pygromos.files.topology package

Submodules

pygromos.files.topology.disres module

class pygromos.files.topology.disres.Disres(in_value: Optional[Union[str, Dict]] = None)

Bases: pygromos.files.topology.disres.Distance_restraints

class pygromos.files.topology.disres.Distance_restraints(in_value: Optional[Union[str, Dict]] = None)

Bases: pygromos.files._basics._general_gromos_file._general_gromos_file

read_blocks()

required_blocks = ['TITLE', 'DISTANCERESPEC']

pygromos.files.topology.ifp module

File: Description:

Author:

class pygromos.files.topology.ifp.Ifp(in_value: Union[str, Dict])

Bases: pygromos.files._basics._general_gromos_file._general_gromos_file

path: str

read_file()

give back the content. WARNING DEAPRECEATED.

Warning

DEAPRECEATED

Returns

key is the block name of the gromos file, any is the content of a block

Return type

Dict[str, any]

pygromos.files.topology.mtb module

File: Description:

Author: Marc Lehner

class pygromos.files.topology.mtb.Mtb(in_value: Union[str, Dict], _future_file: bool = False)

Bases: pygromos.files._basics._general_gromos_file._general_gromos_file

all_res_names: List

mtb_ends: Dict[str, pygromos.files.blocks.mtb_blocks.MTBUILDBLEND]

mtb_solutes: Dict[str, pygromos.files.blocks.mtb_blocks.MTBUILDBLSOLUTE]

mtb_solvents: Dict[str, pygromos.files.blocks.mtb_blocks.MTBUILDBLSOLVENT]

read_file()

give back the content. WARNING DEAPRECEATED.

Warning

DEAPRECEATED

Returns

key is the block name of the gromos file, any is the content of a block

Return type

Dict[str, any]

read_mtb_file(path: str) → List[str]

pygromos.files.topology.ptp module

class pygromos.files.topology.ptp.Pertubation_topology(in_value: Optional[Union[str, dict]] = None)

Bases: pygromos.files._basics._general_gromos_file._general_gromos_file

MPERATOM: pygromos.files.blocks.pertubation_blocks.MPERTATOM

PERTATOMPARAM: pygromos.files.blocks.pertubation_blocks.PERTATOMPARAM

PERTBONDANGLE: pygromos.files.blocks.pertubation_blocks.PERTBONDANGLE

PERTBONDANGLEH: pygromos.files.blocks.pertubation_blocks.PERTBONDANGLEH

PERTBONDSTRETCH: pygromos.files.blocks.pertubation_blocks.PERTBONDSTRETCH

PERTBONDSTRETCHH: pygromos.files.blocks.pertubation_blocks.PERTBONDSTRETCHH

PERTPROPERDIH: pygromos.files.blocks.pertubation_blocks.PERTPROPERDIH

TITLE: pygromos.files.blocks._general_blocks.TITLE

read_blocks()

required_blocks = ['TITLE']

class pygromos.files.topology.ptp.Ptp(in_value: Optional[Union[str, dict]] = None)

Bases: pygromos.files.topology.ptp.Pertubation_topology

MPERATOM: pygromos.files.blocks.pertubation_blocks.MPERTATOM

PERTATOMPARAM: pygromos.files.blocks.pertubation_blocks.PERTATOMPARAM

PERTBONDANGLE: pygromos.files.blocks.pertubation_blocks.PERTBONDANGLE

PERTBONDANGLEH: pygromos.files.blocks.pertubation_blocks.PERTBONDANGLEH

PERTBONDSTRETCH: pygromos.files.blocks.pertubation_blocks.PERTBONDSTRETCH

PERTBONDSTRETCHH: pygromos.files.blocks.pertubation_blocks.PERTBONDSTRETCHH

PERTPROPERDIH: pygromos.files.blocks.pertubation_blocks.PERTPROPERDIH

TITLE: pygromos.files.blocks._general_blocks.TITLE

path: str

pygromos.files.topology.top module

File: gromos++ topo file functions Warnings: this CLASS IS NOT IMPLEMENTED! TODO:REWORK Description:

in this lib, gromos topo file mainpulating functions are gathered

Author: Marc Lehner, Benjamin Ries

class pygromos.files.topology.top.Top(in_value: Union[str, dict, pygromos.utils.typing.Top_Type], _future_file: bool = False)

