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NAME

Bond

SYNOPSIS

use Bond;

use Bond qw(:all);

DESCRIPTION

Bond class provides the following methods:

new, Copy, DeleteBond, GetAtoms, GetBondBeginAtom, GetBondEndAtom, GetBondFromAtom, GetBondToAtom, GetBondedAtom, GetCommonAtom, GetLargestRing, GetNumOfRings, GetNumOfRingsWithEvenSize, GetNumOfRingsWithOddSize, GetNumOfRingsWithSize, GetNumOfRingsWithSizeGreaterThan, GetNumOfRingsWithSizeLessThan, GetRings, GetRingsWithEvenSize, GetRingsWithOddSize, GetRingsWithSize, GetRingsWithSizeGreaterThan, GetRingsWithSizeLessThan, GetSizeOfLargestRing, GetSizeOfSmallestRing, GetSmallestRing, IsAromatic, IsBondStereochemistrySpecified, IsBondTypeSpecified, IsCis, IsCisOrTrans, IsCoordinate, IsDative, IsDouble, IsDown, IsDownward, IsHash, IsInRing, IsInRingOfSize, IsIonic, IsNotInRing, IsOnlyInOneRing, IsQuadruple, IsQuintuple, IsSextuple, IsSingle, IsTautomeric, IsTrans, IsTriple, IsUp, IsUpOrDown, IsUpward, IsWedge, IsWedgeOrHash, SetAtoms, SetBondOrder, SetBondStereochemistry, SetBondType, StringifyBond, SwitchBondFromAndToAtoms

Bond class is derived from ObjectProperty base class which provides methods not explicitly defined in Atom or ObjectProperty class using Perl's AUTOLOAD 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 Atoms invoved in Bond.

GetBondedAtom

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

Returns BondedAtom bonded to Atom in Bond.

GetBondBeginAtom

$BeginAtom = $Bond->GetBondBeginAtom();

Returns BeginAtom corresponding to bond starting atom in Bond.

GetBondEndAtom

$EndAtom = $Bond->GetBondEndAtom();

Returns EndAtom corresponding to bond ending atom in Bond.

GetBondFromAtom

$FromAtom = $Bond->GetBondFromAtom();

Returns FromAtom corresponding to bond starting atom in Bond.

GetBondToAtom

$ToAotm = $Bond->GetBondToAtom();

Returns ToAtom corresponding to bond ending atom in Bond.

GetCommonAtom

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

Returns Atom common to both Bond and $OtherBond.

GetLargestRing

@RingAtoms = $Bond->GetLargestRing();

Returns an array of ring Atoms 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 Atoms 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.

IsBondStereochemistrySpecified

$Status = $Bond->IsBondStereochemistrySpecified();

Returns 1 or 0 based on whether Bond's sterochemistry is specified.

IsBondTypeSpecified

$Status = $Bond->IsBondTypeSpecified();

Returns 1 or 0 based on whether Bond's type is specified.

IsCis

$Status = $Bond->IsCis();

Returns 1 or 0 based on whether it's a cis Bond.

IsCisOrTrans

$Status = $Bond->IsCisOrTrans();

Returns 1 or 0 based on whether it's a cis or trans Bond.

IsCoordinate

$Status = $Bond->IsCoordinate();

Returns 1 or 0 based on whether it's a coordinate or dative Bond.

IsDative

$Status = $Bond->IsDative();

Returns 1 or 0 based on whether it's a coordinate or dative Bond.

IsDouble

$Status =$Bond->IsDouble();

Returns 1 or 0 based on whether it's a double Bond.

IsDown

$Status = $Bond->IsDown();

Returns 1 or 0 based on whether it's a hash or down single Bond.

IsDownward

$Return = $Bond->IsDownward();

Returns 1 or 0 based on whether it's a downward Bond.

IsHash

$Status = $Bond->IsHash();

Returns 1 or 0 based on whether it's a hash or down single 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.

IsIonic

$Status = $Bond->IsIonic();

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

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.

IsQuadruple

$Status = $Bond->IsQuadruple();

Returns 1 or 0 based on whether it's a quadruple Bond.

