Non-physical species model¶

TCKDB backend app models non-physical species (np_species) module

class tckdb.backend.app.models.np_species.NonPhysicalSpecies(**kwargs)[source]¶

A class for representing a TCKDB NonPhysicalSpecies item.

Note

All atom indices in these arguments are 1-indexed unless explicitly stated otherwise.

id¶

The primary key (not a user input).

Type: int

label¶

A free user label for the species (maximum 255 characters).

Type: Optional[str]

# provenance

timestamp¶

The UTC timestamp of uploading the data to TCKDB (not a user input).

Type: float

retracted¶

A reason for retracting this object. Default: None (not a user input).

Type: str

# review

reviewed¶

Whether this entry was reviewed (not a user input).

Type: bool

approved¶

If reviewed, whether it was approved (not a user input).

Type: bool

reviewer_flags¶

Backend flags to assist the review process (automatically determined, but users may add notes to flag items for the reviewer).

Example:

{'general': 'This species has a shallow (1.5 kJ/mol) well along the 4-8-7-10 torsional mode.'}

Type: Dict[str, str]

# chemical identifiers

smiles¶

The canonical SMILES descriptor with chirality information.

Note

Either smiles, inchi, or graph must be specified.

Type: Optional[str]

inchi¶

The InChI descriptor with an explicit H layer and chirality information.

Note

Either smiles, inchi, or graph must be specified.

Type: Optional[str]

inchi_key¶

The InChI key descriptor. Automatically assigned if not given by the user.

Type: Optional[str]

charge¶

The net molecular charge.

Type: int

multiplicity¶

The spin multiplicity.

Type: int

electronic_state¶

The species electronic state at CIS level. Default: 'X' (denoting ground state).

Type: Optional[str]

# geometry and connectivity

coordinates¶

Cartesian coordinates in standard orientation. Keys (values) are:

‘symbols’ (Tuple[str])
Chemical element symbols
‘isotopes’ (Tuple[int])
The respective isotopes
‘coords’ (Tuple[Tuple[float]])
The respective coordinates

Example for methane:

{'symbols': ('C', 'H', 'H', 'H', 'H'),
 'isotopes': (12, 1, 1, 1, 1),
 'coords': ((0.0, 0.0, 0.0),
            (0.6300326, 0.6300326, 0.6300326),
            (-0.6300326, -0.6300326, 0.6300326),
            (-0.6300326, 0.6300326, -0.6300326),
            (0.6300326, -0.6300326, -0.6300326))}

Type: Dict[str, Union[Tuple[Tuple[float, float, float], …], Tuple[int, …], Tuple[str, …]]]

graph¶

A 2D connectivity graph in an RMG adjacency list format. Note that this graph represents a single Lewis structure (resonance structure). These graphs can be generated using RMG’s API or online at https://rmg.mit.edu/molecule_search.

Note

Either smiles, inchi, or graph must be specified.

Example for methane:

multiplicity 1
C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
H u0 p0 c0 {1,S}
H u0 p0 c0 {1,S}
H u0 p0 c0 {1,S}
H u0 p0 c0 {1,S}

Type: Optional[str]

fragments¶

Fragments represented by this species, e.g., VdW wells. Entries are atom index lists of all atoms in a fragment. Default: None (denoting there’s only one fragment).

Type: Optional[List[List[int]]]

fragment_orientation¶

Relative orientation of fragments, starting from the heaviest one. All fragments must be in standard Cartesian orientation prior to determining the following parameters. Entries are dictionaries with the following keys (values):

‘cm’ (List[float])
A vector pointing from a fragment’s center to the center of mass of the next fragment.

Units:
Angstrom

‘x’ (float)
The X axis rotational angle in degrees.

‘y’ (float)
The Y axis rotational angle in degrees.

‘z’ (float)
The Z axis rotational angle in degrees.

Type: Optional[List[Dict[str, Union[float, List[float]]]]]

chirality¶

The species’ chiral centers, following the Cahn–Ingold–Prelog (CIP) notation ('R' or 'S' for atom centers, 'E' or 'Z' for double bond centers). Keys are tuples of atom indices of a chiral center, values are string representations of the respective chiral center.

Note: Non-radical valance 3 nitrogen atoms are also considered chiral if connected to three different groups (considering the lone pair to always be a unique fourth group). In such cases, use a 'NR' or 'NS' notation.

Example

A double bond with chirality 'E' between atoms 1-2, an 'S' chiral center on atom 3, and an 'S' chiral center on atom 6 which is a nitrogen are represented as:

{(1, 2): 'E', (3,): 'S', (6,): 'NS'})

Type: Optional[Dict[Tuple[int], str]]

conformation_method¶

The method used to determine the lowest energy conformer. Required if the species has 4 or more atoms.

Type: Optional[str]

is_well¶

Whether this conformer represents a local well (at the opt level used).

