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124 .\" ========================================================================
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125 .\"
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126 .IX Title "BOND 1"
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127 .TH BOND 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
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128 .\" For nroff, turn off justification. Always turn off hyphenation; it makes
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129 .\" way too many mistakes in technical documents.
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130 .if n .ad l
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131 .nh
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132 .SH "NAME"
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133 Bond
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 use Bond;
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137 .PP
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138 use Bond qw(:all);
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139 .SH "DESCRIPTION"
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140 .IX Header "DESCRIPTION"
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141 \&\fBBond\fR class provides the following methods:
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142 .PP
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143 new, Copy, DeleteBond, GetAtoms, GetBondBeginAtom, GetBondEndAtom,
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144 GetBondFromAtom, GetBondToAtom, GetBondedAtom, GetCommonAtom, GetLargestRing,
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145 GetNumOfRings, GetNumOfRingsWithEvenSize, GetNumOfRingsWithOddSize,
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146 GetNumOfRingsWithSize, GetNumOfRingsWithSizeGreaterThan,
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147 GetNumOfRingsWithSizeLessThan, GetRings, GetRingsWithEvenSize,
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148 GetRingsWithOddSize, GetRingsWithSize, GetRingsWithSizeGreaterThan,
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149 GetRingsWithSizeLessThan, GetSizeOfLargestRing, GetSizeOfSmallestRing,
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150 GetSmallestRing, IsAromatic, IsBondStereochemistrySpecified, IsBondTypeSpecified,
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151 IsCis, IsCisOrTrans, IsCoordinate, IsDative, IsDouble, IsDown, IsDownward, IsHash,
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152 IsInRing, IsInRingOfSize, IsIonic, IsNotInRing, IsOnlyInOneRing, IsQuadruple,
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153 IsQuintuple, IsSextuple, IsSingle, IsTautomeric, IsTrans, IsTriple, IsUp,
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154 IsUpOrDown, IsUpward, IsWedge, IsWedgeOrHash, SetAtoms, SetBondOrder,
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155 SetBondStereochemistry, SetBondType, StringifyBond, SwitchBondFromAndToAtoms
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156 .PP
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157 \&\fBBond\fR class is derived from \fBObjectProperty\fR base class which provides methods not explicitly
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158 defined in \fBAtom\fR or \fBObjectProperty\fR class using Perl's \s-1AUTOLOAD\s0 functionality. These methods
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159 are generated on-the-fly for a specified object property:
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160 .PP
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161 .Vb 3
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162 \& Set<PropertyName>(<PropertyValue>);
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163 \& $PropertyValue = Get<PropertyName>();
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164 \& Delete<PropertyName>();
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165 .Ve
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166 .SS "\s-1METHODS\s0"
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167 .IX Subsection "METHODS"
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168 .IP "\fBnew\fR" 4
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169 .IX Item "new"
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170 .Vb 1
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171 \& $NewBond = new Bond([%PropertyNameAndValues]);
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172 .Ve
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173 .Sp
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174 Using specified \fIBond\fR property names and values hash, \fBnew\fR method creates a new object
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175 and returns a reference to newly created \fBBond\fR object. By default, following properties are
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176 initialized:
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177 .Sp
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178 .Vb 4
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179 \& ID = SequentialObjectID
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180 \& @Atoms = ();
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181 \& BondType = ""
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182 \& BondOrder = ""
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183 .Ve
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184 .Sp
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185 Except for \fI\s-1ID\s0\fR property, all other default properties and other additional properties can
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186 be set during invocation of this method.
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187 .Sp
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188 Examples:
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189 .Sp
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190 .Vb 3
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191 \& $Bond = new Bond();
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192 \& $DoubleBond = new Bond(\*(AqAtoms\*(Aq => [$Atom2, $Atom1],
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193 \& \*(AqBondOrder\*(Aq => 2);
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194 .Ve
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195 .IP "\fBCopy\fR" 4
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196 .IX Item "Copy"
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197 .Vb 1
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198 \& $BondCopy = $Bond\->Copy();
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199 .Ve
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200 .Sp
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201 Copy \fIBond\fR and its associated data using \fBStorable::dclone\fR and return a new
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202 \&\fBBond\fR object.
