annotate mayachemtools/docs/modules/man3/ExtendedConnectivityFingerprints.3 @ 3:e420415a1799 draft

Uploaded
author deepakjadmin
date Wed, 20 Jan 2016 12:16:47 -0500
parents 73ae111cf86f
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 "EXTENDEDCONNECTIVITYFINGERPRINTS 1"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
127 .TH EXTENDEDCONNECTIVITYFINGERPRINTS 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 ExtendedConnectivityFingerprints
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 Fingerprints::ExtendedConnectivityFingerprints;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
137 .PP
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
138 use Fingerprints::ExtendedConnectivityFingerprints 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 ExtendedConnectivityFingerprints [ Ref 48, Ref 52 ] class provides the following methods:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
142 .PP
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
143 new, GenerateFingerprints, GetDescription, SetAtomIdentifierType,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
144 SetAtomicInvariantsToUse, SetFunctionalClassesToUse, SetNeighborhoodRadius,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
145 StringifyExtendedConnectivityFingerprints
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
146 .PP
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
147 \&\fBExtendedConnectivityFingerprints\fR is derived from \fBFingerprints\fR class which in turn
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
148 is derived from \fBObjectProperty\fR base class that provides methods not explicitly defined
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
149 in \fBExtendedConnectivityFingerprints\fR, \fBFingerprints\fR or \fBObjectProperty\fR classes using Perl's
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
150 \&\s-1AUTOLOAD\s0 functionality. These methods are generated on-the-fly for a specified object property:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
151 .PP
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
152 .Vb 3
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
153 \& Set<PropertyName>(<PropertyValue>);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
154 \& $PropertyValue = Get<PropertyName>();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
155 \& Delete<PropertyName>();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
156 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
157 .PP
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
158 The current release of MayaChemTools supports generation of \fBExtendedConnectivityFingerprints\fR
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
159 corresponding to following \fBAtomtomIdentifierTypes\fR:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
160 .PP
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
161 .Vb 3
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
162 \& AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
163 \& FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
164 \& SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
165 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
166 .PP
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
167 Based on the values specified for \fBAtomIdentifierType\fR, \fBAtomicInvariantsToUse\fR
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
168 and \fBFunctionalClassesToUse\fR, initial atom types are assigned to all non-hydrogen atoms in
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
169 a molecule and these atom types strings are converted into initial atom identifier integers using
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
170 \&\fBTextUtil::HashCode\fR function. The duplicate atom identifiers are removed.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
171 .PP
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
172 For \fBNeighborhoodRadius\fR value of \fI0\fR, the initial set of unique atom identifiers comprises
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
173 the molecule fingerprints. Otherwise, atom neighborhoods are generated for each non-hydrogen
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
174 atom up-to specified \fBNeighborhoodRadius\fR value. For each non-hydrogen central atom
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
175 at a specific radius, its neighbors at next radius level along with their bond orders and previously
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
176 calculated atom identifiers are collected which in turn are used to generate a new integer
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
177 atom identifier; the bond orders and atom identifier pairs list is first sorted by bond order
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
178 followed by atom identifiers to make these values graph invariant.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
179 .PP
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
180 After integer atom identifiers have been generated for all non-hydrogen atoms at all specified
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
181 neighborhood radii, the duplicate integer atom identifiers corresponding to same hash code
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
182 value generated using \fBTextUtil::HashCode\fR are tracked by keeping the atom identifiers at
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
183 lower radius. Additionally, all structurally duplicate integer atom identifiers at each specified
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
184 radius are also tracked by identifying equivalent atom and bonds corresponding to substructures
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
185 used for generating atom identifier and keeping integer atom identifier with lowest value.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
186 .PP
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
187 For \fIExtendedConnnectivity\fR value of fingerprints \fBType\fR, the duplicate identifiers are
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
188 removed from the list and the unique atom identifiers constitute the extended connectivity
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
189 fingerprints of a molecule.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
190 .PP
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
191 For \fIExtendedConnnectivityCount\fR value of fingerprints \fBType\fR, the occurrence of each
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
192 unique atom identifiers appears is counted and the unique atom identifiers along with their
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
193 count constitute the extended connectivity fingerprints of a molecule.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
