|
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 "TOPOLOGICALPHARMACOPHOREATOMPAIRSFINGERPRINTS 1"
|
|
|
127 .TH TOPOLOGICALPHARMACOPHOREATOMPAIRSFINGERPRINTS 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 TopologicalPharmacophoreAtomPairsFingerprints
|
|
|
134 .SH "SYNOPSIS"
|
|
|
135 .IX Header "SYNOPSIS"
|
|
|
136 use Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints;
|
|
|
137 .PP
|
|
|
138 use Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints qw(:all);
|
|
|
139 .SH "DESCRIPTION"
|
|
|
140 .IX Header "DESCRIPTION"
|
|
|
141 \&\fBTopologicalPharmacophoreAtomPairsFingerprints\fR [ Ref 60\-62, Ref 65, Ref 68 ] class provides
|
|
|
142 the following methods:
|
|
|
143 .PP
|
|
|
144 new, GenerateFingerprints, GetDescription, GetAtomPairIDs, SetAtomTypesToUse,
|
|
|
145 SetAtomTypesWeight, SetFuzzFactor, SetFuzzificationMethodology,
|
|
|
146 SetFuzzificationMode, SetMaxDistance, SetMinDistance,
|
|
|
147 SetNormalizationMethodology, SetValuesPrecision,
|
|
|
148 StringifyTopologicalPharmacophoreAtomPairsFingerprints
|
|
|
149 .PP
|
|
|
150 \&\fBTopologicalPharmacophoreAtomPairsFingerprints\fR is derived from \fBFingerprints\fR class which in turn
|
|
|
151 is derived from \fBObjectProperty\fR base class that provides methods not explicitly defined
|
|
|
152 in \fBTopologicalPharmacophoreAtomPairsFingerprints\fR, \fBFingerprints\fR or \fBObjectProperty\fR classes using Perl's
|
|
|
153 \&\s-1AUTOLOAD\s0 functionality. These methods are generated on-the-fly for a specified object property:
|
|
|
154 .PP
|
|
|
155 .Vb 3
|
|
|
156 \& Set<PropertyName>(<PropertyValue>);
|
|
|
157 \& $PropertyValue = Get<PropertyName>();
|
|
|
158 \& Delete<PropertyName>();
|
|
|
159 .Ve
|
|
|
160 .PP
|
|
|
161 Based on the values specified for \fBAtomTypesToUse\fR, pharmacophore atom types are
|
|
|
162 assigned to all non-hydrogen atoms in a molecule and a distance matrix is generated.
|
|
|
163 A pharmacophore atom pairs basis set is initialized for all unique possible pairs within
|
|
|
164 \&\fBMinDistance\fR and \fBMaxDistance\fR range.
|
|
|
165 .PP
|
|
|
166 .Vb 1
|
|
|
167 \& Let:
|
|
|
168 \&
|
|
|
169 \& P = Valid pharmacophore atom type
|
|
|
170 \&
|
|
|
171 \& Px = Pharmacophore atom type x
|
|
|
172 \& Py = Pharmacophore atom type y
|
|
|
173 \&
|
|
|
174 \& Dmin = Minimum distance corresponding to number of bonds between two atoms
|
|
|
175 \& Dmax = Maximum distance corresponding to number of bonds between two atoms
|
|
|
176 \& D = Distance corresponding to number of bonds between two atoms
|
|
|
177 \&
|
|
|
178 \& Px\-Dn\-Py = Pharmacophore atom pair ID for atom types Px and Py at distance Dn
|
|
|
179 \&
|
|
|
180 \& P = Number of pharmacophore atom types to consider
|
|
|
181 \& PPDn = Number of possible unique pharmacophore atom pairs at a distance Dn
|
|
|
182 \&
|
|
|
183 \& PPT = Total number of possible pharmacophore atom pairs at all distances between Dmin and Dmax
|
|
|
184 \&
|
|
|
185 \& Then:
|
|
|
186 \&
|
|
|
187 \& PPD = (P * (P \- 1))/2 + P
|
|
|
188 \&
|
|
|
189 \& PPT = ((Dmax \- Dmin) + 1) * ((P * (P \- 1))/2 + P)
|
|
|
190 \& = ((Dmax \- Dmin) + 1) * PPD
|
|
|
191 \&
|
|
|
192 \& So for default values of Dmin = 1, Dmax = 10 and P = 5,
|
|
|
193 \&
|
|
|
194 \& PPD = (5 * (5 \- 1))/2 + 5 = 15
|
|
|
195 \& PPT = ((10 \- 1) + 1) * 15 = 150
|
|
|
196 \&
|
|
|
197 \& The pharmacophore atom pairs bais set includes 150 values.