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203 .IP "\fBDeleteBond\fR" 4
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204 .IX Item "DeleteBond"
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205 .Vb 1
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206 \& $Bond\->DeleteBond();
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207 .Ve
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208 .Sp
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209 Delete \fIBond\fR between atoms in from a molecule.
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210 .IP "\fBGetAtoms\fR" 4
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211 .IX Item "GetAtoms"
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212 .Vb 1
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213 \& @BondedAtoms = $Bond\->GetAtoms();
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214 .Ve
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215 .Sp
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216 Returns an array containing \fIAtoms\fR invoved in \fIBond\fR.
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217 .IP "\fBGetBondedAtom\fR" 4
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218 .IX Item "GetBondedAtom"
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219 .Vb 1
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220 \& $BondedAtom = $Bond\->GetBondedAtom($Atom);
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221 .Ve
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222 .Sp
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223 Returns \fBBondedAtom\fR bonded to \fIAtom\fR in \fIBond\fR.
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224 .IP "\fBGetBondBeginAtom\fR" 4
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225 .IX Item "GetBondBeginAtom"
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226 .Vb 1
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227 \& $BeginAtom = $Bond\->GetBondBeginAtom();
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228 .Ve
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229 .Sp
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230 Returns \fBBeginAtom\fR corresponding to bond starting atom in \fIBond\fR.
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231 .IP "\fBGetBondEndAtom\fR" 4
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232 .IX Item "GetBondEndAtom"
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233 .Vb 1
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234 \& $EndAtom = $Bond\->GetBondEndAtom();
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235 .Ve
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236 .Sp
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237 Returns \fBEndAtom\fR corresponding to bond ending atom in \fIBond\fR.
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238 .IP "\fBGetBondFromAtom\fR" 4
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239 .IX Item "GetBondFromAtom"
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240 .Vb 1
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241 \& $FromAtom = $Bond\->GetBondFromAtom();
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242 .Ve
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243 .Sp
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244 Returns \fBFromAtom\fR corresponding to bond starting atom in \fIBond\fR.
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245 .IP "\fBGetBondToAtom\fR" 4
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246 .IX Item "GetBondToAtom"
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247 .Vb 1
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248 \& $ToAotm = $Bond\->GetBondToAtom();
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249 .Ve
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250 .Sp
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251 Returns \fBToAtom\fR corresponding to bond ending atom in \fIBond\fR.
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252 .IP "\fBGetCommonAtom\fR" 4
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253 .IX Item "GetCommonAtom"
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254 .Vb 1
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255 \& $CommonAtom = $Bond\->GetCommonAtom($OtherBond);
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256 .Ve
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257 .Sp
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258 Returns \fBAtom\fR common to both \fIBond\fR and \fI\f(CI$OtherBond\fI\fR.
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259 .IP "\fBGetLargestRing\fR" 4
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260 .IX Item "GetLargestRing"
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261 .Vb 1
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262 \& @RingAtoms = $Bond\->GetLargestRing();
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263 .Ve
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264 .Sp
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265 Returns an array of ring \fIAtoms\fR corresponding to the largest ring containing \fIBond\fR.
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266 in a molecule
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267 .IP "\fBGetNumOfRings\fR" 4
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268 .IX Item "GetNumOfRings"
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269 .Vb 1
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270 \& $NumOfRings = $Bond\->GetNumOfRings();
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271 .Ve
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272 .Sp
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273 Returns number of rings containing \fIBond\fR in a molecule.
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274 .IP "\fBGetNumOfRingsWithEvenSize\fR" 4
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275 .IX Item "GetNumOfRingsWithEvenSize"
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276 .Vb 1
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277 \& $NumOfRings = $Bond\->GetNumOfRingsWithEvenSize();
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278 .Ve
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279 .Sp
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280 Returns number of rings with even size containing \fIBond\fR in a molecule.
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281 .IP "\fBGetNumOfRingsWithOddSize\fR" 4
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282 .IX Item "GetNumOfRingsWithOddSize"
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283 .Vb 1
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284 \& $NumOfRings = $Bond\->GetNumOfRingsWithOddSize();
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285 .Ve
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286 .Sp
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287 Returns number of rings with odd size containing \fIBond\fR in a molecule.
