diff --git a/genindex.html b/genindex.html index 624a9b99..8e230e81 100644 --- a/genindex.html +++ b/genindex.html @@ -352,7 +352,6 @@

Index

A - | B | C | D | E @@ -360,30 +359,21 @@

Index

| G | H | I - | J | K | L | M - | N | O | P - | Q | R | S | T | U - | V | W - | X

A

+ -
-

B

- - - -
-

C

@@ -518,59 +432,23 @@

C

D

-

E

- +
@@ -578,19 +456,11 @@

E

F

- +
  • fix_CO_openbabel() (in module rdmc.utils)
    • -
  • formed_bonds (rdmc.reaction.Reaction property) -
    • -
  • FourierSeries1D (class in rdmc.mathlib.curvefit) -
    • -
  • freq_viewer() (in module rdmc.view) -
    • -
  • freqs (rdmc.external.logparser.base.CclibLog property) -
    • -
  • from_complex() (rdmc.conformer_generation.align.NaiveAlign class method) -
    • -
  • from_r_and_p_complex() (rdmc.conformer_generation.align.NaiveAlign class method) -
    • -
    @@ -896,58 +596,12 @@

    H

    I

    - -
    - -

    J

    - -
    @@ -975,53 +629,11 @@

    M

    @@ -1077,113 +663,27 @@

    M

  • (rdmc.forcefield.RDKitFF property)
    • -
  • mol_animation() (in module rdmc.view) -
    • -
  • mol_to_dict() (in module rdmc.conformer_generation.utils) + +
    • + +

    O

    + + -
    - -

    N

    - - -
    - -

    O

    - - -
    @@ -1191,59 +691,15 @@

    O

    P

    -
    - -

    Q

    - - -
    @@ -1251,140 +707,15 @@

    Q

    R

    - +
    • rdmc.external.inpwriter.utils @@ -1428,48 +757,8 @@

      R

    • module
    -
  • - rdmc.external.logparser - -
    • -
  • - rdmc.external.logparser.base - -
    • -
  • - rdmc.external.logparser.gaussian - -
    • -
  • - rdmc.external.logparser.orca - -
    • -
  • - rdmc.external.logparser.qchem - -
    • -
  • - rdmc.external.logparser.utils - -
    • +
    • rdmc.external.rmg @@ -1482,34 +771,6 @@

      R

      • -
    • - rdmc.mathlib - -
      • -
    • - rdmc.mathlib.curvefit - -
      • -
    • - rdmc.mathlib.geom - -
      • -
    • - rdmc.mathlib.greedymin - -
    • @@ -1517,20 +778,6 @@

      R

      • -
    • - rdmc.reaction - -
      • -
    • - rdmc.ts - -
    • @@ -1540,15 +787,6 @@

      R

    • module
    -
  • - rdmc.view - -
    • -
  • Reaction (class in rdmc.reaction) -
  • recover_mol() (rdmc.forcefield.RDKitFF method)
  • Reflect() (rdmc.mol.RDKitMol method) @@ -1556,26 +794,10 @@

    R

  • RemoveHs() (rdmc.mol.RDKitMol method)
  • RenumberAtoms() (rdmc.mol.RDKitMol method) -
    • -
  • require_bond_analysis() (rdmc.reaction.Reaction method) -
    • -
  • require_job_type() (rdmc.external.logparser.base.BaseLog method) -
    • -
  • require_ts() (rdmc.external.logparser.base.BaseLog method) -
    • -
  • reset_atom_maps() (rdmc.conf.ConformerFilter method) -
    • -
  • reset_pmol() (in module rdmc.conformer_generation.align)
  • reverse_map() (in module rdmc.utils)
  • rmg_mol_to_rdkit_mol() (in module rdmc.utils) -
    • -
  • RMSDPPGuesser (class in rdmc.conformer_generation.ts_guessers) -
    • -
  • rotate() (in module rdmc.mathlib.geom) -
    • -
  • rotate_fragment_separately() (rdmc.conformer_generation.align.NaiveAlign method)
    • @@ -1593,65 +815,17 @@

    S

  • SaturateMol() (rdmc.mol.RDKitMol method)
    • -
  • save_guesses() (rdmc.conformer_generation.ts_guessers.TSInitialGuesser method) -
    • -
  • save_opt_mols() (rdmc.conformer_generation.optimizers.GaussianOptimizer method) - -
    • -
  • SCGMetric (class in rdmc.conformer_generation.metrics) -
    • -
  • scheme_to_dict() (in module rdmc.external.logparser.utils) -
    • -
  • schemes (rdmc.external.logparser.base.BaseLog property) -
    • -
  • score_bimolecule() (rdmc.conformer_generation.align.NaiveAlign method) -
    • -
  • search_for_a_minimum() (in module rdmc.mathlib.greedymin) -
    • -
  • search_minimum() (in module rdmc.mathlib.greedymin) -
    • -
  • SellaOptimizer (class in rdmc.conformer_generation.ts_optimizers) -
    • -
  • set_config() (rdmc.conformer_generation.generators.StochasticConformerGenerator method) -
    • -
  • set_filter() (rdmc.conformer_generation.generators.ConformerGenerator method) - -
  • SetVdwMatrix() (rdmc.mol.RDKitMol method) -
    • -
  • split_by_energies() (rdmc.conf.ConformerCluster method) -
    • -
  • StochasticConformerGenerator (class in rdmc.conformer_generation.generators) -
    • -
  • success (rdmc.external.logparser.base.BaseLog property)
    • @@ -1673,46 +841,20 @@

    S

    T

    - -
    - -

    V

    - - -

    W

    @@ -1820,8 +898,6 @@

    W

  • write_gaussian_irc() (in module rdmc.external.inpwriter.gaussian)
  • write_gaussian_opt() (in module rdmc.external.inpwriter.gaussian) -
    • -
  • write_mol_data() (rdmc.conformer_generation.embedders.ConfGenEmbedder method)
    • -

    X

    - - - -
    - diff --git a/index.html b/index.html index b59fae93..3add7b4e 100644 --- a/index.html +++ b/index.html @@ -382,7 +382,7 @@

    RDMC Documentationrxn = Reaction('CCO>>CC(=O)O') -

    And see what the mol and rxn are capable of! The full lists of APIs of RDKitMol and Reaction are provided in this documentation.

    +

    And see what the mol and rxn are capable of! The full lists of APIs of RDKitMol and Reaction are provided in this documentation.

    We also provided a few notebooks (available in \ipython and Colab) to demonstrate the usage of RDMC. Please feel invited to try them out!

    RDMC is developed by

  • rdmc.external.logparser
    • diff --git a/reference/external/logparser/base.html b/reference/external/logparser/base.html index 18545e96..5a6ce296 100644 --- a/reference/external/logparser/base.html +++ b/reference/external/logparser/base.html @@ -464,518 +464,8 @@
    -
    -

    rdmc.external.logparser.base#

    -
    -
    -class rdmc.external.logparser.base.BaseLog(path: str, job_type: list | None = None, ts: bool | None = None)#
    -

    Bases: object

    -

    The base class helps to parse the log files and provides information -helpful to analyze the calculation.

    -
    -
    -auto_update_prop()#
    -

    A decorator to update the property automatically.

    -
    -
    Parameters:
    -

    update_fun (str) – The method name for the update function.

    -
    -
    -

    Examples

    -

    This decorator can be used as follows:

    -
    @property
-@auto_update_prop('update_prop1')
-def prop1(self):
-    "docstring for prop1"
-
-def update_prop1(self):
-    # define how to get the value of prop1
-    # and set the value to self._prop1
-
    -
    -
    - -
    -
    -property finished#
    -
    - -
    -
    -property is_ts#
    -
    - -
    -
    -property job_type#
    -
    - -
    -
    -opt_criteria = []#
    -
    - -
    -
    -require_job_type()#
    -

    A decorator to check the job type.

    -
    - -
    -
    -require_ts()#
    -

    A decorator to check if the job involves ts.

    -
    - -
    -
    -property schemes#
    -
    - -
    -
    -property success#
    -
    - -
    -
    -property termination_time#
    -
    - -
    -
    -time_regex = ''#
    -
    - -
    - -
    -
    -class rdmc.external.logparser.base.CclibLog(path: str, job_type: list | None = None, ts: bool | None = None)#
    -

    Bases: BaseLog

    -

    This class parses the log files using cclib.

    -
    -
    -property all_geometries#
    -

    Return all geometries in the file as a numpy array.

    -
    -
    Returns:
    -

    np.ndarray

    -
    -
    -
    - -
    -
    -property cclib_results#
    -

    Get the cclib results.

    -
    - -
    -
    -property charge#
    -

    The charge of the molecule.

    -
    -
    Returns:
    -

    int

    -
    -
    -
    - -
    -
    -property converged_geometries#
    -

    Return converged geometries as a numpy array.

    -
    -
    Returns:
    -

    np.ndarray

    -
    -
    -
    - -
    -
    -property freqs#
    -

    Return the frequency as a numpy array.

    -
    - -
    -
    -get_best_opt_geom(*args, **kwargs)#
    -
    - -
    -
    -get_converged_geom_idx(as_numbers: bool = False)#
    -

    Return the indexes of geometries that are converged. By default, a -numpy array of True and False will be returned. But you can output numeric -results by changing the argument.

    -
    -
    Parameters:
    -

    as_numbers (bool) – Whether returns a list of numbers. Defaults to False for better performance.

    -
    -
    Returns:
    -

    np.array

    -
    -
    -
    - -
    -
    -get_irc_midpoint(*args, **kwargs)#
    -
    - -
    -
    -get_lowest_e_geometry(as_xyz: bool = False)#
    -

    Get the geometry with the lowest energy in a job. By default its ID is returned.

    -
    -
    Parameters:
    -

    as_xyz (bool) – if True, the xyz str is returned rather than ID.

