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

Uploaded
author deepakjadmin
date Wed, 20 Jan 2016 11:55:01 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1 .\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.22)
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
2 .\"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
3 .\" Standard preamble:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
4 .\" ========================================================================
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
5 .de Sp \" Vertical space (when we can't use .PP)
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
6 .if t .sp .5v
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
7 .if n .sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
8 ..
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
9 .de Vb \" Begin verbatim text
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
10 .ft CW
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
11 .nf
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
12 .ne \\$1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
13 ..
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
14 .de Ve \" End verbatim text
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
15 .ft R
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
16 .fi
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
17 ..
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
18 .\" Set up some character translations and predefined strings. \*(-- will
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
19 .\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
20 .\" double quote, and \*(R" will give a right double quote. \*(C+ will
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
21 .\" give a nicer C++. Capital omega is used to do unbreakable dashes and
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
22 .\" therefore won't be available. \*(C` and \*(C' expand to `' in nroff,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
23 .\" nothing in troff, for use with C<>.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
24 .tr \(*W-
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
25 .ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p'
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
26 .ie n \{\
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
27 . ds -- \(*W-
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
28 . ds PI pi
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
29 . if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
30 . if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\" diablo 12 pitch
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
31 . ds L" ""
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
32 . ds R" ""
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
33 . ds C` ""
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
34 . ds C' ""
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
35 'br\}
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
36 .el\{\
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
37 . ds -- \|\(em\|
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
38 . ds PI \(*p
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
39 . ds L" ``
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
40 . ds R" ''
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
41 'br\}
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
42 .\"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
43 .\" Escape single quotes in literal strings from groff's Unicode transform.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
44 .ie \n(.g .ds Aq \(aq
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
45 .el .ds Aq '
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
46 .\"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
47 .\" If the F register is turned on, we'll generate index entries on stderr for
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
48 .\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
49 .\" entries marked with X<> in POD. Of course, you'll have to process the
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
50 .\" output yourself in some meaningful fashion.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
51 .ie \nF \{\
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
52 . de IX
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
53 . tm Index:\\$1\t\\n%\t"\\$2"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
54 ..
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
55 . nr % 0
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
56 . rr F
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
57 .\}
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
58 .el \{\
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
59 . de IX
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
60 ..
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
61 .\}
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
62 .\"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
63 .\" Accent mark definitions (@(#)ms.acc 1.5 88/02/08 SMI; from UCB 4.2).
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
64 .\" Fear. Run. Save yourself. No user-serviceable parts.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
65 . \" fudge factors for nroff and troff
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
66 .if n \{\
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
67 . ds #H 0
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
68 . ds #V .8m
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
69 . ds #F .3m
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
70 . ds #[ \f1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
71 . ds #] \fP
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
72 .\}
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
73 .if t \{\
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
74 . ds #H ((1u-(\\\\n(.fu%2u))*.13m)
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
75 . ds #V .6m
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
76 . ds #F 0
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
77 . ds #[ \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
78 . ds #] \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
79 .\}
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
80 . \" simple accents for nroff and troff
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
81 .if n \{\
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
82 . ds ' \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
83 . ds ` \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
84 . ds ^ \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
85 . ds , \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
86 . ds ~ ~
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
87 . ds /
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
88 .\}
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
89 .if t \{\
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
90 . ds ' \\k:\h'-(\\n(.wu*8/10-\*(#H)'\'\h"|\\n:u"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
91 . ds ` \\k:\h'-(\\n(.wu*8/10-\*(#H)'\`\h'|\\n:u'
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
92 . ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'^\h'|\\n:u'
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
93 . ds , \\k:\h'-(\\n(.wu*8/10)',\h'|\\n:u'
