gaddlemaps.parsers package

Module contents

Simulation Files Parsers

This submodule contains some useful functionalities to read and extract information from files coming from molecular simulation programs. Up to now, only files in the format used by GROMACS are contemplated (.gro and .itp formats).

class gaddlemaps.parsers.CoordinatesParser(path, mode='r')

Bases: object

Attributes

EXTENSIONS

box_matrix

Return a 3x3 matrix with the 3 lattice vectors

comment

A comment/name of the system

natoms

Number of atoms in the file

Methods

close()	Closes the file
next()	Returns next atomline formatted
seek_atom(index)	Displaces the position of the 'cursor' to an atom line
writeline(atomlist)	Writes a line of atom information
writelines(list_atomlist)	Writes several lines of atoms

EXTENSIONS: Optional[Tuple[str, ...]] = None

abstract property box_matrix: ndarray

Return a 3x3 matrix with the 3 lattice vectors

Return type

ndarray

abstract close()

Closes the file

abstract property comment: str

A comment/name of the system

Return type

str

abstract property natoms: int

Number of atoms in the file

Return type

int

abstract next()

Returns next atomline formatted

Return type

Union[Tuple[int, str, str, int, float, float, float], Tuple[int, str, str, int, float, float, float, float, float, float]]

abstract seek_atom(index)

Displaces the position of the ‘cursor’ to an atom line

Displaces the position of the ‘cursor’ to the beginning of the line of the ‘index’ atom, where the first atom index is 0. This function warrants that calling the “next” function the information about atom “index” will be returned.

Parameters

index (int) – The index of the atom to found

abstract writeline(atomlist)

Writes a line of atom information

If there was no content written in the file it creates the header and the number of atoms. If the number of atoms was not provided it will kept empty and the number will be written just before closing the file. This possibility is only compatible with a number of atoms smaller than 1000000.

Parameters

atomlist (list or string) – A list with all the info of the atom, just like the one returned by readline. If it is a string, it will be written directly without parsing.

writelines(list_atomlist)

Writes several lines of atoms

Parameters

list_atomlist (list of list of str or int or float) – A list of lists with all the info of the atom, just like the one returned by readline

class gaddlemaps.parsers.GroFile(path, mode='r')

Bases: CoordinatesParser

Implements a file object for opening and writing .gro files

Grofile verifies the gromacs format, and autodetects the correct way to read the file. It modifies the methods read and write of a common file with methods that take as input lists with all the info of an atom. The readlines and writelines are modified to take (return) lists with the info of an atom in lists (as returned by the read function).

This class can also be initiated with an already opened file.

Note

The “+” modifier for the open mode is not allowed right now

Parameters

• path (str or TextIOWrapper) – The path to the file to be opened or the opened file.

• mode (str) – “r” to open the file in read mode and “w” to open it in write mode.

Raises

IOError – If the gro file has not the correct format

Attributes

box_matrix

numpy.ndarray(3,3): the 3 lattice vectors of the box.

comment

string: The comment of the .gro file.

name

str: The filename of the open file

natoms

integer: The number of atoms in the system.

position_format

tuple of int : the number of total figures and decimal places for the

Methods

close()	Closes the file
determine_format(atomline)	Returns the format of the postion coordinates and whether or not the .gro file has velocities
next()	Returns next atomline formatted
parse_atomline(atomline[, format_dict])	Parses an atom line and returns its content in a list.
parse_atomlist(atomlist[, format_dict])	Convert a list of atom info to string with the appropriate format
readline([parsed])	Returns the next line of the gro file.
readlines()	Returns all the lines of a grofile parsed in lists.
seek_atom(index)	Displaces the position of the 'cursor' to an atom line
validate_string(string)	Validates a string to be valid as resname or as name.
writeline(atomlist)	Writes a line of atom information
writelines(list_atomlist)	Writes several lines of atoms

COORD_START = 20

DEFAULT_COMMENT = "Gro file genereted with 'Gromacs Tools' python module."

DEFAULT_POSTION_FORMAT = (8, 3)

EXTENSIONS: Optional[Tuple[str, ...]] = ('gro', 'GRO')

NUMBER_FIGURES = 9

property box_matrix: ndarray

the 3 lattice vectors of the box.

Type

numpy.ndarray(3,3)

Return type

ndarray

close()

Closes the file

If the file is in write mode it will write al the remaining information.

property comment: str

The comment of the .gro file.

Type

string

Return type

str

classmethod determine_format(atomline)

Returns the format of the postion coordinates and whether or not the .gro file has velocities

Parameters

atomline (str) – An atom line from the .gro file

Returns

form – Dictionary with 2 keys, “position” and “velocities”. The position key leads to a tuple with 2 ints. THe first in is the number of characters in the float format (C) and the second is the number of decimal places in the float (D), i.e. corresponds to the ‘%C.Df’ format.

Return type

dict

property name: str

The filename of the open file

Type

str

Return type

str

property natoms: int

The number of atoms in the system.

Type

integer

Return type

int

next()

Returns next atomline formatted

Return type

Union[Tuple[int, str, str, int, float, float, float], Tuple[int, str, str, int, float, float, float, float, float, float]]

classmethod parse_atomline(atomline, format_dict=None)

Parses an atom line and returns its content in a list.

