本文整理汇总了C#中IAtomContainer.addAtom方法的典型用法代码示例。如果您正苦于以下问题：C# IAtomContainer.addAtom方法的具体用法？C# IAtomContainer.addAtom怎么用？C# IAtomContainer.addAtom使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类IAtomContainer的用法示例。
在下文中一共展示了IAtomContainer.addAtom方法的4个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的C#代码示例。
示例1: processFormula
/// <summary> Processes the content from the formula field of the INChI.
/// Typical values look like C6H6, from INChI=1.12Beta/C6H6/c1-2-4-6-5-3-1/h1-6H.
/// </summary>
public virtual IAtomContainer processFormula(IAtomContainer parsedContent, System.String atomsEncoding)
{
//logger.debug("Parsing atom data: ", atomsEncoding);
Regex pattern = new Regex("([A-Z][a-z]?)(\\d+)?(.*)");
//Pattern pattern = Pattern.compile("([A-Z][a-z]?)(\\d+)?(.*)");
System.String remainder = atomsEncoding;
while (remainder.Length > 0)
{
//logger.debug("Remaining: ", remainder);
Match matcher = pattern.Match(remainder);
//Matcher matcher = pattern.matcher(remainder);
//if (matcher.matches())
if (matcher != null && matcher.Success)
{
System.String symbol = matcher.Groups[1].Value;
//logger.debug("Atom symbol: ", symbol);
if (symbol.Equals("H"))
{
// don't add explicit hydrogens
}
else
{
System.String occurenceStr = matcher.Groups[2].Value;
int occurence = 1;
if (occurenceStr != null)
{
occurence = System.Int32.Parse(occurenceStr);
}
//logger.debug(" occurence: ", occurence);
for (int i = 1; i <= occurence; i++)
{
parsedContent.addAtom(parsedContent.Builder.newAtom(symbol));
}
}
remainder = matcher.Groups[3].Value;
if (remainder == null)
remainder = "";
//logger.debug(" Remaining: ", remainder);
}
else
{
//logger.error("No match found!");
remainder = "";
}
//logger.debug("NO atoms: ", parsedContent.AtomCount);
}
return parsedContent;
}示例2: readAtomBlock
//.........这里部分代码省略.........
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
// parse the element
System.String element = tokenizer.NextToken();
bool isElement = false;
try
{
isElement = IsotopeFactory.getInstance(atom.Builder).isElement(element);
}
catch (System.Exception exception)
{
throw new CDKException("Could not determine if element exists!", exception);
}
if (isPseudoAtom(element))
{
atom = readData.Builder.newPseudoAtom(atom);
}
else if (isElement)
{
atom.Symbol = element;
}
else
{
System.String error = "Cannot parse element of type: " + element;
//logger.error(error);
throw new CDKException("(Possible CDK bug) " + error);
}
// parse atom coordinates (in Angstrom)
try
{
System.String xString = tokenizer.NextToken();
System.String yString = tokenizer.NextToken();
System.String zString = tokenizer.NextToken();
double x = System.Double.Parse(xString);
double y = System.Double.Parse(yString);
double z = System.Double.Parse(zString);
atom.setPoint3d(new Point3d(x, y, z));
atom.setPoint2d(new Point2d(x, y)); // FIXME: dirty!
