public long EstimateRamUsage(System.Object obj)
{
long size = Size(obj);
seen.Clear();
return(size);
}
internal virtual void Clear()
{
terms.Clear();
queries.Clear();
docIDs.Clear();
numTerms = 0;
bytesUsed = 0;
}
public void Visit(object t, object parent, int childIndex, IDictionary <string, object> unusedlabels)
{
// the unusedlabels arg is null as visit on token type doesn't set.
_labels.Clear();
if (_outer.ParseCore(t, _tpattern, _labels))
{
_visitor.Visit(t, parent, childIndex, _labels);
}
}
private static void setGroupSuccessors(System.Collections.IDictionary theSuccessors, System.String theSegName)
{
for (System.Collections.IEnumerator it = new SupportClass.HashSetSupport(theSuccessors.Keys).GetEnumerator(); it.MoveNext();)
{
StructRef from = (StructRef)it.Current;
StructRef to = (StructRef)theSuccessors[from];
from.setSuccessor(theSegName, to);
}
theSuccessors.Clear();
}
protected void odsEquipTypes_OnInserting(object source, ObjectDataSourceMethodEventArgs e)
{
System.Collections.IDictionary paramsFromPage = e.InputParameters;
TrackerDotNet.control.EquipTypeTbl _et = new TrackerDotNet.control.EquipTypeTbl();
_et.EquipTypeName = paramsFromPage["EquipTypeName"].ToString();
_et.EquipTypeDesc = paramsFromPage["EquipTypeDesc"].ToString();
paramsFromPage.Clear();
paramsFromPage.Add("objEquipType", _et);
}
public void Sync()
{
current.Clear();
for (int i = 0; i < keys.Count; ++i)
{
current[keys[i]] = values[i];
}
keys.Clear();
values.Clear();
Reset();
}
internal void ApplyPropertyValue(object target)
{
if (target == null)
{
throw new ArgumentNullException("target");
}
// Do nothing for parameter-based values
if (_property != null)
{
try
{
if (_isDictionary && _property != null && _property.GetSetMethod() == null)
{
System.Collections.IDictionary dictionary = (System.Collections.IDictionary)_property.GetValue(target, null);
dictionary.Clear();
if (HasValue)
{
((IDictionaryHelper)_value).ApplyValues(dictionary);
}
}
else if (!_isDictionary && _isMultiValue && !ArgumentType.IsArray)
{
object collection = _property.GetValue(target, null);
System.Collections.IList list = collection as System.Collections.IList;
if (list != null)
{
list.Clear();
}
else
{
typeof(ICollection <>).MakeGenericType(ElementType).GetMethod("Clear").Invoke(collection, null);
}
if (HasValue)
{
((ICollectionHelper)_value).ApplyValues(collection);
}
}
else if (HasValue || Value != null) // Don't set the value of an unspecified argument with a null default value.
{
_property.SetValue(target, Value, null);
}
}
catch (TargetInvocationException ex)
{
throw new CommandLineArgumentException(string.Format(CultureInfo.CurrentCulture, Properties.Resources.SetValueErrorFormat, ArgumentName, ex.InnerException.Message), ArgumentName, CommandLineArgumentErrorCategory.ApplyValueError, ex.InnerException);
}
}
}
static int _m_Clear(RealStatePtr L)
{
try {
ObjectTranslator translator = ObjectTranslatorPool.Instance.Find(L);
System.Collections.IDictionary gen_to_be_invoked = (System.Collections.IDictionary)translator.FastGetCSObj(L, 1);
{
gen_to_be_invoked.Clear( );
return(0);
}
} catch (System.Exception gen_e) {
return(LuaAPI.luaL_error(L, "c# exception:" + gen_e));
}
}
/// <summary> Removes all statically stored {@link StringResourceRepository}s.</summary>
/// <since> 1.6
/// </since>
public static void ClearRepositories()
{
STATIC_REPOSITORIES.Clear();
}
/// <summary> Read a <code>ChemFile</code> from a file in PDB format. The molecules
/// in the file are stored as <code>BioPolymer</code>s in the
/// <code>ChemFile</code>. The residues are the monomers of the
/// <code>BioPolymer</code>, and their names are the concatenation of the
/// residue, chain id, and the sequence number. Separate chains (denoted by
/// TER records) are stored as separate <code>BioPolymer</code> molecules.
