本文整理汇总了C#中IAtomContainer.addBond方法的典型用法代码示例。如果您正苦于以下问题：C# IAtomContainer.addBond方法的具体用法？C# IAtomContainer.addBond怎么用？C# IAtomContainer.addBond使用的例子？那么, 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.addBond方法的5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: bondAtom
/// <summary>
/// Rebonds one atom by looking up nearby atom using the binary space partition tree.
/// </summary>
private void bondAtom(IAtomContainer container, IAtom atom)
{
double myCovalentRadius = atom.CovalentRadius;
double searchRadius = myCovalentRadius + maxCovalentRadius + bondTolerance;
Point tupleAtom = new Point(atom.X3d, atom.Y3d, atom.Z3d);
Bspt.EnumerateSphere e = bspt.enumHemiSphere(tupleAtom, searchRadius);
while (e.MoveNext())
{
IAtom atomNear = ((TupleAtom)e.Current).Atom;
if (atomNear != atom && container.getBond(atom, atomNear) == null)
{
bool isBonded_ = isBonded(myCovalentRadius, atomNear.CovalentRadius, e.foundDistance2());
if (isBonded_)
{
IBond bond = atom.Builder.newBond(atom, atomNear, 1.0);
container.addBond(bond);
}
}
}
}示例2: processConnections
/// <summary> Processes the content from the connections field of the INChI.
/// Typical values look like 1-2-4-6-5-3-1, from INChI=1.12Beta/C6H6/c1-2-4-6-5-3-1/h1-6H.
///
/// </summary>
/// <param name="bondsEncoding">the content of the INChI connections field
/// </param>
/// <param name="container"> the atomContainer parsed from the formula field
/// </param>
/// <param name="source"> the atom to build the path upon. If -1, then start new path
///
/// </param>
/// <seealso cref="processFormula">
/// </seealso>
public virtual void processConnections(System.String bondsEncoding, IAtomContainer container, int source)
{
//logger.debug("Parsing bond data: ", bondsEncoding);
IBond bondToAdd = null;
/* Fixme: treatment of branching is too limited! */
System.String remainder = bondsEncoding;
while (remainder.Length > 0)
{
//logger.debug("Bond part: ", remainder);
if (remainder[0] == '(')
{
System.String branch = chopBranch(remainder);
processConnections(branch, container, source);
if (branch.Length + 2 <= remainder.Length)
{
remainder = remainder.Substring(branch.Length + 2);
}
else
{
remainder = "";
}
}
else
{
Regex pattern = new Regex("^(\\d+)-?(.*)");
//Pattern pattern = Pattern.compile("^(\\d+)-?(.*)");
//Matcher matcher = pattern.matcher(remainder);
Match matcher = pattern.Match(remainder);
//if (matcher.matches())
if (matcher != null && matcher.Success)
{
System.String targetStr = matcher.Groups[1].Value;
int target = System.Int32.Parse(targetStr);
//logger.debug("Source atom: ", source);
//logger.debug("Target atom: ", targetStr);
IAtom targetAtom = container.getAtomAt(target - 1);
if (source != -1)
{
IAtom sourceAtom = container.getAtomAt(source - 1);
bondToAdd = container.Builder.newBond(sourceAtom, targetAtom, 1.0);
container.addBond(bondToAdd);
}
remainder = matcher.Groups[2].Value;
source = target;
//logger.debug(" remainder: ", remainder);
}
else
{
//logger.error("Could not get next bond info part");
return;
}
}
}
}示例3: readBondBlock
//.........这里部分代码省略.........
//logger.warn("Query order types are not supported (yet). File a bug if you need it");
}
else
{
bond.Order = (double)order;
}
}
catch (System.Exception exception)
{
System.String error = "Error while parsing bond index";
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
// parse index atom 1
try
{
System.String indexAtom1String = tokenizer.NextToken();
int indexAtom1 = System.Int32.Parse(indexAtom1String);
IAtom atom1 = readData.getAtomAt(indexAtom1 - 1);
bond.setAtomAt(atom1, 0);
}
catch (System.Exception exception)
{
System.String error = "Error while parsing index atom 1 in bond";
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
// parse index atom 2
try
{
System.String indexAtom2String = tokenizer.NextToken();
int indexAtom2 = System.Int32.Parse(indexAtom2String);
IAtom atom2 = readData.getAtomAt(indexAtom2 - 1);
bond.setAtomAt(atom2, 1);
}
catch (System.Exception exception)
{
System.String error = "Error while parsing index atom 2 in bond";
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
// the rest are key=value fields
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("CFG"))
{
int configuration = System.Int32.Parse(value_Renamed);
if (configuration == 0)
{
bond.Stereo = CDKConstants.STEREO_BOND_NONE;
}
else if (configuration == 1)
{
bond.Stereo = CDKConstants.STEREO_BOND_UP;
}
else if (configuration == 2)
{
bond.Stereo = CDKConstants.STEREO_BOND_UNDEFINED;
}
else if (configuration == 3)
{
bond.Stereo = CDKConstants.STEREO_BOND_DOWN;
}
}
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);
}
}
}
// storing bond
readData.addBond(bond);
//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 bond: " + bond);
}
}
}示例4: 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5: 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;
}