Mercurial > repos > deepakjadmin > mayatool3_test3

diff mayachemtools/docs/modules/man3/Bond.3 @ 0:73ae111cf86f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author deepakjadmin
date Wed, 20 Jan 2016 11:55:01 -0500
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mayachemtools/docs/modules/man3/Bond.3	Wed Jan 20 11:55:01 2016 -0500
@@ -0,0 +1,715 @@
+.\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.22)
+.\"
+.\" Standard preamble:
+.\" ========================================================================
+.de Sp \" Vertical space (when we can't use .PP)
+.if t .sp .5v
+.if n .sp
+..
+.de Vb \" Begin verbatim text
+.ft CW
+.nf
+.ne \\$1
+..
+.de Ve \" End verbatim text
+.ft R
+.fi
+..
+.\" Set up some character translations and predefined strings.  \*(-- will
+.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left
+.\" double quote, and \*(R" will give a right double quote.  \*(C+ will
+.\" give a nicer C++.  Capital omega is used to do unbreakable dashes and
+.\" therefore won't be available.  \*(C` and \*(C' expand to `' in nroff,
+.\" nothing in troff, for use with C<>.
+.tr \(*W-
+.ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p'
+.ie n \{\
+.    ds -- \(*W-
+.    ds PI pi
+.    if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch
+.    if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\"  diablo 12 pitch
+.    ds L" ""
+.    ds R" ""
+.    ds C` ""
+.    ds C' ""
+'br\}
+.el\{\
+.    ds -- \|\(em\|
+.    ds PI \(*p
+.    ds L" ``
+.    ds R" ''
+'br\}
+.\"
+.\" Escape single quotes in literal strings from groff's Unicode transform.
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\"
+.\" If the F register is turned on, we'll generate index entries on stderr for
+.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
+.\" entries marked with X<> in POD.  Of course, you'll have to process the
+.\" output yourself in some meaningful fashion.
+.ie \nF \{\
+.    de IX
+.    tm Index:\\$1\t\\n%\t"\\$2"
+..
+.    nr % 0
+.    rr F
+.\}
+.el \{\
+.    de IX
+..
+.\}
+.\"
+.\" Accent mark definitions (@(#)ms.acc 1.5 88/02/08 SMI; from UCB 4.2).
+.\" Fear.  Run.  Save yourself.  No user-serviceable parts.
+.    \" fudge factors for nroff and troff
+.if n \{\
+.    ds #H 0
+.    ds #V .8m
+.    ds #F .3m
+.    ds #[ \f1
+.    ds #] \fP
+.\}
+.if t \{\
+.    ds #H ((1u-(\\\\n(.fu%2u))*.13m)
+.    ds #V .6m
+.    ds #F 0
+.    ds #[ \&
+.    ds #] \&
+.\}
+.    \" simple accents for nroff and troff
+.if n \{\
+.    ds ' \&
+.    ds ` \&
+.    ds ^ \&
+.    ds , \&
+.    ds ~ ~
+.    ds /
+.\}
+.if t \{\
+.    ds ' \\k:\h'-(\\n(.wu*8/10-\*(#H)'\'\h"|\\n:u"
+.    ds ` \\k:\h'-(\\n(.wu*8/10-\*(#H)'\`\h'|\\n:u'
+.    ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'^\h'|\\n:u'
+.    ds , \\k:\h'-(\\n(.wu*8/10)',\h'|\\n:u'
+.    ds ~ \\k:\h'-(\\n(.wu-\*(#H-.1m)'~\h'|\\n:u'
+.    ds / \\k:\h'-(\\n(.wu*8/10-\*(#H)'\z\(sl\h'|\\n:u'
+.\}
+.    \" troff and (daisy-wheel) nroff accents