///
/// <p>Connectivity information is not currently read.
///
/// </summary>
/// <returns> The ChemFile that was read from the PDB file.
/// </returns>
private IChemFile readChemFile(IChemFile oFile)
{
int bonds = 0;
// initialize all containers
IChemSequence oSeq = oFile.Builder.newChemSequence();
IChemModel oModel = oFile.Builder.newChemModel();
ISetOfMolecules oSet = oFile.Builder.newSetOfMolecules();
// some variables needed
string cCol;
PDBAtom oAtom;
PDBPolymer oBP = new PDBPolymer();
System.Text.StringBuilder cResidue;
string oObj;
IMonomer oMonomer;
string cRead = "";
char chain = 'A'; // To ensure stringent name giving of monomers
IStrand oStrand;
int lineLength = 0;
atomNumberMap = System.Collections.Hashtable.Synchronized(new System.Collections.Hashtable());
// do the reading of the Input
try
{
do
{
cRead = _oInput.ReadLine();
//logger.debug("Read line: ", cRead);
if (cRead != null)
{
lineLength = cRead.Length;
if (lineLength < 80)
{
//logger.warn("Line is not of the expected length 80!");
}
// make sure the record name is 6 characters long
if (lineLength < 6)
{
cRead = cRead + " ";
}
// check the first column to decide what to do
cCol = cRead.Substring(0, (6) - (0));
if ("ATOM ".ToUpper().Equals(cCol.ToUpper()))
{
// read an atom record
oAtom = readAtom(cRead, lineLength);
// construct a string describing the residue
cResidue = new System.Text.StringBuilder(8);
oObj = oAtom.ResName;
if (oObj != null)
{
cResidue = cResidue.Append(oObj.Trim());
}
oObj = oAtom.ChainID;
if (oObj != null)
{
// cResidue = cResidue.append(((String)oObj).trim());
cResidue = cResidue.Append(System.Convert.ToString(chain));
}
oObj = oAtom.ResSeq;
if (oObj != null)
{
cResidue = cResidue.Append(oObj.Trim());
}
// search for an existing strand or create a new one.
oStrand = oBP.getStrand(System.Convert.ToString(chain));
if (oStrand == null)
{
oStrand = new PDBStrand();
oStrand.StrandName = System.Convert.ToString(chain);
}
// search for an existing monomer or create a new one.
oMonomer = oBP.getMonomer(cResidue.ToString(), System.Convert.ToString(chain));
if (oMonomer == null)
{
PDBMonomer monomer = new PDBMonomer();
monomer.MonomerName = cResidue.ToString();
monomer.MonomerType = oAtom.ResName;
monomer.ChainID = oAtom.ChainID;
monomer.ICode = oAtom.ICode;
oMonomer = monomer;
}
// add the atom
oBP.addAtom(oAtom, oMonomer, oStrand);
System.Object tempObject;
//UPGRADE_WARNING: At least one expression was used more than once in the target code. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1181'"
tempObject = atomNumberMap[(System.Int32)oAtom.Serial];
atomNumberMap[(System.Int32)oAtom.Serial] = oAtom;
if (readConnect.Set && tempObject != null)
{
//logger.warn("Duplicate serial ID found for atom: ", oAtom);
}
// //logger.debug("Added ATOM: ", oAtom);
/** As HETATMs cannot be considered to either belong to a certain monomer or strand,
* they are dealt with seperately.*/
}
else if ("HETATM".ToUpper().Equals(cCol.ToUpper()))
{
// read an atom record
oAtom = readAtom(cRead, lineLength);
oAtom.HetAtom = true;
oBP.addAtom(oAtom);
System.Object tempObject2;
//UPGRADE_WARNING: At least one expression was used more than once in the target code. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1181'"
tempObject2 = atomNumberMap[(System.Int32)oAtom.Serial];
atomNumberMap[(System.Int32)oAtom.Serial] = oAtom;
if (tempObject2 != null)
{
//logger.warn("Duplicate serial ID found for atom: ", oAtom);
}
//logger.debug("Added HETATM: ", oAtom);
}
else if ("TER ".ToUpper().Equals(cCol.ToUpper()))
{
// start new strand
chain++;
oStrand = new PDBStrand();
oStrand.StrandName = System.Convert.ToString(chain);
//logger.debug("Added new STRAND");
}
else if ("END ".ToUpper().Equals(cCol.ToUpper()))
{
atomNumberMap.Clear();
// create bonds and finish the molecule
if (deduceBonding.Set)
{
// OK, try to deduce the bonding patterns
if (oBP.AtomCount != 0)
{
// Create bonds. If bonds could not be created, all bonds are deleted.
