Package schrodinger :: Package application :: Package matsci :: Module zmutils :: Class ZAtom
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Class ZAtom

object --+
         |
        ZAtom

A single atom in a Z-matrix

Instance Methods [hide private]
 
__init__(self, jagin, index)
Create a ZAtom object
 
constrainCoord(self, coord)
Constrain the given coord so it can't be optimized
 
freeCoord(self, coord)
Allow the given coord to be optimized
 
constrainAll(self)
Constrain all the coords so they can't be optimized
 
freeAll(self)
Allow all the coords to be optimized
 
bumpIndexes(self, bump)
Modify all the indexes (both for self and any referenced atoms) by a constant number.
str
getSymbolicLine(self)
Get the line that defines the atoms for the bond, angle and dihedral and also the coordinate names.
 
getVariableLines(self)
Get a series of lines that defines each coordinate.
str
getAtomName(self, element, index)
Get the name of an atom with the given element and index
str
getCoordName(self, coord)
Get the name of a coordinate for this atom, such as r11 or d7
 
addCoord(self, index, element, value)
Add an internal coordinate for this atom referenced to a target atom.
 
changeCoord(self, coord, value, index=None, element=None)
Change the definition of an existing internal coordinate.

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables [hide private]
  COORD_LETTERS = ['r', 'a', 'd']
Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, jagin, index)
(Constructor)

 

Create a ZAtom object

Parameters:
Overrides: object.__init__

constrainCoord(self, coord)

 

Constrain the given coord so it can't be optimized

Parameters:
  • coord (int) - 0 (bond), 1 (angle) or 2 (dihedral)

freeCoord(self, coord)

 

Allow the given coord to be optimized

Parameters:
  • coord (int) - 0 (bond), 1 (angle) or 2 (dihedral)

bumpIndexes(self, bump)

 

Modify all the indexes (both for self and any referenced atoms) by a constant number. Used when this z-matrix is being added to another, and now atom 1 is actually atom 20...

Parameters:
  • bump (int) - The amount to modify each index

getSymbolicLine(self)

 

Get the line that defines the atoms for the bond, angle and dihedral and also the coordinate names. i.e. C11 H1 r11 C2 a11 C7 d11

Returns: str
The string defining the z-matrix coordinates for this atom. Includes the trailing return character

getVariableLines(self)

 

        Get a series of lines that defines each coordinate.
        i.e.:
        r11 = 1.452
a11 = 102.4
d11 = 180.


        @rtype: str
        @return: The string defining the z-matrix coordinate values for this
        atom.  Includes the trailing return character at the end of the block.
        

getAtomName(self, element, index)

 

Get the name of an atom with the given element and index

Parameters:
  • element (str) - The atomic symbol of the atom
  • index (int) - The index of the atom
Returns: str
The name of the atom, such as "C12"

getCoordName(self, coord)

 

Get the name of a coordinate for this atom, such as r11 or d7

Parameters:
  • coord (int) - 0 (bond), 1 (angle) or 2 (dihedral)
Returns: str
The name of the coordinate, such as "r12"

addCoord(self, index, element, value)

 

Add an internal coordinate for this atom referenced to a target atom. Note that coordinates must be added in the order bond, angle, dihedral.

Parameters:
  • index (int) - The atom index of the target atom (such as the atom the bond extends to)
  • element (str) - The element of the target atom
  • value (float) - The value of this coordinate

changeCoord(self, coord, value, index=None, element=None)

 

Change the definition of an existing internal coordinate. If index and element are passed in the target atom for the coordinate will be changed.

Parameters:
  • coord (int) - 0 (bond), 1 (angle) or 2 (dihedral)
  • value (float) - The value of this coordinate
  • index (int) - The atom index of the target atom (such as the atom the bond extends to), 1-based. Both index and element must be supplied for them to be used.
  • element (str) - The element of the target atom. Both index and element must be supplied for them to be used.