}
catch (System.Exception exception)
{
System.String error = "Error while parsing atom coordinates";
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
// atom-atom mapping
System.String mapping = tokenizer.NextToken();
if (!mapping.Equals("0"))
{
//logger.warn("Skipping atom-atom mapping: " + mapping);
} // else: default 0 is no mapping defined
// the rest are key value things
if (command.IndexOf("=") != -1)
{
System.Collections.Hashtable options = parseOptions(exhaustStringTokenizer(tokenizer));
System.Collections.IEnumerator keys = options.Keys.GetEnumerator();
//UPGRADE_TODO: Method 'java.util.Enumeration.hasMoreElements' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilEnumerationhasMoreElements'"
while (keys.MoveNext())
{
//UPGRADE_TODO: Method 'java.util.Enumeration.nextElement' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilEnumerationnextElement'"
System.String key = (System.String)keys.Current;
System.String value_Renamed = (System.String)options[key];
try
{
if (key.Equals("CHG"))
{
int charge = System.Int32.Parse(value_Renamed);
if (charge != 0)
{
// zero is no charge specified
atom.setFormalCharge(charge);
}
}
else
{
//logger.warn("Not parsing key: " + key);
}
}
catch (System.Exception exception)
{
//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'"
System.String error = "Error while parsing key/value " + key + "=" + value_Renamed + ": " + exception.Message;
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
}
}
// store atom
readData.addAtom(atom);
//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'"
//logger.debug("Added atom: " + atom);
}
}
}示例3: addExplicitHydrogensToSatisfyValency
/// <summary> Method that saturates an atom in a molecule by adding explicit hydrogens.
///
/// </summary>
/// <param name="atom"> Atom to saturate
/// </param>
/// <param name="container">AtomContainer containing the atom
/// </param>
/// <param name="count"> Number of hydrogens to add
/// </param>
/// <param name="totalContainer">In case you have a container containing multiple structures, this is the total container, whereas container is a partial structure
///
/// </param>
/// <cdk.keyword> hydrogen, adding </cdk.keyword>
/// <cdk.keyword> explicit hydrogen </cdk.keyword>
public virtual IAtomContainer addExplicitHydrogensToSatisfyValency(IAtomContainer container, IAtom atom, int count, IAtomContainer totalContainer)
{
//boolean create2DCoordinates = GeometryTools.has2DCoordinates(container);
IIsotope isotope = IsotopeFactory.getInstance(container.Builder).getMajorIsotope("H");
atom.setHydrogenCount(0);
IAtomContainer changedAtomsAndBonds = container.Builder.newAtomContainer();
for (int i = 1; i <= count; i++)
{
IAtom hydrogen = container.Builder.newAtom("H");
IsotopeFactory.getInstance(container.Builder).configure(hydrogen, isotope);
totalContainer.addAtom(hydrogen);
IBond newBond = container.Builder.newBond((IAtom) atom, hydrogen, 1.0);
totalContainer.addBond(newBond);
changedAtomsAndBonds.addAtom(hydrogen);
changedAtomsAndBonds.addBond(newBond);
}
return changedAtomsAndBonds;
}示例4: depthFirstTargetSearch
/// <summary> Recursivly perfoms a depth first search in a molecular graphs contained in
/// the AtomContainer molecule, starting at the root atom and returning when it
/// hits the target atom.
/// CAUTION: This recursive method sets the VISITED flag of each atom
/// does not reset it after finishing the search. If you want to do the
/// operation on the same collection of atoms more than once, you have
/// to set all the VISITED flags to false before each operation
/// by looping of the atoms and doing a
/// "atom.setFlag((CDKConstants.VISITED, false));"
///
/// </summary>
/// <param name="molecule">The
/// AtomContainer to be searched
/// </param>
/// <param name="root"> The root atom
/// to start the search at
/// </param>
/// <param name="target"> The target
/// </param>
/// <param name="path"> An
/// AtomContainer to be filled with the path
/// </param>
/// <returns> true if the
/// target atom was found during this function call
/// </returns>
public static bool depthFirstTargetSearch(IAtomContainer molecule, IAtom root, IAtom target, IAtomContainer path)
{
IBond[] bonds = molecule.getConnectedBonds(root);
IAtom nextAtom;
root.setFlag(CDKConstants.VISITED, true);
for (int f = 0; f < bonds.Length; f++)
{
nextAtom = bonds[f].getConnectedAtom(root);
if (!nextAtom.getFlag(CDKConstants.VISITED))
{
path.addAtom(nextAtom);
path.addBond(bonds[f]);
if (nextAtom == target)
{
return true;
}
else
{
if (!depthFirstTargetSearch(molecule, nextAtom, target, path))
{
// we did not find the target
path.removeAtom(nextAtom);
path.removeElectronContainer(bonds[f]);
}
else
{
return true;
}
}
}
}
return false;
}