exporter = new PDBExporter();
+		using var stream = File.Create(filename);
+		exporter.Export(mol, stream);
+	}
+
+	public override void Export(IExportable exportable, Stream stream)
+	{
+		base.Export(exportable, stream);
+		if (Molecule == null) return;
+		var atomsCount = Molecule.Atoms.Count;
+		using var sw = new StreamWriter(stream);
+		sw.WriteLine("HEADER");
+		sw.WriteLine($"TITLE{StringUtil.Spaces(5)}{Molecule.Title}");
+
+		var line = new char[80];
+		for (var i = 0; i < atomsCount; i++)
+		{
+			var atom = Molecule.Atoms[i];
+			Array.Fill(line, ' ');
+			AppendToCharArrayAt(in line, "ATOM", 0, PdbAlign.Left);
+			AppendToCharArrayAt(in line, i.ToString(), 11);
+			AppendToCharArrayAt(in line, atom.Title, 13, PdbAlign.Left);
+			AppendToCharArrayAt(in line, atom.Residue, 20);
+			AppendToCharArrayAt(in line, atom.ChainId != default ? atom.ChainId : ' ', 22);
+			AppendToCharArrayAt(in line, atom.ResidueId.ToString(), 26);
+			AppendToCharArrayAt(in line, atom.Location.X.ToInvariantString(), 38);
+			AppendToCharArrayAt(in line, atom.Location.Y.ToInvariantString(), 46);
+			AppendToCharArrayAt(in line, atom.Location.Z.ToInvariantString(), 54);
+			AppendToCharArrayAt(in line, atom.Symbol, 78);
+			AppendToCharArrayAt(in line, atom.Charge.ToString(), 80);
+			sw.WriteLine(line);
+		}
+	}
+
+	private static void AppendToCharArrayAt(in char[] arr, char chr, int index) => arr[index] = chr;
+
+	//if align is right, give end column index
+	private static void AppendToCharArrayAt(in char[] arr, ReadOnlySpan<char> str, int index,
+		PdbAlign align = PdbAlign.Right)
+	{
+		switch (align)
+		{
+			case PdbAlign.Left:
+			{
+				for (var i = 0; i < str.Length; i++) arr[index + i] = str[i];
+				break;
+			}
+			case PdbAlign.Right:
+			{
+				for (var i = 0; i < str.Length; i++) arr[index - str.Length + i] = str[i];
+				break;
+			}
+			default:
+				throw new ArgumentOutOfRangeException(nameof(align), align, null);
+		}
+	}
+
+	private enum PdbAlign
+	{
+		Left,
+		Right
+	}
+}
diff --git a/ChemSharp.Spectroscopy/ChemSharp.Spectroscopy.csproj b/ChemSharp.Spectroscopy/ChemSharp.Spectroscopy.csproj
@@ -3,7 +3,7 @@
   <PropertyGroup>
     <PackageId>ChemSharp.Spectroscopy</PackageId>
     <Description>Chemsharp: Spectroscopry IO: NMR, EPR, UVVIS, CSV</Description>
-    <TargetFrameworks>netstandard2.0;netstandard2.1;net6.0;net7.0</TargetFrameworks>
+    <TargetFrameworks>netstandard2.1;net6.0;net7.0</TargetFrameworks>
   </PropertyGroup>
 
   <ItemGroup>

diff --git a/ChemSharp.UnitConversion/ChemSharp.UnitConversion.csproj b/ChemSharp.UnitConversion/ChemSharp.UnitConversion.csproj
@@ -2,7 +2,7 @@
   <PropertyGroup>
     <PackageId>ChemSharp.UnitConversion</PackageId>
     <Description>Chemsharp: UnitConversion</Description>
-    <TargetFrameworks>netstandard2.0;netstandard2.1;net6.0;net7.0</TargetFrameworks>
+    <TargetFrameworks>netstandard2.1;net6.0;net7.0</TargetFrameworks>
   </PropertyGroup>
 
   <ItemGroup>

diff --git a/ChemSharp/ChemSharp.csproj b/ChemSharp/ChemSharp.csproj
@@ -3,7 +3,7 @@
   <PropertyGroup>
     <PackageId>ChemSharp</PackageId>
     <Description>Library for processing of chemistry related files (aiming at spectroscopy and structural files)</Description>
-    <TargetFrameworks>netstandard2.0;netstandard2.1;net6.0;net7.0</TargetFrameworks>
+    <TargetFrameworks>netstandard2.1;net6.0;net7.0</TargetFrameworks>
     <Nullable>enable</Nullable>
   </PropertyGroup>