pygromos.files.blocks package¶

Submodules¶

pygromos.files.blocks.coord_blocks module¶

class pygromos.files.blocks.coord_blocks.GENBOX(pbc: pygromos.files.blocks.coord_blocks.Pbc = Pbc.vacuum, length: List[float] = [0.0, 0.0, 0.0], angles: List[float] = [0.0, 0.0, 0.0], euler: List[float] = [0.0, 0.0, 0.0], origin: List[float] = [0.0, 0.0, 0.0], content=None)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_gromos_block

This Block is representing the simulation Box in a coordinate file.

Variables

~GENBOX.pbc (int,Pbc) – Periodic Boundary Condition
~GENBOX.length (List[float]) –
~GENBOX.angles (List[float]) –
~GENBOX.euler (List[float]) –
~GENBOX.origin (List[float]) –

__init__(pbc: pygromos.files.blocks.coord_blocks.Pbc = Pbc.vacuum, length: List[float] = [0.0, 0.0, 0.0], angles: List[float] = [0.0, 0.0, 0.0], euler: List[float] = [0.0, 0.0, 0.0], origin: List[float] = [0.0, 0.0, 0.0], content=None)[source]¶

Parameters

pbc (int,Pbc)
length (List[float])
angles (List[float])
euler (List[float])
origin (List[float])

property angles: List[float]¶

block_to_string() → str[source]¶

comment: str¶

content: Iterable¶

property euler: List[float]¶

property length: List[float]¶

property origin: List[float]¶

property pbc: pygromos.files.blocks.coord_blocks.Pbc¶

read_content_from_str(content: List[str])[source]¶

class pygromos.files.blocks.coord_blocks.LATTICESHIFTS(content: List[pygromos.files.blocks.coord_blocks.lattice_shift])[source]¶

Bases: pygromos.files.blocks._general_blocks._iterable_gromos_block

Parameters: content (List[lattice_shift]) – every element in this list is a lattice shift obj

__init__(content: List[pygromos.files.blocks.coord_blocks.lattice_shift])[source]¶

Parameters: content (List[lattice_shift]) – every element in this list is a lattice shift obj

comment: str¶

read_content_from_str(content: List[str])[source]¶

class pygromos.files.blocks.coord_blocks.PERTDATA(content: List[str])[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_gromos_block

__init__(content: List[str])[source]¶

This block is used for lambda-sampling and gives the lambda value of the current coordinates.

Parameters: lambda_value (float) – current lambda value

content: float¶

property lam: float¶

read_content_from_str(content: List[str])[source]¶

class pygromos.files.blocks.coord_blocks.POSITION(content: List[pygromos.files.blocks.coord_blocks.atomP])[source]¶

Bases: pygromos.files.blocks._general_blocks._iterable_gromos_block

Parameters: content (List[atomP]) – every element in this list is of atom position obj

comment: str¶

read_content_from_str(content: List[str])[source]¶

class pygromos.files.blocks.coord_blocks.POSRESSPEC(content: List[pygromos.files.blocks.coord_blocks.atomP])[source]¶

Bases: pygromos.files.blocks._general_blocks._iterable_gromos_block

POSITION

Parameters: content (List[atomP]) – every element in this list is of atom position obj

comment: str¶

read_content_from_str(content: List[str])[source]¶

class pygromos.files.blocks.coord_blocks.Pbc(value)[source]¶

Bases: enum.Enum

An enumeration.

rectangular = 1¶

triclinic = 2¶

trunc_octahedron = -1¶

vacuum = 0¶

class pygromos.files.blocks.coord_blocks.REFPOSITION(content: List[pygromos.files.blocks.coord_blocks.atomP])[source]¶

Bases: pygromos.files.blocks._general_blocks._iterable_gromos_block

Parameters: content (List[atomP]) – every element in this list is of atom position obj

__init__(content: List[pygromos.files.blocks.coord_blocks.atomP])[source]¶

Parameters: content (List[atomP]) – every element in this list is of atom position obj

comment: str¶

read_content_from_str(content: List[str])[source]¶

class pygromos.files.blocks.coord_blocks.STOCHINT(content: List[pygromos.files.blocks.coord_blocks.atomSI])[source]¶

Bases: pygromos.files.blocks._general_blocks._iterable_gromos_block

Parameters

content (List[atomSI]) – every element in this list is of atom stochastic interval obj
seed (str) – contains the seed for the stochastic dynamics simulation

block_to_string() → str[source]¶

comment: str¶

read_content_from_str(content: List[str])[source]¶

class pygromos.files.blocks.coord_blocks.VELOCITY(content: List[pygromos.files.blocks.coord_blocks.atomV])[source]¶

Bases: pygromos.files.blocks._general_blocks._iterable_gromos_block

Parameters: content (List[atomV]) – every element in this list is of atom velocity obj

comment: str¶

read_content_from_str(content: List[str])[source]¶

class pygromos.files.blocks.coord_blocks.atomP(resID: int, resName: str, atomType: str, atomID: int, xp: float, yp: float, zp: float)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

__init__(resID: int, resName: str, atomType: str, atomID: int, xp: float, yp: float, zp: float)[source]¶

Parameters

resID
resName
atomType
atomID
xp
yp
zp

to_string() → str[source]¶

class pygromos.files.blocks.coord_blocks.atomSI(resID: int, resName: str, atomType: str, atomID: int, sxx: float, sxy: float, sxz: float)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

to_string() → str[source]¶

class pygromos.files.blocks.coord_blocks.atomV(resID: int, resName: str, atomType: str, atomID: int, xv: float, yv: float, zv: float)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

to_string() → str[source]¶

class pygromos.files.blocks.coord_blocks.lattice_shift(atomID: int, x: float, y: float, z: float)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

to_string() → str[source]¶

pygromos.files.blocks.imd_blocks module¶

class pygromos.files.blocks.imd_blocks.AMBER(AMBER: int = 0, AMBSCAL: int = 0, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks.imd_blocks._generic_imd_block

AMBER block

Variables

~AMBER.Amber (bool) –
~AMBER.AMBSCAL (float) –

AMBSCAL: float¶

Amber: bool¶

name: str = 'AMBER'¶

class pygromos.files.blocks.imd_blocks.BOUNDCOND(NTB: int = 0, NDFMIN: int = 0, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks.imd_blocks._generic_imd_block

Boundary Condition Block

This block describes the boundary condition of the coordinate system.

Variables

~BOUNDCOND.NTB (int, optional) –
Boundary conditions, by default 0 -1 : truncated octahedral

0 : vacuum 1 : rectangular 2 : triclinic
~BOUNDCOND.NDFMIN (int, optional) – number of degrees of freedom subtracted for temperature, by default 0

NDFMIN: int¶

NTB: int¶

name: str = 'BOUNDCOND'¶

class pygromos.files.blocks.imd_blocks.COMTRANSROT(NSCM: int = 0, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks.imd_blocks._generic_imd_block

COMTRANSROT block

This block controls the center of mass translation and rotation removal. (flying ice cube problem)

Variables: ~COMTRANSROT.NSCM (int) – controls system centre-of-mass (com) motion removal 0: no com motion removal (default) < 0: com translation and rotation are removed every abs(NSCM) steps. > 0: com translation is removed every NSCM steps.

NSCM: int¶

name: str = 'COMTRANSROT'¶

class pygromos.files.blocks.imd_blocks.CONSTRAINT(NTC: int = 0, NTCP: int = 0, NTCP0: float = 0, NTCS: int = 0, NTCS0: float = 0, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks.imd_blocks._generic_imd_block

CONSTRAINT block: This block is controlling constraining the atoms during a simulation.

Variables

~CONSTRAINT.NTC (int) –
~CONSTRAINT.NTCP (int) –
~CONSTRAINT.NTCP0 (int) –
~CONSTRAINT.NTCS (int) –
~CONSTRAINT.NTCS0 (int) –

NTC: int¶

NTCP: int¶

NTCP0: float¶

NTCS: int¶

NTCS0: float¶

__init__(NTC: int = 0, NTCP: int = 0, NTCP0: float = 0, NTCS: int = 0, NTCS0: float = 0, content: Optional[List[str]] = None)[source]¶

Args:: NTC: NTCP: NTCP0: NTCS: NTCS0:

name: str = 'CONSTRAINT'¶

class pygromos.files.blocks.imd_blocks.COVALENTFORM(NTBBH: int = 0, NTBAH: int = 0, NTBDN: int = 0, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks.imd_blocks._generic_imd_block

COVALENTFORM Block

The COVALENTFORM Block manages the functional form of the Bonded contributions to the force field. It is optional in an imd file to define the block.

Variables

~COVALENTFORM.NTBBH (int) – 0,1 controls bond-stretching potential 0: quartic form (default) 1: harmonic form
~COVALENTFORM.NTBAH (int) – 0,1 controls bond-angle bending potential 0: cosine-harmonic (default) 1: harmonic
~COVALENTFORM.NTBDN (int) – 0,1 controls torsional dihedral potential 0: arbitrary phase shifts (default) 1: phase shifts limited to 0 and 180 degrees.

NTBAH: int¶

NTBBH: int¶

NTBDN: int¶

name = 'COVALENTFORM'¶

class pygromos.files.blocks.imd_blocks.DISTANCERES(NTDIR: int = 0, NTDIRA: int = 0, CDIR: int = 0, DIR0: int = 0, TAUDIR: int = 1, FORCESCALE: int = 0, VDIR: int = 0, NTWDIR: int = 0, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks.imd_blocks._generic_imd_block

DISTANCERES Block

CDIR: int¶

DIR0: int¶

FORCESCALE: int¶

NTDIR: int¶

NTDIRA: int¶

NTWDIR: int¶

TAUDIR: int¶

VDIR: int¶

__init__(NTDIR: int = 0, NTDIRA: int = 0, CDIR: int = 0, DIR0: int = 0, TAUDIR: int = 1, FORCESCALE: int = 0, VDIR: int = 0, NTWDIR: int = 0, content: Optional[List[str]] = None)[source]¶

Args:: NTDIR: NTDIRA: CDIR: DIR0: TAUDIR: FORCESCALE: VDIR: NTWDIR:

name = 'DISTANCERES'¶

class pygromos.files.blocks.imd_blocks.EDS(NUMSTATES: int = 0, S: float = 0, EIR: List[float] = [], EDS: bool = 1, ALPHLJ: float = 0.0, ALPHC: float = 0.0, FUNCTIONAL: int = 1, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks.imd_blocks._generic_imd_block

EDS block

This block is used in an EDS simulation.

Variables

~EDS.NUMSTATES (int) – EDS-States
~EDS.S (float) – smoothness parameter
~EDS.EIR (List[float]) – energy offsets
~EDS.EDS (bool, optional) – turn on EDS_simulation
~EDS.ALPHLJ (float, optional) –
~EDS.ALPHC (float, optional) –
~EDS.FUNCTIONAL (int, optional) – 1: Single s Hamiltonian (default) 2: Hamiltonian with NUMSTATES*(NUMSTATES-1)/2 (pairwise) S parameters ==> changes type of S 3: Hamiltonian with (NUMSTATES-1) S parameters ==> changes type of S

read_content_from_str(content: List[str])[source]¶

class pygromos.files.blocks.imd_blocks.ENERGYMIN(NTEM: int = 0, NCYC: int = 0, DELE: float = 0, DX0: float = 0, DXM: float = 0, NMIN: int = 0, FLIM: float = 0, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks.imd_blocks._generic_imd_block

ENERGYMIN block This block takes care of managing the Energyminimization controls.

Variables

~ENERGYMIN.NTEM (int) – controls energy minimisation mode. 0: do not do energy minimisation (default) 1: steepest-descent minimisation 2: Fletcher-Reeves conjugate-gradient minimisation 3: Polak-Ribiere conjugate-gradient minimisation
~ENERGYMIN.NCYC (int) – >0 number of steps before resetting the conjugate-gradient search direction =0 reset only if the energy grows in the search direction
~ENERGYMIN.DELE (float) – >0.0 energy threshold for convergence >0.0 (conjugate-gradient) RMS force threshold for convergence
~ENERGYMIN.DX0 (float) – >0.0 initial step size
~ENERGYMIN.DXM (float) – >0.0 maximum step size
~ENERGYMIN.NMIN (float) – >0 minimum number of minimisation steps
~ENERGYMIN.FLIM (float) – >=0.0 limit force to maximum value (FLIM > 0.0 is not recommended)

DELE: float¶

DX0: float¶

DXM: float¶

FLIM: float¶

NCYC: int¶

NMIN: int¶

NTEM: int¶

name = 'ENERGYMIN'¶

class pygromos.files.blocks.imd_blocks.FORCE(BONDS: bool = True, ANGLES: bool = True, IMPROPER: bool = True, DIHEDRAL: bool = True, ELECTROSTATIC: bool = True, VDW: bool = True, NEGR: int = 0, NRE: List[int] = [], content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks.imd_blocks._generic_imd_block

FORCE Block: this Block is controlling the forcefield options. It can turn on and of terms, as well as generate force sub groups for analysis.

Variables

~FORCE.BONDS (bool) –
~FORCE.ANGLES (bool) –
~FORCE.IMPROPER (bool) –
~FORCE.DIHEDRAL (bool) –
~FORCE.ELECTROSTATIC (bool) –
~FORCE.VDW (bool) –
~FORCE.NEGR (int) – Number of Energy subgroups
~FORCE.NRE (List[int]) – List of last atoms for Energy subgroups. (NRE len == NEGR)

ANGLES: bool¶

BONDS: bool¶

DIHEDRAL: bool¶

ELECTROSTATIC: bool¶

IMPROPER: bool¶

NEGR: int¶

NRE: List[int]¶

VDW: bool¶

__init__(BONDS: bool = True, ANGLES: bool = True, IMPROPER: bool = True, DIHEDRAL: bool = True, ELECTROSTATIC: bool = True, VDW: bool = True, NEGR: int = 0, NRE: List[int] = [], content: Optional[List[str]] = None)[source]¶

Args:: BONDS: ANGLES: IMPROPER: DIHEDRAL: ELECTROSTATIC: VDW: NEGR: NRE (list):

adapt_energy_groups(energy_groups: Dict[int, int])[source]¶

Change the Force groups.

Parameters

residues (Dict[int, int]) – the dictionary contains the forceGroups with the ID of the respective last atom.

