htmd.builder.builder.
DisulfideBridge
(**kwargs)¶Bases: object
Warning
Deprecated since version 1.12.0. Use <Read builder documentation on argument `disulfide()
>` instead.
htmd.builder.builder.
convertDisulfide
(mol, disu)¶htmd.builder.builder.
detectCisPeptideBonds
(mol)¶htmd.builder.builder.
detectDisulfideBonds
(mol, thresh=3)¶Automatically detects disulfide bonds in a molecule
disubonds – A list of DisulfideBridge
objects
np.ndarray
htmd.builder.builder.
embed
(mol1, mol2, gap=1.3)¶Embeds one molecule into another removing overlaps.
Will remove residues of mol2 which have collisions with atoms of mol1.
newmol – The resulting Molecule object
Molecule
object
Example
>>> all = embed(memb, prot)
htmd.builder.builder.
minimalRotation
(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
htmd.builder.builder.
removeAtomsInHull
(mol1, mol2, hullsel, removesel)¶Calculates the convex hull of an atom selection in mol1 and removes atoms within that hull in mol2.
mol1 (Molecule
object) – Molecule for which to calculate the convex hull
mol2 (Molecule
object) – Molecule which contains the atoms which we check if they are within the hull
hullsel (str) – Atom selection string for atoms in mol1 from which to calculate the convex hull. See more here
removesel (str) – Atom selection string for atoms in mol2 from which to remove the ones which are within the hull. See more here
newmol2 (Molecule) – mol2 but without any atoms located within the convex hull
numrem (int) – Number of fragments removed
htmd.builder.builder.
removeHET
(prot)¶htmd.builder.builder.
removeLipidsInProtein
(prot, memb, lipidsel='lipids')¶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.
htmd.builder.builder.
tileMembrane
(memb, xmin, ymin, xmax, ymax, buffer=1.5)¶Tile a membrane in the X and Y dimensions to reach a specific size.
A big membrane Molecule
megamemb