0
|
1 .\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.22)
|
|
2 .\"
|
|
3 .\" Standard preamble:
|
|
4 .\" ========================================================================
|
|
5 .de Sp \" Vertical space (when we can't use .PP)
|
|
6 .if t .sp .5v
|
|
7 .if n .sp
|
|
8 ..
|
|
9 .de Vb \" Begin verbatim text
|
|
10 .ft CW
|
|
11 .nf
|
|
12 .ne \\$1
|
|
13 ..
|
|
14 .de Ve \" End verbatim text
|
|
15 .ft R
|
|
16 .fi
|
|
17 ..
|
|
18 .\" Set up some character translations and predefined strings. \*(-- will
|
|
19 .\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left
|
|
20 .\" double quote, and \*(R" will give a right double quote. \*(C+ will
|
|
21 .\" give a nicer C++. Capital omega is used to do unbreakable dashes and
|
|
22 .\" therefore won't be available. \*(C` and \*(C' expand to `' in nroff,
|
|
23 .\" nothing in troff, for use with C<>.
|
|
24 .tr \(*W-
|
|
25 .ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p'
|
|
26 .ie n \{\
|
|
27 . ds -- \(*W-
|
|
28 . ds PI pi
|
|
29 . if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch
|
|
30 . if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\" diablo 12 pitch
|
|
31 . ds L" ""
|
|
32 . ds R" ""
|
|
33 . ds C` ""
|
|
34 . ds C' ""
|
|
35 'br\}
|
|
36 .el\{\
|
|
37 . ds -- \|\(em\|
|
|
38 . ds PI \(*p
|
|
39 . ds L" ``
|
|
40 . ds R" ''
|
|
41 'br\}
|
|
42 .\"
|
|
43 .\" Escape single quotes in literal strings from groff's Unicode transform.
|
|
44 .ie \n(.g .ds Aq \(aq
|
|
45 .el .ds Aq '
|
|
46 .\"
|
|
47 .\" If the F register is turned on, we'll generate index entries on stderr for
|
|
48 .\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
|
|
49 .\" entries marked with X<> in POD. Of course, you'll have to process the
|
|
50 .\" output yourself in some meaningful fashion.
|
|
51 .ie \nF \{\
|
|
52 . de IX
|
|
53 . tm Index:\\$1\t\\n%\t"\\$2"
|
|
54 ..
|
|
55 . nr % 0
|
|
56 . rr F
|
|
57 .\}
|
|
58 .el \{\
|
|
59 . de IX
|
|
60 ..
|
|
61 .\}
|
|
62 .\"
|
|
63 .\" Accent mark definitions (@(#)ms.acc 1.5 88/02/08 SMI; from UCB 4.2).
|
|
64 .\" Fear. Run. Save yourself. No user-serviceable parts.
|
|
65 . \" fudge factors for nroff and troff
|
|
66 .if n \{\
|
|
67 . ds #H 0
|
|
68 . ds #V .8m
|
|
69 . ds #F .3m
|
|
70 . ds #[ \f1
|
|
71 . ds #] \fP
|
|
72 .\}
|
|
73 .if t \{\
|
|
74 . ds #H ((1u-(\\\\n(.fu%2u))*.13m)
|
|
75 . ds #V .6m
|
|
76 . ds #F 0
|
|
77 . ds #[ \&
|
|
78 . ds #] \&
|
|
79 .\}
|
|
80 . \" simple accents for nroff and troff
|
|
81 .if n \{\
|
|
82 . ds ' \&
|
|
83 . ds ` \&
|
|
84 . ds ^ \&
|
|
85 . ds , \&
|
|
86 . ds ~ ~
|
|
87 . ds /
|
|
88 .\}
|
|
89 .if t \{\
|
|
90 . ds ' \\k:\h'-(\\n(.wu*8/10-\*(#H)'\'\h"|\\n:u"
|
|
91 . ds ` \\k:\h'-(\\n(.wu*8/10-\*(#H)'\`\h'|\\n:u'
|
|
92 . ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'^\h'|\\n:u'
|
|
93 . ds , \\k:\h'-(\\n(.wu*8/10)',\h'|\\n:u'
|
|
94 . ds ~ \\k:\h'-(\\n(.wu-\*(#H-.1m)'~\h'|\\n:u'
|
|
95 . ds / \\k:\h'-(\\n(.wu*8/10-\*(#H)'\z\(sl\h'|\\n:u'
|
|
96 .\}
|
|