Type: bool

is_global_min¶

If this conformer is a well, whether it is meant to represents the global minimum energy well.

Type: bool

global_min_geometry¶

If this species does not represent the global minimum well, this argument must contain the coordinates of the global minimum energy conformer at the same opt level.

Type: Optional[Dict[str, tuple]]

# TS

is_ts¶

Whether this species represents a transition state. Default: False.

Type: bool

irc_trajectories¶

The two IRC trajectories. Each trajectory is a list of coordinates dictionaries. Required if the species is a transition state. Cannot be specified for non-TS species.

Type: Optional[List[List[Dict[str, tuple]]]]

# relationships - Many to One

literature_id¶

The literature reference from the Literature table.

Type: int

literature¶

An attribute that establishes a bidirectional relationship in a One to Many data model with the Literature table, where the “reverse” side is a Many to One data model.

Type: relationship

bot_id¶

The bot used to generate the object from the Bot table.

Type: int

bot¶

An attribute that establishes a bidirectional relationship in a One to Many data model with the Bot table, where the “reverse” side is a Many to One data model.

Type: relationship

opt_level¶

An attribute that establishes a bidirectional relationship in a One to Many data model with the Level table, where the “reverse” side is a Many to One data model.

Type: Optional[relationship]

freq_level¶

An attribute that establishes a bidirectional relationship in a One to Many data model with the Level table, where the “reverse” side is a Many to One data model.

Type: Optional[relationship]

scan_level¶

An attribute that establishes a bidirectional relationship in a One to Many data model with the Level table, where the “reverse” side is a Many to One data model.

Type: Optional[relationship]

irc_level¶

An attribute that establishes a bidirectional relationship in a One to Many data model with the Level table, where the “reverse” side is a Many to One data model.

Type: Optional[relationship]

sp_level¶

An attribute that establishes a bidirectional relationship in a One to Many data model with the Level table, where the “reverse” side is a Many to One data model. Required.

Type: Optional[relationship]

opt_ess¶

An attribute that establishes a bidirectional relationship in a One to Many data model with the ESS table, where the “reverse” side is a Many to One data model.

Type: Optional[relationship]

freq_ess¶

An attribute that establishes a bidirectional relationship in a One to Many data model with the ESS table, where the “reverse” side is a Many to One data model.

Type: Optional[relationship]

scan_ess¶

An attribute that establishes a bidirectional relationship in a One to Many data model with the ESS table, where the “reverse” side is a Many to One data model.

Type: Optional[relationship]

irc_ess¶

An attribute that establishes a bidirectional relationship in a One to Many data model with the ESS table, where the “reverse” side is a Many to One data model.

Type: Optional[relationship]

sp_ess¶

An attribute that establishes a bidirectional relationship in a One to Many data model with the ESS table, where the “reverse” side is a Many to One data model. Required.

Type: Optional[relationship]

# relationships - Many to Many

authors¶

An attribute that establishes a bidirectional relationship in a Many to Many data model with the Person table representing authors of this object.

Type: relationship

reviewers¶

An attribute that establishes a bidirectional relationship in a Many to Many data model with the Person table representing reviewers of this object.

Type: relationship

# paths

opt_path¶

The path to the optimization output file. Required for polyatomic species (with 2 or more atoms).

Type: Optional[str]

freq_path¶

The path to the frequencies calculation output file. Required for polyatomic species (with 2 or more atoms).

Type: Optional[str]

scan_paths¶

Paths to the torsion scan calculation output files. Keys are tuples of tuples. The number of inner-level tuples corresponds to the torsion dimension. Entries of the inner-level tuple are torsion atom indices. Values are paths to the respective scan calculation log file.

Type: Optional[Dict[Tuple[Tuple[int, int, int, int], …], str]]

irc_paths¶

Entries are paths to the IRC calculation output files. Required for transition states. Either a single path to a forward+reverse IRC, or two respective paths.

Type: Optional[List[str]]

sp_path¶

The path to the single point energy output file. Unlike the Species object, here sp_path is optional.

Type: Optional[str]

# unconverged jobs

unconverged_jobs¶

Any relevant unconverged jobs that were troubleshooted while calculating this Species. Entries are dictionaries, keys (values) are:

‘job type’ (str): 'opt', 'freq', 'scan', 'irc', or 'sp'

‘issue’ (str): The identified issue

‘troubleshooting’ (str): Description of the troubleshooting method(s) that solved the issue

‘comment’ (str): An optional comment explaining the troubleshooting approach

‘path’ (str): The path to the relevant unconverged ESS log file

Type: Optional[List[Dict[str, str]]]

# misc

extras¶

Any additional information in the form of a dictionary Unlike the Species object, here extras is required and should at least contain a reason for declaring this species non-physical.

Type: Dict[str, Any]