//�Private�Methods�(3)�
/// <summary>
/// Checks for boxing.
/// </summary>
/// <param name="customTypeList">The custom type list.</param>
private void CheckForBoxing(List <MethodInfo> customTypeList)
{
foreach (var item in customTypeList)
{
try
{
//Checking if a method attribute has DLLImport which will be ignored.
if (item.GetCustomAttributes(typeof(DllImportAttribute), false).Length > 0)
{
continue;
}
var boxOpCodeList =
new MethodBodyAnalyzer().GetMethodBodyInILFormat(item).FindAll(opCodeItem =>
opCodeItem.OpCode == OpCodes.Box) as List <ILInstructionFormat>;
var pdbSourceData = new PDBReader(_symbolreader).GetMethodSourceFromPDB(item);
FetchSourceLines(boxOpCodeList, pdbSourceData, item);
}
//It is ok to suppress since for some methods, its source code can not be read or
//information can not be read from pdb.
catch (COMException) { }
catch (ExternalException) { }
}
}
public void TestSFBug1085912_1()
{
string filename_pdb = "NCDK.Data.PDB.1CKV.pdb";
var ins1 = ResourceLoader.GetAsStream(this.GetType(), filename_pdb);
ISimpleChemObjectReader reader = new PDBReader(ins1);
IChemFile chemFile1 = (IChemFile)reader.Read(builder.NewChemFile());
reader.Close();
IChemSequence seq1 = chemFile1[0];
IChemModel model1 = seq1[0];
IAtomContainer container = model1.MoleculeSet[0];
IBioPolymer polymer1 = (IBioPolymer)container;
int countchemFile1 = chemFile1.Count;
int countmodel1 = model1.MoleculeSet.Count;
int countpolymer1 = polymer1.Atoms.Count;
StringWriter writer = new StringWriter();
CMLWriter cmlWriter = new CMLWriter(writer);
cmlWriter.RegisterCustomizer(new PDBAtomCustomizer());
cmlWriter.Write(polymer1);
cmlWriter.Close();
string cmlContent1 = writer.ToString();
CMLReader reader2 = new CMLReader(new MemoryStream(Encoding.UTF8.GetBytes(cmlContent1)));
var chemFil2 = reader2.Read(builder.NewChemFile());
reader2.Close();
IChemSequence seq2 = chemFil2[0];
IChemModel model2 = seq2[0];
var polymer2 = (IPDBPolymer)model2.MoleculeSet[0];
int countchemFile2 = chemFil2.Count;
int countmodel2 = model2.MoleculeSet.Count;
int countpolymer2 = polymer2.Atoms.Count;
Assert.AreEqual(countchemFile1, countchemFile2);
Assert.AreEqual(countmodel1, countmodel2);
Assert.AreEqual(countpolymer1, countpolymer2);
writer = new StringWriter();
cmlWriter = new CMLWriter(writer);
cmlWriter.RegisterCustomizer(new PDBAtomCustomizer());
cmlWriter.Write(polymer2);
cmlWriter.Close();
string cmlContent2 = writer.ToString();
string conte1 = cmlContent1.Substring(0, 1000);
string conte2 = cmlContent2.Substring(0, 1000);
Assert.AreEqual(conte1, conte2);
}
public void TestCranbinSurface()
{
var bldr = CDK.Builder;
IChemFile chemFile;
var path = "NCDK.Data.PDB.1CRN.pdb";
using (var pdbr = new PDBReader(ResourceLoader.GetAsStream(path)))
{
chemFile = pdbr.Read(bldr.NewChemFile());
var mol = ChemFileManipulator.GetAllAtomContainers(chemFile).ElementAt(0);
var surface = new NumericalSurface(mol);
var map = surface.GetAtomSurfaceMap();
Assert.AreEqual(222, map.Count);
Assert.AreEqual(327, mol.Atoms.Count);
}
}
public void ReadPDB()
{
PDBReader reader = new PDBReader(this.fileName);
foreach (ClassDef cDef in GetClasses())
{
foreach (MethodDef mDef in cDef.GetMethods())
{
CILInstructions buffer = mDef.GetCodeBuffer();
PDBMethod meth = reader.GetMethod((int)mDef.Token());
if (meth == null)
{
continue; // no symbols for this method
}
PDBSequencePoint[] spList = meth.SequencePoints;
MergeBuffer mergeBuffer = new MergeBuffer(buffer.GetInstructions());
PDBScope outer = meth.Scope;
Scope root = ReadPDBScope(outer, mergeBuffer, null, mDef);
buffer.currentScope = root;
bool hasRootScope = mergeBuffer.hasRootScope();
if (!hasRootScope)
{
mergeBuffer.Add(new OpenScope(root), (uint)0);
}