    -
    -
    Returns:
    -
      -

    • - int – the ID of the conformer

      • -

    • - str – the XYZ of the conformer

      • -
    -
    -
    -
    - -
    -
    -get_mol(refid: int = -1, embed_conformers: bool = True, converged: bool = True, neglect_spin: bool = True, backend: str = 'openbabel', sanitize: bool | None = None) → RDKitMol#
    -

    Perceive the xyzs in the file, create a rdmc.mol.RDKitMol() and convert the geometries to its conformers.

    -
    -
    Parameters:
    -
      -

    • refid (int) –

      The conformer ID in the log file to be used as the reference for mol perception. -Defaults to -1, meaning it is determined by the following criteria:

      -
        -

      • For opt, it is the last geometry if succeeded; otherwise, the initial geometry;

        • -

      • For freq, it is the geometry input;

        • -

      • For scan, it is the geometry input;

        • -

      • For IRC, uses the initial geometry if bidirectional job; uses the last converged -geometry if uni-directional job.

        • -
      -

      • -

    • embed_confs (bool) – Whether to embed intermediate conformers in the file to the obtained molecule. -Defaults to True. To be clear, at least one conformer will be included in -obtained mol, and its geometry is determined by refid.

      • -

    • converged (bool) – Whether to only embed converged conformers to the obtained molecule. This option -is only valid when embed_confs is True.

      • -

    • neglect_spin (bool) – Whether to neglect the error when spin multiplicity are different -between the generated mol and the value in the output file. This -can be useful for calculations involves TS. Defaults to True.

      • -

    • backend (str) – The backend engine for parsing XYZ. Defaults to 'openbabel'.

      • -

    • sanitize (bool) – Whether to sanitize the generated molecule. Defaults to True. -If a TS involved in the job, better to set it False.

      • -
    -
    -
    Returns:
    -

    RDKitMol – a molecule generated from the output file.

    -
    -
    -
    - -
    -
    -get_scannames(*args, **kwargs)#
    -
    - -
    -
    -get_scanparams(*args, **kwargs)#
    -
    - -
    -
    -get_scf_energies(converged: bool = True, only_opt: bool = False, relative: bool = False)#
    -

    Get SCF energies in kcal/mol.

    -
    -
    Parameters:
    -
      -

    • converged (bool) – Only get the SCF energies for converged geometries.’ -Defaults to True.

      • -

    • only_opt (bool) – For composite method like CBS-QB3, you can choose only to -return SCF energies only for the optimization step. Defaults -to False.

      • -

    • relative (bool) – Only return the value relative to the minimum. Defaults to False.

      • -
    -
    -
    Returns:
    -

    np.array – The SCF energies.

    -
    -
    -
    - -
    -
    -get_xyzs(converged: bool = True, initial_geom: bool = True)#
    -

    Get the xyz strings of geometries stored in the output file.

    -
    -
    Parameters:
    -
      -

    • converged (bool) – Only return the xyz strings for converged molecules. -Defaults to True.

      • -

    • initial_geom (bool) – By default cclib_results will replace the geometry 1 (index 0) -with the converged geometry. This options allows to keep the -geometry 1 as the input geometry. Defaults to True.

      • -
    -
    -
    -
    - -
    -
    -guess_rxn_from_irc(*args, **kwargs)#
    -
    - -
    -
    -guess_rxn_from_normal_mode(amplitude: float = 0.25, atom_weighted: bool = False, inverse: bool = False, backend: str = 'openbabel')#
    -

    Guess the reactants and products from the mode of the imaginary frequency. Note: this -result is not deterministic depending on the amplitude you use.

    -
    -
    Parameters:
    -
      -

    • amplitude (int) – The amplitude factor on the displacement matrix to generate the -guess geometry for the reactant and the product. A smaller factor -makes the geometry close to the TS, while a wildly large factor -makes the geometry nonphysical. Can be either a float or a list of floats.

      • -

    • atom_weighted (bool) – If use the sqrt(atom mass) as a scaling factor to the displacement. -The concern is that light atoms (e.g., H) tend to have larger motions -than heavier atoms.

      • -

    • inverse (bool) – Inverse the direction of the reaction. Defaults to False.

      • -

    • backend (str) – The backend engine for parsing XYZ. Defaults to 'openbabel'.

      • -
    -
    -
    -
    - -
    -
    -property initial_geometry#
    -

    Return the initial geometry of the job. For scan jobs and ircs jobs. -Intermediate guesses will not be returned.

    -
    - -
    -
    -interact_freq()#
    -

    Create a IPython interactive widget to investigate the frequency calculation.

    -
    - -
    -
    -interact_irc(sanitize: bool = False, converged: bool = True, backend: str = 'openbabel', continuous_update: bool = False) → <ipywidgets.widgets.interaction._InteractFactory object at 0x7f3e07cf2710>#
    -

    Create a IPython interactive widget to investigate the IRC results.

    -
    -
    Parameters:
    -
      -

    • sanitize (bool) – Whether to sanitize the molecule. Defaults to False.

      • -

    • converged (bool) – Whether to only embed converged conformers to the mol. Defaults to True.

      • -

    • backend (str) – The backend engine for parsing XYZ. Defaults to 'openbabel'.

      • -

    • continuous_update (bool) – Whether to update the widget continuously. Defaults to False.

      • -
    -
    -
    Returns:
    -

    interact

    -
    -
    -
    - -
    -
    -interact_opt(sanitize: bool = True, backend: str = 'openbabel', continuous_update: bool = False) → <ipywidgets.widgets.interaction._InteractFactory object at 0x7f3e07cf2710>#
    -

    Create a IPython interactive widget to investigate the optimization convergence.

    -
    -
    Parameters:
    -
      -

    • sanitize (bool, optional) – Whether to sanitize the molecule. Defaults to True.

      • -

    • backend (str) – The backend engine for parsing XYZ. Defaults to 'openbabel'.

      • -

    • continuous_update (bool) – Whether to update the widget continuously. Defaults to False.

      • -
    -
    -
    Returns:
    -

    interact

    -
    -
    -
    - -
    -
    -interact_scan(*args, **kwargs)#
    -
    - -
    -
    -property multiplicity#
    -

    Get the multiplicity.

    -
    -
    Returns:
    -

    int

    -
    -
    -
    - -
    -
    -property neg_freqs#
    -

    Return the imaginary frequency as a numpy array.

    -
    - -
    -
    -property num_all_geoms#
    -

    Return the number of all geometries.

    -
    -
    Returns:
    -

    int

    -
    -
    -
    - -
    -
    -property num_converged_geoms#
    -

    Return the number of converged geometries. Useful in IRC and SCAN jobs.

    -
    -
    Returns:
    -

    int

    -
    -
    -
    - -
    -
    -property num_neg_freqs#
    -

    Return the number of imaginary frequencies.

    -
    -
    Returns:
    -

    int

    -
    -
    -
    - -
    -
    -property opt_convergence#
    -
    - -
    -
    -property optstatus#
    -

    Return the geometry optimization status

    -
    - -
    -
    -plot_irc_energies(converged: bool = True, relative: bool = True, highlight_index: int | None = None, ax: matplotlib.pyplot.axes = None)#
    -

    Plot the energy curve for the IRC trajectory. Note, the sequence may be altered if -the IRC is a two-way calculation.

    -
    -
    Parameters:
    -
      -

    • converged (bool) – If only returns energies for converged geometries. Defaults to True.

      • -

    • relative (bool) – If plot relative values (to the highest values). Defaults to True.

      • -

    • highlight_index (int) – highlight the data corresponding to the given index.

      • -

    • ax (axes) – An existing matplotlib axes instance.

      • -
    -
    -
    -
    - -
    -
    -plot_opt_convergence(logy: bool = True, relative: bool = True, highlight_index: int | None = None, ax=None)#
    -

    Plot the convergence curve from the convergence table.

    -
    -
    Parameters:
    -
      -

    • logy (bool) – If using log scale for the y axis. Defaults to True.

      • -

    • relative (bool) – If plot relative values (to the target values). Defaults to True.

      • -

    • highlight_index (int) – highlight the data corresponding to the given index.

      • -

    • () (ax) –

      • -
    -
    -
    -
    - -
    -
    -plot_scan_energies(converged: bool = True, relative_x: bool = True, relative_y: bool = True, highlight_index: int | None = None, ax: matplotlib.pyplot.axes = None, draw_fit: bool = True)#
    -

    Plot the energy curve for the scan trajectory.

    -
    -
    Parameters:
    -
      -

    • converged (bool) – If only returns energies for converged geometries. Defaults to True.

      • -

    • relative_x (bool) – If plot relative values (to the initial values). -Only valid for scan trajectories. Defaults to True.

      • -

    • relative_y (bool) – If plot relative values (to the lowest values). Defaults to True.

      • -

    • highlight_index (int) – Highlight the data corresponding to the given index. Defaults to None, no hightlighting.

      • -

    • ax (axes) – Draw on an existing matplotlib axes instance. Defaults to None, creating a new axes.

      • -

    • draw_fit (bool, optional) – Whether to draw a Fouries series fitted to the energies. Only valid for dihedral scans. -It will be drawn as an orange dotted curve. Defaults to True.

      • -
    -
    -
    -
    - -
    -
    -view_freq(mode_idx: int = 0, frames: int = 10, amplitude: float = 1.0, *args, **kwargs) → <ipywidgets.widgets.interaction._InteractFactory object at 0x7f3e07cf2710>#
    -

    Create a Py3DMol viewer for the frequency mode.

    -
    -
    Parameters:
    -
      -

    • mode_idx (int) – The index of the frequency mode to display. Defaults to 0.

      • -

    • frames (int) – The number of frames of the animation. The larger the value, -the slower the change of the animation. Defaults to 10.

      • -

    • amplitude (float) – The magnitude of the mode change. Defaults to 1.0.

      • -
    -
    -
    Returns:
    -

    interact

    -
    -
    -
    - -
    -
    -view_mol(backend: str = 'openbabel', sanitize: bool = False, *args, **kwargs)#
    -

    Create a Py3DMol viewer for the molecule. By default, it will shows either -the initial geometry or the converged geometry depending on what job type -involved in the file.