|
|
|
198 \&
|
|
|
199 \& The atom pair IDs correspond to:
|
|
|
200 \&
|
|
|
201 \& Px\-Dn\-Py = Pharmacophore atom pair ID for atom types Px and Py at distance Dn
|
|
|
202 \&
|
|
|
203 \& For example: H\-D1\-H, H\-D2\-HBA, PI\-D5\-PI and so on
|
|
|
204 .Ve
|
|
|
205 .PP
|
|
|
206 Using distance matrix and pharmacohore atom types, occurrence of unique pharmacohore atom
|
|
|
207 pairs is counted. The contribution of each atom type to atom pair interaction is optionally
|
|
|
208 weighted by specified \fBAtomTypesWeight\fR before assigning its count to appropriate distance
|
|
|
209 bin. Based on \fBNormalizationMethodology\fR option, pharmacophore atom pairs count is optionally
|
|
|
210 normalized. Additionally, pharmacohore atom pairs count is optionally fuzzified before or after
|
|
|
211 the normalization controlled by values of \fBFuzzifyAtomPairsCount\fR, \fBFuzzificationMode\fR,
|
|
|
212 \&\fBFuzzificationMethodology\fR and \fBFuzzFactor\fR.
|
|
|
213 .PP
|
|
|
214 The final pharmacophore atom pairs count along with atom pair identifiers involving all non-hydrogen
|
|
|
215 atoms, with optional normalization and fuzzification, constitute pharmacophore topological atom pairs
|
|
|
216 fingerprints of the molecule.
|
|
|
217 .PP
|
|
|
218 For \fIArbitrarySize\fR value of \fBAtomPairsSetSizeToUse\fR, the fingerprint vector correspond to
|
|
|
219 only those topological pharmacophore atom pairs which are present and have non-zero count. However,
|
|
|
220 for \fIFixedSize\fR value of \fBAtomPairsSetSizeToUse\fR, the fingerprint vector contains all possible
|
|
|
221 valid topological pharmacophore atom pairs with both zero and non-zero count values.
|
|
|
222 .PP
|
|
|
223 The current release of MayaChemTools generates the following types of topological pharmacophore
|
|
|
224 atom pairs fingerprints vector strings:
|
|
|
225 .PP
|
|
|
226 .Vb 7
|
|
|
227 \& FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
|
|
|
228 \& Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H\-D1\-H H
|
|
|
229 \& \-D1\-NI HBA\-D1\-NI HBD\-D1\-NI H\-D2\-H H\-D2\-HBA H\-D2\-HBD HBA\-D2\-HBA HBA\-D2\-
|
|
|
230 \& HBD H\-D3\-H H\-D3\-HBA H\-D3\-HBD H\-D3\-NI HBA\-D3\-NI HBD\-D3\-NI H\-D4\-H H\-D4\-H
|
|
|
231 \& BA H\-D4\-HBD HBA\-D4\-HBA HBA\-D4\-HBD HBD\-D4\-HBD H\-D5\-H H\-D5\-HBA H\-D5\-...;
|
|
|
232 \& 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10
|
|
|
233 \& 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1
|
|
|
234 \&
|
|
|
235 \& FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
|
|
|
236 \& ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
|
|
|
237 \& 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 1 0 0 0 1
|
|
|
238 \& 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 1 0 0 1 0
|
|
|
239 \& 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 0 37 10 8 0 0 0 0 1 0 0 0 0 0 0
|
|
|
240 \& 0 35 10 9 0 0 3 3 0 0 1 0 0 0 0 0 28 7 7 4 0 0 0 0 0 0 0 0 0 0 0 18...