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288 .IP "\fBGetNumOfRingsWithSize\fR" 4
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289 .IX Item "GetNumOfRingsWithSize"
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290 .Vb 1
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291 \& $NumOfRings = $Bond\->GetNumOfRingsWithSize($RingSize);
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292 .Ve
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293 .Sp
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294 Returns number of rings with specific \fIRingSize\fR containing \fIBond\fR in a molecule.
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295 .IP "\fBGetNumOfRingsWithSizeGreaterThan\fR" 4
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296 .IX Item "GetNumOfRingsWithSizeGreaterThan"
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297 .Vb 1
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298 \& $NumOfRings = $Bond\->GetNumOfRingsWithSizeGreaterThan($RingSize);
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299 .Ve
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300 .Sp
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301 Returns number of rings with size greater than specific \fIRingSize\fR containing
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302 \&\fIBond\fR in a molecule.
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303 .IP "\fBGetNumOfRingsWithSizeLessThan\fR" 4
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304 .IX Item "GetNumOfRingsWithSizeLessThan"
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305 .Vb 1
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306 \& $NumOfRings = $Bond\->GetNumOfRingsWithSizeLessThan($RingSize);
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307 .Ve
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308 .Sp
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309 Returns number of rings with size less than specific \fIRingSize\fR containing \fIBond\fR
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310 in a molecule.
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311 .IP "\fBGetRings\fR" 4
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312 .IX Item "GetRings"
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313 .Vb 1
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314 \& @Rings = $Bond\->GetRings();
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315 .Ve
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316 .Sp
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317 Returns an array of references to arrays containing ring atoms corressponding
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318 to all rings containing \fIBond\fR in a molecule.
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319 .IP "\fBGetRingsWithEvenSize\fR" 4
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320 .IX Item "GetRingsWithEvenSize"
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321 .Vb 1
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322 \& @Rings = $Bond\->GetRingsWithEvenSize();
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323 .Ve
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324 .Sp
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325 Returns an array of references to arrays containing ring atoms corressponding to all rings with even size
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326 containing \fIBond\fR in a molecule.
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327 .IP "\fBGetRingsWithOddSize\fR" 4
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328 .IX Item "GetRingsWithOddSize"
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329 .Vb 1
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330 \& @Rings = $Bond\->GetRingsWithOddSize();
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331 .Ve
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332 .Sp
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333 Returns an array of references to arrays containing ring atoms corressponding to all rings with odd size
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334 containing \fIBond\fR in a molecule.
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335 .IP "\fBGetRingsWithSize\fR" 4
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336 .IX Item "GetRingsWithSize"
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337 .Vb 1
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338 \& @Rings = $Bond\->GetRingsWithSize($RingSize);
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339 .Ve
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340 .Sp
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341 Returns an array of references to arrays containing ring atoms corressponding to all rings with specific
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342 \&\fIRingSize \fRcontaining \fIBond\fR in a molecule.
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343 .IP "\fBGetRingsWithSizeGreaterThan\fR" 4
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344 .IX Item "GetRingsWithSizeGreaterThan"
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345 .Vb 1
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346 \& @Rings = $Bond\->GetRingsWithSizeGreaterThan($RingSize);
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347 .Ve
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|
|
348 .Sp
|
|
|
349 Returns an array of references to arrays containing ring atoms corressponding to all rings with size
|
|
|
350 greater than specific \fIRingSize \fRcontaining \fIBond\fR in a molecule.
|
|
|
351 .IP "\fBGetRingsWithSizeLessThan\fR" 4
|
|
|
352 .IX Item "GetRingsWithSizeLessThan"
|
|
|
353 .Vb 1
|
|
|
354 \& @Rings = $Bond\->GetRingsWithSizeLessThan($RingSize);
|
|
|
355 .Ve
|
|
|
356 .Sp
|
|
|
357 Returns an array of references to arrays containing ring atoms corressponding to all rings with size
|
|
|
358 less than specific \fIRingSize \fRcontaining \fIBond\fR in a molecule.
