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The
atom()
method is used to add a new Atom to a Group node.
This method cannot be applied to an Atom
node.
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Method
Name
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Applicable
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Argument
Keywords
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Return
Value
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atom
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Group
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"name",
"existing",
"renumber",
"mass",
"charge",
"atomitype",
"atomxtype",
"mask"
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The
new Atom node
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Keyword
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Argument
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Purpose
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Preset
Value
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name
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required
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the
name of this Atom
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-
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existing
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optional
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A
value of 1 declares this atom to exist. A
value of 0 declares this atom to be
new.
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0
|
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renumber
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optional
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Specify
a value of 0 to prevent atoms from being
renumbered. Specify 1 to
renumber.
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1
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mass
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optional
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atomic
mass
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-
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charge
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optional
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atomic
charge
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-
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atomitype
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optional
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inclusion
atom type
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-
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atomxtype
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optional
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exclusion
atom type
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-
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mask
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optional
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selection
mask
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-
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The
first argument, the name, must always be specified.
No values are assigned to
mass,
charge
and mask
if no values are specified for these keywords. (But
newly created atoms are given sensible default
values for these properties.)
The
newly created atom is assigned null
atomitype
and atomxtype
values if no values are given for these parameters.
Unless proper values are provided, the new atom
will not participate in any force field term
(except for Electrostatics). The values that you
can assign are defined in the library of constants.
This library is named when the top of the hierarchy
is first created.
The
Exclusion Atom Type (specified for the
atomxtype
keyword) is used to determine the force
constants to be applied for force field terms
that use an Exclusion list. In these
terms, interactions are calculated for all pairs
of atoms, except pairs that are specifically
excluded in an Exclusion list. If an atom
is assigned an Exclusion Atom Type that is a
null string "", it is also excluded from all
Exclusion list interactions.
The
Inclusion Atom Type (specified for the
atomxtype
keyword) is used to determine the force
constants to be applied for force terms that use
an Inclusion list. For these terms,
interactions are never implied, only those that
explicitly appear in an Inclusion list
are calculated. Constants for a given force
field term is usually supplied for a limited
number of combinations of Inclusion Atom Types.
It is an error to create a force field term for
a groups of atoms for which no constants exist.
If the force constants library is complete, this
would indicate that the attempted grouping does
not make sense. If an atom is assigned a null
string "" for the Inclusion Atom Type, the atom
is automatically eliminated from in any
Inclusion list interation.
It
is an error to declare a value for the
existing
keyword that is in contradiction to the status of
the atom. If an atom exists, any values specified
for the last five arguments are used to modify the
properties of the atom. There is a method to
specifically modify the properties of an atom, see
modify()
below. The atom()
method may be applied to a Group containing an
existing atom to convert the atom name to the Atom
object.
Usually,
one would allow the renumbering to occur so that
the atoms are always correctly indexed. There are
times when the user may want to have greater
control. For example, if you are adding many atoms
and doing nothing else that require correctly
numbered atoms, you can turn off atom renumbering
as each atom is added. After the last atom has been
added, you can then call the
index()
method to update the atom numbers.
In
the following example, a single atom is attached to
the top of a newly created hierarchy. The first
argument, the name must always be specified so we
did that without the keyword. Finally, since we do
not save the return value of the method call, the
returned object, the newly created Atom node, is
printed:
>>> from Yup.Taro.AtomMap import *
>>> from Yup.Tools.misc import datasource
>>> Model = AtomMap( datasource( 'TestTube' ) )
>>>
>>> Model.atom( "first", mask = 1 )
+first 0:0 1:0 -1:-1 1
>>>
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