matmacore.mol module

class matmacore.mol.Mol(path=None)

Bases: object

A class that can parse log files from different Computational Software. It can parse log files from Gaussian 16, xvg files from Gromacs, out files from ORCA, and log files from CP2K.

connectivity_matrix(distXX=1.65, distXH=1.15)

Creates a connectivity matrix of the molecule. A connectivity matrix holds the information of which atoms are bonded and to what.

Parameters:

• distXX – The max distance between two atoms (not hydrogen) to be considered a bond

• distXH – The max distance between any atom and a hydrogen atom to be considered a bond

cp2k(file=None, job_type='md', colvar=None, timestep=None)

Parses information from CP2K. Right now only works for AIMD Trajectories, plan to implement opt compatability later.

Parameters:

• job_type – (string) Currently only md is supported. Should be manually specified.

• colvar – (list) A list containing the atom numbers that define your collective variable.

• timestep – (float) Timestep of your MD calculation. The function will attempt to extract this from your input file if present.

• traj_file – (string) File containing the CP2K trajectory.

• input_file – (string) File containing your CP2K inputs.

• output_file – (string) File containing your CP2K output.

csv(file, skiprows=1, dtype=<class 'float'>, delimiter: str = ', ')

Parses a csv file and appends the data to the mol object

Parameters:

• file – (string) File containing the csv data.

• skiprows – (int) Number of rows to skip

• dtype – (type) Data type

• delimiter – (str) Delimiter

element_symbol()

A dictionary for atomic number and atomic symbol :param A: either atomic number or atomic symbol for Hydrogen, Carbon, Nitrogen, Oxygen, Fluorine and Silicon :return: the corresponding atomic symbol or atomic number

gaussian()

Parses log files from Gaussian 16 and appends information inside the log file to the mol object.

gromacs(file=None)

Parses information from gromacs *.xvg file

Parameters:

file – (string) File containing the gromacs data.

orca(output_file='input.log', job_type='opt')

Parses information from ORCA input.log file :param output_file: (string) File containing ORCA output file. :param job_type: (string) The type of calculation ORCA run.

class matmacore.mol.Reaction(mol_list, mol_label)

Bases: object

A class that organizes several molecules into a reaction

static combiner(mol_list)

Adds the energies for multiple molecules and returns a new mol object.

Parameters:

mol_list – (list) List of molecule objects.

Returns:

mol

create_mol_list()

Creates Mol objects from user-specified groups of directories and labels.

Parameters:

*groups – Variable number of groups, where each group is a list of directories followed by a label.

Returns:

List of Mol objects. mol_label (list): List of labels for the Mol objects.

Return type:

mol_list (list)

create_reaction_list()

Creates a standardized reaction list with names from input definitions.

Parameters:

*reaction_definitions – Variable number of reaction definitions where each is: (reaction_name, [dir1, dir2, ‘label’], [dir3, ‘label’], …)

Returns:

[(reaction_name, mol_list, labels), …]

Return type:

list

delta()

Calculates the energy differences for a reaction