|
|
|
359 .IP "\fBGetSizeOfLargestRing\fR" 4
|
|
|
360 .IX Item "GetSizeOfLargestRing"
|
|
|
361 .Vb 1
|
|
|
362 \& $Size = $Bond\->GetSizeOfLargestRing();
|
|
|
363 .Ve
|
|
|
364 .Sp
|
|
|
365 Returns size of the largest ring containing \fIBond\fR in a molecule.
|
|
|
366 .IP "\fBGetSizeOfSmallestRing\fR" 4
|
|
|
367 .IX Item "GetSizeOfSmallestRing"
|
|
|
368 .Vb 1
|
|
|
369 \& $Size = $Bond\->GetSizeOfSmallestRing();
|
|
|
370 .Ve
|
|
|
371 .Sp
|
|
|
372 Returns size of the smallest ring containing \fIBond\fR in a molecule.
|
|
|
373 .IP "\fBGetSmallestRing\fR" 4
|
|
|
374 .IX Item "GetSmallestRing"
|
|
|
375 .Vb 1
|
|
|
376 \& @RingAtoms = $Bond\->GetSmallestRing();
|
|
|
377 .Ve
|
|
|
378 .Sp
|
|
|
379 Returns an array of ring \fIAtoms\fR corresponding to the largest ring containing \fIBond\fR
|
|
|
380 in a molecule.
|
|
|
381 .IP "\fBIsAromatic\fR" 4
|
|
|
382 .IX Item "IsAromatic"
|
|
|
383 .Vb 1
|
|
|
384 \& $Status = $Bond\->IsAromatic();
|
|
|
385 .Ve
|
|
|
386 .Sp
|
|
|
387 Returns 1 or 0 based on whether it's an aromatic \fIBond\fR.
|
|
|
388 .IP "\fBIsBondStereochemistrySpecified\fR" 4
|
|
|
389 .IX Item "IsBondStereochemistrySpecified"
|
|
|
390 .Vb 1
|
|
|
391 \& $Status = $Bond\->IsBondStereochemistrySpecified();
|
|
|
392 .Ve
|
|
|
393 .Sp
|
|
|
394 Returns 1 or 0 based on whether \fIBond\fR's sterochemistry is specified.
|
|
|
395 .IP "\fBIsBondTypeSpecified\fR" 4
|
|
|
396 .IX Item "IsBondTypeSpecified"
|
|
|
397 .Vb 1
|
|
|
398 \& $Status = $Bond\->IsBondTypeSpecified();
|
|
|
399 .Ve
|
|
|
400 .Sp
|
|
|
401 Returns 1 or 0 based on whether \fIBond\fR's type is specified.
|
|
|
402 .IP "\fBIsCis\fR" 4
|
|
|
403 .IX Item "IsCis"
|
|
|
404 .Vb 1
|
|
|
405 \& $Status = $Bond\->IsCis();
|
|
|
406 .Ve
|
|
|
407 .Sp
|
|
|
408 Returns 1 or 0 based on whether it's a cis \fIBond\fR.
|
|
|
409 .IP "\fBIsCisOrTrans\fR" 4
|
|
|
410 .IX Item "IsCisOrTrans"
|
|
|
411 .Vb 1
|
|
|
412 \& $Status = $Bond\->IsCisOrTrans();
|
|
|
413 .Ve
|
|
|
414 .Sp
|
|
|
415 Returns 1 or 0 based on whether it's a cis or trans \fIBond\fR.
|
|
|
416 .IP "\fBIsCoordinate\fR" 4
|
|
|
417 .IX Item "IsCoordinate"
|
|
|
418 .Vb 1
|
|
|
419 \& $Status = $Bond\->IsCoordinate();
|
|
|
420 .Ve
|
|
|
421 .Sp
|
|
|
422 Returns 1 or 0 based on whether it's a coordinate or dative \fIBond\fR.
|
|
|
423 .IP "\fBIsDative\fR" 4
|
|
|
424 .IX Item "IsDative"
|
|
|
425 .Vb 1
|
|
|
426 \& $Status = $Bond\->IsDative();