97 . \" troff and (daisy-wheel) nroff accents
|
|
98 .ds : \\k:\h'-(\\n(.wu*8/10-\*(#H+.1m+\*(#F)'\v'-\*(#V'\z.\h'.2m+\*(#F'.\h'|\\n:u'\v'\*(#V'
|
|
99 .ds 8 \h'\*(#H'\(*b\h'-\*(#H'
|
|
100 .ds o \\k:\h'-(\\n(.wu+\w'\(de'u-\*(#H)/2u'\v'-.3n'\*(#[\z\(de\v'.3n'\h'|\\n:u'\*(#]
|
|
101 .ds d- \h'\*(#H'\(pd\h'-\w'~'u'\v'-.25m'\f2\(hy\fP\v'.25m'\h'-\*(#H'
|
|
102 .ds D- D\\k:\h'-\w'D'u'\v'-.11m'\z\(hy\v'.11m'\h'|\\n:u'
|
|
103 .ds th \*(#[\v'.3m'\s+1I\s-1\v'-.3m'\h'-(\w'I'u*2/3)'\s-1o\s+1\*(#]
|
|
104 .ds Th \*(#[\s+2I\s-2\h'-\w'I'u*3/5'\v'-.3m'o\v'.3m'\*(#]
|
|
105 .ds ae a\h'-(\w'a'u*4/10)'e
|
|
106 .ds Ae A\h'-(\w'A'u*4/10)'E
|
|
107 . \" corrections for vroff
|
|
108 .if v .ds ~ \\k:\h'-(\\n(.wu*9/10-\*(#H)'\s-2\u~\d\s+2\h'|\\n:u'
|
|
109 .if v .ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'\v'-.4m'^\v'.4m'\h'|\\n:u'
|
|
110 . \" for low resolution devices (crt and lpr)
|
|
111 .if \n(.H>23 .if \n(.V>19 \
|
|
112 \{\
|
|
113 . ds : e
|
|
114 . ds 8 ss
|
|
115 . ds o a
|
|
116 . ds d- d\h'-1'\(ga
|
|
117 . ds D- D\h'-1'\(hy
|
|
118 . ds th \o'bp'
|
|
119 . ds Th \o'LP'
|
|
120 . ds ae ae
|
|
121 . ds Ae AE
|
|
122 .\}
|
|
123 .rm #[ #] #H #V #F C
|
|
124 .\" ========================================================================
|
|
125 .\"
|
|
126 .IX Title "TOPOLOGICALATOMPAIRSFINGERPRINTS 1"
|
|
127 .TH TOPOLOGICALATOMPAIRSFINGERPRINTS 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
|
|
128 .\" For nroff, turn off justification. Always turn off hyphenation; it makes
|
|
129 .\" way too many mistakes in technical documents.
|
|
130 .if n .ad l
|
|
131 .nh
|
|
132 .SH "NAME"
|
|
133 TopologicalAtomPairsFingerprints
|
|
134 .SH "SYNOPSIS"
|
|
135 .IX Header "SYNOPSIS"
|
|
136 use Fingerprints::TopologicalAtomPairsFingerprints;
|
|
137 .PP
|
|
138 use Fingerprints::TopologicalAtomPairsFingerprints qw(:all);
|
|
139 .SH "DESCRIPTION"
|
|
140 .IX Header "DESCRIPTION"
|
|
141 \&\fBTopologicalAtomPairsFingerprints\fR [ Ref 57, Ref 59, Ref 72 ] class provides the following methods:
|
|
142 .PP
|
|
143 new, GenerateFingerprints, GetAtomPairIDs, GetDescription, SetAtomIdentifierType,
|
|
144 SetAtomicInvariantsToUse, SetFunctionalClassesToUse, SetMaxDistance,
|
|
145 SetMinDistance, StringifyTopologicalAtomPairsFingerprints
|
|
146 .PP
|
|
147 \&\fBTopologicalAtomPairsFingerprints\fR is derived from \fBFingerprints\fR class which in turn
|
|
148 is derived from \fBObjectProperty\fR base class that provides methods not explicitly defined
|
|
149 in \fBTopologicalAtomPairsFingerprints\fR, \fBFingerprints\fR or \fBObjectProperty\fR classes using Perl's
|
|
150 \&\s-1AUTOLOAD\s0 functionality. These methods are generated on-the-fly for a specified object property:
|
|
151 .PP
|
|
152 .Vb 3
|
|
153 \& Set<PropertyName>(<PropertyValue>);
|
|
154 \& $PropertyValue = Get<PropertyName>();
|
|
155 \& Delete<PropertyName>();
|
|
156 .Ve
|
|
157 .PP
|
|
158 The current release of MayaChemTools supports generation of \fBAtomTypesFingerpritns\fR
|
|
