:orphan:

.. status publishable
.. product Molecular Builder
.. sectionauthor Dave
.. SME Dave
.. PR Ray
.. TW Ken
.. date 2018

.. _molbuildDTS:

|medea| |molecularbuilder| -  A Collection of Tools for Building Molecules
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.. admonition:: **At-a-Glance**

   The |medea|\ :sup:`®`\ [#TM]_ *Molecular Builder* allows you to
   create a wide variety of molecular models from simple organic
   fluid systems to coordination complexes encountered in dyes and
   pigments or as homogeneous catalysts used for synthesis of organic
   materials. The builder integrates seamlessly with other |medea| builders
   enabling efficient model construction for any type of materials system.

   **Key Benefits**

   **Productivity** - |medea| |molecularbuilder| lets you draw, use predefined templates, import from a periodic crystal model, access fragment libraries, or use SMILES strings to quickly build the structures you need.

   **Accuracy** - Predifined templates, extensive fragment libraries, and built-in minimization & molecular dynamics to 'clean' structures each ensure that your |medea| |molecularbuilder| models are accurate.

   **Orchestration** - Use in conjunction with other |medea| builders to assemble complex multicomponent, multimolecular models.

Key Features
^^^^^^^^^^^^
The |medea| |molecularbuilder| provides a collection of model-building tools for creating individual molecules, which will either be used directly as inputs
to |medea|\ 's property calculation modules, or will be used in conjunction with other |medea| builders to assemble complex multicomponent, multimolecular models.

Using the *Molecular Builder* you can:

* Control the coordination and local geometry by choosing from a set of templates

* Attach complete pre-built fragments from the extensible library containing dozens of fragments of various types

  * Common aliphatic hydrocarbons

  * Aromatic and fused aromatic ring compounds

  * Fatty acids

  * Common functional groups - ethers, alcohols, halides, amines and amides etc.

  * Ligands

  * Amino acid side groups

* Generate initial coordinates using SMILES representation of the structure, or by extracting one or more molecules from a periodic model

* Transform to periodic cell representation for use with VASP and LAMMPS

.. figure:: /Datasheets/images/MolecularBuilder_panel_graphic-2.png
   :align: center

:myquote:`The extensive collection of builders in MedeA gets you to the important part of modeling fast—namely calculating and analyzing properties of new and existing materials.`

Required Modules
^^^^^^^^^^^^^^^^

* |medea| |menvironment|

Related Modules
^^^^^^^^^^^^^^^

* |medea| |amorphousbuilder|
* |medea| |interfacebuilder|
* |medea| |thermosetbuilder|



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Find Out More
^^^^^^^^^^^^^

Learn more about using the |medea| |molecularbuilder| by viewing the following on-line video tutorials:

* Building small molecules: |youtube01.01|

* Using the fragments library: |youtube01.02|

* Creating molecules from a SMILES string: |youtube01.03|




.. [#TM] |regTMinfo|

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   :download: :download:`pdf </Datasheets/Datasheet-MolecularBuilder.pdf>`