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
- 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
- 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
- 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 thenext
command to iterate over it.- 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.