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NAME

Bond

SYNOPSIS

use Bond;

use Bond qw(:all);

DESCRIPTION

Bond class provides the following methods:

new, Copy, DeleteBond, GetAtoms, GetBondedAtom, GetCommonAtom, GetLargestRing , GetNumOfRings, GetNumOfRingsWithEvenSize, GetNumOfRingsWithOddSize , GetNumOfRingsWithSize, GetNumOfRingsWithSizeGreaterThan , GetNumOfRingsWithSizeLessThan, GetRings, GetRingsWithEvenSize , GetRingsWithOddSize, GetRingsWithSize, GetRingsWithSizeGreaterThan , GetRingsWithSizeLessThan, GetSizeOfLargestRing, GetSizeOfSmallestRing , GetSmallestRing, IsAromatic, IsInRing, IsInRingOfSize, IsNotInRing , IsOnlyInOneRing, SetAtoms, SetBondOrder, SetBondType, SetID, SetStereochemistry , StringifyBond

Bond class is derived from ObjectProperty base class which provides methods not explictly defined in Atom or ObjectProperty class using Perl's AUTOLOD functionality. These methods are generated on-the-fly for a specified object property:

METHODS

new

$NewBond = new Bond([%PropertyNameAndValues]);

Using specified Bond property names and values hash, new method creates a new object and returns a reference to newly created Bond object. By default, following properties are initialized:

ID = SequentialObjectID
@Atoms = ();
BondType = ""
BondOrder = ""

Except for ID property, all other default properties and other additional properties can be set during invocation of this method.

Examples:

$Bond = new Bond();
$DoubleBond = new Bond('Atoms' => [$Atom2, $Atom1], 'BondOrder' => 2);

Copy

$BondCopy = $Bond->Copy();

Copy Bond and its associated data using Storable::dclone and return a new Bond object

DeleteBond

$Bond->DeleteBond();

Delete Bond between atoms in from a molecule.

GetAtoms

@BondedAtoms = $Bond->GetAtoms();

Returns an array containing Atom objects invoved in Bond

GetBondedAtom

$BondedAtom = $Bond->GetBondedAtom($Atom);

Returns BondedAtom object bonded to Atom in Bond

GetCommonAtom

$CommonAtom = $Bond->GetCommonAtom($OtherBond);

Returns Atom object common to bonds Bond and $OtherBond

GetLargestRing

@RingAtoms = $Bond->GetLargestRing();

Returns an array of ring Atom objects corresponding to the largest ring containing Bond in a molecule

GetNumOfRings

$NumOfRings = $Bond->GetNumOfRings();

Returns number of rings containing Bond in a molecule

GetNumOfRingsWithEvenSize

$NumOfRings = $Bond->GetNumOfRingsWithEvenSize();

Returns number of rings with even size containing Bond in a molecule

GetNumOfRingsWithOddSize

$NumOfRings = $Bond->GetNumOfRingsWithOddSize();

Returns number of rings with odd size containing Bond in a molecule

GetNumOfRingsWithSize

$NumOfRings = $Bond->GetNumOfRingsWithSize($RingSize);

Returns number of rings with specific RingSize containing Bond in a molecule

GetNumOfRingsWithSizeGreaterThan

$NumOfRings = $Bond->GetNumOfRingsWithSizeGreaterThan($RingSize);

Returns number of rings with size greater than specific RingSize containing Bond in a molecule

GetNumOfRingsWithSizeLessThan

$NumOfRings = $Bond->GetNumOfRingsWithSizeLessThan($RingSize);

Returns number of rings with size less than specific RingSize containing Bond in a molecule

GetRings

@Rings = $Bond->GetRings();

Returns an array of references to arrays containing ring atoms corressponding to all rings containing Bond in a molecule

GetRingsWithEvenSize

@Rings = $Bond->GetRingsWithEvenSize();

Returns an array of references to arrays containing ring atoms corressponding to all rings with even size containing Bond in a molecule

GetRingsWithOddSize

@Rings = $Bond->GetRingsWithOddSize();

Returns an array of references to arrays containing ring atoms corressponding to all rings with odd size containing Bond in a molecule.

