From 550c3ce8b6c7838a396037d440bb49cf5108fefd Mon Sep 17 00:00:00 2001 From: xiaoruiDong Date: Wed, 18 Oct 2023 01:39:37 +0000 Subject: [PATCH] deploy: ee3663dc470655237cb9426c5a12c9ad313de83a --- genindex.html | 1002 +---------------- index.html | 2 +- objects.inv | Bin 4931 -> 2286 bytes py-modindex.html | 147 +-- reference/conf.html | 651 +---------- .../embedding_geometries/align.html | 257 +---- .../embedding_geometries/embedders.html | 166 +-- .../embedding_geometries/index.html | 26 +- .../embedding_geometries/ts_guessers.html | 261 +---- .../geometry_optimization/index.html | 17 +- .../geometry_optimization/optimizers.html | 168 +-- .../geometry_optimization/ts_optimizers.html | 249 +--- reference/conformer_generation/index.html | 14 +- .../postprocessing/index.html | 29 +- .../postprocessing/pruners.html | 223 +--- .../postprocessing/solvation.html | 80 +- .../postprocessing/ts_verifiers.html | 249 +--- .../postprocessing/verifiers.html | 89 +- reference/conformer_generation/utils.html | 151 +-- .../workflow/generators.html | 157 +-- .../conformer_generation/workflow/index.html | 25 +- .../workflow/metrics.html | 85 +- .../workflow/sampler.html | 155 +-- .../workflow/ts_generators.html | 116 +- reference/external/index.html | 90 +- reference/external/logparser/base.html | 574 +--------- reference/external/logparser/gaussian.html | 36 +- reference/external/logparser/index.html | 94 +- reference/external/logparser/orca.html | 46 +- reference/external/logparser/qchem.html | 82 +- reference/external/logparser/utils.html | 26 +- reference/mathlib/curvefit.html | 63 +- reference/mathlib/geom.html | 170 +-- reference/mathlib/greedymin.html | 113 +- reference/mathlib/index.html | 35 +- reference/mol.html | 6 +- reference/rdmc.html | 277 +---- reference/reaction.html | 246 +--- reference/ts.html | 217 +--- reference/utils.html | 2 +- reference/view.html | 206 +--- searchindex.js | 2 +- 42 files changed, 151 insertions(+), 6453 deletions(-) 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 - - - -     - rdmc.conf - - - -     - rdmc.conformer_generation - - - -     - rdmc.conformer_generation.align - - - -     - rdmc.conformer_generation.embedders - - - -     - rdmc.conformer_generation.generators - - - -     - rdmc.conformer_generation.metrics - - - -     - rdmc.conformer_generation.optimizers - - - -     - rdmc.conformer_generation.pruners - - - -     - rdmc.conformer_generation.sampler - - - -     - rdmc.conformer_generation.solvation - - - -     - rdmc.conformer_generation.ts_generators - - - -     - rdmc.conformer_generation.ts_guessers - - - -     - rdmc.conformer_generation.ts_optimizers - - - -     - rdmc.conformer_generation.ts_verifiers - - - -     - rdmc.conformer_generation.utils - - - -     - rdmc.conformer_generation.verifiers + rdmc @@ -477,36 +397,6 @@

    Python Module Index

        rdmc.external.inpwriter.utils - - -     - rdmc.external.logparser - - - -     - rdmc.external.logparser.base - - - -     - rdmc.external.logparser.gaussian - - - -     - rdmc.external.logparser.orca - - - -     - rdmc.external.logparser.qchem - - - -     - rdmc.external.logparser.utils -     @@ -517,51 +407,16 @@

    Python Module Index

        rdmc.forcefield - - -     - rdmc.mathlib - - - -     - rdmc.mathlib.curvefit - - - -     - rdmc.mathlib.geom - - - -     - rdmc.mathlib.greedymin -     rdmc.mol - - -     - rdmc.reaction - - - -     - rdmc.ts -     rdmc.utils - - -     - rdmc.view - diff --git a/reference/conf.html b/reference/conf.html index a714f16a..b71550f4 100644 --- a/reference/conf.html +++ b/reference/conf.html @@ -39,7 +39,6 @@ - @@ -457,599 +456,8 @@
    -
    -

    rdmc.conf#

    -

    This module provides class and methods for dealing with RDKit Conformer.

    -
    -
    -class rdmc.conf.ConformerCluster(children: array, energies: array | None = None)#
    -

    Bases: object

    -
    -
    -merge(clusters: list)#
    -

    Merge the cluster with a list of clusters.

    -
    -
    Parameters:
    -

    clusters (list) – A list of the ConformerCluster object to be merged in.

    -
    -
    -
    - -
    -
    -split_by_energies(decimals: int = 1, as_dict: bool = True)#
    -

    Split the conformer by energies.

    -
    -
    Parameters:
    -
      -

    • decimals (int, optional) – clustering children based on the number of digit -after the dot of the energy values. -For kcal/mol and J/mol, 0 or 1 is recommended; for -hartree, 3 or 4 is recommended. Defaults to 1.

      • -

    • as_dict (bool, optional) – If True, return a dict object whose keys are -energy values and values are divided ConformerCluster -object. Otherwise, return a list of ConformerClusters. -Defaults to True.

      • -
    -
    -
    -
    - -
    - -
    -
    -class rdmc.conf.ConformerFilter(mol: RDKitMol)#
    -

    Bases: object

    -
    -
    -property atom_maps#
    -

    Store all possible atommappings of the given molecules. There are usually combinatory -explosion.

    -
    - -
    -
    -check_dihed_angle_diff(confs, threshold: float = 5.0, mask: ndarray | None = None, adjust_periodicity: bool = False, as_dict: bool = True, as_list_idx: bool = False)#
    -

    The implementation of checking individual dihedral angle difference. This approach is also -implemented in the MSTor workflow.

    -
    -
    Parameters:
    -
      -

    • confs (list) – A list of conformer IDs.

      • -

    • threshold (float, optional) – The difference (in degree) used for filtering. Defaults to 5.

      • -

    • mask (np.ndarray, optional) – An array that has the same length as torsions and values of True or False to -indicate which torsions are not considered. This can be helpful, e.g., to exclude -methyl torsional symmetry.

      • -

    • adjust_periodicity (bool, optional) – Since dihedral angles have a period of 360 degrees. Defaults to True. -It is suggested to run twice with this value be True and False to -get a better performance.

      • -

    • as_dict (bool) – Return the result as a dict object with keys for the index of clusters and values -of conformer indexes (provided in confs). Otherwise, return as a list of grouped -conformer indexes. Defaults to True.

      • -

    • as_list_idx (bool) – Return the indexes in the confs list other than the value in the confs.

      • -
    -
    -
    Returns:
    -

    dict or list

    -
    -
    -
    - -
    -
    -filter_by_dihed_angles(clusters, threshold: float = 5.0, mask: ndarray | None = None, as_clusters: bool = True) → list#
    -

    A method to filter comformers by calculating the differences of dihedral angles between conformers. -The check will be implemented twice, with and without considering periodicity.

    -
    -
    Parameters:
    -
      -

    • clusters (ConformerCluster or list) – A single ConformerCluster object or a list of conformerClusters.

      • -

    • threshold (float, optional) – The threshold (in degree) used for hierarchy clustering. Defaults to 5.

      • -

    • mask (np.array, optional) – An array that has the same length as torsions and values of True or False to -indicate which torsions are not considered. This can be helpful, e.g., to exclude -methyl torsional symmetry.

