fragmenstein.igor package

The class Igor is split into multiple files. Additionally, the submodule fragmenstein.igor.pyrosetta_import implements a hack to allow Pyrosetta to be mocked for import —for typehinting and Sphinx (RTD) purposes only.

class fragmenstein.igor.Igor[source]

Bases: _IgorInit, _IgorMin, _IgorUtils

Regular Igor(..) accepts pyrosetta pose. Igor.from_pdbblock(..) accepts pdb block as str, while Igor.from_pdbfile(..) accepts filename as str.

ligand can be one of many things. default is ‘LIG’. But it can be

  • pose index (123)

  • PDB index ‘123A’

  • a tuple of (PDB resi, PDB chain)

  • a residue name in uppercase “LIG”

  • a pyrosetta.Vector1 where 1 == the ligand.

If key_residues is None, only the connecting residue is added (if present in the LINK record). This is overridden if one of many options are given. If it is a pyrosetta.Vector1 it is assumed that 1 mean select this residue (as a result of a selector.apply(pose) operation) If it is a list or tuple, the elements are interpreted similarly to ligand.

This class inherits the base classes _IgorInit, _IgorMin, _IgorUtils, which contain the initialisation methods, minimisation methods and extra methods respectively.

MMFF_score(mol: Mol | None = None, delta: bool = False) → float
Warning:

This was moved out of Igor, which still has a method, albeit for calling this. But on the minimised.

mol = victor.igor.mol_from_pose()

Xrepack_neighbors() → None
__init__()

Given a pose with a blended ligand at ligand residue. Load it (ready for minimisation).

Parameters:

  • pose – pose.

  • constraint_file – filename

  • ligand_residue – ligands -see class docstring

  • key_residues – multiple entries -see class docstring

classmethod add_constraint_file()

Add a constraint file to the pose.

Parameters:

  • pose

  • constraint_file

Returns:

angle_constraint = 10
atom_pair_constraint = 10
constraint_file

str

coordinate_constraint = 1
classmethod detailed_scores()

Gets called by Victor too, hence the classmethod :param pose: :return:

display_energy()

Given the minimized_mol display the energy contributions. As Victor has this while Igor is naive of bond orders, if None is passed it will made due with no bond order.

term is the term to use:

  • all will be ['lj_atr', 'lj_rep', 'fa_solv', 'fa_elec']

  • lenard-jones will ['lj_atr', 'lj_rep']

  • while ['lj_atr', 'lj_rep', 'fa_solv', 'fa_elec'] will be the individual ones.

As this is rather obscure, there is an enum as an attribute of display_energy method called Term, with the values .display.Term.ALL, .display.Term.ATTRACTION, .display.Term.REPULSION, .display.Term.LENARDJONES, .display.Term.SOLVATATION, .display.Term.ELECTROSTATIC which is possibly more sane (e.g. igor.display_energy(minimized_mol, term=igor.display.Term.ELECTROSTATIC)).

dock()

Docks the pose the normal way and without constraints.

Returns:

classmethod download_map(pdbcode: str, filename: str)

Download to disk a CCP4 map of a given PDB code :param pdbcode: :param filename: :return:

fa_intra_rep = 0.005
classmethod fix_scorefxn_weights(scorefxn, **constraint_weights)
classmethod from_pdbblock()
classmethod from_pdbfile()

Given a PDB with the ligand load it.

Parameters:

  • pdbfile – pdb file

  • params_file – params file

  • constraint_file – filename

  • ligand_residue – ligand -see class docstring

  • key_residues – multiple entries -see class docstring

Returns:

get_MinMover()

This gets stuck.

Returns:

Move

get_PertMinMover()

This makes a mess of the structure.

Returns:

Move

get_mod_FastRelax()

This is not the usual fastRelax. It uses a modded minimiser protocol!

default_coord_constraint turns on the restrict to starting position, which is mostly redundant/ineffectual with fragmenstein constraint set. Actually, epirically I cannot see a difference. No repacking.

Parameters:

  • cycles – number of cycles

  • weight – 10 is strict. 5 is decent. 1 is traditional.

  • default_coord_constraint – whether to constrain to the start position

Returns:

get_old_FastRelax()
Parameters:

cycles

Returns:

static init_pyrosetta()

Common options for pyrosetta. Does not use pyrosetta_help atm

ligand_score()
make_ligand_only_pose()
Returns:

minimize(cycles: int = 15, default_coord_constraint=True, weight: float = 1.0)
mol_from_pose()

Returns the ligand without the dummy atom!

Returns:

ligand

Return type:

Chem.Mol

per_atom_scores()

Per atom scores are generally a bad idea as a score relative to something else is better. So do treat with the appropriate caution. NB. these scores will not sum to the that of the residue.

Given a pose, a target_res and a scorefxn return a dict of per atom scores:

  • Lenard-Jones attraction 6-term

  • Lenard-Jones repulsion 12-term

  • Solvatation (zero)

  • Electrostatic interactions

Parameters:

  • pose

  • target_res

  • scorefxn

Returns:

a dict of atom names to dict of ‘lj_atr’, ‘lj_rep’, ‘fa_solv’, ‘fa_elec’ to value

pose

pyrosetta.Pose

pose2str()

Convert a pose to a string. Why isn’t this standard?

Parameters:

pose – if no pose is provided self.pose is used.

Returns:

pdb block

Return type:

str

classmethod relax_with_ED()

Relaxes pose based on the ccp4 electron density map provided. See download_map to download one.

Parameters:

  • pose

  • ccp4_file – download map from ePDB

  • constraint_weights – weights for the constraints First run with high weights, then lower.

  • cycles – number of cycles

Returns:

Relaxes pose in place

repack_neighbors() → None

Repacking is done by relax… :return:

residues_in_selector()[source]

This method is just for checking purposes for humans basically.

residues_in_vector()[source]

This method is just for checking purposes for humans basically.

score_split()
classmethod tethered_relax()

Relax by constraining the original pose.

Parameters:

  • original – the pose to relax, but makes a copy

  • constraint_weight – the weight of the constraints (coordinate_constraint, angle_constraint, atom_pair_constraint)

  • cycles – number of cycles

  • relax_to_start_coords – relax to the start coords or not

Returns:

the relaxed pose

relax_to_start_coords is the same as constraint_weight=0 if the original pose has no custom constraints

fragmenstein.igor.pyrosetta_import submodule