|
|
|
241 \&
|
|
|
242 \& FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
|
|
|
243 \& ance1:MaxDistance10;150;OrderedNumericalValues;IDsAndValuesString;H\-D1
|
|
|
244 \& \-H H\-D1\-HBA H\-D1\-HBD H\-D1\-NI H\-D1\-PI HBA\-D1\-HBA HBA\-D1\-HBD HBA\-D1\-NI H
|
|
|
245 \& BA\-D1\-PI HBD\-D1\-HBD HBD\-D1\-NI HBD\-D1\-PI NI\-D1\-NI NI\-D1\-PI PI\-D1\-PI H\-D
|
|
|
246 \& 2\-H H\-D2\-HBA H\-D2\-HBD H\-D2\-NI H\-D2\-PI HBA\-D2\-HBA HBA\-D2\-HBD HBA\-D2...;
|
|
|
247 \& 18 0 0 1 0 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3
|
|
|
248 \& 1 0 0 0 1 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0
|
|
|
249 \& 1 0 0 1 0 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0
|
|
|
250 .Ve
|
|
|
251 .SS "\s-1METHODS\s0"
|
|
|
252 .IX Subsection "METHODS"
|
|
|
253 .IP "\fBnew\fR" 4
|
|
|
254 .IX Item "new"
|
|
|
255 .Vb 2
|
|
|
256 \& $TPAPFP = new TopologicalPharmacophoreAtomPairsFingerprints(
|
|
|
257 \& %NamesAndValues);
|
|
|
258 .Ve
|
|
|
259 .Sp
|
|
|
260 Using specified \fITopologicalPharmacophoreAtomPairsFingerprints\fR property names and
|
|
|
261 values hash, \fBnew\fR method creates a new object and returns a reference to newly created
|
|
|
262 \&\fBTopologicalPharmacophoreAtomPairsFingerprints\fR object. By default, the following properties
|
|
|
263 are initialized:
|
|
|
264 .Sp
|
|
|
265 .Vb 6
|
|
|
266 \& Molecule = \*(Aq\*(Aq
|
|
|
267 \& Type = \*(AqTopologicalPharmacophoreAtomPairs\*(Aq
|
|
|
268 \& MinDistance = 1
|
|
|
269 \& MaxDistance = 10
|
|
|
270 \& NormalizationMethodology = \*(AqNone\*(Aq
|
|
|
271 \& AtomTypesToUse = [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqH\*(Aq]
|
|
|
272 \&
|
|
|
273 \& FuzzifyAtomPairsCount = 0
|
|
|
274 \& FuzzificationMode = \*(AqAfterNormalization\*(Aq
|
|
|
275 \& FuzzificationMethodology = \*(AqFuzzyBinning\*(Aq
|
|
|
276 \& FuzzFactor = 0.15
|
|
|
277 \&
|
|
|
278 \& ValuesPrecision = 2
|
|
|
279 .Ve
|
|
|
280 .Sp
|
|
|
281 Examples:
|
|
|
282 .Sp
|
|
|
283 .Vb 2
|
|
|
284 \& $TPAPFP = new TopologicalPharmacophoreAtomPairsFingerprints(
|
|
|
285 \& \*(AqMolecule\*(Aq => $Molecule);
|
|
|
286 \&
|
|
|
287 \& $TPAPFP = new TopologicalPharmacophoreAtomPairsFingerprints(
|
|
|
288 \& \*(AqMolecule\*(Aq => $Molecule,
|
|
|
