Atom¶

class Atom(atnum=0, symbol=None, coords=None, unit='angstrom', bonds=None, mol=None, **other)[source]¶

A class representing a single atom in three dimensional space.

An instance of this class has the following attributes:

atnum – atomic number (zero for “dummy atoms”)
coords – tuple of length 3 storing spatial coordinates
bonds – list of bonds (see Bond) this atom is a part of
mol – Molecule this atom belongs to
properties – Settings instance storing all other information about this atom (initially it is populated with **other)

The above attributes can be accessed either directly or using one of the following properties:

x, y, z – allow to read or modify each coordinate separately
symbol – allows to read or write the atomic symbol directly. Atomic symbol is not stored as an attribute, instead of that the atomic number (atnum) indicates the type of atom. In fact, symbol this is just a wrapper around atnum that uses PeriodicTable as a translator:
```
>>> a = Atom(atnum=8)
>>> print(a.symbol)
O
>>> a.symbol = 'Ca'
>>> print(a.atnum)
20
```
mass – atomic mass, obtained from PeriodicTable, read only
radius – atomic radius, obtained from PeriodicTable, read only
connectors – number of connectors, obtained from PeriodicTable, read only

Note

When creating a new atom, its type can be chosen either by setting an atomic number or a symbol (atnum and symbol constructor arguments). The symbol argument takes precedence – if it is supplied, the atnum argument is ignored.

Values stored in coords tuple do not necessarily have to be numeric, you can also store any string there. This might come handy for programs that allow parametrization of coordinates in the input file (to enforce some geometry constraints for example):

>>> a = Atom(symbol='C', coords=(1,2,3))
>>> print(a)
         C       1.00000       2.00000       3.00000
>>> a.y = 'param1'
>>> print(a)
         C       1.00000        param1       3.00000

However, non-numerical coordinates cannot be used together with some methods (for example distance_to() or translate()). An attempt to do this raises an exception.

Internally, atomic coordinates are always expressed in angstroms. Most of methods that read or modify atomic coordinates accept a keyword argument unit allowing to choose unit in which results and/or arguments are expressed (see Units for details). Throughout the entire code angstrom is the default length unit. If you don’t specify unit parameter in any place of your script, all the automatic unit handling described above boils down to occasional multiplication/division by 1.0.

__init__(atnum=0, symbol=None, coords=None, unit='angstrom', bonds=None, mol=None, **other)[source]¶: Initialize self. See help(type(self)) for accurate signature.

str(symbol=True, suffix='', suffix_dict={}, unit='angstrom', space=14, decimal=6)[source]¶

Return a string representation of this atom.

Returned string is a single line (no newline characters) that always contains atomic coordinates (and maybe more). Each atomic coordinate is printed using space characters, with decimal characters reserved for decimal digits. Coordinates values are expressed in unit.

If symbol is True, atomic symbol is added at the beginning of the line. If symbol is a string, this exact string is printed there.

suffix is an arbitrary string that is appended at the end of returned line. It can contain identifiers in curly brackets (like for example f={fragment}) that will be replaced by values of corresponding keys from suffix_dict dictionary. See Format String Syntax for details.

Example:

>>> a = Atom(atnum=6, coords=(1,1.5,2))
>>> print(a.str())
         C      1.000000      1.500000      2.000000
>>> print(a.str(unit='bohr'))
         C      1.889726      2.834589      3.779452
>>> print(a.str(symbol=False))
      1.000000      1.500000      2.000000
>>> print(a.str(symbol='C2.13'))
     C2.13      1.000000      1.500000      2.000000
>>> print(a.str(suffix='protein1'))
         C      1.000000      1.500000      2.000000 protein1
>>> a.properties.info = 'membrane'
>>> print(a.str(suffix='subsystem={info}', suffix_dict=a.properties))
         C      1.000000      1.500000      2.000000 subsystem=membrane

__str__()[source]¶: Return a string representation of this atom. Simplified version of str() to work as a magic method.

__iter__()[source]¶: Iteration through atom yields coordinates. Thanks to that instances of Atom can be passed to any method requiring as an argument a point or a vector in 3D space.

translate(vector, unit='angstrom')[source]¶

Move this atom in space by vector, expressed in unit.

vector should be an iterable container of length 3 (usually tuple, list or numpy array). unit describes unit of values stored in vector.