|
|
|
427 .Ve
|
|
|
428 .Sp
|
|
|
429 Returns 1 or 0 based on whether it's a coordinate or dative \fIBond\fR.
|
|
|
430 .IP "\fBIsDouble\fR" 4
|
|
|
431 .IX Item "IsDouble"
|
|
|
432 .Vb 1
|
|
|
433 \& $Status =$Bond\->IsDouble();
|
|
|
434 .Ve
|
|
|
435 .Sp
|
|
|
436 Returns 1 or 0 based on whether it's a double \fIBond\fR.
|
|
|
437 .IP "\fBIsDown\fR" 4
|
|
|
438 .IX Item "IsDown"
|
|
|
439 .Vb 1
|
|
|
440 \& $Status = $Bond\->IsDown();
|
|
|
441 .Ve
|
|
|
442 .Sp
|
|
|
443 Returns 1 or 0 based on whether it's a hash or down single \fIBond\fR.
|
|
|
444 .IP "\fBIsDownward\fR" 4
|
|
|
445 .IX Item "IsDownward"
|
|
|
446 .Vb 1
|
|
|
447 \& $Return = $Bond\->IsDownward();
|
|
|
448 .Ve
|
|
|
449 .Sp
|
|
|
450 Returns 1 or 0 based on whether it's a downward \fIBond\fR.
|
|
|
451 .IP "\fBIsHash\fR" 4
|
|
|
452 .IX Item "IsHash"
|
|
|
453 .Vb 1
|
|
|
454 \& $Status = $Bond\->IsHash();
|
|
|
455 .Ve
|
|
|
456 .Sp
|
|
|
457 Returns 1 or 0 based on whether it's a hash or down single \fIBond\fR.
|
|
|
458 .IP "\fBIsInRing\fR" 4
|
|
|
459 .IX Item "IsInRing"
|
|
|
460 .Vb 1
|
|
|
461 \& $Status = $Bond\->IsInRing();
|
|
|
462 .Ve
|
|
|
463 .Sp
|
|
|
464 Returns 1 or 0 based on whether \fIBond\fR is present in a ring.
|
|
|
465 .IP "\fBIsInRingOfSize\fR" 4
|
|
|
466 .IX Item "IsInRingOfSize"
|
|
|
467 .Vb 1
|
|
|
468 \& $Status = $Bond\->IsInRingOfSize($Size);
|
|
|
469 .Ve
|
|
|
470 .Sp
|
|
|
471 Returns 1 or 0 based on whether \fIBond\fR is present in a ring of specific \fISize\fR.
|
|
|
472 .IP "\fBIsIonic\fR" 4
|
|
|
473 .IX Item "IsIonic"
|
|
|
474 .Vb 1
|
|
|
475 \& $Status = $Bond\->IsIonic();
|
|
|
476 .Ve
|
|
|
477 .Sp
|
|
|
478 Returns 1 or 0 based on whether it's an ionic \fIBond\fR.
|
|
|
479 .IP "\fBIsNotInRing\fR" 4
|
|
|
480 .IX Item "IsNotInRing"
|
|
|
481 .Vb 1
|
|
|
482 \& $Status = $Bond\->IsNotInRing();
|
|
|
483 .Ve
|
|
|
484 .Sp
|
|
|
485 Returns 1 or 0 based on whether \fIBond\fR is not present in a ring.
|
|
|
486 .IP "\fBIsOnlyInOneRing\fR" 4
|
|
|
487 .IX Item "IsOnlyInOneRing"
|
|
|
488 .Vb 1
|
|
|
489 \& $Status = $Bond\->IsOnlyInOneRing();
|
|
|
490 .Ve
|
|
|
491 .Sp
|
|
|
492 Returns 1 or 0 based on whether \fIBond\fR is only present in one ring.
|
|
|
493 .IP "\fBIsQuadruple\fR" 4
|
|
|
494 .IX Item "IsQuadruple"
|
|
|
495 .Vb 1
|
|
|
496 \& $Status = $Bond\->IsQuadruple();