      • -

    • as_clusters (bool, optional) – Return the results as a list of ConformerClusters (True) or a list of -grouped conformer indexes (True). Defaults to True.

      • -
    -
    -
    Returns:
    -

    list

    -
    -
    -
    - -
    -
    -filter_by_iter_hcluster(clusters: list | ConformerCluster, threshold: float = 5.0, criterion: str = 'distance', method: str = 'average', max_iter: int = 10, as_clusters: bool = True)#
    -

    A method to filter comformers by iteratively applying hierarchy clustering. -In a new iteration, only the distinguishable representative conformers will be used that are -generated in the previous iteration.

    -
    -
    Parameters:
    -
      -

    • clusters (ConformerCluster or list) – A single ConformerCluster object or a list of conformerClusters.

      • -

    • threshold (float, optional) – The threshold (in degree) used for hierarchy clustering. Defaults to 5.

      • -

    • criterion (str, optional) – Specifies the criterion for forming flat clusters. Valid values are ‘inconsistent’, -‘distance’ (default), or ‘maxclust’ cluster formation algorithms

      • -

    • method (str, optional) – The linkage method to use. Valid values are single, complete, average (default), -weighted, median centroid, and ward. Except median centroid (O(n^3)), others have a -computational cost scaled by O(n^2).

      • -

    • adjust_periodicity (bool, optional) – Since dihedral angles have a period of 360 degrees. Defaults to True. -It is suggested to run twice with this value be True and False to -get a better performance.

      • -

    • max_iter (int, optional) – The max number of iterations. Defaults to 10. There is a early-stopping techinque -if number of clusters doesn’t change with increasing number of iterations.

      • -

    • as_clusters (bool, optional) – Return the results as a list of ConformerClusters (True) or a list of -grouped conformer indexes (True). Defaults to True.

      • -
    -
    -
    Returns:
    -

    list

    -
    -
    -
    - -
    -
    -generate_rmsds_of_cluster(cluster, reflect: bool = False, reorder: bool = True, max_iters: int = 1000)#
    -

    Get the RMSDs between the representative conformer and each conformer in the cluster.

    -
    - -
    -
    -get_tor_matrix(confs: array | list, adjust_periodicity: bool = True) → ndarray#
    -

    Get the torsional matrix consists of torsional angles for the input list of conformer indexes.

    -
    -
    Parameters:
    -
      -

    • confid (int) – The conformer ID

      • -

    • adjust_periodicity (bool) – Whether to adjust the periodicity for torsional angles.

      • -
    -
    -
    Returns:
    -

    np.array – a M (the number of conformers indicated by confs) x N (the number of torsional angles) matrix

    -
    -
    -
    - -
    -
    -get_torsional_angles(confid: int, adjust_periodicity: bool = True) → array#
    -

    Get torsional angles for a given conformers.

    -
    -
    Parameters:
    -
      -

    • confid (int) – The conformer ID.

      • -

    • adjust_periodicity (bool) – Whether to adjust the periodicity for torsional angles. -Defaults to True.

      • -
    -
    -
    Returns:
    -

    np.array – A 1D array of torsional angles.

    -
    -
    -
    - -
    -
    -hierarchy_cluster(confs, threshold: float = 5.0, criterion: str = 'distance', method: str = 'average', adjust_periodicity: bool = False, as_dict: bool = True, as_list_idx: bool = False)#
    -

    The implementation of an hierarchy clustering method based on scipy. -It is basically defining clusters based on points within a hypercube defined by threshold. -More details refer to scipy.

    -
    -
    Parameters:
    -
      -

    • confs (list) – A list of conformer IDs.

      • -

    • threshold (float, optional) – The threshold (in degree) used for hierarchy clustering. Defaults to 5.

      • -

    • criterion (str, optional) – Specifies the criterion for forming flat clusters. Valid values are 'inconsistent', -'distance' (default), or 'maxclust' cluster formation algorithms.

      • -

    • method (str, optional) – The linkage method to use. Valid values are 'single', 'complete', 'average' (default), -'weighted', 'median centroid', and 'ward'. Except median centroid (\(O(n^3)\)), others have a -computational cost scaled by \(O(n^2)\).

      • -

    • adjust_periodicity (bool, optional) – Since dihedral angles have a period of 360 degrees, adjusting for periodicity helps -create better clustering results. Defaults to True. -It is suggested to run twice with this value be True and False to -get a better performance.

      • -

    • as_dict (bool) – Return the result as a dict object with keys for the index of clusters and values -of conformer indexes (provided in confs). Otherwise, return as a list of grouped -conformer indexes. Defaults to True.

      • -

    • as_list_idx (bool) – Return the indexes in the confs list other than the value in the confs. -Default to False.

      • -
    -
    -
    -
    - -
    -
    -pairwise_rmsd(i: int, j: int, reflect: bool = False, reorder: bool = True, max_iters: int = 1000)#
    -

    The implementation of calculating pairwise RMSD values.

    -
    -
    Parameters:
    -
      -

    • i (int) – Index of one of the conformer. Usually, used as the ‘reference’.

      • -

    • j (int) – Index of the other conformer.

      • -

    • reflect (bool, optional) – Whether to reflect the j conformer to rule out -mirror symmetry. Defaults to False.

      • -

    • reorder (bool, optional) – Whether to allow atom index order to change (based -on isomorphism check to rule out torsional symmetry -and rotational symmetry).

      • -

    • max_iters (int, optional) – The max iteration in mimizing the RMSD.

      • -
    -
    -
    -
    - -
    -
    -reset_atom_maps(max_atom_maps=100000)#
    -

    Reset the stored matches.

    -
    -
    Parameters:
    -

    max_atom_maps (int) – The maximum number of atom maps to generate To avoid combinatory explosion, -it is set to avoid the program to run forever. As a cost, you may miss some mappings.

    -
    -
    -
    - -
    - -
    -
    -class rdmc.conf.RDKitConf(conf)#
    -

    Bases: object

    -

    A wrapper for rdchem.Conformer.

    -

    The method nomenclature follows the Camel style to be consistent with RDKit.

    -
    -
    -classmethod FromConformer(conf: Conformer) → RDKitConf#
    -

    Convert a RDKit Chem.rdchem.Conformer to a RDKitConf. This allows a more -capable and flexible Conformer class.

    -
    -
    Parameters:
    -

    conf (Chem.rdchem.Conformer) – A RDKit Conformer instance to be converted.

    -
    -
    Returns:
    -

    RDKitConf – The conformer corresponding to the RDKit Conformer in RDKitConf

    -
    -
    -
    - -
    -
    -classmethod FromMol(mol: RWMol | Mol, id: int = 0) → RDkitConf#
    -

    Get a RDKitConf instance from a Chem.rdchem.Mol/RWMol instance.

    -
    -
    Parameters:
    -
      -

    • mol (Union[RWMol, Mol]) – a Molecule in RDKit Default format.

      • -

    • id (int) – The id of the conformer to be extracted from the molecule.

      • -
    -
    -
    Returns:
    -

    RDKitConf – A Conformer in RDKitConf of the given molecule

    -
    -
    -
    - -
    -
    -classmethod FromRDKitMol(rdkitmol: RDKitMol, id: int = 0) → RDkitConf#
    -

    Get a RDKitConf instance from a RDKitMol instance. The owning molecule -of the generated conformer is RDKitMol instead of Chem.rdchem.Mol.