try
{
if (useRebondTool.Set)
{
if (!createBondsWithRebondTool(oBP))
{
// Get rid of all potentially created bonds.
//logger.info("Bonds could not be created using the RebondTool when PDB file was read.");
oBP.removeAllBonds();
}
}
else
{
if (!createBonds(oBP))
{
// Get rid of all potentially created bonds.
//logger.info("Bonds could not be created when PDB file was read.");
oBP.removeAllBonds();
}
}
}
catch (System.Exception exception)
{
//logger.info("Bonds could not be created when PDB file was read.");
//logger.debug(exception);
}
}
}
oSet.addMolecule(oBP);
// oBP = new BioPolymer();
// } else if (cCol.equals("USER ")) {
// System.out.println(cLine);
// System.out.println(cLine);
// } else if (cCol.equals("ENDMDL")) {
// System.out.println(cLine);
}
else if (cCol.Equals("MODEL "))
{
// OK, start a new model and save the current one first *if* it contains atoms
if (oBP.AtomCount > 0)
{
// save the model
oSet.addAtomContainer(oBP);
oModel.SetOfMolecules = oSet;
oSeq.addChemModel(oModel);
// setup a new one
oBP = new PDBPolymer();
oModel = oFile.Builder.newChemModel();
oSet = oFile.Builder.newSetOfMolecules();
}
}
else if ("REMARK".ToUpper().Equals(cCol.ToUpper()))
{
System.Object comment = oFile.getProperty(CDKConstants.COMMENT);
if (comment == null)
{
comment = "";
}
if (lineLength > 12)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Object.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
comment = comment.ToString() + cRead.Substring(11).Trim() + "\n";
oFile.setProperty(CDKConstants.COMMENT, comment);
}
else
{
//logger.warn("REMARK line found without any comment!");
}
}
else if ("COMPND".ToUpper().Equals(cCol.ToUpper()))
{
string title = cRead.Substring(10).Trim();
oFile.setProperty(CDKConstants.TITLE, title);
}
/*************************************************************
* Read connectivity information from CONECT records.
* Only covalent bonds are dealt with. Perhaps salt bridges
* should be dealt with in the same way..?
*/
else if (readConnect.Set && "CONECT".ToUpper().Equals(cCol.ToUpper()))
{
cRead.Trim();
if (cRead.Length < 16)
{
//logger.debug("Skipping unexpected empty CONECT line! : ", cRead);
}
else
{
string bondAtom = cRead.Substring(7, 5).Trim();
int bondAtomNo = System.Int32.Parse(bondAtom);
for (int b = 0; b < 9; b += (b == 5 ? 2 : 1))
{
string bondedAtom = cRead.Substring((b * 5) + 11, 5).Trim();
int bondedAtomNo;
if (int.TryParse(bondedAtom, out bondedAtomNo))
{
bonds++;
addBond(oBP, bondAtomNo, bondedAtomNo);
}
}
//string bondedAtom = cRead.Substring(12, 5).Trim();
//int bondedAtomNo = -1;
//try
//{
// bondedAtomNo = System.Int32.Parse(bondedAtom);
//}
//catch (System.Exception e)
//{
// bondedAtomNo = -1;
//}
//if (bondedAtomNo != -1)
//{
// bonds++;
// addBond(oBP, bondAtomNo, bondedAtomNo);
// //logger.warn("Bonded " + bondAtomNo + " with " + bondedAtomNo);
//}
//else
//{
//}
//if (cRead.Length > 17)
//{
// bondedAtom = cRead.Substring(16, 5);
// bondedAtom = bondedAtom.Trim();
// try
// {
// bondedAtomNo = System.Int32.Parse(bondedAtom);
// }
// catch (System.Exception e)
// {
// bondedAtomNo = -1;
// }
// if (bondedAtomNo != -1)
// {
// bonds++;
// addBond(oBP, bondAtomNo, bondedAtomNo);
// //logger.warn("Bonded " + bondAtomNo + " with " + bondedAtomNo);
// }
//}
//if (cRead.Length > 22)
//{
// bondedAtom = cRead.Substring(22, 5);