{forceGroupID: lastAtom} = {1:12, 2:26, 3:128}

name: str = 'FORCE'¶

read_content_from_str(content: List[str])[source]¶

class pygromos.files.blocks.imd_blocks.INITIALISE(NTIVEL: bool = False, NTISHK: int = 0, NTINHT: bool = False, NTINHB: bool = False, NTISHI: bool = False, NTIRTC: bool = False, NTICOM: int = 0, NTISTI: bool = False, IG: int = 0, TEMPI: float = 0, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks.imd_blocks._generic_imd_block

INITIALISE block

This block controls the Initialisation of a simulation.

Variables

~INITIALISE.NTIVEL (bool) – 0,1 controls generation of initial velocities 0: read from configuration (default) 1: generate from Maxell distribution at temperature TEMPI
~INITIALISE.NTISHK (int) – 0..3 controls shaking of initial configuration 0: no intial SHAKE (default) 1: initial SHAKE on coordinates only 2: initial SHAKE on velocities only 3: initial SHAKE on coordinates and velocities
~INITIALISE.NTINHT (bool) – 0,1 controls generation of initial Nose-Hoover chain variables 0: read from configuration (default) 1: reset variables to zero.
~INITIALISE.NTINHB (bool) – 0,1 controls generation of initial Nose-Hoover (chain) barostat variables 0: read from strartup file (if applicable) (default) 1: reset variables to zero
~INITIALISE.NTISHI (bool) – 0,1 controls initial setting for lattice shift vectors 0: read from configuration (default) 1: reset shifts to zero.
~INITIALISE.NTIRTC (bool) – 0,1 controls initial setting of positions and orientations for roto-translational constraints 0: read from configuration (default) 1: reset based on initial configuraion of startup file
~INITIALISE.NTICOM (int) – 0,1,2 controls initial removal of COM motion 0: no initial system COM motion removal (default) 1: initial COM translation is removed 2: initial COM rotation is removed
~INITIALISE.NTISTI (bool) – 0,1 controls generation of stochastic integrals 0: read stochastic integrals and IG from configuration (default) 1: set stochastic integrals to zero and use IG from here.
~INITIALISE.IG (int) – random number generator seed
~INITIALISE.TEMPI (float) – initial temperature

IG: int¶

NTICOM: int¶

NTINHB: bool¶

NTINHT: bool¶

NTIRTC: bool¶

NTISHI: bool¶

NTISHK: int¶

NTISTI: bool¶

NTIVEL: bool¶

TEMPI: float¶

__init__(NTIVEL: bool = False, NTISHK: int = 0, NTINHT: bool = False, NTINHB: bool = False, NTISHI: bool = False, NTIRTC: bool = False, NTICOM: int = 0, NTISTI: bool = False, IG: int = 0, TEMPI: float = 0, content: Optional[List[str]] = None)[source]¶

Args:: NTIVEL: NTISHK: NTINHT: NTINHB: NTISHI: NTIRTC: NTICOM: NTISTI: IG: TEMPI:

name = 'INITIALISE'¶

class pygromos.files.blocks.imd_blocks.INNERLOOP(NTILM: int = 0, NTILS: int = 0, NGPUS: int = 0, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks.imd_blocks._generic_imd_block

INNERLOOP block

Variables

~INNERLOOP.NTILM (int) –
~INNERLOOP.NTILS (int) –
~INNERLOOP.NGPUS (int) –

NGPUS: int¶

NTILM: int¶

NTILS: int¶

name = 'INNERLOOP'¶

class pygromos.files.blocks.imd_blocks.LAMBDA(NTIL: int = 0, NTLI: List[int] = [], NILG1: List[int] = [], NILG2: List[int] = [], ALI: List[float] = [], BLI: List[float] = [], CLI: List[float] = [], DLI: List[float] = [], ELI: List[float] = [], content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks.imd_blocks._generic_imd_block

LAMBDA block: This block is controlling the perturbation for free energy calculations.

Variables

~LAMBDA.NTIL (int) –
~LAMBDA.NTLI(1) (int or List[int]) –
~LAMBDA.NILG1(1) (int or List[int]) –
~LAMBDA.NILG2(1) (int or List[int]) –
~LAMBDA.ALI(1) (float or List[float]) –
~LAMBDA.BLI(1) (float or List[float]) –
~LAMBDA.CLI(1) (float or List[float]) –
~LAMBDA.DLI(1) (float or List[float]) –
~LAMBDA.ELI(1) (float or List[float]) –

ALI: List[float]¶

BLI: List[float]¶

CLI: List[float]¶

DLI: List[float]¶

ELI: List[float]¶

NILG1: List[int]¶

NILG2: List[int]¶

NTIL: int¶

NTLI: List[int]¶

name: str = 'LAMBDA'¶

class pygromos.files.blocks.imd_blocks.MULTIBATH(ALGORITHM: int = 0, NBATHS: int = 0, TEMP0: List[float] = [], TAU: List[float] = [], DOFSET: int = 0, LAST: List[int] = [], COMBATH: List[int] = [], IRBATH: List[int] = [], NUM: Optional[int] = None, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks.imd_blocks._generic_imd_block

MULTIBATH Block

This block controls the Thermostat of a simulation. Multiple temperature baths can be coupled.

Variables

~MULTIBATH.ALGORITHM (int) – temperature coupling algorithm weak-coupling(0) nose-hoover(1) nose-hoover-chains(2) num (where num is the number of chains to use)
~MULTIBATH.NUM (int, optional) – Mumber of chains in Nosé Hoover chains scheme [only specify when needed]
~MULTIBATH.NBATHS (int) – Number of temperature baths
~MULTIBATH.TEMP0 (List[float]) – temperature of each bath (list len == NBATHS)
~MULTIBATH.TAU (List[float]) – coupling of the temperaturebath to the system (list len == NBATHS)
~MULTIBATH.DOFSET (int) – Number of set of Degrees of freedom.
~MULTIBATH.LAST (List[int] (list len == DOFSET)) – Last atoms of each DOFSet
~MULTIBATH.COMBATH (List[int] (list len == DOFSET)) – Index of the temperature baths
~MULTIBATH.IRBATH (List[int] (list len == DOFSET)) – IRBAHT?

ALGORITHM: int¶

COMBATH: List[int]¶

DOFSET: int¶

IRBATH: List[int]¶

LAST: List[int]¶

NBATHS: int¶

NUM: int¶

TAU: List[float]¶

TEMP0: List[float]¶

adapt_multibath(last_atoms_bath: Dict[int, int], algorithm: Optional[int] = None, num: Optional[int] = None, T: Optional[Union[float, List[float]]] = None, TAU: Optional[float] = None) → None[source]¶

This function is adding each atom set into a single multibath.: #TODO implementation not correct with com_bath and irbath! Works for super simple cases though

Parameters

last_atoms_bath (Dict[int,int]) – lastatom:bath
algorithm (int) – int code for algorihtm
T (float,List[float], optional) – temperature value
TAU (float, optional) – coupling var

Return type

None

block_to_string() → str[source]¶

name: str = 'MULTIBATH'¶

read_content_from_str(content: List[str])[source]¶

class pygromos.files.blocks.imd_blocks.NEW_REPLICA_EDS(REEDS: bool = False, NRES: int = 0, NUMSTATES: int = 0, NEOFF: int = 0, RES: List[float] = [], EIR: List[List[float]] = [[]], NRETRIAL: int = 0, NREQUIL: int = 0, EDS_STAT_OUT: int = 0, CONT: bool = False, PERIODIC: int = 0, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks.imd_blocks._generic_imd_block

REPLICA_EDS Block

This block is controlling the REPLICA_EDS settings in gromos and is basically a mixture of EDS and RE block. (Don’t use them when using this block!)

Variables

~NEW_REPLICA_EDS.REEDS (bool) – Shall REEDS be activated?
~NEW_REPLICA_EDS.NRES (int) – Number of s-Values
~NEW_REPLICA_EDS.NEOFF (int) – number of replica exchange eds energy Offset vectors (only used for 2D REEDS - still needs to be present ;))
~NEW_REPLICA_EDS.NUMSTATES (int) – Number of EDS-states
~NEW_REPLICA_EDS.RES (List[float]) – s_values for all replicas
~NEW_REPLICA_EDS.EIR (List[List[float]]) – energy offsets for all replicas and all states List[List[float]] = REPLICA[EDS_STATE[EIR]]
~NEW_REPLICA_EDS.NERTRIAL (int) – How many replica exchanges trials should be executed? (NRETRIAL*STEP.NSTLIM == total simulation time)
~NEW_REPLICA_EDS.NREQUIL (int) – How many equilibration runs shall be exectured? (NREQUIL*STEP.NSTLIM == total simulation time)
~NEW_REPLICA_EDS.EDS_STAT_OUT (int) – Shall the replica exchange information be outputted? (__future__ frequency of output.)
~NEW_REPLICA_EDS.CONT (bool) – Is this a continuation run?

CONT: bool¶

EDS_STAT_OUT: int¶

EIR: List[float]¶

NEOFF: int¶

NREQUIL: int¶

NRES: int¶

NRETRIAL: int¶

NUMSTATES: int¶

PERIODIC: int¶

REEDS: bool¶

RES: List[float]¶

name: str = 'REPLICA_EDS'¶

read_content_from_str(content: List[str])[source]¶

class pygromos.files.blocks.imd_blocks.NONBONDED(NLRELE: int = 0, APPAK: float = 0, RCRF: float = 0, EPSRF: float = 0, NSLFEXCL: bool = False, NSHAPE: int = 0, ASHAPE: float = 0, NA2CLC: int = 0, TOLA2: str = 0, EPSLS: float = 0, NKX: int = 0, NKY: int = 0, NKZ: int = 0, KCUT: float = 0, NGX: int = 0, NGY: int = 0, NGZ: int = 0, NASORD: int = 0, NFDORD: int = 0, NALIAS: int = 0, NSPORD: int = 0, NQEVAL: int = 0, FACCUR: float = 0, NRDGRD: bool = False, NWRGRD: bool = False, NLRLJ: bool = False, SLVDNS: float = 0, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks.imd_blocks._generic_imd_block

NONBONDED block

This block is controlling the Nonbonded term evaluation

Variables

~NONBONDED.NLRELE (int) – 1-3 method to handle electrostatic interactions -1 : reaction-field (LSERF compatibility mode) 0 : no electrostatic interactions 1 : reaction-field 2 : Ewald method 3 : P3M method
~NONBONDED.APPAK (float) – >= 0.0 reaction-field inverse Debye screening length
~NONBONDED.RCRF (float) – >= 0.0 reaction-field radius
~NONBONDED.EPSRF (float) – = 0.0 || > 1.0 reaction-field permittivity
~NONBONDED.NSLFEXCL (bool) – contribution of excluded atoms to reaction field false=off/true=on
~NONBONDED.NSHAPE (float) – -1..10 lattice sum charge-shaping function -1 : gaussian 0..10 : polynomial
~NONBONDED.ASHAPE (float) – > 0.0 width of the lattice sum charge-shaping function
~NONBONDED.NA2CLC (int) – 0..4 controls evaluation of lattice sum A2 term 0 : A2 = A2~ = 0 1 : A2~ exact, A2 = A2~ 2 : A2 numerical, A2~ = A2 3 : A2~ exact from Ewald or from mesh and atom coords, A2 numerical 4 : A2~ averaged from mesh only, A2 numerical
~NONBONDED.TOLA2 (float) – > 0.0 tolerance for numerical A2 evaluation
~NONBONDED.EPSLS (float) – = 0.0 || > 1.0 lattice sum permittivity (0.0 = tinfoil)
NKZ (NKX, NKY,) – > 0 maximum absolute Ewald k-vector components
~NONBONDED.KCUT (float) – > 0.0 Ewald k-space cutoff
NGZ (NGX, NGY,) – > 0 P3M number of grid points
~NONBONDED.NASORD (int) – 1..5 order of mesh charge assignment function
~NONBONDED.NFDORD (int) – 0..5 order of the mesh finite difference operator 0 : ik - differentiation 1..5 : finite differentiation
~NONBONDED.NALIAS (float) – > 0 number of mesh alias vectors considered
~NONBONDED.NSPORD (float) – order of SPME B-spline functions (not available)
~NONBONDED.NQEVAL (float) – >= 0 controls accuracy reevaluation 0 : do not reevaluate > 0 : evaluate every NQEVAL steps
~NONBONDED.FACCUR (float) – > 0.0 rms force error threshold to recompute influence function
~NONBONDED.NRDGRD (bool) – 0,1 read influence function 0 : calculate influence function at simulation start up 1 : read influence function from file (not yet implemented)
~NONBONDED.NWRGRD (bool) – 0,1 write influence function 0 : do not write 1 : write at the end of the simulation (not yet implemented)
~NONBONDED.NLRLJ (bool) – 0,1 controls long-range Lennard-Jones corrections 0 : no corrections 1 : do corrections (not yet implemented)
~NONBONDED.SLVDNS (float) – > 0.0 average solvent density for long-range LJ correction (ignored)

APPAK: float¶

ASHAPE: float¶

EPSLS: float¶

EPSRF: float¶

FACCUR: float¶

KCUT: float¶

NA2CLC: int¶

NALIAS: int¶

NASORD: int¶

NFDORD: int¶

NGX: int¶

NGY: int¶

NGZ: int¶

NKX: int¶

NKY: int¶

NKZ: int¶

NLRELE: int¶

NLRLJ: bool¶

NQEVAL: int¶

NRDGRD: bool¶

NSHAPE: int¶

NSLFEXCL: bool¶

NSPORD: int¶

NWRGRD: bool¶

RCRF: float¶

SLVDNS: float¶

TOLA2: str¶

name: str = 'NONBONDED'¶

class pygromos.files.blocks.imd_blocks.PAIRLIST(ALGORITHM: int = 0, NSNB: int = 0, RCUTP: float = 0, RCUTL: float = 0, SIZE: Union[str, float] = 0, TYPE: Union[str, bool] = False, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks.imd_blocks._generic_imd_block

PAIRLIST Block

This block is controlling the pairlist control.