159 corresponding to following \fBAtomtomIdentifierTypes\fR:
|
|
160 .PP
|
|
161 .Vb 3
|
|
162 \& AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
|
|
163 \& FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
|
|
164 \& SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
|
|
165 .Ve
|
|
166 .PP
|
|
167 Based on the values specified for \fBAtomIdentifierType\fR along with other specified
|
|
168 parameters such as \fBAtomicInvariantsToUse\fR and \fBFunctionalClassesToUse\fR, initial
|
|
169 atom types are assigned to all non-hydrogen atoms in a molecule. Using the distance
|
|
170 matrix for the molecule and initial atom types assigned to non-hydrogen atoms, all unique atom
|
|
171 pairs within \fBMinDistance\fR and \fBMaxDistance\fR are identified and counted. An atom pair
|
|
172 identifier is generated for each unique atom pair; the format of atom pair identifier is:
|
|
173 .PP
|
|
174 .Vb 1
|
|
175 \& <AtomType1>\-D<n>\-<AtomType2>
|
|
176 \&
|
|
177 \& AtomType1, AtomType2: Atom types assigned to atom1 and atom2
|
|
178 \& D: Distance between atom1 and atom2
|
|
179 \&
|
|
180 \& where AtomType1 <= AtomType2
|
|
181 .Ve
|
|
182 .PP
|
|
183 The atom pair identifiers for all unique atom pairs corresponding to non-hydrogen atoms constitute
|
|
184 topological atom pairs fingerprints of the molecule.
|
|
185 .PP
|
|
186 The current release of MayaChemTools generates the following types of topological atom pairs
|
|
187 fingerprints vector strings:
|
|
188 .PP
|
|
189 .Vb 6
|
|
190 \& FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
|
|
191 \& istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
|
|
192 \& .H3\-D1\-C.X3.BO3.H1 C.X2.BO2.H2\-D1\-C.X2.BO2.H2 C.X2.BO2.H2\-D1\-C.X3.BO3.
|
|
193 \& H1 C.X2.BO2.H2\-D1\-C.X3.BO4 C.X2.BO2.H2\-D1\-N.X3.BO3 C.X2.BO3.H1\-D1\-...;
|
|
194 \& 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
|
|
195 \& 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1...
|
|
196 \&
|
|
197 \& FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
|
|
198 \& istance1:MaxDistance10;223;NumericalValues;IDsAndValuesPairsString;C.X
|
|
199 \& 1.BO1.H3\-D1\-C.X3.BO3.H1 2 C.X2.BO2.H2\-D1\-C.X2.BO2.H2 1 C.X2.BO2.H2\-D1\-
|
|
200 \& C.X3.BO3.H1 4 C.X2.BO2.H2\-D1\-C.X3.BO4 1 C.X2.BO2.H2\-D1\-N.X3.BO3 1 C.X2
|
|
201 \& .BO3.H1\-D1\-C.X2.BO3.H1 10 C.X2.BO3.H1\-D1\-C.X3.BO4 8 C.X3.BO3.H1\-D1\-C.X
|
|
202 \& 3.BO4 1 C.X3.BO3.H1\-D1\-O.X1.BO1.H1 2 C.X3.BO4\-D1\-C.X3.BO4 6 C.X3.BO...
|
|
203 \&
|
|
204 \& FingerprintsVector;TopologicalAtomPairs:DREIDINGAtomTypes:MinDistance1
|
|
205 \& :MaxDistance10;157;NumericalValues;IDsAndValuesString;C_2\-D1\-C_3 C_2\-D
|
|
206 \& 1\-C_R C_2\-D1\-N_3 C_2\-D1\-O_2 C_2\-D1\-O_3 C_3\-D1\-C_3 C_3\-D1\-C_R C_3\-D1\-N_
|
|
207 \& R C_3\-D1\-O_3 C_R\-D1\-C_R C_R\-D1\-F_ C_R\-D1\-N_3 C_R\-D1\-N_R C_2\-D2\-C_3 C_2
|
|
208 \& 1 1 1 2 1 7 1 1 2 23 1 1 2 1 3 5 5 2 1 5 28 2 3 3 1 1 1 2 4 1 1 4 9 3
|
|
209 \& 1 4 24 2 4 3 3 4 5 5 14 1 1 2 3 22 1 3 4 4 1 1 1 1 2 2 5 1 4 21 3 1...