Bases: pygromos.files._basics._general_gromos_file._general_gromos_file

_add_top(top: Optional[pygromos.utils.typing.Top_Type], solvFrom1: bool = True, verbose: bool = False) → pygromos.utils.typing.Top_Type

combines two topologies. Parameters are taken from the initial topology. But missing parameters from the second topology will be added. Can be used like com_top from Gromos++

Parameters

• top (TopType) – second topology to add to the first topology

• solvFrom1 (bool, optional) – should the solvent be taken from the first topology? (else second), by default True

• verbose (bool, optional) – extra print statements, by default True

• sanityCheck (bool, optional) – feature and compatibility check, by default True

Returns

returns a topology made by combing two topologies

Return type

TopType

add_new_CONSTRAINT(IC: int, JC: int, ICC: float, verbose: bool = False)

adds a CONSTRAINT entry to the topology

Parameters

• IC (int) – atom index I

• JC (int) – atom index J

• ICC (float) – constraint length

• verbose (bool, optional)

add_new_LJparameter(C6: float, C12: float, CS6: float = 0, CS12: float = 0, combination_rule: str = 'geometric', verbose=False, AddATOMTYPENAME: Optional[str] = None, lowerBound: float = 1e-100)

add a LJ entry to the LJ parameter block

Parameters

• C6 (float)

• C12 (float)

• CS6 (float, optional)

• CS12 (float, optional)

• combination_rule (str, optional) – no other options supported rigth now, by default “geometric”

• AddATOMTYPENAME (str, optional) – if not None a new atomtype is made, by default None

• lowerBound (float, optional) – saftey, by default 1e-100

add_new_PRESSUREGROUPS(number: int, verbose: bool = False)

add_new_SOLUTEMOLECULES(number: int, verbose: bool = False)

add_new_TEMPERATUREGROUPS(number: int, verbose: bool = False)

add_new_angle(k: float, kh: float, b0: float, atomI: int, atomJ: int, atomK: int, includesH: bool = False, verbose: bool = False, convertToQuartic: bool = False)

add a angle between atom I, J and K to the ANGLE block

Parameters

• k (float) – force konstant

• kh (float) – force konstant harmonic

• b0 (float) – angle at which the force is 0

• atomI (int) – atom I

• atomJ (int) – atom J

• atomK (int) – atom K

• includesH (bool, optional) – ANGLE or ANGLEH, by default False

• convertToQuartic (bool, optional) – auto convert, by default False

add_new_atom(ATNM: int = 0, MRES: int = 0, PANM: str = '_', IAC: int = 1, MASS: float = 1.0, CG: int = 0, CGC: int = 1, INE: list = [], INE14: list = [], verbose=False, C6: Optional[float] = None, C12: Optional[float] = None, CS6: float = 0, CS12: float = 0, IACname: Optional[str] = None)

add a atom to a system (with creating a new atomtype if needed and adding LJ parameters if needed)

Parameters

• ATNM (int, optional) – number of the atom in the system, by default 0

• MRES (int, optional) – residue number, by default 0

• PANM (str, optional) – name of the atom, by default ‘_’

• IAC (int, optional) – atomtype number of the atom, by default 1

• MASS (float, optional) – mass of the atom, by default 1.0

• CG (int, optional) – charge of the atom, by default 0

• CGC (int, optional) – charge group bool, by default 1

• INE (list, optional) – INE list, by default []

• INE14 (list, optional) – INE14 list, by default []