+.ds : \\k:\h'-(\\n(.wu*8/10-\*(#H+.1m+\*(#F)'\v'-\*(#V'\z.\h'.2m+\*(#F'.\h'|\\n:u'\v'\*(#V'
+.ds 8 \h'\*(#H'\(*b\h'-\*(#H'
+.ds o \\k:\h'-(\\n(.wu+\w'\(de'u-\*(#H)/2u'\v'-.3n'\*(#[\z\(de\v'.3n'\h'|\\n:u'\*(#]
+.ds d- \h'\*(#H'\(pd\h'-\w'~'u'\v'-.25m'\f2\(hy\fP\v'.25m'\h'-\*(#H'
+.ds D- D\\k:\h'-\w'D'u'\v'-.11m'\z\(hy\v'.11m'\h'|\\n:u'
+.ds th \*(#[\v'.3m'\s+1I\s-1\v'-.3m'\h'-(\w'I'u*2/3)'\s-1o\s+1\*(#]
+.ds Th \*(#[\s+2I\s-2\h'-\w'I'u*3/5'\v'-.3m'o\v'.3m'\*(#]
+.ds ae a\h'-(\w'a'u*4/10)'e
+.ds Ae A\h'-(\w'A'u*4/10)'E
+.    \" corrections for vroff
+.if v .ds ~ \\k:\h'-(\\n(.wu*9/10-\*(#H)'\s-2\u~\d\s+2\h'|\\n:u'
+.if v .ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'\v'-.4m'^\v'.4m'\h'|\\n:u'
+.    \" for low resolution devices (crt and lpr)
+.if \n(.H>23 .if \n(.V>19 \
+\{\
+.    ds : e
+.    ds 8 ss
+.    ds o a
+.    ds d- d\h'-1'\(ga
+.    ds D- D\h'-1'\(hy
+.    ds th \o'bp'
+.    ds Th \o'LP'
+.    ds ae ae
+.    ds Ae AE
+.\}
+.rm #[ #] #H #V #F C
+.\" ========================================================================
+.\"
+.IX Title "BOND 1"
+.TH BOND 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
+.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
+.\" way too many mistakes in technical documents.
+.if n .ad l
+.nh
+.SH "NAME"
+Bond
+.SH "SYNOPSIS"
+.IX Header "SYNOPSIS"
+use Bond;
+.PP
+use Bond qw(:all);
+.SH "DESCRIPTION"
+.IX Header "DESCRIPTION"
+\&\fBBond\fR class provides the following methods:
+.PP
+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
+.PP
+\&\fBBond\fR class is derived from \fBObjectProperty\fR base class which provides methods not explicitly
+defined in \fBAtom\fR or \fBObjectProperty\fR class using Perl's \s-1AUTOLOAD\s0 functionality. These methods
+are generated on-the-fly for a specified object property:
+.PP
+.Vb 3
+\&    Set<PropertyName>(<PropertyValue>);
+\&    $PropertyValue = Get<PropertyName>();
+\&    Delete<PropertyName>();
+.Ve
+.SS "\s-1METHODS\s0"
+.IX Subsection "METHODS"
+.IP "\fBnew\fR" 4
+.IX Item "new"
+.Vb 1
+\&    $NewBond = new Bond([%PropertyNameAndValues]);
+.Ve
+.Sp
+Using specified \fIBond\fR property names and values hash, \fBnew\fR method creates a new object
+and returns a reference to newly created \fBBond\fR object. By default, following properties are
+initialized:
+.Sp
+.Vb 4
+\&    ID = SequentialObjectID
+\&    @Atoms = ();
+\&    BondType = ""
+\&    BondOrder = ""
+.Ve
+.Sp
+Except for \fI\s-1ID\s0\fR property, all other default properties and other additional properties can
+be set during invocation of this method.
+.Sp
+Examples:
+.Sp
+.Vb 3
+\&    $Bond = new Bond();
+\&    $DoubleBond = new Bond(\*(AqAtoms\*(Aq => [$Atom2, $Atom1],
+\&                           \*(AqBondOrder\*(Aq => 2);
+.Ve
+.IP "\fBCopy\fR" 4
+.IX Item "Copy"
+.Vb 1
+\&    $BondCopy = $Bond\->Copy();
+.Ve
+.Sp
+Copy \fIBond\fR and its associated data using \fBStorable::dclone\fR and return a new
+\&\fBBond\fR object.