|
|
210 \&
|
|
211 \& FingerprintsVector;TopologicalAtomPairs:EStateAtomTypes:MinDistance1:M
|
|
212 \& axDistance10;251;NumericalValues;IDsAndValuesString;aaCH\-D1\-aaCH aaCH\-
|
|
213 \& D1\-aasC aasC\-D1\-aasC aasC\-D1\-aasN aasC\-D1\-dssC aasC\-D1\-sF aasC\-D1\-ssNH
|
|
214 \& aasC\-D1\-sssCH aasN\-D1\-ssCH2 dO\-D1\-dssC dssC\-D1\-sOH dssC\-D1\-ssCH2 d...;
|
|
215 \& 10 8 5 2 1 1 1 1 1 2 1 1 1 2 2 1 4 10 12 2 2 6 3 1 3 2 2 1 1 1 1 1 1 1
|
|
216 \& 1 1 5 2 1 1 6 12 2 2 2 2 6 1 3 2 2 5 2 2 1 2 1 1 1 1 1 1 3 1 3 19 2...
|
|
217 \&
|
|
218 \& FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
|
|
219 \& stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar\-D1\-Ar
|
|
220 \& Ar\-D1\-Ar.HBA Ar\-D1\-HBD Ar\-D1\-Hal Ar\-D1\-None Ar.HBA\-D1\-None HBA\-D1\-NI H
|
|
221 \& BA\-D1\-None HBA.HBD\-D1\-NI HBA.HBD\-D1\-None HBD\-D1\-None NI\-D1\-None No...;
|
|
222 \& 23 2 1 1 2 1 1 1 1 2 1 1 7 28 3 1 3 2 8 2 1 1 1 5 1 5 24 3 3 4 2 13 4
|
|
223 \& 1 1 4 1 5 22 4 4 3 1 19 1 1 1 1 1 2 2 3 1 1 8 25 4 5 2 3 1 26 1 4 1 ...
|
|
224 \&
|
|
225 \& FingerprintsVector;TopologicalAtomPairs:MMFF94AtomTypes:MinDistance1:M
|
|
226 \& axDistance10;227;NumericalValues;IDsAndValuesPairsString;C5A\-D1\-C5B 2
|
|
227 \& C5A\-D1\-CB 1 C5A\-D1\-CR 1 C5A\-D1\-N5 2 C5B\-D1\-C5B 1 C5B\-D1\-C=ON 1 C5B\-D1\-
|
|
228 \& CB 1 C=ON\-D1\-NC=O 1 C=ON\-D1\-O=CN 1 CB\-D1\-CB 18 CB\-D1\-F 1 CB\-D1\-NC=O 1
|
|
229 \& COO\-D1\-CR 1 COO\-D1\-O=CO 1 COO\-D1\-OC=O 1 CR\-D1\-CR 7 CR\-D1\-N5 1 CR\-D1\-OR
|
|
230 \& 2 C5A\-D2\-C5A 1 C5A\-D2\-C5B 2 C5A\-D2\-C=ON 1 C5A\-D2\-CB 3 C5A\-D2\-CR 4 ...
|
|
231 \&
|
|
232 \& FingerprintsVector;TopologicalAtomPairs:SLogPAtomTypes:MinDistance1:Ma
|
|
233 \& xDistance10;329;NumericalValues;IDsAndValuesPairsString;C1\-D1\-C10 1 C1
|
|
234 \& \-D1\-C11 2 C1\-D1\-C5 1 C1\-D1\-CS 4 C10\-D1\-N11 1 C11\-D1\-C21 1 C14\-D1\-C18 2
|
|
235 \& C14\-D1\-F 1 C18\-D1\-C18 10 C18\-D1\-C20 4 C18\-D1\-C22 2 C20\-D1\-C20 3 C20\-D
|
|
236 \& 1\-C21 1 C20\-D1\-N11 1 C21\-D1\-C21 1 C21\-D1\-C5 1 C21\-D1\-N11 1 C22\-D1\-N4 1
|
|
237 \& C5\-D1\-N4 1 C5\-D1\-O10 1 C5\-D1\-O2 1 C5\-D1\-O9 1 CS\-D1\-O2 2 C1\-D2\-C1 3...
