FileWriter class

class AaronTools.fileIO.FileWriter

class for handling file writing

classmethod write_file(geom, style=None, append=False, outfile=None, *args, **kwargs)

Writes file from geometry in the specified style

Parameters:

• geom (Geometry) – the Geometry to use

• style (str) –

  the file type style to generate Currently supported options: “xyz” (default), “com”, “inp”, “inq”, “in”, “sqmin”, “cube”, “xtb”, “crest”, “mol”

  if outfile has one of these extensions, default is that style

• append (bool) – for *.xyz, append geometry to the same file

• outfile (str|None|False) – output destination - default is [geometry name] + [extension] or [geometry name] + [step] + [extension]

• kwargs (str) –

  allowed kwargs: * oniom * models * theory

  if outfile is False, no output file will be written, but the contents will be returned

• theory (Theory) – for com, inp, and in files, an object with a get_header and get_footer method

classmethod write_xyz(geom, append, outfile=None, comment=None, **kwargs)

write xyz file (file with coordinate system of input geometry)

Parameters:

• geom (Geometry) – molecule(s) to be written to the output

• append (bool) – whether the output should be appended to a file (True) or overwrite (False)

• outfile (str) – filename to append/write output to

Default/None: output file is the name of the geometry object provided (e.g. benzene.xyz if geom.name = ‘benzene’)

False: method simply returns the contents of the output file instead of writing/appending.

Parameters:

comment (str) – comment to be added to the output Default/None: comment is the same as the geom object’s comment

Returns:

xyz file contents if outfile=False, otherwise no return value

Return type:

str

classmethod write_multi_xyz(geom, append, outfile=None, **kwargs)

write multiple oniom xyz files from geometry with multiple poses such as a pdb derived geometry

Parameters:

• geom (Geometry) – molecule(s) to be written to the outputs

• append (bool) – whether the output should be appended to a file (True) or overwrite (False)

• outfile (str) – filename to append/write output to

Default/None: output file is the name of the geometry object provided (e.g. benzene.xyz if geom.name = ‘benzene’)

False: method simply returns the contents of the output file instead of writing/appending.

kwargs[“models”] can be string “all”, string of model number e.g. “2”, string of model range e.g. “1-5”,

or list of model numbers including ranges e.g. [“1”, “3-5”, “10”]

kwargs[“oniom”] can be string “all” or string “frag” which requires a specification of the fragment in another kwarg kwargs[“layer”] can be defined if kwargs[“oniom”] == “frag”, can be “H”, “M”, or “L”

classmethod write_oniom_xyz(geom, append, outfile=None, **kwargs)

write xyz files with additional columns for atomtype, charge, and link atom info

Parameters:

• geom (Geometry) – molecule(s) to be written to the outputs

• append (bool) – whether the output should be appended to a file (True) or overwrite (False)

• outfile (str) – filename to append/write output to

Default/None: output file is the name of the geometry object provided (e.g. benzene.xyz if geom.name = ‘benzene’)

False: method simply returns the contents of the output file instead of writing/appending.

kwargs[“oniom”] can be string “all” or string “frag” which requires a specification of the fragment in another kwarg kwargs[“layer”] can be defined if kwargs[“oniom”] == “frag”, can be “H”, “M”, or “L”

classmethod write_mol(geom, outfile=None, **kwargs)

write V2000 mol file

Parameters:

• geom (Geometry) – molecule(s) to be written

• outfile (str) – file to be written to

Default/None: output file is the name of the geometry object provided (e.g. benzene.mol if geom.name = ‘benzene’)

False: method simply returns the contents of the output file instead of writing.

classmethod write_com(geom, theory, outfile=None, return_warnings=False, **kwargs)

write Gaussian input file for given Theory and Geometry

Parameters:

• geom (Geometry) – structure

• theory (Theory) – input file parameters

• outfile (None|False|str) –

  output file option

  • None - geom.name + “.com” is used as output destination

  • False - return contents of the input file as a str

  • str - output destination

• return_warnings (bool) – True to return a list of warnings (e.g. basis set might be misspelled

• kwargs – passed to Theory methods (make_header, make_molecule, etc.)

classmethod write_inp(geom, theory, outfile=None, return_warnings=False, **kwargs)

write ORCA input file for the given Theory() and Geometry()

Parameters:

• geom (Geometry) – structure

• theory (Theory) – input file parameters

• outfile (None|False|str) –

  • None - geom.name + “.inp” is used as output destination

  • False - return contents of the input file as a str

  • str - output destination

• return_warnings (bool) – True to return a list of warnings (e.g. basis set might be misspelled

