restraintmaker.io.Files package

Submodules

restraintmaker.io.Files.Gromacs_files module

Gromacs_files TODO:write DOCU! and code :)

class restraintmaker.io.Files.Gromacs_files.Gromacs_distanceRestraint_file(disres_funct: int = 1, disres_factor: int = 1, standard_up1: bool = False, standard_up2: bool = False)

Bases: object

block_name = 'distance_restraints'

build_disres(selected_restraints: List)

disres = []

header: List[str] = ['i', 'j', 'type', 'index', "type'", 'low', 'up1', 'up2', 'fac']

static load(in_path: str) → List[Tuple[int, int]]

This function is a very simple loading function, that gets the atom IDs of selected restratins in the in_file.

std_index: int = 1

std_low: float = 0.0

std_up1: float = 0.0

std_up2: float = 0.15

write(out_path: str) → str

class restraintmaker.io.Files.Gromacs_files.Gromacs_positionRestraint_file(std_funct: int = 1, std_fc: float = (1000, 1000, 1000))

Bases: object

block_name = 'position_restraints'

build_posres(selected_restraints: List)

header: List[str] = ['ai', 'funct', 'fc']

static load(in_path: str) → List[Tuple[int, int]]

This function is a very simple loading function, that gets the atom IDs of selected restratins in the in_file.

posres = []

std_fc: float = (1000, 1000, 1000)

std_funct: float = 0.0

write(out_path: str) → str

restraintmaker.io.Files.Gromacs_files.gmx_disres

alias of restraintmaker.io.Files.Gromacs_files.distanceRestraint

restraintmaker.io.Files.Gromacs_files.gmx_posres

alias of restraintmaker.io.Files.Gromacs_files.positionRestraint

restraintmaker.io.Files.Gromos_blocks module

THIS CODE WAS BORROWED FROM PYGROMOSTOOLS - Check it out :)

class restraintmaker.io.Files.Gromos_blocks.atomP(resID, resName, atomType, atomID, xp, yp, zp)

Bases: restraintmaker.io.Files.Gromos_blocks._generic_field

__init__(resID, resName, atomType, atomID, xp, yp, zp)

Args:

resID: resName: atomType: atomID: xp: yp: zp:

to_string() → str

class restraintmaker.io.Files.Gromos_blocks.atomV(resID, resName, atomType, atomID, xv, yv, zv)

Bases: restraintmaker.io.Files.Gromos_blocks._generic_field

__init__(resID, resName, atomType, atomID, xv, yv, zv)

Args:

resID: resName: atomType: atomID: xv: yv: zv:

to_string() → str

class restraintmaker.io.Files.Gromos_blocks.atom_pair_distanceRes(i1: int, j1: int, k1: int, l1: int, type1: restraintmaker.io.Files.Gromos_blocks.geometric_code, i2: int, j2: int, k2: int, l2: int, type2: restraintmaker.io.Files.Gromos_blocks.geometric_code, r0: float, w0: float, rah: restraintmaker.io.Files.Gromos_blocks.distant_Restraint_Type, comment: str = '')

Bases: restraintmaker.io.Files.Gromos_blocks._generic_field

__init__(i1: int, j1: int, k1: int, l1: int, type1: restraintmaker.io.Files.Gromos_blocks.geometric_code, i2: int, j2: int, k2: int, l2: int, type2: restraintmaker.io.Files.Gromos_blocks.geometric_code, r0: float, w0: float, rah: restraintmaker.io.Files.Gromos_blocks.distant_Restraint_Type, comment: str = '')

..function: Constructor of Gromos atom_pair_distanceRes

Args:

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: 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: r0 (float): radius_0 of restraint w0 (float): weighting of restraint rah: restraint_type comment (str):

to_string()

class restraintmaker.io.Files.Gromos_blocks.atom_pos_block(content: List[restraintmaker.io.Files.Gromos_blocks.atomP])

Bases: restraintmaker.io.Files.Gromos_blocks._generic_gromos_block

__init__(content: List[restraintmaker.io.Files.Gromos_blocks.atomP])

Args:

content:

block_to_string() → str

class restraintmaker.io.Files.Gromos_blocks.atom_ref_pos_block(content: list)