GetRingsWithSize

@Rings = $Bond->GetRingsWithSize($RingSize);

Returns an array of references to arrays containing ring atoms corressponding to all rings with specific RingSize containing Bond in a molecule

GetRingsWithSizeGreaterThan

@Rings = $Bond->GetRingsWithSizeGreaterThan($RingSize);

Returns an array of references to arrays containing ring atoms corressponding to all rings with size greater than specific RingSize containing Bond in a molecule

GetRingsWithSizeLessThan

@Rings = $Bond->GetRingsWithSizeLessThan($RingSize);

Returns an array of references to arrays containing ring atoms corressponding to all rings with size less than specific RingSize containing Bond in a molecule

GetSizeOfLargestRing

$Size = $Bond->GetSizeOfLargestRing();

Returns size of the largest ring containing Bond in a molecule

GetSizeOfSmallestRing

$Size = $Bond->GetSizeOfSmallestRing();

Returns size of the smallest ring containing Bond in a molecule

GetSmallestRing

@RingAtoms = $Bond->GetSmallestRing();

Returns an array of ring Atom objects corresponding to the largest ring containing Bond in a molecule

IsAromatic

$Status = $Bond->IsAromatic();

Returns 1 or 0 based on whether it's an aromatic Bond

IsInRing

$Status = $Bond->IsInRing();

Returns 1 or 0 based on whether Bond is present in a ring

IsInRingOfSize

$Status = $Bond->IsInRingOfSize($Size);

Returns 1 or 0 based on whether Bond is present in a ring of specific Size

IsNotInRing

$Status = $Bond->IsNotInRing();

Returns 1 or 0 based on whether Bond is not present in a ring

IsOnlyInOneRing

$Status = $Bond->IsOnlyInOneRing();

Returns 1 or 0 based on whether Bond is only present in one ring

SetAtoms

$Bond->SetAtoms($AtomsRef);
$Bond->SetAtoms(@Atoms);

Set atoms of Bond to atoms in Atoms array or in a reference to an array of atoms and return Bond

SetBondOrder

$Bond->SetBondOrder($BondOrder);

Sets bond order of Bond to specified BondOrder and returns Bond. Possible bond order values: 1 = Single, 1.5 = Atomatic, 2 = Double, 3 = Triple, 4 = Quadruple.

Notes:

o BondType property is automatially assiged using default BondType values for specified BondOrder.
o BondType values can also be explicit set.
o To make bonds aromatic in a ring, explicitly set "Aromatic" property for bond/atoms and make sure apporpriate BondOrder values are assgined.
o Dative bond types are treated as single bond types with explicit formal charge of + and - on first and second bond atoms.

SetBondType

$Bond->SetBondType($BondType);

Sets bond type for Bond to specified BondType and returns Bond. Possible bond type values for different bond orders are:

1 : Single, SingleWedge (Up), SingleHash (Down), SingleWavy, Dative
2 : Double, DoubleCross (Cis/Trans)
3 : Triple
4 : Quadruple
1.5 : Aromatic (Single/Double), Tautomeric(Single/Double)

Notes:

o BondOrder property is automatially assiged using default BondOrder values for specified BondType.

SetStereochemistry

$Bond->SetStereochemistry($Stereochemistry);

Sets bond stereochemistry for Bond to specified Stereochemistry and returns Bond. Possible Stereochemistry values: Z, cis, E, trans

StringifyBond

$BondString = $Bond->StringifyBond();

Returns a string containing information about Bond object

AUTHOR

Manish Sud

SEE ALSO

Atom.pm, Molecule.pm

COPYRIGHT

Copyright (C) 2004-2008 Manish Sud. All rights reserved.

This file is part of MayaChemTools.

MayaChemTools is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.