289 \& \*(AqAtomPairsSetSizeToUse\*(Aq => \*(AqArbitrarySize\*(Aq,
|
|
|
290 \& \*(AqMinDistance\*(Aq => 1,
|
|
|
291 \& \*(AqMaxDistance\*(Aq => 10,
|
|
|
292 \& \*(AqNormalizationMethodology\*(Aq => \*(AqNone\*(Aq,
|
|
|
293 \& \*(AqAtomTypesToUse\*(Aq => [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqH\*(Aq],
|
|
|
294 \& \*(AqFuzzifyAtomPairsCount\*(Aq => 0);
|
|
|
295 \&
|
|
|
296 \& $TPAPFP = new TopologicalPharmacophoreAtomPairsFingerprints(
|
|
|
297 \& \*(AqMolecule\*(Aq => $Molecule,
|
|
|
298 \& \*(AqAtomPairsSetSizeToUse\*(Aq => \*(AqFizedSize\*(Aq,
|
|
|
299 \& \*(AqMinDistance\*(Aq => 1,
|
|
|
300 \& \*(AqMaxDistance\*(Aq => 10,
|
|
|
301 \& \*(AqNormalizationMethodology\*(Aq => \*(AqNone\*(Aq,
|
|
|
302 \& \*(AqAtomTypesToUse\*(Aq => [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqH\*(Aq],
|
|
|
303 \& \*(AqFuzzifyAtomPairsCount\*(Aq => 1,
|
|
|
304 \& \*(AqFuzzificationMethodology\*(Aq => \*(AqFuzzyBinning\*(Aq,
|
|
|
305 \& \*(AqFuzzFactor\*(Aq => 0.15,
|
|
|
306 \& \*(AqValuesPrecision\*(Aq => 2);
|
|
|
307 \&
|
|
|
308 \& $TPAPFP\->GenerateFingerprints();
|
|
|
309 \& print "$TPAPFP\en";
|
|
|
310 .Ve
|
|
|
311 .IP "\fBGetDescription\fR" 4
|
|
|
312 .IX Item "GetDescription"
|
|
|
313 .Vb 1
|
|
|
314 \& $Description = $TopologicalPharmacophoreAtomPairsFP\->GetDescription();
|
|
|
315 .Ve
|
|
|
316 .Sp
|
|
|
317 Returns a string containing description of topological pharmacophore atom pairs fingerprints.
|
|
|
318 .IP "\fBGenerateFingerprints\fR" 4
|
|
|
319 .IX Item "GenerateFingerprints"
|
|
|
320 .Vb 1
|
|
|
321 \& $TopologicalPharmacophoreAtomPairsFP\->GenerateFingerprints();
|
|
|
322 .Ve
|
|
|
323 .Sp
|
|
|
324 Generates topological pharmacophore atom pairs fingerprints and returns
|
|
|
325 \&\fITopologicalPharmacophoreAtomPairsFP\fR.
|
|
|
326 .IP "\fBGetAtomPairIDs\fR" 4
|
|
|
327 .IX Item "GetAtomPairIDs"
|
|
|
328 .Vb 2
|
|
|
329 \& $AtomPairIDsRef = $TopologicalPharmacophoreAtomPairsFP\->GetAtomPairIDs();
|
|
|
330 \& @AtomPairIDs = $TopologicalPharmacophoreAtomPairsFP\->GetAtomPairIDs();
|
|
|
331 .Ve
|
|
|
332 .Sp
|
|
|
333 Returns atom pair IDs corresponding to atom pairs count values in topological pharmacophore
|
|
|
334 atom pairs fingerprints vector as an array or reference to an array.