+.IP "\fBDeleteBond\fR" 4
+.IX Item "DeleteBond"
+.Vb 1
+\&    $Bond\->DeleteBond();
+.Ve
+.Sp
+Delete \fIBond\fR between atoms in from a molecule.
+.IP "\fBGetAtoms\fR" 4
+.IX Item "GetAtoms"
+.Vb 1
+\&    @BondedAtoms = $Bond\->GetAtoms();
+.Ve
+.Sp
+Returns an array containing \fIAtoms\fR invoved in \fIBond\fR.
+.IP "\fBGetBondedAtom\fR" 4
+.IX Item "GetBondedAtom"
+.Vb 1
+\&    $BondedAtom = $Bond\->GetBondedAtom($Atom);
+.Ve
+.Sp
+Returns \fBBondedAtom\fR bonded to \fIAtom\fR in  \fIBond\fR.
+.IP "\fBGetBondBeginAtom\fR" 4
+.IX Item "GetBondBeginAtom"
+.Vb 1
+\&    $BeginAtom = $Bond\->GetBondBeginAtom();
+.Ve
+.Sp
+Returns \fBBeginAtom\fR corresponding to bond starting atom in \fIBond\fR.
+.IP "\fBGetBondEndAtom\fR" 4
+.IX Item "GetBondEndAtom"
+.Vb 1
+\&    $EndAtom = $Bond\->GetBondEndAtom();
+.Ve
+.Sp
+Returns \fBEndAtom\fR corresponding to bond ending atom in \fIBond\fR.
+.IP "\fBGetBondFromAtom\fR" 4
+.IX Item "GetBondFromAtom"
+.Vb 1
+\&    $FromAtom = $Bond\->GetBondFromAtom();
+.Ve
+.Sp
+Returns \fBFromAtom\fR corresponding to bond starting atom in \fIBond\fR.
+.IP "\fBGetBondToAtom\fR" 4
+.IX Item "GetBondToAtom"
+.Vb 1
+\&    $ToAotm = $Bond\->GetBondToAtom();
+.Ve
+.Sp
+Returns \fBToAtom\fR corresponding to bond ending atom in \fIBond\fR.
+.IP "\fBGetCommonAtom\fR" 4
+.IX Item "GetCommonAtom"
+.Vb 1
+\&    $CommonAtom = $Bond\->GetCommonAtom($OtherBond);
+.Ve
+.Sp
+Returns \fBAtom\fR common to both \fIBond\fR and \fI\f(CI$OtherBond\fI\fR.
+.IP "\fBGetLargestRing\fR" 4
+.IX Item "GetLargestRing"
+.Vb 1
+\&    @RingAtoms = $Bond\->GetLargestRing();
+.Ve
+.Sp
+Returns an array of ring \fIAtoms\fR corresponding to the largest ring containing \fIBond\fR.
+in a molecule
+.IP "\fBGetNumOfRings\fR" 4
+.IX Item "GetNumOfRings"
+.Vb 1
+\&    $NumOfRings = $Bond\->GetNumOfRings();
+.Ve
+.Sp
+Returns number of rings containing \fIBond\fR in a molecule.
+.IP "\fBGetNumOfRingsWithEvenSize\fR" 4
+.IX Item "GetNumOfRingsWithEvenSize"
+.Vb 1
+\&    $NumOfRings = $Bond\->GetNumOfRingsWithEvenSize();
+.Ve
+.Sp
+Returns number of rings with even size containing \fIBond\fR in a molecule.
+.IP "\fBGetNumOfRingsWithOddSize\fR" 4
+.IX Item "GetNumOfRingsWithOddSize"
+.Vb 1
+\&    $NumOfRings = $Bond\->GetNumOfRingsWithOddSize();
+.Ve
+.Sp
+Returns number of rings with odd size containing \fIBond\fR in a molecule.
+.IP "\fBGetNumOfRingsWithSize\fR" 4
+.IX Item "GetNumOfRingsWithSize"
+.Vb 1
+\&    $NumOfRings = $Bond\->GetNumOfRingsWithSize($RingSize);
+.Ve
+.Sp
+Returns number of rings with specific \fIRingSize\fR containing \fIBond\fR in a molecule.