// bondedAtom = bondedAtom.Trim();
// try
// {
// bondedAtomNo = System.Int32.Parse(bondedAtom);
// }
// catch (System.Exception e)
// {
// bondedAtomNo = -1;
// }
// if (bondedAtomNo != -1)
// {
// bonds++;
// addBond(oBP, bondAtomNo, bondedAtomNo);
// //logger.warn("Bonded " + bondAtomNo + " with " + bondedAtomNo);
// }
//}
//if (cRead.Length > 27)
//{
// bondedAtom = cRead.Substring(27, 5);
// bondedAtom = bondedAtom.Trim();
// try
// {
// bondedAtomNo = System.Int32.Parse(bondedAtom);
// }
// catch (System.Exception e)
// {
// bondedAtomNo = -1;
// }
// if (bondedAtomNo != -1)
// {
// bonds++;
// addBond(oBP, bondAtomNo, bondedAtomNo);
// //logger.warn("Bonded " + bondAtomNo + " with " + bondedAtomNo);
// }
//}
}
}
/*************************************************************/
else if ("HELIX ".ToUpper().Equals(cCol.ToUpper()))
{
// HELIX 1 H1A CYS A 11 LYS A 18 1 RESIDUE 18 HAS POSITIVE PHI 1D66 72
// 1 2 3 4 5 6 7
// 01234567890123456789012345678901234567890123456789012345678901234567890123456789
PDBStructure structure = new PDBStructure();
structure.StructureType = PDBStructure.HELIX;
structure.StartChainID = cRead[19];
structure.StartSequenceNumber = System.Int32.Parse(cRead.Substring(21, (25) - (21)).Trim());
structure.StartInsertionCode = cRead[25];
structure.EndChainID = cRead[31];
structure.EndSequenceNumber = System.Int32.Parse(cRead.Substring(33, (37) - (33)).Trim());
structure.EndInsertionCode = cRead[37];
oBP.addStructure(structure);
}
else if ("SHEET ".ToUpper().Equals(cCol.ToUpper()))
{
PDBStructure structure = new PDBStructure();
structure.StructureType = PDBStructure.SHEET;
structure.StartChainID = cRead[21];
structure.StartSequenceNumber = System.Int32.Parse(cRead.Substring(22, (26) - (22)).Trim());
structure.StartInsertionCode = cRead[26];
structure.EndChainID = cRead[32];
structure.EndSequenceNumber = System.Int32.Parse(cRead.Substring(33, (37) - (33)).Trim());
structure.EndInsertionCode = cRead[37];
oBP.addStructure(structure);
}
else if ("TURN ".ToUpper().Equals(cCol.ToUpper()))
{
PDBStructure structure = new PDBStructure();
structure.StructureType = PDBStructure.TURN;
structure.StartChainID = cRead[19];
structure.StartSequenceNumber = System.Int32.Parse(cRead.Substring(20, (24) - (20)).Trim());
structure.StartInsertionCode = cRead[24];
structure.EndChainID = cRead[30];
structure.EndSequenceNumber = System.Int32.Parse(cRead.Substring(31, (35) - (31)).Trim());
structure.EndInsertionCode = cRead[35];
oBP.addStructure(structure);
} // ignore all other commands
}
}
while (_oInput.Peek() != -1 && (cRead != null));
}
catch (System.Exception e)
{
//logger.error("Found a problem at line:\n");
//logger.error(cRead);
//logger.error("01234567890123456789012345678901234567890123456789012345678901234567890123456789");
//logger.error(" 1 2 3 4 5 6 7 ");
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
//logger.error(" error: " + e.Message);
//logger.debug(e);
}
// try to close the Input
try
{
_oInput.Close();
}
catch (System.Exception e)
{
//logger.debug(e);
}
// Set all the dependencies
oModel.SetOfMolecules = oSet;
oSeq.addChemModel(oModel);
oFile.addChemSequence(oSeq);
return oFile;
}
internal virtual void removeAllLocals()
{
m_locals.Clear(); m_activationObject = null;
}
internal virtual void removeAllArguments()
{
m_args.Clear();
}
/* doc location == msgID & curPath together.