Variables

~PAIRLIST.ALGORITHM (int) – standard(0) (gromos96 like pairlist) grid(1) (md++ grid pairlist) grid_cell(2) (creates a mask)
~PAIRLIST.NSNB (int) – frequency (number of steps) a pairlist is constructed
~PAIRLIST.RCUTPL (float) – short-range cut-off in twin-range
~PAIRLIST.RCUTL (float) – intermediate-range cut-off in twin-range
~PAIRLIST.SIZE (str, float) – grid cell size (or auto = 0.5 * RCUTP)
~PAIRLIST.TYPE (str, bool) – chargegoup(0) (chargegroup based cutoff) atomic(1) (atom based cutoff)

ALGORITHM: int¶

NSNB: int¶

RCUTL: float¶

RCUTPL: float¶

SIZE: Union[str, float]¶

TYPE: Union[str, bool]¶

__init__(ALGORITHM: int = 0, NSNB: int = 0, RCUTP: float = 0, RCUTL: float = 0, SIZE: Union[str, float] = 0, TYPE: Union[str, bool] = False, content: Optional[List[str]] = None)[source]¶

Args:: ALGORITHM: NSNB: RCUTP: RCUTL: SIZE: TYPE:

name: str = 'PAIRLIST'¶

class pygromos.files.blocks.imd_blocks.PERTURBATION(NTG: int = 0, NRDGL: int = 0, RLAM: float = 0, DLAMT: float = 0, ALPHLJ: float = 0, ALPHC: float = 0, NLAM: int = 0, NSCALE: int = 0, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks.imd_blocks._generic_imd_block

Pertubation Block

This block is for Thermodynamic integration

Variables

~PERTURBATION.NTG (int) – 0..1 controls use of free-energy calculation. 0: no free-energy calculation (default) 1: calculate dH/dRLAM
~PERTURBATION.NRDGL (int) – 0,1 controls reading of initial value for RLAM. 0: use initial RLAM parameter from PERTURBATION block 1: read from configuration
~PERTURBATION.RLAM (float) – 0.0..1.0 initial value for lambda
~PERTURBATION.DLAMT (float) – >= 0.0 rate of lambda increase in time.
~PERTURBATION.ALPHLJ (float) – >= 0.0 Lennard-Jones soft-core parameter
~PERTURBATION.ALPHC (float) – >= 0.0 Coulomb-RF soft-core parameter
~PERTURBATION.NLAM (int) – > 0 power dependence of lambda coupling
~PERTURBATION.NSCALE (int) –
0..2 controls use of interaction scaling 0: no interaction scaling 1: interaction scaling 2: perturbation for all atom pairs with scaled

interactions. No perturbation for others.
~PERTURBATION.ExampleBlock –
~PERTURBATION.____________ –
DLAMT (# NTG NRDGL RLAM) – 1 0 0.0 0.0
NSCALE (# ALPHLJ ALPHC NLAM) – 0.5 0.5 2 0

ALPHC: float¶

ALPHLJ: float¶

DLAMT: float¶

NLAM: int¶

NRDGL: int¶

NSCALE: int¶

NTG: int¶

RLAM: float¶

name: str = 'PERTURBATION'¶

class pygromos.files.blocks.imd_blocks.POSITIONRES(NTPOR: int = 0, NTPORB: int = 0, NTPORS: int = 0, CPOR: int = 0, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks.imd_blocks._generic_imd_block

POSITIONRES block

This block allows the managment of the Position Restraints during the Simulation.

Variables

~POSITIONRES.NTPOR (int) – 0..3 controls atom positions re(con)straining. 0: no position re(con)straints (default) 1: restraining with force constant CPOR 2: restraining with force constant CPOR weighted by atomic B-factors 3: constraining
~POSITIONRES.NTPORB (int) – 0,1 controls reading of reference positions and B-factors 0: read reference positions from startup file. 1: read reference positions and B-factors from special file
~POSITIONRES.NTPORS (int) – 0,1 controls scaling of reference positions upon pressure scaling 0: do not scale reference positions 1: scale reference positions
~POSITIONRES.CPOR (int) – >= 0 position restraining force constant

CPOR: int¶

NTPOR: int¶

NTPORB: int¶

NTPORS: int¶

name = 'POSITIONRES'¶

class pygromos.files.blocks.imd_blocks.PRECALCLAM(NRLAM: int = 0, MINLAM: float = 0, MAXLAM: float = 0, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks.imd_blocks._generic_imd_block

Variables: ~PRECALCLAM.NTG (int) –

MAXLAM: float¶

MINLAM: float¶

NRLAM: int¶

__init__(NRLAM: int = 0, MINLAM: float = 0, MAXLAM: float = 0, content: Optional[List[str]] = None)[source]¶

Can be used to caluclate multiple extra lambda values

Parameters

NRLAM (int) – 0 : off >1 : precalculating energies for NRLAM extra lambda values
MINLAM – between 0 and 1: minimum lambda value to precalculate energies
MAXLAM – between MINLAM and 1: maximum lambda value to precalculate energies

name = 'PRECALCLAM'¶

class pygromos.files.blocks.imd_blocks.PRESSURESCALE(COUPLE: int = 0, SCALE: int = 0, COMP: float = 0, TAUP: float = 0, VIRIAL: int = 0, SEMIANISOTROPIC: List[int] = [], PRES0: List[List[float]] = [[0, 0, 0], [0, 0, 0], [0, 0, 0]], content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks.imd_blocks._generic_imd_block

PRESSURESCALE Block This block controls the barostat of the simulation

Variables

~PRESSURESCALE.COUPLE (int) – off(0), calc(1), scale(2)
~PRESSURESCALE.SCALE (int) – off(0), iso(1), aniso(2), full(3), semianiso(4)
~PRESSURESCALE.COMP (float) – compessibility
~PRESSURESCALE.TAUP (float) – coupling strength
~PRESSURESCALE.VIRIAL (int) – none(0), atomic(1), group(2)
~PRESSURESCALE.SEMIANISOTROPIC (List[int]) – (semianisotropic couplings: X, Y, Z) e.g. 1 1 2: x and y jointly coupled and z separately coupled e.g. 0 0 1: constant area (xy-plane) and z coupled to a bath
~PRESSURESCALE.PRES0 (List[List[float]]) – reference pressure

COMP: float¶

COUPLE: int¶

PRES0: List[List[float]]¶

SCALE: int¶

SEMIANISOTROPIC: List[int]¶

TAUP: float¶

VIRIAL: int¶

name: str = 'PRESSURESCALE'¶

read_content_from_str(content: List[str])[source]¶

class pygromos.files.blocks.imd_blocks.PRINTOUT(NTPR: int = 0, NTPP: int = 0, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks.imd_blocks._generic_imd_block

PRINTOUT block

This Block manages the output frequency into the .omd/std-out file.

Variables

~PRINTOUT.NTPR (int) – print out energies, etc. every NTPR steps
~PRINTOUT.NTPP (int) – =1 perform dihedral angle transition monitoring

NTPP: int¶

NTPR: int¶

name: str = 'PRINTOUT'¶

class pygromos.files.blocks.imd_blocks.QMMM(NTQMMM: int = 0, NTQMSW: int = 0, RCUTQ: float = 0.0, NTWQMMM: int = 0, QMLJ: int = 0, MMSCAL: float = - 1.0, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks.imd_blocks._generic_imd_block

QMMM Block

The QMMM block describes how to treat an embedded QM zone

Variables

~QMMM.NTQMMM (int) – Define if QM/MM is applied (1) or not (0, default)
~QMMM.NTQMSW (int) – QM software package to use. Available options are MNDO (0, default), Turbomole (1), DFTB (2), MOPAC (3), ORCA (4), and XTB (5)
~QMMM.RCUTQ (float) – Cutoff for inclusion of MM charge groups. If the value is 0, all particles are considered.
~QMMM.NTWQMMM (int) – Write QM/MM related data to special trajectory every NTWQMMM step. Switch off with 0.
~QMMM.QMLJ (int) – Define if LJ interaction is activated in the QM zone (1) or not (0).
~QMMM.MMSCAL (float) – Scale MM charges with (2/pi)*atan(x*(r_{mm}-r_{mm})). Values > 0.0 describe the scaling factor, values < 0.0 turn off scaling (default).

MMSCAL: float¶

NTQMMM: int¶

NTQMSW: int¶

NTWQMMM: int¶

QMLJ: int¶

RCUTQ: float¶

name: str = 'QMMM'¶

class pygromos.files.blocks.imd_blocks.RANDOMNUMBERS(NTRNG: int = 0, NTGSL: int = 0, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks.imd_blocks._generic_imd_block

Random Numbers Block

NTGSL: int¶

NTRNG: int¶

name: str = 'RANDOMNUMBERS'¶

class pygromos.files.blocks.imd_blocks.REPLICA(RETL: bool = False, NRET: int = 0, RET: List[float] = [], LRESCALE: int = 0, NRELAM: int = 0, RELAM: List[float] = [], RETS: List[float] = [], NRETRIAL: int = 0, NREQUIL: int = 0, CONT: bool = False, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks.imd_blocks._generic_imd_block

REPLICA Block

This block is controlling the REPLICA settings in gromos. It works both for T-REMD and H-REMD

Variables

~REPLICA.RETL (bool) – Do you want to rund an RE simulation or not? RETL=0 : turn off RE RETL=1 : turn on RE
~REPLICA.NRET (int) – Number of temperatures
~REPLICA.RET (List[float]) – List of temperature at each replica
~REPLICA.LRESCALE (bool) – controls temperature scaling 0 don’t scale temperatures after exchange trial 1 scale temperatures after exchange trial
~REPLICA.NRELAM (int) – number of lambda values
~REPLICA.RELAM (List[float]) – lambda value for each lambda-replica
~REPLICA.RETS (List[float]) – timestep of each LAMBDA replica
~REPLICA.NRETRIAL (int) – How many replica exchanges trials should be executed? (NRETRIAL*STEP.NSTLIM == total simulation time)
~REPLICA.NREQUIL (int) – How many equilibration runs shall be exectured? (NREQUIL*STEP.NSTLIM == total simulation time)
~REPLICA.CONT (bool) – Is this a continuation run? 0 start from one configuration file 1 start from multiple configuration files

# RETL 1 # NRET 10 # RET(1..NRET) 300.0 320.0 340.0 360.0 380.0 400.0 420.0 440.0 460.0 480.0 # LRESCALE 1 # NRELAM 10 # RELAM(1..NRELAM 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 # RETS(1..NRELAM) 0.002 0.001 0.001 0.001 0.002 0.003 0.002 0.001 0.001 0.002 # NRETRIAL 100 # NREQUIL 10 # CONT 0 END

CONT: bool¶

LRESCALE: bool¶

NRELAM: int¶

NREQUIL: int¶

NRET: int¶

NRETRIAL: int¶

RELAM: List[float]¶

RET: List[float]¶

RETL: bool¶

RETS: List[float]¶

name: str = 'REPLICA'¶

read_content_from_str(content: List[str])[source]¶

class pygromos.files.blocks.imd_blocks.REPLICA_EDS(REEDS: bool = True, NRES: int = 0, NUMSTATES: int = 0, RES: List[float] = [0], EIR: List[List[float]] = [[0]], NRETRIAL: int = 0, NREQUIL: int = 0, EDS_STAT_OUT: int = 0, CONT: bool = True, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks.imd_blocks._generic_imd_block

CONT: bool¶

EDS_STAT_OUT: int¶

EIR: List[float]¶

NREQUIL: int¶

NRES: int¶

NRETRIAL: int¶

NUMSTATES: int¶

REEDS: bool¶

RES: List[float]¶

__init__(REEDS: bool = True, NRES: int = 0, NUMSTATES: int = 0, RES: List[float] = [0], EIR: List[List[float]] = [[0]], NRETRIAL: int = 0, NREQUIL: int = 0, EDS_STAT_OUT: int = 0, CONT: bool = True, content: Optional[List[str]] = None)[source]¶

REPLICA_EDS Block

This block is controlling the REPLICA_EDS settings in gromos and is basically a mixture of EDS and RE block. (Don’t use them when using this block!)

Variables

~REPLICA_EDS.__init__.REEDS (bool) – Shall REEDS be activated?
~REPLICA_EDS.__init__.NRES (int) – Number of s-Values
~REPLICA_EDS.__init__.NUMSTATES (int) – Number of EDS-states
~REPLICA_EDS.__init__.RES (List[float]) – s_values for all replicas
~REPLICA_EDS.__init__.EIR (List[List[float]]) – energy offsets for all replicas and all states List[List[float]] = REPLICA[EDS_STATE[EIR]]
~REPLICA_EDS.__init__.NERTRIAL (int) – How many replica exchanges trials should be executed? (NRETRIAL*STEP.NSTLIM == total simulation time)
~REPLICA_EDS.__init__.NREQUIL (int) – How many equilibration runs shall be exectured? (NREQUIL*STEP.NSTLIM == total simulation time)
~REPLICA_EDS.__init__.EDS_STAT_OUT (int) – Shall the replica exchange information be outputted? (__future__ frequency of output.)
~REPLICA_EDS.__init__.CONT (bool) – Is this a continuation run?

name: str = 'REPLICA_EDS'¶

read_content_from_str(content: List[str])[source]¶

class pygromos.files.blocks.imd_blocks.ROTTRANS(RTC: int = 0, RTCLAST: int = 0, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks.imd_blocks._generic_imd_block

Roto-translational block

This block is for roto-translational constraints. Note: use either centre of mass removal or roto-translational constraints but not both!

Variables

~ROTTRANS.RTC (int) – turn roto-translational constraints on (1)
~ROTTRANS.RTCLAST (int) – last atom of subset to be roto-translationally constrained

RTC: int¶

RTCLAST: int¶

name: str = 'ROTTRANS'¶

class pygromos.files.blocks.imd_blocks.STEP(NSTLIM: int = 0, T: float = 0, DT: float = 0, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks.imd_blocks._generic_imd_block

Step Block

This Block gives the number of simulation steps,

Variables

~STEP.NSTLIM (int) – number of simulations Step till terminating.
~STEP.T (float) – Starting Time
~STEP.DT (float) – time step [fs]

DT: float¶

NSTLIM: int¶

T: float¶

name: str = 'STEP'¶

class pygromos.files.blocks.imd_blocks.STOCHDYN(NTSD: int = 0, NTFR: int = 0, NSFR: int = 0, NBREF: int = 0, RCUTF: float = 0, CFRIC: float = 0, TEMPSD: float = 0, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks.imd_blocks._generic_imd_block

Stochastic Dynamics block

This block is for Stochastic Dynamics

Variables

~STOCHDYN.NTSD (int) –
~STOCHDYN.NTFR (int) –
~STOCHDYN.NSFR (int) –
~STOCHDYN.NBREF (int) –
~STOCHDYN.RCUTF (float) –
~STOCHDYN.CFRIC (float) –
~STOCHDYN.TEMPSD (float) –

CFRIC: float¶

NBREF: int¶

NSFR: int¶

NTFR: int¶

NTSD: int¶

RCUTF: float¶

TEMPSD: float¶

name: str = 'STOCHDYN'¶

class pygromos.files.blocks.imd_blocks.SYSTEM(NPM: int = 0, NSM: int = 0, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks.imd_blocks._generic_imd_block

System Block

The system block defines the number of solute molecules and solvent molecules

Variables

~SYSTEM.NPM (int) – Number of Solute Molecules
~SYSTEM.NSM (int) – Number of Solvent Molecules

NPM: int¶

NSM: int¶

name: str = 'SYSTEM'¶

class pygromos.files.blocks.imd_blocks.WRITETRAJ(NTWX: int = 0, NTWSE: int = 0, NTWV: int = 0, NTWF: int = 0, NTWE: int = 0, NTWG: int = 0, NTWB: int = 0, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks.imd_blocks._generic_imd_block

The WRITETRAJ Block manages the output frequency of GROMOS. Here you can determine how often a file should be written.