    -
    -
    Parameters:
    -
      -

    • backend (str) – The backend engine for parsing XYZ. Defaults to 'openbabel'.

      • -

    • sanitize (bool) – Whether to sanitize the generated mol. Defaults to False.

      • -
    -
    -
    -
    - -
    -
    -view_traj(align_scan: bool = True, align_frag_idx: int = 1, backend: str = 'openbabel', converged: bool = True, **kwargs)#
    -

    View the trajectory as a Py3DMol animation.

    -
    -
    Parameters:
    -
      -

    • align_scan (bool) – If align the molecule to make the animation cleaner. -Defaults to True

      • -

    • align_frag_idx (int) – Value should be either 1 or 2. Assign which of the part to be -aligned. Defaults to 1.

      • -

    • backend (str) – The backend engine for parsing XYZ. Defaults to 'openbabel'.

      • -
    -
    -
    -
    - -
    - +
    +

    rdmc.external.logparser.base#

    @@ -1015,66 +505,6 @@
    -
    -
    - On this page -
    -
    -
    diff --git a/reference/external/logparser/gaussian.html b/reference/external/logparser/gaussian.html index 7a366634..907b8916 100644 --- a/reference/external/logparser/gaussian.html +++ b/reference/external/logparser/gaussian.html @@ -464,26 +464,8 @@
    -
    -

    rdmc.external.logparser.gaussian#

    -
    -
    -class rdmc.external.logparser.gaussian.GaussianLog(path: str, job_type: list | None = None, ts: bool | None = None)#
    -

    Bases: CclibLog

    -

    A class helps to parse the Gaussian log files and provides information -helpful to analyze the calculation.

    -
    -
    -opt_criteria = ['Force Maximum', 'Force RMS', 'Displacement Maximum', 'Displacement RMS']#
    -
    - -
    -
    -time_regex = '[a-zA-Z]+\\s+\\d+\\s+\\d{2}\\:\\d{2}\\:\\d{2}\\s+\\d{4}'#
    -
    - -
    - +
    +

    rdmc.external.logparser.gaussian#

    @@ -523,20 +505,6 @@
    -
    -
    - On this page -
    -
    -
    diff --git a/reference/external/logparser/index.html b/reference/external/logparser/index.html index 5d2af1a8..12381e89 100644 --- a/reference/external/logparser/index.html +++ b/reference/external/logparser/index.html @@ -459,95 +459,15 @@
    -
    -

    rdmc.external.logparser#

    +
    +

    rdmc.external.logparser#

    diff --git a/reference/external/logparser/orca.html b/reference/external/logparser/orca.html index 9631f2b5..12678aa2 100644 --- a/reference/external/logparser/orca.html +++ b/reference/external/logparser/orca.html @@ -464,35 +464,8 @@
    -
    -

    rdmc.external.logparser.orca#

    -
    -
    -class rdmc.external.logparser.orca.ORCALog(path: str, job_type: list | None = None, ts: bool | None = None)#
    -

    Bases: CclibLog

    -

    A class helps to parse the Gaussian log files and provides information -helpful to analyze the calculation.

    -

    # Todo: -Test this class. most implementation hasn’t been tested yet.

    -
    -
    -property multiplicity#
    -

    Get the multiplicity of the molecule.

    -

    # For unknown reason sometimes multiplicity is not parsed correctly by cclib

    -
    - -
    -
    -opt_criteria = ['TolE', 'TolRMSG', 'TolMaxG', 'TolRMSD', 'TolMaxD']#
    -
    - -
    -
    -time_regex = ''#
    -
    - -
    - +
    +

    rdmc.external.logparser.orca#

    @@ -532,21 +505,6 @@
    -
    -
    - On this page -
    -
    -
    diff --git a/reference/external/logparser/qchem.html b/reference/external/logparser/qchem.html index 43765ff7..7233c64b 100644 --- a/reference/external/logparser/qchem.html +++ b/reference/external/logparser/qchem.html @@ -464,70 +464,8 @@
    -
    -

    rdmc.external.logparser.qchem#

    -
    -
    -class rdmc.external.logparser.qchem.QChemLog(path: str, job_type: list | None = None, ts: bool | None = None)#
    -

    Bases: CclibLog

    -

    A class helps to parse the Gaussian log files and provides information -helpful to analyze the calculation.

    -
    -
    -get_mol(refid: int = -1, embed_conformers: bool = True, neglect_spin: bool = True, backend: str = 'openbabel', sanitize: bool = True) → RDKitMol#
    -

    Perceive the xyzs in the file and turn the geometries to conformers.

    -
    -
    Parameters:
    -
      -

    • refid (int) – The conformer ID in the log file to be used as the reference for mol perception. -Defaults to -1, meaning it is determined by the following criteria: -- For opt, it is the last geometry if succeeded; otherwise, the initial geometry; -- For freq, it is the geometry input; -- For scan, it is the geometry input; -- For IRC, uses the initial geometry.

      • -

    • embed_confs (bool) – Whether to embed intermediate conformers in the file to the mol. -Defaults to True. To clear, at least one conformer will be included in -obtained mol, and its geometry is determined by refid.

      • -

    • neglect_spin (bool) – Whether to neglect the error when spin multiplicity are different -between the generated mol and the value in the output file. This -can be useful for calculations involves TS. Defaults to True.

      • -

    • backend (str) – The backend engine for parsing XYZ. Defaults to 'openbabel'.

      • -

    • sanitize (bool) – Whether to sanitize the generated mol. Defaults to True. -If a TS involved in the job, better to set it False

      • -
    -
    -
    Returns:
    -

    RDKitMol – a molecule generated from the output file.

    -
    -
    -
    - -
    -
    -get_scf_energies(relative: bool = False)#
    -

    Get SCF energies in kcal/mol.

    -
    -
    Parameters:
    -

    relative (bool) – Only return the value relative to the minimum. Defaults to False.

    -
    -
    Returns:
    -

    np.array – The SCF energies.

    -
    -
    -
    - -
    -
    -opt_critieria = ['Gradient', 'Displacement', 'Energy change']#
    -
    - -
    -
    -time_regex = '[a-zA-Z]+\\s+\\d+\\s+\\d{2}\\:\\d{2}\\:\\d{2}\\s+\\d{4}'#
    -
    - -
    - +
    +

    rdmc.external.logparser.qchem#

    @@ -567,22 +505,6 @@
    -
    -
    - On this page -
    -
    -
    diff --git a/reference/external/logparser/utils.html b/reference/external/logparser/utils.html index e95e9f14..4a926912 100644 --- a/reference/external/logparser/utils.html +++ b/reference/external/logparser/utils.html @@ -464,20 +464,8 @@
    -
    -

    rdmc.external.logparser.utils#

    -

    A module contains functions to read Gaussian output file.

    -
    -
    -rdmc.external.logparser.utils.scheme_to_dict(scheme_str: str) → dict#
    -

    A function to transform scheme to a dict.

    -
    -
    Parameters:
    -

    scheme_str (str) – the calculation scheme used in a Gaussian job.

    -
    -
    -
    - +
    +

    rdmc.external.logparser.utils#

    @@ -517,16 +505,6 @@
    -
    -
    - On this page -
    -
    -
    diff --git a/reference/mathlib/curvefit.html b/reference/mathlib/curvefit.html index 4e2482ea..b5d70f75 100644 --- a/reference/mathlib/curvefit.html +++ b/reference/mathlib/curvefit.html @@ -39,7 +39,6 @@ - @@ -460,51 +459,8 @@
    -
    -

    rdmc.mathlib.curvefit#

    -

    A module used to fit curves or surfaces. Potentially useful in characterize PES.

    -
    -
    -class rdmc.mathlib.curvefit.FourierSeries1D(max_num_term: int | None = None, verbose: bool = False)#
    -

    Bases: object

    -

    FourierSeries1D helps to fit the potential energy surface to a 1D -Fourier Series, and evaluate the values using the fitted curve.

    -
    -
    -fit(X: ndarray, y: ndarray)#
    -

    Fit the 1D Fourier series.

    -
    -
    Parameters:
    -
      -

    • X (np.ndarray) – _description_

      • -

    • y (np.ndarray) – 1D array. It is assumed to be a periodic function of x with -a periodicity of \(2 \pi\).

      • -
    -
    -
    -
    - -
    -
    -max_num_term = None#
    -
    - -
    -
    -predict(X: ndarray)#
    -

    Predict the value using Fourier Series. This function forces y=0 at the origin.

    -
    -
    Parameters:
    -

    X (np.ndarray) – The X variable that should be a 1D array.

    -
    -
    Returns:
    -

    _type_ – _description_

    -
    -
    -
    - -
    - +
    +

    rdmc.mathlib.curvefit#

    @@ -544,21 +500,6 @@
    -
    -
    - On this page -
    -
    -
    diff --git a/reference/mathlib/geom.html b/reference/mathlib/geom.html index dedb11f7..f33c315e 100644 --- a/reference/mathlib/geom.html +++ b/reference/mathlib/geom.html @@ -39,7 +39,6 @@ - @@ -460,156 +459,8 @@
    -
    -

    rdmc.mathlib.geom#

    -

    This module provides class and methods for dealing with 3D geometry operations.

    -
    -
    -rdmc.mathlib.geom.get_centroid(coords: array, keepdims=False) → array#
    -

    Get the centroid given the coords of each item.

    -
    -
    Parameters:
    -
      -

    • coords (np.array) – The 3D coordinates in numpy array with a size of N x 3.

      • -

    • keepdims (bool) – Defaults to False (export 1D array); otherwise output an array of a size of 1 x 3.

      • -
    -
    -
    Returns:
    -

    np.array – 1D array indicate the coordinates of the centroid.

    -
    -
    -
    - -
    -
    -rdmc.mathlib.geom.get_distances_from_a_point(coords: array, pos: array, keepdims: bool = False)#
    -

    Get the Euclidiean distance to a point for all elements.

    -
    -
    Parameters:
    -
      -

    • coords (np.array) – The 3D coordinates in numpy array with a size of N x 3.

      • -

    • pos (np.array) – The coordinates of the point.

