BigDFT.IO module

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

read_pdb(ifile, include_chain=False, disable_warnings=False, ignore_connectivity=False, ignore_unit_cell=False, charmm_format=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.
charmm_format (bool) – Accepts Charmm-format.

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)

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.

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)

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_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.

read_yaml(ifile)[source]

Read a system from a yaml file. This assumes that we’re getting something in the posinp format: i.e. we have a position and unit key.

Parameters:: ifile (TextIOBase) – the file to read from.
Returns:: the system file.
Return type:: (BigDFT.Systems.System)

write_yaml(sys, ofile)[source]

Write a system to a yaml file with the posinp format.

Parameters:

sys (BigDFT.Systems.System) – the system to write.
ofile (TextIOBase) – the file to write to.

class XYZReader(filename)[source]

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.

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

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.

write(atomdict)[source]

Write an atom to the file.

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

_example()[source]

The following is an example of module usage:

"""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()