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To
create an atomic hierarchy, first create the top of
the hierarchy by calling
AtomMap()
from the AtomMap
module. Then attach other
AtomGroup
objects by using two AtomGroup
methods atom()
and group().
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Function
Name
|
Argument
Keywords
|
Return
Value
|
|
AtomMap
|
"libdir",
"initial",
"capacity",
"increment"
|
The
AtomGroup
object representing the top of a new
hierarchy
|
|
Keyword
|
Purpose
|
Preset
Value
|
|
libdir
|
Directory
containing the library of constants
files.
|
There
is no preset value. This argument must
always be specified.
|
|
initial
|
Preallocate
space to hold this many local Groups and
Atoms in this node.
|
1
|
|
capacity
|
Preallocate
space for this number of Atoms in the
entire hierarchy.
|
100
|
|
increment
|
Expand
space for this many more Atoms as
needed.
|
10
|
The
first argument must always be supplied. Other
arguments are optional.
The
"libdir"
keyword is used to specify a directory containing a
library of constants files. These files are
produced by the fpf
program. The value specified with the
"initial"
keyword is used to allocate space to hold this many
Atom and Group directly in the top node. (The
future Groups under the top node may hold other
Groups and Atoms but no space is needed in the top
node for their contents.) Space in the top node is
expanded one at a time when needed. The properties
of all the Atoms in the entire hierarchy are held
in a separate table. The value specified for the
"capacity"
keyword is used to size this table. When the table
is full, it is expanded by the amount specified
with the "increment"
keyword.
If
you know the eventual population of Atoms and
Groups that are held directly in the top node,
specify the value for
"initial".
If you know the total number of atoms, including
deleted atoms, specify the value for
"capacity".
This will avoid memory reallocation and the risk of
memory "holes". Otherwise, it is best to accept the
preset values.
Example:
>>> from Yup.Taro.AtomMap import *
>>> from Yup.Tools.misc import datasource
>>> Model = AtomMap( datasource( 'TestTube' ), capacity = 4500 )
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Create
the top of the hierarchy for an eventual population
of about 4500 atoms and store the return value in
the variable Model.
The return value contains the reference to the
newly created top node. You need to save this value
so that you can continue to build the atom
hierarchy. This model is bound to the constants
library 'TestTube'. This is one of the standard
libraries so its location can be specified simply
by giving the name of the library, with the help of
the datasource()
function imported from the
Tools.misc
module in the Yup
package.
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