• kwargs – passed to Theory methods (make_header, make_molecule, etc.)

classmethod write_inq(geom, theory, outfile=None, return_warnings=False, **kwargs)

write QChem input file for the given Theory() and Geometry()

Parameters:

• geom (Geometry) – structure

• theory (Theory) – input file parameters

• outfile (None|False|str) –

  • None - geom.name + “.inq” is used as output destination

  • False - return contents of the input file as a str

  • str - output destination

• return_warnings (bool) – True to return a list of warnings (e.g. basis set might be misspelled

• kwargs – passed to Theory methods (make_header, make_molecule, etc.)

classmethod write_in(geom, theory, outfile=None, return_warnings=False, **kwargs)

write Psi4 input file for the given Theory() and Geometry()

Parameters:

• geom (Geometry) – structure

• theory (Theory) – input file parameters

• outfile (None|False|str) –

  • None - geom.name + “.in” is used as output destination

  • False - return contents of the input file as a str

  • str - output destination

• return_warnings (bool) – True to return a list of warnings (e.g. basis set might be misspelled

• kwargs – passed to Theory methods (make_header, make_molecule, etc.)

classmethod write_sqm(geom, theory, outfile=None, return_warnings=False, **kwargs)

write SQM input file for the given Theory() and Geometry()

Parameters:

• geom (Geometry) – structure

• theory (Theory) – input file parameters

• outfile (None|False|str) –

  • None - geom.name + “.sqmin” is used as output destination

  • False - return contents of the input file as a str

  • str - output destination

• return_warnings (bool) – True to return a list of warnings (e.g. basis set might be misspelled

• kwargs – passed to Theory methods (make_header, make_molecule, etc.)

classmethod write_cube(geom, orbitals=None, outfile=None, kind='homo', padding=4.0, spacing=0.2, alpha=True, xyz=False, n_jobs=1, delta=0.1, **kwargs)

write a cube file for a molecular orbital

Parameters:

• geom (Geometry) – structure

• orbitals (Orbitals) – orbital data

• outfile (str) – output destination

• kind (str|int) – index of molecular orbital or “homo” for ground state highest occupied molecular orbital or “lumo” for first ground state unoccupied MO can also be an array of MO coefficients

• alpha (bool) –

• xyz (bool) –

• ao (str|int) – index of atomic orbital to print

• padding (float) – padding around geom’s coordinates

• spacing (float) – targeted spacing between points

• n_jobs (int) – number of parallel threads to use this is on top of NumPy’s multithreading, so if NumPy uses 8 threads and n_jobs=2, you can expect to see 16 threads in use

• delta (float) – see Orbitals.fukui_donor_value or fukui_acceptor_value

classmethod write_pdb(geom, append, outfile=None, qt=False)

write input files for pdb

Parameters:

• geom (Geometry) – molecule to be written/appended

• append (bool) – appends instead of overwrites if True

• outfile (str) – file to be written to

Default/None: output file is the name of the geometry object provided (e.g. benzene.mol if geom.name = ‘benzene’)

False: method simply returns the contents of the output file instead of writing.

Parameters:

qt (bool) – determines charge spacing to be used for writing; True is 2, False is 10

classmethod write_xtb(geom, theory, outfile=None, return_warnings=False, **kwargs)

write input files for xtb

Parameters:

• geom (Geometry) – molecule to be written/appended

• theory (Theory) – theory to be used for xtb

• outfile (str) – file to be written to

Default/None: output file is the name of the geometry object provided (e.g. benzene.mol if geom.name = ‘benzene’)

False: method simply returns the contents of the output file instead of writing.

Parameters:

return_warnings (bool) – whether or not warnings should be returned

classmethod write_crest(geom, theory, outfile=None, return_warnings=False, **kwargs)

write crest input files

Parameters:

• geom (Geometry) – molecule to be written/appended

• theory (Theory) – theory to be used for crest

• outfile (str) – file to be written to

Default/None: output file is the name of the geometry object provided (e.g. benzene.mol if geom.name = ‘benzene’)

False: method simply returns the contents of the output file instead of writing.

Parameters:

return_warnings (bool) – whether or not warnings should be returned

static write_dict_files(contents, dirname, name)

write data to different files

Parameters:

• contents (dict) – keys are either a file name (includes a “.”) or a file extension (no “.”)

• dirname (str) –

  where to write files e.g. calling with contents as

  {“run.sh”: “cat {{ name }}.txt”, “txt”: “hi”}

  and name as “test” will write run.sh and test.txt to dirname

• name (str) – name of file to be written