static void Main(string[] args)
{
CambridgeSoft.ChemScript14.Environment.SetVerbosity(true);
CambridgeSoft.ChemScript14.Environment.SetThrowExceptions(true);
Console.WriteLine(CambridgeSoft.ChemScript14.Environment.Version());
Console.WriteLine("This .NET session will demonstrate many of the features in ChemScript.\n\n");
string oldDir = SetCurrentDirectory();
if (!IsInputFilesReady())
{
Console.WriteLine("Press <Enter> to quit ...");
Console.ReadLine();
return;
}
try
{
Console.WriteLine(" 0. Loading the ChemScript module");
Console.WriteLine(" 1. Creating a StructureData object");
Console.WriteLine(" 2. Writing a StructureData object to a string or a file");
Console.WriteLine(" 3. Working with Atom and Bond objects");
Console.WriteLine(" 4. Converting names to structures and structures to names");
Console.WriteLine(" 5. Converting 2D structures to 3D");
Console.WriteLine(" 6. Minimizing MM2 and energy calculations for 3D structures");
Console.WriteLine(" 7. Salt stripping");
Console.WriteLine(" 8. Searching structures atom by atom");
Console.WriteLine(" 9. Finding the largest common substructure");
Console.WriteLine("10. Overlaying structures");
Console.WriteLine("11. Computing molecular topological properties");
Console.WriteLine("12. Working with ReactionData objects");
Console.WriteLine("13. Reading and writing SD files");
Console.WriteLine("\n");
Console.WriteLine("Press <Enter> to continue ...");
Console.ReadLine();
Console.WriteLine("\n\n\n 0. Loading the ChemScript module\n--------------------------------------");
Console.WriteLine("\nBefore starting, you must load the ChemScript module by typing the following:\n(Note: This is case-sensitive)");
Console.WriteLine("\nusing CambridgeSoft.ChemScript14;");
Console.WriteLine("\n\nIt will now load ChemScript14");
Console.WriteLine("\n\n\n 1. Creating a StructureData object\n--------------------------------------");
Console.ReadLine();
Console.WriteLine("\nCreating a StructureData object from a SMILES string.");
Console.ReadLine();
Console.WriteLine("StructureData m = StructureData.LoadData(\"C=CCO\");");
StructureData m = StructureData.LoadData("C=CCO");
Console.WriteLine("\nLet's take a look at what's in this StructureData object:");
Console.ReadLine();
Console.WriteLine("m.List();");
m.List();
Console.WriteLine("\nCreating a StructureData object from a file.");
Console.ReadLine();
Console.WriteLine("m = StructureData.LoadFile(\"demo.cdx\");");
m = StructureData.LoadFile("demo.cdx");
Console.WriteLine("\nYou can create a StructureData object first, and then load data into it.");
Console.ReadLine();
Console.WriteLine("m = new StructureData();");
m = new StructureData();
Console.WriteLine("m.ReadFile(\"demo.cdx\");");
m.ReadFile("demo.cdx");
Console.WriteLine("\nWhen loading data or files, you can specify a mimetype. This will speed the loading because ChemScript will not need to determine the data type from the file contents.");
Console.ReadLine();
Console.WriteLine("m = StructureData.LoadData(\"C=CCO\", \"smiles\");");
m = StructureData.LoadData("C=CCO", "smiles");
Console.WriteLine("\nIt is also possible to use the full mimetype name:");
Console.ReadLine();
Console.WriteLine("m = StructureData.LoadData(\"C=CCO\", \"chemical/smiles\");");
m = StructureData.LoadData("C=CCO", "chemical/smiles");
try
{
Console.WriteLine("\nBut if the given mimetype does not match, the loading will fail.");
Console.ReadLine();
Console.WriteLine("m = StructureData.LoadData(\"C=CCO\", \"cdx\");");
m = StructureData.LoadData("C=CCO", "cdx");
Console.WriteLine("Console.WriteLine(m)");
Console.WriteLine(m);
}
catch (Exception e)
{
Console.WriteLine(e.Message);
}
