Functions | |
def | RunAntechamber |
def | AddFromFiles |
def | AddFromPath |
def | AddIon |
Variables | |
tuple | __all__ = ('RunAntechamber', 'AddFromFiles', 'AddFromPath', 'AddIon',) |
def ost::mol::mm::antechamber::AddFromFiles | ( | force_field, | ||
frcmod_filename, | ||||
mpdb_filename | ||||
) |
Add data from a frcmod and an mpdb file to a force field. This will add a new :class:`~ost.mol.mm.BuildingBlock` to `force_field` for the residue defined in those files (residue name is extracted from the mpdb file which can only contain a single residue). Charges for each atom are extracted from the mpdb file. According to the frcmod file, an :class:`~ost.mol.mm.Interaction` is added for each bond, angle, dihedral and improper. Atom types with masses and non-bonded interactions are added to `force_field` as needed. :param force_field: A force field object to which the new parameters are added. :type force_field: :class:`~ost.mol.mm.Forcefield` :param frcmod_filename: Path to ``frcmod`` file as generated by ``parmchk2``. :type frcmod_filename: :class:`str` :param mpdb_filename: Path to mpdb file as generated by ``antechamber``. :type mpdb_filename: :class:`str` :return: The updated force field (same as `force_field`). :rtype: :class:`~ost.mol.mm.Forcefield`
Definition at line 403 of file antechamber.py.
def ost::mol::mm::antechamber::AddFromPath | ( | force_field, | ||
out_dir | ||||
) |
Add data from a directory created with :meth:`Run` to a force field. See :meth:`AddFromFiles` for details. :param force_field: A force field object to which the new parameters are added. :type force_field: :class:`~ost.mol.mm.Forcefield` :param out_dir: Output directory as created with :meth:`Run`. Must contain files ``frcmod`` and ``out.mpdb``. :type out_dir: :class:`str` :return: The updated force field (same as `force_field`). :rtype: :class:`~ost.mol.mm.Forcefield`
Definition at line 461 of file antechamber.py.
def ost::mol::mm::antechamber::AddIon | ( | force_field, | ||
res_name, | ||||
atom_name, | ||||
atom_mass, | ||||
atom_charge, | ||||
lj_sigma, | ||||
lj_epsilon | ||||
) |
Add a single atom as an ion to a force field. Since Antechamber cannot deal with ions, you can add simple ones easily with this function. This adds a :class:`~ost.mol.mm.BuildingBlock` to `force_field` for the given residue name containing a single atom. The atom will have a type with the same name as the atom name and the given mass, charge and non-bonded (LJ) interaction parameters. :param force_field: A force field object to which the ion is added. :type force_field: :class:`~ost.mol.mm.Forcefield` :param res_name: Residue name for the ion to be added. :type res_name: :class:`str` :param atom_name: Atom name which is also used as atom type name. :type atom_name: :class:`str` :param atom_mass: Mass of the atom. :type atom_mass: :class:`float` :param atom_charge: Charge of the atom. :type atom_charge: :class:`float` :param lj_sigma: The sigma parameter for the non-bonded LJ interaction. :type lj_sigma: :class:`float` in nm :param lj_epsilon: The sigma parameter for the non-bonded LJ interaction. :type lj_epsilon: :class:`float` in kJ/mol
Definition at line 478 of file antechamber.py.
def ost::mol::mm::antechamber::RunAntechamber | ( | res_name, | ||
filename, | ||||
format = 'ccif' , |
||||
amberhome = None , |
||||
base_out_dir = None | ||||
) |
Run Antechamber to guess force field parameters for a given residue name. This requires an installation of AmberTools (tested with AmberTools15) with binaries ``antechamber`` and ``parmchk2``. This has the same restrictions as Antechamber itself and we assume the input to be uncharged. Note that Antechamber cannot deal with metal ions and other non-organic elements. The results are stored in a separate folder named `res_name` within `base_out_dir` (if given, otherwise the current working directory). The main output files are ``frcmod`` and ``out.mpdb``. The former contains force field parameters and masses. The latter maps atom names to atom types and defines the partial charges. The same output could be obtained as follows: .. code-block:: console $ antechamber -i <FILENAME> -fi <FORMAT> -bk '<RES_NAME>' -o out.mol2 -fo mol2 -c bcc -pf yes $ parmchk2 -i out.mol2 -f mol2 -o frcmod -a Y $ antechamber -i out.mol2 -fi mol2 -o out.mpdb -fo mpdb -pf yes The force field parameters can be manually modified if needed. It can for instance happen that some parameters cannot be identified. Those lines will be marked with a comment "ATTN, need revision". :param res_name: Residue name for which we desire force field parameters. :type res_name: :class:`str` :param filename: Path to a file which contains the necessary information for `res_name`. It must include all hydrogens. :type filename: :class:`str` :param format: Format of file given with `filename`. Common formats are 'ccif' for PDB's component dictionary or 'pdb' for a PDB file containing the desired residue with all hydrogens. :type format: :class:`str` :param amberhome: Base path of your AmberTools installation. If not None, we look for ``antechamber`` and ``parmchk2`` within ``AMBERHOME/bin`` additionally to the system's ``PATH``. :type amberhome: :class:`str` :param base_out_dir: Path to a base path, where the output will be stored. If None, the current working directory is used. :type base_out_dir: :class:`str`
Definition at line 293 of file antechamber.py.
tuple __all__ = ('RunAntechamber', 'AddFromFiles', 'AddFromPath', 'AddIon',) |
Definition at line 515 of file antechamber.py.