VinaApp
#
- class biotite.application.autodock.VinaApp(ligand, receptor, center, size, flexible=None, bin_path='vina')[source]#
Bases:
LocalApp
Dock a ligand to a receptor molecule using AutoDock Vina.
- Parameters:
- ligandAtomArray
The structure of the receptor molecule. Must have an associated
BondList
. An associatedcharge
annotation is recommended for proper calculation of partial charges.- receptorAtomArray, shape=(n,)
The structure of the receptor molecule. Must have an associated
BondList
. An associatedcharge
annotation is recommended for proper calculation of partial charges.- centerndarray, shape=(3,), dtype=float
The xyz coordinates for the center of the search space.
- sizendarray, shape=(3,), dtype=float
The size of the search space in xyz directions.
- flexiblendarray, shape=(n,), dtype=bool, optional
A boolean mask that indicates flexible amino acid side chains in receptor. Each residue, where at least one atom index is
True
in flexible, is considered flexible. By default, the receptor has no flexibility.- bin_pathstr, optional
Path to the Vina binary.
Examples
>>> # A dummy receptor and ligand >>> ligand = residue("ASP") >>> receptor = atom_array >>> app = VinaApp( ... ligand, receptor, ... # Binding pocket is in the center of the receptor ... center=centroid(receptor), ... # 20 Å x 20 Å x 20 Å search space ... size=[20, 20, 20], ... # Handle residues 2 and 5 as flexible ... flexible=(receptor.res_id == 2) | (receptor.res_id == 5) ... )
- add_additional_options(options)#
Add additional options for the command line program. These options are put before the arguments automatically determined by the respective
LocalApp
subclass.This method is focused on advanced users, who have knowledge on the available options of the command line program and the options already used by the
LocalApp
subclasses. Ignoring the already used options may result in conflicting CLI arguments and potential unexpected results. It is recommended to use this method only, when the respectiveLocalApp
subclass does not provide a method to set the desired option.- Parameters:
- optionslist of str
A list of strings representing the command line options.
Notes
In order to see which options the command line execution used, try the
get_command()
method.Examples
>>> seq1 = ProteinSequence("BIQTITE") >>> seq2 = ProteinSequence("TITANITE") >>> seq3 = ProteinSequence("BISMITE") >>> seq4 = ProteinSequence("IQLITE") >>> # Run application without additional arguments >>> app = ClustalOmegaApp([seq1, seq2, seq3, seq4]) >>> app.start() >>> app.join() >>> print(app.get_command()) clustalo --in ...fa --out ...fa --force --output-order=tree-order --seqtype Protein --guidetree-out ...tree >>> # Run application with additional argument >>> app = ClustalOmegaApp([seq1, seq2, seq3, seq4]) >>> app.add_additional_options(["--full"]) >>> app.start() >>> app.join() >>> print(app.get_command()) clustalo --full --in ...fa --out ...fa --force --output-order=tree-order --seqtype Protein --guidetree-out ...tree
- cancel()#
Cancel the application when in RUNNING or FINISHED state.
- clean_up()#
Do clean up work after the application terminates.
PROTECTED: Optionally override when inheriting.
- static dock(ligand, receptor, center, size, flexible=None, bin_path='vina')#
Dock a ligand to a receptor molecule using AutoDock Vina.
This is a convenience function, that wraps the
VinaApp
execution.- Parameters:
- ligandAtomArray
The structure of the receptor molecule. Must have an associated
BondList
. An associatedcharge
annotation is recommended for proper calculation of partial charges.- receptorAtomArray, shape=(n,)
The structure of the receptor molecule. Must have an associated
BondList
. An associatedcharge
annotation is recommended for proper calculation of partial charges.- centerndarray, shape=(3,), dtype=float
The xyz coordinates for the center of the search space.
- sizendarray, shape=(3,), dtype=float
The size of the search space in xyz directions.
- flexiblendarray, shape=(n,), dtype=bool, optional
A boolean mask that indicates flexible amino acid side chains in receptor. Each residue, where at least one atom index is
True
in flexible, is considered flexible. By default, the receptor has no flexibility.- bin_pathstr, optional
Path to the Vina binary.
- Returns:
- coordndarray, shape=(m,n,3), dtype=float
The docked ligand coordinates for m binding modes and n atoms of the input ligand. The models are sorted from best to worst predicted binding affinity. Missing coordinates due to the removed nonpolar hydrogen atoms are set to NaN.
- energiesndarray, shape=(m,), dtype=float
The corresponding predicted binding energies (kcal/mol).
- get_app_state()#
Get the current app state.
- Returns:
- app_stateAppState
The current app state.
- get_command()#
Get the executed command.
Cannot be called until the application has been started.
- Returns:
- commandstr
The executed command.
Examples
>>> seq1 = ProteinSequence("BIQTITE") >>> seq2 = ProteinSequence("TITANITE") >>> seq3 = ProteinSequence("BISMITE") >>> seq4 = ProteinSequence("IQLITE") >>> app = ClustalOmegaApp([seq1, seq2, seq3, seq4]) >>> app.start() >>> print(app.get_command()) clustalo --in ...fa --out ...fa --force --output-order=tree-order --seqtype Protein --guidetree-out ...tree
- get_energies()#
Get the predicted binding energy for each generated binding mode.
