meeko.molecule_pdbqt module

meeko.molecule_pdbqt module#

class meeko.molecule_pdbqt.PDBQTMolecule(pdbqt_string, name=None, poses_to_read=None, energy_range=None, is_dlg=False, skip_typing=False)[source]#

Bases: object

PDBQTMolecule class for reading PDBQT (or dlg) files from AutoDock4, AutoDock-GPU or AutoDock-Vina.

_current_pose#

Index of the current pose.

Type:

int

_pdbqt_filename#

Filename of the PDBQT file.

Type:

str

_atoms#

Array of atoms.

Type:

ndarray.

_positions#

Array of positions.

Type:

ndarray

_bonds#

Dictionary of bonds.

Type:

dict

_atom_annotations#

Dictionary of atom annotations.

Type:

dict

_pose_data#

Dictionary of pose data.

Type:

dict

_name#

Name of the molecule.

Type:

str

_KDTrees#

List of KDTree objects for each pose.

Type:

list

classmethod from_file(pdbqt_filename, name=None, poses_to_read=None, energy_range=None, is_dlg=False, skip_typing=False)[source]#

Read PDBQT file and return PDBQTMolecule object.

Parameters:

  • pdbqt_filename (str) – Filename of the PDBQT file.

  • name (str, optional) – Name of the molecule. De is None (use filename without pdbqt suffix).

  • poses_to_read (int, optional) – Total number of poses to read. Default is None (read all).

  • energy_range (float, optional) – Read docked poses until the maximum energy difference from best pose is reach, for example 2.5 kcal/mol. Default is None (read all).

  • is_dlg (bool, optional) – Input file is in dlg (AutoDock docking log) format. Default is False (input file is not in dlg format).

  • skip_typing (bool, optional) – Flag indicating that atomtyping should be skipped. Default is False (do not skip typing).

property name#

Return the name of the molecule.

property pose_id#

Return the index of the current pose.

property score#

Return the score (kcal/mol) of the current pose.

available_atom_properties(ignore_properties=None)[source]#

Return all the available atom properties for that molecule. The following properties are awlays ignored:

  • ligand

  • flexible_residue

  • water

Parameters:

ignore_properties (list, optional) – List of properties to ignore. Default is None (no properties are ignored).

Returns:

list – List of available atom properties.

Return type:

list

has_flexible_residues()[source]#

Tell if the molecule contains a flexible residue or not.

Returns:

True if contains flexible residues, otherwise False.

Return type:

bool

has_water_molecules()[source]#

Tell if the molecules contains water molecules or not in the current pose.

Returns:

True if contains water molecules in the current pose, otherwise False.

Return type:

bool

atoms(atom_idx=None, only_active=True)[source]#

Return the ith atom.

Parameters:

  • atom_idx (int, list, optional) – Index of one or multiple atoms (0-based). Default is None (return all atoms).

  • only_active (bool, optional) – Return only active atoms. Default is True (return only active atoms).

Returns:

atoms – ndarray (atom_id, atom_name, resname, resid, chainid, xyz, q, t).

Return type:

ndarray

positions(atom_idx=None, only_active=True)[source]#

Return coordinates (xyz) of all atoms or a certain atom.

Parameters:

  • atom_idx (int, list, optional) – Index of one or multiple atoms (0-based). Default is None (return all atoms).

  • only_active (bool, optional) – Return only active atoms. Default is True (return only active atoms).

Returns:

ndarray of coordinates (xyz).

Return type:

ndarray

atoms_by_properties(atom_properties, only_active=True)[source]#

Return atom based on their properties.

Parameters:

  • atom_properties (str or list) – Property of the atoms to retrieve (properties: ligand, flexible_residue, vdw, hb_don, hb_acc, metal, water, reactive, glue).

  • only_active (bool, optional) – Return only active atoms. Default is True (return only active atoms).

Returns:

ndarray of atoms (atom_id, atom_name, resname, resid, chainid, xyz, q, t).

Return type:

ndarray

Raises:

KeyError – If the atom property is not valid.

closest_atoms_from_positions(xyz, radius, atom_properties=None, ignore=None)[source]#

Retrieve indices of the closest atoms around a positions/coordinates at a certain radius.

Parameters:

  • xyz (np.ndarray) – array of 3D coordinates.

  • radius (float) – radius.

  • atom_properties (str or list, optional) – Property of the atoms to retrieve (properties: ligand, flexible_residue, vdw, hb_don, hb_acc, metal, water, reactive, glue).

  • ignore (int or list, optional) – Ignore atom for the search using atom id (0-based). Default is None (no atoms are ignored).

Returns:

ndarray (atom_id, atom_name, resname, resid, chainid, xyz, q, t).

Return type:

ndarray

Raises:

KeyError – If the atom property is not valid.

closest_atoms(atom_idx, radius, atom_properties=None)[source]#

Retrieve indices of the closest atoms around a positions/coordinates at a certain radius.

Parameters:

  • atom_idx (int, list) – index of one or multiple atoms (0-based).

  • radius (float) – radius.

  • atom_properties (str or list, optional) – Property of the atoms to retrieve (properties: ligand, flexible_residue, vdw, hb_don, hb_acc, metal, water, reactive, glue).

Returns:

ndarray (atom_id, atom_name, resname, resid, chainid, xyz, q, t).

Return type:

ndarray

neighbor_atoms(atom_idx)[source]#

Return neighbor (bonded) atoms of certain atom(s) by their index.

Parameters:

atom_idx (int, list) – index of one or multiple atoms (0-based).

Returns:

list of lists containing the neighbor (bonded) atoms (0-based).

Return type:

list

write_pdbqt_string(as_model=True)[source]#

Write PDBQT output string of the current pose.

Parameters:

as_model (bool, optional) – Add MODEL/ENDMDL keywords to the output PDBQT string Default is True (add MODEL/ENDMDL keywords).

Returns:

PDBQT string of the current pose.

Return type:

str

write_pdbqt_file(output_pdbqtfilename, overwrite=False, as_model=False)[source]#

Write PDBQT file of the current pose

Parameters:

  • output_pdbqtfilename (str) – Filename of the output PDBQT file.

  • overwrite (bool, optional) – Overwrite on existing PDBQT file. Default is False (do not overwrite).

  • as_model (bool, optional) – Add MODEL/ENDMDL keywords to the output PDBQT string. Default is False (do not add MODEL/ENDMDL keywords).

Raises:

RuntimeError – If the output PDBQT file already exists and overwrite is False.

Return type:

None

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