public void WriteImageFile(string fname, IndigoObject mol, string format, string comment,float weight)
{
switch (format)
{
case "png":{indigo.setOption("render-output-format", "png");break;}
case "svg":{indigo.setOption("render-output-format", "svg");break;}
case "pdf":{indigo.setOption("render-output-format", "pdf");break;}
case "emf":{indigo.setOption("render-output-format", "emf");break;}
default: throw new Exception("format not handled by Indigo: " + format);
}
// http://ggasoftware.com/opensource/indigo/api/options#rendering
//png, svg, pdf are allowed. On Windows, emf is also allowed.
indigo.setOption ("render-bond-length","18");
indigo.setOption ("render-relative-thickness", Math.Round (weight,2).ToString ());
indigo.setOption("render-coloring", true);
indigo.setOption("render-margins", 1, 1);
//indigo.setOption("render-atom-ids-visible", true);
indigo.setOption("render-comment", comment);
indigo.setOption("render-implicit-hydrogens-visible", false);
indigo.setOption("render-label-mode", "hetero");
indigo.setOption("render-comment-font-size", "15");
indigo.setOption("render-comment-offset", "6");
mol.layout();
renderer.renderToFile(mol, fname);
//indigo.setOption("render-output-format", "svg");
}
public void renderGridToFile(IndigoObject items, int[] refatoms, int ncolumns, string filename)
{
if (refatoms != null)
if (refatoms.Length != items.count ())
throw new IndigoException ("renderGridToFile(): refatoms[] size must be equal to the number of objects");
_indigo.checkResult(_renderer_lib.indigoRenderGridToFile (items.self, refatoms, ncolumns, filename));
}
public byte[] renderGridToBuffer(IndigoObject items, int[] refatoms, int ncolumns)
{
IndigoObject bufh = _indigo.writeBuffer ();
if (refatoms != null)
if (refatoms.Length != items.count ())
throw new IndigoException ("renderGridToFile(): refatoms[] size must be equal to the number of objects");
_indigo.checkResult (_renderer_lib.indigoRenderGrid (items.self, refatoms, ncolumns, bufh.self));
return bufh.toBuffer ();
}
public Bitmap renderToBitmap (IndigoObject obj)
{
_indigo.setSessionID ();
_indigo.checkResult (_indigo._indigo_lib.indigoSetOption ("render-output-format", "png"));
byte[] res = renderToBuffer (obj);
MemoryStream stream = new MemoryStream ();
stream.Write (res, 0, res.Length);
stream.Seek (0, SeekOrigin.Begin);
return (Bitmap)Image.FromStream (stream);
}
public byte[] renderToBuffer (IndigoObject obj)
{
_indigo.setSessionID ();
using (IndigoObject bufh = _indigo.writeBuffer()) {
_indigo.checkResult (_renderer_lib.indigoRender (obj.self, bufh.self));
byte* buf;
int bufsize;
_indigo.checkResult (_indigo._indigo_lib.indigoToBuffer (bufh.self, &buf, &bufsize));
byte[] res = new byte[bufsize];
for (int i = 0; i < bufsize; ++i)
res [i] = buf [i];
return res;
}
}
public IndigoObject createSaver(IndigoObject output, string format)
{
setSessionID();
return(new IndigoObject(this, output, _indigo_lib.indigoCreateSaver(output.self, format)));
}
public void addCatalyst(IndigoObject molecule)
{
dispatcher.setSessionID();
_indigo_lib.indigoAddCatalyst(self, molecule.self);
}
public void renderToFile(IndigoObject obj, string filename)
{
_indigo.setSessionID ();
_indigo.checkResult (_renderer_lib.indigoRenderToFile (obj.self, filename));
}
public int arrayAdd(IndigoObject item)
{
dispatcher.setSessionID();
return dispatcher.checkResult(_indigo_lib.indigoArrayAdd(self, item.self));
}
public void setAtomMappingNumber(IndigoObject reaction_atom, int number)