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
94 . ds ~ \\k:\h'-(\\n(.wu-\*(#H-.1m)'~\h'|\\n:u'
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
95 . ds / \\k:\h'-(\\n(.wu*8/10-\*(#H)'\z\(sl\h'|\\n:u'
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
96 .\}
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
97 . \" troff and (daisy-wheel) nroff accents
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
98 .ds : \\k:\h'-(\\n(.wu*8/10-\*(#H+.1m+\*(#F)'\v'-\*(#V'\z.\h'.2m+\*(#F'.\h'|\\n:u'\v'\*(#V'
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
99 .ds 8 \h'\*(#H'\(*b\h'-\*(#H'
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
100 .ds o \\k:\h'-(\\n(.wu+\w'\(de'u-\*(#H)/2u'\v'-.3n'\*(#[\z\(de\v'.3n'\h'|\\n:u'\*(#]
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
101 .ds d- \h'\*(#H'\(pd\h'-\w'~'u'\v'-.25m'\f2\(hy\fP\v'.25m'\h'-\*(#H'
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
102 .ds D- D\\k:\h'-\w'D'u'\v'-.11m'\z\(hy\v'.11m'\h'|\\n:u'
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
103 .ds th \*(#[\v'.3m'\s+1I\s-1\v'-.3m'\h'-(\w'I'u*2/3)'\s-1o\s+1\*(#]
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
104 .ds Th \*(#[\s+2I\s-2\h'-\w'I'u*3/5'\v'-.3m'o\v'.3m'\*(#]
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
105 .ds ae a\h'-(\w'a'u*4/10)'e
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
106 .ds Ae A\h'-(\w'A'u*4/10)'E
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
107 . \" corrections for vroff
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
108 .if v .ds ~ \\k:\h'-(\\n(.wu*9/10-\*(#H)'\s-2\u~\d\s+2\h'|\\n:u'
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
109 .if v .ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'\v'-.4m'^\v'.4m'\h'|\\n:u'
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
110 . \" for low resolution devices (crt and lpr)
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
111 .if \n(.H>23 .if \n(.V>19 \
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
112 \{\
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
113 . ds : e
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
114 . ds 8 ss
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
115 . ds o a
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
116 . ds d- d\h'-1'\(ga
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
117 . ds D- D\h'-1'\(hy
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
118 . ds th \o'bp'
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
119 . ds Th \o'LP'
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
120 . ds ae ae
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
121 . ds Ae AE
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
122 .\}
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
123 .rm #[ #] #H #V #F C
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
124 .\" ========================================================================
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
125 .\"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
126 .IX Title "BOND 1"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
127 .TH BOND 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
128 .\" For nroff, turn off justification. Always turn off hyphenation; it makes
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
129 .\" way too many mistakes in technical documents.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
130 .if n .ad l
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
131 .nh
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
132 .SH "NAME"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
133 Bond
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
134 .SH "SYNOPSIS"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
135 .IX Header "SYNOPSIS"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
136 use Bond;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
137 .PP
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
138 use Bond qw(:all);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
139 .SH "DESCRIPTION"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
140 .IX Header "DESCRIPTION"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
141 \&\fBBond\fR class provides the following methods:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
142 .PP
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
143 new, Copy, DeleteBond, GetAtoms, GetBondBeginAtom, GetBondEndAtom,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
144 GetBondFromAtom, GetBondToAtom, GetBondedAtom, GetCommonAtom, GetLargestRing,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
145 GetNumOfRings, GetNumOfRingsWithEvenSize, GetNumOfRingsWithOddSize,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
146 GetNumOfRingsWithSize, GetNumOfRingsWithSizeGreaterThan,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
147 GetNumOfRingsWithSizeLessThan, GetRings, GetRingsWithEvenSize,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
148 GetRingsWithOddSize, GetRingsWithSize, GetRingsWithSizeGreaterThan,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
149 GetRingsWithSizeLessThan, GetSizeOfLargestRing, GetSizeOfSmallestRing,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
150 GetSmallestRing, IsAromatic, IsBondStereochemistrySpecified, IsBondTypeSpecified,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
151 IsCis, IsCisOrTrans, IsCoordinate, IsDative, IsDouble, IsDown, IsDownward, IsHash,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
152 IsInRing, IsInRingOfSize, IsIonic, IsNotInRing, IsOnlyInOneRing, IsQuadruple,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
153 IsQuintuple, IsSextuple, IsSingle, IsTautomeric, IsTrans, IsTriple, IsUp,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
154 IsUpOrDown, IsUpward, IsWedge, IsWedgeOrHash, SetAtoms, SetBondOrder,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
155 SetBondStereochemistry, SetBondType, StringifyBond, SwitchBondFromAndToAtoms
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
156 .PP
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
157 \&\fBBond\fR class is derived from \fBObjectProperty\fR base class which provides methods not explicitly
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
158 defined in \fBAtom\fR or \fBObjectProperty\fR class using Perl's \s-1AUTOLOAD\s0 functionality. These methods
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
159 are generated on-the-fly for a specified object property:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
160 .PP
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
161 .Vb 3
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
162 \& Set<PropertyName>(<PropertyValue>);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
163 \& $PropertyValue = Get<PropertyName>();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
164 \& Delete<PropertyName>();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
165 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
166 .SS "\s-1METHODS\s0"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
167 .IX Subsection "METHODS"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
168 .IP "\fBnew\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
169 .IX Item "new"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
170 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
