|
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 "TOPOLOGICALATOMTORSIONSFINGERPRINTS 1"
|
|
|
127 .TH TOPOLOGICALATOMTORSIONSFINGERPRINTS 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 TopologicalAtomTorsionsFingerprints
|
|
|
134 .SH "SYNOPSIS"
|
|
|
135 .IX Header "SYNOPSIS"
|
|
|
136 use Fingerprints::TopologicalAtomTorsionsFingerprints;
|
|
|
137 .PP
|
|
|
138 use Fingerprints::TopologicalAtomTorsionsFingerprints qw(:all);
|
|
|
139 .SH "DESCRIPTION"
|
|
|
140 .IX Header "DESCRIPTION"
|
|
|
141 \&\fBTopologicalAtomTorsionsFingerprints\fR class provides the following methods:
|
|
|
142 .PP
|
|
|
143 new, GenerateFingerprints, GetAtomTorsionsIDs, GetDescription,
|
|
|
144 SetAtomIdentifierType, SetAtomicInvariantsToUse, SetFunctionalClassesToUse,
|
|
|
145 StringifyTopologicalAtomTorsionsFingerprints
|
|
|
146 .PP
|
|
|
147 \&\fBTopologicalAtomTorsionsFingerprints\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 \fBTopologicalAtomTorsionsFingerprints\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 \fBTopologicalAtomTorsionsFingerprints\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 in a molecule. All unique atom torsions
|
|
|
170 are identified and an atom torsion identifier is generated; the format of atom torsion identifier is:
|
|
|
171 .PP
|
|
|
172 .Vb 1
|
|
|
173 \& <AtomType1>\-<AtomType2>\-<AtomType3>\-<AtomType4>
|
|
|
174 \&
|
|
|
175 \& AtomType1, AtomType2, AtomType3, AtomTyp4: Assigned atom types
|
|
|
176 \&
|
|
|
177 \& where AtomType1 <= AtomType2 <= AtomType3 <= AtomType4
|
|
|
178 .Ve
|
|
|
179 .PP
|
|
|
180 The atom torsion identifiers for all unique atom torsions corresponding to non-hydrogen atoms constitute
|
|
|
181 topological atom torsions fingerprints of the molecule.
|
|
|
182 .PP
|
|
|
183 The current release of MayaChemTools generates the following types of topological atom torsions
|
|
|
184 fingerprints vector strings:
|
|
|
185 .PP
|
|
|
186 .Vb 5
|
|
|
187 \& FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
|
|
|
188 \& 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-
|
|
|
189 \& C.X3.BO4 C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-N.X3.BO3 C.X2.BO2.H2\-C.X2.BO
|
|
|
190 \& 2.H2\-C.X3.BO3.H1\-C.X2.BO2.H2 C.X2.BO2.H2\-C.X2.BO2.H2\-C.X3.BO3.H1\-O...;
|
|
|
191 \& 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1
|
|
|
192 \&
|
|
|
193 \& FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
|
|
|
194 \& 3;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3
|
|
|
195 \& .BO4\-C.X3.BO4 2 C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-N.X3.BO3 2 C.X2.BO2.H
|
|
|
196 \& 2\-C.X2.BO2.H2\-C.X3.BO3.H1\-C.X2.BO2.H2 1 C.X2.BO2.H2\-C.X2.BO2.H2\-C.X3.B
|
|
|
197 \& O3.H1\-O.X1.BO1.H1 1 C.X2.BO2.H2\-C.X2.BO2.H2\-N.X3.BO3\-C.X3.BO4 2 C.X2.B
|
|
|
198 \& O2.H2\-C.X3.BO3.H1\-C.X2.BO2.H2\-C.X3.BO3.H1 2 C.X2.BO2.H2\-C.X3.BO3.H1...