+.IP "\fBGetNumOfRingsWithSizeGreaterThan\fR" 4
+.IX Item "GetNumOfRingsWithSizeGreaterThan"
+.Vb 1
+\&    $NumOfRings = $Bond\->GetNumOfRingsWithSizeGreaterThan($RingSize);
+.Ve
+.Sp
+Returns number of rings with size greater than specific \fIRingSize\fR containing
+\&\fIBond\fR in a molecule.
+.IP "\fBGetNumOfRingsWithSizeLessThan\fR" 4
+.IX Item "GetNumOfRingsWithSizeLessThan"
+.Vb 1
+\&    $NumOfRings = $Bond\->GetNumOfRingsWithSizeLessThan($RingSize);
+.Ve
+.Sp
+Returns number of rings with size less than specific \fIRingSize\fR containing \fIBond\fR
+in a molecule.
+.IP "\fBGetRings\fR" 4
+.IX Item "GetRings"
+.Vb 1
+\&    @Rings = $Bond\->GetRings();
+.Ve
+.Sp
+Returns an array of references to arrays containing ring atoms corressponding
+to all rings containing \fIBond\fR in a molecule.
+.IP "\fBGetRingsWithEvenSize\fR" 4
+.IX Item "GetRingsWithEvenSize"
+.Vb 1
+\&    @Rings = $Bond\->GetRingsWithEvenSize();
+.Ve
+.Sp
+Returns an array of references to arrays containing ring atoms corressponding to all rings with even size
+containing \fIBond\fR in a molecule.
+.IP "\fBGetRingsWithOddSize\fR" 4
+.IX Item "GetRingsWithOddSize"
+.Vb 1
+\&    @Rings = $Bond\->GetRingsWithOddSize();
+.Ve
+.Sp
+Returns an array of references to arrays containing ring atoms corressponding to all rings with odd size
+containing \fIBond\fR in a molecule.
+.IP "\fBGetRingsWithSize\fR" 4
+.IX Item "GetRingsWithSize"
+.Vb 1
+\&    @Rings = $Bond\->GetRingsWithSize($RingSize);
+.Ve
+.Sp
+Returns an array of references to arrays containing ring atoms corressponding to all rings with specific
+\&\fIRingSize \fRcontaining \fIBond\fR in a molecule.
+.IP "\fBGetRingsWithSizeGreaterThan\fR" 4
+.IX Item "GetRingsWithSizeGreaterThan"
+.Vb 1
+\&    @Rings = $Bond\->GetRingsWithSizeGreaterThan($RingSize);
+.Ve
+.Sp
+Returns an array of references to arrays containing ring atoms corressponding to all rings with size
+greater than specific \fIRingSize \fRcontaining \fIBond\fR in a molecule.
+.IP "\fBGetRingsWithSizeLessThan\fR" 4
+.IX Item "GetRingsWithSizeLessThan"
+.Vb 1
+\&    @Rings = $Bond\->GetRingsWithSizeLessThan($RingSize);
+.Ve
+.Sp
+Returns an array of references to arrays containing ring atoms corressponding to all rings with size
+less than specific \fIRingSize \fRcontaining \fIBond\fR in a molecule.
+.IP "\fBGetSizeOfLargestRing\fR" 4
+.IX Item "GetSizeOfLargestRing"
+.Vb 1
+\&    $Size = $Bond\->GetSizeOfLargestRing();
+.Ve
+.Sp
+Returns size of the largest ring containing \fIBond\fR in a molecule.
+.IP "\fBGetSizeOfSmallestRing\fR" 4
+.IX Item "GetSizeOfSmallestRing"
+.Vb 1
+\&    $Size = $Bond\->GetSizeOfSmallestRing();
+.Ve
+.Sp
+Returns size of the smallest ring containing \fIBond\fR in a molecule.