|
|
|
335 .IP "\fBSetAtomPairsSetSizeToUse\fR" 4
|
|
|
336 .IX Item "SetAtomPairsSetSizeToUse"
|
|
|
337 .Vb 1
|
|
|
338 \& $TopologicalPharmacophoreAtomPairsFP\->SetAtomPairsSetSizeToUse($Values);
|
|
|
339 .Ve
|
|
|
340 .Sp
|
|
|
341 Sets pharmacophore atom pairs set size to use for topological pharmacophore fingerprints
|
|
|
342 generation and returns \fITopologicalPharmacophoreAtomPairsFingerprints\fR.
|
|
|
343 .Sp
|
|
|
344 Possible values for pharmacophore atom pairs set size are: \fIArbitrarySize, FizedSize\fR.
|
|
|
345 Default value: \fIArbitrarySize\fR.
|
|
|
346 .Sp
|
|
|
347 For \fIArbitrarySize\fR value of \fBAtomPairsSetSizeToUse\fR, the fingerprint vector correspond to
|
|
|
348 only those topological pharmacophore atom pairs which are present and have non-zero count. However,
|
|
|
349 for \fIFixedSize\fR value of \fBAtomPairsSetSizeToUse\fR, the fingerprint vector contains all possible
|
|
|
350 valid topological pharmacophore atom pairs with both zero and non-zero count values.
|
|
|
351 .IP "\fBSetAtomTypesToUse\fR" 4
|
|
|
352 .IX Item "SetAtomTypesToUse"
|
|
|
353 .Vb 2
|
|
|
354 \& $TopologicalPharmacophoreAtomPairsFP\->SetAtomTypesToUse($ValuesRef);
|
|
|
355 \& $TopologicalPharmacophoreAtomPairsFP\->SetAtomTypesToUse(@Values);
|
|
|
356 .Ve
|
|
|
357 .Sp
|
|
|
358 Sets pharmacophore atom types to use for topological pharmacophore fingerprints
|
|
|
359 generation and returns \fITopologicalPharmacophoreAtomPairsFingerprints\fR.
|
|
|
360 .Sp
|
|
|
361 Possible values for pharmacophore atom types are: \fIAr, \s-1CA\s0, H, \s-1HBA\s0, \s-1HBD\s0, Hal, \s-1NI\s0, \s-1PI\s0, \s-1RA\s0\fR.
|
|
|
362 Default value [ Ref 60\-62 ] : \fI\s-1HBD\s0,HBA,PI,NI,H\fR.
|
|
|
363 .Sp
|
|
|
364 The pharmacophore atom types abbreviations correspond to:
|
|
|
365 .Sp
|
|
|
366 .Vb 9
|
|
|
367 \& HBD: HydrogenBondDonor
|
|
|
368 \& HBA: HydrogenBondAcceptor
|
|
|
369 \& PI : PositivelyIonizable
|
|
|
370 \& NI : NegativelyIonizable
|
|
|
371 \& Ar : Aromatic
|
|
|
372 \& Hal : Halogen
|
|
|
373 \& H : Hydrophobic
|
|
|
374 \& RA : RingAtom
|
|
|
375 \& CA : ChainAtom
|
|
|
376 .Ve
|
|
|
377 .Sp
|
|
|
378 \&\fIAtomTypes::FunctionalClassAtomTypes\fR module is used to assign pharmacophore atom
|
|
|
379 types. It uses following definitions [ Ref 60\-61, Ref 65\-66 ]:
|
|
|
380 .Sp
|
|
|
381 .Vb 4
|
|
|
382 \& HydrogenBondDonor: NH, NH2, OH
|
|
|
383 \& HydrogenBondAcceptor: N[!H], O
|
|
|
384 \& PositivelyIonizable: +, NH2
|
|
|
385 \& NegativelyIonizable: \-, C(=O)OH, S(=O)OH, P(=O)OH
|
|
|
386 .Ve
|
|
|
387 .IP "\fBSetAtomTypesWeight\fR" 4
|
|
|
388 .IX Item "SetAtomTypesWeight"
|
|
|
389 .Vb 2
|
|
|
390 \& $TopologicalPharmacophoreAtomPairsFP\->SetAtomTypesWeight(
|
|
|
391 \& %AtomTypesToWeight);
|
|
|
392 .Ve
|
|
|
393 .Sp
|
|
|
394 Sets weights of specified pharmacophore atom types to use during calculation of their contribution
|
|
|
395 to atom pair count and returns \fITopologicalPharmacophoreAtomPairsFP\fR. Default values: \fI1 for
|
|
|
396 each atom type\fR.