* If we've encountered an element called "elementNam", then this tries
* to determine what it is, based on what we already know about the document.
* returns true if we can make sense of this new element name given the
* position we're at (represented by msgID / curPath),
* false if we can't (which probably means this should be a useless element).
* returning true doesn't mean that we actually changed msgID or curPath, it
* might mean that we just passed through a segment group element OK.
*/
protected internal static bool tryToGrowDocLocationFromElementName(System.Text.StringBuilder msgID, NuGenDatumPath curPath, System.Collections.IDictionary segmentId2nextRepIdx, NuGenDatumPath lastDumpedPath, System.String elementName)
{
bool ok = false; // ok == can we make sense of this new element?
// hmm ... where are we in the document:
if ((msgID.Length == 0) && (curPath.size() == 0))
{
// we're entering a message
msgID.Replace(msgID.ToString(0, msgID.Length - 0), elementName, 0, msgID.Length - 0);
segmentId2nextRepIdx.Clear();
ok = true;
}
else if ((msgID.Length > 0) && (curPath.size() == 0))
{
// we're entering either a segment-group element (eg. <ADT_A01.PROCEDURE>)
// or an actual segment element.
if (!(elementName.StartsWith("" + msgID + '.')))
{
// must be an actual segment.
curPath.add(elementName);
if (segmentId2nextRepIdx.Contains(elementName))
{
curPath.add(segmentId2nextRepIdx[elementName]);
}
else
{
curPath.add((System.Object) 0);
}
segmentId2nextRepIdx[elementName] = (System.Int32)(((System.Int32)curPath.get_Renamed(curPath.size() - 1)) + 1);
}
ok = true;
}
else if ((msgID.Length > 0) && (curPath.size() > 0))
{
// we're entering a field or a component or a subcomponent.
if (curPath.size() == 2)
{
// we're entering a field element
// all fields should start with segment-ID + '.'
if (elementName.StartsWith("" + curPath.get_Renamed(0) + '.'))
{
try
{
int fieldIdxFromElementName = System.Int32.Parse(elementName.Substring(elementName.IndexOf('.') + 1));
curPath.add((System.Object)fieldIdxFromElementName);
// now add the repetition idx to curPath:
if ((lastDumpedPath.size() >= 4) && (((System.Int32)lastDumpedPath.get_Renamed(2)) == fieldIdxFromElementName))
{
// lastDumpedPath has a fieldIdx and a fieldRepIdx.
curPath.add((System.Object)(((System.Int32)lastDumpedPath.get_Renamed(3)) + 1));
}
else
{
curPath.add((System.Object) 0);
}
ok = true;
}
catch (System.FormatException)
{
}
} // else => this isn't a field -- must be useless.
}
else if ((curPath.size() == 4) || (curPath.size() == 5))
{
// we're entering a component or subcomponent element
try
{
int idxFromElementName = System.Int32.Parse(elementName.Substring(elementName.IndexOf('.') + 1));
curPath.add((System.Object)idxFromElementName);
ok = true;
}
catch (System.FormatException)
{
}
}
}
return(ok);
}
/// <summary> Read a <code>ChemFile</code> from a file in PDB format. The molecules
/// in the file are stored as <code>BioPolymer</code>s in the
/// <code>ChemFile</code>. The residues are the monomers of the
/// <code>BioPolymer</code>, and their names are the concatenation of the
/// residue, chain id, and the sequence number. Separate chains (denoted by
/// TER records) are stored as separate <code>BioPolymer</code> molecules.
///
/// <p>Connectivity information is not currently read.
///
/// </summary>
/// <returns> The ChemFile that was read from the PDB file.
