Biobuild is a molecular building suite designed to facilitate the creation of large biomolecules such as glycans.
It allows for an easy molecule creation process in a jupyter-notebook environment. Biobuild offers direct integrations
to [PubChem](https://pubchem.ncbi.nlm.nih.gov), and the [PDBE component library](https://www.google.com/search?client=safari&rls=en&q=pdbe+component+library&ie=UTF-8&oe=UTF-8) as well as the [CHARMM project](http://charmm-gui.org) for pre-defined component structures and linkage types.
Biobuild allows users to:
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- build any larger molecular structure they like
- improve the conformation of an existing structure
- convert data formats
- visualize the structures as they build them
- quickly obtain molecular structures for chemical compounds
Biobuild cannot:
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- generate circular structures (users need to choose suitable templates with rings already present)
- imitate real-life chemical reaction mechanisms
- perform molecular dynamics or quantum chemistry computations
- generate molecules _for_ the user - the user needs to know what they want to build...
Example - building a dendrimer
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Let's build a polyphenylene dendrimer
python
import biobuild as bb
bb.load_small_molecules()
benzene = bb.molecule("benzene")
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make the periphery
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periphery = benzene.copy()
set up the linkage instructions
always shifting the carbon at which to attach
link = bb.linkage("C1", "C1")
for carbon in range(1, 6):
link.atom1 = f"C{carbon}"
periphery.attach(benzene, link, at_residue=1)
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assemble the molecule
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mol = benzene.copy()
link2 = bb.linkage("C1", "C4")
and attach the periphery to the core
for carbon in mol.get_atoms("C", by="element"):
link2.atom1 = carbon
mol.attach(periphery, link2, at_residue=1, other_residue=2)
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optimize the conformation
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mol.optimize()
mol.to_pdb("polyphenylene.pdb")