171 \& $NewBond = new Bond([%PropertyNameAndValues]);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
172 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
173 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
174 Using specified \fIBond\fR property names and values hash, \fBnew\fR method creates a new object
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
175 and returns a reference to newly created \fBBond\fR object. By default, following properties are
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
176 initialized:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
177 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
178 .Vb 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
179 \& ID = SequentialObjectID
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
180 \& @Atoms = ();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
181 \& BondType = ""
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
182 \& BondOrder = ""
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
183 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
184 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
185 Except for \fI\s-1ID\s0\fR property, all other default properties and other additional properties can
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
186 be set during invocation of this method.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
187 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
188 Examples:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
189 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
190 .Vb 3
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
191 \& $Bond = new Bond();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
192 \& $DoubleBond = new Bond(\*(AqAtoms\*(Aq => [$Atom2, $Atom1],
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
193 \& \*(AqBondOrder\*(Aq => 2);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
194 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
195 .IP "\fBCopy\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
196 .IX Item "Copy"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
197 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
198 \& $BondCopy = $Bond\->Copy();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
199 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
200 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
201 Copy \fIBond\fR and its associated data using \fBStorable::dclone\fR and return a new
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
202 \&\fBBond\fR object.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
203 .IP "\fBDeleteBond\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
204 .IX Item "DeleteBond"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
205 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
206 \& $Bond\->DeleteBond();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
207 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
208 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
209 Delete \fIBond\fR between atoms in from a molecule.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
210 .IP "\fBGetAtoms\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
211 .IX Item "GetAtoms"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
212 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
213 \& @BondedAtoms = $Bond\->GetAtoms();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
214 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
215 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
216 Returns an array containing \fIAtoms\fR invoved in \fIBond\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
217 .IP "\fBGetBondedAtom\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
218 .IX Item "GetBondedAtom"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
219 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
220 \& $BondedAtom = $Bond\->GetBondedAtom($Atom);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
221 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
222 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
223 Returns \fBBondedAtom\fR bonded to \fIAtom\fR in \fIBond\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
224 .IP "\fBGetBondBeginAtom\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
225 .IX Item "GetBondBeginAtom"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
226 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
227 \& $BeginAtom = $Bond\->GetBondBeginAtom();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
228 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
229 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
230 Returns \fBBeginAtom\fR corresponding to bond starting atom in \fIBond\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
231 .IP "\fBGetBondEndAtom\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
232 .IX Item "GetBondEndAtom"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
233 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
234 \& $EndAtom = $Bond\->GetBondEndAtom();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
235 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
236 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
237 Returns \fBEndAtom\fR corresponding to bond ending atom in \fIBond\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
238 .IP "\fBGetBondFromAtom\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
239 .IX Item "GetBondFromAtom"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
240 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
241 \& $FromAtom = $Bond\->GetBondFromAtom();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
242 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
243 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
244 Returns \fBFromAtom\fR corresponding to bond starting atom in \fIBond\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
245 .IP "\fBGetBondToAtom\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
246 .IX Item "GetBondToAtom"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
247 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
248 \& $ToAotm = $Bond\->GetBondToAtom();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
249 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
250 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
251 Returns \fBToAtom\fR corresponding to bond ending atom in \fIBond\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
252 .IP "\fBGetCommonAtom\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
253 .IX Item "GetCommonAtom"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
254 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
255 \& $CommonAtom = $Bond\->GetCommonAtom($OtherBond);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
256 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
257 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
258 Returns \fBAtom\fR common to both \fIBond\fR and \fI\f(CI$OtherBond\fI\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
259 .IP "\fBGetLargestRing\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
260 .IX Item "GetLargestRing"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
261 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
262 \& @RingAtoms = $Bond\->GetLargestRing();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
263 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