|
|
|
199 \&
|
|
|
200 \& FingerprintsVector;TopologicalAtomTorsions:DREIDINGAtomTypes;27;Numeri
|
|
|
201 \& calValues;IDsAndValuesString;C_2\-C_3\-C_3\-C_3 C_2\-C_3\-C_3\-O_3 C_2\-C_R\-C
|
|
|
202 \& _R\-C_3 C_2\-C_R\-C_R\-C_R C_2\-C_R\-C_R\-N_R C_2\-N_3\-C_R\-C_R C_3\-C_3\-C_2\-O_2
|
|
|
203 \& C_3\-C_3\-C_2\-O_3 C_3\-C_3\-C_3\-C_3 C_3\-C_3\-C_3\-N_R C_3\-C_3\-C_3\-O_3 C_...;
|
|
|
204 \& 1 1 1 2 1 2 1 1 3 1 3 2 2 2 1 1 1 3 1 2 2 32 2 2 5 3 1
|
|
|
205 \&
|
|
|
206 \& FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
|
|
|
207 \& lValues;IDsAndValuesString;aaCH\-aaCH\-aaCH\-aaCH aaCH\-aaCH\-aaCH\-aasC aaC
|
|
|
208 \& H\-aaCH\-aasC\-aaCH aaCH\-aaCH\-aasC\-aasC aaCH\-aaCH\-aasC\-sF aaCH\-aaCH\-aasC\-
|
|
|
209 \& ssNH aaCH\-aasC\-aasC\-aasC aaCH\-aasC\-aasC\-aasN aaCH\-aasC\-ssNH\-dssC a...;
|
|
|
210 \& 4 4 8 4 2 2 6 2 2 2 4 3 2 1 3 3 2 2 2 1 2 1 1 1 2 1 1 1 1 1 1 1 2 1 1 2
|
|
|
211 \&
|
|
|
212 \& FingerprintsVector;TopologicalAtomTorsions:FunctionalClassAtomTypes;26
|
|
|
213 \& ;NumericalValues;IDsAndValuesString;Ar\-Ar\-Ar\-Ar Ar\-Ar\-Ar\-Ar.HBA Ar\-Ar\-
|
|
|
214 \& Ar\-HBD Ar\-Ar\-Ar\-Hal Ar\-Ar\-Ar\-None Ar\-Ar\-Ar.HBA\-Ar Ar\-Ar\-Ar.HBA\-None Ar
|
|
|
215 \& \-Ar\-HBD\-None Ar\-Ar\-None\-HBA Ar\-Ar\-None\-HBD Ar\-Ar\-None\-None Ar\-Ar.H...;
|
|
|
216 \& 32 5 2 2 3 3 3 2 2 2 2 1 2 1 1 1 2 1 1 1 1 3 1 1 1 3
|
|
|
217 \&
|
|
|
218 \& FingerprintsVector;TopologicalAtomTorsions:MMFF94AtomTypes;43;Numerica
|
|
|
219 \& lValues;IDsAndValuesString;C5A\-C5B\-C5B\-C5A C5A\-C5B\-C5B\-C=ON C5A\-C5B\-C5
|
|
|
220 \& B\-CB C5A\-C5B\-C=ON\-NC=O C5A\-C5B\-C=ON\-O=CN C5A\-C5B\-CB\-CB C5A\-CB\-CB\-CB C5
|
|
|
221 \& A\-N5\-C5A\-C5B C5A\-N5\-C5A\-CB C5A\-N5\-C5A\-CR C5A\-N5\-CR\-CR C5B\-C5A\-CB\-C...;
|
|
|
222 \& 1 1 1 1 1 2 2 2 1 1 2 2 2 2 1 1 2 1 1 2 1 2 1 1 1 2 1 1 1 2 18 2 2 1 1
|
|
|
223 \& 1 1 2 1 1 3 1 3
|
|
|
224 \&
|
|
|
225 \& FingerprintsVector;TopologicalAtomTorsions:SLogPAtomTypes;49;Numerical
|
|
|
226 \& Values;IDsAndValuesPairsString;C1\-C10\-N11\-C20 1 C1\-C10\-N11\-C21 1 C1\-C1
|
|
|
227 \& 1\-C21\-C21 2 C1\-C11\-C21\-N11 2 C1\-CS\-C1\-C10 1 C1\-CS\-C1\-C5 1 C1\-CS\-C1\-CS
|
|
|
228 \& 2 C10\-C1\-CS\-O2 1 C10\-N11\-C20\-C20 2 C10\-N11\-C21\-C11 1 C10\-N11\-C21\-C21 1
|
|
|
229 \& C11\-C21\-C21\-C20 1 C11\-C21\-C21\-C5 1 C11\-C21\-N11\-C20 1 C14\-C18\-C18\-C20
|
|
|
230 \& 2 C18\-C14\-C18\-C18 2 C18\-C18\-C14\-F 2 C18\-C18\-C18\-C18 4 C18\-C18\-C18\-C...