|
|
|
497 .Ve
|
|
|
498 .Sp
|
|
|
499 Returns 1 or 0 based on whether it's a quadruple \fIBond\fR.
|
|
|
500 .IP "\fBIsQuintuple\fR" 4
|
|
|
501 .IX Item "IsQuintuple"
|
|
|
502 .Vb 1
|
|
|
503 \& $Status = $Bond\->IsQuintuple();
|
|
|
504 .Ve
|
|
|
505 .Sp
|
|
|
506 Returns 1 or 0 based on whether it's a quintuple \fIBond\fR.
|
|
|
507 .IP "\fBIsSextuple\fR" 4
|
|
|
508 .IX Item "IsSextuple"
|
|
|
509 .Vb 1
|
|
|
510 \& $Status = $Bond\->IsSextuple();
|
|
|
511 .Ve
|
|
|
512 .Sp
|
|
|
513 Returns 1 or 0 based on whether it's a sextuple \fIBond\fR.
|
|
|
514 .IP "\fBIsSingle\fR" 4
|
|
|
515 .IX Item "IsSingle"
|
|
|
516 .Vb 1
|
|
|
517 \& $Status =$Bond\->IsSingle();
|
|
|
518 .Ve
|
|
|
519 .Sp
|
|
|
520 Returns 1 or 0 based on whether it's a single \fIBond\fR.
|
|
|
521 .IP "\fBIsTriple\fR" 4
|
|
|
522 .IX Item "IsTriple"
|
|
|
523 .Vb 1
|
|
|
524 \& $Status =$Bond\->IsTriple();
|
|
|
525 .Ve
|
|
|
526 .Sp
|
|
|
527 Returns 1 or 0 based on whether it's a triple \fIBond\fR.
|
|
|
528 .IP "\fBIsTautomeric\fR" 4
|
|
|
529 .IX Item "IsTautomeric"
|
|
|
530 .Vb 1
|
|
|
531 \& $Status = $Bond\->IsTautomeric();
|
|
|
532 .Ve
|
|
|
533 .Sp
|
|
|
534 Returns 1 or 0 based on whether it's a \fIBond\fR.
|
|
|
535 .IP "\fBIsTrans\fR" 4
|
|
|
536 .IX Item "IsTrans"
|
|
|
537 .Vb 1
|
|
|
538 \& $Status = $Bond\->IsTrans();
|
|
|
539 .Ve
|
|
|
540 .Sp
|
|
|
541 Returns 1 or 0 based on whether it's a trans \fIBond\fR.
|
|
|
542 .IP "\fBIsUp\fR" 4
|
|
|
543 .IX Item "IsUp"
|
|
|
544 .Vb 1
|
|
|
545 \& $Status = $Bond\->IsUp();
|
|
|
546 .Ve
|
|
|
547 .Sp
|
|
|
548 Returns 1 or 0 based on whether it's a up \fIBond\fR.
|
|
|
549 .IP "\fBIsUpOrDown\fR" 4
|
|
|
550 .IX Item "IsUpOrDown"
|
|
|
551 .Vb 1
|
|
|
552 \& $Status = $Bond\->IsUpOrDown();
|
|
|
553 .Ve
|
|
|
554 .Sp
|
|
|
555 Returns 1 or 0 based on whether it's an up or down \fIBond\fR.
|
|
|
556 .IP "\fBIsUpward\fR" 4
|
|
|
557 .IX Item "IsUpward"
|
|
|
558 .Vb 1
|
|
|
559 \& $Status = $Bond\->IsUpward();
|
|
|
560 .Ve
|
|
|
561 .Sp
|
|
|
562 Returns 1 or 0 based on whether it's an upward \fIBond\fR.
|
|
|
563 .IP "\fBIsWedge\fR" 4
|
|
|
564 .IX Item "IsWedge"
|
|
|
565 .Vb 1
|
|
|
566 \& $Status = $Bond\->IsWedge();
