pygromos.files.coord package¶

Submodules¶

pygromos.files.coord.cnf module¶

class pygromos.files.coord.cnf.Cnf(in_value: Optional[Union[str, dict]], clean_resiNumbers_by_Name: bool = False, verbose: bool = False, _future_file: bool = False)[source]¶

Bases: pygromos.files._basics._general_gromos_file._general_gromos_file

This class is a representation of the gromos .cnf coordinate files. It allows reading, analysis and modifying of the coordinate files.

is a child of general_gromos_file

GENBOX: pygromos.files.blocks.coord_blocks.GENBOX¶

LATTICESHIFTS: pygromos.files.blocks.coord_blocks.LATTICESHIFTS¶

PERTDATA: pygromos.files.blocks.coord_blocks.PERTDATA¶

POSITION: pygromos.files.blocks.coord_blocks.POSITION¶

TIMESTEP: pygromos.files.blocks._general_blocks.TIMESTEP¶

TITLE: pygromos.files.blocks._general_blocks.TITLE¶

VELOCITY: pygromos.files.blocks.coord_blocks.VELOCITY¶

add_empty_box()[source]¶

add_residue_positions(coords: object)[source]¶

This function adds all residues of an coords file to @DEVELOP

This is a very crude functio at the moment! It only takes positions of a residue and merges them! if there are residues with the same name, this might lead to problems, as clean_posiresnumbyname function is not sensitive for that! todo: make more robust! bschroed

Parameters: coords (function_libs.gromos.files.coord.Cnf obj) – object - CNF object

atom_ref_pos_block: pygromos.files.blocks.coord_blocks.REFPOSITION¶

center_of_geometry(selectedAtoms: Optional[List[int]] = None) → list[source]¶

calculates the center of geometry for asingle molecule or the selected Atoms

Returns: cog
Return type: list

clean_posiResNums()[source]¶

This function recount the Residue number with respect to residue name and residue number.

Warning

only in “Position_BLOCK!@development

Return type: None

count_residue_atoms(resID: int = False, resName: str = False, verbose=False) → int[source]¶

createRDKITconf(mol: rdkit.Chem.rdchem.Mol, conversionFactor: float = 0.1)[source]¶

creates a PyGromosTools CNF type from a rdkit molecule. If a conformation exists the first one will be used.

Parameters

mol (Chem.rdchem.Mol) – Molecule, possibly with a conformation
conversionFactor (float) – the factor used to convert length from rdkit to Gromos (default: angstrom -> nano meter = 0.1)

delete_atom(resID: int = False, resName: str = False, atomID: int = False, atomType: str = False)[source]¶

delete_residue(resID: int = False, resName: str = False, verbose=False) → int[source]¶

this function is deleting residues from a cnf file with taking following _blocks into account:: “POSITION”, “VELOCITY”, “LATTICESHIFTS”, “REFPOSITION”

it additionally recounts all atomIds and residueIDs afterwards. you can provide a residue ID or a residue Name or both (than only exact match will be deleted).

Parameters

resID (int) – Id of the residue to be deleted
resName (str) – Name of the residue to be deleted
verbose (bool) – Text… lots of it!

Returns

0 if succesfull

Return type

int

gen_possrespec(residues: Union[Dict[str, List[int]], List[int]], keep_residues: bool = True, verbose: bool = False) → pygromos.utils.typing.Position_Restraints_Type[source]¶

This function writes out a gromos file, containing a atom list. that is to be position restrained! Raises not Implemented error, if a input variant of the residues

Parameters

residues (dict, list) – residues to be restrained (dict containing resname:[res ids] or list of resnames or residue IDs)
keep_residues (bool, optional) – should the passed residues be kept or deleted?
verbose (bool, optional) – loud and noisy?

Returns

str – out_path
Position_Restraints – posrespec-file-obj

gen_refpos() → pygromos.utils.typing.Reference_Position_Type[source]¶

generate_position_restraints(out_path_prefix: str, residues: Union[Dict[str, List[int]], List[int]], verbose: bool = False) → Tuple[str, str][source]¶

This function generates position restraints for the selected residues.

Parameters

out_path_prefix (str) – target path prefix for the out files.
residues (dict or list) – residues to be restrained (dict containing resname:[res ids] or list of resnames or residue IDs)
verbose (bool, optional) – Loud and noisy, by default False

Returns

return the two resulting paths to the generated files.

Return type

Tuple[str, str]

get_atomP(atomID: Optional[int] = None, atomType: Optional[str] = None, resID: Optional[int] = None, resName: str = False) → list[source]¶

get_atom_coordinates() → numpy.array[source]¶

This function returns a np.array containing all system coordinates.

Returns: dims are atoms[x,y,z]
Return type: np.array

get_atoms_distance(atomI: Optional[Union[int, List[int]]] = None, atomJ: Optional[int] = None, atoms: Optional[Union[List[int], Dict[int, int]]] = None) → Union[float, List[float]][source]¶

get_density(mass: float = 1, autoCalcMass: bool = False) → float[source]¶

This function calculates the density of the cnf.

Returns: density of the cnf.
Return type: float

get_last_atomID() → int[source]¶

get_last atom: A very simple convenience function that returns the last atom

Returns: Returns the last atom of the system.
Return type: int

get_mass() → float[source]¶

This function calculates the mass of the cnf.

Returns: mass of the cnf.
Return type: float

get_mdtraj()[source]¶

get_pdb(rdkit_ready: bool = False, connectivity_top=None) → str[source]¶

translate cnf to pdb.

Parameters

rdkit_ready (bool, optional) – str output was tested with RDKIT (default: False)
connectivity_top (top.Top, optional) – if the pygromos top class is provided (containing a BOND block), then the pdb gets a connect block.