Variables

~WRITETRAJ.NTWX (int) – controls writing of coordinate trajectory 0: no coordinate trajectory is written (default) >0: write solute and solvent coordinates every NTWX steps <0: write solute coordinates every |NTWX| steps
~WRITETRAJ.NTWSE (int) – >= 0 selection criteria for coordinate trajectory writing 0: write normal coordinate trajectory >0: write minimum-energy coordinate and energy trajectory (based on the energy entry selected by NTWSE and as blocks of length NTWX) (see configuration/energy.cc or ene_ana library for indices)
~WRITETRAJ.NTWV (int) – controls writing of velocity trajectory 0: no velocity trajectory is written (default) >0: write solute and solvent velocities every NTWV steps <0: write solute velocities every |NTWV| steps
~WRITETRAJ.NTWF (int) – controls writing of force trajectory 0: no force trajectory is written (default) >0: write solute and solvent forces every NTWF steps <0: write solute forces every |NTWF| steps
~WRITETRAJ.NTWE (int) – >= 0 controls writing of energy trajectory 0: no energy trajectory is written (default) >0: write energy trajectory every NTWE steps
~WRITETRAJ.NTWG (int) – >= 0 controls writing of free energy trajectory 0: no free energy trajectory is written (default) >0: write free energy trajectory every NTWG steps
~WRITETRAJ.NTWB (int) –
>= 0 controls writing of block-averaged energy trajectory 0: no block averaged energy trajectory is written (default) >0: write block-averaged energy variables every |NTWB| steps

(and free energies if NTWG > 0) trajectory

NTWB: int¶

NTWE: int¶

NTWF: int¶

NTWG: int¶

NTWSE: int¶

NTWV: int¶

NTWX: int¶

__init__(NTWX: int = 0, NTWSE: int = 0, NTWV: int = 0, NTWF: int = 0, NTWE: int = 0, NTWG: int = 0, NTWB: int = 0, content: Optional[List[str]] = None)[source]¶

Args:: NTWX: NTWSE: NTWV: NTWF: NTWE: NTWG: NTWB:

name = 'WRITETRAJ'¶

pygromos.files.blocks.miscBlocks module¶

class pygromos.files.blocks.miscBlocks.ATOMNAMELIB(content: Union[List[str], Dict[str, Dict[str, str]]])[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_gromos_block

__init__(content: Union[List[str], Dict[str, Dict[str, str]]])[source]¶

atom name translation lib part of the resn lib

Parameters: content (Union[List[str], Dict[str, Dict[str, str]]])

block_to_string() → str[source]¶

fields = ['top_resn', 'atom_pdb', 'atom_top']¶

pdb_top: defaultdict(<class 'dict'>, {})¶

read_content_from_str(content: Union[List[str], Dict[str, Dict[str, str]]])[source]¶

class pygromos.files.blocks.miscBlocks.RESIDUENAMELIB(content: Union[str, List[str], Dict[str, Dict[str, str]]])[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_gromos_block

__init__(content: Union[str, List[str], Dict[str, Dict[str, str]]])[source]¶

content is the content for the residuenamelib

Parameters: content (Union[List[str], Dict[str, Dict[str, str]]])

block_to_string() → str[source]¶

fields = ['pdb_name', 'g96top_name']¶

pdb_top: defaultdict(<class 'list'>, {})¶

read_content_from_str(content: List[str])[source]¶

pygromos.files.blocks.mtb_blocks module¶

class pygromos.files.blocks.mtb_blocks.LINKEXCLUSIONS(FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, content=None)[source]¶

Bases: pygromos.files.blocks.mtb_blocks.mtb_blocks

FORCEFIELD: pygromos.files.blocks.topology_blocks.FORCEFIELD¶

MAKETOPVERSION: pygromos.files.blocks.topology_blocks.MAKETOPVERSION¶

NRNE: int¶

block_to_string() → str[source]¶

read_content_from_str(content: str)[source]¶

class pygromos.files.blocks.mtb_blocks.MTBUILDBLEND(FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, content=None)[source]¶

Bases: pygromos.files.blocks.mtb_blocks.mtb_blocks

FORCEFIELD: pygromos.files.blocks.topology_blocks.FORCEFIELD¶

MAKETOPVERSION: pygromos.files.blocks.topology_blocks.MAKETOPVERSION¶

angles: List[pygromos.files.blocks.mtb_blocks.mtb_angles_field]¶

atoms: List[pygromos.files.blocks.mtb_blocks.mtb_atoms_field]¶

block_to_string() → str[source]¶

bonds: List[pygromos.files.blocks.mtb_blocks.mtb_bonds_field]¶

dihedrals: List[pygromos.files.blocks.mtb_blocks.mtb_dihedral_field]¶

improper_dihedrals: List[pygromos.files.blocks.mtb_blocks.mtb_dihedral_field]¶

lj_exceptions: List[pygromos.files.blocks.mtb_blocks.mtb_lj_exceptions_field]¶

read_content_from_str(content: str)[source]¶

replacing_atoms: List[pygromos.files.blocks.mtb_blocks.mtb_trailing_atoms_field]¶

skip_lines: int = 2¶

class pygromos.files.blocks.mtb_blocks.MTBUILDBLSOLUTE(FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, content=None)[source]¶

Bases: pygromos.files.blocks.mtb_blocks.mtb_blocks

FORCEFIELD: pygromos.files.blocks.topology_blocks.FORCEFIELD¶

MAKETOPVERSION: pygromos.files.blocks.topology_blocks.MAKETOPVERSION¶

angles: List[pygromos.files.blocks.mtb_blocks.mtb_angles_field]¶

atoms: List[pygromos.files.blocks.mtb_blocks.mtb_atoms_field]¶

block_to_string() → str[source]¶

bonds: List[pygromos.files.blocks.mtb_blocks.mtb_bonds_field]¶

dihedrals: List[pygromos.files.blocks.mtb_blocks.mtb_dihedral_field]¶

improper_dihedrals: List[pygromos.files.blocks.mtb_blocks.mtb_dihedral_field]¶

lj_exceptions: List[pygromos.files.blocks.mtb_blocks.mtb_lj_exceptions_field]¶

preceding_exclusions: List[pygromos.files.blocks.mtb_blocks.mtb_preceding_exclusions_field]¶

read_content_from_str(content: str)[source]¶

skip_lines: int = 2¶

trailing_atoms: List[pygromos.files.blocks.mtb_blocks.mtb_trailing_atoms_field]¶

class pygromos.files.blocks.mtb_blocks.MTBUILDBLSOLVENT(FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, content=None)[source]¶

Bases: pygromos.files.blocks.mtb_blocks.mtb_blocks

FORCEFIELD: pygromos.files.blocks.topology_blocks.FORCEFIELD¶

MAKETOPVERSION: pygromos.files.blocks.topology_blocks.MAKETOPVERSION¶

atoms: List[pygromos.files.blocks.mtb_blocks.mtb_atoms_field]¶

block_to_string() → str[source]¶

constraints: List[pygromos.files.blocks.mtb_blocks.mtb_constraints_field]¶

read_content_from_str(content: str)[source]¶

class pygromos.files.blocks.mtb_blocks.mtb_angles_field(IB: int, JB: int, KB: int, MCB: int)[source]¶

Bases: pygromos.files.blocks.mtb_blocks.mtb_fields

to_string() → str[source]¶

class pygromos.files.blocks.mtb_blocks.mtb_atoms_field(ATOM: int, ANM: str, IACM: int, MASS: int, CGMI: float, CGM: int, MAE: int, MSAE: List[int])[source]¶

Bases: pygromos.files.blocks.mtb_blocks.mtb_fields

to_string() → str[source]¶

class pygromos.files.blocks.mtb_blocks.mtb_atoms_solvent_field(ATOM: int, ANM: str, IACM: int, MASS: int, CG: float)[source]¶

Bases: pygromos.files.blocks.mtb_blocks.mtb_fields

to_string() → str[source]¶

class pygromos.files.blocks.mtb_blocks.mtb_blocks(name: Optional[str] = None, used: Optional[bool] = None, content: Optional[str] = None)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_gromos_block

comment: str¶

content: Iterable¶

class pygromos.files.blocks.mtb_blocks.mtb_bonds_field(IB: int, JB: int, MCB: int)[source]¶

Bases: pygromos.files.blocks.mtb_blocks.mtb_fields

to_string() → str[source]¶

class pygromos.files.blocks.mtb_blocks.mtb_constraints_field(IB: int, JB: int, LENGTH: float)[source]¶

Bases: pygromos.files.blocks.mtb_blocks.mtb_fields

to_string() → str[source]¶

class pygromos.files.blocks.mtb_blocks.mtb_dihedral_field(IB: int, JB: int, KB: int, LB: int, MCB: int)[source]¶

Bases: pygromos.files.blocks.mtb_blocks.mtb_fields

to_string() → str[source]¶

class pygromos.files.blocks.mtb_blocks.mtb_fields[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

field_continue_next_line = '\n\t\t\t\t\t\t\t\t\t\t'¶

fieldseperator = ' '¶

lineseperator = ' \n'¶

class pygromos.files.blocks.mtb_blocks.mtb_lj_exceptions_field(iac: int, jac: int, mcb: int)[source]¶

Bases: pygromos.files.blocks.mtb_blocks.mtb_fields

to_string() → str[source]¶

class pygromos.files.blocks.mtb_blocks.mtb_preceding_exclusions_field(ATOM: int, MAE: int, MSAE: List[int])[source]¶

Bases: pygromos.files.blocks.mtb_blocks.mtb_fields

to_string() → str[source]¶

class pygromos.files.blocks.mtb_blocks.mtb_trailing_atoms_field(ATOM: int, ANM: str, IACM: int, MASS: int, CGMI: float, CGM: int)[source]¶

Bases: pygromos.files.blocks.mtb_blocks.mtb_fields

to_string() → str[source]¶

pygromos.files.blocks.pertubation_blocks module¶

class pygromos.files.blocks.pertubation_blocks.MPERTATOM(NJLA: Optional[int] = None, NPTB: Optional[int] = None, STATEIDENTIFIERS: List[str] = [], STATEATOMHEADER: Tuple[str] = ['NR', 'NAME', 'ALPHLJ', 'ALPHCRF'], STATEATOMS: List[pygromos.files.blocks.pertubation_blocks.atom_eds_pertubation_state] = [], dummy_IAC: int = 22, dummy_CHARGE: float = 0.0, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_gromos_block

__init__(NJLA: Optional[int] = None, NPTB: Optional[int] = None, STATEIDENTIFIERS: List[str] = [], STATEATOMHEADER: Tuple[str] = ['NR', 'NAME', 'ALPHLJ', 'ALPHCRF'], STATEATOMS: List[pygromos.files.blocks.pertubation_blocks.atom_eds_pertubation_state] = [], dummy_IAC: int = 22, dummy_CHARGE: float = 0.0, content: Optional[List[str]] = None)[source]¶

This block is used for lambda sampling to define the different states.

Parameters

NJLA (int) – number of perturbed atoms
NPTB (int) – number of pertubation states
STATEIDENTIFIERS (List[str]) – string names for states
STATEATOMHEADER – header for the atom description table
STATEATOMS – list of atoms, that shall be perturbed
dummy_IAC – dummy atom VdW type for perturbed atoms
dummy_CHARGE – dummy atom charge type for perturbed atoms

add_state_atoms(state_atoms: List[pygromos.files.blocks.pertubation_blocks.atom_eds_pertubation_state])[source]¶

This function can add states and atoms, but also overwrite state values of existing atoms. If a new state is defined only for a subset of atoms, all other atoms are set to the default dummy. If a new atom misses a state definition, this state will be set to dummy.

Parameters: state_atoms (List[atom_eds_pertubation_state])

block_to_string() → str[source]¶

comment: str¶

content: Iterable¶

delete_atom(atomNR: Union[int, List[int]])[source]¶

This function removes atom lines from the ptp file.

Parameters: atomNR (int) – atom to be removed.

delete_state(stateIDs: Optional[Union[int, List[int]]] = None, stateNames: Optional[Union[str, List[str]]] = None)[source]¶

This function deletes an state column.

Parameters: stateIDs (int) – number of the state

property nStates: int¶

property nTotalStateAtoms: int¶

read_content_from_str(content: List[str])[source]¶

property states: dict¶

class pygromos.files.blocks.pertubation_blocks.PERTATOMPARAM(STATEATOMS: Optional[List[pygromos.files.blocks.pertubation_blocks.atom_lam_pertubation_state]] = None, STATEATOMHEADER: Optional[Tuple[str]] = None, NJLA: Optional[int] = None, STATEIDENTIFIERS=None, dummy_IAC=22, dummy_CHARGE=0.0, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_gromos_block

add_state_atoms(state_atoms: List[pygromos.files.blocks.pertubation_blocks.atom_lam_pertubation_state])[source]¶

This function can add states and atoms, but also overwrite state values of existing atoms. If a new state is defined only for a subset of atoms, all other atoms are set to the default dummy. If a new atom misses a state definition, this state will be set to dummy.

Parameters: state_atoms (List[atom_eds_pertubation_state])

block_to_string() → str[source]¶

comment: str¶

content: Iterable¶

delete_atom(atomNR: Union[int, List[int]])[source]¶

This function removes atom lines from the ptp file.

Parameters: atomNR (int) – atom to be removed.

delete_state(stateIDs: Optional[Union[int, List[int]]] = None, stateNames: Optional[Union[str, List[str]]] = None)[source]¶

This function deletes an state column.