264 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
265 Returns an array of ring \fIAtoms\fR corresponding to the largest ring containing \fIBond\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
266 in a molecule
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
267 .IP "\fBGetNumOfRings\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
268 .IX Item "GetNumOfRings"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
269 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
270 \& $NumOfRings = $Bond\->GetNumOfRings();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
271 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
272 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
273 Returns number of rings containing \fIBond\fR in a molecule.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
274 .IP "\fBGetNumOfRingsWithEvenSize\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
275 .IX Item "GetNumOfRingsWithEvenSize"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
276 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
277 \& $NumOfRings = $Bond\->GetNumOfRingsWithEvenSize();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
278 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
279 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
280 Returns number of rings with even size containing \fIBond\fR in a molecule.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
281 .IP "\fBGetNumOfRingsWithOddSize\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
282 .IX Item "GetNumOfRingsWithOddSize"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
283 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
284 \& $NumOfRings = $Bond\->GetNumOfRingsWithOddSize();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
285 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
286 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
287 Returns number of rings with odd size containing \fIBond\fR in a molecule.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
288 .IP "\fBGetNumOfRingsWithSize\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
289 .IX Item "GetNumOfRingsWithSize"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
290 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
291 \& $NumOfRings = $Bond\->GetNumOfRingsWithSize($RingSize);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
292 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
293 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
294 Returns number of rings with specific \fIRingSize\fR containing \fIBond\fR in a molecule.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
295 .IP "\fBGetNumOfRingsWithSizeGreaterThan\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
296 .IX Item "GetNumOfRingsWithSizeGreaterThan"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
297 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
298 \& $NumOfRings = $Bond\->GetNumOfRingsWithSizeGreaterThan($RingSize);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
299 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
300 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
301 Returns number of rings with size greater than specific \fIRingSize\fR containing
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
302 \&\fIBond\fR in a molecule.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
303 .IP "\fBGetNumOfRingsWithSizeLessThan\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
304 .IX Item "GetNumOfRingsWithSizeLessThan"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
305 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
306 \& $NumOfRings = $Bond\->GetNumOfRingsWithSizeLessThan($RingSize);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
307 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
308 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
309 Returns number of rings with size less than specific \fIRingSize\fR containing \fIBond\fR
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
310 in a molecule.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
311 .IP "\fBGetRings\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
312 .IX Item "GetRings"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
313 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
314 \& @Rings = $Bond\->GetRings();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
315 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
316 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
317 Returns an array of references to arrays containing ring atoms corressponding
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
318 to all rings containing \fIBond\fR in a molecule.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
319 .IP "\fBGetRingsWithEvenSize\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
320 .IX Item "GetRingsWithEvenSize"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
321 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
322 \& @Rings = $Bond\->GetRingsWithEvenSize();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
323 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
324 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
325 Returns an array of references to arrays containing ring atoms corressponding to all rings with even size
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
326 containing \fIBond\fR in a molecule.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
327 .IP "\fBGetRingsWithOddSize\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
328 .IX Item "GetRingsWithOddSize"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
329 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
330 \& @Rings = $Bond\->GetRingsWithOddSize();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
331 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
332 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
333 Returns an array of references to arrays containing ring atoms corressponding to all rings with odd size
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
334 containing \fIBond\fR in a molecule.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
335 .IP "\fBGetRingsWithSize\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
336 .IX Item "GetRingsWithSize"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
337 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
338 \& @Rings = $Bond\->GetRingsWithSize($RingSize);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
339 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
340 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
341 Returns an array of references to arrays containing ring atoms corressponding to all rings with specific
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
342 \&\fIRingSize \fRcontaining \fIBond\fR in a molecule.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
343 .IP "\fBGetRingsWithSizeGreaterThan\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
344 .IX Item "GetRingsWithSizeGreaterThan"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
345 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
346 \& @Rings = $Bond\->GetRingsWithSizeGreaterThan($RingSize);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
347 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
348 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
349 Returns an array of references to arrays containing ring atoms corressponding to all rings with size
