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java.lang.Objectinfo.mrupp.isoak1.MolecularGraph
public class MolecularGraph
Query-only data structure for molecular graphs. Contains all information about one molecule. Designed as a constant data structure, i.e. once created no modifications are possible. Optimized for fast access.
Nested Class Summary | |
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static class |
MolecularGraph.FileFormat
The supported chemical file formats (currently only SDF). |
Field Summary | |
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static int |
MAX_DEGREE
Maximum degree of any vertex. |
Constructor Summary | |
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MolecularGraph(java.io.LineNumberReader reader,
MolecularGraph.FileFormat format)
Creates a new molecular graph from a given source. |
Method Summary | |
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float |
atomDescriptor(int atom,
int descriptor)
Returns the value of the given descriptor for the given atom. |
float |
bondDescriptor(int bond,
int descriptor)
Returns the value of the given descriptor for the given bond. |
int |
bondIndex(int a,
int b)
Returns the index of the bond between two atoms. |
java.lang.String |
name()
Returns an identifier for the molecular graph. |
int |
neighbour(int atom,
int n)
Returns the n-th neighbour (index) of given atom. |
int |
numAtoms()
Returns the total number of atoms in the molecular graph. |
int |
numBonds()
Returns the total number of bonds in the molecular graph. |
int |
numNeighbours(int atom)
Returns the degree of given atom. |
Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final int MAX_DEGREE
Constructor Detail |
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public MolecularGraph(java.io.LineNumberReader reader, MolecularGraph.FileFormat format) throws java.io.IOException, java.text.ParseException
reader
- the source from which a textual representation of the molecule is read.format
- the file format of the textual source.
java.io.IOException
java.text.ParseException
Method Detail |
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public float atomDescriptor(int atom, int descriptor)
public float bondDescriptor(int bond, int descriptor)
public int bondIndex(int a, int b)
public java.lang.String name()
public int neighbour(int atom, int n)
public int numAtoms()
public int numBonds()
public int numNeighbours(int atom)
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