|
|
238 \&
|
|
239 \& FingerprintsVector;TopologicalAtomPairs:SYBYLAtomTypes:MinDistance1:Ma
|
|
240 \& xDistance10;159;NumericalValues;IDsAndValuesPairsString;C.2\-D1\-C.3 1 C
|
|
241 \& .2\-D1\-C.ar 1 C.2\-D1\-N.am 1 C.2\-D1\-O.2 1 C.2\-D1\-O.co2 2 C.3\-D1\-C.3 7 C.
|
|
242 \& 3\-D1\-C.ar 1 C.3\-D1\-N.ar 1 C.3\-D1\-O.3 2 C.ar\-D1\-C.ar 23 C.ar\-D1\-F 1 C.a
|
|
243 \& r\-D1\-N.am 1 C.ar\-D1\-N.ar 2 C.2\-D2\-C.3 1 C.2\-D2\-C.ar 3 C.3\-D2\-C.3 5 C.3
|
|
244 \& \-D2\-C.ar 5 C.3\-D2\-N.ar 2 C.3\-D2\-O.3 4 C.3\-D2\-O.co2 2 C.ar\-D2\-C.ar 2...
|
|
245 \&
|
|
246 \& FingerprintsVector;TopologicalAtomPairs:TPSAAtomTypes:MinDistance1:Max
|
|
247 \& Distance10;64;NumericalValues;IDsAndValuesPairsString;N21\-D1\-None 3 N7
|
|
248 \& \-D1\-None 2 None\-D1\-None 34 None\-D1\-O3 2 None\-D1\-O4 3 N21\-D2\-None 5 N7\-
|
|
249 \& D2\-None 3 N7\-D2\-O3 1 None\-D2\-None 44 None\-D2\-O3 2 None\-D2\-O4 5 O3\-D2\-O
|
|
250 \& 4 1 N21\-D3\-None 7 N7\-D3\-None 4 None\-D3\-None 45 None\-D3\-O3 4 None\-D3\-O4
|
|
251 \& 5 N21\-D4\-N7 1 N21\-D4\-None 5 N21\-D4\-O3 1 N21\-D4\-O4 1 N7\-D4\-None 4 N...
|
|
252 \&
|
|
253 \& FingerprintsVector;TopologicalAtomPairs:UFFAtomTypes:MinDistance1:MaxD
|
|
254 \& istance10;157;NumericalValues;IDsAndValuesPairsString;C_2\-D1\-C_3 1 C_2
|
|
255 \& \-D1\-C_R 1 C_2\-D1\-N_3 1 C_2\-D1\-O_2 2 C_2\-D1\-O_3 1 C_3\-D1\-C_3 7 C_3\-D1\-C
|
|
256 \& _R 1 C_3\-D1\-N_R 1 C_3\-D1\-O_3 2 C_R\-D1\-C_R 23 C_R\-D1\-F_ 1 C_R\-D1\-N_3 1
|
|
257 \& C_R\-D1\-N_R 2 C_2\-D2\-C_3 1 C_2\-D2\-C_R 3 C_3\-D2\-C_3 5 C_3\-D2\-C_R 5 C_3\-D
|
|
258 \& 2\-N_R 2 C_3\-D2\-O_2 1 C_3\-D2\-O_3 5 C_R\-D2\-C_R 28 C_R\-D2\-F_ 2 C_R\-D2\-...