    -
    -
    Parameters:
    -
      -

    • rdkitmol (RDKitMol) – a Molecule in RDKitMol.

      • -

    • id (int) – The id of the conformer to be extracted from the molecule.

      • -
    -
    -
    Returns:
    -

    RDKitConf – A Conformer in RDKitConf of the given molecule

    -
    -
    -
    - -
    -
    -GetAllTorsionsDeg() → list#
    -

    Get the dihedral angles of all torsional modes (rotors) of the Conformer. The sequence of the -values are corresponding to the torsions of the molecule (GetTorsionalModes).

    -
    -
    Returns:
    -

    list – A list of dihedral angles of all torsional modes.

    -
    -
    -
    - -
    -
    -GetAngleDeg(atomIds: Sequence[int]) → float#
    -

    Get the angle between atoms in degrees.

    -
    -
    Parameters:
    -

    atomIds (Sequence) – A 3-element sequence object containing atom indexes.

    -
    -
    Returns:
    -

    float – Angle value in degrees.

    -
    -
    -
    - -
    -
    -GetAngleRad(atomIds: Sequence[int]) → float#
    -

    Get the angle between atoms in rads.

    -
    -
    Parameters:
    -

    atomIds (Sequence) – A 3-element sequence object containing atom indexes.

    -
    -
    Returns:
    -

    float – Angle value in rads.

    -
    -
    -
    - -
    -
    -GetBondLength(atomIds: Sequence[int]) → float#
    -

    Get the bond length between atoms in Angstrom.

    -
    -
    Parameters:
    -

    atomIds (Sequence) – A 3-element sequence object containing atom indexes.

    -
    -
    Returns:
    -

    float – Bond length in Angstrom.

    -
    -
    -
    - -
    -
    -GetDistanceMatrix() → ndarray#
    -

    Get the distance matrix of the conformer.

    -
    -
    Returns:
    -

    array – n x n distance matrix such that n is the number of atom.

    -
    -
    -
    - -
    -
    -GetOwningMol()#
    -

    Get the owning molecule of the conformer.

    -
    -
    Returns:
    -

    Union[Mol, RWMol, RDKitMol] – The owning molecule

    -
    -
    -
    - -
    -
    -GetTorsionDeg(torsion: list) → float#
    -

    Get the dihedral angle of the torsion in degrees. The torsion can be defined -by any atoms in the molecule (not necessarily bonded atoms.)

    -
    -
    Parameters:
    -

    torsion (list) – A list of four atom indexes.

    -
    -
    Returns:
    -

    float – The dihedral angle of the torsion.

    -
    -
    -
    - -
    -
    -GetTorsionalModes(indexed1: bool = False, excludeMethyl: bool = False, includeRings: bool = False) → list#
    -

    Get all of the torsional modes (rotors) of the Conformer. This information -is obtained from its owning molecule.

    -
    -
    Parameters:
    -
      -

    • indexed1 – The atom index in RDKit starts from 0. If you want to have -indexed 1 atom indexes, please set this argument to True.

      • -

    • excludeMethyl (bool) – Whether exclude the torsions with methyl groups. Defaults to False.

      • -

    • includeRings (bool) – Whether or not to include ring torsions. Defaults to False.

      • -
    -
    -
    Returns:
    -

    Optinal[list] – A list of four-atom-indice to indicating the torsional modes.

    -
    -
    -
    - -
    -
    -GetVdwMatrix(threshold=0.4) → ndarray | None#
    -

    Get the derived Van der Waals matrix, which can be used to analyze -the collision of atoms. More information can be found from generate_vdw_mat.

    -
    -
    Parameters:
    -

    threshold – float indicating the threshold to use in the vdw matrix

    -
    -
    Returns:
    -

    Optional[np.ndarray] – A 2D array of the derived Van der Waals Matrix, if the -the matrix exists, otherwise None.

    -
    -
    -
    - -
    -
    -HasCollidingAtoms(threshold=0.4) → ndarray#
    -
    -
    Parameters:
    -

    threshold – float indicating the threshold to use in the vdw matrix

    -
    -
    -
    - -
    -
    -HasOwningMol()#
    -

    Whether the conformer has a owning molecule.

    -
    -
    Returns:
    -

    bool – True if the conformer has a owning molecule.

    -
    -
    -
    - -
    -
    -SetAllTorsionsDeg(angles: list)#
    -

    Set the dihedral angles of all torsional modes (rotors) of the Conformer. The sequence of the -values are corresponding to the torsions of the molecule (GetTorsionalModes).

    -
    -
    Parameters:
    -

    angles (list) – A list of dihedral angles of all torsional modes.

    -
    -
    -
    - -
    -
    -SetAngleDeg(atomIds: Sequence[int], value: int | float) → float#
    -

    Set the angle between atoms in degrees.

    -
    -
    Parameters:
    -
      -

    • atomIds (Sequence) – A 3-element sequence object containing atom indexes.

      • -

    • value (int or float, optional) – Bond angle in degrees.

      • -
    -
    -
    -
    - -
    -
    -SetAngleRad(atomIds: Sequence[int], value: int | float) → float#
    -

    Set the angle between atoms in rads.

    -
    -
    Parameters:
    -
      -

    • atomIds (Sequence) – A 3-element sequence object containing atom indexes.

      • -

    • value (int or float, optional) – Bond angle in rads.

      • -
    -
    -
    -
    - -
    -
    -SetBondLength(atomIds: Sequence[int], value: int | float) → float#
    -

    Set the bond length between atoms in Angstrom.

    -
    -
    Parameters:
    -
      -

    • atomIds (Sequence) – A 3-element sequence object containing atom indexes.

      • -

    • value (int or float, optional) – Bond length in Angstrom.

      • -
    -
    -
    -
    - -
    -
    -SetOwningMol(owningMol: RDKitMol | Mol | RWMol)#
    -

    Set the owning molecule of the conformer. It can be either RDKitMol -or Chem.rdchem.Mol.

    -
    -
    Parameters:
    -

    owningMol – Union[RDKitMol, Chem.rdchem.Mol] The owning molecule of the conformer.

    -
    -
    Raises:
    -

    ValueError – Not a valid owning_mol input, when giving something else.

    -
    -
    -
    - -
    -
    -SetPositions(coords: tuple | list)#
    -

    Set the Positions of atoms of the conformer.

    -
    -
    Parameters:
    -

    coords – a list of tuple of atom coordinates.

    -
    -
    -
    - -
    -
    -SetTorsionDeg(torsion: list, degree: float | int)#
    -

    Set the dihedral angle of the torsion in degrees. The torsion can only be defined -by a chain of bonded atoms.

    -
    -
    Parameters:
    -
      -

    • torsion (list) – A list of four atom indexes.

      • -

    • degree (float, int) – The dihedral angle of the torsion.

      • -
    -
    -
    -
    - -
    -
    -SetTorsionalModes(torsions: list | tuple)#
    -

    Set the torsional modes (rotors) of the Conformer. This is useful when the -default torsion is not correct.

    -
    -
    Parameters:
    -

    torsions (Union[list, tuple]) – A list of four-atom-lists indicating the torsional modes.

    -
    -
    Raises:
    -

    ValueError – The torsional mode used is not valid.

    -
    -
    -
    - -
    -
    -ToConformer() → Conformer#
    -

    Get its backend RDKit Conformer object.

    -
    -
    Returns:
    -

    Conformer – The backend conformer

    -
    -
    -
    - -
    -
    -ToMol() → RDKitMol#
    -

    Convert conformer to mol.