+.IP "\fBGetSmallestRing\fR" 4
+.IX Item "GetSmallestRing"
+.Vb 1
+\&    @RingAtoms = $Bond\->GetSmallestRing();
+.Ve
+.Sp
+Returns an array of ring \fIAtoms\fR corresponding to the largest ring containing \fIBond\fR
+in a molecule.
+.IP "\fBIsAromatic\fR" 4
+.IX Item "IsAromatic"
+.Vb 1
+\&    $Status = $Bond\->IsAromatic();
+.Ve
+.Sp
+Returns 1 or 0 based on whether it's an aromatic \fIBond\fR.
+.IP "\fBIsBondStereochemistrySpecified\fR" 4
+.IX Item "IsBondStereochemistrySpecified"
+.Vb 1
+\&    $Status = $Bond\->IsBondStereochemistrySpecified();
+.Ve
+.Sp
+Returns 1 or 0 based on whether \fIBond\fR's sterochemistry is specified.
+.IP "\fBIsBondTypeSpecified\fR" 4
+.IX Item "IsBondTypeSpecified"
+.Vb 1
+\&    $Status = $Bond\->IsBondTypeSpecified();
+.Ve
+.Sp
+Returns 1 or 0 based on whether \fIBond\fR's type is specified.
+.IP "\fBIsCis\fR" 4
+.IX Item "IsCis"
+.Vb 1
+\&    $Status = $Bond\->IsCis();
+.Ve
+.Sp
+Returns 1 or 0 based on whether it's a cis \fIBond\fR.
+.IP "\fBIsCisOrTrans\fR" 4
+.IX Item "IsCisOrTrans"
+.Vb 1
+\&    $Status = $Bond\->IsCisOrTrans();
+.Ve
+.Sp
+Returns 1 or 0 based on whether it's a cis or trans \fIBond\fR.
+.IP "\fBIsCoordinate\fR" 4
+.IX Item "IsCoordinate"
+.Vb 1
+\&    $Status = $Bond\->IsCoordinate();
+.Ve
+.Sp
+Returns 1 or 0 based on whether it's a coordinate or dative  \fIBond\fR.
+.IP "\fBIsDative\fR" 4
+.IX Item "IsDative"
+.Vb 1
+\&    $Status = $Bond\->IsDative();
+.Ve
+.Sp
+Returns 1 or 0 based on whether it's a coordinate or dative  \fIBond\fR.
+.IP "\fBIsDouble\fR" 4
+.IX Item "IsDouble"
+.Vb 1
+\&    $Status =$Bond\->IsDouble();
+.Ve
+.Sp
+Returns 1 or 0 based on whether it's a double \fIBond\fR.
+.IP "\fBIsDown\fR" 4
+.IX Item "IsDown"
+.Vb 1
+\&    $Status = $Bond\->IsDown();
+.Ve
+.Sp
+Returns 1 or 0 based on whether it's a hash or down single \fIBond\fR.
+.IP "\fBIsDownward\fR" 4
+.IX Item "IsDownward"
+.Vb 1
+\&    $Return = $Bond\->IsDownward();
+.Ve
+.Sp
+Returns 1 or 0 based on whether it's a downward \fIBond\fR.
+.IP "\fBIsHash\fR" 4
+.IX Item "IsHash"
+.Vb 1
+\&    $Status = $Bond\->IsHash();
+.Ve
+.Sp
+Returns 1 or 0 based on whether it's a hash or down single \fIBond\fR.
+.IP "\fBIsInRing\fR" 4
+.IX Item "IsInRing"
+.Vb 1
+\&    $Status = $Bond\->IsInRing();
+.Ve
+.Sp
+Returns 1 or 0 based on whether \fIBond\fR is present in a ring.
+.IP "\fBIsInRingOfSize\fR" 4
+.IX Item "IsInRingOfSize"
+.Vb 1
+\&    $Status = $Bond\->IsInRingOfSize($Size);
+.Ve
+.Sp
+Returns 1 or 0 based on whether \fIBond\fR is present in a ring of specific \fISize\fR.