Parameters: stateIDs (int) – number of the state

property nStates: int¶

property nTotalStateAtoms: int¶

read_content_from_str(content: List[str])[source]¶

property states: Dict¶

class pygromos.files.blocks.pertubation_blocks.PERTBONDANGLE(STATEATOMS: Optional[List[pygromos.files.blocks.pertubation_blocks.atom_lam_pertubation_state_angle]] = None, STATEATOMHEADER: Optional[Tuple[str]] = None, NPA: Optional[int] = None, dummy_ANGLE=22, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_gromos_block

block_to_string() → str[source]¶

comment: str¶

content: Iterable¶

property nStates: int¶

property nTotalStateAtoms: int¶

read_content_from_str(content: List[str])[source]¶

property states: dict¶

class pygromos.files.blocks.pertubation_blocks.PERTBONDANGLEH(STATEATOMS: Optional[List[pygromos.files.blocks.pertubation_blocks.atom_lam_pertubation_state_angle]] = None, STATEATOMHEADER: Optional[Tuple[str]] = None, NPA: Optional[int] = None, dummy_ANGLE=22, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_gromos_block

block_to_string() → str[source]¶

comment: str¶

content: Iterable¶

property nStates: int¶

property nTotalStateAtoms: int¶

read_content_from_str(content: List[str])[source]¶

property states: dict¶

class pygromos.files.blocks.pertubation_blocks.PERTBONDSTRETCH(STATEATOMS: Optional[List[pygromos.files.blocks.pertubation_blocks.atom_lam_pertubation_state_bond]] = None, STATEATOMHEADER: Optional[Tuple[str]] = None, NPB: Optional[int] = None, dummy_BOND=22, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_gromos_block

block_to_string() → str[source]¶

comment: str¶

content: Iterable¶

property nStates: int¶

property nTotalStateAtoms: int¶

read_content_from_str(content: List[str])[source]¶

property states: dict¶

class pygromos.files.blocks.pertubation_blocks.PERTBONDSTRETCHH(STATEATOMS: Optional[List[pygromos.files.blocks.pertubation_blocks.atom_lam_pertubation_state_bond]] = None, STATEATOMHEADER: Optional[Tuple[str]] = None, NPB: Optional[int] = None, dummy_BOND=22, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_gromos_block

block_to_string() → str[source]¶

comment: str¶

content: Iterable¶

property nStates: int¶

property nTotalStateAtoms: int¶

read_content_from_str(content: List[str])[source]¶

property states: dict¶

class pygromos.files.blocks.pertubation_blocks.PERTIMROPERDIH(STATEATOMS: Optional[List[pygromos.files.blocks.pertubation_blocks.atom_lam_pertubation_state_dihedral]] = None, STATEATOMHEADER: Optional[Tuple[str]] = None, NPD: Optional[int] = None, dummy_IMP=22, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_gromos_block

block_to_string() → str[source]¶

comment: str¶

content: Iterable¶

property nStates: int¶

property nTotalStateAtoms: int¶

read_content_from_str(content: List[str])[source]¶

property states: dict¶

class pygromos.files.blocks.pertubation_blocks.PERTIMROPERDIHH(STATEATOMS: Optional[List[pygromos.files.blocks.pertubation_blocks.atom_lam_pertubation_state_dihedral]] = None, STATEATOMHEADER: Optional[Tuple[str]] = None, NPD: Optional[int] = None, dummy_IMP=22, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_gromos_block

block_to_string() → str[source]¶

comment: str¶

content: Iterable¶

property nStates: int¶

property nTotalStateAtoms: int¶

read_content_from_str(content: List[str])[source]¶

property states: dict¶

class pygromos.files.blocks.pertubation_blocks.PERTPROPERDIH(STATEATOMS: Optional[List[pygromos.files.blocks.pertubation_blocks.atom_lam_pertubation_state_dihedral]] = None, STATEATOMHEADER: Optional[Tuple[str]] = None, NPD: Optional[int] = None, dummy_DIH=22, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_gromos_block

block_to_string() → str[source]¶

comment: str¶

content: Iterable¶

property nStates: int¶

property nTotalStateAtoms: int¶

read_content_from_str(content: List[str])[source]¶

property states: dict¶

class pygromos.files.blocks.pertubation_blocks.PERTPROPERDIHH(STATEATOMS: Optional[List[pygromos.files.blocks.pertubation_blocks.atom_lam_pertubation_state_dihedral]] = None, STATEATOMHEADER: Optional[Tuple[str]] = None, NPD: Optional[int] = None, dummy_DIH=22, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_gromos_block

class PERTPROPERDIH(STATEATOMS: Optional[List[pygromos.files.blocks.pertubation_blocks.atom_lam_pertubation_state_dihedral]] = None, STATEATOMHEADER: Optional[Tuple[str]] = None, NPD: Optional[int] = None, dummy_DIH=22, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_gromos_block

block_to_string() → str[source]¶

comment: str¶

content: Iterable¶

property nStates: int¶

property nTotalStateAtoms: int¶

read_content_from_str(content: List[str])[source]¶

property states: dict¶

block_to_string() → str[source]¶

comment: str¶

content: Iterable¶

property nStates: int¶

property nTotalStateAtoms: int¶

read_content_from_str(content: List[str])[source]¶

property states: dict¶

class pygromos.files.blocks.pertubation_blocks.TITLE(content: str, field_seperator: str = '\t', line_seperator: str = '\n', name: str = 'TITLE', used: bool = True)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_gromos_block

block_to_string() → str[source]¶

content: str¶

field_seperator: str = '\t'¶

line_seperator: str = '\n'¶

order = [[['content']]]¶

pyGromosWatermark: str = '>>> Generated with PyGromosTools (riniker group) <<<'¶

read_content_from_str(content: List[str])[source]¶

class pygromos.files.blocks.pertubation_blocks.atom_eds_pertubation_state(NR: int, NAME: str, STATES: Dict[int, __main__.pertubationEdsState], ALPHLJ: float = 1.0, ALPHCRF: float = 1.0)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

state_format_pattern = ' {:>3} {:>10.5f}'¶

to_string() → str[source]¶

class pygromos.files.blocks.pertubation_blocks.atom_lam_pertubation_state(NR: int, RES: int, NAME: str, STATES: Dict[int, __main__.pertubationLamState], ALPHLJ: float = 1.0, ALPHCRF: float = 1.0)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

state_format_pattern = ' {:>5} {:>5} {:>10.5f}'¶

to_string() → str[source]¶

class pygromos.files.blocks.pertubation_blocks.atom_lam_pertubation_state_angle(NR: int, atomI: int, atomJ: int, atomK: int, STATES: Dict[int, int])[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

state_format_pattern = ' {:>5}'¶

to_string() → str[source]¶

class pygromos.files.blocks.pertubation_blocks.atom_lam_pertubation_state_bond(NR: int, atomI: int, atomJ: int, STATES: Dict[int, int])[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

state_format_pattern = ' {:>5}'¶

to_string() → str[source]¶

class pygromos.files.blocks.pertubation_blocks.atom_lam_pertubation_state_dihedral(NR: int, atomI: int, atomJ: int, atomK: int, atomL: int, STATES: Dict[int, int])[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

state_format_pattern = ' {:>5}'¶

to_string() → str[source]¶

class pygromos.files.blocks.pertubation_blocks.atom_mass_type(N: int, ATMAS: float, ATMASN: str, comment: str = '')[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

to_string() → str[source]¶

pygromos.files.blocks.qmmm_blocks module¶

class pygromos.files.blocks.qmmm_blocks.DFTBELEMENTS(content: Union[str, dict, pygromos.utils.typing.DFTBELEMENTS_Type])[source]¶

Bases: pygromos.files.blocks.topology_blocks._topology_block

FORCEFIELD: pygromos.files.blocks.topology_blocks.FORCEFIELD¶

MAKETOPVERSION: pygromos.files.blocks.topology_blocks.MAKETOPVERSION¶

class pygromos.files.blocks.qmmm_blocks.MNDOELEMENTS(content: Union[str, dict, pygromos.utils.typing.MNDOELEMENTS_Type])[source]¶

Bases: pygromos.files.blocks.topology_blocks._topology_block

FORCEFIELD: pygromos.files.blocks.topology_blocks.FORCEFIELD¶

MAKETOPVERSION: pygromos.files.blocks.topology_blocks.MAKETOPVERSION¶

class pygromos.files.blocks.qmmm_blocks.MOPACELEMENTS(content: Union[str, dict, pygromos.utils.typing.MOPACELEMENTS_Type])[source]¶

Bases: pygromos.files.blocks.topology_blocks._topology_block

FORCEFIELD: pygromos.files.blocks.topology_blocks.FORCEFIELD¶

MAKETOPVERSION: pygromos.files.blocks.topology_blocks.MAKETOPVERSION¶

class pygromos.files.blocks.qmmm_blocks.ORCAELEMENTS(content: Union[str, dict, pygromos.utils.typing.ORCAELEMENTS_Type])[source]¶

Bases: pygromos.files.blocks.topology_blocks._topology_block

FORCEFIELD: pygromos.files.blocks.topology_blocks.FORCEFIELD¶

MAKETOPVERSION: pygromos.files.blocks.topology_blocks.MAKETOPVERSION¶

class pygromos.files.blocks.qmmm_blocks.QMUNIT(content: Union[str, dict, pygromos.utils.typing.QMUNIT_Type], QLGL: float = 0.052918, QEGE: float = 2625.5, QCGC: float = 1.0, QIGI: float = 0.1)[source]¶

Bases: pygromos.files.blocks.topology_blocks._topology_block

block_to_string() → str[source]¶

read_content_from_str(content: str)[source]¶

table_header: Iterable[str] = ['QLGL', 'QEGE', 'QCGC', 'QIGI']¶

The QMUNIT block

Parameters

QLGL (float) – QM length to Gromos length (e.g. Bohr to nm)
QEGE (float) – QM energy to Gromos energy (e.g. Hartree to kJ / mol)
QCGC (float) – Gromos charge to QM charge
QIGI (float) – QM input units to Gromos input units (e.g. Angstrom to nm)

class pygromos.files.blocks.qmmm_blocks.QMZONE(content: Union[Iterable[pygromos.files.blocks.qmmm_blocks.qmzone_field], str])[source]¶

Bases: pygromos.files.blocks.topology_blocks._topology_table_block

NBON: int = 1¶

block_to_string() → str[source]¶

table_header: Iterable[str] = ['QMEN', 'QMEI', 'QMEZ', 'QMEB']¶

table_line_type¶: alias of pygromos.files.blocks.qmmm_blocks.qmzone_field

class pygromos.files.blocks.qmmm_blocks.TURBOMOLEELEMENTS(content: Union[str, dict, pygromos.utils.typing.TURBOMOLEELEMENTS_Type])[source]¶

Bases: pygromos.files.blocks.topology_blocks._topology_block

FORCEFIELD: pygromos.files.blocks.topology_blocks.FORCEFIELD¶

MAKETOPVERSION: pygromos.files.blocks.topology_blocks.MAKETOPVERSION¶

class pygromos.files.blocks.qmmm_blocks.XTBELEMENTS(content: Union[str, dict, pygromos.utils.typing.XTBELEMENTS_Type])[source]¶

Bases: pygromos.files.blocks.topology_blocks._topology_block

FORCEFIELD: pygromos.files.blocks.topology_blocks.FORCEFIELD¶

MAKETOPVERSION: pygromos.files.blocks.topology_blocks.MAKETOPVERSION¶

class pygromos.files.blocks.qmmm_blocks.qmzone_field(QMEN: str, QMEI: int, QMEZ: int, QMEB: int)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

__init__(QMEN: str, QMEI: int, QMEZ: int, QMEB: int)[source]¶

One line of the QMZONE block

Parameters

QMEN (str) – (QM element name), indicates the atom identifier for this position
QMEI (int) – (QM element iterator), specifies an iterator over the atom positions
QMEZ (int) – (QM element Z), specifies the nuclear charge Z of the atom position
QMEB (int) – (QM element bond), specifies whether a bond can be broken or not (== 0)

to_string()[source]¶

pygromos.files.blocks.replica_exchange_blocks module¶

class pygromos.files.blocks.replica_exchange_blocks.repex_system(s: list, T: float, state_eir: dict)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_gromos_block

block_to_string() → str[source]¶

comment: str¶

content: Iterable¶

class pygromos.files.blocks.replica_exchange_blocks.replica_stat(ID: int, partner: int, run: int, Ti: float, Epoti: float, Tj: float, Epotj: float, p: float, s: bool, si: float, sj: float, state_potentials: Optional[dict] = None, potentials: Optional[dict] = None, li: Optional[float] = None, lj: Optional[float] = None)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

Epoti: float¶

Epotj: float¶

ID: int¶

Ti: float¶

Tj: float¶

__init__(ID: int, partner: int, run: int, Ti: float, Epoti: float, Tj: float, Epotj: float, p: float, s: bool, si: float, sj: float, state_potentials: Optional[dict] = None, potentials: Optional[dict] = None, li: Optional[float] = None, lj: Optional[float] = None)[source]¶

Parameters

ID
partner
run
Ti
Epoti
Tj
Epotj
p
s
si
sj
state_potentials
potentials
li
lj

li: float¶

lj: float¶

p: float¶

partner: int¶

run: int¶

s: bool¶

si: float¶

sj: float¶

state_potentials: Dict[str, float]¶

to_string() → str[source]¶

pygromos.files.blocks.topology_blocks module¶

class pygromos.files.blocks.topology_blocks.ATOMTYPENAME(content: Union[str, Dict[str, str], pygromos.utils.typing.ATOMTYPENAME_Type], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._topology_block

FORCEFIELD: pygromos.files.blocks.topology_blocks.FORCEFIELD¶

MAKETOPVERSION: pygromos.files.blocks.topology_blocks.MAKETOPVERSION¶

class pygromos.files.blocks.topology_blocks.BOND(content: Union[Iterable[pygromos.files.blocks.topology_blocks.top_bond_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NBON: Optional[int] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._topology_table_block

NBON: int = 1¶

__init__(content: Union[Iterable[pygromos.files.blocks.topology_blocks.top_bond_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NBON: Optional[int] = None)[source]¶

GROMOS BOND block

Parameters

content (Union[Iterable[top_bond_type], str])
FORCEFIELD (FORCEFIELD)
MAKETOPVERSION (MAKETOPVERSION)
NBON (int, optional) – Number of bonds

block_to_string() → str[source]¶

read_content_from_str(content: str)[source]¶

table_header: Iterable[str] = ['IB', 'JB', 'ICB']¶

table_line_type¶: alias of pygromos.files.blocks.topology_blocks.top_bond_type

class pygromos.files.blocks.topology_blocks.BONDANGLE(content: Union[Iterable[pygromos.files.blocks.topology_blocks.bondangle_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NTHE: Optional[int] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._topology_table_block