|
|
|
397 .Sp
|
|
|
398 The weight values allow to increase the importance of specific pharmacophore atom type
|
|
|
399 in the generated fingerprints. A weight value of 0 for an atom type eliminates its contribution to
|
|
|
400 atom pair count where as weight value of 2 doubles its contribution.
|
|
|
401 .IP "\fBSetFuzzFactor\fR" 4
|
|
|
402 .IX Item "SetFuzzFactor"
|
|
|
403 .Vb 1
|
|
|
404 \& $TopologicalPharmacophoreAtomPairsFP\->SetFuzzFactor($Value);
|
|
|
405 .Ve
|
|
|
406 .Sp
|
|
|
407 Sets fuzz factor value to use during fuzzification of atom pairs count and returns
|
|
|
408 \&\fITopologicalPharmacophoreAtomPairsFP\fR. Default value: \fI0.15\fR.
|
|
|
409 .Sp
|
|
|
410 Valid values: For \fIFuzzyBinning\fR value of \fBFuzzificationMethodology\fR: \fIbetween 0 and 1.0\fR; For
|
|
|
411 \&\fIFuzzyBinSmoothing\fR value of \fBFuzzificationMethodology\fR: \fIbetween 0 and 0.5\fR.
|
|
|
412 .IP "\fBSetFuzzificationMethodology\fR" 4
|
|
|
413 .IX Item "SetFuzzificationMethodology"
|
|
|
414 .Vb 1
|
|
|
415 \& $TopologicalPharmacophoreAtomPairsFP\->SetFuzzificationMethodology($Value);
|
|
|
416 .Ve
|
|
|
417 .Sp
|
|
|
418 Sets fuzzification methodology to use for fuzzification of atom pairs count and returns
|
|
|
419 \&\fITopologicalPharmacophoreAtomPairsFP\fR. Default value: \fIFuzzyBinning\fR. Possible values:
|
|
|
420 \&\fIFuzzyBinning | FuzzyBinSmoothing\fR.
|
|
|
421 .Sp
|
|
|
422 In conjunction with values for options \fBFuzzifyAtomPairsCount\fR, \fBFuzzificationMode\fR and
|
|
|
423 \&\fBFuzzFactor\fR, \fBFuzzificationMethodology\fR option is used to fuzzify pharmacophore atom
|
|
|
424 pairs count.