- Returns:
- energiesndarray, dtype=float
The predicted binding energies (kcal/mol). The energies are sorted from best to worst.
- get_exit_code()#
Get the exit code of the process.
PROTECTED: Do not call from outside.
- Returns:
- codeint
The exit code.
- get_flexible_residue_models()#
Get the structure for the flexible side chains with the conformations for each generated binding mode.
If no flexible side chains were defined, the returned
AtomArrayStack
contains no atoms.- Returns:
- side_chainsAtomArrayStack
The docked side chains. Each model corresponds to one binding mode. The models are sorted from best to worst predicted binding affinity.
Notes
The returned structure may contain less atoms than the input structure, as Vina removes nonpolar hydrogen atoms. Furthermore, the returned structure contains AutoDock atom types as
element
annotation.
- get_ligand_coord()#
Get the ligand coordinates for each generated binding mode.
- Returns:
- coordndarray, shape=(m,n,3), dtype=float
The coordinates for m binding modes and n atoms of the input ligand. The models are sorted from best to worst predicted binding affinity. Missing coordinates due to the removed nonpolar hydrogen atoms are set to NaN.
- get_ligand_models()#
Get the ligand structure with the conformations for each generated binding mode.
- Returns:
- ligandAtomArrayStack
The docked ligand. Each model corresponds to one binding mode. The models are sorted from best to worst predicted binding affinity.
Notes
The returned structure may contain less atoms than the input structure, as Vina removes nonpolar hydrogen atoms. Furthermore, the returned structure contains AutoDock atom types as
element
annotation.
- get_process()#
Get the Popen instance.
PROTECTED: Do not call from outside.
- Returns:
- processPopen
The Popen instance
- get_receptor_coord()#
Get the get_receptor_coord coordinates for each generated binding mode.
- Returns:
- coordndarray, shape=(m,n,3), dtype=float
The coordinates for m binding modes and n atoms of the input receptor. The models are sorted from best to worst predicted binding affinity. Missing coordinates due to the removed nonpolar hydrogen atoms from flexible side chains are set to NaN.
Notes
The output is only meaningful, if flexible side chains were defined. Otherwise, the returned coordinates are simply m repetitions of the input receptor coordinates.
- get_stderr()#
Get the STDERR pipe content of the process.
PROTECTED: Do not call from outside.
- Returns:
- stdoutstr
The standard error.
- get_stdout()#
Get the STDOUT pipe content of the process.
PROTECTED: Do not call from outside.
- Returns:
- stdoutstr
The standard output.
- is_finished()#
Check if the application has finished.
PROTECTED: Override when inheriting.
- Returns:
- finishedbool
True of the application has finished, false otherwise
- join(timeout=None)#
Conclude the application run and set its state to JOINED. This can only be done from the RUNNING or FINISHED state.
If the application is FINISHED the joining process happens immediately, if otherwise the application is RUNNING, this method waits until the application is FINISHED.
- Parameters:
- timeoutfloat, optional
If this parameter is specified, the
Application
only waits for finishing until this value (in seconds) runs out. After this time is exceeded aTimeoutError
is raised and the application is cancelled.
- Raises:
- TimeoutError
If the joining process exceeds the timeout value.
- set_arguments(arguments)#
Set command line arguments for the application run.
PROTECTED: Do not call from outside.
- Parameters:
- argumentslist of str
A list of strings representing the command line options.
- set_energy_range(energy_range)#
Set the maximum energy range of the generated models.
Vina will ignore binding modes if the difference between this mode and the best mode is greater than this value. By default, the range is
3.0
.- Parameters:
- numberfloat
The energy range (kcal/mol).
- set_exec_dir(exec_dir)#
Set the directory where the application should be executed. If not set, it will be executed in the working directory at the time the application was created.
PROTECTED: Do not call from outside.
- Parameters:
- exec_dirstr
The execution directory.
- set_exhaustiveness(exhaustiveness)#
Set the exhaustiveness parameter for Vina.
A higher exhaustiveness may lead to better docking results, but also increases the computation time. By default, the exhaustiveness is
8
.- Parameters:
- exhaustivenessint
The value for the exhaustiveness parameter. Must be greater than 0.
- set_max_number_of_models(number)#
Set the maximum number of binding modes to generate.
Vina may generate less modes, if the docking process does not find enough distinct conformations. By default, the maximum number is
9
.- Parameters:
- numberint
The maximum number of generated modes/models.
- set_seed(seed)#
Fix the seed for the random number generator to get reproducible results.
By default, the seed is chosen randomly.
- Parameters:
- seedint
The seed for the random number generator.
- set_stdin(file)#
Set a file as standard input for the application run.
PROTECTED: Do not call from outside.
- Parameters:
- filefile object
The file for the standard input. Must have a valid file descriptor, e.g. file-like objects such as StringIO are invalid.
- start()#
Start the application run and set its state to RUNNING. This can only be done from the CREATED state.
- wait_interval()#
The time interval of
is_finished()
calls in the joining process.PROTECTED: Override when inheriting.
- Returns:
- intervalfloat
Time (in seconds) between calls of
is_finished()
injoin()