/// </returns>
private IChemFile readChemFile(IChemFile oFile)
{
int bonds = 0;
// initialize all containers
IChemSequence oSeq = oFile.Builder.newChemSequence();
IChemModel oModel = oFile.Builder.newChemModel();
ISetOfMolecules oSet = oFile.Builder.newSetOfMolecules();
// some variables needed
string cCol;
PDBAtom oAtom;
PDBPolymer oBP = new PDBPolymer();
System.Text.StringBuilder cResidue;
string oObj;
IMonomer oMonomer;
string cRead = "";
char chain = 'A'; // To ensure stringent name giving of monomers
IStrand oStrand;
int lineLength = 0;
atomNumberMap = System.Collections.Hashtable.Synchronized(new System.Collections.Hashtable());
// do the reading of the Input
try
{
do
{
cRead = _oInput.ReadLine();
//logger.debug("Read line: ", cRead);
if (cRead != null)
{
lineLength = cRead.Length;
if (lineLength < 80)
{
//logger.warn("Line is not of the expected length 80!");
}
// make sure the record name is 6 characters long
if (lineLength < 6)
{
cRead = cRead + " ";
}
// check the first column to decide what to do
cCol = cRead.Substring(0, (6) - (0));
if ("ATOM ".ToUpper().Equals(cCol.ToUpper()))
{
// read an atom record
oAtom = readAtom(cRead, lineLength);
// construct a string describing the residue
cResidue = new System.Text.StringBuilder(8);
oObj = oAtom.ResName;
if (oObj != null)
{
cResidue = cResidue.Append(oObj.Trim());
}
oObj = oAtom.ChainID;
if (oObj != null)
{
// cResidue = cResidue.append(((String)oObj).trim());
cResidue = cResidue.Append(System.Convert.ToString(chain));
}
oObj = oAtom.ResSeq;
if (oObj != null)
{
cResidue = cResidue.Append(oObj.Trim());
}
// search for an existing strand or create a new one.
oStrand = oBP.getStrand(System.Convert.ToString(chain));
if (oStrand == null)
{
oStrand = new PDBStrand();
oStrand.StrandName = System.Convert.ToString(chain);
}
// search for an existing monomer or create a new one.
oMonomer = oBP.getMonomer(cResidue.ToString(), System.Convert.ToString(chain));
if (oMonomer == null)
{
PDBMonomer monomer = new PDBMonomer();
monomer.MonomerName = cResidue.ToString();
monomer.MonomerType = oAtom.ResName;
monomer.ChainID = oAtom.ChainID;
monomer.ICode = oAtom.ICode;
oMonomer = monomer;
}
// add the atom
oBP.addAtom(oAtom, oMonomer, oStrand);
System.Object tempObject;
//UPGRADE_WARNING: At least one expression was used more than once in the target code. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1181'"
tempObject = atomNumberMap[(System.Int32)oAtom.Serial];
atomNumberMap[(System.Int32)oAtom.Serial] = oAtom;
if (readConnect.Set && tempObject != null)
{
//logger.warn("Duplicate serial ID found for atom: ", oAtom);
}
// //logger.debug("Added ATOM: ", oAtom);
/** As HETATMs cannot be considered to either belong to a certain monomer or strand,
* they are dealt with seperately.*/
}
else if ("HETATM".ToUpper().Equals(cCol.ToUpper()))
{
// read an atom record
oAtom = readAtom(cRead, lineLength);
oAtom.HetAtom = true;
oBP.addAtom(oAtom);
System.Object tempObject2;
//UPGRADE_WARNING: At least one expression was used more than once in the target code. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1181'"
tempObject2 = atomNumberMap[(System.Int32)oAtom.Serial];
atomNumberMap[(System.Int32)oAtom.Serial] = oAtom;
if (tempObject2 != null)
{
//logger.warn("Duplicate serial ID found for atom: ", oAtom);
}
//logger.debug("Added HETATM: ", oAtom);
}
else if ("TER ".ToUpper().Equals(cCol.ToUpper()))
{
// start new strand
chain++;
oStrand = new PDBStrand();
oStrand.StrandName = System.Convert.ToString(chain);
//logger.debug("Added new STRAND");
}
else if ("END ".ToUpper().Equals(cCol.ToUpper()))
{
atomNumberMap.Clear();
// create bonds and finish the molecule
if (deduceBonding.Set)
{
// OK, try to deduce the bonding patterns
if (oBP.AtomCount != 0)
{
// Create bonds. If bonds could not be created, all bonds are deleted.
try
{
if (useRebondTool.Set)
{
if (!createBondsWithRebondTool(oBP))
{
// Get rid of all potentially created bonds.