|
|
|
567 .Ve
|
|
|
568 .Sp
|
|
|
569 Returns 1 or 0 based on whether it's a wedge \fIBond\fR.
|
|
|
570 .IP "\fBIsWedgeOrHash\fR" 4
|
|
|
571 .IX Item "IsWedgeOrHash"
|
|
|
572 .Vb 1
|
|
|
573 \& $Status = $Bond\->IsWedgeOrHash();
|
|
|
574 .Ve
|
|
|
575 .Sp
|
|
|
576 Returns 1 or 0 based on whether it's a wedge or hash \fIBond\fR.
|
|
|
577 .IP "\fBSetAtoms\fR" 4
|
|
|
578 .IX Item "SetAtoms"
|
|
|
579 .Vb 2
|
|
|
580 \& $Bond\->SetAtoms($AtomsRef);
|
|
|
581 \& $Bond\->SetAtoms(@Atoms);
|
|
|
582 .Ve
|
|
|
583 .Sp
|
|
|
584 Set atoms of \fIBond\fR to atoms in \fIAtoms\fR array or in a reference to an array of atoms
|
|
|
585 and return \fIBond\fR.
|
|
|
586 .IP "\fBSetBondOrder\fR" 4
|
|
|
587 .IX Item "SetBondOrder"
|
|
|
588 .Vb 1
|
|
|
589 \& $Bond\->SetBondOrder($BondOrder);
|
|
|
590 .Ve
|
|
|
591 .Sp
|
|
|
592 Sets bond order of \fIBond\fR to specified \fIBondOrder\fR and returns \fIBond\fR. Possible bond order
|
|
|
593 values: 1 = Single, 1.5 = Aromatic, 2 = Double, 3 = Triple, 4 = Quadruple, 5 = Quintuple,
|
|
|
594 6 = Sextuple, 7 = Septuple
|
|
|
595 .Sp
|
|
|
596 Notes:
|
|
|
597 .Sp
|
|
|
598 .Vb 8
|
|
|
599 \& . BondType property is automatically assigned using default BondType
|
|
|
600 \& values for specified BondOrder.
|
|
|
601 \& . BondType values can also be explicit set.
|
|
|
602 \& . To make bonds aromatic in a ring, explicitly set "Aromatic"
|
|
|
603 \& property for bond/atoms and make sure appropriate BondOrder
|
|
|
604 \& values are assigned.
|
|
|
605 \& . Dative or coordinate bond types are treated as single bond types with
|
|
|
606 \& explicit formal charge of + and \- on first and second bond atoms.
|
|
|
607 .Ve
|
|
|
608 .IP "\fBSetBondType\fR" 4
|
|
|
609 .IX Item "SetBondType"
|
|
|
610 .Vb 1
|
|
|
611 \& $Bond\->SetBondType($BondType);
|
|
|
612 .Ve
|
|
|
613 .Sp
|
|
|
614 Sets bond type for \fIBond\fR to specified \fIBondType\fR and returns \fIBond\fR. Possible bond type
|
|
|
615 values for different bond orders are:
|
|
|
616 .Sp
|
|
|
617 .Vb 9
|
|
|
618 \& 0: None, Ionic, Unspecified
|
|
|
619 \& 1 : Single, Dative, Coordinate, SingleOrDouble, SingleOrAromatic, Tautomeric
|
|
|
620 \& 2 : Double, SingleOrDouble, DoubleOrAromatic, Tautomeric
|
|
|
621 \& 3 : Triple
|
|
|
622 \& 4 : Quadruple
|
|
|
623 \& 5 : Quintuple
|
|
|
624 \& 6 : Sextuple
|
|
|
625 \& 7 : Septuple
|
|
|
626 \& 1.5 : Aromatic, Resonance, SingleOrAromatic, DoubleOrAromatic
|
|
|
627 .Ve
|
|
|
628 .Sp
|
|
|
629 Notes:
|
|
|
630 .Sp
|
|
|
631 .Vb 3
|
|
|
632 \& o BondType Any is valid for all BondOrders.
|
|
|
633 \& o BondOrder property is automatically assigned using default BondOrder
|
|
|
634 \& values for specified BondType.