NTHE: int¶

__init__(content: Union[Iterable[pygromos.files.blocks.topology_blocks.bondangle_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NTHE: Optional[int] = None)[source]¶

GROMOS BONDSTRETCHTYPE block

Parameters

content (Union[Iterable[bondangle_type], str])
FORCEFIELD (FORCEFIELD)
MAKETOPVERSION (MAKETOPVERSION)
NTHE (int, optional) – Number of bondangles

block_to_string() → str[source]¶

read_content_from_str(content: str)[source]¶

table_header: Iterable[str] = ['IT', 'JT', 'KT', 'ICT']¶

table_line_type¶: alias of pygromos.files.blocks.topology_blocks.bondangle_type

class pygromos.files.blocks.topology_blocks.BONDANGLEBENDTYPE(content: Union[Iterable[pygromos.files.blocks.topology_blocks.bondanglebendtype_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NBTY: Optional[int] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._topology_table_block

NBTY: int¶

__init__(content: Union[Iterable[pygromos.files.blocks.topology_blocks.bondanglebendtype_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NBTY: Optional[int] = None)[source]¶

GROMOS BONDSTRETCHTYPE block

Parameters

content (Union[Iterable[bondanglebendtype_type], str])
FORCEFIELD (FORCEFIELD)
MAKETOPVERSION (MAKETOPVERSION)
NBTY (int, optional) – Number of bondstretchtypes

block_to_string() → str[source]¶

read_content_from_str(content: str)[source]¶

table_header: Iterable[str] = ['CT', 'CHT', 'T0']¶

table_line_type¶: alias of pygromos.files.blocks.topology_blocks.bondanglebendtype_type

class pygromos.files.blocks.topology_blocks.BONDANGLEBENDTYPECODE(content: Union[Iterable[pygromos.files.blocks.topology_blocks.angle_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NRTTY: Optional[int] = None, NTTY: Optional[int] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._iterable_topology_block

NRTTY: int¶

NTTY: int¶

__init__(content: Union[Iterable[pygromos.files.blocks.topology_blocks.angle_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NRTTY: Optional[int] = None, NTTY: Optional[int] = None)[source]¶

GROMOS bond-stretching parameters

Parameters

content (Union[Iterable[atom_mass_type], str])
FORCEFIELD (FORCEFIELD)
MAKETOPVERSION (MAKETOPVERSION)
NRBTY (int, optional) – Number of bond types
NBTY (int, optional) – Number of maximal bond index.rst

block_to_string() → str[source]¶

read_content_from_str(content: str)[source]¶

table_header: Iterable[str] = ['ICT(H)[N]', 'CT[N]', 'CHT[N]', '(T0[N])']¶

class pygromos.files.blocks.topology_blocks.BONDANGLEH(content: Union[Iterable[pygromos.files.blocks.topology_blocks.bondangle_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NTHEH: Optional[int] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._topology_table_block

NTHEH: int¶

__init__(content: Union[Iterable[pygromos.files.blocks.topology_blocks.bondangle_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NTHEH: Optional[int] = None)[source]¶

GROMOS BONDANGLEH block

Parameters

content (Union[Iterable[bondangle_type], str])
FORCEFIELD (FORCEFIELD)
MAKETOPVERSION (MAKETOPVERSION)
NTHEH (int, optional) – Number of bondangles

block_to_string() → str[source]¶

read_content_from_str(content: str)[source]¶

table_header: Iterable[str] = ['ITH', 'JTH', 'KTH', 'ICTH']¶

table_line_type¶: alias of pygromos.files.blocks.topology_blocks.bondangle_type

class pygromos.files.blocks.topology_blocks.BONDH(content: Union[Iterable[pygromos.files.blocks.topology_blocks.top_bond_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NBONH: Optional[int] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._topology_table_block

NBONH: int = 1¶

__init__(content: Union[Iterable[pygromos.files.blocks.topology_blocks.top_bond_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NBONH: Optional[int] = None)[source]¶

GROMOS BONDH block

Parameters

content (Union[Iterable[top_bond_type], str])
FORCEFIELD (FORCEFIELD)
MAKETOPVERSION (MAKETOPVERSION)
NBONH (int, optional) – Number of bonds with H

block_to_string() → str[source]¶

read_content_from_str(content: str)[source]¶

table_header: Iterable[str] = ['IBH', 'JBH', 'ICBH']¶

table_line_type¶: alias of pygromos.files.blocks.topology_blocks.top_bond_type

class pygromos.files.blocks.topology_blocks.BONDSTRETCHTYPE(content: Union[Iterable[pygromos.files.blocks.topology_blocks.bondstretchtype_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NBTY: Optional[int] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._topology_table_block

NBTY: int¶

__init__(content: Union[Iterable[pygromos.files.blocks.topology_blocks.bondstretchtype_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NBTY: Optional[int] = None)[source]¶

GROMOS BONDSTRETCHTYPE block

Parameters

content (Union[Iterable[bondstretchtype_type], str])
FORCEFIELD (FORCEFIELD)
MAKETOPVERSION (MAKETOPVERSION)
NBTY (int, optional) – Number of bondstretchtypes

block_to_string() → str[source]¶

read_content_from_str(content: str)[source]¶

table_header: Iterable[str] = ['CB', 'CHB', 'B0']¶

table_line_type¶: alias of pygromos.files.blocks.topology_blocks.bondstretchtype_type

class pygromos.files.blocks.topology_blocks.BONDSTRETCHTYPECODE(content: Union[Iterable[pygromos.files.blocks.topology_blocks.bond_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NRBTY: Optional[int] = None, NBTY: Optional[int] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._iterable_topology_block

NBTY: int¶

NRBTY: int¶

__init__(content: Union[Iterable[pygromos.files.blocks.topology_blocks.bond_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NRBTY: Optional[int] = None, NBTY: Optional[int] = None)[source]¶

GROMOS bond-stretching parameters

Parameters

content (Union[Iterable[atom_mass_type], str])
FORCEFIELD (FORCEFIELD)
MAKETOPVERSION (MAKETOPVERSION)
NRBTY (int, optional) – Number of bond types
NBTY (int, optional) – Number of maximal bond index.rst

block_to_string() → str[source]¶

read_content_from_str(content: str)[source]¶

table_header: Iterable[str] = ['ICB(H)[N]', 'CB[N]', 'HB[N]', 'B0[N]']¶

class pygromos.files.blocks.topology_blocks.CONSTRAINT(content: str, FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NCON: Optional[int] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._topology_table_block

NCON: int¶

block_to_string() → str[source]¶

read_content_from_str(content: str)[source]¶

table_header: Iterable[str] = ['IC', 'JC', 'ICC']¶

table_line_type¶: alias of pygromos.files.blocks.topology_blocks.constraint_type

class pygromos.files.blocks.topology_blocks.CROSSDIHEDRAL(content: Union[Iterable[pygromos.files.blocks.topology_blocks.crossgihedral_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NPHI: Optional[int] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._topology_table_block

NPHI: int¶

__init__(content: Union[Iterable[pygromos.files.blocks.topology_blocks.crossgihedral_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NPHI: Optional[int] = None)[source]¶

[summary]

Parameters

content (Union[Iterable[crossgihedral_type], str]) – [description]
FORCEFIELD (FORCEFIELD, optional) – [description], by default None
MAKETOPVERSION (MAKETOPVERSION, optional) – [description], by default None
NPHI ([type], optional) – number of cross dihedrals NOT involving H atoms in solute, by default None

block_to_string() → str[source]¶

read_content_from_str(content: str)[source]¶

table_header: Iterable[str] = ['AP', 'BP', 'CP', 'DP', 'EP', 'FP', 'GP', 'HP', 'ICC']¶

table_line_type¶: alias of pygromos.files.blocks.topology_blocks.crossgihedralh_type

class pygromos.files.blocks.topology_blocks.CROSSDIHEDRALH(content: Union[Iterable[pygromos.files.blocks.topology_blocks.crossgihedralh_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NPHIH: Optional[int] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._topology_table_block

NPHIH: int¶

__init__(content: Union[Iterable[pygromos.files.blocks.topology_blocks.crossgihedralh_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NPHIH: Optional[int] = None)[source]¶

[summary]

Parameters

content (Union[Iterable[crossgihedralh_type], str]) – [description]
FORCEFIELD (FORCEFIELD, optional) – [description], by default None
MAKETOPVERSION (MAKETOPVERSION, optional) – [description], by default None
NPHIH ([type], optional) – number of cross dihedrals involving H atoms in solute, by default None

block_to_string() → str[source]¶

read_content_from_str(content: str)[source]¶

table_header: Iterable[str] = ['APH', 'BPH', 'CPH', 'DPH', 'EPH', 'FPH', 'GPH', 'HPH', 'ICCH']¶

table_line_type¶: alias of pygromos.files.blocks.topology_blocks.crossgihedralh_type

class pygromos.files.blocks.topology_blocks.DIHEDRAL(content: Union[Iterable[pygromos.files.blocks.topology_blocks.top_dihedral_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NPHI: Optional[int] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._topology_table_block

NPHI: int¶

__init__(content: Union[Iterable[pygromos.files.blocks.topology_blocks.top_dihedral_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NPHI: Optional[int] = None)[source]¶

GROMOS DIHEDRAL block

Parameters

content (Union[Iterable[top_dihedral_type], str])
FORCEFIELD (FORCEFIELD)
MAKETOPVERSION (MAKETOPVERSION)
NPHI (int, optional) – Number of tors dihedral

block_to_string() → str[source]¶

read_content_from_str(content: str)[source]¶

table_header: Iterable[str] = ['IP', 'JP', 'KP', 'LP', 'ICP']¶

table_line_type¶: alias of pygromos.files.blocks.topology_blocks.top_dihedral_type

class pygromos.files.blocks.topology_blocks.DIHEDRALH(content: Union[Iterable[pygromos.files.blocks.topology_blocks.dihedralh_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NPHIH: Optional[int] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._topology_table_block

NPHIH: int¶

__init__(content: Union[Iterable[pygromos.files.blocks.topology_blocks.dihedralh_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NPHIH: Optional[int] = None)[source]¶

GROMOS DIHEDRAL block

Parameters

content (Union[Iterable[dihedralh_type], str])
FORCEFIELD (FORCEFIELD)
MAKETOPVERSION (MAKETOPVERSION)
NPHIH (int, optional) – Number of dihedralH

block_to_string() → str[source]¶

read_content_from_str(content: str)[source]¶

table_header: Iterable[str] = ['IPH', 'JPH', 'KPH', 'LPH', 'ICPH']¶

table_line_type¶: alias of pygromos.files.blocks.topology_blocks.dihedralh_type

class pygromos.files.blocks.topology_blocks.DISTANCERESSPEC(KDISH: Optional[int] = None, KDISC: Optional[int] = None, RESTRAINTHEADER: Optional[list] = None, RESTRAINTS: Optional[list] = None, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_gromos_block

__init__(KDISH: Optional[int] = None, KDISC: Optional[int] = None, RESTRAINTHEADER: Optional[list] = None, RESTRAINTS: Optional[list] = None, content: Optional[List[str]] = None)[source]¶

Parameters

KDISH
KDISC
RESTRAINTHEADER
RESTRAINTS

block_to_string() → str[source]¶

comment: str¶

content: Iterable¶

read_content_from_str(content: List[str])[source]¶

class pygromos.files.blocks.topology_blocks.FORCEFIELD(NAME: Optional[str] = None, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_gromos_block

NAME: str¶

block_to_string() → str[source]¶

class pygromos.files.blocks.topology_blocks.IMPDIHEDRAL(content: Union[Iterable[pygromos.files.blocks.topology_blocks.impdihedral_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NQHI: Optional[int] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._topology_table_block

NQHI: int¶

__init__(content: Union[Iterable[pygromos.files.blocks.topology_blocks.impdihedral_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NQHI: Optional[int] = None)[source]¶

GROMOS IMPDIHEDRAL block

Parameters

content (Union[Iterable[impdihedral_type], str])
FORCEFIELD (FORCEFIELD)
MAKETOPVERSION (MAKETOPVERSION)
NQHI (int, optional) – Number of impdihedral

block_to_string() → str[source]¶

read_content_from_str(content: str)[source]¶

table_header: Iterable[str] = ['IQ', 'JQ', 'KQ', 'LQ', 'ICQ']¶

table_line_type¶: alias of pygromos.files.blocks.topology_blocks.impdihedral_type

class pygromos.files.blocks.topology_blocks.IMPDIHEDRALH(content: Union[Iterable[pygromos.files.blocks.topology_blocks.impdihedralh_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NQHIH: Optional[int] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._topology_table_block

NQHIH: int¶

__init__(content: Union[Iterable[pygromos.files.blocks.topology_blocks.impdihedralh_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NQHIH: Optional[int] = None)[source]¶

GROMOS IMPDIHEDRALH block

Parameters

content (Union[Iterable[impdihedralh_type], str])
FORCEFIELD (FORCEFIELD)
MAKETOPVERSION (MAKETOPVERSION)
NQHIH (int, optional) – Number of impdihedralH

block_to_string() → str[source]¶

read_content_from_str(content: str)[source]¶

table_header: Iterable[str] = ['IQH', 'JQH', 'KQH', 'LQH', 'ICQH']¶

table_line_type¶: alias of pygromos.files.blocks.topology_blocks.impdihedralh_type

class pygromos.files.blocks.topology_blocks.IMPDIHEDRALTYPE(content: Union[Iterable[pygromos.files.blocks.topology_blocks.impdihedraltype_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NQTY: Optional[int] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._topology_table_block

NQTY: int¶

__init__(content: Union[Iterable[pygromos.files.blocks.topology_blocks.impdihedraltype_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NQTY: Optional[int] = None)[source]¶

GROMOS IMPDIHEDRALTYPE block

Parameters

content (Union[Iterable[impdihedraltype_type], str])
FORCEFIELD (FORCEFIELD)
MAKETOPVERSION (MAKETOPVERSION)
NQTY (int, optional) – Number of impdihedraltype

block_to_string() → str[source]¶

read_content_from_str(content: str)[source]¶

table_header: Iterable[str] = ['CQ', 'Q0']¶

table_line_type¶: alias of pygromos.files.blocks.topology_blocks.impdihedraltype_type

class pygromos.files.blocks.topology_blocks.IMPDIHEDRALTYPECODE(content: Union[Iterable[pygromos.files.blocks.topology_blocks.improper_dihedral_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NRQTY: Optional[int] = None, NQTY: Optional[int] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._iterable_topology_block