|
|
|
425 .Sp
|
|
|
426 Let:
|
|
|
427 .Sp
|
|
|
428 .Vb 3
|
|
|
429 \& Px = Pharmacophore atom type x
|
|
|
430 \& Py = Pharmacophore atom type y
|
|
|
431 \& PPxy = Pharmacophore atom pair between atom type Px and Py
|
|
|
432 \&
|
|
|
433 \& PPxyDn = Pharmacophore atom pairs count between atom type Px and Py
|
|
|
434 \& at distance Dn
|
|
|
435 \& PPxyDn\-1 = Pharmacophore atom pairs count between atom type Px and Py
|
|
|
436 \& at distance Dn \- 1
|
|
|
437 \& PPxyDn+1 = Pharmacophore atom pairs count between atom type Px and Py
|
|
|
438 \& at distance Dn + 1
|
|
|
439 \&
|
|
|
440 \& FF = FuzzFactor for FuzzyBinning and FuzzyBinSmoothing
|
|
|
441 .Ve
|
|
|
442 .Sp
|
|
|
443 Then:
|
|
|
444 .Sp
|
|
|
445 For \fIFuzzyBinning\fR:
|
|
|
446 .Sp
|
|
|
447 .Vb 1
|
|
|
448 \& PPxyDn = PPxyDn (Unchanged)
|
|
|
449 \&
|
|
|
450 \& PPxyDn\-1 = PPxyDn\-1 + PPxyDn * FF
|
|
|
451 \& PPxyDn+1 = PPxyDn+1 + PPxyDn * FF
|
|
|
452 .Ve
|
|
|
453 .Sp
|
|
|
454 For \fIFuzzyBinSmoothing\fR:
|
|
|
455 .Sp
|
|
|
456 .Vb 2
|
|
|
457 \& PPxyDn = PPxyDn \- PPxyDn * 2FF for Dmin < Dn < Dmax
|
|
|
458 \& PPxyDn = PPxyDn \- PPxyDn * FF for Dn = Dmin or Dmax
|
|
|
459 \&
|
|
|
460 \& PPxyDn\-1 = PPxyDn\-1 + PPxyDn * FF
|
|
|
461 \& PPxyDn+1 = PPxyDn+1 + PPxyDn * FF
|
|
|
462 .Ve
|
|
|
463 .Sp
|
|
|
464 In both fuzzification schemes, a value of 0 for \s-1FF\s0 implies no fuzzification of occurrence counts.
|
|
|
465 A value of 1 during \fIFuzzyBinning\fR corresponds to maximum fuzzification of occurrence counts;
|
|
|
466 however, a value of 1 during \fIFuzzyBinSmoothing\fR ends up completely distributing the value over
|
|
|
467 the previous and next distance bins.
|
|
|
468 .Sp
|
|
|
469 So for default value of \fBFuzzFactor\fR (\s-1FF\s0) 0.15, the occurrence count of pharmacohore atom pairs
|
|
|
470 at distance Dn during FuzzyBinning is left unchanged and the counts at distances Dn \-1 and Dn + 1
|
|
|
471 are incremented by PPxyDn * 0.15.
|
|
|
472 .Sp
|
|
|
473 And during \fIFuzzyBinSmoothing\fR the occurrence counts at Distance Dn is scaled back using multiplicative
|
|
|
474 factor of (1 \- 2*0.15) and the occurrence counts at distances Dn \-1 and Dn + 1 are incremented by
|
|
|
475 PPxyDn * 0.15. In other words, occurrence bin count is smoothed out by distributing it over the
|
|
|
476 previous and next distance value.
|
|
|
477 .IP "\fBSetFuzzificationMode\fR" 4
|
|
|
478 .IX Item "SetFuzzificationMode"
|
|
|
479 .Vb 1
|
|
|
480 \& $TopologicalPharmacophoreAtomPairsFP\->SetFuzzificationMode($Value);
|
|
|
481 .Ve
|
|
|
482 .Sp
|
|
|
483 Sets fuzzification mode to use for fuzzification of atom pairs count and returns
|
|
|
484 \&\fITopologicalPharmacophoreAtomPairsFP\fR. Default value: \fIAfterNormalization\fR. Possible values:
|
|
|
485 \&\fIBeforeNormalization | AfterNormalization\fR.
|
|
|
486 .IP "\fBSetMaxDistance\fR" 4
|
|
|
487 .IX Item "SetMaxDistance"
|
|
|
488 .Vb 1
|
|
|
489 \& $TopologicalPharmacophoreAtomPairsFP\->SetMaxDistance($Value);
|
|
|
490 .Ve
|
|
|
491 .Sp
|
|
|
492 Sets maximum bond distance between atom pairs for generating topological pharmacophore atom
|
|
|
493 pairs fingerprints and returns \fITopologicalPharmacophoreAtomPairsFP\fR.
