Chem4D

Chem4D is a python plugin collection for Cinema 4D, which enables you to import chemical structure files in Cinema 4D.

Installation

1. Download the release package and unzip it in your C4D plugins folder "XXX\Maxon Cinema 4D RXX\plugins"
2. Cut __init__.py and PDT.py to C4D's python lib folder "C:\Users\XXX\AppData\Roaming\Maxon\Maxon Cinema 4D RXX_XXXXXX\python39\libs"
3. Chem4D relies on third party python module rdkit and pymatgen. To install these to C4D python environment, go to C4D installation folder "XXX\Maxon Cinema 4D R26\resource\modules\python\libs\python39.win64.framework" or "XXX\Maxon Cinema 4D 2024\resource\modules\python\libs\win64", backup this folder, then hold shift and click right mouse button to open powershell, input following command and hit enter one by one.
   ./python -m ensurepip --upgrade
./python -m pip install rdkit
./python -m pip install pymatgen
4. Done!

Tips

• Use .mol2 file for Molecule whenever possible, it supports more molecular data.
• Press C (make editable) and you will find that this molecule is built with Cloners.
• Open C4D console to see outputs of this plugin when it doesn't work right.
• It is a good habit to backup your work when using Chem4D, it may be unstable :)
• The plugin is only tested on C4D R26.107, other versions may work.

Change list

v1.0.0

Features in initial release.

1. Import .mol and .mol2 files.
2. Change overall atom radius, atom segements and bond radius.
3. Change atom color and radius for each element in the molecular.
4. Chem4D reads the AtomProperties.txt file to set initial atom radius and color, you can add element symbols and modify this file. e.g. H radius R G B

Issues.

• Can NOT undo if you delete the Chem4D object in Attribute Manager.

v2.0.0

Major feature release.
Add a new plugin Crystal for reading small structure cif file. Original mol reader plugin has been renamed as Molecule.

Features

1. Crystal Import inorganic structure .cif file.
2. Crystal Change overall atom radius, atom segements and bond radius.
3. Crystal Change atom color and radius for each element in the crystal.
4. Crystal and Molecule Reads the elements.txt file to set initial atom radius and color, you can add element symbols and modify this file. e.g. H radius R G B
5. Crystal You can choose where to generate polyhedral.
   Guess mode will guess charge on each site, and polyhedral will be build on site with positive charge. Do not use guess mode when a unit cell is big, it is very slow e.g. ZIF-8
   Symbol or Label mode will use input symbol or label as polyhedral center. Label can be found in cif file under _atom_site_label, and symbol is pure element symbol. Multiple words should be seperated by space.
   
6. Crystal Change cell a, b, c dimention
7. Molecule Adopted to new PDT.py

Limitations

1. Crystal Cannot identify molecule piece on the cell boundary. To get full molecule, generate 3*3*3 structure and delete outer atoms.
2. Crystal Due to the brute force algorithm to remove overlaped atoms and bonds, it is slow to generate supercell larger than 100.
3. Crystal _atom_site_occupancy must be 1.
4. Crystal Some unit cell structure may missing a corner, this is a bug in pymatgen. e.g. Fe3O4_spinel.cif
5. Crystal and Molecule Do not use Enabel toggle in ObjectManager, there is a bug that has not been resolved.
6. Crystal and Molecule Dynamic parameters (Atom property) will loss when undo during regenrating geometry