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
350 greater than specific \fIRingSize \fRcontaining \fIBond\fR in a molecule.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
351 .IP "\fBGetRingsWithSizeLessThan\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
352 .IX Item "GetRingsWithSizeLessThan"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
353 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
354 \& @Rings = $Bond\->GetRingsWithSizeLessThan($RingSize);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
355 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
356 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
357 Returns an array of references to arrays containing ring atoms corressponding to all rings with size
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
358 less than specific \fIRingSize \fRcontaining \fIBond\fR in a molecule.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
359 .IP "\fBGetSizeOfLargestRing\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
360 .IX Item "GetSizeOfLargestRing"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
361 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
362 \& $Size = $Bond\->GetSizeOfLargestRing();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
363 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
364 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
365 Returns size of the largest ring containing \fIBond\fR in a molecule.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
366 .IP "\fBGetSizeOfSmallestRing\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
367 .IX Item "GetSizeOfSmallestRing"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
368 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
369 \& $Size = $Bond\->GetSizeOfSmallestRing();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
370 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
371 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
372 Returns size of the smallest ring containing \fIBond\fR in a molecule.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
373 .IP "\fBGetSmallestRing\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
374 .IX Item "GetSmallestRing"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
375 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
376 \& @RingAtoms = $Bond\->GetSmallestRing();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
377 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
378 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
379 Returns an array of ring \fIAtoms\fR corresponding to the largest ring containing \fIBond\fR
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
380 in a molecule.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
381 .IP "\fBIsAromatic\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
382 .IX Item "IsAromatic"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
383 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
384 \& $Status = $Bond\->IsAromatic();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
385 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
386 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
387 Returns 1 or 0 based on whether it's an aromatic \fIBond\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
388 .IP "\fBIsBondStereochemistrySpecified\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
389 .IX Item "IsBondStereochemistrySpecified"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
390 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
391 \& $Status = $Bond\->IsBondStereochemistrySpecified();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
392 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
393 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
394 Returns 1 or 0 based on whether \fIBond\fR's sterochemistry is specified.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
395 .IP "\fBIsBondTypeSpecified\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
396 .IX Item "IsBondTypeSpecified"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
397 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
398 \& $Status = $Bond\->IsBondTypeSpecified();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
399 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
400 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
401 Returns 1 or 0 based on whether \fIBond\fR's type is specified.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
402 .IP "\fBIsCis\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
403 .IX Item "IsCis"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
404 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
405 \& $Status = $Bond\->IsCis();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
406 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
407 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
408 Returns 1 or 0 based on whether it's a cis \fIBond\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
409 .IP "\fBIsCisOrTrans\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
410 .IX Item "IsCisOrTrans"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
411 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
412 \& $Status = $Bond\->IsCisOrTrans();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
413 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
414 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
415 Returns 1 or 0 based on whether it's a cis or trans \fIBond\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
416 .IP "\fBIsCoordinate\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
417 .IX Item "IsCoordinate"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
418 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
419 \& $Status = $Bond\->IsCoordinate();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
420 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
421 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
422 Returns 1 or 0 based on whether it's a coordinate or dative \fIBond\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
423 .IP "\fBIsDative\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
424 .IX Item "IsDative"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
425 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
426 \& $Status = $Bond\->IsDative();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
427 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
428 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
429 Returns 1 or 0 based on whether it's a coordinate or dative \fIBond\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
430 .IP "\fBIsDouble\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
431 .IX Item "IsDouble"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
432 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
433 \& $Status =$Bond\->IsDouble();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
434 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
435 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
436 Returns 1 or 0 based on whether it's a double \fIBond\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
437 .IP "\fBIsDown\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
438 .IX Item "IsDown"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
439 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