      • -

    • keepdims (bool) – Defaults to False (export 1D array); otherwise output an array of a size of 1 x 3.

      • -
    -
    -
    Returns:
    -

    np.array – 1D array indicate the distances.

    -
    -
    -
    - -
    -
    -rdmc.mathlib.geom.get_mass_center(coords: array, atommasses: Iterable, keepdims=False) → array#
    -

    Get the mass center given the coords of each item and its corresponding mass.

    -
    -
    Parameters:
    -
      -

    • coords (np.array) – The 3D coordinates in numpy array with a size of N x 3.

      • -

    • atommasses (Iterable) – A list or an array of mass values.

      • -

    • keepdims (bool) – Defaults to False (export 1D array); otherwise output an array of a size of 1 x 3.

      • -
    -
    -
    Returns:
    -

    np.array – 1D array indicate the coordinates of the mass center.

    -
    -
    -
    - -
    -
    -rdmc.mathlib.geom.get_max_distance_from_center(coords: array) → float#
    -

    Get the maximum distance from the center of a set of coordinates

    -
    -
    Parameters:
    -

    coords (np.array) – The 3D coordinates in numpy array with a size of N x 3.

    -
    -
    Returns:
    -

    float – The distance between the center and the farthest item.

    -
    -
    -
    - -
    -
    -rdmc.mathlib.geom.get_weighted_center(coords: array, weights: Iterable, keepdims=False) → array#
    -

    Get the mass center given the coords of each item and its corresponding weight.

    -
    -
    Parameters:
    -
      -

    • coords (np.array) – The 3D coordinates in numpy array with a size of N x 3.

      • -

    • weights (Iterable) – A list or an array of weights corresponding to each element.

      • -

    • keepdims (bool) – Defaults to False (export 1D array); otherwise output an array of a size of 1 x 3.

      • -
    -
    -
    Returns:
    -

    np.array – 1D array indicate the coordinates of the mass center.

    -
    -
    -
    - -
    -
    -rdmc.mathlib.geom.rotate(coords: array, angles: array, degrees: bool = False, about_center: bool = False, about: array | None = None)#
    -

    Rotate the coordinates according to the angles about the x, y, and z axes. The rotation is -about the origin, but there are a few options about choosing the about location.

    -
    -
    Parameters:
    -
      -

    • coords (np.array) – The 3D coordinates in numpy array with a size of \(N \times 3\).

      • -

    • angles (np.array) – An array with a size of (1,3) indicates the rotation angles about the -x, y, and z axes, respectively.

      • -

    • degrees (bool) – If the angles are defined as degrees. Defaults to False.

      • -

    • about_center (bool) – Whether to rotate the coordinates about their center. -Defaults to False. Note about_center cannot be assigned simultaneously with about.

      • -

    • about (np.array) – The coordinate that the rotation is about. Should be a vector with a length of 3. -It is defaults to None, rotating about the origin. -about cannot be specified along with about_center.

      • -
    -
    -
    Returns:
    -

    np.array – coordinates after the rotation.

    -
    -
    -
    - -
    -
    -rdmc.mathlib.geom.translate(coords: array, tran_vec: array) → array#
    -

    Translate the coordinates according to the tran_vec vector.

    -
    -
    Parameters:
    -
      -

    • coords (np.array) – The 3D coordinates in numpy array with a size of N x 3.

      • -

    • tran_vec (np.array) – A vector indicate the direction and the magnitude of the translational operation. -It should be a numpy array with a size of (3,) or (1,3).

      • -
    -
    -
    Returns:
    -

    np.array – An numpy array with the same size as the original coords.

    -
    -
    -
    - -
    -
    -rdmc.mathlib.geom.translate_centroid(coords: array, new_ctr: array = array([0., 0., 0.]))#
    -

    Translate the coordinates according to the tran_vec vector.

    -
    -
    Parameters:
    -
      -

    • coords (np.array) – The 3D coordinates in numpy array with a size of N x 3.

      • -

    • new_ctr (np.array) – A vector indicate the new position of the centroid. -It should be a numpy array with a size of (3,) or (1,3). -By defaults, the centroid will be moved to the origin.

      • -
    -
    -
    Returns:
    -

    np.array – An numpy array with the same size as the original coords.

    -
    -
    -
    - +
    +

    rdmc.mathlib.geom#

    @@ -649,23 +500,6 @@
    -
    -
    - On this page -
    -
    -
    diff --git a/reference/mathlib/greedymin.html b/reference/mathlib/greedymin.html index 38b70106..f417ddd6 100644 --- a/reference/mathlib/greedymin.html +++ b/reference/mathlib/greedymin.html @@ -459,103 +459,8 @@
    -
    -

    rdmc.mathlib.greedymin#

    -

    Modules for finding local minima on the scanned potential energy surface -by a greedy algorithm. Need to parallelize this.

    -
    -
    -rdmc.mathlib.greedymin.compare_to_adjacent_point(coord: List[Tuple], energies: ndarray, unchecked_points: List[Tuple], filters: List[Tuple]) → Tuple#
    -

    Compare the energy of current point and those of other points.

    -
    -
    Parameters:
    -
      -

    • coord (list of tuples) – The coordinate of the current point.

      • -

    • energies (np.ndarray) – The energies of all points.

      • -

    • unchecked_points (list of tuples) – The points that have not been checked.

      • -

    • filters (list of tuples) – The filters for searching adjacent points.

      • -
    -
    -
    Returns:
    -

    The coordinate of the adjacent point with the lowest energy.

    -
    -
    -
    - -
    -
    -rdmc.mathlib.greedymin.get_energy(coord: List[Tuple], energies: ndarray) → float#
    -

    Get the energies of adjacent points considering periodic boundary condition.

    -
    -
    Parameters:
    -
      -

    • coord – The coordinate of a point.

      • -

    • energies – The energies of all points.

      • -
    -
    -
    Returns:
    -

    float – The energy of the point.

    -
    -
    -
    - -
    -
    -rdmc.mathlib.greedymin.get_step_to_adjacent_points(fsize: int, dim: int = 2, cutoff: float = inf) → generator#
    -

    Get a generator containing the adjacent points.

    -
    -
    Parameters:
    -
      -

    • fsize – The filter size as positive integer.

      • -

    • dim – The dimension of the PES. Default is 2.

      • -

    • cutoff – The cutoff distance. only consider steps with -distance smaller than the cutoff. Default is -infinity, meaning no cutoff is applied.

      • -
    -
    -
    Returns:
    -

    A generator containing the adjacent coordinates.

    -
    -
    -
    - -
    -
    -rdmc.mathlib.greedymin.search_for_a_minimum(coord: tuple, energies: ndarray, unchecked_points: List[Tuple], filters: List[Tuple]) → Tuple#
    -

    Search a local minimum on a given PES.

    -
    -
    Parameters:
    -
      -

    • coord (tuple) – The coordinate of the current point.

      • -

    • energies (np.ndarray) – The energies of all points.

      • -

    • unchecked_points (list of tuples) – The points that have not been checked.

      • -

    • filters (list of tuples) – The filters for searching adjacent points.

      • -

    • minimum. (The coordinate of a local) –

      • -
    -
    -
    -
    - -
    -
    -rdmc.mathlib.greedymin.search_minimum(energies: ndarray, fsize: int, cutoff: float = inf) → List[Tuple]#
    -

    Search all the minimums on a given PES.

    -
    -
    Parameters:
    -
      -

    • energies (np.ndarray) – The energies of all points.

      • -

    • fsize (int) – The filter size as positive integer.

      • -

    • cutoff (float) – The cutoff distance. only consider steps with -distance smaller than the cutoff. Default is -infinity, meaning no cutoff is applied.

      • -
    -
    -
    Returns:
    -

    A list of coordinates of the minimums.

    -
    -
    -
    - +
    +

    rdmc.mathlib.greedymin#

    @@ -595,20 +500,6 @@
    -
    -
    - On this page -
    -
    -
    diff --git a/reference/mathlib/index.html b/reference/mathlib/index.html index 59df7302..06b2b0a4 100644 --- a/reference/mathlib/index.html +++ b/reference/mathlib/index.html @@ -456,38 +456,13 @@
    -
    -

    rdmc.mathlib#

    +
    +

    rdmc.mathlib#

    diff --git a/reference/mol.html b/reference/mol.html index ebbdad1f..9fc8e4a0 100644 --- a/reference/mol.html +++ b/reference/mol.html @@ -894,7 +894,7 @@
    -GetAllConformers() → List[RDKitConf]#
    +GetAllConformers() → List[RDKitConf]#

    Get all of the embedded conformers.

    Returns:
    @@ -986,7 +986,7 @@
    -GetConformer(id: int = 0) → RDKitConf#
    +GetConformer(id: int = 0) → RDKitConf#

    Get the embedded conformer according to ID.

    Parameters:
    @@ -1003,7 +1003,7 @@
    -GetConformers(ids: list | tuple = [0]) → List[RDKitConf]#
    +GetConformers(ids: list | tuple = [0]) → List[RDKitConf]#

    Get the embedded conformers according to IDs.

    Parameters:
    diff --git a/reference/rdmc.html b/reference/rdmc.html index c1ca8e52..45789ac9 100644 --- a/reference/rdmc.html +++ b/reference/rdmc.html @@ -453,8 +453,8 @@
    -
    -

    RDMC APIs#

    +
    +

    RDMC APIs#

  • rdmc.mathlib
  • rdmc.conformer_generation
    • diff --git a/reference/reaction.html b/reference/reaction.html index 2dff4a59..470a10c5 100644 --- a/reference/reaction.html +++ b/reference/reaction.html @@ -456,209 +456,8 @@
    -
    -

    rdmc.reaction#

    -

    Module for Reaction

    -
    -
    -class rdmc.reaction.Reaction(reactant: List[RDKitMol] | RDKitMol, product: List[RDKitMol] | RDKitMol, ts: RDKitMol | None = None)#
    -

    Bases: object

    -

    The Reaction class that stores the reactant, product, and transition state information.