• C6 (float, optional) – C6 value, by default None

• C12 (float, optional) – C12 value, by default None

• CS6 (float, optional) – CS6 value, by default 0

• CS12 (float, optional) – CS12 value, by default 0

• IACname (str, optional) – new IACname if NONE PANM is used, by default None

add_new_atomtype(name: str, verbose: bool = False)

add a atomtype to ATOMTYPENAME block

Parameters

• name (str) – new atomtype name

• verbose (bool, optional) – by default False

add_new_bond(k: float, b0: float, atomI: int, atomJ: int, includesH: bool = False, verbose: bool = False)

add a bond between atom I and J to the BOND block

Parameters

• k (float) – force konstant

• b0 (float) – distance at which the force is 0

• atomI (int) – atom I

• atomJ (int) – atom J

• includesH (bool, optional) – wheter it should be added to BOND or BONDH, by default False

add_new_crossdihedral(verbose: bool = False)

add_new_impdihedral(CQ: float, Q0: float, atomI: int, atomJ: int, atomK: int, atomL: int, includesH: bool = False, verbose: bool = False)

add a new impdihedral

Parameters

• CQ (float) – force constant

• Q0 (float) – Q0

• atomI (int) – atom I

• atomJ (int) – atom J

• atomK (int) – atom K

• atomL (int) – atom L

• includesH (bool, optional) – IMPDIHEDRALH or IMPDIHEDRAL, by default False

add_new_impdihedral_type(CQ: float, Q0: float, verbose: bool = False)

add a new impodihedraltype

Parameters

• CQ (float) – force constant

• Q0 (float) – Q0

add_new_resname(name: str, verbose: bool = False)

add a resname to the RESNAME block

Parameters

• name (str) – resname name

• verbose (bool, optional) – by default False

add_new_soluteatom(ATNM: int = 0, MRES: int = 0, PANM: str = '', IAC: int = 0, MASS: float = 0, CG: float = 0, CGC: int = 0, INE: list = [], INE14: list = [], verbose: bool = False)

add a soluteatom to the SOLUTEATOM block

add_new_torsiondihedral(CP: float, PD: float, NP: int, atomI: int, atomJ: int, atomK: int, atomL: int, includesH: bool = False, verbose: bool = False)

add a torsiondihedral between atom I, J, K and L to the TORSIONDIHEDRAL block

Parameters

• CP (float) – force constant

• PD (float) – phase

• NP (int) – multiplicity

• atomI (int) – atom I

• atomJ (int) – atom J

• atomK (int) – atom K

• atomL (int) – atom L

• includesH (bool, optional) – DIHEDRAL or DIHEDRALH, by default False

find_LJparameterNumber(C12: float, C6: float) → int

find the LJ parameter number

get_LJparameter_from_IAC(IAC: int)

get the LJ parameter from the IAC number

Parameters

IAC (int) – [description]

get_diff_to_top(top: pygromos.utils.typing.Top_Type)

get_mass() → float

Calculates the total mass of the solute molecule

Returns

total mass in a.u.

Return type

float

get_num_atomtypes() → int

harmonic2quarticAngleConversion(kh: float, b0: float)

conversion of a harmonic bondanglebending force constant to a cubic in cosine/quartic one

Parameters

• kh (float) – harmonic bondanglebending force constant (CHT)

• b0 (float) – bondangle 0

Returns

cubic in cosine force constant (CT)

Return type

float

make_ordered(orderList: Optional[list] = None)

multiply_top(n_muliplication: int, unifyGroups: bool = False, verbose: bool = False) → pygromos.utils.typing.Top_Type

read_file()

give back the content. WARNING DEAPRECEATED.

Warning

DEAPRECEATED

Returns

key is the block name of the gromos file, any is the content of a block

Return type

Dict[str, any]

pygromos.files.topology.top.check_top()

pygromos.files.topology.top.combine_topologies()

pygromos.files.topology.top.make_topolog(input_arg, build, param, seq, solve='H2O')

Module contents