440 \& $Status = $Bond\->IsDown();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
441 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
442 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
443 Returns 1 or 0 based on whether it's a hash or down single \fIBond\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
444 .IP "\fBIsDownward\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
445 .IX Item "IsDownward"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
446 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
447 \& $Return = $Bond\->IsDownward();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
448 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
449 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
450 Returns 1 or 0 based on whether it's a downward \fIBond\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
451 .IP "\fBIsHash\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
452 .IX Item "IsHash"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
453 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
454 \& $Status = $Bond\->IsHash();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
455 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
456 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
457 Returns 1 or 0 based on whether it's a hash or down single \fIBond\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
458 .IP "\fBIsInRing\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
459 .IX Item "IsInRing"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
460 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
461 \& $Status = $Bond\->IsInRing();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
462 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
463 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
464 Returns 1 or 0 based on whether \fIBond\fR is present in a ring.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
465 .IP "\fBIsInRingOfSize\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
466 .IX Item "IsInRingOfSize"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
467 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
468 \& $Status = $Bond\->IsInRingOfSize($Size);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
469 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
470 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
471 Returns 1 or 0 based on whether \fIBond\fR is present in a ring of specific \fISize\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
472 .IP "\fBIsIonic\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
473 .IX Item "IsIonic"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
474 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
475 \& $Status = $Bond\->IsIonic();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
476 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
477 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
478 Returns 1 or 0 based on whether it's an ionic \fIBond\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
479 .IP "\fBIsNotInRing\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
480 .IX Item "IsNotInRing"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
481 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
482 \& $Status = $Bond\->IsNotInRing();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
483 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
484 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
485 Returns 1 or 0 based on whether \fIBond\fR is not present in a ring.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
486 .IP "\fBIsOnlyInOneRing\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
487 .IX Item "IsOnlyInOneRing"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
488 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
489 \& $Status = $Bond\->IsOnlyInOneRing();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
490 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
491 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
492 Returns 1 or 0 based on whether \fIBond\fR is only present in one ring.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
493 .IP "\fBIsQuadruple\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
494 .IX Item "IsQuadruple"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
495 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
496 \& $Status = $Bond\->IsQuadruple();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
497 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
498 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
499 Returns 1 or 0 based on whether it's a quadruple \fIBond\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
500 .IP "\fBIsQuintuple\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
501 .IX Item "IsQuintuple"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
502 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
503 \& $Status = $Bond\->IsQuintuple();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
504 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
505 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
506 Returns 1 or 0 based on whether it's a quintuple \fIBond\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
507 .IP "\fBIsSextuple\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
508 .IX Item "IsSextuple"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
509 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
510 \& $Status = $Bond\->IsSextuple();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
511 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
512 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
513 Returns 1 or 0 based on whether it's a sextuple \fIBond\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
514 .IP "\fBIsSingle\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
515 .IX Item "IsSingle"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
516 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
517 \& $Status =$Bond\->IsSingle();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
518 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
519 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
520 Returns 1 or 0 based on whether it's a single \fIBond\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
521 .IP "\fBIsTriple\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
522 .IX Item "IsTriple"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
523 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
524 \& $Status =$Bond\->IsTriple();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
525 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
526 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
527 Returns 1 or 0 based on whether it's a triple \fIBond\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
528 .IP "\fBIsTautomeric\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
529 .IX Item "IsTautomeric"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
530 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
531 \& $Status = $Bond\->IsTautomeric();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
532 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
533 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
534 Returns 1 or 0 based on whether it's a \fIBond\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
535 .IP "\fBIsTrans\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
