Automatically detects disulfide bonds in a molecule
Embeds one molecule into another removing overlaps.
Will remove residues of mol2 which have collisions with atoms of mol1.
newmol – The resulting Molecule object
>>> all = embed(memb, prot)
Find the rotation around Z that minimizes the X and Y dimensions of the protein to best fit in a box.
Essentially PCA in 2D
Calculates the convex hull of an atom selection in mol1 and removes atoms within that hull in mol2.
Molecule object) – Molecule for which to calculate the convex hull
Molecule object) – Molecule which contains the atoms which we check if they are within the hull
newmol2 (Molecule) – mol2 but without any atoms located within the convex hull
numrem (int) – Number of fragments removed
Calculates the convex hull of the protein. If a lipid lies inside the hull it gets removed.
This does not work well for lipids crossing out of the hull. If even one atom of the lipid is outside it will change the hull and will not get removed. I assume it will get removed by the clashes with the protein though.
Tile a membrane in the X and Y dimensions to reach a specific size.
A big membrane Molecule