Console.WriteLine("\nYou have to use \"smiles\" instead of \"cdx\".");
Console.ReadLine();
Console.WriteLine("m = StructureData.LoadData(\"C=CCO\", \"smiles\");");
m = StructureData.LoadData("C=CCO", "smiles");
Console.WriteLine("\nHere are all of the mimetypes you can use.");
Console.ReadLine();
Console.WriteLine("foreach (String types in StructureData.MimeTypes())");
Console.WriteLine(" Console.WriteLine(types);");
foreach (String types in StructureData.MimeTypes())
{
Console.WriteLine(types);
}
Console.WriteLine("\n\n\n 2. Writing a StructureData object to a string or a file\n--------------------------------------");
Console.ReadLine();
Console.WriteLine("\nWrite the StructureData object into a base64 encoded CDX string.");
Console.ReadLine();
Console.WriteLine("Console.WriteLine(m.WriteData(\"cdx\", true));");
Console.WriteLine(m.WriteData("cdx", true));
Console.WriteLine("\nGet a SMILES string representation of the StructureData object.");
Console.ReadLine();
Console.WriteLine("Console.WriteLine(m.WriteData(\"smiles\"));");
Console.WriteLine(m.WriteData("smiles"));
Console.WriteLine("\nGet an InChI string representation of the StructureData object.");
Console.ReadLine();
Console.WriteLine("Console.WriteLine(m.WriteData(\"inchi\"));");
Console.WriteLine(m.WriteData("inchi"));
Console.WriteLine("\nWrite a file.");
Console.ReadLine();
Console.WriteLine("m.WriteFile(\"output.cdx\", \"cdx\");");
m.WriteFile("output.cdx", "cdx");
Console.WriteLine("\nIf no mimetype is specified, the file extension is used to determine the file format.");
Console.ReadLine();
Console.WriteLine("m.WriteFile(\"output.cdx\");");
m.WriteFile("output.cdx");
Console.WriteLine("\n\n\n 3. Working with Atom and Bond objects\n--------------------------------------");
Console.ReadLine();
Console.WriteLine("\nIterate over all atoms");
Console.ReadLine();
Console.WriteLine("foreach (Atom a in m.Atoms);");
Console.WriteLine(" Console.WriteLine(a.Name + \", \" + a.GetCartesian().ToString());");
foreach (Atom a in m.Atoms)
{
Console.WriteLine(a.Name + ", " + a.GetCartesian().ToString());
}
Console.WriteLine("\nIterate over all bonds");
Console.ReadLine();
Console.WriteLine("foreach (Bond b in m.Bonds);");
Console.WriteLine(" Console.WriteLine(b.Atom1.Name + \", \" + b.Atom2.Name + \", \" + b.Order.Name)");
foreach (Bond b in m.Bonds)
{
Console.WriteLine(b.Atom1.Name + "," + b.Atom2.Name + "," + b.Order.Name);
}
Console.WriteLine("\nAdd an atom");
Console.ReadLine();
Console.WriteLine("Atom a1 = m.CreateAtom(\"O\");");
Atom a1 = m.CreateAtom("O");
Console.WriteLine("\nAdd a bond");
Console.ReadLine();
Console.WriteLine("Bond b1 = m.CreateBond(a1, m.Atoms[0], null);");
Bond b1 = m.CreateBond(a1, m.Atoms[0], null);
Console.WriteLine("\nRemove an atom");
Console.ReadLine();
Console.WriteLine("m.RemoveAtom(m.Atoms[0]);");
m.RemoveAtom(m.Atoms[0]);
Console.WriteLine("\nRemove a bond");
Console.ReadLine();
Console.WriteLine("m.RemoveBond(m.Bonds[0]);");
m.RemoveBond(m.Bonds[0]);
Console.WriteLine("\nRemove a bond and its bonded atoms");
Console.ReadLine();
Console.WriteLine("m.RemoveBond(m.bonds[0], true);");
m.RemoveBond(m.Bonds[0], true);
Console.WriteLine("\n\n\n 4. Converting names to structures and structures to names\n--------------------------------------");
Console.ReadLine();
Console.WriteLine("\nConvert a chemical name into a structure.");
Console.ReadLine();
Console.WriteLine("m = StructureData.LoadData(\"benzene\", \"name\");");
m = StructureData.LoadData("benzene", "name");
Console.WriteLine("\nGet the chemical name of a structure.");
Console.ReadLine();
Console.WriteLine("Console.WriteLine(m.WriteData(\"name\"));");
Console.WriteLine(m.WriteData("name"));