536 .IX Item "IsTrans"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
537 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
538 \& $Status = $Bond\->IsTrans();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
539 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
540 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
541 Returns 1 or 0 based on whether it's a trans \fIBond\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
542 .IP "\fBIsUp\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
543 .IX Item "IsUp"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
544 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
545 \& $Status = $Bond\->IsUp();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
546 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
547 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
548 Returns 1 or 0 based on whether it's a up \fIBond\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
549 .IP "\fBIsUpOrDown\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
550 .IX Item "IsUpOrDown"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
551 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
552 \& $Status = $Bond\->IsUpOrDown();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
553 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
554 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
555 Returns 1 or 0 based on whether it's an up or down \fIBond\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
556 .IP "\fBIsUpward\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
557 .IX Item "IsUpward"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
558 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
559 \& $Status = $Bond\->IsUpward();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
560 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
561 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
562 Returns 1 or 0 based on whether it's an upward \fIBond\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
563 .IP "\fBIsWedge\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
564 .IX Item "IsWedge"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
565 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
566 \& $Status = $Bond\->IsWedge();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
567 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
568 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
569 Returns 1 or 0 based on whether it's a wedge \fIBond\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
570 .IP "\fBIsWedgeOrHash\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
571 .IX Item "IsWedgeOrHash"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
572 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
573 \& $Status = $Bond\->IsWedgeOrHash();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
574 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
575 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
576 Returns 1 or 0 based on whether it's a wedge or hash \fIBond\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
577 .IP "\fBSetAtoms\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
578 .IX Item "SetAtoms"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
579 .Vb 2
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
580 \& $Bond\->SetAtoms($AtomsRef);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
581 \& $Bond\->SetAtoms(@Atoms);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
582 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
583 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
584 Set atoms of \fIBond\fR to atoms in \fIAtoms\fR array or in a reference to an array of atoms
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
585 and return \fIBond\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
586 .IP "\fBSetBondOrder\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
587 .IX Item "SetBondOrder"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
588 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
589 \& $Bond\->SetBondOrder($BondOrder);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
590 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
591 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
592 Sets bond order of \fIBond\fR to specified \fIBondOrder\fR and returns \fIBond\fR. Possible bond order
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
593 values: 1 = Single, 1.5 = Aromatic, 2 = Double, 3 = Triple, 4 = Quadruple, 5 = Quintuple,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
594 6 = Sextuple, 7 = Septuple
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
595 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
596 Notes:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
597 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
598 .Vb 8
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
599 \& . BondType property is automatically assigned using default BondType
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
600 \& values for specified BondOrder.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
601 \& . BondType values can also be explicit set.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
602 \& . To make bonds aromatic in a ring, explicitly set "Aromatic"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
603 \& property for bond/atoms and make sure appropriate BondOrder
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
604 \& values are assigned.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
605 \& . Dative or coordinate bond types are treated as single bond types with
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
606 \& explicit formal charge of + and \- on first and second bond atoms.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
607 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
608 .IP "\fBSetBondType\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
609 .IX Item "SetBondType"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
610 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
611 \& $Bond\->SetBondType($BondType);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
612 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
613 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
614 Sets bond type for \fIBond\fR to specified \fIBondType\fR and returns \fIBond\fR. Possible bond type
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
615 values for different bond orders are:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
616 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
617 .Vb 9
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
618 \& 0: None, Ionic, Unspecified
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
619 \& 1 : Single, Dative, Coordinate, SingleOrDouble, SingleOrAromatic, Tautomeric
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
620 \& 2 : Double, SingleOrDouble, DoubleOrAromatic, Tautomeric
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
621 \& 3 : Triple
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
622 \& 4 : Quadruple
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
623 \& 5 : Quintuple
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
624 \& 6 : Sextuple
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
625 \& 7 : Septuple
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