|
|
|
231 \&
|
|
|
232 \& FingerprintsVector;TopologicalAtomTorsions:SYBYLAtomTypes;26;Numerical
|
|
|
233 \& Values;IDsAndValuesPairsString;C.2\-C.3\-C.3\-C.3 1 C.2\-C.3\-C.3\-O.3 1 C.2
|
|
|
234 \& \-C.ar\-C.ar\-C.3 1 C.2\-C.ar\-C.ar\-C.ar 2 C.2\-C.ar\-C.ar\-N.ar 1 C.2\-N.am\-C.
|
|
|
235 \& ar\-C.ar 2 C.3\-C.3\-C.2\-O.co2 2 C.3\-C.3\-C.3\-C.3 3 C.3\-C.3\-C.3\-N.ar 1 C.3
|
|
|
236 \& \-C.3\-C.3\-O.3 3 C.3\-C.3\-C.ar\-C.ar 2 C.3\-C.3\-C.ar\-N.ar 2 C.3\-C.3\-N.ar\-C.
|
|
|
237 \& ar 2 C.3\-C.ar\-C.ar\-C.ar 1 C.3\-C.ar\-N.ar\-C.3 1 C.3\-C.ar\-N.ar\-C.ar 1 ...
|
|
|
238 \&
|
|
|
239 \& FingerprintsVector;TopologicalAtomTorsions:TPSAAtomTypes;8;NumericalVa
|
|
|
240 \& lues;IDsAndValuesPairsString;N21\-None\-None\-None 9 N7\-None\-None\-None 4
|
|
|
241 \& None\-N21\-None\-None 10 None\-N7\-None\-None 3 None\-N7\-None\-O3 1 None\-None\-
|
|
|
242 \& None\-None 44 None\-None\-None\-O3 3 None\-None\-None\-O4 5
|
|
|
243 \&
|
|
|
244 \& FingerprintsVector;TopologicalAtomTorsions:UFFAtomTypes;27;NumericalVa
|
|
|
245 \& lues;IDsAndValuesPairsString;C_2\-C_3\-C_3\-C_3 1 C_2\-C_3\-C_3\-O_3 1 C_2\-C
|
|
|
246 \& _R\-C_R\-C_3 1 C_2\-C_R\-C_R\-C_R 2 C_2\-C_R\-C_R\-N_R 1 C_2\-N_3\-C_R\-C_R 2 C_3
|
|
|
247 \& \-C_3\-C_2\-O_2 1 C_3\-C_3\-C_2\-O_3 1 C_3\-C_3\-C_3\-C_3 3 C_3\-C_3\-C_3\-N_R 1 C
|
|
|
248 \& _3\-C_3\-C_3\-O_3 3 C_3\-C_3\-C_R\-C_R 2 C_3\-C_3\-C_R\-N_R 2 C_3\-C_3\-N_R\-C_R 2
|
|
|
249 \& C_3\-C_R\-C_R\-C_R 1 C_3\-C_R\-N_R\-C_3 1 C_3\-C_R\-N_R\-C_R 1 C_3\-N_R\-C_R\-...
|
|
|
250 .Ve
|
|
|
251 .SS "\s-1METHODS\s0"
|
|
|
252 .IX Subsection "METHODS"
|
|
|
253 .IP "\fBnew\fR" 4
|
|
|
254 .IX Item "new"
|
|
|
255 .Vb 2
|
|
|
256 \& $NewTopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints(
|
|
|
257 \& %NamesAndValues);
|
|
|
258 .Ve
|
|
|
259 .Sp
|
|
|
260 Using specified \fITopologicalAtomTorsionsFingerprints\fR property names and values hash, \fBnew\fR
|
|
|
261 method creates a new object and returns a reference to newly created \fBTopologicalAtomTorsionsFingerprints\fR
|
|
|
262 object. By default, the following properties are initialized:
|
|
|
263 .Sp
|
|
|
264 .Vb 5
|
|
|
265 \& Molecule = \*(Aq\*(Aq
|
|
|
266 \& Type = \*(AqTopologicalAtomTorsions\*(Aq
|
|
|
267 \& AtomIdentifierType = \*(Aq\*(Aq
|
|
|
268 \& AtomicInvariantsToUse = [\*(AqAS\*(Aq, \*(AqX\*(Aq, \*(AqBO\*(Aq, \*(AqH\*(Aq, \*(AqFC\*(Aq]
|
|
|
269 \& FunctionalClassesToUse = [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqAr\*(Aq, \*(AqHal\*(Aq]
|
|
|
270 .Ve
|
|
|
271 .Sp
|
|
|
272 Examples:
|
|
|
273 .Sp
|
|
|
274 .Vb 4
|
|
|
275 \& $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints(
|
|
|
276 \& \*(AqMolecule\*(Aq => $Molecule,
|
|
|
277 \& \*(AqAtomIdentifierType\*(Aq =>
|