|
|
|
635 .Ve
|
|
|
636 .Sp
|
|
|
637 Possible bond stereochemistry values for different bond orders are:
|
|
|
638 .Sp
|
|
|
639 .Vb 4
|
|
|
640 \& 0 : None, Unspecified
|
|
|
641 \& 1 : Wedge, Up, Hash, Down, Wavy, WedgeOrHash, UpOrDown, Upward, Downward,
|
|
|
642 \& None, Unspecified
|
|
|
643 \& 2 : Cis, Trans, Z, E, DoubleCross, CisOrTrans, None, Unspecified
|
|
|
644 .Ve
|
|
|
645 .IP "\fBSetBondStereochemistry\fR" 4
|
|
|
646 .IX Item "SetBondStereochemistry"
|
|
|
647 .Vb 1
|
|
|
648 \& $Bond = $Bond\->SetBondStereochemistry($BondStereochemistry);
|
|
|
649 .Ve
|
|
|
650 .Sp
|
|
|
651 Sets bond stereochemistry of \fIBond\fR to specified \fIBondStereochemistry\fR and
|
|
|
652 returns \fIBond\fR. Possible \fIBondStereoChemistry\fR values for different bond orders
|
|
|
653 are:
|
|
|
654 .Sp
|
|
|
655 BondOrder: 1
|
|
|
656 .Sp
|
|
|
657 .Vb 1
|
|
|
658 \& None, Unspecified: Not a stereo bond or unspecified
|
|
|
659 \&
|
|
|
660 \& Wedge, Up : Wedge end pointing up
|
|
|
661 \& Hash, Down: Wedge end pointing down
|
|
|
662 \& Wavy, WedgeOrHash, UpOrDown: Wedge end up or down
|
|
|
663 \&
|
|
|
664 \& Upward: Single bond around cis/trans double bonds pointing upward
|
|
|
665 \& Downward: Single bond around cis/trans double bonds pointing upward
|
|
|
666 .Ve
|
|
|
667 .Sp
|
|
|
668 Notes:
|
|
|
669 .Sp
|
|
|
670 .Vb 3
|
|
|
671 \& o Wedge starts at begin atom of a bond making wedge pointed end always
|
|
|
672 \& at this atom.
|
|
|
673 \& o Upward/downward bonds start at atoms involved in cis/trans double bonds.
|
|
|
674 .Ve
|
|
|
675 .Sp
|
|
|
676 BondOrder: 2
|
|
|
677 .Sp
|
|
|
678 .Vb 1
|
|
|
679 \& None, Unspecified: Not a stereo bond or unspecified
|
|
|
680 \&
|
|
|
681 \& Z, cis: Similar groups on same side of double bond
|
|
|
682 \& E, trans: Similar groups on different side of double bond
|
|
|
683 \&
|
|
|
684 \& CisOrTrans, DoubleCross: cis or trans
|
|
|
685 .Ve
|
|
|
686 .IP "\fBStringifyBond\fR" 4
|
|
|
687 .IX Item "StringifyBond"
|
|
|
688 .Vb 1
|
|
|
689 \& $BondString = $Bond\->StringifyBond();
|
|
|
690 .Ve
|
|
|
691 .Sp
|
|
|
692 Returns a string containing information about \fIbond\fR object.
|
|
|
693 .IP "\fBSwitchBondFromAndToAtoms\fR" 4
|
|
|
694 .IX Item "SwitchBondFromAndToAtoms"
|
|
|
695 .Vb 1
|
|
|
696 \& $Bond = $Bond\->SwitchBondFromAndToAtoms();
|
|
|
697 .Ve
|
|
|
698 .Sp
|
|
|
699 Swaps bond from and to atoms in \fIBond\fR and returns \fIBond\fR.
|
|
|
700 .SH "AUTHOR"
|
|
|
701 .IX Header "AUTHOR"
|
|
|
702 Manish Sud <msud@san.rr.com>
|
|
|
703 .SH "SEE ALSO"
|
|
|
704 .IX Header "SEE ALSO"
|
|
|
705 Atom.pm, Molecule.pm
|
|
|
706 .SH "COPYRIGHT"
|
|
|
707 .IX Header "COPYRIGHT"
|
|
|
708 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
709 .PP
|
|
|
710 This file is part of MayaChemTools.
|
|
|
711 .PP
|
|
|
712 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
713 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
|
|
|
714 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
715 any later version.
|