|
|
259 .Ve
|
|
260 .SS "\s-1METHODS\s0"
|
|
261 .IX Subsection "METHODS"
|
|
262 .IP "\fBnew\fR" 4
|
|
263 .IX Item "new"
|
|
264 .Vb 2
|
|
265 \& $NewTopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
|
|
266 \& %NamesAndValues);
|
|
267 .Ve
|
|
268 .Sp
|
|
269 Using specified \fITopologicalAtomPairsFingerprints\fR property names and values hash, \fBnew\fR
|
|
270 method creates a new object and returns a reference to newly created \fBTopologicalAtomPairsFingerprints\fR
|
|
271 object. By default, the following properties are initialized:
|
|
272 .Sp
|
|
273 .Vb 7
|
|
274 \& Molecule = \*(Aq\*(Aq
|
|
275 \& Type = \*(AqTopologicalAtomPairs\*(Aq
|
|
276 \& MinDistance = 1
|
|
277 \& MaxDistance = 10
|
|
278 \& AtomIdentifierType = \*(Aq\*(Aq
|
|
279 \& AtomicInvariantsToUse = [\*(AqAS\*(Aq, \*(AqX\*(Aq, \*(AqBO\*(Aq, \*(AqH\*(Aq, \*(AqFC\*(Aq]
|
|
280 \& FunctionalClassesToUse = [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqAr\*(Aq, \*(AqHal\*(Aq]
|
|
281 .Ve
|
|
282 .Sp
|
|
283 Examples:
|
|
284 .Sp
|
|
285 .Vb 4
|
|
286 \& $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
|
|
287 \& \*(AqMolecule\*(Aq => $Molecule,
|
|
288 \& \*(AqAtomIdentifierType\*(Aq =>
|
|
289 \& \*(AqAtomicInvariantsAtomTypes\*(Aq);
|
|
290 \&
|
|
291 \& $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
|
|
292 \& \*(AqMolecule\*(Aq => $Molecule,
|
|
293 \& \*(AqMinDistance\*(Aq => 1,
|
|
294 \& \*(AqMaxDistance\*(Aq => 10,
|
|
295 \& \*(AqAtomIdentifierType\*(Aq =>
|
|
296 \& \*(AqAtomicInvariantsAtomTypes\*(Aq,
|
|
297 \& \*(AqAtomicInvariantsToUse\*(Aq =>
|
|
298 \& [\*(AqAS\*(Aq, \*(AqX\*(Aq, \*(AqBO\*(Aq, \*(AqH\*(Aq, \*(AqFC\*(Aq] );
|
|
299 \&
|
|
300 \& $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
|
|
301 \& \*(AqMolecule\*(Aq => $Molecule,
|
|
302 \& \*(AqAtomIdentifierType\*(Aq =>
|
|
303 \& \*(AqEStateAtomTypes\*(Aq);
|
|
304 \&
|
|
305 \& $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
|
|
306 \& \*(AqMolecule\*(Aq => $Molecule,
|
|
307 \& \*(AqAtomIdentifierType\*(Aq =>
|
|
308 \& \*(AqSLogPAtomTypes\*(Aq);
|
|
309 \&
|
|
310 \& $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
|
|
311 \& \*(AqMolecule\*(Aq => $Molecule,
|
|
312 \& \*(AqMinDistance\*(Aq => 1,
|
|
313 \& \*(AqMaxDistance\*(Aq => 10,
|
|
314 \& \*(AqAtomIdentifierType\*(Aq =>
|
|
315 \& \*(AqFunctionalClassAtomTypes\*(Aq,
|
|
316 \& \*(AqFunctionalClassesToUse\*(Aq =>
|
|
317 \& [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqAr\*(Aq, \*(AqHal\*(Aq]);
|
|
318 \&
|
|
319 \&
|
|
320 \& $TopologicalAtomPairsFingerprints\->GenerateFingerprints();
|
|
321 \& print "$TopologicalAtomPairsFingerprints\en";
|
|
322 .Ve
|
|
323 .IP "\fBGetDescription\fR" 4
|
|
324 .IX Item "GetDescription"
|
|
325 .Vb 1
|
|
326 \& $Description = $TopologicalAtomPairsFingerprints\->GetDescription();
|
|
327 .Ve
|
|
328 .Sp
|
|
329 Returns a string containing description of topological atom pairs fingerprints fingerprints.
|
|
330 .IP "\fBGenerateFingerprints\fR" 4
|
|
331 .IX Item "GenerateFingerprints"
|
|
332 .Vb 1
|
|
333 \& $TopologicalAtomPairsFingerprints\->GenerateFingerprints();
|
|
334 .Ve
|
|
335 .Sp
|
|
336 Generates topological atom pairs fingerprints and returns \fITopologicalAtomPairsFingerprints\fR.
|
|
337 .IP "\fBGetAtomPairIDs\fR" 4
|
|
338 .IX Item "GetAtomPairIDs"
|
|
339 .Vb 2
|
|
340 \& $AtomPairIDsRef = $TopologicalAtomPairsFingerprints\->GetAtomPairIDs();
|
|
341 \& @AtomPairIDs = $TopologicalAtomPairsFingerprints\->GetAtomPairIDs();
|
|
342 .Ve
|
|
343 .Sp
|
|
344 Returns atom pair IDs corresponding to atom pairs count values in topological atom pairs
|
|
345 fingerprints vector as an array or reference to an array.
|
|
346 .IP "\fBSetAtomIdentifierType\fR" 4
|
|
347 .IX Item "SetAtomIdentifierType"
|
|
348 .Vb 1
|
|
349 \& $TopologicalAtomPairsFingerprints\->SetAtomIdentifierType($IdentifierType);
|
|
350 .Ve
|
|
351 .Sp
|
|
352 Sets atom \fIIdentifierType\fR to use during atom pairs fingerprints generation and
|
|
353 returns \fITopologicalAtomPairsFingerprints\fR.