NQTY: int¶

NRQTY: int¶

__init__(content: Union[Iterable[pygromos.files.blocks.topology_blocks.improper_dihedral_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NRQTY: Optional[int] = None, NQTY: Optional[int] = None)[source]¶

GROMOS improper dihedral type parameters

Parameters

content (Union[Iterable[atom_mass_type], str])
FORCEFIELD (FORCEFIELD)
MAKETOPVERSION (MAKETOPVERSION)
NRQTY (int, optional) – Number of improperDihedrals types
NQTY (int, optional) – Number of maximal improperDihedrals index.rst

block_to_string() → str[source]¶

read_content_from_str(content: str)[source]¶

table_header: Iterable[str] = ['ICQ', 'CQ', 'Q0']¶

class pygromos.files.blocks.topology_blocks.LJEXCEPTIONS(content: Union[Iterable[pygromos.files.blocks.topology_blocks.ljexception_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NEX: Optional[int] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._topology_table_block

NEX: int¶

__init__(content: Union[Iterable[pygromos.files.blocks.topology_blocks.ljexception_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NEX: Optional[int] = None)[source]¶

GROMOS LJEXCEPTIONS block

Parameters

content (Union[Iterable[ljexception_type], str])
FORCEFIELD (FORCEFIELD)
MAKETOPVERSION (MAKETOPVERSION)
NEX (int, optional) – Number of LJEXCEPTIONS

block_to_string() → str[source]¶

read_content_from_str(content: str)[source]¶

table_header: Iterable[str] = ['AT1', 'AT2', 'C12', 'C6']¶

table_line_type¶: alias of pygromos.files.blocks.topology_blocks.ljexception_type

class pygromos.files.blocks.topology_blocks.LJPARAMETERS(content: Union[Iterable[pygromos.files.blocks.topology_blocks.ljparameters_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NRATT2: Optional[int] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._topology_table_block

NRATT2: int¶

__init__(content: Union[Iterable[pygromos.files.blocks.topology_blocks.ljparameters_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NRATT2: Optional[int] = None)[source]¶

GROMOS LJPARAMETERS block

Parameters

content (Union[Iterable[ljparameters_type], str])
FORCEFIELD (FORCEFIELD)
MAKETOPVERSION (MAKETOPVERSION)
NRATT2 (int, optional) – Number of LJPARAMETERS

block_to_string() → str[source]¶

read_content_from_str(content: str)[source]¶

table_header: Iterable[str] = ['IAC', 'JAC', 'C12', 'C6', 'CS12', 'CS6']¶

table_line_type¶: alias of pygromos.files.blocks.topology_blocks.ljparameters_type

class pygromos.files.blocks.topology_blocks.MAKETOPVERSION(VERSION: Optional[str] = None, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_gromos_block

VERSION: str¶

block_to_string() → str[source]¶

class pygromos.files.blocks.topology_blocks.MASSATOMTYPECODE(content: Union[Iterable[pygromos.files.blocks.topology_blocks.atom_mass_type], Iterable[str]], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NRMATY: Optional[int] = None, NMATY: Optional[int] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._iterable_topology_block

NMATY: int¶

NRMATY: int¶

block_to_string() → str[source]¶

read_content_from_str(content: Union[str, List[str]])[source]¶

table_header: Iterable[str] = ['N', 'ATMAS', 'ATMASN']¶

class pygromos.files.blocks.topology_blocks.MIXEDATOMLJPAIR(content: List[str], NRMTT: Optional[int] = None, FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._iterable_topology_block

NRMTT: int¶

__init__(content: List[str], NRMTT: Optional[int] = None, FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None)[source]¶

Parameters

content
NRATT
FORCEFIELD
MAKETOPVERSION

block_to_string() → str[source]¶

read_content_from_str(content: str)[source]¶

table_header: Iterable[str] = ['IACI', 'IACJ', 'C6', 'C12_1', 'C12_2', 'C12_3']¶: GROMOS 43A1 normal van der Waals parameters for mixed atom type pairs (I,J)

class pygromos.files.blocks.topology_blocks.PERTATOMPARAM(STATEATOMS: Optional[List[pygromos.files.blocks.topology_blocks.atom_lam_pertubation_state]] = None, STATEATOMHEADER: Optional[Tuple[str]] = None, NJLA: Optional[int] = None, STATEIDENTIFIERS: Optional[List[str]] = None, dummy_IAC: int = 22, dummy_CHARGE: int = 0.0, content: Optional[List[str]] = None)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_gromos_block

add_state_atoms(state_atoms: List[pygromos.files.blocks.topology_blocks.atom_lam_pertubation_state])[source]¶: This function can add states and atoms, but also overwrite state values of existing atoms. If a new state is defined only for a subset of atoms, all other atoms are set to the default dummy. If a new atom misses a state definition, this state will be set to dummy. :Parameters: state_atoms (List[atom_eds_pertubation_state])

block_to_string() → str[source]¶

comment: str¶

content: Iterable¶

delete_atom(atomNR: Union[int, List[int]])[source]¶: This function removes atom lines from the ptp file. :Parameters: atomNR (int) – atom to be removed.

delete_state(stateIDs: Optional[Union[int, List[int]]] = None, stateNames: Optional[Union[str, List[str]]] = None)[source]¶: This function deletes an state column. :Parameters: stateIDs (int) – number of the state

property nStates: int¶

property nTotalStateAtoms: int¶

read_content_from_str(content: List[str])[source]¶

property states: dict¶

class pygromos.files.blocks.topology_blocks.PHYSICALCONSTANTS(content: Union[str, dict, pygromos.utils.typing.PHYSICALCONSTANTS_Type], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._topology_block

FORCEFIELD: pygromos.files.blocks.topology_blocks.FORCEFIELD¶

MAKETOPVERSION: pygromos.files.blocks.topology_blocks.MAKETOPVERSION¶

block_to_string() → str[source]¶

read_content_from_str(content: str)[source]¶

class pygromos.files.blocks.topology_blocks.PRESSUREGROUPS(content: Optional[Union[str, dict]] = None, FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NSM: Optional[int] = None, NSP: Optional[List[int]] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._generic_topology_groups

NSM: int¶

NSP: List[int]¶

class pygromos.files.blocks.topology_blocks.RESNAME(content: Union[str, Dict[str, str], pygromos.utils.typing.RESNAME_Type], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._topology_block

FORCEFIELD: pygromos.files.blocks.topology_blocks.FORCEFIELD¶

MAKETOPVERSION: pygromos.files.blocks.topology_blocks.MAKETOPVERSION¶

class pygromos.files.blocks.topology_blocks.SCALEDINTERACTIONS(values=None, content=None)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_gromos_block

__init__(values=None, content=None)[source]¶: Not exactly sure what these parameters do

block_to_string() → str[source]¶

comment: str¶

content: Iterable¶

read_content_from_str(content)[source]¶

class pygromos.files.blocks.topology_blocks.SINGLEATOMLJPAIR(content: List[str], NRATT: Optional[int] = None, FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._iterable_topology_block

NRATT: int¶

__init__(content: List[str], NRATT: Optional[int] = None, FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None)[source]¶

Parameters

content
NRATT
FORCEFIELD
MAKETOPVERSION

block_to_string() → str[source]¶

read_content_from_str(content: str)[source]¶

table_header = ['IAC', 'TYPE', 'C6', 'C12(1)', 'C12(2)', 'C12(3)']¶

class pygromos.files.blocks.topology_blocks.SOLUTEATOM(content: Union[str, Dict[str, str], pygromos.utils.typing._iterable_topology_block_Type], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._iterable_topology_block

NRP: int¶

block_to_string() → str[source]¶

read_content_from_str(content: str)[source]¶

table_header: Iterable[str] = ['IB', 'JB', 'ICB']¶

class pygromos.files.blocks.topology_blocks.SOLUTEMOLECULES(content: Optional[Union[str, dict]] = None, FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NSM: Optional[int] = None, NSP: Optional[List[int]] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._generic_topology_groups

NSM: int¶

NSP: List[int]¶

class pygromos.files.blocks.topology_blocks.SOLVENTATOM(content: Union[Iterable[pygromos.files.blocks.topology_blocks.solventatom_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NRAM: Optional[int] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._topology_table_block

NRAM: int¶

__init__(content: Union[Iterable[pygromos.files.blocks.topology_blocks.solventatom_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NRAM: Optional[int] = None)[source]¶

GROMOS solventatom block

Parameters

content (Union[Iterable[solventatom_type], str])
FORCEFIELD (FORCEFIELD)
MAKETOPVERSION (MAKETOPVERSION)
NRAM (int, optional) – Number of solventatom

block_to_string() → str[source]¶

read_content_from_str(content: str)[source]¶

table_header: Iterable[str] = ['I', 'ANMS', 'IACS', 'MASS', 'CGS']¶

table_line_type¶: alias of pygromos.files.blocks.topology_blocks.solventatom_type

class pygromos.files.blocks.topology_blocks.SOLVENTCONSTR(content: Union[Iterable[pygromos.files.blocks.topology_blocks.solventconstr_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NCONS: Optional[int] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._topology_table_block

NCONS: int¶

__init__(content: Union[Iterable[pygromos.files.blocks.topology_blocks.solventconstr_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NCONS: Optional[int] = None)[source]¶

GROMOS SOLVENTCONSTR block

Parameters

content (Union[Iterable[solventconstr_type], str])
FORCEFIELD (FORCEFIELD)
MAKETOPVERSION (MAKETOPVERSION)
NCONS (int, optional) – Number of SOLVENTCONSTR

block_to_string() → str[source]¶

read_content_from_str(content: str)[source]¶

table_header: Iterable[str] = ['ICONS', 'JCONS', 'CONS']¶

table_line_type¶: alias of pygromos.files.blocks.topology_blocks.solventconstr_type

class pygromos.files.blocks.topology_blocks.SPECATOMLJPAIR(content: List[str], NRST: Optional[int] = None, FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._iterable_topology_block

NRST: int¶

__init__(content: List[str], NRST: Optional[int] = None, FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None)[source]¶

Parameters

content
NRATT
FORCEFIELD
MAKETOPVERSION

read_content_from_str(content: str)[source]¶

table_header: Iterable[str] = ['???']¶

class pygromos.files.blocks.topology_blocks.TEMPERATUREGROUPS(content: Optional[Union[str, dict]] = None, FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NSM: Optional[int] = None, NSP: Optional[List[int]] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._generic_topology_groups

NSM: int¶

NSP: List[int]¶

class pygromos.files.blocks.topology_blocks.TOPVERSION(content: Union[str, Dict[str, str], pygromos.utils.typing.TOPVERSION_Type], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._topology_block

FORCEFIELD: pygromos.files.blocks.topology_blocks.FORCEFIELD¶

MAKETOPVERSION: pygromos.files.blocks.topology_blocks.MAKETOPVERSION¶

class pygromos.files.blocks.topology_blocks.TORSDIHEDRALTYPE(content: Union[Iterable[pygromos.files.blocks.topology_blocks.torsdihedraltype_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NPTY: Optional[int] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._topology_table_block

NPTY: int¶

__init__(content: Union[Iterable[pygromos.files.blocks.topology_blocks.torsdihedraltype_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NPTY: Optional[int] = None)[source]¶

GROMOS IMPDIHEDRAL block

Parameters

content (Union[Iterable[torsdihedraltype_type], str])
FORCEFIELD (FORCEFIELD)
MAKETOPVERSION (MAKETOPVERSION)
NQTY (int, optional) – Number of torsion dihedrals

block_to_string() → str[source]¶

read_content_from_str(content: str)[source]¶

table_header: Iterable[str] = ['CP', 'PD', 'NP']¶

table_line_type¶: alias of pygromos.files.blocks.topology_blocks.torsdihedraltype_type

class pygromos.files.blocks.topology_blocks.TORSDIHEDRALTYPECODE(content: Union[Iterable[pygromos.files.blocks.topology_blocks.dihedral_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NRPTY: Optional[int] = None, NPTY: Optional[int] = None)[source]¶

Bases: pygromos.files.blocks.topology_blocks._iterable_topology_block

NPTY: int¶

NRPTY: int¶

__init__(content: Union[Iterable[pygromos.files.blocks.topology_blocks.dihedral_type], str], FORCEFIELD: Optional[pygromos.files.blocks.topology_blocks.FORCEFIELD] = None, MAKETOPVERSION: Optional[pygromos.files.blocks.topology_blocks.MAKETOPVERSION] = None, NRPTY: Optional[int] = None, NPTY: Optional[int] = None)[source]¶

GROMOS (trigonometric) dihedral torsional angle parameters

Parameters

content (Union[Iterable[atom_mass_type], str])
FORCEFIELD (FORCEFIELD)
MAKETOPVERSION (MAKETOPVERSION)
NRPTY (int, optional) – Number of dihedral-angle types
NPTY (int, optional) – Number of maximal dihedral-angle index.rst

block_to_string() → str[source]¶

read_content_from_str(content: str)[source]¶

table_header: Iterable[str] = ['ICP(H)[N]', 'CP[N]', 'PD', 'NP']¶

class pygromos.files.blocks.topology_blocks.angle_type(ICT: int, CT: float, CHT: float, T0: float, atomI: Union[str, Iterable[str]], atomJ: Union[str, Iterable[str]], atomK: Union[str, Iterable[str]], specialNumber: int)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

__init__(ICT: int, CT: float, CHT: float, T0: float, atomI: Union[str, Iterable[str]], atomJ: Union[str, Iterable[str]], atomK: Union[str, Iterable[str]], specialNumber: int)[source]¶

GROMOS bond-stretching parameters for one possible bond

Parameters

ICT (int) – Bond-angle type code
CT (float) – Non-harmonic force constant
CHT (float) – Harmonic force constant
T0 (float) – Ideal bond angle
atomI (str, Iterable[str]) – possible atom I useages
atomJ (str, Iterable[str]) – possible atom J useages
atomK (str, Iterable[str]) – possible atom K useages
specialNumber (int) – No Idea @Todo: refactor later!