{
dispatcher.setSessionID();
_indigo_lib.indigoSetAtomMappingNumber(self, reaction_atom.self, number);
}
/// <summary>
/// Inserts a structure under a specified id
/// </summary>
/// <param name="record">Indigo object with a chemical structure (molecule or reaction)</param>
/// <param name="id">record id</param>
/// <returns> inserted record id</returns>
public int insert(IndigoObject record, int id)
{
_indigo.setSessionID();
return(Bingo.checkResult(_indigo, _lib.bingoInsertRecordObjWithId(_id, record.self, id)));
}
public System.Collections.IEnumerable iterateMatches(IndigoObject query)
{
dispatcher.setSessionID();
return new IndigoObject(dispatcher, dispatcher.checkResult(_indigo_lib.indigoIterateMatches(self, query.self)), this);
}
public System.Collections.IEnumerable iterateMatches(IndigoObject query)
{
dispatcher.setSessionID();
return(new IndigoObject(dispatcher, this, _indigo_lib.indigoIterateMatches(self, query.self)));
}
public int countMatches(IndigoObject query)
{
dispatcher.setSessionID();
return dispatcher.checkResult(_indigo_lib.indigoCountMatches(self, query.self));
}
public int countMatchesWithLimit(IndigoObject query, int embeddings_limit)
{
dispatcher.setSessionID();
return dispatcher.checkResult(_indigo_lib.indigoCountMatchesWithLimit(self, query.self, embeddings_limit));
}
public IndigoObject match(IndigoObject query)
{
dispatcher.setSessionID();
int res = dispatcher.checkResult(_indigo_lib.indigoMatch(self, query.self));
if (res == 0)
return null;
return new IndigoObject(dispatcher, res, this);
}
public void unignoreAtom(IndigoObject atom)
{
dispatcher.setSessionID();
dispatcher.checkResult(_indigo_lib.indigoUnignoreAtom(self, atom.self));
}
public void addCatalyst(IndigoObject molecule)
{
dispatcher.setSessionID();
dispatcher.checkResult(_indigo_lib.indigoAddCatalyst(self, molecule.self));
}
public int arrayAdd(IndigoObject item)
{
dispatcher.setSessionID();
return(_indigo_lib.indigoArrayAdd(self, item.self));
}
public IndigoObject mapMolecule(IndigoObject query_reaction_molecule)
{
dispatcher.setSessionID();
int mapped = dispatcher.checkResult(_indigo_lib.indigoMapMolecule(self, query_reaction_molecule.self));
if (mapped == 0)
return null;
return new IndigoObject(dispatcher, mapped);
}
public int countMatches(IndigoObject query)
{
dispatcher.setSessionID();
return(_indigo_lib.indigoCountMatches(self, query.self));
}
public IndigoObject mapBond(IndigoObject query_bond)
{
dispatcher.setSessionID();
int mapped = dispatcher.checkResult(_indigo_lib.indigoMapBond(self, query_bond.self));
if (mapped == 0)
return null;
return new IndigoObject(dispatcher, mapped);
}
public void append(IndigoObject obj)
{
dispatcher.setSessionID();
_indigo_lib.indigoAppend(self, obj.self);
}
public IndigoObject decomposeMolecule(IndigoObject mol)
{
dispatcher.setSessionID();
int res = dispatcher.checkResult(_indigo_lib.indigoDecomposeMolecule(self, mol.self));
if (res == 0)
return null;
return new IndigoObject(dispatcher, res, this);
}
public IndigoObject addBond(IndigoObject dest, int order)
{
dispatcher.setSessionID();
return(new IndigoObject(dispatcher, this, _indigo_lib.indigoAddBond(self, dest.self, order)));
}
public void addDecomposition(IndigoObject q_match)
{
dispatcher.setSessionID();
dispatcher.checkResult(_indigo_lib.indigoAddDecomposition(self, q_match.self));
}
/// <summary>
/// Execute similarity search operation
/// </summary>
/// <param name="query">indigo object (molecule or reaction)</param>
