An Entire Atom Vector (AV) may be extracted, by subscripting, and the Extract AV that results can be treated like any other AV with regards to operators, methods and functions. Only an Entire and mapped AV can be subscripted. The key must be an AtomGroup object and the key and the Entire AV must share the same atom map. Thus: X = N[m] X is a new Extract AV formed from the Entire AV N from the key m where N and m share an Atom Map. >>> print `Top` /5:a1:b1/3:a2:b2/4:a3/2:a4:b4\b3:c3:d3/5:c4:d4/0\e4:f4:g4\\c2\c1:d1/2:d2:e2\e1/2:f2/2:e3:f3\g2/0\\\ >>> print `Gd3` /5:c4:d4/0\e4:f4:g4\ >>> from Yup.Taro.AtomVect import * >>> A = AtomVector( Top ) >>> B = A[Gd3] >>> print A.numatom, A.numdimen, A.firstatom, A.lastatom, A.type 16 3 0 15 Entire-Mapped >>> print B.numatom, B.numdimen, B.firstatom, B.lastatom, B.type 4 3 6 9 Extract-Mapped >>> In the above example, Top is the root node of an Atom Map and Gd3 is a descendent node. A is an AV mapped to Top and B is an extract of A formed by subscripting A with the Gd3 node as key. The vital statistics are printed in the last two commands. You can assign to a subscripted AV. The source must be conformal with the subscripted AV. For example: >>> A AtomVector[16:3] { 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 } >>> A[Gd3] = AtomVector( numatom=Gd3.numatoms, sample='UNIFORM' ) >>> A AtomVector[16:3] { 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0.131382 0.0241401 -0.213294 0.16831 0.739189 0.488083 0.928526 -0.954222 0.770989 0.243873 -0.293435 0.299112 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 } >>> This works with inplace operators as well. Note that the following: B = A[Gd3] B = AtomVector( numatom=Gd3.numatoms, sample='UNIFORM' ) would not have the outcome that some may expect. In the first line, the Gd3 slice of A forms a new Extract AV which is assigned to the variable B. In the second line, this reference is removed and B is pointed to a new Entire AV. A does not receive any new values. The len() function returns the length of the vector in the AV which is the product of the number of atoms and the number of dimensions. An extract can also be formed using the Extract() function, see the Functions page. An Anonymous Atom Vector cannot be subscripted to form an extract but any Entire Atom Vector can be sliced using the Extract() function. Intro New Print Compare Operators Data Methods Functions Subscript Files