foreach (PDBSequencePoint sp in spList)
{
PDBDocument doc = sp.Document;
mergeBuffer.Add(
new Line((uint)sp.Line, (uint)sp.Column, (uint)sp.EndLine, (uint)sp.EndColumn,
SourceFile.GetSourceFile(doc.URL, doc.Language, doc.LanguageVendor, doc.DocumentType)),
(uint)sp.Offset);
}
if (!hasRootScope)
{
mergeBuffer.Add(new CloseScope(root), (uint)outer.EndOffset);
}
buffer.SetInstructions(mergeBuffer.Instructions);
}
}
}
public void makeProtein(string filename)
{
//Uses PDBReader to read a file
//Then extracts the information needed to instantiate the protein
PDBReader reader = new PDBReader();
reader.readFile(filename);
AtomData[] proteinAtoms = reader.getProteinAtoms();
AtomData[] extraAtoms = reader.getExtraAtoms();
string[] aminoAcidCodes = reader.getAminoAcidCodes();
BondData[] extraBonds = reader.getExtraBonds();
//Gets instance of ProteinHelper
helper = ProteinHelper.getHelperInstance();
//Initalizes array of atoms
atoms = new GameObject[proteinAtoms.Length + extraAtoms.Length];
int i = 0;
//Instantiates atoms present in amino acids and adds object to array of Atoms
foreach (AtomData atom in proteinAtoms)
{
atoms[i++] = createAtom(atom.x, atom.y, atom.z, helper.getColor(atom.element));
}
//Instantiates atoms not present in amino acids and adds object to array of Atoms
foreach (AtomData atom in extraAtoms)
{
atoms[i++] = createAtom(atom.x, atom.y, atom.z, helper.getColor(atom.element));
}
//Instantiates bonds present in amino acid sequence and adds them to array of bonds
List <GameObject> bonds = new List <GameObject>();
BondData[] bondData;
i = 0;
int previousEnd = 0;
foreach (string aminoAcid in aminoAcidCodes)
{
//Instantiates bonds in the backbone of the amino acid
bonds.Add(createBond(atoms[i], atoms[i + 1]));
bonds.Add(createBond(atoms[i + 1], atoms[i + 2]));
bonds.Add(createBond(atoms[i + 2], atoms[i + 3])); //should be a double bond in future
//Instantiates bond connecting current amino acid to previous one
if (previousEnd != 0)
{
bonds.Add(createBond(atoms[previousEnd], atoms[i]));
}
//Grabs bonds in R group of current amino acid
bondData = helper.getRGroupBonds(aminoAcid);
//Instantiates each of the bonds in the R group
foreach (BondData bond in bondData)
{
bonds.Add(createBond(atoms[i + bond.atom1Index], atoms[i + bond.atom2Index]));
}
//Increases iterator and stores carboxyl end for next amino acid
previousEnd = i + 2;
i += helper.getNumAtoms(aminoAcid);
}
//Instantiates bonds not present in amino acid sequence and adds them to list of bonds
foreach (BondData bond in extraBonds)
{
bonds.Add(createBond(atoms[bond.atom1Index], atoms[bond.atom2Index]));
}
this.bonds = bonds.ToArray();
}
public void ReadPDB()
{
PDBReader reader = new PDBReader(this.fileName);
foreach (ClassDef cDef in GetClasses())
foreach (MethodDef mDef in cDef.GetMethods())
{
CILInstructions buffer = mDef.GetCodeBuffer();
PDBMethod meth = reader.GetMethod((int)mDef.Token());
if (meth == null)
continue; // no symbols for this method
PDBSequencePoint[] spList = meth.SequencePoints;
MergeBuffer mergeBuffer = new MergeBuffer(buffer.GetInstructions());
PDBScope outer = meth.Scope;
Scope root = ReadPDBScope(outer, mergeBuffer, null, mDef);
buffer.currentScope = root;
bool hasRootScope = mergeBuffer.hasRootScope();
if (!hasRootScope)
mergeBuffer.Add(new OpenScope(root), (uint)0);
foreach (PDBSequencePoint sp in spList)
{
PDBDocument doc = sp.Document;
mergeBuffer.Add(
new Line((uint)sp.Line, (uint)sp.Column, (uint)sp.EndLine, (uint)sp.EndColumn,
SourceFile.GetSourceFile(doc.URL, doc.Language, doc.LanguageVendor, doc.DocumentType)),
(uint)sp.Offset);
}
if (!hasRootScope)
mergeBuffer.Add(new CloseScope(root), (uint)outer.EndOffset);
buffer.SetInstructions(mergeBuffer.Instructions);
}
}