/// <param name="min">Minimum similarity value</param>
/// <param name="max">Maximum similairy value</param>
/// <returns>Bingo search object instance</returns>
public BingoObject searchSim(IndigoObject query, float min, float max)
{
return(searchSim(query, min, max, null));
}
public void append(IndigoObject obj)
{
dispatcher.setSessionID();
dispatcher.checkResult(_indigo_lib.indigoAppend(self, obj.self));
}
public Metafile renderToMetafile(IndigoObject obj)
{
_indigo.setSessionID ();
_indigo.checkResult (_indigo._indigo_lib.indigoSetOption ("render-output-format", "emf"));
byte[] res = renderToBuffer (obj);
MemoryStream ms = new MemoryStream (res);
Metafile mf = new Metafile (ms);
return mf;
}
public int atomMappingNumber(IndigoObject reaction_atom)
{
dispatcher.setSessionID();
return dispatcher.checkResult(_indigo_lib.indigoGetAtomMappingNumber(self, reaction_atom.self));
}
public IndigoObject reactionProductEnumerate(IndigoObject reaction, IndigoObject monomers)
{
setSessionID();
return(new IndigoObject(this, _indigo_lib.indigoReactionProductEnumerate(reaction.self, monomers.self)));
}
public void setAtomMappingNumber(IndigoObject reaction_atom, int number)
{
dispatcher.setSessionID();
dispatcher.checkResult(_indigo_lib.indigoSetAtomMappingNumber(self, reaction_atom.self, number));
}
public void transform(IndigoObject reaction, IndigoObject monomer)
{
setSessionID();
_indigo_lib.indigoTransform(reaction.self, monomer.self);
}
public ReactingCenter reactingCenter(IndigoObject bond)
{
int c;
dispatcher.setSessionID();
if (dispatcher.checkResult(_indigo_lib.indigoGetReactingCenter(self, bond.self, &c)) == 1)
return (ReactingCenter)c;
throw new IndigoException("reactingCenter(): unexpected result");
}
public void cmlAppend(IndigoObject item)
{
dispatcher.setSessionID();
_indigo_lib.indigoCmlAppend(self, item.self);
}
public void setReactingCenter(IndigoObject bond, ReactingCenter type)
{
dispatcher.setSessionID();
dispatcher.checkResult(_indigo_lib.indigoSetReactingCenter(self, bond.self, (int)type));
}
public void unignoreAtom(IndigoObject atom)
{
dispatcher.setSessionID();
_indigo_lib.indigoUnignoreAtom(self, atom.self);
}
public IndigoObject addBond(IndigoObject dest, int order)
{
dispatcher.setSessionID();
return new IndigoObject(dispatcher, dispatcher.checkResult(_indigo_lib.indigoAddBond(self, dest.self, order)), this);
}
public int countMatchesWithLimit(IndigoObject query, int embeddings_limit)
{
dispatcher.setSessionID();
return(_indigo_lib.indigoCountMatchesWithLimit(self, query.self, embeddings_limit));
}
public IndigoObject merge(IndigoObject what)
{
dispatcher.setSessionID();
return new IndigoObject(dispatcher, dispatcher.checkResult(_indigo_lib.indigoMerge(self, what.self)), this);
}
public void addDecomposition(IndigoObject q_match)
{
dispatcher.setSessionID();
_indigo_lib.indigoAddDecomposition(self, q_match.self);
}
public IndigoObject exactMatch(IndigoObject obj1, IndigoObject obj2)
{
return(exactMatch(obj1, obj2, ""));
}
public int atomMappingNumber(IndigoObject reaction_atom)
{
dispatcher.setSessionID();
return(_indigo_lib.indigoGetAtomMappingNumber(self, reaction_atom.self));
}
public int commonBits(IndigoObject obj1, IndigoObject obj2)
{
setSessionID();
return(_indigo_lib.indigoCommonBits(obj1.self, obj2.self));
}
public void setReactingCenter(IndigoObject bond, ReactingCenter type)
{
dispatcher.setSessionID();
_indigo_lib.indigoSetReactingCenter(self, bond.self, (int)type);
