ACCeL is a python package that enables batch processing of conformational isomers, making it easy to create, run, and analyze files for computational chemistry programs and automate calculation processes.

Installation

pip install accel

Examples

from accel import Box
Box("*.log").read_atoms().read_energy().energy_limit().rmsd_limit().write_input("template_file.inp")

How to use "Box"

add(contents)

Adds files to the Box. Contents can be specified flexibly as directory name, filename, wildcard, iterative object, etc.

read_atoms(filetype=None, **options)

Read coordinate information and other information from files.

check_end(filetype=None, **options)

Verify that output files are terminated successfully.

read_energy(filetype=None, **options)

Read energy values from output files.

read_correction(filetype=None, **options)

Read thermodynamic correction values from output files.

check_freq(filetype=None, **options)

Read frequencis from files and check the number of imaginary frequencies.

run(filetype=None, **options)

Execute files and wait for them to complete.

submit(filetype=None, **options)

Execute all files immediately.

calc_free_energy(filetype=None, **options)

Calculate the free energy using loaded values.

labeling(separator="_", index_list=[0, 1])

Set the label name (isomer name other than the conformational isomer) automatically. By default, a conformation with the name KEF20958_a_256 will have the label KEF20958_a. Therefore, it is recommended that the file name handled in ACCeL be BaseName_IsomerName_Number.

set_data(key, value=None)

Set data in batches.

set_state(flag=True)

Set state at once.

set_label(label="")

Set label names in batches.

zero_fill(digit=3, separator="_", position=3)

Fill in the numbers in the name with zeros. By default, KEF20958_a_2 is set to KEF20958_a_002.

count(comment="")

Count up the number of active systems with their respective labels.

export_data(filepath)

Output information on the conformers to a CSV file.

energy_limit(threshold=3.0, max_limit=None, in_label=True)

Enable only stable conformation (default 3.0 kcal/mol) per label.

calc_rel_energy(in_label=True)

Convert energy values to relative values.

calc_distribution(in_label=True, temperature=298.15)

The Boltzmann distribution is calculated according to energy values. By default, it is calculated for each label.

calc_energy(keys=[], unit=Units.kcal_mol)

The data specified for keys are added together and the energy value is calculated.

copy_files(directory, change_path=False, suffix=None)

Duplicate the file in directory.

search(directory=None, existing_check=True, suffix=None)

Search for files with the same name in directory.

read_xyz()

Read coordinate information, etc. from XYZ files (.xyz).

write_xyz(directory=None, change_path=True, centering=True)

Export XYZ files.

read_mol()

Read coordinate information, etc. from MOL files (.mol, .sdf, .sd).

write_mol(directory=None, change_path=True, centering=True)

Export MOL files.

write_input(template, directory=None, change_path=True)

Create an input file. The following keywords in the template will be replaced. #NAME# -> name #LABEL# -> label name #AXYZ# -> Element name + XYZ list #ATOMS# -> number of atoms #CHG# -> charge #MULT# -> multiplicity #ENRGY# -> energy value #PATH# -> file path #DATA[]# -> data value

calc_bonds(cov_scaling=1.1, vdw_scaling=1.0)

Embed bonding information. Necessary to calculate the symmetric information.

calc_symm(calc_all=True)

Embed symmetry information; required for RMSD calculations.

rmsd_limit(threshold=0.01, all_combinations_of_confs=False, redundant_check=3, all_perturbation_of_rotamers=False)

Disable one conformation among the conformations whose RMSD is less than a certain value. In other words, it removes the identical conformations. The default value is 0.01 angstrom.

map_numbers(reference_box=None)

Correct misnumbering of the same substituent (e.g., two H's in methylene) between conformations.

calc_length(number_a, number_b, key="")

Calculate the distance between atoms.

calc_dihedral(number_a, number_b, number_c, number_d, key="")

Calculate the dihedral angle between atoms.

calc_angle(number_a, number_b, number_c, key="")

Calculate the angle between atoms.

modify_length(number_a, number_b, target, fix_a=False, fix_b=False, numbers_along_with_a=[], numbers_along_with_b=[])

Correct the distance between atoms.

convert_to_mirror(centering=True)

Convert to a mirror image.

only_minimum(in_label=True)

Enable only the most stable conformation. The default is to calculate with the respective label.

get() -> Systems

Returns the Systems of the active coordination group.

get_average(keys=[], keys_for_atoms=[]) -> Systems

Return Systems for the locus group with energy-weighted average data for each label.

duplicate() -> Box

Returns a duplicate Box.