194 .PP
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
195 For \fIExtendedConnectivityBits\fR value of fingerprints \fB\-m, \-\-mode\fR, the unique atom identifiers
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
196 are used as a random number seed to generate a random integer value between 0 and \fB\-\-Size\fR which
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
197 in turn is used to set corresponding bits in the fingerprint bit-vector string.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
198 .PP
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
199 The current release of MayaChemTools generates the following types of extended connectivity
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
200 fingerprints vector strings:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
201 .PP
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
202 .Vb 6
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
203 \& FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
204 \& us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
205 \& 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
206 \& 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
207 \& 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
208 \& 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
209 \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
210 \& FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
211 \& :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
212 \& 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
213 \& 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
214 \& 3 2 1 1 14 1 2 10 4 3 1 1 1 1 2 1 2 1 1 1 2 3 1 1 2 1 3 3 8 2 2 2 6 2
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
215 \& 1 2 1 1 2 1 1 1 2 1 1 2 1 2 1 1 1 1 1 1 1 1 1 2 1 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
216 \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
217 \& FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
218 \& es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
219 \& 0000000001010000000110000011000000000000100000000000000000000000100001
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
220 \& 1000000110000000000000000000000000010011000000000000000000000000010000
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
221 \& 0000000000000000000000000010000000000000000001000000000000000000000000
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
222 \& 0000000000010000100001000000000000101000000000000000100000000000000...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
223 \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
224 \& FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
225 \& es:Radius2;1024;HexadecimalString;Ascending;000000010050c0600800000803
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
226 \& 0300000091000004000000020000100000000124008200020000000040020000000000
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
227 \& 2080000000820040010020000000008040000000000080001000000000400000000000
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
228 \& 4040000090000061010000000800200000000000001400000000020080000000000020
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
229 \& 00008020200000408000
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
230 \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
231 \& FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
232 \& s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
233 \& 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
234 \& 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
235 \& 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
236 \& 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
237 \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
238 \& FingerprintsVector;ExtendedConnectivityCount:FunctionalClassAtomTypes:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
239 \& Radius2;57;NumericalValues;IDsAndValuesString;24769214 508787397 85039
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
240 \& 3286 862102353 981185303 1231636850 1649386610 1941540674 263599683 32
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
241 \& 9205671 571109041 639579325 683993318 723853089 810600886 885767127...;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
242 \& 1 1 1 10 2 22 3 1 3 3 1 1 1 3 2 2 1 2 2 2 3 1 1 1 1 1 14 1 1 1 1 1 1 2
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
243 \& 1 2 1 1 2 2 1 1 2 1 1 1 2 1 1 2 1 1 1 1 1 1 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
244 \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
245 \& FingerprintsBitVector;ExtendedConnectivityBits:FunctionalClassAtomType
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
246 \& s:Radius2;1024;BinaryString;Ascending;00000000000000000000100000000000
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
247 \& 0000000001000100000000001000000000000000000000000000000000101000000010
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
248 \& 0000001000000000010000000000000000000000000000000000000000000000000100
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
249 \& 0000000000001000000000000001000000000001001000000000000000000000000000
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
250 \& 0000000000000000100000000000001000000000000000000000000000000000000...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
251 \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
252 \& FingerprintsVector;ExtendedConnectivity:DREIDINGAtomTypes:Radius2;56;A
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
253 \& lphaNumericalValues;ValuesString;280305427 357928343 721790579 1151822
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
254 \& 898 1207111054 1380963747 1568213839 1603445250 4559268 55012922 18094
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
255 \& 0813 335715751 534801009 684609658 829361048 972945982 999881534 10076
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
256 \& 55741 1213692591 1222032501 1224517934 1235687794 1244268533 152812070
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
257 \& 0 1629595024 1856308891 1978806036 2001865095 2096549435 172675415 ...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
258 \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
259 \& FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
260 \& haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
261 \& 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
262 \& 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
263 \& 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
264 \& 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
265 \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