|
|
278 \& \*(AqAtomicInvariantsAtomTypes\*(Aq);
|
|
|
279 \&
|
|
|
280 \& $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints(
|
|
|
281 \& \*(AqMolecule\*(Aq => $Molecule,
|
|
|
282 \& \*(AqAtomIdentifierType\*(Aq =>
|
|
|
283 \& \*(AqAtomicInvariantsAtomTypes\*(Aq,
|
|
|
284 \& \*(AqAtomicInvariantsToUse\*(Aq =>
|
|
|
285 \& [\*(AqAS\*(Aq, \*(AqX\*(Aq, \*(AqBO\*(Aq, \*(AqH\*(Aq, \*(AqFC\*(Aq] );
|
|
|
286 \&
|
|
|
287 \& $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints(
|
|
|
288 \& \*(AqMolecule\*(Aq => $Molecule,
|
|
|
289 \& \*(AqAtomIdentifierType\*(Aq =>
|
|
|
290 \& \*(AqDREIDINGAtomTypes\*(Aq);
|
|
|
291 \&
|
|
|
292 \& $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints(
|
|
|
293 \& \*(AqMolecule\*(Aq => $Molecule,
|
|
|
294 \& \*(AqAtomIdentifierType\*(Aq =>
|
|
|
295 \& \*(AqSYBYLAtomTypes\*(Aq);
|
|
|
296 \&
|
|
|
297 \& $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints(
|
|
|
298 \& \*(AqMolecule\*(Aq => $Molecule,
|
|
|
299 \& \*(AqAtomIdentifierType\*(Aq =>
|
|
|
300 \& \*(AqSLogPAtomTypes\*(Aq);
|
|
|
301 \&
|
|
|
302 \& $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints(
|
|
|
303 \& \*(AqMolecule\*(Aq => $Molecule,
|
|
|
304 \& \*(AqAtomIdentifierType\*(Aq =>
|
|
|
305 \& \*(AqFunctionalClassAtomTypes\*(Aq,
|
|
|
306 \& \*(AqFunctionalClassesToUse\*(Aq =>
|
|
|
307 \& [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqAr\*(Aq, \*(AqHal\*(Aq] );
|
|
|
308 \&
|
|
|
309 \&
|
|
|
310 \& $TopologicalAtomTorsionsFingerprints\->GenerateFingerprints();
|
|
|
311 \& print "$TopologicalAtomTorsionsFingerprints\en";
|
|
|
312 .Ve
|
|
|
313 .IP "\fBGetDescription\fR" 4
|
|
|
314 .IX Item "GetDescription"
|
|
|
315 .Vb 1
|
|
|
316 \& $Description = $TopologicalAtomTorsionsFingerprints\->GetDescription();
|
|
|
317 .Ve
|
|
|
318 .Sp
|
|
|
319 Returns a string containing description of topological atom torsions fingerprints.
|
|
|
320 .IP "\fBGenerateFingerprints\fR" 4
|
|
|
321 .IX Item "GenerateFingerprints"
|
|
|
322 .Vb 1
|
|
|
323 \& $TopologicalAtomTorsionsFingerprints\->GenerateFingerprints();
|
|
|
324 .Ve
|
|
|
325 .Sp
|
|
|
326 Generates topological atom torsions fingerprints and returns \fITopologicalAtomTorsionsFingerprints\fR.
|
|
|
327 .IP "\fBGetAtomTorsionsIDs\fR" 4
|
|
|
328 .IX Item "GetAtomTorsionsIDs"
|
|
|
329 .Vb 2
|
|
|
330 \& $AtomPairIDsRef = $TopologicalAtomTorsionsFingerprints\->GetAtomTorsionsIDs();
|
|
|
331 \& @AtomPairIDs = $TopologicalAtomTorsionsFingerprints\->GetAtomTorsionsIDs();
|
|
|
332 .Ve
|
|
|
333 .Sp
|
|
|
334 Returns atom torsion IDs corresponding to atom torsion count values in topological atom torsions
|
|
|
335 fingerprints vector as an array or reference to an array.
