atom
index
/home/schwitrs/bzr-repo/xplor-python3/bin.Linux_x86_64/atom.py


Atom Object
 
constructor:
 
  Atom(simulation,index)
 
    references the specified atom in the given simulation. Note that the
index is 0-offset, unlike XPLOR's id specifier (which is 1-offest).
 
The following methods return the constructor arguments:
 
  simulation()
  index()
 
The following accessor methods are defined:
 
  string()      - a unique descriptive string
  segmentName() 
  residueName() - residue name (e.g. 'ALA')
  atomName()    - atom name (e.g. 'HN')
  chemType()    - chemical type used for type-based parameters
  residueNum()  - residue number (note that this is an integer)
  pos()         - a vec3.Vec3 describing Cartesian position
  vel()         - a Vec3 describing Cartesian velocoty
  mass()        - atomic mass
  fric()        - friction used for bath-coupling by dynamics engines
  charge()      - atomic partial charge.
 
The above functions get the named quantities. These quantities may be
set using functions named setQuantity(arg), where Quantiy is the
appropriate name and arg is the desired new value.
 
Atom objects can be compared using the equality operator (==), and they are
hashable, so they can be used in Python sets.
 
Additionally, there are the following methods:
  isValid()  - specifying whether the atom pos has been set.
  bondedTo() - return a list of atoms bonded to this atom.
 
 
 
# This file was automatically generated by SWIG (http://www.swig.org).
# Version 4.0.2
#
# Do not make changes to this file unless you know what you are doing--modify
# the SWIG interface file instead.

 
Classes
       
builtins.object
Atom

 
class Atom(builtins.object)
    Atom(*args)
 

 
  Methods defined here:
__eq__(self, other)
Return self==value.
__hash__(self)
Return hash(self).
__init__(self, *args)
Initialize self.  See help(type(self)) for accurate signature.
__ne__(self, other)
Return self!=value.
__repr__ = _swig_repr(self)
atomName(self, *args, **kwargs) -> 'String const'
bondedTo(self, *args, **kwargs) -> 'CDSList< Atom >'
charge(self, *args, **kwargs) -> 'float_type const &'
chemType(self, *args, **kwargs) -> 'String const'
fric(self, *args, **kwargs) -> 'float_type const &'
index(self, *args, **kwargs) -> 'int'
isValid(self, *args, **kwargs) -> 'bool'
mass(self, *args, **kwargs) -> 'float_type const &'
pos(self)
pos_ref(self, *args, **kwargs) -> 'Vec3 const &'
pyXplorHelp(self, *args, **kwargs) -> 'String'
residueName(self, *args, **kwargs) -> 'String const'
residueNum(self, *args, **kwargs) -> 'int'
segmentName(self, *args, **kwargs) -> 'String const'
setAtomName(self, *args, **kwargs) -> 'void'
setCharge(self, *args, **kwargs) -> 'void'
setChemType(self, *args, **kwargs) -> 'void'
setFric(self, *args, **kwargs) -> 'void'
setMass(self, *args, **kwargs) -> 'void'
setPos(self, *args, **kwargs) -> 'void'
setResidueName(self, *args, **kwargs) -> 'void'
setResidueNum(self, *args, **kwargs) -> 'void'
setSegmentName(self, *args, **kwargs) -> 'void'
setVel(self, *args, **kwargs) -> 'void'
simulation(self, *args) -> 'Simulation const *'
string(self, *args, **kwargs) -> 'String'
vel(self)
vel_ref(self, *args, **kwargs) -> 'Vec3 const &'

Static methods defined here:
__swig_destroy__ = delete_Atom(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
thisown

 
The membership flag

Data and other attributes defined here:
INVALID_COORD = 9999.0

 
Functions
       
cdsMapConvertToInt(*args, **kwargs) -> 'int'
pyXplorHelp(*args) -> 'String'

 
Data
        cvar = <Swig global variables>