Bases: restraintmaker.io.Files.Gromos_blocks._generic_gromos_block

__init__(content: list)

Args:

content (list):

block_to_string() → str

class restraintmaker.io.Files.Gromos_blocks.atom_vel_block(content: List[restraintmaker.io.Files.Gromos_blocks.atomV])

Bases: restraintmaker.io.Files.Gromos_blocks._generic_gromos_block

__init__(content: List[restraintmaker.io.Files.Gromos_blocks.atomV])

Args:

content:

block_to_string() → str

class restraintmaker.io.Files.Gromos_blocks.distance_res_spec_block(KDISH: int, KDISC: int, RESTRAINTHEADER: list, RESTRAINTS: list)

Bases: restraintmaker.io.Files.Gromos_blocks._generic_gromos_block

__init__(KDISH: int, KDISC: int, RESTRAINTHEADER: list, RESTRAINTS: list)

Args:

KDISH (int): KDISC (int): RESTRAINTHEADER (list): RESTRAINTS (list):

block_to_string() → str

class restraintmaker.io.Files.Gromos_blocks.distant_Restraint_Type(value)

Bases: enum.Enum

An enumeration.

full_harmonic_distance_restraint = 0

half_harmonic_attractive = 1

half_harmonic_repulsive = -1

class restraintmaker.io.Files.Gromos_blocks.genbox_block(pbc: enum.Enum, length: list, angles: list, euler: list, origin: list)

Bases: restraintmaker.io.Files.Gromos_blocks._generic_gromos_block

__init__(pbc: enum.Enum, length: list, angles: list, euler: list, origin: list)

Args:

pbc (Enum): length (list): angles (list): euler (list): origin (list):

block_to_string() → str

class restraintmaker.io.Files.Gromos_blocks.geometric_code(value)

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 restraintmaker.io.Files.Gromos_blocks.lattice_shift(atomID, x, y, z)

Bases: restraintmaker.io.Files.Gromos_blocks._generic_field

__init__(atomID, x, y, z)

Args:

atomID: x: y: z:

to_string() → str

class restraintmaker.io.Files.Gromos_blocks.lattice_shifts_block(content: List[restraintmaker.io.Files.Gromos_blocks.lattice_shift])

Bases: restraintmaker.io.Files.Gromos_blocks._generic_gromos_block

__init__(content: List[restraintmaker.io.Files.Gromos_blocks.lattice_shift])

Args:

content:

block_to_string() → str

class restraintmaker.io.Files.Gromos_blocks.timestep_block(t: float, step: int, subcontent=False)

Bases: restraintmaker.io.Files.Gromos_blocks._generic_gromos_block

__init__(t: float, step: int, subcontent=False)

Args:

t (float): step (int): subcontent:

block_to_string() → str

class restraintmaker.io.Files.Gromos_blocks.title_block(content)

Bases: restraintmaker.io.Files.Gromos_blocks._generic_gromos_block

__init__(content)

Args:

content:

block_to_string() → str

order = [[['content']]]

restraintmaker.io.Files.Gromos_files module

THIS CODE WAS BORROWED FROM PYGROMOSTOOLS - Check it out :)

class restraintmaker.io.Files.Gromos_files.disres(in_path: Optional[str] = None)

Bases: restraintmaker.io.Files.Gromos_files.general_gromos_file

__init__(in_path: Optional[str] = None)

Args:

in_path:

parse_disres_file(path: str) → dict

Args:

path (str):

read_disres_file(path: str)

Args:

path (str):

required_blocks: List[str] = ['TITLE', 'DISTANCERESPEC']

class restraintmaker.io.Files.Gromos_files.general_gromos_file(in_path: Optional[str] = None)

Bases: object

__init__(in_path: Optional[str] = None)

Args:

in_path:

_read_gromos_block(lines: list)

Args:

lines (list):

add_block(blocktitle: str, content: dict, verbose: bool = False)

Args:

blocktitle (str): content (dict): verbose (bool):

blocksset: List[dict] = []

content: Dict[str, Any]

path: str

required_blocks: List[str] = ['TITLE']

write(path)

Args:

path:

Module contents