Parses an atom line and returns its content in a list. In its default behaviour the input line is analyzed and the number of decimals are guessed. It is also possible to insert the format in a format dictionary. This is a dictionary with 2 keys, “position” and “velocities”. The position key leads to a tuple with 2 ints. The first in is the number of characters in the float format (C) and the second is the number of decimal places in the float (D), i.e. corresponds to the ‘%C.Df’ format.

Parameters

• atomline (str) – An string with a line from a grofile

• format_dict (dict_format (optional)) – None or dictionary with 2 keys, “position” and “velocities”. The position key leads to a tuple with 2 ints. THe first in is the number of characters in the float format (C) and the second is the number of decimal places in the float (D), i.e. corresponds to the ‘%C.Df’ format. If None the format will be automatically guessed. Default None.

Returns

info –

A list with the following information:

• mol_index(integer)

• resname (string)

• name (string)

• global_index (integer)

• x, y, z (floats)

• vx, vy ,vz (floats) [optional]

Return type

list

classmethod parse_atomlist(atomlist, format_dict=None)

Convert a list of atom info to string with the appropriate format

Parses a list with the atom information and returns its content in a string with the correct format to write in a .gro file. In its default behaviour the input line is analyzed and the number of decimals are guessed. It is also possible to insert the format in a format dictionary. This is a dictionary with 2 keys, “position” and “velocities”. The position key leads to a tuple with 2 ints. The first is the number of characters in the float format (C) and the second is the number of decimal places in the float (D), i.e. corresponds to the ‘%C.Df’ format.

Parameters

• atomlist (list) –

  A list with the following information:

  • mol_index(integer)

  • resname (string)

  • name (string)

  • global_index (integer)

  • x, y, z (floats)

  • vx, vy ,vz (floats) [optional]]

• format_dict (dict (optional)) – None or dictionary with 2 keys, “position” and “velocities”. The position key leads to a tuple with 2 ints. THe first in is the number of characters in the float format (C) and the second is the number of decimal places in the float (D), i.e. corresponds to the ‘%C.Df’ format. If None the format will be automatically guessed. Default None.

Returns

atomline – An string with a line from a .gro file

Return type

str

property position_format: Tuple[int, int]

the number of total figures and decimal places for the positions.

Type

tuple of int

Return type

Tuple[int, int]

readline(parsed=True)

Returns the next line of the gro file.

If parsed=True (default) the data on the atom line is parsed and returned in a list. If false the line is returned as an string (just like if it were opened as a common file.)

Parameters

parsed (bool (optional)) – Wether the data of the line should be parsed or not. Default: True

Returns

info – Returns the info of the line, i alist if it was parsed or in a string if not

Return type

str or list

readlines()

Returns all the lines of a grofile parsed in lists.

Returns

info – Returns a list with the info of all the atom lines in lists

Return type

list(list)

seek_atom(index)

Displaces the position of the ‘cursor’ to an atom line

Displaces the position of the ‘cursor’ to the beginning of the line of the ‘index’ atom, where the first atom index is 0. If the index is equal to the number of atoms the beginning of the box lattice line is found.

Parameters

index (int) – The index of the atom to found

static validate_string(string)

Validates a string to be valid as resname or as name.

If the input name has more than 5 characters, new name is returned cutting the input one.

Parameters

string (str) – The string to validate.

Returns

new_string – The properly formatted string.

Return type

str

writeline(atomlist)

Writes a line of atom information

If there was no content written in the file it creates the header and the number of atoms. If the number of atoms was not provided it will kept empty and the number will be written just before closing the file. This possibility is only compatible with a number of atoms smaller than 1000000.

Parameters

atomlist (list or string) – A list with all the info of the atom, just like the one returned by readline. If it is a string, it will be written directly without parsing.

writelines(list_atomlist)

Writes several lines of atoms

If there was no content written in the file it creates the header and the number of atoms. If the number of atoms was not provided it will kept empty and the number will be written just before closing the file. This possibility is only compatible with a number of atoms smaller than 1000000.

Parameters

list_atomlist (list of list of str or int or float) – A list of lists with all the info of the atom, just like the one returned by readline

class gaddlemaps.parsers.ParserManager

Bases: object

Methods

register

parsers: Dict[str, Type[CoordinatesParser]] = {'GRO': <class 'gaddlemaps.parsers.GroFile'>, 'gro': <class 'gaddlemaps.parsers.GroFile'>}

classmethod register(parser)

class gaddlemaps.parsers.ParserRegistered(name, bases, attrs)

Bases: ABCMeta

Methods

__call__(*args, **kwargs)	Call self as a function.
mro(/)	Return a type's method resolution order.
register(subclass)	Register a virtual subclass of an ABC.

mro(/)

Return a type’s method resolution order.

register(subclass)

Register a virtual subclass of an ABC.

Returns the subclass, to allow usage as a class decorator.

gaddlemaps.parsers.dump_lattice_gro(vectors)

Extracts final line of a .gro file from the lattice vectors for pbc.

Parameters

vectors (numpy.ndarray((3,3))) – An array with a lattice vector in each row.

Returns

line – The final line of a .gro file.

Return type

string

gaddlemaps.parsers.extract_lattice_gro(line)

Extracts the lattice vectors for pbc from the final line of a .gro file.

Parameters

line (string) – The final line of a .gro file.

Returns

vectors – An array with a lattice vector in each row.

Return type

numpy.ndarray((3,3))

gaddlemaps.parsers.open_coordinate_file(filename, mode='r')

Return type

CoordinatesParser