|
|
354 .Sp
|
|
355 Possible values: \fIAtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
|
|
356 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
|
|
357 TPSAAtomTypes, UFFAtomTypes\fR.
|
|
358 .IP "\fBSetAtomicInvariantsToUse\fR" 4
|
|
359 .IX Item "SetAtomicInvariantsToUse"
|
|
360 .Vb 2
|
|
361 \& $TopologicalAtomPairsFingerprints\->SetAtomicInvariantsToUse($ValuesRef);
|
|
362 \& $TopologicalAtomPairsFingerprints\->SetAtomicInvariantsToUse(@Values);
|
|
363 .Ve
|
|
364 .Sp
|
|
365 Sets atomic invariants to use during \fIAtomicInvariantsAtomTypes\fR value of \fIAtomIdentifierType\fR
|
|
366 for topological atom pairs fingerprints generation and returns \fITopologicalAtomPairsFingerprints\fR.
|
|
367 .Sp
|
|
368 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,
|
|
369 H, Ar, \s-1RA\s0, \s-1FC\s0, \s-1MN\s0, \s-1SM\s0\fR. Default value: \fI\s-1AS\s0,X,BO,H,FC\fR.
|
|
370 .Sp
|
|
371 The atomic invariants abbreviations correspond to:
|
|
372 .Sp
|
|
373 .Vb 1
|
|
374 \& AS = Atom symbol corresponding to element symbol
|
|
375 \&
|
|
376 \& X<n> = Number of non\-hydrogen atom neighbors or heavy atoms
|
|
377 \& BO<n> = Sum of bond orders to non\-hydrogen atom neighbors or heavy atoms
|
|
378 \& LBO<n> = Largest bond order of non\-hydrogen atom neighbors or heavy atoms
|
|
379 \& SB<n> = Number of single bonds to non\-hydrogen atom neighbors or heavy atoms
|
|
380 \& DB<n> = Number of double bonds to non\-hydrogen atom neighbors or heavy atoms
|
|
381 \& TB<n> = Number of triple bonds to non\-hydrogen atom neighbors or heavy atoms
|
|
382 \& H<n> = Number of implicit and explicit hydrogens for atom
|
|
383 \& Ar = Aromatic annotation indicating whether atom is aromatic
|
|
384 \& RA = Ring atom annotation indicating whether atom is a ring
|
|
385 \& FC<+n/\-n> = Formal charge assigned to atom
|
|
386 \& MN<n> = Mass number indicating isotope other than most abundant isotope
|
|
387 \& SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
|
|
388 \& 3 (triplet)
|
|
389 .Ve
|
|
390 .Sp
|
|
391 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
|
|
392 .Sp
|
|
393 .Vb 1
|
|
394 \& AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/\-n>.MN<n>.SM<n>
|
|
395 .Ve
|
|
396 .Sp
|
|
397 Except for \s-1AS\s0 which is a required atomic invariant in atom types, all other atomic invariants are
|
|
398 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.
|
|
399 .Sp
|
|
400 In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
|
|
401 are also allowed:
|
|
402 .Sp
|
|
403 .Vb 12
|
|
404 \& X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
|
|
405 \& BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
|
|
406 \& LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
|
|
407 \& SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
|
|
408 \& DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
|
|
409 \& TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
|
|
410 \& H : NumOfImplicitAndExplicitHydrogens
|
|
411 \& Ar : Aromatic
|
|
412 \& RA : RingAtom
|
|
413 \& FC : FormalCharge
|
|
414 \& MN : MassNumber
|
|
415 \& SM : SpinMultiplicity
|
|
416 .Ve
|
|
417 .Sp
|
|
418 \&\fIAtomTypes::AtomicInvariantsAtomTypes\fR module is used to assign atomic invariant
|
|
419 atom types.
|
|
420 .IP "\fBSetFunctionalClassesToUse\fR" 4
|
|
421 .IX Item "SetFunctionalClassesToUse"
|
|
422 .Vb 2
|
|
423 \& $TopologicalAtomPairsFingerprints\->SetFunctionalClassesToUse($ValuesRef);
|
|
424 \& $TopologicalAtomPairsFingerprints\->SetFunctionalClassesToUse(@Values);
|
|
425 .Ve
|
|
426 .Sp
|
|
427 Sets functional classes invariants to use during \fIFunctionalClassAtomTypes\fR value of \fIAtomIdentifierType\fR
|
|
428 for topological atom pairs fingerprints generation and returns \fITopologicalAtomPairsFingerprints\fR.
