Fragments

Molecular fragments and inorganic ligands for rapidly building structures

• a variety of ligands for inorganic complexes, including haptic structures
• many kinds of functional group pieces for "click to add" (e.g., phenyl groups)
• amino acids for a peptide builder
• monomers for a polymer builder

Programmatic addition of fragments

Complement a virtual environment of Python with the requirements.txt. This as well as the required scripts are compiled in sub folder scripts.

For functional groups, SMILES are recorded in the groups.smi files, assuming the attachment point is on the left-hand side, e.g.

SC#N thiocyanate

The functional group files can then be generated:

python scripts/rdkit-fragments.py new-groups.smi

In general, it is safer to create a new SMILES file for new functional groups - and then append to the groups.smi after generation. This way, only new files are created and the existing files are not overwritten.

The rdkit-fragments.py script will generate SVG using rdkit depiction and PNG (using cairosvg) preview images for each functional group. Only the PNG images should be added to the repository, since Avogadro does not support SVG icons currently.

It will also generate a SDF / Molfile using rdkit ETKDGv3 conformer generation and MMFF94 geometry optimization.

The SDF should be converted to CJSON by Open Babel or Avogadro before adding to the repository.

If RDKit depictions need revision, edit the SVG file (or create a new one from a program like ChemDraw or ChemDoodle). The svg2png.py script uses cairosvg to generate a new PNG image with the appropriate resolution.

Manual Creation of Ligands

In some cases, the geometry produced by the scripts is poor and a ligand or functional group needs to be created manually. To manually build new ligands, follow the instructions on https://two.avogadro.cc/docs/tools/template-tool.html#creating-new-ligands.

The structure preview by depict-ligands.py of .smi by Avogadro highlights the site of complexation temporarily occupied by the dummy atom * by a dot colored in rgb(255,127,127), or #ff7f7f.