|
AtomGroup
objects have several data attribute which you can
view. These attributes cannot be modified by
assignment.
These
attributes are defined for all
AtomGroup
objects.
|
Attribute
|
Description
|
|
nodename
|
The
name of this node. The top node has no
name.
|
|
nodeorder
|
The
sequence number (the order of insertion
starting from 0) of this node in the
parent node.
|
|
nodetype
|
Whether
an "Atom" or a "Group" node.
|
|
pathname
|
The
full pathname of this node starting from
the top of the hierarchy.
|
|
CXType
|
The
string "AtomMap"
|
|
version
|
The
version string from the parameter
library
|
|
rootmap
|
The
root AtomMap
|
Python
will identify the AtomMap module as a user defined
C Type. If you wish to determine if a module is an
AtomMap you can first use the built-in function
hasattr
to determine if the CXType
attribute is defined and then test the value of the
attribute against the string
'AtomMap'.
Example:
assuming we have defined the hierarchy in the
concrete example:
>>> print Ab4.nodename, "---", Ab4.nodetype, "---", Ab4.pathname
b4 --- Atom --- :b1:b2:a3:b4
|
The
following attributes are defined only for Atom
nodes:
|
Attribute
|
Description
|
|
atomindex
|
Atom
Number or Atom Index starting from
0.
|
|
atomitype
|
Inclusion
Atom Type. Blank if not specified, error
string if incorrect
specification.
|
|
atomxtype
|
Exclusion
Atom Type. Blank if not specified, error
string if incorrect
specification.
|
|
charge
|
Atomic
Charge. 0 if not specified.
|
|
mask
|
Value
of the Selection Mask
|
|
mass
|
Atomic
Mass. 1 if not specified.
|
|
reference
|
Reference
number starting from 0. This is equal to
atomindex
if the atoms are inserted in strict
depth-first order.
|
The
following attributes are defined only for Group
nodes:
|
Attribute
|
Description
|
|
capacity
|
Amount
of space allocated in this Group to hold
local Groups and Atoms.
|
|
firstatom
|
The
atom number or index of the first atom in
this Group (which may be in a descendent
of this Group).
|
|
nextatom
|
One
plus the atom number or index of the last
atom in this Group (which may be in a
descendent of this group). Or, the
firstatom
attribute for the next AtomGroup
node.
|
|
numatoms
|
The
total number of Atoms contained in this
Group and in descendent Groups.
|
|
numgroups
|
This
Group and the total number of Groups
contained in this Group and in descendent
Groups.
|
|
numlocal
|
The
total number of Atoms and Groups contained
locally in this Group. This must never
exceed capacity.
|
|
numnames
|
This
Group and the total number of Atoms and
Groups contained in this Group and in
descendent Groups.
|
Example:
>>> print Gb2.capacity, Gb2.numatoms, Gb2.numgroups, Gb2.numlocal, Gb2.numnames
4 8 4 4 12
|
|