//logger.info("Bonds could not be created using the RebondTool when PDB file was read.");
oBP.removeAllBonds();
}
}
else
{
if (!createBonds(oBP))
{
// Get rid of all potentially created bonds.
//logger.info("Bonds could not be created when PDB file was read.");
oBP.removeAllBonds();
}
}
}
catch (System.Exception exception)
{
//logger.info("Bonds could not be created when PDB file was read.");
//logger.debug(exception);
}
}
}
oSet.addMolecule(oBP);
// oBP = new BioPolymer();
// } else if (cCol.equals("USER ")) {
// System.out.println(cLine);
// System.out.println(cLine);
// } else if (cCol.equals("ENDMDL")) {
// System.out.println(cLine);
}
else if (cCol.Equals("MODEL "))
{
// OK, start a new model and save the current one first *if* it contains atoms
if (oBP.AtomCount > 0)
{
// save the model
oSet.addAtomContainer(oBP);
oModel.SetOfMolecules = oSet;
oSeq.addChemModel(oModel);
// setup a new one
oBP = new PDBPolymer();
oModel = oFile.Builder.newChemModel();
oSet = oFile.Builder.newSetOfMolecules();
}
}
else if ("REMARK".ToUpper().Equals(cCol.ToUpper()))
{
System.Object comment = oFile.getProperty(CDKConstants.COMMENT);
if (comment == null)
{
comment = "";
}
if (lineLength > 12)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Object.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
comment = comment.ToString() + cRead.Substring(11).Trim() + "\n";
oFile.setProperty(CDKConstants.COMMENT, comment);
}
else
{
//logger.warn("REMARK line found without any comment!");
}
}
else if ("COMPND".ToUpper().Equals(cCol.ToUpper()))
{
string title = cRead.Substring(10).Trim();
oFile.setProperty(CDKConstants.TITLE, title);
}
/*************************************************************
* Read connectivity information from CONECT records.
* Only covalent bonds are dealt with. Perhaps salt bridges
* should be dealt with in the same way..?
*/
else if (readConnect.Set && "CONECT".ToUpper().Equals(cCol.ToUpper()))
{
cRead.Trim();
if (cRead.Length < 16)
{
//logger.debug("Skipping unexpected empty CONECT line! : ", cRead);
}
else
{
string bondAtom = cRead.Substring(7, 5).Trim();
int bondAtomNo = System.Int32.Parse(bondAtom);
for (int b = 0; b < 9; b += (b == 5 ? 2 : 1))
{
string bondedAtom = cRead.Substring((b * 5) + 11, 5).Trim();
int bondedAtomNo;
if (int.TryParse(bondedAtom, out bondedAtomNo))
{
bonds++;
addBond(oBP, bondAtomNo, bondedAtomNo);
}
}
//string bondedAtom = cRead.Substring(12, 5).Trim();
//int bondedAtomNo = -1;
//try
//{
// bondedAtomNo = System.Int32.Parse(bondedAtom);
//}
//catch (System.Exception e)
//{
// bondedAtomNo = -1;
//}
//if (bondedAtomNo != -1)
//{
// bonds++;
// addBond(oBP, bondAtomNo, bondedAtomNo);
// //logger.warn("Bonded " + bondAtomNo + " with " + bondedAtomNo);
//}
//else
//{
//}
//if (cRead.Length > 17)
//{
// bondedAtom = cRead.Substring(16, 5);
// bondedAtom = bondedAtom.Trim();
// try
// {
// bondedAtomNo = System.Int32.Parse(bondedAtom);
// }
// catch (System.Exception e)
// {
// bondedAtomNo = -1;
// }
// if (bondedAtomNo != -1)
// {
// bonds++;
// addBond(oBP, bondAtomNo, bondedAtomNo);
// //logger.warn("Bonded " + bondAtomNo + " with " + bondedAtomNo);
// }
//}
//if (cRead.Length > 22)
//{
// bondedAtom = cRead.Substring(22, 5);