|
|
|
336 .IP "\fBSetAtomIdentifierType\fR" 4
|
|
|
337 .IX Item "SetAtomIdentifierType"
|
|
|
338 .Vb 1
|
|
|
339 \& $TopologicalAtomTorsionsFingerprints\->SetAtomIdentifierType($IdentifierType);
|
|
|
340 .Ve
|
|
|
341 .Sp
|
|
|
342 Sets atom \fIIdentifierType\fR to use during atom torsions fingerprints generation and
|
|
|
343 returns \fITopologicalAtomTorsionsFingerprints\fR.
|
|
|
344 .Sp
|
|
|
345 Possible values: \fIAtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
|
|
|
346 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
|
|
|
347 TPSAAtomTypes, UFFAtomTypes\fR.
|
|
|
348 .IP "\fBSetAtomicInvariantsToUse\fR" 4
|
|
|
349 .IX Item "SetAtomicInvariantsToUse"
|
|
|
350 .Vb 2
|
|
|
351 \& $TopologicalAtomTorsionsFingerprints\->SetAtomicInvariantsToUse($ValuesRef);
|
|
|
352 \& $TopologicalAtomTorsionsFingerprints\->SetAtomicInvariantsToUse(@Values);
|
|
|
353 .Ve
|
|
|
354 .Sp
|
|
|
355 Sets atomic invariants to use during \fIAtomicInvariantsAtomTypes\fR value of \fIAtomIdentifierType\fR
|
|
|
356 for topological atom torsions fingerprints generation and returns \fITopologicalAtomTorsionsFingerprints\fR.
|
|
|
357 .Sp
|
|
|
358 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,
|
|
|
359 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.
|
|
|
360 .Sp
|
|
|
361 The atomic invariants abbreviations correspond to:
|
|
|
362 .Sp
|
|
|
363 .Vb 1
|
|
|
364 \& AS = Atom symbol corresponding to element symbol
|
|
|
365 \&
|
|
|
366 \& X<n> = Number of non\-hydrogen atom neighbors or heavy atoms
|
|
|
367 \& BO<n> = Sum of bond orders to non\-hydrogen atom neighbors or heavy atoms
|
|
|
368 \& LBO<n> = Largest bond order of non\-hydrogen atom neighbors or heavy atoms
|
|
|
369 \& SB<n> = Number of single bonds to non\-hydrogen atom neighbors or heavy atoms
|
|
|
370 \& DB<n> = Number of double bonds to non\-hydrogen atom neighbors or heavy atoms
|
|
|
371 \& TB<n> = Number of triple bonds to non\-hydrogen atom neighbors or heavy atoms
|
|
|
372 \& H<n> = Number of implicit and explicit hydrogens for atom
|
|
|
373 \& Ar = Aromatic annotation indicating whether atom is aromatic
|
|
|
374 \& RA = Ring atom annotation indicating whether atom is a ring
|
|
|
375 \& FC<+n/\-n> = Formal charge assigned to atom
|
|
|
376 \& MN<n> = Mass number indicating isotope other than most abundant isotope
|
|
|
377 \& SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
|
|
|
378 \& 3 (triplet)
|
|
|
379 .Ve
|
|
|
380 .Sp
|
|
|
381 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
|
|
|
382 .Sp
|
|
|
383 .Vb 1
|
|
|
384 \& AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/\-n>.MN<n>.SM<n>
|
|
|
385 .Ve
|
|
|
386 .Sp
|
|
|
387 Except for \s-1AS\s0 which is a required atomic invariant in atom types, all other atomic invariants are
|
|
|
388 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.
|
|
|
389 .Sp
|
|
|
390 In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
|
|
|
391 are also allowed:
|
|
|
392 .Sp
|
|
|
393 .Vb 12
|
|
|
394 \& X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
|
|
|
395 \& BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
|
|
|
396 \& LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
|
|
|
397 \& SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
|
|
|
398 \& DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
|
|
|
399 \& TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
|
|
|
400 \& H : NumOfImplicitAndExplicitHydrogens
|
|
|
401 \& Ar : Aromatic
|
|
|
402 \& RA : RingAtom
|
|
|
403 \& FC : FormalCharge
|
|
|
404 \& MN : MassNumber
|
|
|
405 \& SM : SpinMultiplicity
|
|
|
406 .Ve
|
|
|
407 .Sp
|
|
|
408 \&\fIAtomTypes::AtomicInvariantsAtomTypes\fR module is used to assign atomic invariant
|
|
|
409 atom types.
