MolBond
The chemaxon.struc.MolBond class is used to represent chemical bond. To create a MolBond object, one of these constructor methods can be used:
-
MolBond(MolAtom a1, MolAtom a2, int f)
-
MolBond(MolAtom a1, MolAtom a2)
-
MolBond(MolBond b)
The two MolAtom objects in the constructors defines between which atoms is the bond defined. The int f constant defines the type of the bond. The value can be:
-
1 - single bond
-
2 - double bond
-
3 - triple bond
-
MolBond.AROMATIC - aromatic bond
-
MolBond.SINGLE_OR_DOUBLE - bond, that can be both single and double
-
MolBond.SINGLE_OR_AROMATIC - bond, that can be both single and aromatic
-
MolBond.DOUBLE_OR_AROMATIC - bond, that can be both double and aromatic
-
MolBond.CONJUGATED - conjugated bond
-
MolBond.COORDINATE - coordinated bond
-
MolBond.UP - single bond up
-
MolBond.DOWN - single bond down
-
MolBond.WAVY - single bond up or down
-
MolBond.STEREO1_MASK - single bond stereo mask. It is the same as UP | DOWN
-
MolBond.STEREO2_CARE - Cis/trans info of this bond is taken care of during the SSS process, used only for query bonds
-
MolBond.STEREO_MASK - Single and double bond stereo mask. It is the same as STEREO1_MASK | CTUMASK | STEREO2_CARE
-
MolBond.ANY - any bond
If this constant is omitted, single bond object will be created.
Similarly to the MolAtom the constructed MolBond object should be added to the molecule it belongs to.
Code examples
package
chemaxon.examples.strucrep
import
chemaxon.struc.*;
/**
* Example class for structure manipulation. Creates water.
*
* @author Andras Volford
*
*/
public
class
BuildMoleculeWater {
public
static
void
main(String[] args) {
// create an empty Molecule
Molecule m =
new
Molecule();
// create the Carbon atom
MolAtom a1 =
new
MolAtom(
8
);
// and add it to the molecule
m.add(a1);
// create the Hydrogen atom
MolAtom a2 =
new
MolAtom(
1
);
// and add it to the molecule
m.add(a2);
// create the Hydrogen atom
MolAtom a3 =
new
MolAtom(
1
);
// and add it to the molecule
m.add(a3);
System.out.println(m.toFormat(
"smiles"
));
// this prints [H+].[H+].O as no bond has been defined yet
// create a bond between atoms, bond order
MolBond b1 =
new
MolBond(a1, a2,
1
);
m.add(b1);
MolBond b2 =
new
MolBond(a1, a3,
1
);
m.add(b2);
System.out.println(m.toFormat(
"smiles"
));
// this prints water
}
}
/*
* Copyright (c) 1998-2014 ChemAxon Ltd. All Rights Reserved.
*/
import
java.io.IOException;
import
chemaxon.formats.MolFormatException;
import
chemaxon.formats.MolImporter;
import
chemaxon.struc.Molecule;
import
chemaxon.struc.MolAtom;
import
chemaxon.struc.MolBond;
/**
* Example class to demonstrate how to access atoms and bonds
* of the molecule.
*
* @author Andras Volford, Miklos Vargyas
*
*/
public
class
MoleculeAtoms {
public
static
void
main(String[] args) {
String filename = args[
0
];
try
{
// create a molecule importer for the given file
MolImporter mi =
new
MolImporter(filename);
// read the first molecule from the file
Molecule m = mi.read();
while
(m !=
null
) {
printAtoms(m);
printBonds(m);
// read the next molecule from the input file
m = mi.read();
}
mi.close();
}
catch
(MolFormatException e) {
System.err.println(
"Molecule format not recognised."
);
}
catch
(IOException e) {
System.err.println(
"I/O error:"
+ e);
}
}
private
static
void
printAtoms( Molecule m ) {
m.calcHybridization();
System.out.println(
"Atoms in the molecule\natomic number\tcharge\thybridisation"
);
for
(
int
i =
0
; i < m.getAtomCount(); i++) {
MolAtom a = m.getAtom(i);
System.out.println( i +
"th atom: "
+ a.getAtno() +
"\t\t"
+ a.getCharge() +
"\t"
+ a.getHybridizationState());
}
}
private
static
void
printBonds( Molecule m ) {
System.out.println(
"Bonds in the molecule\nbond order\tcoodinate"
);
for
(
int
i =
0
; i < m.getBondCount(); i++) {
MolBond b = m.getBond(i);
System.out.println( b.getType() +
"\t\t"
+ b.isCoordinate() +
" "
+ m.indexOf( b.getAtom1()) +
"-"
+ m.indexOf( b.getAtom2()));
}
}
}
The following table summarizes if the properties of the MolBond have set or get methods.
property |
set |
get |
note |
Index |
|
|
assigned automatically |
2 endpoints – 2 nodes |
|
|
|
Type |
|
|
|
Stereo information |
|
|
wedge / double bond stereo detailed in stereo chemistry |