    -
    -
    Returns:
    -

    RDKitMol – The new mol generated from the conformer

    -
    -
    -
    - -
    - -
    -
    -rdmc.conf.edit_conf_by_add_bonds(conf, function_name, atoms, value)#
    -

    RDKit forbids modifying internal coordinates with non-bonding atoms. -This function tries to provide a workaround.

    -
    -
    Parameters:
    -
      -

    • conf (RDKitConf) – The conformer to be modified.

      • -

    • function_name (str) – The function name of the edit.

      • -

    • atoms (list) – A list of atoms representing the internal coordinates.

      • -

    • value (float) – Value to be set.

      • -
    -
    -
    -
    - +
    +

    rdmc.conf#

    @@ -1089,61 +497,6 @@
    -
    -
    - On this page -
    -
    -
    diff --git a/reference/conformer_generation/embedding_geometries/align.html b/reference/conformer_generation/embedding_geometries/align.html index cef0b66b..26a35a21 100644 --- a/reference/conformer_generation/embedding_geometries/align.html +++ b/reference/conformer_generation/embedding_geometries/align.html @@ -464,236 +464,8 @@
    -
    -

    rdmc.conformer_generation.align#

    -

    This module provides class and methods for reaction path analysis.

    -
    -
    -class rdmc.conformer_generation.align.NaiveAlign(coords: array, atom_maps: List[List], formed_bonds: List[tuple], broken_bonds: List[tuple])#
    -

    Bases: object

    -

    This is a naive alignment algorithm aligns reactant conformers.

    -
      -

    • For 1 reactant system, the algorithm simply put the center of the reactant at the origin.

      • -

    • For 2 reactant system, the resulting alignment has the following characteristics:

      -
        -

      • the centroid for fragment 1 is at the origin.

        • -

      • the centroid for fragment 2 is at (R1 + R2 + D), where R1 is the radius of fragment 1, R2 is the radius -of fragment 2, and D is a pre-set distance value defined by the user.

        • -

      • the centroid of the reacting atoms in fragment 1 should be around the line (0,0,0) => (1,0,0).

        • -

      • the centroid of the reacting atoms in fragment 2 should be around the line (0,0,0) => (1,0,0).

        • -

      • the distance between atoms to form bonds are minimized.

        • -
      -
      • -
    -

    The following are under development:

    -
      -

    • For 3 reactant system, the feature is under-development. There should be two cases: close-linear alignment and triangle alignment, -depending on the max number of interactions among fragments.

      • -

    • For 4 reactant system, the feature is under-development. There should be three cases: close-linear, square, and tetrahedron alignment, -depending on the max number of interactions among fragments.

      • -
    -
    -
    -dist = 2.0#
    -
    - -
    -
    -classmethod from_complex(r_complex: RDKitMol, formed_bonds: List[tuple], broken_bonds: List[tuple], conf_id: int = 0)#
    -

    Initialize from a reactant complex.

    -
    -
    Parameters:
    -
      -

    • r_complex (RDKitMol) – The reactant complex.

      • -

    • formed_bonds (List[tuple]) – bonds formed in the reaction.

      • -

    • broken_bonds (List[tuple]) – bonds broken in the reaction.

      • -

    • conf_id (int, optional) – The conformer id to be used in the r_complex. Defaults to 0.

      • -
    -
    -
    -
    - -
    -
    -classmethod from_r_and_p_complex(r_complex: RDKitMol, p_complex: RDKitMol, conf_id: int = 0)#
    -

    Initialize from the reactant complex and the product complex. The product complex -does not need to have conformers embedded, however, it should be atom mapped with -the reactant complex.

    -
    -
    Parameters:
    -
      -

    • r_complex (RDKitMol) – The reactant complex.

      • -

    • p_complex (RDKitMol) – The product complex.

      • -

    • conf_id (int, optional) – The conformer id to be used in the reactant complex r_complex. Defaults to 0.

      • -
    -
    -
    -
    - -
    -
    -classmethod from_reactants(mols: List[RDKitMol], formed_bonds: List[tuple], broken_bonds: List[tuple], conf_ids: List[int] | None = None)#
    -

    Create a complex in place by stacking the molecules together.

    -
    -
    Parameters:
    -
      -

    • mols (RDKitMol) – A list of reactants.

      • -

    • formed_bonds (List[tuple]) – bonds formed in the reaction.

      • -

    • broken_bonds (List[tuple]) – bonds broken in the reaction.

      • -

    • conf_id1 (int, optional) – The conformer id to be used in mol1. Defaults to 0.

      • -

    • conf_id2 (int, optional) – The conformer id to be used in mol2. Defaults to 0.

      • -
    -
    -
    -
    - -
    -
    -get_alignment_coords(dist: float | None = None) → array#
    -

    Get coordinates of the alignment.

    -
    -
    Parameters:
    -

    dist (float, optional) – The a preset distance used to separate molecules. -Defaults to None meaning using the value of dist.

    -
    -
    Returns:
    -

    np.array – The coordinates of the alignment.

    -
    -
    -
    - -
    -
    -get_fragment_radii() → List[float]#
    -

    Get the radius of each fragment defined by the distance between the centroid to the farthest element.

    -
    -
    Returns:
    -

    list – A list of radius.

    -
    -
    -
    - -
    -
    -get_reacting_atoms_in_fragments() → List[list]#
    -

    Get the reacting atoms in each reactant.

    -
    -
    Returns:
    -
      -

    • - A list of the list of reacting atoms in each reactant.

      • -

    • - A list of the list of non reacting atoms in each reactant.

      • -
    -
    -
    -
    - -
    -
    -initialize_align(dist: float | None = None)#
    -

    Initialize the alignment for the reactants. Currently only available for 1 reactant and 2 reactant systems.

    -
    -
    Parameters:
    -

    dist (float, optional) – The a preset distance used to separate molecules. Defaults to None, -meaning using the default value of dist.

    -
    -
    -
    - -
    -
    -rotate_fragment_separately(*angles: array, about_reacting: bool = False) → array#
    -

    Rotate the molecule fragments in the complex by angles. The length of angles should be same as the length of -self.atom_maps.

    -
    -
    Parameters:
    -
      -

    • angles (np.array) – Rotation angles for molecule fragment 1. It should be an array with a -size of (1,3) indicate the rotation angles about the x, y, and z axes, respectively.

      • -

    • about_reacting (bool, optional) – If rotate about the reactor center instead of the centroid. Defaults to False.

      • -
    -
    -
    Returns:
    -

    np.array – The coordinates after the rotation operation.

    -
    -
    -
    - -
    -
    -score_bimolecule(angles: array) → float#
    -

    Calculate the score of bimolecular reaction alignment.

    -
    -
    Parameters:
    -

    angles (np.array) – an array with 6 elements. The first 3 angles correspond to the rotation of the first fragment, -and the last 3 angles correspond to the rotation of the second fragment.

    -
    -
    Returns:
    -

    float – The score value.

    -
    -
    -
    - -
    - -
    -
    -rdmc.conformer_generation.align.align_reactant_fragments(r_mol: RDKitMol, p_mol: RDKitMol) → RDKitMol#
    -

    Given reactant and product mols, find details of formed and broken bonds and generate reacting reactant complex.

    -
    -
    Parameters:
    -
      -

    • r_mol ('RDKitMol' or 'Mol') – An RDKit Mol object for reactant.

      • -

    • p_mol ('RDKitMol' or 'Mol') – An RDKit Mol object for product.