+.IP "\fBIsIonic\fR" 4
+.IX Item "IsIonic"
+.Vb 1
+\&    $Status = $Bond\->IsIonic();
+.Ve
+.Sp
+Returns 1 or 0 based on whether it's an ionic \fIBond\fR.
+.IP "\fBIsNotInRing\fR" 4
+.IX Item "IsNotInRing"
+.Vb 1
+\&    $Status = $Bond\->IsNotInRing();
+.Ve
+.Sp
+Returns 1 or 0 based on whether \fIBond\fR is not present in a ring.
+.IP "\fBIsOnlyInOneRing\fR" 4
+.IX Item "IsOnlyInOneRing"
+.Vb 1
+\&    $Status = $Bond\->IsOnlyInOneRing();
+.Ve
+.Sp
+Returns 1 or 0 based on whether \fIBond\fR is only present in one ring.
+.IP "\fBIsQuadruple\fR" 4
+.IX Item "IsQuadruple"
+.Vb 1
+\&    $Status = $Bond\->IsQuadruple();
+.Ve
+.Sp
+Returns 1 or 0 based on whether it's a quadruple \fIBond\fR.
+.IP "\fBIsQuintuple\fR" 4
+.IX Item "IsQuintuple"
+.Vb 1
+\&    $Status = $Bond\->IsQuintuple();
+.Ve
+.Sp
+Returns 1 or 0 based on whether it's a quintuple \fIBond\fR.
+.IP "\fBIsSextuple\fR" 4
+.IX Item "IsSextuple"
+.Vb 1
+\&    $Status = $Bond\->IsSextuple();
+.Ve
+.Sp
+Returns 1 or 0 based on whether it's a sextuple \fIBond\fR.
+.IP "\fBIsSingle\fR" 4
+.IX Item "IsSingle"
+.Vb 1
+\&    $Status =$Bond\->IsSingle();
+.Ve
+.Sp
+Returns 1 or 0 based on whether it's a single \fIBond\fR.
+.IP "\fBIsTriple\fR" 4
+.IX Item "IsTriple"
+.Vb 1
+\&    $Status =$Bond\->IsTriple();
+.Ve
+.Sp
+Returns 1 or 0 based on whether it's a triple \fIBond\fR.
+.IP "\fBIsTautomeric\fR" 4
+.IX Item "IsTautomeric"
+.Vb 1
+\&    $Status = $Bond\->IsTautomeric();
+.Ve
+.Sp
+Returns 1 or 0 based on whether it's a \fIBond\fR.
+.IP "\fBIsTrans\fR" 4
+.IX Item "IsTrans"
+.Vb 1
+\&    $Status = $Bond\->IsTrans();
+.Ve
+.Sp
+Returns 1 or 0 based on whether it's a trans \fIBond\fR.
+.IP "\fBIsUp\fR" 4
+.IX Item "IsUp"
+.Vb 1
+\&    $Status = $Bond\->IsUp();
+.Ve
+.Sp
+Returns 1 or 0 based on whether it's a up \fIBond\fR.
+.IP "\fBIsUpOrDown\fR" 4
+.IX Item "IsUpOrDown"
+.Vb 1
+\&    $Status = $Bond\->IsUpOrDown();
+.Ve
+.Sp
+Returns 1 or 0 based on whether it's an up or down \fIBond\fR.
+.IP "\fBIsUpward\fR" 4
+.IX Item "IsUpward"
+.Vb 1
+\&    $Status = $Bond\->IsUpward();
+.Ve
+.Sp
+Returns 1 or 0 based on whether it's an upward \fIBond\fR.
+.IP "\fBIsWedge\fR" 4
+.IX Item "IsWedge"
+.Vb 1
+\&    $Status = $Bond\->IsWedge();
+.Ve
+.Sp
+Returns 1 or 0 based on whether it's a wedge \fIBond\fR.
+.IP "\fBIsWedgeOrHash\fR" 4
+.IX Item "IsWedgeOrHash"
+.Vb 1
+\&    $Status = $Bond\->IsWedgeOrHash();
+.Ve
+.Sp
+Returns 1 or 0 based on whether it's a wedge or hash \fIBond\fR.
