molsysmt.thirds.tleap package

Submodules

molsysmt.thirds.tleap.tleap module

class molsysmt.thirds.tleap.tleap.TLeap

Bases: object

Programmatic interface to write and run AmberTools’ tLEaP scripts. To avoid problems with special characters in file paths, the class run the tleap script in a temporary folder with hardcoded names for files and then copy the output files in their respective folders. .. attribute:: script

add_commands(*args)

Append commands to the script :param args: Individual commands to add to the script written in full as strings.

Newline characters are added after each command

add_ions(unit_name, ion, num_ions=0, replace_solvent=False)

Add ions to a unit in LEaP This adds to the script :param unit_name: Name of the existing LEaP unit which Ions will be added into :type unit_name: str :param ion: LEaP recognized name of ion to add :type ion: str :param num_ions: Number of ions of type ion to add to unit_name. If 0, the unit

is neutralized (default is 0).

Parameters:

replace_solvent (bool, optional) – If True, ions will replace solvent molecules rather than being added.

check_unit(unit_name)

Checking for internal inconsistencies in a Unit such as: long or short bonds, non-integral total charge, missing atoms, unwanted steric clashes between atoms. :param unit_name: Name of the unit as it should be represented in LEaP :type unit_name: str

combine(unit_name, *args)

Combine units in LEaP This adds to the script :param unit_name: Name of LEaP unit to assign the combination to :type unit_name: str :param args: Name of LEaP units to combine into a single unit called leap_name :type args: iterable of strings

export_script(file_path)

Write script to file :param file_path: Full file path with extension of the script to save :type file_path: str

get_total_charge(unit_name)

Getting the total charge of a Unit :param unit_name: Name of the unit as it should be represented in LEaP :type unit_name: str

load_parameters(*args)

Load the LEaP parameters into the working TLEaP script if not already loaded This adds to the script Uses loadAmberParams for frcmod.* files Uses loadOff for *.off and *.lib files Uses source for other files. :param args: File names for each type of leap file that can be loaded.

Method to load them is automatically determined from file extension or base name

load_unit(unit_name, file_path)

Load a Unit into LEaP, this is typically a molecule or small complex. This adds to the script Accepts *.mol2 or *.pdb files :param unit_name: Name of the unit as it should be represented in LEaP :type unit_name: str :param file_path: Full file path with extension of the file to read into LEaP as a new unit :type file_path: str

make_sequence(unit_name, sequence)

Define a Unit with a sequence of residue names :param unit_name: Name of the unit as it should be represented in LEaP :type unit_name: str :param file_path: Space separated equence of residue names (3-letters code) :type file_path: str

new_section(comment)

Adds a comment line to the script

run(working_directory=None, verbose=False)

Run script and return warning messages in leap log file.

save_unit(unit_name, output_path)

Write a LEaP unit to file. Accepts either *.prmtop, *.inpcrd, or *.pdb files This adds to the script :param unit_name: Name of the unit to save :type unit_name: str :param output_path: Full file path with extension to save.

Outputs with multiple files (e.g. Amber Parameters) have their names derived from this instead

property script

Complete and return the finalized script string Adds a quit command to the end of the script.

set_global_parameter(**kwargs)

Set global parameter value with command ‘set default’. See the Amber manual: ‘set’ subsection of section ‘Commands’ in Leap chapter. :param OldPrmtopFormat: “on” or “off” (default) to write the prmtop file in Amber 6 and earlier format :type OldPrmtopFormat: str :param Dielectric: “constant” or “distance” (default) for constant or distance dependent dielectric :type Dielectric: str :param PdbWriteCharges: “on” or “off” (default) to write withe savePDB the atom charges in the B-factors

columnt

Parameters:

• PBRadii (str) – “bondi”, “mbondi” (default), “mbondi2”, “mbondi3” or “amber6” to choose the set of atomic radii for generalized Born or Poisson-Boltzmann calculations.

• nocenter (str) – “on” or “off” (default) to deactivate recentering coordinates.

• reorder_residues (str) – “on” (default) or “off” to place non-solvent residues before sovent residues

solvate(unit_name, solvent_model, clearance, box_geometry='cubic')

Solvate a unit in LEaP isometrically This adds to the script :param unit_name: Name of the existing LEaP unit which will be solvated :type unit_name: str :param solvent_model: LEaP recognized name of the solvent model to use, e.g. “TIP3PBOX” :type solvent_model: str :param clearance: Add solvent up to clearance distance away (units of length) from the unit_name (radial) :type clearance: unit.Quantity :param box_geometry: Shape of the box to be solvated (Default is “cubic”). :type box_geometry: “cubic” or “truncated octahedral”

transform(unit_name, transformation)

Transformation is an array-like representing the affine transformation matrix.

Module contents