// bondedAtom = bondedAtom.Trim();
// try
// {
// bondedAtomNo = System.Int32.Parse(bondedAtom);
// }
// catch (System.Exception e)
// {
// bondedAtomNo = -1;
// }
// if (bondedAtomNo != -1)
// {
// bonds++;
// addBond(oBP, bondAtomNo, bondedAtomNo);
// //logger.warn("Bonded " + bondAtomNo + " with " + bondedAtomNo);
// }
//}
//if (cRead.Length > 27)
//{
// bondedAtom = cRead.Substring(27, 5);
// bondedAtom = bondedAtom.Trim();
// try
// {
// bondedAtomNo = System.Int32.Parse(bondedAtom);
// }
// catch (System.Exception e)
// {
// bondedAtomNo = -1;
// }
// if (bondedAtomNo != -1)
// {
// bonds++;
// addBond(oBP, bondAtomNo, bondedAtomNo);
// //logger.warn("Bonded " + bondAtomNo + " with " + bondedAtomNo);
// }
//}
}
}
/*************************************************************/
else if ("HELIX ".ToUpper().Equals(cCol.ToUpper()))
{
// HELIX 1 H1A CYS A 11 LYS A 18 1 RESIDUE 18 HAS POSITIVE PHI 1D66 72
// 1 2 3 4 5 6 7
// 01234567890123456789012345678901234567890123456789012345678901234567890123456789
PDBStructure structure = new PDBStructure();
structure.StructureType = PDBStructure.HELIX;
structure.StartChainID = cRead[19];
structure.StartSequenceNumber = System.Int32.Parse(cRead.Substring(21, (25) - (21)).Trim());
structure.StartInsertionCode = cRead[25];
structure.EndChainID = cRead[31];
structure.EndSequenceNumber = System.Int32.Parse(cRead.Substring(33, (37) - (33)).Trim());
structure.EndInsertionCode = cRead[37];
oBP.addStructure(structure);
}
else if ("SHEET ".ToUpper().Equals(cCol.ToUpper()))
{
PDBStructure structure = new PDBStructure();
structure.StructureType = PDBStructure.SHEET;
structure.StartChainID = cRead[21];
structure.StartSequenceNumber = System.Int32.Parse(cRead.Substring(22, (26) - (22)).Trim());
structure.StartInsertionCode = cRead[26];
structure.EndChainID = cRead[32];
structure.EndSequenceNumber = System.Int32.Parse(cRead.Substring(33, (37) - (33)).Trim());
structure.EndInsertionCode = cRead[37];
oBP.addStructure(structure);
}
else if ("TURN ".ToUpper().Equals(cCol.ToUpper()))
{
PDBStructure structure = new PDBStructure();
structure.StructureType = PDBStructure.TURN;
structure.StartChainID = cRead[19];
structure.StartSequenceNumber = System.Int32.Parse(cRead.Substring(20, (24) - (20)).Trim());
structure.StartInsertionCode = cRead[24];
structure.EndChainID = cRead[30];
structure.EndSequenceNumber = System.Int32.Parse(cRead.Substring(31, (35) - (31)).Trim());
structure.EndInsertionCode = cRead[35];
oBP.addStructure(structure);
} // ignore all other commands
}
}while (_oInput.Peek() != -1 && (cRead != null));
}
catch (System.Exception e)
{
//logger.error("Found a problem at line:\n");
//logger.error(cRead);
//logger.error("01234567890123456789012345678901234567890123456789012345678901234567890123456789");
//logger.error(" 1 2 3 4 5 6 7 ");
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
//logger.error(" error: " + e.Message);
//logger.debug(e);
}
// try to close the Input
try
{
_oInput.Close();
}
catch (System.Exception e)
{
//logger.debug(e);
}
// Set all the dependencies
oModel.SetOfMolecules = oSet;
oSeq.addChemModel(oModel);
oFile.addChemSequence(oSeq);
return(oFile);
}
public void Clear()
{
dict.Clear();
}