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)[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)

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.

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.