debump

Routines for biomolecule optimization.

Code author: Jens Erik Nielsen

Code author: Todd Dolinsky

Code author: Yong Huang

Code author: Nathan Baker

class pdb2pqr.debump.Debump(biomolecule, definition=None)

Grab bag of random stuff that apparently didn’t fit elsewhere.

Todo

This class needs to be susbtantially refactored in to multiple classes with clear responsibilities.

__init__(biomolecule, definition=None)

Initialize the Debump object.

Parameters:

• biomolecule (Biomolecule) – the biomolecule to debump

• definition (Definition) – topology definition file

debump_biomolecule()

Minimize bump score for molecule.

Make sure that none of the added atoms were rebuilt on top of existing atoms. See each called function for more information.

Raises:

ValueError – if missing (backbone) atoms are encountered

debump_residue(residue, conflict_names)

Debump a specific residue.

Only should be called if the residue has been detected to have a conflict. If called, try to rotate about dihedral angles to resolve the conflict.

Parameters:

• residue (Residue) – the residue in question

• conflict_names ([str]) – a list of atomnames that were rebuilt too close to other atoms

Returns:

True if successful, False otherwise

Return type:

bool

find_nearby_atoms(atom)

Find nearby atoms for conflict-checking.

Uses neighboring cells to compare atoms rather than an all versus all O(n^2) algorithm, which saves a great deal of time. There are several instances where we ignore potential conflicts; these include donor/acceptor pairs, atoms in the same residue, and bonded CYS bridges.

Parameters:

atom (Atom) – find nearby atoms to this atom

Returns:

a dictionary of Atom too close to amount of overlap for that atom

Return type:

dict

find_residue_conflicts(residue, *, write_conflict_info=False)

Find conflicts between residues.

Parameters:

• residue (Residue) – residue to check

• write_conflict_info (bool) – write verbose output about conflict

Returns:

list of conflicts

Return type:

[str]

get_bump_score(residue)

Get a bump score for a residue.

Parameters:

residue (Residue) – residue with bumping to evaluate

Returns:

bump score

Return type:

float

get_bump_score_atom(atom)

Find nearby atoms for conflict-checking.

Uses neighboring cells to compare atoms rather than an all versus all O(n^2) algorithm, which saves a great deal of time. There are several instances where we ignore potential conflicts; these include donor/acceptor pairs, atoms in the same residue, and bonded CYS bridges.

Parameters:

atom (Atom) – find nearby atoms to this atom

Returns:

a bump score sum((dist-cutoff)**20 for all nearby atoms

Return type:

float

get_closest_atom(atom)

Get the closest atom that does not form a donor/acceptor pair.

Used to detect potential conflicts.

Note

Cells must be set before using this function.

Parameters:

atom (Atom) – the atom to test

Returns:

the closest atom to the input atom that does not satisfy a donor/acceptor pair.

Return type:

Atom

score_dihedral_angle(residue, anglenum)

Assign score to dihedral angle.

Parameters:

• residue (Residue) – residue with dihedral angles to score

• anglenum (int) – specific dihedral angle index

Returns:

score for dihedral angle

Return type:

float

set_dihedral_angle(residue, anglenum, angle)

Rotate a residue about a given angle.

Uses quatfit methods to perform the matrix mathematics.

Parameters:

• residue (Residue) – residue to rotate

• anglenum – specific dihedral angle index

• angle (float) – the angle to set the dihedral to