266 \& FingerprintsVector;ExtendedConnectivity:MMFF94AtomTypes:Radius2;64;Alp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
267 \& haNumericalValues;ValuesString;224051550 746527773 998750766 103704190
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
268 \& 2 1239701709 1248384926 1259447756 1521678386 1631549126 1909437580 20
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
269 \& 37095052 2104274756 2117729376 8770364 31445800 81450228 314289324 344
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
270 \& 041929 581773587 638555787 692022098 811840536 929651561 936421792 988
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
271 \& 636432 1048624296 1054288509 1369487579 1454058929 1519352190 17271...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
272 \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
273 \& FingerprintsVector;ExtendedConnectivity:SLogPAtomTypes:Radius2;71;Alph
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
274 \& aNumericalValues;ValuesString;78989290 116507218 489454042 888737940 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
275 \& 162561799 1241797255 1251494264 1263717127 1471206899 1538061784 17654
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
276 \& 07295 1795036542 1809833874 2020454493 2055310842 2117729376 11868981
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
277 \& 56731842 149505242 184525155 196984339 288181334 481409282 556716568 6
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
278 \& 41915747 679881756 721736571 794256218 908276640 992898760 10987549...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
279 \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
280 \& FingerprintsVector;ExtendedConnectivity:SYBYLAtomTypes:Radius2;58;Alph
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
281 \& aNumericalValues;ValuesString;199957044 313356892 455463968 465982819
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
282 \& 1225318176 1678585943 1883366064 1963811677 2117729376 113784599 19153
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
283 \& 8837 196629033 263865277 416380653 477036669 681527491 730724924 90906
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
284 \& 5537 1021959189 1133014972 1174311016 1359441203 1573452838 1661585138
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
285 \& 1668649038 1684198062 1812312554 1859266290 1891651106 2072549404 ...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
286 \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
287 \& FingerprintsVector;ExtendedConnectivity:TPSAAtomTypes:Radius2;47;Alpha
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
288 \& NumericalValues;ValuesString;20818206 259344053 862102353 1331904542 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
289 \& 700688206 265614156 363161397 681332588 810600886 885767127 950172500
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
290 \& 951454814 1059668746 1247054493 1382302230 1399502637 1805025917 19189
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
291 \& 39561 2114677228 2126402271 8130483 17645742 32278373 149975755 160327
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
292 \& 654 256360355 279492740 291251259 317592700 333763396 972105960 101...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
293 \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
294 \& FingerprintsVector;ExtendedConnectivity:UFFAtomTypes:Radius2;56;AlphaN
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
295 \& umericalValues;ValuesString;280305427 357928343 721790579 1151822898 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
296 \& 207111054 1380963747 1568213839 1603445250 4559268 55012922 180940813
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
297 \& 335715751 534801009 684609658 829361048 972945982 999881534 1007655741
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
298 \& 1213692591 1222032501 1224517934 1235687794 1244268533 1528120700 162
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
299 \& 9595024 1856308891 1978806036 2001865095 2096549435 172675415 18344...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
300 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
301 .SS "\s-1METHODS\s0"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
302 .IX Subsection "METHODS"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
303 .IP "\fBnew\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
304 .IX Item "new"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
305 .Vb 2
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
306 \& $NewExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
307 \& %NamesAndValues);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
308 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
309 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
310 Using specified \fIExtendedConnectivityFingerprints\fR property names and values hash, \fBnew\fR
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
311 method creates a new object and returns a reference to newly created \fBExtendedConnectivityFingerprints\fR
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
312 object. By default, the following properties are initialized:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
313 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
314 .Vb 6
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
315 \& Molecule = \*(Aq\*(Aq
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
316 \& Type = \*(AqExtendedConnectivity\*(Aq
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
317 \& NeighborhoodRadius = 2
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
318 \& AtomIdentifierType = \*(Aq\*(Aq
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
319 \& AtomicInvariantsToUse = [\*(AqAS\*(Aq, \*(AqX\*(Aq, \*(AqBO\*(Aq, \*(AqH\*(Aq, \*(AqFC\*(Aq, \*(AqMN\*(Aq]
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
320 \& FunctionalClassesToUse = [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqAr\*(Aq, \*(AqHal\*(Aq]
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
321 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
322 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
323 Examples:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
324 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
325 .Vb 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
326 \& $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
327 \& \*(AqMolecule\*(Aq => $Molecule,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
328 \& \*(AqAtomIdentifierType\*(Aq =>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
329 \& \*(AqAtomicInvariantsAtomTypes\*(Aq);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
330 \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
331 \& $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