|
|
429 .Sp
|
|
430 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.
|
|
431 Default value [ Ref 24 ]: \fI\s-1HBD\s0,HBA,PI,NI,Ar,Hal\fR.
|
|
432 .Sp
|
|
433 The functional class abbreviations correspond to:
|
|
434 .Sp
|
|
435 .Vb 9
|
|
436 \& HBD: HydrogenBondDonor
|
|
437 \& HBA: HydrogenBondAcceptor
|
|
438 \& PI : PositivelyIonizable
|
|
439 \& NI : NegativelyIonizable
|
|
440 \& Ar : Aromatic
|
|
441 \& Hal : Halogen
|
|
442 \& H : Hydrophobic
|
|
443 \& RA : RingAtom
|
|
444 \& CA : ChainAtom
|
|
445 \&
|
|
446 \& Functional class atom type specification for an atom corresponds to:
|
|
447 \&
|
|
448 \& Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None
|
|
449 .Ve
|
|
450 .Sp
|
|
451 \&\fIAtomTypes::FunctionalClassAtomTypes\fR module is used to assign functional class atom
|
|
452 types. It uses following definitions [ Ref 60\-61, Ref 65\-66 ]:
|
|
453 .Sp
|
|
454 .Vb 4
|
|
455 \& HydrogenBondDonor: NH, NH2, OH
|
|
456 \& HydrogenBondAcceptor: N[!H], O
|
|
457 \& PositivelyIonizable: +, NH2
|
|
458 \& NegativelyIonizable: \-, C(=O)OH, S(=O)OH, P(=O)OH
|
|
459 .Ve
|
|
460 .IP "\fBSetMaxDistance\fR" 4
|
|
461 .IX Item "SetMaxDistance"
|
|
462 .Vb 1
|
|
463 \& $TopologicalAtomPairsFingerprints\->SetMaxDistance($Distance);
|
|
464 .Ve
|
|
465 .Sp
|
|
466 Sets maximum distance to use during topological atom pairs fingerprints generation and
|
|
467 returns \fITopologicalAtomPairsFingerprints\fR.
|
|
468 .IP "\fBSetMinDistance\fR" 4
|
|
469 .IX Item "SetMinDistance"
|
|
470 .Vb 1
|
|
471 \& $TopologicalAtomPairsFingerprints\->SetMinDistance($Distance);
|
|
472 .Ve
|
|
473 .Sp
|
|
474 Sets minimum distance to use during topological atom pairs fingerprints generation and
|
|
475 returns \fITopologicalAtomPairsFingerprints\fR.
|
|
476 .IP "\fBStringifyTopologicalAtomPairsFingerprints\fR" 4
|
|
477 .IX Item "StringifyTopologicalAtomPairsFingerprints"
|
|
478 .Vb 2
|
|
479 \& $String = $TopologicalAtomPairsFingerprints\->
|
|
480 \& StringifyTopologicalAtomPairsFingerprints();
|
|
481 .Ve
|
|
482 .Sp
|
|
483 Returns a string containing information about \fITopologicalAtomPairsFingerprints\fR object.
|
|
484 .SH "AUTHOR"
|
|
485 .IX Header "AUTHOR"
|
|
486 Manish Sud <msud@san.rr.com>
|
|
487 .SH "SEE ALSO"
|
|
488 .IX Header "SEE ALSO"
|
|
489 Fingerprints.pm, FingerprintsStringUtil.pm, AtomNeighborhoodsFingerprints.pm,
|
|
490 AtomTypesFingerprints.pm, EStateIndiciesFingerprints.pm, ExtendedConnectivityFingerprints.pm,
|
|
491 MACCSKeys.pm, PathLengthFingerprints.pm, TopologicalAtomTripletsFingerprints.pm,
|
|
492 TopologicalAtomTorsionsFingerprints.pm, TopologicalPharmacophoreAtomPairsFingerprints.pm,
|
|
493 TopologicalPharmacophoreAtomTripletsFingerprints.pm
|
|
494 .SH "COPYRIGHT"
|
|
495 .IX Header "COPYRIGHT"
|
|
496 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
497 .PP
|
|
498 This file is part of MayaChemTools.
|
|
499 .PP
|
|
500 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
501 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
|
|
502 Software Foundation; either version 3 of the License, or (at your option)
|
|
503 any later version.
|