      • -
    -
    -
    Returns:
    -

    RDKitMol – The new reactant with aligned fragments.

    -
    -
    -
    - -
    -
    -rdmc.conformer_generation.align.prepare_mols(r_mol: RDKitMol, p_mol: RDKitMol, align_bimolecular: bool = True) → Tuple[RDKitMol, RDKitMol]#
    -

    Prepare mols for reaction path analysis. If reactant has multiple fragments, first orient reactants in reacting -orientation. Then, reinitialize coordinates of product using reset_pmol function.

    -
    -
    Parameters:
    -
      -

    • r_mol ('RDKitMol' or 'Mol') – An RDKit Mol object for reactant.

      • -

    • p_mol ('RDKitMol' or 'Mol') – An RDKit Mol object for product.

      • -

    • align_bimolecular (bool, optional) – Whether or not to use alignment algorithm on bimolecular reactions. -Defaults to True

      • -
    -
    -
    Returns:
    -
      -

    • r_mol (‘RDKitMol’) – The new reactant molecule.

      • -

    • p_mol_new (‘RDKitMol’) – The new product molecule.

      • -
    -
    -
    -
    - -
    -
    -rdmc.conformer_generation.align.reset_pmol(r_mol: RDKitMol, p_mol: RDKitMol) → RDKitMol#
    -

    Reset the product mol to best align with the reactant. This procedure consists of initializing the product 3D -structure with the reactant coordinates and then 1) minimizing the product structure with constraints for broken -bonds and 2) performing a second minimization with no constraints.

    -
    -
    Parameters:
    -
      -

    • r_mol ('RDKitMol' or 'Mol') – An RDKit Mol object for reactant.

      • -

    • p_mol ('RDKitMol' or 'Mol') – An RDKit Mol object for product.

      • -
    -
    -
    Returns:
    -

    RDKitMol – The new product mol with changed coordinates.

    -
    -
    -
    - +
    +

    rdmc.conformer_generation.align#

    @@ -733,31 +505,6 @@
    -
    -
    - On this page -
    -
    -
    diff --git a/reference/conformer_generation/embedding_geometries/embedders.html b/reference/conformer_generation/embedding_geometries/embedders.html index d25a63b1..a172482a 100644 --- a/reference/conformer_generation/embedding_geometries/embedders.html +++ b/reference/conformer_generation/embedding_geometries/embedders.html @@ -464,142 +464,8 @@
    -
    -

    rdmc.conformer_generation.embedders#

    -

    Modules for providing initial guess geometries

    -
    -
    -class rdmc.conformer_generation.embedders.ConfGenEmbedder(track_stats=False)#
    -

    Bases: object

    -

    Base class for conformer generation embedders.

    -
    -
    -embed_conformers(n_conformers: int)#
    -

    Embed conformers according to the molecule graph.

    -
    -
    Parameters:
    -

    n_conformers (int) – Number of conformers to generate.

    -
    -
    Raises:
    -

    NotImplementedError – This method needs to be implemented in the subclass.

    -
    -
    -
    - -
    -
    -update_mol(smiles: str)#
    -

    Update the molecule graph based on the SMILES string.

    -
    -
    Parameters:
    -

    smiles (str) – SMILES string of the molecule

    -
    -
    -
    - -
    -
    -update_stats(n_trials: int, time: float = 0.0) → dict#
    -

    Update the statistics of the conformer generation.

    -
    -
    Parameters:
    -
      -

    • n_trials (int) – Number of trials

      • -

    • time (float, optional) – Time spent on conformer generation. Defaults to 0..

      • -
    -
    -
    Returns:
    -

    dict – Statistics of the conformer generation

    -
    -
    -
    - -
    -
    -write_mol_data()#
    -

    Write the molecule data.

    -
    -
    Returns:
    -

    dict – Molecule data.

    -
    -
    -
    - -
    - -
    -
    -class rdmc.conformer_generation.embedders.ETKDGEmbedder(track_stats=False)#
    -

    Bases: ConfGenEmbedder

    -

    Embed conformers using ETKDG.

    -
    -
    -embed_conformers(n_conformers: int)#
    -

    Embed conformers according to the molecule graph.

    -
    -
    Parameters:
    -

    n_conformers (int) – Number of conformers to generate.

    -
    -
    Returns:
    -

    mol – Molecule with conformers.

    -
    -
    -
    - -
    - -
    -
    -class rdmc.conformer_generation.embedders.GeoMolEmbedder(trained_model_dir: str, dataset: str = 'drugs', temp_schedule: str = 'linear', track_stats: bool = False)#
    -

    Bases: ConfGenEmbedder

    -

    Embed conformers using GeoMol.

    -
    -
    Parameters:
    -
      -

    • trained_model_dir (str) – Directory of the trained model.

      • -

    • dataset (str, optional) – Dataset used for training. Defaults to "drugs".

      • -

    • temp_schedule (str, optional) – Temperature schedule. Defaults to "linear".

      • -

    • track_stats (bool, optional) – Whether to track the statistics of the conformer generation. Defaults to False.

      • -
    -
    -
    -
    -
    -embed_conformers(n_conformers: int)#
    -

    Embed conformers according to the molecule graph.

    -
    -
    Parameters:
    -

    n_conformers (int) – Number of conformers to generate.

    -
    -
    Returns:
    -

    mol – Molecule with conformers.

    -
    -
    -
    - -
    - -
    -
    -class rdmc.conformer_generation.embedders.RandomEmbedder(track_stats=False)#
    -

    Bases: ConfGenEmbedder

    -

    Embed conformers with coordinates of random numbers.

    -
    -
    -embed_conformers(n_conformers: int)#
    -

    Embed conformers according to the molecule graph.

    -
    -
    Parameters:
    -

    n_conformers (int) – Number of conformers to generate.

    -
    -
    Returns:
    -

    mol – Molecule with conformers.

    -
    -
    -
    - -
    - +
    +

    rdmc.conformer_generation.embedders#

    @@ -639,34 +505,6 @@
    -
    -
    - On this page -
    -
    -
    diff --git a/reference/conformer_generation/embedding_geometries/index.html b/reference/conformer_generation/embedding_geometries/index.html index 6c56e176..daf00aa3 100644 --- a/reference/conformer_generation/embedding_geometries/index.html +++ b/reference/conformer_generation/embedding_geometries/index.html @@ -463,29 +463,9 @@

    Embedding Geometries#

    diff --git a/reference/conformer_generation/embedding_geometries/ts_guessers.html b/reference/conformer_generation/embedding_geometries/ts_guessers.html index f656b523..e2e331bf 100644 --- a/reference/conformer_generation/embedding_geometries/ts_guessers.html +++ b/reference/conformer_generation/embedding_geometries/ts_guessers.html @@ -464,229 +464,8 @@
    -
    -

    rdmc.conformer_generation.ts_guessers#

    -

    Modules for providing transition state initial guess geometries.

    -
    -
    -class rdmc.conformer_generation.ts_guessers.AutoNEBGuesser(optimizer: Calculator = 'xtb-python not installed', track_stats: bool | None = False)#
    -

    Bases: TSInitialGuesser

    -

    The class for generating TS guesses using the AutoNEB method.

    -
    -
    Parameters:
    -
      -

    • optimizer (ase.calculator.calculator.Calculator) – ASE calculator. Defaults to the XTB implementation xtb.ase.calculator.XTB.

      • -

    • track_stats (bool, optional) – Whether to track the status. Defaults to False.