332 \& \*(AqType\*(Aq => \*(AqExtendedConnectivityCount\*(Aq,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
333 \& \*(AqMolecule\*(Aq => $Molecule,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
334 \& \*(AqAtomIdentifierType\*(Aq =>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
335 \& \*(AqAtomicInvariantsAtomTypes\*(Aq);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
336 \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
337 \& $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
338 \& \*(AqType\*(Aq => \*(AqExtendedConnectivityBits\*(Aq,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
339 \& \*(AqMolecule\*(Aq => $Molecule,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
340 \& \*(AqSize\*(Aq => 1024,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
341 \& \*(AqAtomIdentifierType\*(Aq =>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
342 \& \*(AqAtomicInvariantsAtomTypes\*(Aq);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
343 \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
344 \& $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
345 \& \*(AqType\*(Aq => \*(AqExtendedConnectivity\*(Aq,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
346 \& \*(AqMolecule\*(Aq => $Molecule,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
347 \& \*(AqNeighborhoodRadius\*(Aq => 2,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
348 \& \*(AqAtomIdentifierType\*(Aq =>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
349 \& \*(AqAtomicInvariantsAtomTypes\*(Aq,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
350 \& \*(AqAtomicInvariantsToUse\*(Aq =>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
351 \& [\*(AqAS\*(Aq, \*(AqX\*(Aq, \*(AqBO\*(Aq, \*(AqH\*(Aq, \*(AqFC\*(Aq, \*(AqMN\*(Aq] );
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
352 \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
353 \& $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
354 \& \*(AqType\*(Aq => \*(AqExtendedConnectivity\*(Aq,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
355 \& \*(AqMolecule\*(Aq => $Molecule,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
356 \& \*(AqNeighborhoodRadius\*(Aq => 2,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
357 \& \*(AqAtomIdentifierType\*(Aq =>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
358 \& \*(AqFunctionalClassAtomTypes\*(Aq,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
359 \& \*(AqFunctionalClassesToUse\*(Aq =>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
360 \& [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqAr\*(Aq, \*(AqHal\*(Aq] );
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
361 \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
362 \& $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
363 \& \*(AqType\*(Aq => \*(AqExtendedConnectivity\*(Aq,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
364 \& \*(AqMolecule\*(Aq => $Molecule,;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
365 \& \*(AqAtomIdentifierType\*(Aq =>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
366 \& \*(AqMMFF94AtomTypes\*(Aq);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
367 \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
368 \& $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
369 \& \*(AqType\*(Aq => \*(AqExtendedConnectivityCount\*(Aq,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
370 \& \*(AqMolecule\*(Aq => $Molecule,;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
371 \& \*(AqAtomIdentifierType\*(Aq =>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
372 \& \*(AqMMFF94AtomTypes\*(Aq);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
373 \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
374 \& $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
375 \& \*(AqType\*(Aq => \*(AqExtendedConnectivityCount\*(Aq,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
376 \& \*(AqMolecule\*(Aq => $Molecule,;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
377 \& \*(AqAtomIdentifierType\*(Aq =>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
378 \& \*(AqSLogPAtomTypes\*(Aq);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
379 \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
380 \& $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
381 \& \*(AqType\*(Aq => \*(AqExtendedConnectivity\*(Aq,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
382 \& \*(AqMolecule\*(Aq => $Molecule,;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
383 \& \*(AqAtomIdentifierType\*(Aq =>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
384 \& \*(AqSLogPAtomTypes\*(Aq);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
385 \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
386 \& $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
387 \& \*(AqType\*(Aq => \*(AqExtendedConnectivity\*(Aq,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
388 \& \*(AqMolecule\*(Aq => $Molecule,;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
389 \& \*(AqAtomIdentifierType\*(Aq =>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
390 \& \*(AqSYBYLAtomTypes\*(Aq);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
391 \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
392 \& $ExtendedConnectivityFingerprints\->GenerateFingerprints();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
393 \& print "$ExtendedConnectivityFingerprints\en";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
394 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
395 .IP "\fBGenerateFingerprints\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
396 .IX Item "GenerateFingerprints"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
397 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
398 \& $ExtendedConnectivityFingerprints\->GenerateFingerprints();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
399 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
400 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
401 Generates extended connectivity fingerprints and returns \fIExtendedConnectivityFingerprints\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
402 .IP "\fBGetDescription\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
403 .IX Item "GetDescription"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
404 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
405 \& $Description = $ExtendedConnectivityFingerprints\->GetDescription();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
406 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
407 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
408 Returns a string containing description of extended connectivity fingerprints
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
