Reading and Writing Other File Formats

  • import cctk is assumed.

  • cctk was originally designed with Gaussian in mind, but has some limited support for other file formats. Please consider OpenBabel for more extensive file conversion needs.

XYZ Files

  • cctk assumes the first line is the number of atoms, the second line is the title, and the third and subsequent lines are geometry specifications of the form atom_symbol x_position y_position z_position.

  • For xyz files containing multiple structures, concatenate blocks of the above form without any separating blank lines.

# read xyz
path = "test/static/test_peptide.xyz"
file = cctk.XYZFile.read_file(path)

# file contents
file.titles[0] == "peptide example"
ensemble = file.ensemble

# convenient accessor
molecule = file.get_molecule()

# if the file contains multiple molecules
for molecule, title in zip(ensemble.molecule_list(), file.titles):
    print(title)
    print(molecule)
    break

# write xyz
assert isinstance(molecule2, Molecule)
XYZFile.write_molecule_to_file(filename, molecule2, title="title"):

MOL2 Files

  • Both single and multiple structures per .mol2 are supported.

# read a single structure
path = "test/static/dodecane.mol2"
file = cctk.MOL2File.read_file(path)
assert isinstance(file, cctk.MOL2File)
ensemble = file.ensemble
assert isinstance(ensemble, cctk.ConformationalEnsemble)
len(ensemble) == 1
molecule = ensemble.molecules[0]

# read multiple structures
path = "test/static/dodecane-csearch.mol2"
file = cctk.MOL2File.read_file(path)
assert isinstance(file, cctk.MOL2File)
ensemble = file.ensemble
assert isinstance(ensemble, cctk.ConformationalEnsemble)
len(ensemble) == 597

# write one structure
filename2 = "my_filename.mol2"
cctk.MOL2File.write_molecule_to_file(filename2, molecule, title)

# write multiple structures
filename3 = "your_filename.mol2"
cctk.MOL2File.write_ensemble_to_file(filename3, ensemble)

  • Setting print_status_messages to True will print progress to stdout.

  • For large files that contain only conformers, set contains_conformers to True.

  • This will skip many consistency checks and avoid the redundant copying of many data structures. This speeds up performance by over 10x.

# faster reading of MOL2 files with conformers
file = cctk.MOL2File.read_file(path, print_status_messages=False, contains_conformers=True)

Maestro Files

  • Only reading is supported.

  • Both single and multiple structures are supported.

# read .mae file
path = "test/static/dodecane_csearch-out.mae"
file, pnames, pvals = cctk.MAEFile.read_file(path)
assert isinstance(file, cctk.MAEFile)

# file contents
ensemble = file.ensemble
assert isinstance(ensemble, cctk.ConformationalEnsemble)
len(ensemble) == 597
len(pnames) == 597
len(pvals) == 597