      • -
    -
    -
    -
    -
    -property attach_calculators#
    -

    Set the calculator for each image.

    -
    - -
    -
    -generate_ts_guesses(mols, multiplicity: int | None = None, save_dir: str | None = None)#
    -

    Generate TS guesser.

    -
    -
    Parameters:
    -
      -

    • mols (list) – A list of reactant and product pairs.

      • -

    • multiplicity (int, optional) – The spin multiplicity of the reaction. Defaults to None.

      • -

    • save_dir (Optional[str], optional) – The path to save the results. Defaults to None.

      • -
    -
    -
    Returns:
    -

    RDKitMol – The TS molecule in RDKitMol with 3D conformer saved with the molecule.

    -
    -
    -
    - -
    -
    -property optimizer#
    -

    Optimizer used by the AutoNEB method.

    -
    - -
    - -
    -
    -class rdmc.conformer_generation.ts_guessers.DEGSMGuesser(method: str = 'GFN2-xTB', nprocs: int = 1, memory: int = 1, gsm_args: str | None = '', track_stats: bool | None = False)#
    -

    Bases: TSInitialGuesser

    -

    The class for generating TS guesses using the DE-GSM method.

    -
    -
    Parameters:
    -

    track_stats (bool, optional) – Whether to track the status. Defaults to False.

    -
    -
    -
    -
    -generate_ts_guesses(mols: list, multiplicity: int | None = None, save_dir: str | None = None)#
    -

    Generate TS guesser.

    -
    -
    Parameters:
    -
      -

    • mols (list) – A list of reactant and product pairs.

      • -

    • multiplicity (int, optional) – The spin multiplicity of the reaction. Defaults to None.

      • -

    • save_dir (Optional[str], optional) – The path to save the results. Defaults to None.

      • -
    -
    -
    Returns:
    -

    RDKitMol – The TS molecule in RDKitMol with 3D conformer saved with the molecule.

    -
    -
    -
    - -
    - -
    -
    -class rdmc.conformer_generation.ts_guessers.RMSDPPGuesser(track_stats: bool | None = False)#
    -

    Bases: TSInitialGuesser

    -

    The class for generating TS guesses using the RMSD-PP method.

    -
    -
    Parameters:
    -

    track_stats (bool, optional) – Whether to track the status. Defaults to False.

    -
    -
    -
    -
    -generate_ts_guesses(mols, multiplicity: int | None = None, save_dir: str | None = None)#
    -

    Generate TS guesser.

    -
    -
    Parameters:
    -
      -

    • mols (list) – A list of reactant and product pairs.

      • -

    • multiplicity (int, optional) – The spin multiplicity of the reaction. Defaults to None.

      • -

    • save_dir (Optional[str], optional) – The path to save the results. Defaults to None.

      • -
    -
    -
    Returns:
    -

    RDKitMol – The TS molecule in RDKitMol with 3D conformer saved with the molecule.

    -
    -
    -
    - -
    - -
    -
    -class rdmc.conformer_generation.ts_guessers.TSEGNNGuesser(trained_model_dir: str, track_stats: bool | None = False)#
    -

    Bases: TSInitialGuesser

    -

    The class for generating TS guesses using the TS-EGNN model.

    -
    -
    Parameters:
    -
      -

    • trained_model_dir (str) – The path to the directory storing the trained TS-EGNN model.

      • -

    • track_stats (bool, optional) – Whether to track the status. Defaults to False.

      • -
    -
    -
    -
    -
    -generate_ts_guesses(mols: list, multiplicity: int | None = None, save_dir: str | None = None)#
    -

    Generate TS guesser.

    -
    -
    Parameters:
    -
      -

    • mols (list) – A list of reactant and product pairs.

      • -

    • multiplicity (int, optional) – The spin multiplicity of the reaction. Defaults to None.

      • -

    • save_dir (Optional[str], optional) – The path to save the results. Defaults to None.

      • -
    -
    -
    Returns:
    -

    RDKitMol – The TS molecule in RDKitMol with 3D conformer saved with the molecule.

    -
    -
    -
    - -
    - -
    -
    -class rdmc.conformer_generation.ts_guessers.TSGCNGuesser(trained_model_dir: str, track_stats: bool | None = False)#
    -

    Bases: TSInitialGuesser

    -

    The class for generating TS guesses using the TS-GCN model.

    -
    -
    Parameters:
    -
      -

    • trained_model_dir (str) – The path to the directory storing the trained TS-GCN model.

      • -

    • track_stats (bool, optional) – Whether to track the status. Defaults to False.

      • -
    -
    -
    -
    -
    -generate_ts_guesses(mols: list, multiplicity: int | None = None, save_dir: str | None = None)#
    -

    Generate TS guesser.

    -
    -
    Parameters:
    -
      -

    • mols (list) – A list of reactant and product pairs.

      • -

    • multiplicity (int, optional) – The spin multiplicity of the reaction. Defaults to None.

      • -

    • save_dir (Optional[str], optional) – The path to save the results. Defaults to None.

      • -
    -
    -
    Returns:
    -

    RDKitMol – The TS molecule in RDKitMol with 3D conformer saved with the molecule.

    -
    -
    -
    - -
    - -
    -
    -class rdmc.conformer_generation.ts_guessers.TSInitialGuesser(track_stats: bool | None = False)#
    -

    Bases: object

    -

    The abstract class for TS initial Guesser.

    -
    -
    Parameters:
    -

    track_stats (bool, optional) – Whether to track the status. Defaults to False.

    -
    -
    -
    -
    -generate_ts_guesses(mols: list, save_dir: str | None = None) → RDKitMol#
    -

    The key function used to generate TS guesses. It varies by the actual classes and need to implemented inside each class. -The function should at least take mols and save_dir as input arguments. The returned value should be a RDKitMol with TS -geometries.

    -
    -
    Parameters:
    -
      -

    • mols (list) – A list of reactant and product pairs.

      • -

    • save_dir (Optional[str], optional) – The path to save the results. Defaults to None for not saving.

      • -
    -
    -
    Returns:
    -

    RDKitMol – The TS molecule in RDKitMol with 3D conformer saved with the molecule.

    -
    -
    Raises:
    -

    NotImplementedError – This method needs to be implemented in the subclass.

    -
    -
    -
    - -
    -
    -save_guesses(save_dir: str, rp_combos: list, ts_mol: RDKitMol)#
    -

    Save the generated guesses into the given save_dir.

    -
    -
    Parameters:
    -
      -

    • save_dir (str) – The path to the directory to save the results.

      • -

    • rp_combos (list) – A list of reactant and product complex pairs used to generate transition states.

      • -

    • ts_mol (RDKitMol) – The TS molecule in RDKitMol with 3D conformer saved with the molecule.

      • -
    -
    -
    -
    - -
    - +
    +

    rdmc.conformer_generation.ts_guessers#

    @@ -726,42 +505,6 @@
    -
    -
    - On this page -
    -
    -
    diff --git a/reference/conformer_generation/geometry_optimization/index.html b/reference/conformer_generation/geometry_optimization/index.html index 1b86a940..f123be08 100644 --- a/reference/conformer_generation/geometry_optimization/index.html +++ b/reference/conformer_generation/geometry_optimization/index.html @@ -463,21 +463,8 @@

    Geometry Optimization#

    diff --git a/reference/conformer_generation/geometry_optimization/optimizers.html b/reference/conformer_generation/geometry_optimization/optimizers.html index 78775989..f5d54ae8 100644 --- a/reference/conformer_generation/geometry_optimization/optimizers.html +++ b/reference/conformer_generation/geometry_optimization/optimizers.html @@ -464,146 +464,8 @@
    -
    -

    rdmc.conformer_generation.optimizers#

    -

    Modules for optimizing initial guess geometries.