IsQuintuple

$Status = $Bond->IsQuintuple();

Returns 1 or 0 based on whether it's a quintuple Bond.

IsSextuple

$Status = $Bond->IsSextuple();

Returns 1 or 0 based on whether it's a sextuple Bond.

IsSingle

$Status =$Bond->IsSingle();

Returns 1 or 0 based on whether it's a single Bond.

IsTriple

$Status =$Bond->IsTriple();

Returns 1 or 0 based on whether it's a triple Bond.

IsTautomeric

$Status = $Bond->IsTautomeric();

Returns 1 or 0 based on whether it's a Bond.

IsTrans

$Status = $Bond->IsTrans();

Returns 1 or 0 based on whether it's a trans Bond.

IsUp

$Status = $Bond->IsUp();

Returns 1 or 0 based on whether it's a up Bond.

IsUpOrDown

$Status = $Bond->IsUpOrDown();

Returns 1 or 0 based on whether it's an up or down Bond.

IsUpward

$Status = $Bond->IsUpward();

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

IsWedge

$Status = $Bond->IsWedge();

Returns 1 or 0 based on whether it's a wedge Bond.

IsWedgeOrHash

$Status = $Bond->IsWedgeOrHash();

Returns 1 or 0 based on whether it's a wedge or hash Bond.

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 = Aromatic, 2 = Double, 3 = Triple, 4 = Quadruple, 5 = Quintuple, 6 = Sextuple, 7 = Septuple

Notes:

. BondType property is automatically assigned using default BondType values for specified BondOrder.
. BondType values can also be explicit set.
. To make bonds aromatic in a ring, explicitly set "Aromatic" property for bond/atoms and make sure appropriate BondOrder values are assigned.
. Dative or coordinate 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:

0: None, Ionic, Unspecified
1 : Single, Dative, Coordinate, SingleOrDouble, SingleOrAromatic, Tautomeric
2 : Double, SingleOrDouble, DoubleOrAromatic, Tautomeric
3 : Triple
4 : Quadruple
5 : Quintuple
6 : Sextuple
7 : Septuple
1.5 : Aromatic, Resonance, SingleOrAromatic, DoubleOrAromatic

Notes:

o BondType Any is valid for all BondOrders.
o BondOrder property is automatically assigned using default BondOrder values for specified BondType.

Possible bond stereochemistry values for different bond orders are:

0 : None, Unspecified
1 : Wedge, Up, Hash, Down, Wavy, WedgeOrHash, UpOrDown, Upward, Downward,
     None, Unspecified
2 : Cis, Trans, Z, E, DoubleCross, CisOrTrans, None, Unspecified

SetBondStereochemistry

$Bond = $Bond->SetBondStereochemistry($BondStereochemistry);

Sets bond stereochemistry of Bond to specified BondStereochemistry and returns Bond. Possible BondStereoChemistry values for different bond orders are:

BondOrder: 1

None, Unspecified: Not a stereo bond or unspecified

Wedge, Up : Wedge end pointing up
Hash, Down: Wedge end pointing down
Wavy, WedgeOrHash, UpOrDown: Wedge end up or down

Upward: Single bond around cis/trans double bonds pointing upward
Downward: Single bond around cis/trans double bonds pointing upward

Notes:

o Wedge starts at begin atom of a bond making wedge pointed end always at this atom.
o Upward/downward bonds start at atoms involved in cis/trans double bonds.

BondOrder: 2

None, Unspecified: Not a stereo bond or unspecified

Z, cis: Similar groups on same side of double bond
E, trans: Similar groups on different side of double bond

CisOrTrans, DoubleCross: cis or trans

StringifyBond

$BondString = $Bond->StringifyBond();

Returns a string containing information about bond object.

SwitchBondFromAndToAtoms

$Bond = $Bond->SwitchBondFromAndToAtoms();

Swaps bond from and to atoms in Bond and returns Bond.

AUTHOR

Manish Sud

SEE ALSO

Atom.pm, Molecule.pm

COPYRIGHT

Copyright (C) 2024 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.