Returns

pdb str.

Return type

str

get_residues(verbose: bool = False) → Dict[str, Dict[str, int]][source]¶

This function is getting all residues of the used cnf file.: it gives back,

Parameters: verbose (bool, optional) – texty?
Returns: returns dict containing all residues, numbers and atoms.
Return type: Dict[str, Dict[str, Any]]

get_system_information(not_ligand_residues: List[str] = [], ligand_resn_prefix: Optional[Union[str, List[str]]] = None, solvent_name: str = 'SOLV') → Tuple[Dict[str, Dict[int, int]], collections.namedtuple, collections.namedtuple, collections.namedtuple, collections.namedtuple][source]¶

This function utilizes a dictionary containing all residues and atom numbers (e.g. cnf.get_residues()) and modifies them such, that the result can be used to set up a standard REEDS gromos_simulation

Parameters

residues (Dict[str, Dict[int,int]]) – input a cnf.residues:dict that shall be cleaned and return a reduced form for parameter file.
not_ligand_residues (List[str]) – here all molecules, that are not considered as ligand or protein.
ligand_resn_prefix (List[str]) – here all molecules, that are considered as ligand are listed.

Returns

Dict[str, Dict[int,int]] – cleaned_residue dict
NamedTuple – ligands
NamedTuple – protein
NamedTuple – non_ligands

get_volume() → float[source]¶

This function calculates the volume of the cnf.

Returns: volume of the cnf.
Return type: float

get_xyz() → str[source]¶

translate cnf to xyz

Returns: in xyz format
Return type: str

read_file() → Dict[str, any][source]¶

Parameters: path

recenter_pbc()[source]¶: This function is shifting the coordinates such that the solute molecule is centered, if it is placed in the corners. However, this function might break down with more complicated situations. Careful the function is not fail safe ;)

recreate_view() → nglview.widget.NGLWidget[source]¶

rename_residue(new_resName: str, resID: int = False, resName: str = False, verbose: bool = False) → int[source]¶

this function is renaming residues from a cnf file with taking following _blocks into account:: “POSITION”, “VELOCITY”

it additionally recounts all atomIds and residueIDs afterwards. you can provide a residue ID or a residue Name or both (than only exact match will be deleted).

Parameters

new_resName (str) – new Name of the residue
resID (int, optional) – Id of the residue to be renamed
resName (str, optional) – Name of the residue to be renamed
verbose (bool, optional) – Text… lots of it!

Returns

0 if succesfull

Return type

int

residues: Dict[str, Dict[str, int]]¶

rotate(rotationCenter: Optional[numpy.array] = None, selectedAtoms=None, alpha: float = 0, beta: float = 0, gamma: float = 0)[source]¶

shift_periodic_boundary()[source]¶: This function is shifting the coordinates such that the solute molecule is centered, if it is placed in the corners. However, this function might break down with more complicated situations. Careful the function is not fail safe ;)

supress_atomPosition_singulrarities() → None[source]¶

This function adds a very small deviation to the position of an atom, dependent on the atom number. This might be needed to avoid singularities in gromosXX.

Return type: None

property view: nglview.widget.NGLWidget¶

write_pdb(out_path: str) → str[source]¶

This function converts the atom POS db of the traj into a pdb traj.

Parameters: out_path (str) – path, were the file should be written to.
Returns: outpath of the file
Return type: str

write_possrespec(out_path: str, residues: dict, verbose: bool = False) → str[source]¶

This function writes out a gromos file, containing a atom list. that is to be position restrained!: Raises not Implemented error, if a input variant of the residues

Parameters

out_path (str) – path to the outputfile
residues (dict, list) – residues to be restrained (dict containing resname:[res ids] or list of resnames or residue IDs)
verbose (bool, optional) – loud and noisy?

Raises

NotImplementedError –

Returns

str – out_path
Position_Restraints – posrespec-file-obj

write_refpos(out_path: str) → str[source]¶

write_xyz(out_path: str) → str[source]¶

This function converts the atom POS db of the traj into a xyz structure.

Parameters: out_path (str) – path, were the file should be written to.
Returns: outpath of the file
Return type: str

pygromos.files.coord.cnf.non_ligand_infos¶: alias of pygromos.files.coord.cnf.ligands_info

pygromos.files.coord.cnf.protein_infos¶: alias of pygromos.files.coord.cnf.protein_info

pygromos.files.coord.cnf.solute_infos¶: alias of pygromos.files.coord.cnf.solute_info

pygromos.files.coord.cnf.solvent_infos¶: alias of pygromos.files.coord.cnf.solvent_info

pygromos.files.coord.posres module¶

class pygromos.files.coord.posres.Position_Restraints(in_value: Union[str, dict, pygromos.utils.typing.Position_Restraints_Type, pygromos.utils.typing.Cnf_Type], clean_resiNumbers_by_Name: bool = False, verbose: bool = False, _future_file: bool = False)[source]¶

Bases: pygromos.files.coord.cnf.Cnf

This class is a representation of the gromos .cnf coordinate files. It allows reading, analysis and modifying of the coordinate files.

is a child of general_gromos_file

LATTICESHIFTS: pygromos.files.blocks.coord_blocks.LATTICESHIFTS¶

POSRESSPEC: pygromos.files.blocks.coord_blocks.POSRESSPEC¶

TITLE: pygromos.files.blocks._general_blocks.TITLE¶

path: str¶

residues: Dict[str, Dict[str, int]]¶

pygromos.files.coord.refpos module¶

class pygromos.files.coord.refpos.Reference_Position(in_value: Union[str, dict, pygromos.utils.typing.Reference_Position_Type, pygromos.utils.typing.Cnf_Type], verbose: bool = False, _future_file: bool = False)[source]¶