to_string()[source]¶

class pygromos.files.blocks.topology_blocks.atom_lam_pertubation_state(NR: int, RES: int, NAME: str, STATES: Dict[int, __main__.pertubationLamState], ALPHLJ: float = 1.0, ALPHCRF: float = 1.0)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

state_format_pattern = ' {:>5} {:>5} {:>10.5f}'¶

to_string()[source]¶

class pygromos.files.blocks.topology_blocks.atom_mass_type(N: int, ATMAS: float, ATMASN: str, comment: str = '')[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

to_string()[source]¶

class pygromos.files.blocks.topology_blocks.atom_pair_distanceRes(i1: int, j1: int, k1: int, l1: int, type1: Union[pygromos.files.blocks.topology_blocks.geometric_code, int], i2: int, j2: int, k2: int, l2: int, type2: Union[pygromos.files.blocks.topology_blocks.geometric_code, int], r0: float, w0: float, rah: Union[pygromos.files.blocks.topology_blocks.distant_Restraint_Type, int], comment: str = '')[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

__init__(i1: int, j1: int, k1: int, l1: int, type1: Union[pygromos.files.blocks.topology_blocks.geometric_code, int], i2: int, j2: int, k2: int, l2: int, type2: Union[pygromos.files.blocks.topology_blocks.geometric_code, int], r0: float, w0: float, rah: Union[pygromos.files.blocks.topology_blocks.distant_Restraint_Type, int], comment: str = '')[source]¶

Parameters

i1 (int) – id of atom i of first molecule
j1 (int) – id of atom j of first molecule
k1 (int) – id of atom k of first molecule
l1 (int) – id of atom l of first molecule
type1 (int) – geometric restraintype of first molecule
i2 (int) – id of atom i of second molecule
j2 (int) – id of atom j of second molecule
k2 (int) – id of atom k of second molecule
l2 (int) – id of atom l of second molecule
type2 (int) – geometric restraintype of second molecule
r0 (float) – radius_0 of restraint
w0 (float) – weighting of restraint
rah (int) – restraint_type
comment (str, optional) – comment for this restraint

to_string()[source]¶

class pygromos.files.blocks.topology_blocks.bond_type(ICB: int, CB: float, HB: float, B0: float, atomI: Union[str, Iterable[str]], atomJ: Union[str, Iterable[str]], specialNumber: int)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

__init__(ICB: int, CB: float, HB: float, B0: float, atomI: Union[str, Iterable[str]], atomJ: Union[str, Iterable[str]], specialNumber: int)[source]¶

GROMOS bond-stretching parameters for one possible bond

Parameters

ICB (int) – Bond type code
CB (float) – Quartic bond-stretch force constant
HB (float) – Harmonic bond-stretch force constant
B0 (float) – Ideal bond length
atomI (str, Iterable[str]) – possible atom I useages
atomJ (str, Iterable[str]) – possible atom J useages
specialNumber (int) – No Idea @Todo: refactor later!

to_string()[source]¶

class pygromos.files.blocks.topology_blocks.bondangle_type(IT: int, JT: int, KT: int, ICT: int)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

__init__(IT: int, JT: int, KT: int, ICT: int)[source]¶

GROMOS bondangleype for a single pair

Parameters

IT (int) – atom number in angle
JT (int) – atom number in angle
KT (int) – atom number in angle
ICT (int) – bond angle type code

to_string()[source]¶

class pygromos.files.blocks.topology_blocks.bondanglebendtype_type(CT: float, CHT: float, T0: float)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

__init__(CT: float, CHT: float, T0: float)[source]¶

GROMOS bondanglebendtype for a single angle

Parameters

CT (float) – quartic force constant
CHT (float) – harmonic force constant
T0 (float) – angle at minimum energy

to_string()[source]¶

class pygromos.files.blocks.topology_blocks.bondstretchtype_type(CB: float, CHB: float, B0: float)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

__init__(CB: float, CHB: float, B0: float)[source]¶

GROMOS bondstretchtype for a single pair

Parameters

CB (float) – quartic force constant
CHB (float) – harmonic force constant
B0 (float) – bond length at minimum energy

to_string()[source]¶

class pygromos.files.blocks.topology_blocks.constraint_type(IC: int, JC: int, ICC: float)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

__init__(IC: int, JC: int, ICC: float)[source]¶

[summary]

Parameters

IC (int) – [description]
JC (int) – [description]
ICC (float) – [description]

to_string()[source]¶

class pygromos.files.blocks.topology_blocks.crossgihedral_type(AP: int, BP: int, CP: int, DP: int, EP: int, FP: int, GP: int, HP: int, ICC: int)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

__init__(AP: int, BP: int, CP: int, DP: int, EP: int, FP: int, GP: int, HP: int, ICC: int)[source]¶

GROMOS Cross Dihedral type for NON H Atoms

Parameters

AP (int) – number of atoms forming a dihedral
BP (int) – number of atoms forming a dihedral
CP (int) – number of atoms forming a dihedral
DP (int) – number of atoms forming a dihedral
EP (int) – number of atoms forming a dihedral
FP (int) – number of atoms forming a dihedral
GP (int) – number of atoms forming a dihedral
HP (int) – number of atoms forming a dihedral
ICC (int) – dihedral type code

to_string()[source]¶

class pygromos.files.blocks.topology_blocks.crossgihedralh_type(APH: int, BPH: int, CPH: int, DPH: int, EPH: int, FPH: int, GPH: int, HPH: int, ICCH: int)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

__init__(APH: int, BPH: int, CPH: int, DPH: int, EPH: int, FPH: int, GPH: int, HPH: int, ICCH: int)[source]¶

GROMOS Cross Dihedral type for H

Parameters

APH (int) – number of atoms forming a dihedral
BPH (int) – number of atoms forming a dihedral
CPH (int) – number of atoms forming a dihedral
DPH (int) – number of atoms forming a dihedral
EPH (int) – number of atoms forming a dihedral
FPH (int) – number of atoms forming a dihedral
GPH (int) – number of atoms forming a dihedral
HPH (int) – number of atoms forming a dihedral
ICCH (int) – dihedral type code

to_string()[source]¶

class pygromos.files.blocks.topology_blocks.dihedral_type(ICP: int, CP: float, PD: float, NP: int, atomI: str, atomJ: str, atomK: str, atomL: str, special_number: float, concrete_example: str = '')[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

__init__(ICP: int, CP: float, PD: float, NP: int, atomI: str, atomJ: str, atomK: str, atomL: str, special_number: float, concrete_example: str = '')[source]¶

GROMOS improper (harmonic) dihedral angle parameters

Parameters

ICQ (int) – Dihedral-angle type code
CQ (float) – Force constant
Q0 (float) – Phase shift
NP (float) – Multiplicity
atomI (str) – Examples for atomI
atomJ (str) – Examples for atomJ
atomK (str) – Examples for atomK
atomL (str) – Examples for atomL
special_number (int) – No Idea @Todo: refactor later!
concrete_example (str, optional) – giving a concrete example

to_string()[source]¶

class pygromos.files.blocks.topology_blocks.dihedralh_type(IPH: int, JPH: int, KPH: int, LPH: int, ICPH: int)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

__init__(IPH: int, JPH: int, KPH: int, LPH: int, ICPH: int)[source]¶: GROMOS dihedral for a single pair

to_string()[source]¶

class pygromos.files.blocks.topology_blocks.distant_Restraint_Type(value)[source]¶

Bases: enum.Enum

An enumeration.

full_harmonic_distance_restraint = 0¶

half_harmonic_attractive = 1¶

half_harmonic_repulsive = -1¶

class pygromos.files.blocks.topology_blocks.geometric_code(value)[source]¶

Bases: enum.Enum

An enumeration.

pseudo_H_atom_goc_H_atoms_CH3 = 5¶

pseudo_H_atoms_goc_of_three_CH3 = 7¶

pseudo_H_atoms_goc_of_two_CH3 = 6¶

real_atom = 0¶

virtual_H_atom_aliphaticC = 1¶

virtual_H_atom_aliphaticC_strange = 4¶

virtual_H_atom_aromaticC = 2¶

virtual_H_atoms_goc_aliph = 3¶

virtual_atoms_cog = -1¶

virtual_atoms_com = -2¶

class pygromos.files.blocks.topology_blocks.impdihedral_type(IQ: int, JQ: int, KQ: int, LQ: int, ICQ: int)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

__init__(IQ: int, JQ: int, KQ: int, LQ: int, ICQ: int)[source]¶

GROMOS impdihedral for a single pair

Parameters

IQ (int)
JQ (int)
KQ (int)
LQ (int) – IQ,JQ,KQ,LQ: atom sequence numbers of atoms forming an improper dihedral
ICQ (int) – improper dihedral type code

to_string()[source]¶

class pygromos.files.blocks.topology_blocks.impdihedralh_type(IQH: int, JQH: int, KQH: int, LQH: int, ICQH: int)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

__init__(IQH: int, JQH: int, KQH: int, LQH: int, ICQH: int)[source]¶

GROMOS impdihedralH for a single pair

Parameters

IQH (int)
JQH (int)
KQH (int)
LQH (int) – IQH,JQH,KQH,LQH: atom sequence numbers of atoms forming an improper dihedral
ICQH (int) – improper dihedral type code

to_string()[source]¶

class pygromos.files.blocks.topology_blocks.impdihedraltype_type(CQ: float, Q0: float)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

__init__(CQ: float, Q0: float)[source]¶

GROMOS impdihedraltype for a single pair

Parameters

CQ (float) – force constant of improper dihedral per degrees square
Q0 (float) – improper dihedral angle at minimum energy in degrees

to_string()[source]¶

class pygromos.files.blocks.topology_blocks.improper_dihedral_type(ICQ: int, CQ: float, Q0: float, group_type: str, special_number: int)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

__init__(ICQ: int, CQ: float, Q0: float, group_type: str, special_number: int)[source]¶

GROMOS improper (harmonic) dihedral angle parameters

Parameters

ICQ (int) – Improper dihedral-angle type code
CQ (float) – Force constant
Q0 (float) – Ideal improper dihedral angle
group_type (str) – Example Useage
special_number (int) – No Idea @Todo: refactor later!

to_string()[source]¶

class pygromos.files.blocks.topology_blocks.ljexception_type(AT1: int, AT2: int, C12: float, C6: float)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

__init__(AT1: int, AT2: int, C12: float, C6: float)[source]¶: GROMOS LJ exception pair

to_string()[source]¶

class pygromos.files.blocks.topology_blocks.ljparameters_type(IAC: int, JAC: int, C12: float, C6: float, CS12: float, CS6: float)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

__init__(IAC: int, JAC: int, C12: float, C6: float, CS12: float, CS6: float)[source]¶: GROMOS LJ parameter pair

to_string()[source]¶

class pygromos.files.blocks.topology_blocks.mixed_atom_lj_pair_type(IACI: int, IACJ: int, C6: float, C12_1: float, C12_2: float, C12_3: float)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

to_string()[source]¶

class pygromos.files.blocks.topology_blocks.single_atom_lj_pair_type(IAC: int, TYPE: str, C6: float, C12_1: float, C12_2: float, C12_3: float, CS6: float, CS12: float, LJ14PAIR: Iterable[float])[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

__init__(IAC: int, TYPE: str, C6: float, C12_1: float, C12_2: float, C12_3: float, CS6: float, CS12: float, LJ14PAIR: Iterable[float])[source]¶

Parameters

IAC (int) – vander wals type index.rst
TYPE (str) – atom type
C6 (float) – square-root of C6
C12_2 (float) – square-root of C6
C12_3 (float) – square-root of C6
CS6 (float) – No Idea @Todo: refactor later!
CS12 (float) – No Idea @Todo: refactor later!
LJ14PAIR (Iterable[float]) – No Idea @Todo: refactor later!

to_string()[source]¶

class pygromos.files.blocks.topology_blocks.soluteatom_type(ATNM: int, MRES: int, PANM: str, IAC: int, MASS: float, CG: float, CGC: int, INE: int, INEvalues: List[int], INE14: int, INE14values: List[int])[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

__init__(ATNM: int, MRES: int, PANM: str, IAC: int, MASS: float, CG: float, CGC: int, INE: int, INEvalues: List[int], INE14: int, INE14values: List[int])[source]¶

soluteatom_type

Parameters

ATNM (int) – [description]
MRES (int) – [description]
PANM (str) – [description]
IAC (int) – [description]
MASS (float) – [description]
CG (float) – [description]
CGC (int) – [description]
INE (int) – [description]
INEvalues ([type]) – [description]
INE14 (int) – [description]
INE14values ([type]) – [description]

to_string()[source]¶

class pygromos.files.blocks.topology_blocks.solventatom_type(I: int, ANMS: str, IACS: int, MASS: float, CGS: float)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

__init__(I: int, ANMS: str, IACS: int, MASS: float, CGS: float)[source]¶: GROMOS solventatom line

to_string()[source]¶

class pygromos.files.blocks.topology_blocks.solventconstr_type(ICONS: int, JCONS: int, CONS: float)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

__init__(ICONS: int, JCONS: int, CONS: float)[source]¶: GROMOS SOLVENTCONSTR entry

to_string()[source]¶

class pygromos.files.blocks.topology_blocks.special_atom_lj_pair_type(c)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

__init__(c)[source]¶

Parameters

IAC (int) – vander wals type index.rst
TYPE (str) – atom type
C6 (float) – square-root of C6
C12_2 (float) – square-root of C6
C12_3 (float) – square-root of C6
CS6 (float) – No Idea @Todo: refactor later!
CS12 (float) – No Idea @Todo: refactor later!
LJ14PAIR (Iterable[float]) – No Idea @Todo: refactor later!

to_string()[source]¶

class pygromos.files.blocks.topology_blocks.top_bond_type(IB: int, JB: int, ICB: int)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

__init__(IB: int, JB: int, ICB: int)[source]¶

GROMOS bond definition for a single pair

Parameters

IB (int) – Atom number i
JB (int) – Atom number j
ICB (int) – Bond type code

to_string()[source]¶

class pygromos.files.blocks.topology_blocks.top_dihedral_type(IP: int, JP: int, KP: int, LP: int, ICP: int)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

__init__(IP: int, JP: int, KP: int, LP: int, ICP: int)[source]¶: GROMOS dihedral for a single pair

to_string()[source]¶

class pygromos.files.blocks.topology_blocks.torsdihedraltype_type(CP: float, PD: float, NP: int)[source]¶

Bases: pygromos.files.blocks._general_blocks._generic_field

__init__(CP: float, PD: float, NP: int)[source]¶

GROMOS dihedraltype for a single pair

Parameters

CP (float) – force constant
PD (float) – phase-shift angle
NP (int) – multiplicity

to_string()[source]¶

Module contents¶

class pygromos.files.blocks.all_blocks_class[source]¶

Bases: object

This class is a very simplistic block library containing all present gromos blocks.

get_all_blocks() → dict[source]¶