    -
    -
    -property active_atoms#
    -
    - -
    -
    -property active_bonds#
    -
    - -
    -
    -apply_resonance_correction(inplace: bool = True, kekulize: bool = True) → Reaction#
    -

    Apply resonance correction to the reactant and product complexes.

    -
    - -
    -
    -bond_analysis()#
    -

    Perform bond analysis on the reaction.

    -
    - -
    -
    -property broken_bonds#
    -
    - -
    -
    -property changed_bonds#
    -
    - -
    -
    -draw_2d(font_scale: float = 1.0, highlight_by_reactant: bool = True) → str#
    -

    This is a modified version of the drawReaction2D function in RDKit.

    -
    -
    Parameters:
    -
      -

    • font_scale (float, optional) – The font scale for the atom map number. Defaults to 1.0.

      • -

    • highlightByReactant (bool, optional) – Whether to highlight the reactant(s) or product(s). Defaults to True.

      • -
    -
    -
    Returns:
    -

    str – The SVG string. To display the SVG, use IPython.display.SVG(svg_string).

    -
    -
    -
    - -
    -
    -property formed_bonds#
    -
    - -
    -
    -classmethod from_reactant_and_product_smiles(rsmi: List[str] | str, psmi: List[str] | str)#
    -

    Initialize the Reaction class from reactant and product smile(s).

    -

    Args:

    -
    - -
    -
    -classmethod from_reaction_smiles(smiles: str)#
    -

    Initialize the Reaction class from reaction SMILES.

    -
    -
    Parameters:
    -

    smiles (str) – The reaction SMILES.

    -
    -
    Returns:
    -

    Reaction – The Reaction class.

    -
    -
    -
    - -
    -
    -get_reverse_reaction()#
    -

    Get the reverse reaction.

    -
    - -
    -
    -init_reactant_product(reactant: List[RDKitMol] | RDKitMol, product: List[RDKitMol] | RDKitMol)#
    -
    - -
    -
    -property involved_atoms#
    -
    - -
    -
    -property involved_bonds#
    -
    - -
    -
    -property is_charge_balanced: bool#
    -

    Whether the charge in the reactant(s) and product(s) are balanced.

    -
    - -
    -
    -property is_element_balanced: bool#
    -

    Whether the elements in the reactant(s) and product(s) are balanced.

    -
    - -
    -
    -property is_mult_equal: bool#
    -

    Whether the spin multiplicity in the reactant(s) and product(s) are equal.

    -
    - -
    -
    -property is_num_atoms_balanced: bool#
    -

    Whether the number of atoms in the reactant(s) and product(s) are balanced.

    -
    - -
    -
    -make_ts()#
    -

    Make the transition state of the reaction based on the reactant and product. -This method assumes that the reactant complex and product complex are atom-mapped -already.

    -
    - -
    -
    -property num_atoms: bool#
    -

    The number of atoms involved in the reactant(s) and product(s).

    -
    - -
    -
    -property num_broken_bonds#
    -
    - -
    -
    -property num_changed_bonds#
    -
    - -
    -
    -property num_formed_bonds#
    -
    - -
    -
    -property num_products: int#
    -

    The number of products.

    -
    - -
    -
    -property num_reactants: int#
    -

    The number of reactants.

    -
    - -
    -
    -require_bond_analysis()#
    -

    Timer decorator for recording the time of a function.

    -
    -
    Parameters:
    -

    func (function) – The function to be decorated.

    -
    -
    Returns:
    -

    function – The decorated function.

    -
    -
    -
    - -
    -
    -to_rdkit_reaction() → ChemicalReaction#
    -

    Convert the reaction to RDKit ChemicalReaction.

    -
    - -
    -
    -to_smiles(remove_hs: bool = False, remove_atom_map: bool = False, **kwargs) → str#
    -

    Convert the reaction to reaction SMILES.

    -
    - -
    -
    -property ts#
    -

    The transition state of the reaction.

    -
    - -
    - +
    +

    rdmc.reaction#

    @@ -698,47 +497,6 @@
    -
    -
    - On this page -
    -
    -
    diff --git a/reference/ts.html b/reference/ts.html index 5705d6fe..4b580218 100644 --- a/reference/ts.html +++ b/reference/ts.html @@ -39,7 +39,6 @@ - @@ -457,203 +456,8 @@
    -
    -

    rdmc.ts#

    -

    This module provides class and methods for dealing with Transition states.

    -
    -
    -rdmc.ts.clean_ts(r_mol: RDKitMol, p_mol: RDKitMol, ts_mol: RDKitMol)#
    -

    Cleans transition state ts_mol by removing all bonds that correspond to broken or formed bonds. -r_mol, p_mol, and ts_mol need to be atom mapped. Bond order changes are not considered.

    -
    -
    Parameters:
    -
      -

    • r_mol (RDKitMol) – the reactant complex.

      • -

    • p_mol (RDKitMol) – the product complex.

      • -

    • ts_mol (RDKitMol) – the transition state corresponding to r_mol and p_mol.

      • -
    -
    -
    Returns:
    -
      -

    • RDKitMol – an edited version of ts_mol, which is the original ts_mol with cleaned bonding.

      • -

    • list –

      -
        -

      • broken bonds: A list of length-2 tuples that contains the atom indexes of the bonds broken in the reaction.

        • -

      • formed bonds: A list of length-2 tuples that contains the atom indexes of the bonds formed in the reaction.

        • -
      -
      • -
    -
    -
    -
    - -
    -
    -rdmc.ts.examine_normal_mode(r_mol: RDKitMol, p_mol: RDKitMol, ts_xyz: array, disp: array, amplitude: float | list = 0.25, weights: bool | array = True, verbose: bool = True, as_factors: bool = True)#
    -

    Examine a TS’s imaginary frequency given a known reactant complex and a -product complex. The function checks if the bond changes are corresponding -to the most significant change in the normal mode. The reactant and product -complex need to be atom mapped.

    -
    -
    Parameters:
    -
      -

    • r_mol ('RDKitMol') – the reactant complex.

      • -

    • p_mol ('RDKitMol') – the product complex.

      • -

    • ts_xyz (np.array) – The xyz coordinates of the transition state. It should have a -size of N x 3.

      • -

    • disp (np.array) – The displacement of the normal mode. It should have a size of -N x 3.

      • -

    • amplitude (float) – The amplitude of the motion. Defaults to 0.25.

      • -

    • weights (bool or np.array) – If True, use the sqrt(atom mass) as a scaling factor to the displacement. -If False, use the identity weights. If a N x 1 np.array is provided, then -The concern is that light atoms (e.g., H) tend to have larger motions -than heavier atoms.

      • -

    • verbose (bool) – If print detailed information. Defaults to True.

      • -

    • as_factors (bool) – If return the value of factors instead of a judgment. -Defaults to False

      • -
    -
    -
    Returns:
    -
      -

    • - bool – True for pass the examination, False otherwise.

      • -

    • - list – If as_factors == True, two factors will be returned.

      • -
    -
    -
    -
    - -
    -
    -rdmc.ts.get_all_changing_bonds(r_mol: RDKitMol | Mol, p_mol: RDKitMol | Mol) → List#
    -

    Get all bonds changed in the reaction. Both reactant and product complexes -need to be atom-mapped.

    -
    -
    Parameters:
    -
      -

    • r_mol ('RDKitMol' or 'Mol') – the reactant complex.

      • -

    • p_mol ('RDKitMol' or 'Mol') – the product complex.

      • -
    -
    -
    Returns:
    -

    list –

    -
      -

    • formed bonds: A list of length-2 tuples that contain the atom indexes of the bonded atoms.

      • -

    • broken bonds: A list of length-2 tuples that contain the atom indexes of the bonded atoms.

      • -

    • bonds with BO changed: A list of length-2 tuples that contain the atom indexes of the bonded atoms.

      • -
    -
    -
    -
    - -
    -
    -rdmc.ts.get_broken_bonds(r_mol: RDKitMol | Mol, p_mol: RDKitMol | Mol) → List#
    -

    Get all bonds broken in the reaction. Both reactant and product complexes -need to be atom-mapped.

    -
    -
    Parameters:
    -
      -

    • r_mol ('RDKitMol' or 'Mol') – the reactant complex.

      • -

    • p_mol ('RDKitMol' or 'Mol') – the product complex.

      • -
    -
    -
    Returns:
    -

    list – A list of length-2 tuples that contain the atom indexes of the bonded atoms.

    -
    -
    -
    - -
    -
    -rdmc.ts.get_formed_and_broken_bonds(r_mol: RDKitMol | Mol, p_mol: RDKitMol | Mol) → List#
    -

    Get all bonds broken in the reaction. Both reactant and product complexes -need to be atom-mapped. This function doesn’t count bonds whose bond order -is lowered but not equal to zero.

    -
    -
    Parameters:
    -
      -

    • r_mol ('RDKitMol' or 'Mol') – the reactant complex.

      • -

    • p_mol ('RDKitMol' or 'Mol') – the product complex.

      • -
    -
    -
    Returns:
    -

    list –

    -
      -

    • formed bonds: A list of length-2 tuples that contain the atom indexes of the bonded atoms.

      • -

    • broken bonds: A list of length-2 tuples that contain the atom indexes of the bonded atoms.

      • -
    -
    -
    -
    - -
    -
    -rdmc.ts.get_formed_bonds(r_mol: RDKitMol | Mol, p_mol: RDKitMol | Mol) → List#
    -

    Get all bonds formed in the reaction. Both reactant and product complexes -need to be atom-mapped.

    -
    -
    Parameters:
    -
      -

    • r_mol ('RDKitMol' or 'Mol') – the reactant complex.

      • -

    • p_mol ('RDKitMol' or 'Mol') – the product complex.

      • -
    -
    -
    -
    -
    Returns

    list: A list of length-2 tuples that contain the atom indexes of the bonded atoms.

    -
    -
    -
    - -
    -
    -rdmc.ts.guess_rxn_from_normal_mode(xyz: array, symbols: array, disp: array, amplitude: float | list = 0.25, weights: bool | array = True, backend: str = 'openbabel', multiplicity: int = 1)#
    -

    Guess reaction according to the normal mode analysis for a transition state.