Console.WriteLine("\nAnother way to get the chemical name.");
Console.ReadLine();
Console.WriteLine("Console.WriteLine(m.ChemicalName());");
Console.WriteLine(m.ChemicalName());
Console.WriteLine("\n\n\n 5. Converting 2D structures to 3D\n--------------------------------------");
Console.ReadLine();
Console.WriteLine("\nFirst we will create a 2D structure.");
Console.ReadLine();
Console.WriteLine("m = StructureData.LoadData(\"C=CCO\");");
m = StructureData.LoadData("C=CCO");
Console.WriteLine("m.List(true, true, true)");
m.List(true, true, true);
Console.WriteLine("\nConvert 2D to 3D.");
Console.ReadLine();
Console.WriteLine("m.ConvertTo3DStructure();");
m.ConvertTo3DStructure();
Console.WriteLine("m.List(true, true, true);");
m.List(true, true, true);
Console.WriteLine("\nRemove Z coordinates.");
Console.ReadLine();
Console.WriteLine("m.ClearZCoordinates();");
m.ClearZCoordinates();
Console.WriteLine("\nConvert a structure to a 2D structure and clean it up");
Console.ReadLine();
Console.WriteLine("m.CleanupStructure();");
m.CleanupStructure();
Console.WriteLine("\n\n\n 6. Minimizing MM2 and energy calculations for 3D structures\n--------------------------------------");
Console.ReadLine();
Console.WriteLine("\nMM2 minimization");
Console.ReadLine();
Console.WriteLine("m.Mm2OptimizeGeometry();");
m.Mm2OptimizeGeometry();
Console.WriteLine("\nCompute MM2 energy");
Console.ReadLine();
Console.WriteLine("Console.WriteLine(m.Mm2Energy());");
Console.WriteLine(m.Mm2Energy());
Console.WriteLine("\n\n\n 7. Salt stripping\n--------------------------------------");
Console.ReadLine();
Console.WriteLine("\nLet's load a StructureData object with a salt");
Console.ReadLine();
Console.WriteLine("m = StructureData.LoadData(\"CCCCCN.[Na+].[Na+].c1ccccc1.[O]\");");
m = StructureData.LoadData("CCCCCN.[Na+].[Na+].c1ccccc1.[O]");
Console.WriteLine("\nSplit salt");
Console.ReadLine();
Console.WriteLine("SaltTable st = new SaltTable();");
SaltTable st = new SaltTable();
Console.ReadLine();
Console.WriteLine("st.RegisterWithSmiles(\"[Na+]\", false);");
st.RegisterWithSmiles("[Na+]", false);
Console.ReadLine();
Console.WriteLine("st.RegisterWithSmiles(\"c1ccccc1\", true);");
st.RegisterWithSmiles("c1ccccc1", true);
Console.ReadLine();
Console.WriteLine("st.RegisterWithSmiles(\"[O]\", true);");
st.RegisterWithSmiles("[O]", true);
Console.ReadLine();
Console.WriteLine("VectorOfStructVector list = st.SplitSaltsAndSolvents(m);");
VectorOfStructVector list = st.SplitSaltsAndSolvents(m);
Console.ReadLine();
Console.WriteLine("StructureDataList mainStructureData = list[0];");
StructureDataList mainStructureData = list[0];
Console.ReadLine();
Console.WriteLine("StructureDataList saltPart = list[1];");
StructureDataList saltPart = list[1];
Console.ReadLine();
Console.WriteLine("Console.WriteLine(\"main StructureData:\" + mainStructureData[0].Smiles + \", salt:\" + saltPart[0].Smiles)");
Console.WriteLine("main StructureData:" + mainStructureData[0].Smiles + ", salt:" + saltPart[0].Smiles);
Console.WriteLine("\n\n\n 8. Searching structures atom by atom\n--------------------------------------");
Console.ReadLine();
Console.WriteLine("\nLet's load two molecules");
Console.ReadLine();
Console.WriteLine("StructureData target = StructureData.LoadData(\"C1CCCCC1C\");");
StructureData target = StructureData.LoadData("C1CCCCC1C");
Console.WriteLine("StructureData query = StructureData.LoadData(\"C1CCCCC1\");");
StructureData query = StructureData.LoadData("C1CCCCC1");
Console.WriteLine("\nNow start the atom-by-atom searching. This results in a map from the target to query");
Console.ReadLine();
Console.WriteLine("AtomsMapVector maps = query.AtomByAtomSearch(target);");
