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Structures can be manipulated directly using the
chemaxon.util.MolHandler
and
chemaxon.struc.Molecule
classes. In usual cases, developers will not need to access
Molecule directly, however MolHandler
might be needed occasionally.
After creating the MolHandler object from a
Molecule, several operations can be performed on the
structure using methods of MolHandler:
addHydrogens
|
Adds the implicit Hydrogen atoms to the molecule. |
addHydrogensToHeteroAtoms
|
Adds the implicit Hydrogen atoms to heteroatoms. |
aromatize
|
Converts the bonds in an aromatic system entered using single and double bonds to aromatic bonds. |
removeHydrogens
|
Removes the Hydrogen atoms from the molecule. |
toFormat
|
Converts the molecule to the specified text format (mol, csmol, smiles, ...) |
The following methods can be used to retrieve information on a structure:
calcMolFormula
|
Calculates the formula of the molecule. |
calcMolWeight
|
Calculates the molecular weight of the molecule. |
containsHydrogens
|
True if the molecule contains explicit Hydrogen atoms, false otherwise. |
getAtomCount
|
Retrieves the number of atoms in the Molecule stored in the MolHandler object. |
getFingerprintInBytes
|
Retrieves a chemical hashed fingerprint for the molecule in bytes. |
getFingerprintInInts
|
Retrieves a chemical hashed fingerprint for the molecule in
int units.
|
getHeavyAtomCount
|
Retrieves the number of atoms in the Molecule stored in the MolHandler object. |
getMolecule
|
Retrieves the Molecule from the MolHandler object. |
Steps of working with MolHandler:
MolHandler object.
To speed up the manipulation of structures by decreasing
the burden on the garbage collector, MolHandler
supports recycling. For this purpose, it is recommended to
apply the same MolHandler object to process a list of structures.
Java example:
MolHandler mh = new MolHandler();
while(...) {
String molfile = ...;
mh.setMolecule(molfile);
mh.addHydrogensToHeteroAtoms();
mh.aromatize();
Molecule molecule = mh.getMolecule();
...
}
The JChem API provides three levels of API support for hit coloring and
alignment. The first two higher-level methods return a colored Molecule object,
which can be directly set for a Marvin GUI component (e.g.
MViewPane
). In other cases the Molecule should be exported to Marvin Documents (MRV)
format, which preserves coloring. Then it can be displayed with coloring
by the Marvin Applet on a web page or other ChemAxon applications.
If the hits are the result of a database search performed with
JChemSearch use
JChemSearch.getHitsAsMolecules() to retrieve the hit
structures. This is also useful for displaying the hit structures in their
original format (coloring and alignment are optional).
During a substructure search the match can be visualized by coloring the matching atoms
in the target structure. Two classes are used in the following examples,
HitColoringAndAlignmentOptions and
HitDisplayTool.
HitColoringAndAlignmentOptions contains information about colouring and rotating the match. Its main parameters are:
| true, if match should be coloured | |
| colour of hit and non-hit atoms | |
| can be one of the following constants: | |
|
HitColoringAndAlignmentOptions colouringOptions =
new HitColoringAndAlignmentOptions();
colouringOptions.coloring = true;
colouringOptions.hitColor = Color.RED;
colouringOptions.nonHitColor = Color.GREEN;
colouringOptions.alignmentMode
= HitColoringAndAlignmentOptions.ALIGNMENT_ROTATE;
HitDisplayTool performs a search with the given query, target, search options and colouring options and returns a coloured / aligned molecule that can be displayed.
Molecule query = MoleculeImport.importMol("Q1.mrv", true);
MolSearchOptions searchOptions =
new MolSearchOptions();
hdt = new HitDisplayTool(colouringOptions, searchOptions,
null, query);
Molecule result = hdt.getHit(target);
A simple example application:
VisualizationExample.java
The two methods above perform the graph search internally, which enables
them to select the "best fit" from multiple hits for alignment.
In some cases one may already have the hit atom indexes, so for performance
or other reasons the older, lower-level methods of
MolHandler may be useful:
align
|
susbstructure hit alignment |
getNonHitBonds
|
returns bonds that are not part of substructure search hit |
getNonHitBondEndpoints
|
returns bond endpoints (atom indexes) that are not part of substructure search hit |
Usually a string containing a structure or other
information in text format has
to be converted before it is inserted into a web page.
For example each line in multiline applet parameters have to be
ended with backslash (\) character.
The chemaxon.util.HTMLTools has methods
for such conversions.
convertForAppletParameter
|
Converts a string to a format that can be used as a value of an applet parameter in an HTML page. |
convertForJavaScript
|
Converts a string to a format that can be used as a value of JavaScript variable in an HTML page. |
convertToUNIXStyle
|
Converts a string to UNIX style. |
insertStringBeforeLineEnds
|
Inserts the specified string before the ends of lines. |
replaceString
|
Replaces occurrences of a string with another one in a third string. |
JSP example (writing a string into JavaScript code):
...
<script LANGUAGE="JavaScript">
<!--
...
s = "<%= HTMLTools.convertForJavaScript(molfile) %>";
...
//-->
</script>
...
Methods useful for printing error messages into a web page:
exceptionToPage
|
Creates an HTML page that displays the message(s) of an exception. |
exceptionToString
|
Prints the message(s) of an exception in HTML format |
stringToPage
|
Creates an HTML page that displays the specified HTML text. |
JSP example (printing an error message to a web page):
try {
...
} catch(Throwable e) {
e.printStackTrace();
try {
%><%= HTMLTools.exceptionToString(e) %><%
} catch(Exception nf) {
%>Error: JChem repository not found<%
}
}