409 fingerprints.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
410 .IP "\fBSetAtomIdentifierType\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
411 .IX Item "SetAtomIdentifierType"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
412 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
413 \& $ExtendedConnectivityFingerprints\->SetAtomIdentifierType($IdentifierType);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
414 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
415 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
416 Sets atom \fIIdentifierType\fR to use during extended connectivity fingerprints generation and
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
417 returns \fIExtendedConnectivityFingerprints\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
418 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
419 Possible values: \fIAtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
420 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
421 TPSAAtomTypes, UFFAtomTypes\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
422 .IP "\fBSetAtomicInvariantsToUse\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
423 .IX Item "SetAtomicInvariantsToUse"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
424 .Vb 2
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
425 \& $ExtendedConnectivityFingerprints\->SetAtomicInvariantsToUse($ValuesRef);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
426 \& $ExtendedConnectivityFingerprints\->SetAtomicInvariantsToUse(@Values);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
427 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
428 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
429 Sets atomic invariants to use during \fIAtomicInvariantsAtomTypes\fR value of \fIAtomIdentifierType\fR
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
430 for extended connectivity fingerprints generation and returns \fIExtendedConnectivityFingerprints\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
431 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
432 Possible values for atomic invariants are: \fI\s-1AS\s0, X, \s-1BO\s0, \s-1LBO\s0, \s-1SB\s0, \s-1DB\s0, \s-1TB\s0,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
433 H, Ar, \s-1RA\s0, \s-1FC\s0, \s-1MN\s0, \s-1SM\s0\fR. Default value [ Ref 24 ]: \fI\s-1AS\s0,X,BO,H,FC,MN\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
434 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
435 The atomic invariants abbreviations correspond to:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
436 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
437 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
438 \& AS = Atom symbol corresponding to element symbol
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
439 \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
440 \& X<n> = Number of non\-hydrogen atom neighbors or heavy atoms
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
441 \& BO<n> = Sum of bond orders to non\-hydrogen atom neighbors or heavy atoms
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
442 \& LBO<n> = Largest bond order of non\-hydrogen atom neighbors or heavy atoms
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
443 \& SB<n> = Number of single bonds to non\-hydrogen atom neighbors or heavy atoms
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
444 \& DB<n> = Number of double bonds to non\-hydrogen atom neighbors or heavy atoms
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
445 \& TB<n> = Number of triple bonds to non\-hydrogen atom neighbors or heavy atoms
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
446 \& H<n> = Number of implicit and explicit hydrogens for atom
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
447 \& Ar = Aromatic annotation indicating whether atom is aromatic
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
448 \& RA = Ring atom annotation indicating whether atom is a ring
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
449 \& FC<+n/\-n> = Formal charge assigned to atom
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
450 \& MN<n> = Mass number indicating isotope other than most abundant isotope
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
451 \& SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
452 \& 3 (triplet)
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
453 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
454 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
455 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
456 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
457 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
458 \& AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/\-n>.MN<n>.SM<n>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
459 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
460 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
461 Except for \s-1AS\s0 which is a required atomic invariant in atom types, all other atomic invariants are
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
462 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
463 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
464 In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
465 are also allowed:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
466 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
467 .Vb 12
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
468 \& X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
469 \& BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
470 \& LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
471 \& SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
472 \& DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
473 \& TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
474 \& H : NumOfImplicitAndExplicitHydrogens
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
475 \& Ar : Aromatic
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
476 \& RA : RingAtom
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
477 \& FC : FormalCharge
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
478 \& MN : MassNumber
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
479 \& SM : SpinMultiplicity
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
480 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
481 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
482 \&\fIAtomTypes::AtomicInvariantsAtomTypes\fR module is used to assign atomic invariant
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
483 atom types.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
484 .IP "\fBSetFunctionalClassesToUse\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