    -
    -
    -class rdmc.conformer_generation.optimizers.ConfGenOptimizer(track_stats=False)#
    -

    Bases: object

    -

    Base class for the geometry optimizers used in conformer generation.

    -
    -
    Parameters:
    -

    track_stats (bool, optional) – Whether to track the status. Defaults to False.

    -
    -
    -
    -
    -optimize_conformers(mol_data: List[dict])#
    -

    Optimize the conformers.

    -
    -
    Parameters:
    -

    mol_data (List[dict]) – The list of conformers to be optimized.

    -
    -
    Raises:
    -

    NotImplementedError – This function should be implemented in the child class.

    -
    -
    -
    - -
    - -
    -
    -class rdmc.conformer_generation.optimizers.GaussianOptimizer(method: str = 'GFN2-xTB', nprocs: int = 1, memory: int = 1, track_stats: bool = False)#
    -

    Bases: ConfGenOptimizer

    -

    Optimizer using the Gaussian.

    -
    -
    Parameters:
    -
      -

    • method (str, optional) – The method to be used for species optimization. You can use the level of theory available in Gaussian. -Defaults to "GFN2-xTB", which is realized by additional scripts provided in the rdmc package.

      • -

    • nprocs (int, optional) – The number of processors to use. Defaults to 1.

      • -

    • memory (int, optional) – Memory in GB used by Gaussian. Defaults to 1.

      • -

    • track_stats (bool, optional) – Whether to track the status. Defaults to False.

      • -
    -
    -
    -
    -
    -optimize_conformers(mol: RDKitMol, multiplicity: int = 1, save_dir: str | None = None, **kwargs) → RDKitMol#
    -

    Optimize the conformers.

    -
    -
    Parameters:
    -
      -

    • mol (RDKitMol) – An RDKitMol object with all guess geometries embedded as conformers.

      • -

    • multiplicity (int) – The multiplicity of the molecule. Defaults to 1.

      • -

    • save_dir (Optional[str], optional) – The path to save the results. Defaults to None.

      • -
    -
    -
    Returns:
    -

    RDKitMol – The optimized molecule as RDKitMol with 3D geometries embedded.

    -
    -
    -
    - -
    -
    -save_opt_mols(save_dir: str, opt_mol: RDKitMol, keep_ids: dict, energies: dict)#
    -

    Save the information of the optimized stable species into the directory.

    -
    -
    Parameters:
    -
      -

    • save_dir (str) – The path to the directory to save the results.

      • -

    • opt_mol (RDKitMol) – The optimized stable species in RDKitMol with 3D conformer saved with the molecule.

      • -

    • keep_ids (dict) – Dictionary of which opts succeeded and which failed.

      • -

    • energies (dict) – Dictionary of energies for each conformer.

      • -
    -
    -
    -
    - -
    - -
    -
    -class rdmc.conformer_generation.optimizers.MMFFOptimizer(method: str = 'rdkit', track_stats: bool = False)#
    -

    Bases: ConfGenOptimizer

    -

    Optimizer using the MMFF force field.

    -
    -
    Parameters:
    -
      -

    • method (str, optional) – The method to be used for stable species optimization. Defaults to "rdkit".

      • -

    • track_stats (bool, optional) – Whether to track the status. Defaults to False.

      • -
    -
    -
    -
    -
    -optimize_conformers(mol_data: List[dict]) → List[dict]#
    -

    Optimize the conformers.

    -
    -
    Parameters:
    -

    mol_data (List[dict]) – The list of conformers to be optimized.

    -
    -
    Returns:
    -

    List[dict] – The list of optimized conformers sorted by energy.

    -
    -
    -
    - -
    - -
    -
    -class rdmc.conformer_generation.optimizers.XTBOptimizer(method: str = 'gff', level: str = 'normal', track_stats: bool = False)#
    -

    Bases: ConfGenOptimizer

    -

    Optimizer using the xTB.

    -
    -
    Parameters:
    -
      -

    • method (str, optional) – The method to be used for species optimization. Defaults to "gff".

      • -

    • level (str, optional) – The level of theory. Defaults to "normal".

      • -

    • track_stats (bool, optional) – Whether to track the status. Defaults to False.

      • -
    -
    -
    -
    -
    -optimize_conformers(mol_data: List[dict]) → List[dict]#
    -

    Optimize the conformers.

    -
    -
    Parameters:
    -

    mol_data (List[dict]) – The list of conformers to be optimized.

    -
    -
    Returns:
    -

    List[dict] – The list of optimized conformers sorted by energy.

    -
    -
    -
    - -
    - +
    +

    rdmc.conformer_generation.optimizers#

    @@ -643,32 +505,6 @@
    -
    -
    - On this page -
    -
    -
    diff --git a/reference/conformer_generation/geometry_optimization/ts_optimizers.html b/reference/conformer_generation/geometry_optimization/ts_optimizers.html index ef7e259d..ae9948eb 100644 --- a/reference/conformer_generation/geometry_optimization/ts_optimizers.html +++ b/reference/conformer_generation/geometry_optimization/ts_optimizers.html @@ -464,222 +464,8 @@
    -
    -

    rdmc.conformer_generation.ts_optimizers#

    -

    Modules for optimizing transition state geometries.

    -
    -
    -class rdmc.conformer_generation.ts_optimizers.GaussianOptimizer(method: str = 'GFN2-xTB', nprocs: int = 1, memory: int = 1, track_stats: bool = False)#
    -

    Bases: TSOptimizer

    -

    The class to optimize TS geometries using the Berny algorithm built in Gaussian. -You have to have the Gaussian package installed to run this optimizer

    -
    -
    Parameters:
    -
      -

    • method (str, optional) – The method to be used for TS optimization. you can use the level of theory available in Gaussian. -We provided a script to run XTB using Gaussian, but there are some extra steps to do. -Defaults to "GFN2-xTB".

      • -

    • nprocs (int, optional) – The number of processors to use. Defaults to 1.

      • -

    • memory (int, optional) – Memory in GB used by Gaussian. Defaults to 1.

      • -

    • track_stats (bool, optional) – Whether to track the status. Defaults to False.

      • -
    -
    -
    -
    -
    -optimize_ts_guesses(mol: RDKitMol, multiplicity: int = 1, save_dir: str | None = None, **kwargs)#
    -

    Optimize the TS guesses.

    -
    -
    Parameters:
    -
      -

    • mol (RDKitMol) – An RDKitMol object with all guess geometries embedded as conformers.

      • -

    • multiplicity (int) – The multiplicity of the molecule. Defaults to 1.

      • -

    • save_dir (Optional[str], optional) – The path to save the results. Defaults to None.

      • -
    -
    -
    Returns:
    -

    RDKitMol – The optimized TS molecule in RDKitMol with 3D conformer saved with the molecule.

    -
    -
    -
    - -
    - -
    -
    -class rdmc.conformer_generation.ts_optimizers.OrcaOptimizer(method: str = 'XTB2', nprocs: int = 1, track_stats: bool = False)#
    -

    Bases: TSOptimizer

    -

    The class to optimize TS geometries using the Berny algorithm built in Orca. -You have to have the Orca package installed to run this optimizer.