    -
    -
    Parameters:
    -
      -

    • xyz (np.array) – The xyz coordinates of the transition state. It should have a -size of \(N \times 3\).

      • -

    • symbols (np.array) – The symbols of each atoms. It should have a size of \(N\).

      • -

    • disp (np.array) – The displacement of the normal mode. It should have a size of -\(N \times 3\).

      • -

    • amplitude (float) – The amplitude of the motion. If a single value is provided then the guess -will be unique (if available). 0.25 will be the default. Otherwise, a list -can be provided, and all possible results will be returned.

      • -

    • weights (bool or np.array) – If True, use the \(\sqrt(atom mass)\) as a scaling factor to the displacement. -If False, use the identity weights. If a \(N \times 1\) np.ndarray is provided, -then use the provided weights. The concern is that light atoms (e.g., H) -tend to have larger motions than heavier atoms.

      • -

    • backend (str) – The backend used to perceive xyz. Defaults to 'openbabel'.

      • -

    • multiplicity (int) – The spin multiplicity of the transition states. Defaults to 1.

      • -
    -
    -
    Returns:
    -
      -

    • list – Potential reactants

      • -

    • list – Potential products

      • -
    -
    -
    -
    - -
    -
    -rdmc.ts.is_DA_rxn_endo(r_mol: RDKitMol, p_mol: RDKitMol, embed: bool = False)#
    -

    Determine the Diels Alder reaction stereo type (endo or exo), -based on the provided reactants and products.

    -
    -
    Parameters:
    -
      -

    • r_mol (RDKitMol) – the reactant complex.

      • -

    • p_mol (RDKitMol) – the product complex.

      • -

    • embed (bool) – bool. If the DA product has no conformer embedded. -Whether to embed a conformer. Defaults to False.

      • -
    -
    -
    -
    - +
    +

    rdmc.ts#

    @@ -693,23 +497,6 @@
    -
    -
    - On this page -
    -
    -
    diff --git a/reference/utils.html b/reference/utils.html index 1cc3e652..3b00f374 100644 --- a/reference/utils.html +++ b/reference/utils.html @@ -746,7 +746,7 @@
    -rdmc.utils.set_rdconf_coordinates(conf: Conformer | RDKitConf, coords: tuple | list | ndarray)#
    +rdmc.utils.set_rdconf_coordinates(conf: Conformer | RDKitConf, coords: tuple | list | ndarray)#

    Set the Positions of atoms of the conformer.

    Parameters:
    diff --git a/reference/view.html b/reference/view.html index 9dd27614..1d0e3306 100644 --- a/reference/view.html +++ b/reference/view.html @@ -456,194 +456,8 @@
    -
    -

    rdmc.view#

    -

    A module contains py3Dmol functions to draw molecules

    -
    -
    -rdmc.view.conformer_viewer(mol: RDKitMol, conf_ids: list | None = None, highlight_ids: list | None = None, opacity: float = 0.5, style_spec: dict | None = None, viewer: view | None = None, viewer_size: tuple = (400, 400), viewer_loc: tuple | None = None) → view#
    -

    This is a viewer for viewing multiple overlaid conformers.

    -
    -
    Parameters:
    -
      -

    • mol (RDKitMol) – An RDKitMol object with embedded conformers.

      • -

    • conf_ids (list, optional) – A list of conformer ids (as int) to be overlaid and viewed. -If not provided, all embedded conformers will be used.

      • -

    • highlight_ids (list, optional) – It is possible to highlight some of the conformers while greying out -other conformers by providing the conformer IDs you want to highlight.

      • -

    • opacity (float, optional) – Set the opacity of the non-highlighted conformers and is only used with the highlighting feature. -the value should be a float between 0.0 to 1.0. The default value is 0.5. -Values below 0.3 may be hard to see.

      • -

    • style_spec (dict, Optional) –

      Style of the shown molecule. The default setting is:

      -
      {'stick': {'radius': 0.05,
-           'color': '#f2f2f2'},
- 'sphere': {'scale': 0.25},}
-
      -
      -

      which set both bond width/color and atom sizes. For more details, please refer to the -original APIs in 3DMol.js.

      -

      • -

    • viewer (py3Dmol.view, optional) – Provide an existing viewer, instead of create a new one.

      • -

    • viewer_size (tuple, optional) – Set the viewer size. Only useful if viewer is not provided. -Defaults to (400, 400).

      • -

    • viewer_loc (tuple, optional) – The location of the viewer in the grid. E.g., (0, 1). Only useful if viewer is not provided.

      • -
    -
    -
    Returns:
    -

    py3Dmol.view – The conformer viewer.

    -
    -
    -
    - -
    -
    -rdmc.view.freq_viewer(obj: str, model: str = 'xyz', frames: int = 10, amplitude: float = 1.0, atom_index: bool = True, style_spec: dict | None = None, viewer: view | None = None, viewer_size: tuple = (400, 400), viewer_loc: tuple | None = None) → view#
    -

    This is the viewer for frequency.

    -
    -
    Parameters:
    -
      -

    • obj (str) – A string representation of the molecule can be xyz string, -sdf string, etc.

      • -

    • model (str, optional) – The model (format) of the molecule representation, e.g., 'xyz'. -Defaults to 'xyz'.

      • -

    • frames (int, optional) – Number of frames to be created.

      • -

    • amplitude (float, optional) – amplitude of distortion.

      • -

    • atom_index (bool, optional) – Whether to show atom index. Defaults to True.

      • -

    • style_spec (dict, Optional) – Style of the shown molecule. The default is showing both -both atoms and bonds.

      • -

    • viewer (py3Dmol.view, optional) – Provide an existing viewer, instead of create a new one.

      • -

    • viewer_size (tuple, optional) – Set the viewer size. Only useful if viewer is not provided. -Defaults to (400, 400).

      • -

    • viewer_loc (tuple, optional) – The location of the viewer in the grid. E.g., (0, 1). Defaults to None.

      • -
    -
    -
    Returns:
    -

    py3Dmol.view – The molecule frequency viewer.

    -
    -
    -
    - -
    -
    -rdmc.view.grid_viewer(viewer_grid: tuple, linked: bool = False, viewer_size: tuple | None = None) → view#
    -

    Create a empty grid viewer.

    -
    -
    Parameters:
    -
      -

    • viewer_grid (tuple) – The layout of the grid, e.g., (1, 4) or (2, 2).

      • -

    • linked (bool, optional) – Whether changes in different sub viewers are linked. Defaults to False.

      • -

    • viewer_size (tuple, optional) – The size of the viewer in (width, height). By Default, each block -is 250 width and 400 height.

      • -
    -
    -
    -
    - -
    -
    -rdmc.view.interactive_conformer_viewer(mol, **kwargs)#
    -

    This is a viewer for individually viewing multiple conformers using an ipython slider widget. -Uses keywords from mol_viewer function, so all arguments of that function are available here.

    -
    -
    Parameters:
    -

    mol (RDKitMol) – An RDKitMol object with embedded conformers.

    -
    -
    Returns:
    -

    py3Dmol.view – The molecule viewer with slider to view different conformers.

    -
    -
    -
    - -
    -
    -rdmc.view.mol_animation(obj: str, model: str = 'xyz', model_extra: dict | None = None, animate: dict | None = None, atom_index: bool = True, style_spec: dict | None = None, viewer: view | None = None, viewer_size: tuple = (400, 400), viewer_loc: tuple | None = None) → view#
    -

    This is the most general function to view a molecule powered by py3Dmol

    -
    -
    Parameters:
    -
      -

    • obj (str) – A string representation of the molecule can be xyz string, -sdf string, etc.

      • -

    • model (str, optional) – The model (format) of the molecule representation, e.g., 'xyz'. -Defaults to 'xyz'.

      • -

    • model_extra (dict, optional) – Extra specs for the model. E.g., frequency specs -Can be provided here. Default to None

      • -

    • animate (dict, optional) – Specs for animation. E.g., {'loop': 'backAndForth'}.

      • -

    • atom_index (bool, optional) – Whether to show atom index. Defaults to True.

      • -

    • style_spec (dict, Optional) – Style of the shown molecule. The default is showing both -both atoms and bonds.

      • -

    • viewer (py3Dmol.view, optional) – Provide an existing viewer, instead of create a new one.

      • -

    • viewer_size (tuple, optional) – Set the viewer size. Only useful if viewer is not provided. -Defaults to (400, 400).

      • -

    • viewer_loc (tuple, optional) – The location of the viewer in the grid. E.g., (0, 1). Defaults to None.

      • -
    -
    -
    Returns:
    -

    py3Dmol.view – The molecule viewer.

    -
    -
    -
    - -
    -
    -rdmc.view.mol_viewer(obj: str, model: str = 'xyz', model_extra: dict | None = None, animate: dict | None = None, atom_index: bool = True, style_spec: dict | None = None, viewer: view | None = None, viewer_size: tuple = (400, 400), viewer_loc: tuple | None = None, gv_background: bool = False, confId: int = 0) → view#
    -

    This is the most general function to view a molecule powered by py3Dmol

    -
    -
    Parameters:
    -
      -

    • obj (str) – A string representation of the molecule can be xyz string, -sdf string, etc. Or an RDKitMol object.

      • -

    • model (str, optional) – The model (format) of the molecule representation, e.g., 'xyz'. -Defaults to 'xyz'. If RDKitMol is feed in, the model will forced to be -sdf.

      • -

    • model_extra (dict, optional) – Extra specs for the model. E.g., frequency specs -Can be provided here. Default to None

      • -

    • animate (dict, optional) – Specs for animation. E.g., {'loop': 'backAndForth'}.

      • -

    • atom_index (bool, optional) – Whether to show atom index. Defaults to True.

      • -

    • style_spec (dict, Optional) – Style of the shown molecule. The default is showing both -both atoms and bonds.

      • -

    • viewer (py3Dmol.view, optional) – Provide an existing viewer, instead of create a new one.