626 \& 1.5 : Aromatic, Resonance, SingleOrAromatic, DoubleOrAromatic
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
627 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
628 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
629 Notes:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
630 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
631 .Vb 3
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
632 \& o BondType Any is valid for all BondOrders.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
633 \& o BondOrder property is automatically assigned using default BondOrder
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
634 \& values for specified BondType.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
635 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
636 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
637 Possible bond stereochemistry values for different bond orders are:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
638 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
639 .Vb 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
640 \& 0 : None, Unspecified
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
641 \& 1 : Wedge, Up, Hash, Down, Wavy, WedgeOrHash, UpOrDown, Upward, Downward,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
642 \& None, Unspecified
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
643 \& 2 : Cis, Trans, Z, E, DoubleCross, CisOrTrans, None, Unspecified
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
644 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
645 .IP "\fBSetBondStereochemistry\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
646 .IX Item "SetBondStereochemistry"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
647 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
648 \& $Bond = $Bond\->SetBondStereochemistry($BondStereochemistry);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
649 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
650 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
651 Sets bond stereochemistry of \fIBond\fR to specified \fIBondStereochemistry\fR and
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
652 returns \fIBond\fR. Possible \fIBondStereoChemistry\fR values for different bond orders
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
653 are:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
654 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
655 BondOrder: 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
656 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
657 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
658 \& None, Unspecified: Not a stereo bond or unspecified
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
659 \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
660 \& Wedge, Up : Wedge end pointing up
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
661 \& Hash, Down: Wedge end pointing down
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
662 \& Wavy, WedgeOrHash, UpOrDown: Wedge end up or down
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
663 \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
664 \& Upward: Single bond around cis/trans double bonds pointing upward
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
665 \& Downward: Single bond around cis/trans double bonds pointing upward
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
666 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
667 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
668 Notes:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
669 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
670 .Vb 3
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
671 \& o Wedge starts at begin atom of a bond making wedge pointed end always
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
672 \& at this atom.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
673 \& o Upward/downward bonds start at atoms involved in cis/trans double bonds.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
674 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
675 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
676 BondOrder: 2
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
677 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
678 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
679 \& None, Unspecified: Not a stereo bond or unspecified
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
680 \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
681 \& Z, cis: Similar groups on same side of double bond
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
682 \& E, trans: Similar groups on different side of double bond
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
683 \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
684 \& CisOrTrans, DoubleCross: cis or trans
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
685 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
686 .IP "\fBStringifyBond\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
687 .IX Item "StringifyBond"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
688 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
689 \& $BondString = $Bond\->StringifyBond();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
690 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
691 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
692 Returns a string containing information about \fIbond\fR object.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
693 .IP "\fBSwitchBondFromAndToAtoms\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
694 .IX Item "SwitchBondFromAndToAtoms"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
695 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
696 \& $Bond = $Bond\->SwitchBondFromAndToAtoms();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
697 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
698 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
699 Swaps bond from and to atoms in \fIBond\fR and returns \fIBond\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
700 .SH "AUTHOR"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
701 .IX Header "AUTHOR"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
702 Manish Sud <msud@san.rr.com>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
703 .SH "SEE ALSO"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
704 .IX Header "SEE ALSO"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
705 Atom.pm, Molecule.pm
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
706 .SH "COPYRIGHT"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
707 .IX Header "COPYRIGHT"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
708 Copyright (C) 2015 Manish Sud. All rights reserved.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
709 .PP
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
710 This file is part of MayaChemTools.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
711 .PP
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
712 MayaChemTools is free software; you can redistribute it and/or modify it under
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
713 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
714 Software Foundation; either version 3 of the License, or (at your option)
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
715 any later version.