5.2. ligandparam.io.gaussianIO

class ligandparam.io.gaussianIO.GaussianInput(command='# HF/6-31G* OPT', elements=None, initial_coordinates=None, charge=0, multiplicity=1, header=None)[source]

Bases: object

Initialize a Gaussian block with the specified parameters.

Parameters:

command (str, optional) – The command for the Gaussian calculation
elements (list, optional) – A list of atomic symbols
initial_coordinates (np.array, optional) – A numpy array of atomic coordinates
charge (int, optional) – The charge of the molecule
multiplicity (int, optional) – The multiplicity of the molecule
header (list, optional) – A list of strings to be included in the header of the Gaussian input file

Methods

generate_block()

Generates the gaussina input block as a list of strings

print

generate_block()[source]

Generates the gaussina input block as a list of strings

This function generates the Gaussian input block as a list of strings. This is useful for writing the block to a file, or printing it to the screen.

Parameters:: None
Return type:: None

print()[source]

class ligandparam.io.gaussianIO.GaussianReader(filename)[source]

Bases: object

This is a class for reading Gaussian log files and pulling out information from them.

Parameters:: filename (str) – The name of the Gaussian log file to read

Methods

`check_complete`()	Check if the Gaussian calculation is complete
`read_log`()	Read the Gaussian log file, and extract information from it.

check_complete()[source]

Check if the Gaussian calculation is complete

This function checks if the Gaussian calculation is complete. This is done by reading the Gaussian log file and checking for the presence of the “Normal termination” string.

Parameters:: None
Returns:: True if the calculation is complete, False otherwise
Return type:: bool

read_log()[source]

Read the Gaussian log file, and extract information from it.

This is adapted from ReadGauOutput in Tim Giese’s parmutils package. This reads the shebang at the end of the file, which contains information about the calculation final results. This works by parsing based on the delimiter in this section.

Parameters:

None

Returns:

atn (list) – A list of atomic symbols
coords (list) – A list of atomic coordinates
charge (int) – The charge of the molecule
multiplicity (int) – The multiplicity of the molecule
To Do
—–
- Add error handling for missing data
- Check that this reads only the FINAL geometry

class ligandparam.io.gaussianIO.GaussianWriter(filename)[source]

Bases: object

Class for writing Gaussian input files

The filename selected will be the name of the Gaussian input file that is written to disk. The class also initializes the number of links to zero, and creates an empty list to store the GaussianInput objects.

Parameters:: filename (str) – The name of the file to write
Return type:: None

Methods

`add_block`(block)	Add a GaussianInput block to the GaussianWriter
`get_run_command`([extension])	Get the command to run the Gaussian input file
`print`()	Print the Gaussian input file to the screen
`write`([dry_run])	Write the Gaussian input file to a file

add_block(block)[source]

Add a GaussianInput block to the GaussianWriter

This function adds a GaussianInput block to the GaussianWriter. This block will be written to the Gaussian input file when the write() function is called.

Parameters:: block (GaussianInput) – The GaussianInput block to add to the GaussianWriter
Return type:: None

get_run_command(extension='.com')[source]

Get the command to run the Gaussian input file

This function returns a string that can be used to run the Gaussian input file. This is useful for debugging, or for running the Gaussian input file from a script.

Parameters:: extension (str, optional) – The extension of the Gaussian input file
Returns:: The command to run the Gaussian input file
Return type:: str

print()[source]

Print the Gaussian input file to the screen

This function prints the Gaussian input file to the screen. This is useful for debugging, or for checking the contents of the file before writing it to disk.

Parameters:: None
Return type:: None

write(dry_run=False)[source]

Write the Gaussian input file to a file

This function writes the Gaussian input file to disk. If dry_run is set to True, the file will not be written to disk, but will be printed to the screen instead. This is useful for debugging. The file is written in the Gaussian input file format, with the LINK1 blocks separated by the –Link1– delimiter.

Parameters:: dry_run (bool, optional) – If True, the file will not be written to disk
Return type:: None