Modules for modeling of molecular structure
===========================================

Module for class 'Structure'
----------------------------

There is a module, that realizes data structure - molecule and methods for its modification.

.. automodule:: kvazar.core.structure
	:members:

There are some overrided methods for structure, as ``__add__``, ``__iadd__``, ``__getslice__``, ``__delitem__``.

And here is a python code of example of usage of module:

.. code-block:: python

	struct_data = dict()
	n_atoms = 2
	n_links = 10
	struct_data['n_atoms'] = n_atoms
	struct_data['n_links'] = n_links
	struct_data['atom_names'] = ['Carbon','Carbon']
	struct_data['coords'] = numpy.zeros((n_atoms,3), numpy.float)
	struct_data['coords'][1][0] = 1.42
	struct_data['links'] = numpy.zeros((n_atoms,n_links), numpy.int32)-1
	struct_data['links'][0][0] = 1
	struct_data['num_links'] = numpy.zeros(n_atoms, numpy.float)
	struct_data['num_links'][0] = 1
	A = structure.Structure(struct_data)
	B = A.copy()
	B.coords[0][1] = B.coords[1][1] = 1.42
	C = A + B 
		
You will get new structure with 4 atoms, where coordinates are concatenated, when velocities, links are still the same as in original A and B

.. code-block:: python

	A += B

You will get modified structure A (A = A + B)

.. code-block:: python

	D = A[1:2]

You will get new structure, which is a part of structure A and has 2 atoms (from 1 to 2 inclusive).

.. code-block:: python

	del A[[(0,0), (1,2)]]

It deletes atoms of structure: 0,1,2. It changes initial structure.

.. code-block:: python

	E = C.getsubstr([(1,2)])

You will get new structure, that made of atoms 1,2.

Module of class for structure loading and saving
------------------------------------------------

.. automodule:: kvazar.fileman
	:members:

There is an example of fileman.py usage in package:

.. code-block:: python

	from kvazar.fileman import FileManager
	fm = FileManager()
	struct1 = fm.load("path/to/c28.ACD")

It loads model of fullerene C28

.. code-block:: python

	fm.set_struct(struct1)
	fm.save("path/to/c28_new.ACD")

It saves copy of model of fullerene in new file.
Examples of input files can be found in kvazar's directory: Path_to_kvazar + "/test/test_data/"

Module for saving output file
-----------------------------

.. automodule:: kvazar.record
	:members:

It provides an interface to the molecular dynamic data. It allows:

* To load any state of calculated file. States are from 0 to the last of states

.. code-block:: python

	python
	from kvazar.record import Record
	rec = Record('path/to/file.nmd', 'a')
	rec.update_state(1)

* To see parameters, that were calculated, for any state:

.. code-block:: python

	rec.params

There are two possible modifiers in initializing of object of class ``Record``:

* 'a' - it will append new data to already existed

* 'w' - it will rewrite data