      • -

    • viewer_size (tuple, optional) – Set the viewer size. Only useful if viewer is not provided. -Defaults to (400, 400).

      • -

    • viewer_loc (tuple, optional) – The location of the viewer in the grid. E.g., (0, 1). Defaults to None.

      • -

    • gv_background (optional, bool) – To use a background that is similar to the style of GaussView. -Defaults to False.

      • -

    • confId (int) – Integer of embedded conformer to view

      • -
    -
    -
    Returns:
    -

    py3Dmol.view – The molecule viewer.

    -
    -
    -
    - -
    -
    -rdmc.view.ts_viewer(r_mol: RDKitMol, p_mol: RDKitMol, ts_mol: RDKitMol, only_ts: bool = False, alignment: list = ['r', 'p', 'ts'], vertically_aligned: bool = True, ts_bond_color: str | Tuple[str] = ('red', 'green'), ts_bond_width: float = 0.1, **kwargs)#
    -

    View reactant, product and ts of a given reaction. The broken bonds in the TS will be shown with red -lines while the formed bonds in the TS will be shown with green lines. Uses keywords from mol_viewer -function, so all arguments of that function are available here.

    -
    -
    Parameters:
    -
      -

    • r_mol (RDKitMol) – The reactant complex.

      • -

    • p_mol (RDKitMol) – The product complex.

      • -

    • ts_mol (RDKitMol) – The ts corresponding to r_mol and p_mol.

      • -

    • only_ts (bool, optional) – Only shows TS. Defaults to showing reactant, product, and TS. Defaults to False.

      • -

    • alignment (list, optional) – The alignment of reactant, product, and TS. Defaults to [‘r’, ‘p’, ‘ts’]. -It can be changed to [‘r’, ‘ts’, ‘p’] to make TS in the middle. You can even remove -‘r’ or ‘p’ to only show TS and one side of the reaction, e.g., [‘r’, ‘ts’]. -This argument is only valid when only_ts is False.

      • -

    • vertically_aligned (bool, optional) – Reactant, product, and TS are vertically aligned. Defaults to True. -Only valid when only_ts is False.

      • -

    • ts_bond_color (tuple or str, optional) – The TS bond color for broken bonds (defaults to “red”) and formed bonds (defaults to “green”). -If a single str is input, the same color will be used. If a length-2 tuple is provided, then the -first color will be used as the broken bond color. As a reference, normal bond color is ‘#f2f2f2’.

      • -

    • ts_bond_width (float) – The width of the TS bonds. Defaults to 0.1. As a reference, normal bond width is 0.05.

