htmd.builder.builder module#

exception htmd.builder.builder.BuildError(text, errors=())#

Bases: Exception

exception htmd.builder.builder.MissingAngleError(text, values=())#

Bases: _MissingErrorType

exception htmd.builder.builder.MissingAtomTypeError(text, values=())#

Bases: _MissingErrorType

exception htmd.builder.builder.MissingBondError(text, values=())#

Bases: _MissingErrorType

exception htmd.builder.builder.MissingParameterError(text, values=())#

Bases: _MissingErrorType

exception htmd.builder.builder.MissingResidueError(text, values=())#

Bases: _MissingErrorType

exception htmd.builder.builder.MissingTorsionError(text, values=())#

Bases: _MissingErrorType

exception htmd.builder.builder.MixedSegmentError#

Bases: Exception

exception htmd.builder.builder.ResidueInsertionError#

Bases: Exception

htmd.builder.builder.convertDisulfide(mol, disu)#

Convert disulfide selection-string pairs to UniqueResidueID pairs.

Parameters:

  • mol (Molecule) – The molecule the selections refer to.

  • disu (list) – A list of pairs of atom selection strings, each pair identifying the two residues forming a disulfide bond.

Returns:

newdisu – The same pairs with each selection string resolved to a UniqueResidueID.

Return type:

list

htmd.builder.builder.detectCisPeptideBonds(mol, respect_bonds=False)#

Detect and warn about cis peptide bonds in a protein.

Projects the protein omega dihedrals and logs a warning for every frame and residue whose omega angle indicates a cis peptide bond.

Parameters:

  • mol (Molecule) – The molecule to check for cis peptide bonds.

  • respect_bonds (bool) – If True, only report cis bonds whose backbone atoms form a connected component in the molecule’s bond graph.

Return type:

None

htmd.builder.builder.detectDisulfideBonds(mol, thresh=3)#

Automatically detect disulfide bonds in a molecule.

Finds all SG atoms in cysteine-like residues (resnames starting with “CY”) and returns pairs whose inter-sulfur distance is below thresh.

Parameters:

  • mol (Molecule) – The molecule for which to detect disulfide bonds.

  • thresh (float) – Distance threshold in Angstroms below which two sulfur atoms are considered bonded.

Returns:

disubonds – A list of pairs of UniqueResidueID objects representing the detected disulfide bonds, sorted by residue ID.

Return type:

list

Raises:

RuntimeError – If segment names are not defined, if multiple SG atoms are found in the same residue, or if a sulfur atom has more than one possible bond partner.

htmd.builder.builder.embed(mol1, mol2, gap=1.3)#

Embed one molecule into another, removing overlapping residues.

Removes residues of mol2 that have collisions with atoms of mol1, then appends mol1 into mol2.

Parameters:

  • mol1 (Molecule) – The first Molecule object (embedded into mol2).

  • mol2 (Molecule) – The second Molecule object (residues clashing with mol1 are removed).

  • gap (float) – Minimum distance in Angstroms between atoms of the two molecules below which a residue is considered to clash.

Returns:

newmol – The resulting Molecule object with mol1 embedded into mol2.

Return type:

Molecule

Examples

>>> merged = 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)#

Calculate the convex hull of an atom selection in mol1 and remove atoms within that hull in mol2.

Parameters:

  • mol1 (Molecule) – Molecule for which to calculate the convex hull.

  • mol2 (Molecule) – Molecule containing atoms to check for hull membership.

  • hullsel (str | ndarray) – An atom selection string, a boolean mask, or an integer index array (see Molecule.atomselect) for atoms in mol1 from which to calculate the convex hull.

  • removesel (str | ndarray) – An atom selection string, a boolean mask, or an integer index array (see Molecule.atomselect) for atoms in mol2 from which to remove those located within the hull.

Return type:

tuple

Returns:

  • newmol2 (Molecule) – mol2 without atoms located within the convex hull.

  • numrem (int) – Number of fragments removed.

htmd.builder.builder.removeHET(prot)#

Remove all HETATM residues from a structure.

Each unique HETATM residue name is removed, assuming it is a bound ligand or other heteroatom group.

Parameters:

prot (Molecule) – The molecule to clean.

Returns:

prot – A copy of the input molecule with all HETATM residues removed.

Return type:

Molecule

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.

Parameters:

  • memb (Molecule) – The membrane to be tiled.

  • xmin (float) – Minimum x coordinate.

  • ymin (float) – Minimum y coordinate.

  • xmax (float) – Maximum x coordinate.

  • ymax (float) – Maximum y coordinate.

  • buffer (float) – Buffer distance in Angstroms between tiles.

Returns:

megamemb – A tiled membrane Molecule covering the specified dimensions.

Return type:

Molecule