diff docs/modules/txt/Bond.txt @ 0:4816e4a8ae95 draft default tip

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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:
+
+        Set<PropertyName>(<PropertyValue>);
+        $PropertyValue = Get<PropertyName>();
+        Delete<PropertyName>();
+
+  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 <[e-mail]>
+
+SEE ALSO
+    Atom.pm, Molecule.pm
+
+COPYRIGHT
+    Copyright (C) 2015 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.
+