BigDFT.IO module¶

This module defines some tools used for reading/writing fragment files.

class XYZReader(filename)[source]¶

Bases: object

A class which can be used to read from xyz files.

This class should behave like a standard file, which means you can use it in with statements, and use the next command to iterate over it.

closed¶

check if a file is open or not.

Type: bool

units¶

the units that the xyz file was in.

Type: str

natoms¶

the number of atoms in the xyz file.

Type: int

cell¶

a list of floats describing the cell.

Type: list

Parameters: filename (str) – the file to read from. You can also specify a molecule that might be in the database.

close()[source]¶

property closed¶

next()[source]¶

open()[source]¶

class XYZWriter(filename, natoms, units='angstroem', cell=None)[source]¶

Bases: object

A class for writing XYZ files.

This class should behave like a standard file, which means you can use it in with statements and write.

Parameters

filename (str) – the file to write to.
natoms (int) – how many atoms we will write.
units (str) – the units of the file. Defaults to angstroem.
cell (BigDFT.UnitCells.UnitCell) – the unit cell.

close()[source]¶

property closed¶

open()[source]¶

write(atomdict)[source]¶

Write an atom to the file.

Parameters: atom (dict) – a dictionary describing the atom.

read_mol2(ifile, disable_warnings=False)[source]¶

Read a system from a mol2 file.

Parameters

ifile (TextIOBase) – the file to read from.
disable_warnings (bool) – whether to print warnings about possible file issues.

Returns

the system file.

Return type

(BigDFT.Systems.System)

read_pdb(ifile, include_chain=False, disable_warnings=False, ignore_connectivity=False, ignore_unit_cell=False)[source]¶

Read a system from a PDB file.

Parameters

ifile (TextIOBase) – the file to read from.
disable_warnings (bool) – whether to print warnings about possible file issues.
include_chain (bool) – include the chain id if True
ignore_connectivity (bool) – if True do not store the information about the connectivity matrix.
ignore_unit_cell (bool) – assumes free boundary conditions if true.

Warning

This will read in the connectivity information from the pdb as well. However, a pdb file does not provide any information about the bond order. Thus, the bond order of each bond will be set to one.

Returns: the system file.
Return type: (BigDFT.Systems.System)

read_xyz(ifile, fragmentation='atomic')[source]¶

Read a system from an xyz file. XYZ files do not contain any information about fragments, so this routine will make each atom its own fragment.

Parameters

ifile (TextIOBase) – the file to read from.
fragmentation (str) – either “atomic” or “single”.

Returns

the system file.

Return type

(BigDFT.Systems.System)

reorder_fragments(frags)[source]¶

write_mol2(system, ofile)[source]¶

Write out a system to a string in the mol2 format.

Parameters

system (BigDFT.Systems.System) – the system to write.
ofile (TextIOBase) – the output stream to write to.

Returns

a string representation of the file.

Return type

(str)

write_pdb(system, ofile)[source]¶

Write out a system to a string in the pdb format.

Parameters

system (BigDFT.Systems.System) – the system to write.
ofile (TextIOBase) – the output stream to write to.

write_xyz(system, ofile)[source]¶

Write out a system to a file in the xyz format.

Parameters

system (BigDFT.Systems.System) – the system to write.
ofile (TextIOBase) – the output stream to write to.
cell (list) – the unit cell.

BigDFT.IO example¶

Below we show an example of using the IO routines.

def _example():
    """Test the XYZ Module"""
    from BigDFT.Systems import System
    from BigDFT.Fragments import Fragment
    from BigDFT.UnitCells import UnitCell
    file = "Si4"

    safe_print("First let's try reading an XYZ file.")
    atom_list = []
    with XYZReader(file) as reader:
        safe_print(reader.closed)
        for at in reader:
            atom_list.append(at)
    safe_print(reader.closed)
    safe_print(atom_list)
    safe_print()

    safe_print("Now let's try writing an XYZ file.")
    safe_print()
    with XYZWriter("test.xyz", len(atom_list),
                   units=reader.units) as writer:
        safe_print(writer.closed)
        for at in atom_list:
            writer.write(at)
    safe_print(writer.closed)
    safe_print()
    with open("test.xyz") as ifile:
        for line in ifile:
            safe_print(line, end='')
    safe_print()

    safe_print("Print with various boundary conditions")
    with XYZWriter("test.xyz", len(atom_list), reader.units,
                   cell=UnitCell()) as writer:
        for at in atom_list:
            writer.write(at)
    with XYZReader("test.xyz") as ifile:
        print(ifile.cell.get_boundary_condition())

    with XYZWriter("test.xyz", len(atom_list), reader.units,
                   cell=UnitCell([5, 5, 5])) as writer:
        for at in atom_list:
            writer.write(at)
    with XYZReader("test.xyz") as ifile:
        print(ifile.cell.get_boundary_condition())

    with XYZWriter("test.xyz", len(atom_list), reader.units,
                   cell=UnitCell([5, float("inf"), 5])) as writer:
        for at in atom_list:
            writer.write(at)
    with XYZReader("test.xyz") as ifile:
        print(ifile.cell.get_boundary_condition())

    with XYZWriter("test.xyz", len(atom_list), reader.units,
                   cell=UnitCell([float("inf"), float("inf"), 5])) as writer:
        for at in atom_list:
            writer.write(at)
    with XYZReader("test.xyz") as ifile:
        print(ifile.cell.get_boundary_condition())
    safe_print()

    safe_print("Now let's demonstrate the pdb and mol2 writer")
    sys = System()
    sys["FRAG:0"] = Fragment(atom_list)
    with open("test.pdb", "w") as ofile:
        write_pdb(sys, ofile)
    with open("test.pdb") as ifile:
        for line in ifile:
            safe_print(line, end='')
    safe_print()

    with open("test.mol2", "w") as ofile:
        write_mol2(sys, ofile)
    with open("test.mol2") as ifile:
        for line in ifile:
            safe_print(line, end='')
    safe_print()