Package schrodinger :: Package application :: Package desmond :: Package packages :: Package msys :: Class Atom

Class Atom

object --+    
         |    
    Handle --+
             |
            Atom

Represents an atom (or pseudoparticle) in a chemical system

Instance Methods

[hide private]

__repr__(self)
repr(x)

data(self)

remove(self)
remove this Atom from the System

__setitem__(self, key, val)
set atom property key to val

__getitem__(self, key)
get atom property key

__contains__(self, key)
does atom property key exist?

addBond(self, other)
create and return a Bond from self to other

findBond(self, other)
Find the bond between self and Atom other; None if not found

Inherited from Handle: __eq__, __hash__, __init__, __ne__

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

Properties

[hide private]

fullname

pos
position

vel
velocity

residue

bonds
Bonds connected to this atom

bonded_atoms
Atoms bonded to this atom

nbonds
number of bonds to this atom

nhydrogens
number of bonded hydrogens

valence
sum of bond orders

aromatic
aromatic

atomic_number
atomic_number

charge
charge

formal_charge
formal_charge

fragid
fragid

mass
mass

name
name

vx
vx

vy
vy

vz
vz

x
x

y
y

z
z

Inherited from Handle: id, system

Inherited from Handle (private): _id, _ptr

Inherited from object: __class__

Method Details

[hide private]

repr(self)
(Representation operator)

repr(x)

Overrides: object.__repr__: (inherited documentation)

Property Details

[hide private]

fullname

Get Method:: unreachable.fullname(self)

pos

position

Get Method:: unreachable.pos(self) - position
Set Method:: unreachable.pos(self, xyz)

vel

velocity

Get Method:: unreachable.vel(self) - velocity
Set Method:: unreachable.vel(self, xyz)

residue

Get Method:: unreachable.residue(self)
Set Method:: unreachable.residue(self, res)

bonds

Bonds connected to this atom

Get Method:: unreachable.bonds(self) - Bonds connected to this atom

bonded_atoms

Atoms bonded to this atom

Get Method:: unreachable.bonded_atoms(self) - Atoms bonded to this atom

nbonds

number of bonds to this atom

Get Method:: unreachable.nbonds(self) - number of bonds to this atom

nhydrogens

number of bonded hydrogens

Get Method:: unreachable.nhydrogens(self) - number of bonded hydrogens

valence

sum of bond orders

Get Method:: unreachable.valence(self) - sum of bond orders

aromatic

Get Method:: unreachable(self, x='aromatic')
Set Method:: unreachable(self, val, x='aromatic')

atomic_number

Get Method:: unreachable(self, x='atomic_number')
Set Method:: unreachable(self, val, x='atomic_number')

charge

Get Method:: unreachable(self, x='charge')
Set Method:: unreachable(self, val, x='charge')

formal_charge

Get Method:: unreachable(self, x='formal_charge')
Set Method:: unreachable(self, val, x='formal_charge')

fragid

Get Method:: unreachable(self, x='fragid')
Set Method:: unreachable(self, val, x='fragid')

mass

Get Method:: unreachable(self, x='mass')
Set Method:: unreachable(self, val, x='mass')

name

Get Method:: unreachable(self, x='name')
Set Method:: unreachable(self, val, x='name')

vx

Get Method:: unreachable(self, x='vx')
Set Method:: unreachable(self, val, x='vx')

vy

Get Method:: unreachable(self, x='vy')
Set Method:: unreachable(self, val, x='vy')

vz

Get Method:: unreachable(self, x='vz')
Set Method:: unreachable(self, val, x='vz')

x

Get Method:: unreachable(self, x='x')
Set Method:: unreachable(self, val, x='x')

y

Get Method:: unreachable(self, x='y')
Set Method:: unreachable(self, val, x='y')

z

Get Method:: unreachable(self, x='z')
Set Method:: unreachable(self, val, x='z')

Class Atom

__repr__(self) (Representation operator)

fullname

pos

vel

residue

bonds

bonded_atoms

nbonds

nhydrogens

valence

aromatic

atomic_number

charge

formal_charge

fragid

mass

name

vx

vy

vz

x

y

z

repr(self)
(Representation operator)