+.IP "\fBSetAtoms\fR" 4
+.IX Item "SetAtoms"
+.Vb 2
+\&    $Bond\->SetAtoms($AtomsRef);
+\&    $Bond\->SetAtoms(@Atoms);
+.Ve
+.Sp
+Set atoms of \fIBond\fR to atoms in \fIAtoms\fR array or in a reference to an array of atoms
+and return \fIBond\fR.
+.IP "\fBSetBondOrder\fR" 4
+.IX Item "SetBondOrder"
+.Vb 1
+\&    $Bond\->SetBondOrder($BondOrder);
+.Ve
+.Sp
+Sets bond order of \fIBond\fR to specified \fIBondOrder\fR and returns \fIBond\fR. Possible bond order
+values: 1 = Single, 1.5 = Aromatic, 2 = Double, 3 = Triple, 4 = Quadruple, 5 = Quintuple,
+6 = Sextuple, 7 = Septuple
+.Sp
+Notes:
+.Sp
+.Vb 8
+\&    . 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.
+.Ve
+.IP "\fBSetBondType\fR" 4
+.IX Item "SetBondType"
+.Vb 1
+\&    $Bond\->SetBondType($BondType);
+.Ve
+.Sp
+Sets bond type for \fIBond\fR to specified \fIBondType\fR and returns \fIBond\fR. Possible bond type
+values for different bond orders are:
+.Sp
+.Vb 9
+\&    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
+.Ve
+.Sp
+Notes:
+.Sp
+.Vb 3
+\&    o BondType Any is valid for all BondOrders.
+\&    o BondOrder property is automatically assigned using default BondOrder
+\&      values for specified BondType.
+.Ve
+.Sp
+Possible bond stereochemistry values for different bond orders are:
+.Sp
+.Vb 4
+\&    0 : None, Unspecified
+\&    1 : Wedge, Up, Hash, Down, Wavy, WedgeOrHash, UpOrDown, Upward, Downward,
+\&        None, Unspecified
+\&    2 : Cis, Trans, Z, E, DoubleCross, CisOrTrans, None, Unspecified
+.Ve
+.IP "\fBSetBondStereochemistry\fR" 4
+.IX Item "SetBondStereochemistry"
+.Vb 1
+\&    $Bond = $Bond\->SetBondStereochemistry($BondStereochemistry);
+.Ve
+.Sp
+Sets bond stereochemistry of \fIBond\fR to specified \fIBondStereochemistry\fR and
+returns \fIBond\fR. Possible \fIBondStereoChemistry\fR values for different bond orders
+are:
+.Sp
+BondOrder: 1
+.Sp
+.Vb 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
+.Ve
+.Sp
+Notes:
+.Sp
+.Vb 3
+\&    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.
+.Ve
+.Sp
+BondOrder: 2
+.Sp
+.Vb 1
+\&    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
+.Ve
+.IP "\fBStringifyBond\fR" 4
+.IX Item "StringifyBond"
+.Vb 1
+\&    $BondString = $Bond\->StringifyBond();
+.Ve
+.Sp
+Returns a string containing information about \fIbond\fR object.
+.IP "\fBSwitchBondFromAndToAtoms\fR" 4
+.IX Item "SwitchBondFromAndToAtoms"
+.Vb 1
+\&    $Bond = $Bond\->SwitchBondFromAndToAtoms();
+.Ve
+.Sp
+Swaps bond from and to atoms in \fIBond\fR and returns \fIBond\fR.
+.SH "AUTHOR"
+.IX Header "AUTHOR"
+Manish Sud <msud@san.rr.com>
+.SH "SEE ALSO"
+.IX Header "SEE ALSO"
+Atom.pm, Molecule.pm
+.SH "COPYRIGHT"
+.IX Header "COPYRIGHT"
+Copyright (C) 2015 Manish Sud. All rights reserved.
+.PP
+This file is part of MayaChemTools.
+.PP
+MayaChemTools is free software; you can redistribute it and/or modify it under
+the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
+Software Foundation; either version 3 of the License, or (at your option)
+any later version.