485 .IX Item "SetFunctionalClassesToUse"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
486 .Vb 2
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
487 \& $ExtendedConnectivityFingerprints\->SetFunctionalClassesToUse($ValuesRef);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
488 \& $ExtendedConnectivityFingerprints\->SetFunctionalClassesToUse(@Values);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
489 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
490 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
491 Sets functional classes invariants to use during \fIFunctionalClassAtomTypes\fR value of \fIAtomIdentifierType\fR
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
492 for extended connectivity fingerprints generation and returns \fIExtendedConnectivityFingerprints\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
493 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
494 Possible values for atom functional classes are: \fIAr, \s-1CA\s0, H, \s-1HBA\s0, \s-1HBD\s0, Hal, \s-1NI\s0, \s-1PI\s0, \s-1RA\s0\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
495 Default value [ Ref 24 ]: \fI\s-1HBD\s0,HBA,PI,NI,Ar,Hal\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
496 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
497 The functional class abbreviations correspond to:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
498 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
499 .Vb 9
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
500 \& HBD: HydrogenBondDonor
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
501 \& HBA: HydrogenBondAcceptor
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
502 \& PI : PositivelyIonizable
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
503 \& NI : NegativelyIonizable
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
504 \& Ar : Aromatic
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
505 \& Hal : Halogen
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
506 \& H : Hydrophobic
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
507 \& RA : RingAtom
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
508 \& CA : ChainAtom
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
509 \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
510 \& Functional class atom type specification for an atom corresponds to:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
511 \&
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
512 \& Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
513 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
514 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
515 \&\fIAtomTypes::FunctionalClassAtomTypes\fR module is used to assign functional class atom
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
516 types. It uses following definitions [ Ref 60\-61, Ref 65\-66 ]:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
517 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
518 .Vb 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
519 \& HydrogenBondDonor: NH, NH2, OH
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
520 \& HydrogenBondAcceptor: N[!H], O
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
521 \& PositivelyIonizable: +, NH2
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
522 \& NegativelyIonizable: \-, C(=O)OH, S(=O)OH, P(=O)OH
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
523 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
524 .IP "\fBSetNeighborhoodRadius\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
525 .IX Item "SetNeighborhoodRadius"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
526 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
527 \& $ExtendedConnectivityFingerprints\->SetNeighborhoodRadius($Radius);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
528 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
529 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
530 Sets neighborhood radius to use during extended connectivity fingerprints generation and
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
531 returns \fIExtendedConnectivityFingerprints\fR.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
532 .IP "\fBStringifyExtendedConnectivityFingerprints\fR" 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
533 .IX Item "StringifyExtendedConnectivityFingerprints"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
534 .Vb 1
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
535 \& $String = $Fingerprints\->StringifyExtendedConnectivityFingerprints();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
536 .Ve
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
537 .Sp
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
538 Returns a string containing information about \fIExtendedConnectivityFingerprints\fR object.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
539 .SH "AUTHOR"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
540 .IX Header "AUTHOR"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
541 Manish Sud <msud@san.rr.com>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
542 .SH "SEE ALSO"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
543 .IX Header "SEE ALSO"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
544 Fingerprints.pm, FingerprintsStringUtil.pm, AtomNeighborhoodsFingerprints.pm,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
545 AtomTypesFingerprints.pm, EStateIndiciesFingerprints.pm, MACCSKeys.pm,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
546 PathLengthFingerprints.pm, TopologicalAtomPairsFingerprints.pm,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
547 TopologicalAtomTripletsFingerprints.pm, TopologicalAtomTorsionsFingerprints.pm,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
548 TopologicalPharmacophoreAtomPairsFingerprints.pm,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
549 TopologicalPharmacophoreAtomTripletsFingerprints.pm
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
550 .SH "COPYRIGHT"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
551 .IX Header "COPYRIGHT"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
552 Copyright (C) 2015 Manish Sud. All rights reserved.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
553 .PP
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
554 This file is part of MayaChemTools.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
555 .PP
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
556 MayaChemTools is free software; you can redistribute it and/or modify it under
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
557 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
558 Software Foundation; either version 3 of the License, or (at your option)
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
559 any later version.