AtomsMapVector maps = query.AtomByAtomSearch(target);
Console.WriteLine("foreach(AtomAtomMap dict in maps){");
Console.WriteLine(" Console.WriteLine(\"one dict:\");");
Console.WriteLine(" foreach(Atom aa in dict.Keys){");
Console.WriteLine(" String r = aa.Name + \" -> \" + dict[aa].Name;");
Console.WriteLine(" Console.WriteLine(r);");
Console.WriteLine(" }");
Console.WriteLine("}");
foreach (AtomAtomMap dict in maps)
{
Console.WriteLine("one dict:");
foreach (Atom aa in dict.Keys)
{
String r0 = aa.Name + " -> " + dict[aa].Name;
Console.WriteLine(r0);
}
}
Console.WriteLine("\nIf you don't care about these atom maps and just want the substructure search result, you can use \"ContainsSubstructure\".");
Console.ReadLine();
Console.WriteLine("Console.WriteLine(target.ContainsSubstructure(query));");
Console.WriteLine(target.ContainsSubstructure(query));
Console.WriteLine("\n\n\n 9. Finding the largest common substructure\n--------------------------------------");
Console.ReadLine();
Console.WriteLine("\nLet's load two molecules");
Console.ReadLine();
Console.WriteLine("StructureData structure1 = StructureData.LoadData(\"C1(C)CCCC1CCO\");");
StructureData structure1 = StructureData.LoadData("C1(C)CCCC1CCO");
Console.WriteLine("StructureData structure2 = StructureData.LoadData(\"C1CCCC1C\");");
StructureData structure2 = StructureData.LoadData("C1CCCC1C");
Console.WriteLine("Use class LargestCommonSubstructure to compute the most common structure\n");
Console.ReadLine();
Console.WriteLine("LargestCommonSubstructure common = LargestCommonSubstructure.Compute(structure1, structure2)");
LargestCommonSubstructure common = LargestCommonSubstructure.Compute(structure1, structure2);
Console.WriteLine("AtomAtomMap atommap1 = common.AtomMapM1()");
Console.WriteLine("AtomAtomMap bondmap1 = common.BondMapM1()");
Console.WriteLine("AtomAtomMap atommap2 = common.AtomMapM2()");
Console.WriteLine("AtomAtomMap bondmap2 = common.BondMapM2()");
AtomAtomMap atommap1 = common.AtomMapM1();
BondBondMap bondmap1 = common.BondMapM1();
AtomAtomMap atommap2 = common.AtomMapM2();
BondBondMap bondmap2 = common.BondMapM2();
Console.WriteLine("foreach(Atom a in atommap1.Keys){");
Console.WriteLine(" r0 = a.Name + \"->\" + atommap1[a].Name + \"->\" + atommap2[a].Name;");
Console.WriteLine(" Console.WriteLine(r0);");
Console.WriteLine("}");
foreach (Atom a in atommap1.Keys)
{
String r0 = a.Name + "->" + atommap1[a].Name + "->" + atommap2[a].Name;
Console.WriteLine(r0);
}
Console.WriteLine("\n\n\n 10. Overlaying structures\n--------------------------------------");
Console.ReadLine();
Console.WriteLine("\n(1). 2D alignment");
Console.ReadLine();
Console.WriteLine("\nFirst let's load two cdx (2D)");
Console.ReadLine();
Console.WriteLine("m = StructureData.LoadFile(\"m.cdx\");");
m = StructureData.LoadFile("m.cdx");
Console.WriteLine("target = StructureData.LoadFile(\"target.cdx\");");
target = StructureData.LoadFile("target.cdx");
Console.WriteLine("\nMake 2D alignment");
Console.ReadLine();
Console.WriteLine("Console.WriteLine(m.Overlay(target));");
Console.WriteLine(m.Overlay(target));
Console.WriteLine("\nWrite the output into a file");
Console.ReadLine();
Console.WriteLine("m.WriteFile(\"m_output.cdx\");");
m.WriteFile("m_output.cdx");
Console.WriteLine("\n(2). 3D Overlay");
Console.WriteLine("\nIf the input consists of 3D structures, the overlay will operate on the 3D coordinates");
Console.ReadLine();
Console.WriteLine("\n\n\n 11. Computing molecular topological properties\n--------------------------------------");
Console.ReadLine();
Console.WriteLine("\nFirst create a Topology object");
Console.ReadLine();
Console.WriteLine("Topology top = m.Topology();");
Topology top = m.Topology();