|
|
|
494 .IP "\fBSetMinDistance\fR" 4
|
|
|
495 .IX Item "SetMinDistance"
|
|
|
496 .Vb 1
|
|
|
497 \& $TopologicalPharmacophoreAtomPairsFP\->SetMinDistance($Value);
|
|
|
498 .Ve
|
|
|
499 .Sp
|
|
|
500 Sets minimum bond distance between atom pairs for generating topological pharmacophore atom
|
|
|
501 pairs fingerprints and returns \fITopologicalPharmacophoreAtomPairsFP\fR.
|
|
|
502 .IP "\fBSetNormalizationMethodology\fR" 4
|
|
|
503 .IX Item "SetNormalizationMethodology"
|
|
|
504 .Vb 1
|
|
|
505 \& $TopologicalPharmacophoreAtomPairsFP\->SetNormalizationMethodology($Value);
|
|
|
506 .Ve
|
|
|
507 .Sp
|
|
|
508 Sets normalization methodology to use for scaling the occurrence count of pharmacophore atom
|
|
|
509 pairs within specified distance range and returns \fITopologicalPharmacophoreAtomPairsFP\fR.
|
|
|
510 Default value: \fINone\fR. Possible values: \fINone, ByHeavyAtomsCount or ByAtomTypesCount\fR.
|
|
|
511 .IP "\fBSetValuesPrecision\fR" 4
|
|
|
512 .IX Item "SetValuesPrecision"
|
|
|
513 .Vb 1
|
|
|
514 \& $TopologicalPharmacophoreAtomPairsFP\->SetValuesPrecision($Value);
|
|
|
515 .Ve
|
|
|
516 .Sp
|
|
|
517 Sets precision of atom pairs count real values which might be generated after normalization
|
|
|
518 or fuzzification and returns \fITopologicalPharmacophoreAtomPairsFP\fR. Default: up to \fI2\fR decimal
|
|
|
519 places.
|
|
|
520 .IP "\fBStringifyTopologicalPharmacophoreAtomPairsFingerprints\fR" 4
|
|
|
521 .IX Item "StringifyTopologicalPharmacophoreAtomPairsFingerprints"
|
|
|
522 .Vb 2
|
|
|
523 \& $String = $TopologicalPharmacophoreAtomPairsFP\->
|
|
|
524 \& StringifyTopologicalPharmacophoreAtomPairsFingerprints();
|
|
|
525 .Ve
|
|
|
526 .Sp
|
|
|
527 Returns a string containing information about \fITopologicalPharmacophoreAtomPairsFingerprints\fR object.
|
|
|
528 .SH "AUTHOR"
|
|
|
529 .IX Header "AUTHOR"
|
|
|
530 Manish Sud <msud@san.rr.com>
|
|
|
531 .SH "SEE ALSO"
|
|
|
532 .IX Header "SEE ALSO"
|
|
|
533 Fingerprints.pm, FingerprintsStringUtil.pm, AtomNeighborhoodsFingerprints.pm,
|
|
|
534 AtomTypesFingerprints.pm, EStateIndiciesFingerprints.pm, ExtendedConnectivityFingerprints.pm,
|
|
|
535 MACCSKeys.pm, PathLengthFingerprints.pm, TopologicalAtomPairsFingerprints.pm,
|
|
|
536 TopologicalAtomTripletsFingerprints.pm, TopologicalAtomTorsionsFingerprints.pm,
|
|
|
537 TopologicalPharmacophoreAtomTripletsFingerprints.pm
|
|
|
538 .SH "COPYRIGHT"
|
|
|
539 .IX Header "COPYRIGHT"
|
|
|
540 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
541 .PP
|
|
|
542 This file is part of MayaChemTools.
|
|
|
543 .PP
|
|
|
544 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
545 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
|
|
|
546 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
547 any later version.
|