|
|
|
410 .IP "\fBSetFunctionalClassesToUse\fR" 4
|
|
|
411 .IX Item "SetFunctionalClassesToUse"
|
|
|
412 .Vb 2
|
|
|
413 \& $TopologicalTorsionsFingerprints\->SetFunctionalClassesToUse($ValuesRef);
|
|
|
414 \& $TopologicalTorsionsFingerprints\->SetFunctionalClassesToUse(@Values);
|
|
|
415 .Ve
|
|
|
416 .Sp
|
|
|
417 Sets functional classes invariants to use during \fIFunctionalClassAtomTypes\fR value of \fIAtomIdentifierType\fR
|
|
|
418 for topological atom torsions fingerprints generation and returns \fITopologicalAtomTorsionsFingerprints\fR.
|
|
|
419 .Sp
|
|
|
420 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.
|
|
|
421 Default value [ Ref 24 ]: \fI\s-1HBD\s0,HBA,PI,NI,Ar,Hal\fR.
|
|
|
422 .Sp
|
|
|
423 The functional class abbreviations correspond to:
|
|
|
424 .Sp
|
|
|
425 .Vb 9
|
|
|
426 \& HBD: HydrogenBondDonor
|
|
|
427 \& HBA: HydrogenBondAcceptor
|
|
|
428 \& PI : PositivelyIonizable
|
|
|
429 \& NI : NegativelyIonizable
|
|
|
430 \& Ar : Aromatic
|
|
|
431 \& Hal : Halogen
|
|
|
432 \& H : Hydrophobic
|
|
|
433 \& RA : RingAtom
|
|
|
434 \& CA : ChainAtom
|
|
|
435 \&
|
|
|
436 \& Functional class atom type specification for an atom corresponds to:
|
|
|
437 \&
|
|
|
438 \& Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None
|
|
|
439 .Ve
|
|
|
440 .Sp
|
|
|
441 \&\fIAtomTypes::FunctionalClassAtomTypes\fR module is used to assign functional class atom
|
|
|
442 types. It uses following definitions [ Ref 60\-61, Ref 65\-66 ]:
|
|
|
443 .Sp
|
|
|
444 .Vb 4
|
|
|
445 \& HydrogenBondDonor: NH, NH2, OH
|
|
|
446 \& HydrogenBondAcceptor: N[!H], O
|
|
|
447 \& PositivelyIonizable: +, NH2
|
|
|
448 \& NegativelyIonizable: \-, C(=O)OH, S(=O)OH, P(=O)OH
|
|
|
449 .Ve
|
|
|
450 .IP "\fBStringifyTopologicalAtomTorsionsFingerprints\fR" 4
|
|
|
451 .IX Item "StringifyTopologicalAtomTorsionsFingerprints"
|
|
|
452 .Vb 2
|
|
|
453 \& $String = $TopologicalAtomTorsionsFingerprints\->
|
|
|
454 \& StringifyTopologicalAtomTorsionsFingerprints();
|
|
|
455 .Ve
|
|
|
456 .Sp
|
|
|
457 Returns a string containing information about \fITopologicalAtomTorsionsFingerprints\fR object.
|
|
|
458 .SH "AUTHOR"
|
|
|
459 .IX Header "AUTHOR"
|
|
|
460 Manish Sud <msud@san.rr.com>
|
|
|
461 .SH "SEE ALSO"
|
|
|
462 .IX Header "SEE ALSO"
|
|
|
463 Fingerprints.pm, FingerprintsStringUtil.pm, AtomNeighborhoodsFingerprints.pm,
|
|
|
464 AtomTypesFingerprints.pm, EStateIndiciesFingerprints.pm, ExtendedConnectivityFingerprints.pm,
|
|
|
465 MACCSKeys.pm, PathLengthFingerprints.pm, TopologicalAtomPairsFingerprints.pm,
|
|
|
466 TopologicalAtomTripletsFingerprints.pm, TopologicalPharmacophoreAtomPairsFingerprints.pm,
|
|
|
467 TopologicalPharmacophoreAtomTripletsFingerprints.pm
|
|
|
468 .SH "COPYRIGHT"
|
|
|
469 .IX Header "COPYRIGHT"
|
|
|
470 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
471 .PP
|
|
|
472 This file is part of MayaChemTools.
|
|
|
473 .PP
|
|
|
474 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
475 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
|
|
|
476 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
477 any later version.
|
