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xyz_file

parse_traj_file(filename)

Convert a provided xmol .xyz file into an array of atomic numbers and cartesian positions

Parameters:

Name Type Description Default
filename

path to the .xyz file to read

 required

Returns:

Type Description

array of (N) atomic numbers and (N, 3) Cartesian positions read from

the given file
Source code in chmpy/fmt/xyz_file.py 
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def parse_traj_file(filename):
    """Convert a provided xmol .xyz file into an array of
    atomic numbers and cartesian positions

    Args:
        filename: path to the .xyz file to read

    Returns:
        array of (N) atomic numbers and (N, 3) Cartesian positions read from
        the given file
    """
    path = Path(filename)
    return parse_traj_string(path.read_text(), filename=str(path.absolute()))

parse_traj_string(contents, filename=None)

Convert provided xmol .xyz file contents into list of arrays of atomic numbers and cartesian positions

Parameters:

Name Type Description Default
contents

text contents of the .xyz file to read

 required

Returns:

Type Description

list of (N) :obj:Element and (N, 3) Cartesian positions read from

the given file
Source code in chmpy/fmt/xyz_file.py 
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def parse_traj_string(contents, filename=None):
    """Convert provided xmol .xyz file contents into list of arrays of
    atomic numbers and cartesian positions

    Args:
        contents: text contents of the .xyz file to read

    Returns:
        list of (N) :obj:`Element` and (N, 3) Cartesian positions read from
        the given file
    """
    lines = contents.splitlines()
    i = 0
    frames = []
    while i < len(lines):
        natom = int(lines[i].strip())
        elements = []
        positions = []
        i += 1
        comment = lines[i]
        i += 1
        for line in lines[i : i + natom]:
            if not line.strip():
                continue
            tokens = line.strip().split()
            xyz = tuple(float(x) for x in tokens[1:4])
            positions.append(xyz)
            elements.append(Element[tokens[0]])
        frames.append((elements, comment, np.asarray(positions)))
        i += natom
    return frames

parse_xyz_file(filename)

Convert a provided xmol .xyz file into an array of atomic numbers and cartesian positions

Parameters:

Name Type Description Default
filename

path to the .xyz file to read

 required

Returns:

Type Description

array of (N) atomic numbers and (N, 3) Cartesian positions read from

the given file
Source code in chmpy/fmt/xyz_file.py 
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def parse_xyz_file(filename):
    """Convert a provided xmol .xyz file into an array of
    atomic numbers and cartesian positions

    Args:
        filename: path to the .xyz file to read

    Returns:
        array of (N) atomic numbers and (N, 3) Cartesian positions read from
        the given file
    """
    path = Path(filename)
    return parse_xyz_string(path.read_text(), filename=str(path.absolute()))

parse_xyz_string(contents, filename=None)

Convert provided xmol .xyz file contents into an array of atomic numbers and cartesian positions

Parameters:

Name Type Description Default
contents

text contents of the .xyz file to read

 required

Returns:

Type Description

array of (N) atomic numbers and (N, 3) Cartesian positions read from

the given file
Source code in chmpy/fmt/xyz_file.py 
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def parse_xyz_string(contents, filename=None):
    """Convert provided xmol .xyz file contents into an array of
    atomic numbers and cartesian positions

    Args:
        contents: text contents of the .xyz file to read

    Returns:
        array of (N) atomic numbers and (N, 3) Cartesian positions read from
        the given file
    """
    lines = contents.splitlines()
    natom = int(lines[0].strip())
    LOG.debug("Expecting %d atoms %s", natom, "in " + filename if filename else "")
    elements = []
    positions = []
    for line in lines[2:]:
        if not line.strip():
            break
        tokens = line.strip().split()
        xyz = tuple(float(x) for x in tokens[1:4])
        positions.append(xyz)
        elements.append(Element[tokens[0]])
    LOG.debug(
        "Found %d atoms lines in %s",
        len(elements),
        "in " + filename if filename else "",
    )
    return elements, np.asarray(positions)