Console.WriteLine("\nThen you are able to get many topology properties");
Console.ReadLine();
Console.WriteLine("Console.WriteLine(top.WienerIndex);");
Console.WriteLine(top.WienerIndex);
Console.WriteLine("Console.WriteLine(top.BalabanIndex);");
Console.WriteLine(top.BalabanIndex);
Console.WriteLine("Console.WriteLine(top.ShapeCoefficient);");
Console.WriteLine(top.ShapeCoefficient);
Console.WriteLine("\n\n and more ...");
Console.WriteLine("\n\n\n 12. Working with ReactionData objects\n--------------------------------------");
Console.ReadLine();
Console.WriteLine("\nCreate a reaction from a SMILES string");
Console.ReadLine();
Console.WriteLine("ReactionData r = ReactionData.LoadData(\"C1CCC=CC1>>CCCCCC\", \"smiles\");");
ReactionData r = ReactionData.LoadData("C1CCC=CC1>>CCCCCC", "smiles");
Console.WriteLine("\nLoad a reaction from a file");
Console.ReadLine();
Console.WriteLine("r = ReactionData.LoadFile(\"reaction.cdx\");");
r = ReactionData.LoadFile("reaction.cdx");
Console.WriteLine("Console.WriteLine(r.Formula());");
Console.WriteLine(r.Formula());
Console.WriteLine("\nGet reactants as a StructureData list");
Console.ReadLine();
Console.WriteLine("foreach (StructureData rtn in r.Reactants)");
Console.WriteLine(" Console.WriteLine(rtn.ToString())");
foreach (StructureData rtn in r.Reactants)
{
Console.WriteLine(rtn.ToString());
}
Console.WriteLine("\nGet products as a StructureData list");
Console.ReadLine();
Console.WriteLine("foreach(StructureData prod in r.Products)");
Console.WriteLine(" Console.WriteLine(prod.ToString())");
foreach (StructureData prod in r.Products)
{
Console.WriteLine(prod.ToString());
}
Console.WriteLine("\n\n\n 13. Reading and writing SD files\n--------------------------------------");
Console.ReadLine();
Console.WriteLine("\nRead StructureData from an SD file");
Console.ReadLine();
Console.WriteLine("SDFileReader sd = SDFileReader.OpenFile(\"input.sdf\");");
SDFileReader sd = SDFileReader.OpenFile("input.sdf");
Console.WriteLine("m = sd.ReadNext()");
Console.WriteLine("while (m != null){");
Console.WriteLine(" Console.WriteLine(m.Formula());");
Console.WriteLine(" Dictionary_String_String items = m.GetDataItems();");
Console.WriteLine(" foreach(String item in items.Keys){");
Console.WriteLine(" r0 = item + \"->\" + items[item];");
Console.WriteLine(" Console.WriteLine(r0)");
Console.WriteLine(" }");
Console.WriteLine(" m = sd.ReadNext();");
Console.WriteLine("}");
m = sd.ReadNext();
while (m != null)
{
Console.WriteLine(m.Formula());
Dictionary_String_String items = m.GetDataItems();
foreach (String item in items.Keys)
{
String r0 = item + "->" + items[item];
Console.WriteLine(r0);
}
m = sd.ReadNext();
}
Console.WriteLine("\nWrite StructureData into an SD file");
Console.ReadLine();
Console.WriteLine("SDFileWriter sw = SDFileWriter.OpenFile(\"out.sdf\", FileOpenMode.OverWrite);");
Console.WriteLine("StructureData m = StructureData.LoadData(\"CCC\");");
Console.WriteLine("m.SetDataItem(\"atomcount\", \"3\");");
Console.WriteLine("sd.WriteStructure(m)");
Console.WriteLine("m = StructureData.LoadData(\"C1CCCCC1\");");
Console.WriteLine("m.SetDataItem(\"atomcount\", \"6\");");
Console.WriteLine("sd.WriteStructure(m)");
SDFileWriter sw = SDFileWriter.OpenFile("out.sdf", FileOpenMode.OverWrite);
m = StructureData.LoadData("CCC");
m.SetDataItem("atomcount", "3");
sw.WriteStructure(m);
m = StructureData.LoadData("C1CCCCC1");
m.SetDataItem("atomcount", "6");
sw.WriteStructure(m);
Console.WriteLine("\nWelcome to ChemScript!");
}
catch (System.Exception e)
{
Console.WriteLine(e.Message);
}
Console.WriteLine("Press <Enter> to quit ...");
Console.ReadLine();
RestoreCurrentDirectory(oldDir);
}