}
public IndigoObject substructureMatcher(IndigoObject target, string mode)
{
setSessionID();
return(new IndigoObject(this, target, _indigo_lib.indigoSubstructureMatcher(target.self, mode)));
}
public IndigoObject merge(IndigoObject what)
{
dispatcher.setSessionID();
return(new IndigoObject(dispatcher, this, _indigo_lib.indigoMerge(self, what.self)));
}
public IndigoObject substructureMatcher(IndigoObject target)
{
return(substructureMatcher(target, ""));
}
/// <summary>
/// Execute substructure search operation
/// </summary>
/// <param name="query">Indigo query object (molecule or reaction)</param>
/// <returns>Bingo search object instance</returns>
public BingoObject searchSub(IndigoObject query)
{
return(searchSub(query, null));
}
/// <summary>
/// Perform exact search operation
/// </summary>
/// <param name="query">indigo object (molecule or reaction)</param>
/// <param name="options">exact search options</param>
/// <returns>Bingo search object instance</returns>
public BingoObject searchExact(IndigoObject query, string options)
{
if (options == null)
{
options = "";
}
_indigo.setSessionID();
return new BingoObject(Bingo.checkResult(_indigo, _lib.bingoSearchExact(_id, query.self, options)), _indigo, _lib);
}
/// <summary>
/// Perform exact search operation
/// </summary>
/// <param name="query">indigo object (molecule or reaction)</param>
/// <returns>Bingo search object instance</returns>
public BingoObject searchExact(IndigoObject query)
{
return(searchExact(query, null));
}
/// <summary>
/// Perform exact search operation
/// </summary>
/// <param name="query">indigo object (molecule or reaction)</param>
/// <returns>Bingo search object instance</returns>
public BingoObject searchExact(IndigoObject query)
{
return searchExact(query, null);
}
public void renderToHDC(IndigoObject obj, IntPtr hdc, bool printing)
{
_indigo.setSessionID ();
int hdch = _indigo.checkResult (_renderer_lib.indigoRenderWriteHDC ((void*)hdc, printing ? 1 : 0));
_indigo.checkResult (_renderer_lib.indigoRender (obj.self, hdch));
}
/// <summary>
/// Execute similarity search operation
/// </summary>
/// <param name="query">indigo object (molecule or reaction)</param>
/// <param name="min">Minimum similarity value</param>
/// <param name="max">Maximum similairy value</param>
/// <returns>Bingo search object instance</returns>
public BingoObject searchSim(IndigoObject query, float min, float max)
{
return searchSim(query, min, max, null);
}
public IndigoObject decomposeMolecules(IndigoObject scaffold, IndigoObject structures)
{
setSessionID();
return(new IndigoObject(this, _indigo_lib.indigoDecomposeMolecules(scaffold.self, structures.self)));
}
public void cmlAppend(IndigoObject item)
{
dispatcher.setSessionID();
dispatcher.checkResult(_indigo_lib.indigoCmlAppend(self, item.self));
}
public void renderToFile(IndigoObject obj, string filename)
{
_indigo.setSessionID();
_indigo.checkResult(_renderer_lib.indigoRenderToFile(obj.self, filename));
}
public IndigoObject decomposeMolecules(IndigoObject scaffold, IEnumerable structures)
{
return(decomposeMolecules(scaffold, toIndigoArray(structures)));
}
public String getInchi(IndigoObject molecule)
{
_indigo.setSessionID();
return(new String(_indigo.checkResult(_inchi_lib.indigoInchiGetInchi(molecule.self))));
}
public IndigoObject createDecomposer(IndigoObject scaffold)
{
setSessionID();
return(new IndigoObject(this, _indigo_lib.indigoCreateDecomposer(scaffold.self)));
}