      • -
    -
    -
    -
    - +
    +

    rdmc.view#

    @@ -683,22 +497,6 @@
    -
    -
    - On this page -
    -
    -
    diff --git a/searchindex.js b/searchindex.js index 75d3d04e..b88536c0 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["index", "reference/cite", "reference/conf", "reference/conformer_generation/embedding_geometries/align", "reference/conformer_generation/embedding_geometries/embedders", "reference/conformer_generation/embedding_geometries/index", "reference/conformer_generation/embedding_geometries/ts_guessers", "reference/conformer_generation/geometry_optimization/index", "reference/conformer_generation/geometry_optimization/optimizers", "reference/conformer_generation/geometry_optimization/ts_optimizers", "reference/conformer_generation/index", "reference/conformer_generation/postprocessing/index", "reference/conformer_generation/postprocessing/pruners", "reference/conformer_generation/postprocessing/solvation", "reference/conformer_generation/postprocessing/ts_verifiers", "reference/conformer_generation/postprocessing/verifiers", 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(rdmc.external.logparser.base.baselog property)": [[29, "rdmc.external.logparser.base.BaseLog.termination_time"]], "time_regex (rdmc.external.logparser.base.baselog attribute)": [[29, "rdmc.external.logparser.base.BaseLog.time_regex"]], "view_freq() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.view_freq"]], "view_mol() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.view_mol"]], "view_traj() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.view_traj"]], "gaussianlog (class in rdmc.external.logparser.gaussian)": [[30, "rdmc.external.logparser.gaussian.GaussianLog"]], "opt_criteria (rdmc.external.logparser.gaussian.gaussianlog attribute)": [[30, "rdmc.external.logparser.gaussian.GaussianLog.opt_criteria"]], "rdmc.external.logparser.gaussian": [[30, "module-rdmc.external.logparser.gaussian"]], "time_regex (rdmc.external.logparser.gaussian.gaussianlog attribute)": [[30, "rdmc.external.logparser.gaussian.GaussianLog.time_regex"]], "rdmc.external.logparser": [[31, "module-rdmc.external.logparser"]], "orcalog (class in rdmc.external.logparser.orca)": [[32, "rdmc.external.logparser.orca.ORCALog"]], "multiplicity (rdmc.external.logparser.orca.orcalog property)": [[32, "rdmc.external.logparser.orca.ORCALog.multiplicity"]], "opt_criteria (rdmc.external.logparser.orca.orcalog attribute)": [[32, "rdmc.external.logparser.orca.ORCALog.opt_criteria"]], "rdmc.external.logparser.orca": [[32, "module-rdmc.external.logparser.orca"]], "time_regex (rdmc.external.logparser.orca.orcalog attribute)": [[32, "rdmc.external.logparser.orca.ORCALog.time_regex"]], "qchemlog (class in rdmc.external.logparser.qchem)": [[33, "rdmc.external.logparser.qchem.QChemLog"]], "get_mol() (rdmc.external.logparser.qchem.qchemlog method)": [[33, "rdmc.external.logparser.qchem.QChemLog.get_mol"]], "get_scf_energies() (rdmc.external.logparser.qchem.qchemlog method)": [[33, "rdmc.external.logparser.qchem.QChemLog.get_scf_energies"]], "opt_critieria (rdmc.external.logparser.qchem.qchemlog attribute)": [[33, "rdmc.external.logparser.qchem.QChemLog.opt_critieria"]], "rdmc.external.logparser.qchem": [[33, "module-rdmc.external.logparser.qchem"]], "time_regex (rdmc.external.logparser.qchem.qchemlog attribute)": [[33, "rdmc.external.logparser.qchem.QChemLog.time_regex"]], "rdmc.external.logparser.utils": [[34, "module-rdmc.external.logparser.utils"]], "scheme_to_dict() (in module rdmc.external.logparser.utils)": [[34, "rdmc.external.logparser.utils.scheme_to_dict"]], "check_isomorphic_molecules() (in module rdmc.external.rmg)": [[35, "rdmc.external.rmg.check_isomorphic_molecules"]], "find_reaction_family() (in module rdmc.external.rmg)": [[35, "rdmc.external.rmg.find_reaction_family"]], "from_rdkit_mol() (in module rdmc.external.rmg)": [[35, "rdmc.external.rmg.from_rdkit_mol"]], "generate_reaction_complex() (in module rdmc.external.rmg)": [[35, "rdmc.external.rmg.generate_reaction_complex"]], "load_rmg_database() (in module rdmc.external.rmg)": [[35, "rdmc.external.rmg.load_rmg_database"]], "load_rxn_family_database() (in module rdmc.external.rmg)": [[35, "rdmc.external.rmg.load_rxn_family_database"]], "rdmc.external.rmg": [[35, "module-rdmc.external.rmg"]], "openbabelff (class in rdmc.forcefield)": [[36, "rdmc.forcefield.OpenBabelFF"]], "rdkitff (class in rdmc.forcefield)": [[36, "rdmc.forcefield.RDKitFF"]], "add_angle_constraint() (rdmc.forcefield.openbabelff method)": [[36, "rdmc.forcefield.OpenBabelFF.add_angle_constraint"]], "add_angle_constraint() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.add_angle_constraint"]], "add_distance_constraint() (rdmc.forcefield.openbabelff method)": [[36, "rdmc.forcefield.OpenBabelFF.add_distance_constraint"]], "add_distance_constraint() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.add_distance_constraint"]], "add_torsion_constraint() (rdmc.forcefield.openbabelff method)": [[36, "rdmc.forcefield.OpenBabelFF.add_torsion_constraint"]], "add_torsion_constraint() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.add_torsion_constraint"]], "available_force_field (rdmc.forcefield.openbabelff attribute)": [[36, "rdmc.forcefield.OpenBabelFF.available_force_field"]], "available_force_field (rdmc.forcefield.rdkitff attribute)": [[36, "rdmc.forcefield.RDKitFF.available_force_field"]], "available_solver (rdmc.forcefield.openbabelff attribute)": [[36, "rdmc.forcefield.OpenBabelFF.available_solver"]], "fix_atom() (rdmc.forcefield.openbabelff method)": [[36, "rdmc.forcefield.OpenBabelFF.fix_atom"]], "fix_atom() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.fix_atom"]], "get_conformer_energies() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.get_conformer_energies"]], "get_energy() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.get_energy"]], "get_optimized_mol() (rdmc.forcefield.openbabelff method)": [[36, "rdmc.forcefield.OpenBabelFF.get_optimized_mol"]], "get_optimized_mol() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.get_optimized_mol"]], "get_roo_radical_atoms() (in module rdmc.forcefield)": [[36, "rdmc.forcefield.get_roo_radical_atoms"]], "is_optimizable() (rdmc.forcefield.openbabelff method)": [[36, "rdmc.forcefield.OpenBabelFF.is_optimizable"]], "is_optimizable() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.is_optimizable"]], "make_optimizable() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.make_optimizable"]], "mol (rdmc.forcefield.openbabelff property)": [[36, "rdmc.forcefield.OpenBabelFF.mol"]], "mol (rdmc.forcefield.rdkitff property)": [[36, "rdmc.forcefield.RDKitFF.mol"]], "optimize() (rdmc.forcefield.openbabelff method)": [[36, "rdmc.forcefield.OpenBabelFF.optimize"]], "optimize() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.optimize"]], "optimize_confs() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.optimize_confs"]], "optimize_mol() (in module rdmc.forcefield)": [[36, "rdmc.forcefield.optimize_mol"]], "rdmc.forcefield": [[36, "module-rdmc.forcefield"]], "recover_mol() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.recover_mol"]], "set_solver() (rdmc.forcefield.openbabelff method)": [[36, "rdmc.forcefield.OpenBabelFF.set_solver"]], "setup() (rdmc.forcefield.openbabelff method)": [[36, "rdmc.forcefield.OpenBabelFF.setup"]], "setup() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.setup"]], "torsional_scan_1d() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.torsional_scan_1d"]], "type (rdmc.forcefield.openbabelff property)": [[36, "rdmc.forcefield.OpenBabelFF.type"]], "type (rdmc.forcefield.rdkitff property)": [[36, "rdmc.forcefield.RDKitFF.type"]], "update_atom_idx() (rdmc.forcefield.openbabelff method)": [[36, "rdmc.forcefield.OpenBabelFF.update_atom_idx"]], "update_atom_idx() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.update_atom_idx"]], "fourierseries1d (class in rdmc.mathlib.curvefit)": [[38, "rdmc.mathlib.curvefit.FourierSeries1D"]], "fit() (rdmc.mathlib.curvefit.fourierseries1d method)": [[38, "rdmc.mathlib.curvefit.FourierSeries1D.fit"]], "max_num_term (rdmc.mathlib.curvefit.fourierseries1d attribute)": [[38, "rdmc.mathlib.curvefit.FourierSeries1D.max_num_term"]], "predict() (rdmc.mathlib.curvefit.fourierseries1d method)": [[38, "rdmc.mathlib.curvefit.FourierSeries1D.predict"]], "rdmc.mathlib.curvefit": [[38, "module-rdmc.mathlib.curvefit"]], "get_centroid() (in module rdmc.mathlib.geom)": [[39, "rdmc.mathlib.geom.get_centroid"]], "get_distances_from_a_point() (in module rdmc.mathlib.geom)": [[39, "rdmc.mathlib.geom.get_distances_from_a_point"]], "get_mass_center() (in module rdmc.mathlib.geom)": [[39, "rdmc.mathlib.geom.get_mass_center"]], "get_max_distance_from_center() (in module rdmc.mathlib.geom)": [[39, "rdmc.mathlib.geom.get_max_distance_from_center"]], "get_weighted_center() (in module rdmc.mathlib.geom)": [[39, "rdmc.mathlib.geom.get_weighted_center"]], "rdmc.mathlib.geom": [[39, "module-rdmc.mathlib.geom"]], "rotate() (in module rdmc.mathlib.geom)": [[39, "rdmc.mathlib.geom.rotate"]], "translate() (in module rdmc.mathlib.geom)": [[39, "rdmc.mathlib.geom.translate"]], "translate_centroid() (in module rdmc.mathlib.geom)": [[39, "rdmc.mathlib.geom.translate_centroid"]], "compare_to_adjacent_point() (in module rdmc.mathlib.greedymin)": [[40, "rdmc.mathlib.greedymin.compare_to_adjacent_point"]], "get_energy() (in module rdmc.mathlib.greedymin)": [[40, "rdmc.mathlib.greedymin.get_energy"]], "get_step_to_adjacent_points() (in module rdmc.mathlib.greedymin)": [[40, "rdmc.mathlib.greedymin.get_step_to_adjacent_points"]], "rdmc.mathlib.greedymin": [[40, "module-rdmc.mathlib.greedymin"]], "search_for_a_minimum() (in module rdmc.mathlib.greedymin)": [[40, "rdmc.mathlib.greedymin.search_for_a_minimum"]], "search_minimum() (in module rdmc.mathlib.greedymin)": [[40, "rdmc.mathlib.greedymin.search_minimum"]], "rdmc.mathlib": [[41, "module-rdmc.mathlib"]], "addnullconformer() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.AddNullConformer"]], "addredundantbonds() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.AddRedundantBonds"]], "alignmol() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.AlignMol"]], "assignstereochemistryfrom3d() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.AssignStereochemistryFrom3D"]], "calcrmsd() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.CalcRMSD"]], "combinemol() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.CombineMol"]], "copy() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.Copy"]], "embedconformer() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.EmbedConformer"]], "embedmultipleconfs() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.EmbedMultipleConfs"]], "embedmultiplenullconfs() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.EmbedMultipleNullConfs"]], "embednullconformer() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.EmbedNullConformer"]], "fromfile() (rdmc.mol.rdkitmol class method)": [[42, "rdmc.mol.RDKitMol.FromFile"]], "frominchi() (rdmc.mol.rdkitmol class method)": [[42, "rdmc.mol.RDKitMol.FromInchi"]], "frommol() (rdmc.mol.rdkitmol class method)": [[42, "rdmc.mol.RDKitMol.FromMol"]], "fromobmol() (rdmc.mol.rdkitmol class method)": [[42, "rdmc.mol.RDKitMol.FromOBMol"]], "fromrmgmol() (rdmc.mol.rdkitmol class method)": [[42, "rdmc.mol.RDKitMol.FromRMGMol"]], "fromsdf() (rdmc.mol.rdkitmol class method)": [[42, "rdmc.mol.RDKitMol.FromSDF"]], "fromsmarts() (rdmc.mol.rdkitmol class method)": [[42, "rdmc.mol.RDKitMol.FromSmarts"]], "fromsmiles() (rdmc.mol.rdkitmol class method)": [[42, "rdmc.mol.RDKitMol.FromSmiles"]], "fromxyz() (rdmc.mol.rdkitmol class method)": [[42, "rdmc.mol.RDKitMol.FromXYZ"]], "getadjacencymatrix() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetAdjacencyMatrix"]], "getallconformers() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetAllConformers"]], "getatommapnumbers() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetAtomMapNumbers"]], "getatommasses() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetAtomMasses"]], "getatomicnumbers() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetAtomicNumbers"]], "getatoms() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetAtoms"]], "getbestalign() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetBestAlign"]], "getbondsastuples() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetBondsAsTuples"]], "getconformer() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetConformer"]], "getconformers() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetConformers"]], "getdistancematrix() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetDistanceMatrix"]], "getelementsymbols() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetElementSymbols"]], "getfingerprint() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetFingerprint"]], "getformalcharge() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetFormalCharge"]], "getinternalcoordinates() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetInternalCoordinates"]], "getmolfrags() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetMolFrags"]], "getpositions() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetPositions"]], "getspinmultiplicity() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetSpinMultiplicity"]], "getsubstructmatch() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetSubstructMatch"]], "getsubstructmatches() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetSubstructMatches"]], "getsymmsssr() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetSymmSSSR"]], "gettorsiontops() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetTorsionTops"]], "gettorsionalmodes() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetTorsionalModes"]], "getvdwmatrix() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetVdwMatrix"]], "hascollidingatoms() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.HasCollidingAtoms"]], "hassameconnectivity() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.HasSameConnectivity"]], "kekulize() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.Kekulize"]], "prepareoutputmol() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.PrepareOutputMol"]], "rdkitmol (class in rdmc.mol)": [[42, "rdmc.mol.RDKitMol"]], "reflect() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.Reflect"]], "removehs() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.RemoveHs"]], "renumberatoms() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.RenumberAtoms"]], "sanitize() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.Sanitize"]], "saturatebiradicalsites12() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.SaturateBiradicalSites12"]], "saturatebiradicalsitescdb() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.SaturateBiradicalSitesCDB"]], "saturatecarbene() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.SaturateCarbene"]], "saturatemol() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.SaturateMol"]], "setatommapnumbers() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.SetAtomMapNumbers"]], "setpositions() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.SetPositions"]], "setvdwmatrix() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.SetVdwMatrix"]], "toatoms() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.ToAtoms"]], "tograph() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.ToGraph"]], "toinchi() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.ToInchi"]], "tomolblock() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.ToMolBlock"]], "toobmol() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.ToOBMol"]], "torwmol() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.ToRWMol"]], "tosdffile() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.ToSDFFile"]], "tosmiles() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.ToSmiles"]], "toxyz() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.ToXYZ"]], "generate_radical_resonance_structures() (in module rdmc.mol)": [[42, "rdmc.mol.generate_radical_resonance_structures"]], "generate_vdw_mat() (in module rdmc.mol)": [[42, "rdmc.mol.generate_vdw_mat"]], "get_unique_mols() (in module rdmc.mol)": [[42, "rdmc.mol.get_unique_mols"]], "has_matched_mol() (in module rdmc.mol)": [[42, "rdmc.mol.has_matched_mol"]], "parse_xyz_or_smiles_list() (in module rdmc.mol)": [[42, "rdmc.mol.parse_xyz_or_smiles_list"]], "rdmc.mol": [[42, "module-rdmc.mol"]], "rdmc": [[43, "module-rdmc"]], "reaction (class in rdmc.reaction)": [[44, "rdmc.reaction.Reaction"]], "active_atoms (rdmc.reaction.reaction property)": [[44, "rdmc.reaction.Reaction.active_atoms"]], "active_bonds (rdmc.reaction.reaction property)": [[44, "rdmc.reaction.Reaction.active_bonds"]], "apply_resonance_correction() (rdmc.reaction.reaction method)": [[44, "rdmc.reaction.Reaction.apply_resonance_correction"]], "bond_analysis() (rdmc.reaction.reaction method)": [[44, "rdmc.reaction.Reaction.bond_analysis"]], "broken_bonds (rdmc.reaction.reaction property)": [[44, "rdmc.reaction.Reaction.broken_bonds"]], "changed_bonds (rdmc.reaction.reaction property)": [[44, "rdmc.reaction.Reaction.changed_bonds"]], "draw_2d() (rdmc.reaction.reaction method)": [[44, "rdmc.reaction.Reaction.draw_2d"]], "formed_bonds (rdmc.reaction.reaction property)": [[44, "rdmc.reaction.Reaction.formed_bonds"]], "from_reactant_and_product_smiles() (rdmc.reaction.reaction class method)": [[44, "rdmc.reaction.Reaction.from_reactant_and_product_smiles"]], "from_reaction_smiles() 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