    -
    -
    Parameters:
    -
      -

    • method (str, optional) – The method to be used for TS optimization. you can use the level of theory available in Orca. -If you want to use XTB methods, you need to put the xtb binary into the Orca directory. -Defaults to "XTB2".

      • -

    • nprocs (int, optional) – The number of processors to use. Defaults to 1.

      • -

    • track_stats (bool, optional) – Whether to track the status. Defaults to False.

      • -
    -
    -
    -
    -
    -extract_frequencies(save_dir: str, n_atoms: int)#
    -

    Extract frequencies from the Orca opt job.

    -
    -
    Parameters:
    -
      -

    • save_dir (str) – Path where Orca logs are saved.

      • -

    • n_atoms (int) – The number of atoms in the molecule.

      • -
    -
    -
    Returns:
    -

    np.ndarray – The frequencies in cm-1.

    -
    -
    -
    - -
    -
    -optimize_ts_guesses(mol: RDKitMol, multiplicity: int = 1, save_dir: str | None = None, **kwargs)#
    -

    Optimize the TS guesses.

    -
    -
    Parameters:
    -
      -

    • mol (RDKitMol) – An RDKitMol object with all guess geometries embedded as conformers.

      • -

    • multiplicity (int) – The multiplicity of the molecule. Defaults to 1.

      • -

    • save_dir (Optional[str], optional) – The path to save the results. Defaults to None.

      • -
    -
    -
    Returns:
    -

    RDKitMol – The optimized TS molecule in RDKitMol with 3D conformer saved with the molecule.

    -
    -
    -
    - -
    - -
    -
    -class rdmc.conformer_generation.ts_optimizers.QChemOptimizer(method: str = 'wB97x-d3', basis: str = 'def2-tzvp', nprocs: int = 1, track_stats: bool = False)#
    -

    Bases: TSOptimizer

    -

    The class to optimize TS geometries using the Baker’s eigenvector-following (EF) algorithm built in QChem. -You have to have the QChem package installed to run this optimizer.

    -
    -
    Parameters:
    -
      -

    • method (str, optional) – The method to be used for TS optimization. you can use the method available in QChem. -Defaults to "wB97x-d3".

      • -

    • basis (str, optional) – The method to be used for TS optimization. you can use the basis available in QChem. -Defaults to "def2-tzvp".

      • -

    • nprocs (int, optional) – The number of processors to use. Defaults to 1.

      • -

    • track_stats (bool, optional) – Whether to track the status. Defaults to False.

      • -
    -
    -
    -
    -
    -optimize_ts_guesses(mol: RDKitMol, multiplicity: int = 1, save_dir: str | None = None, **kwargs)#
    -

    Optimize the TS guesses.

    -
    -
    Parameters:
    -
      -

    • mol (RDKitMol) – An RDKitMol object with all guess geometries embedded as conformers.

      • -

    • multiplicity (int) – The multiplicity of the molecule. Defaults to 1.

      • -

    • save_dir (Optional[str], optional) – The path to save the results. Defaults to None.

      • -
    -
    -
    Returns:
    -

    RDKitMol – The optimized TS molecule in RDKitMol with 3D conformer saved with the molecule.

    -
    -
    -
    - -
    - -
    -
    -class rdmc.conformer_generation.ts_optimizers.SellaOptimizer(method: str = 'GFN2-xTB', fmax: float = 0.001, steps: int = 1000, track_stats: bool = False)#
    -

    Bases: TSOptimizer

    -

    The class to optimize TS geometries using the Sella algorithm. -It uses XTB as the backend calculator, ASE as the interface, and Sella module from the Sella repo.

    -
    -
    Parameters:
    -
      -

    • method (str, optional) – The method in XTB used to optimize the geometry. Options are -'GFN1-xTB' and 'GFN2-xTB'. Defaults to "GFN2-xTB".

      • -

    • fmax (float, optional) – The force threshold used in the optimization. Defaults to 1e-3.

      • -

    • steps (int, optional) – Max number of steps allowed in the optimization. Defaults to 1000.

      • -

    • track_stats (bool, optional) – Whether to track the status. Defaults to False.

      • -
    -
    -
    -
    -
    -optimize_ts_guesses(mol: RDKitMol, save_dir: str | None = None, **kwargs)#
    -

    Optimize the TS guesses.

    -
    -
    Parameters:
    -
      -

    • mol (RDKitMol) – An RDKitMol object with all guess geometries embedded as conformers.

      • -

    • save_dir (str, optional) – The path to save results. Defaults to None.

      • -
    -
    -
    Returns:
    -

    RDKitMol – The optimized TS molecule in RDKitMol with 3D conformer saved with the molecule.

    -
    -
    -
    - -
    - -
    -
    -class rdmc.conformer_generation.ts_optimizers.TSOptimizer(track_stats: bool | None = False)#
    -

    Bases: object

    -

    The abstract class for TS optimizer.

    -
    -
    Parameters:
    -

    track_stats (bool, optional) – Whether to track the status. Defaults to False.

    -
    -
    -
    -
    -optimize_ts_guesses(mol: RDKitMol, save_dir: str, **kwargs)#
    -

    The abstract method for optimizing TS guesses. It will be implemented in actual classes. -The method needs to take mol in RDKitMol and save_dir as str as input arguments, and -return the optimized molecule as RDKitMol.

    -
    -
    Parameters:
    -
      -

    • mol (RDKitMol) – The TS in RDKitMol object with geometries embedded as conformers.

      • -

    • save_dir (Optional[str], optional) – The path to save the results. Defaults to None.

      • -
    -
    -
    Returns:
    -

    RDKitMol – The optimized TS molecule in RDKitMol with 3D conformer saved with the molecule.

    -
    -
    -
    - -
    -
    -save_opt_mols(save_dir: str, opt_mol: RDKitMol, keep_ids: dict, energies: dict)#
    -

    Save the information of the optimized TS geometries into the directory.

    -
    -
    Parameters:
    -
      -

    • save_dir (str) – The path to the directory to save the results.

      • -

    • opt_mol (RDKitMol) – The optimized TS molecule in RDKitMol with 3D conformer saved with the molecule.

      • -

    • keep_ids (dict) – Dictionary of which opts succeeded and which failed.

      • -

    • energies (dict) – Dictionary of energies for each conformer.

      • -
    -
    -
    -
    - -
    - +
    +

    rdmc.conformer_generation.ts_optimizers#

    @@ -719,37 +505,6 @@
    -
    -
    - On this page -
    -
    -
    diff --git a/reference/conformer_generation/index.html b/reference/conformer_generation/index.html index fb8f026f..6eaca92a 100644 --- a/reference/conformer_generation/index.html +++ b/reference/conformer_generation/index.html @@ -456,8 +456,8 @@
    -
    -

    rdmc.conformer_generation#

    +
    +

    rdmc.conformer_generation#

    diff --git a/reference/conformer_generation/postprocessing/index.html b/reference/conformer_generation/postprocessing/index.html index 079d9935..97b75bf9 100644 --- a/reference/conformer_generation/postprocessing/index.html +++ b/reference/conformer_generation/postprocessing/index.html @@ -463,31 +463,10 @@

    Postprocessing#

    diff --git a/reference/conformer_generation/postprocessing/pruners.html b/reference/conformer_generation/postprocessing/pruners.html index 6062cc90..be562a13 100644 --- a/reference/conformer_generation/postprocessing/pruners.html +++ b/reference/conformer_generation/postprocessing/pruners.html @@ -464,201 +464,8 @@
    -
    -

    rdmc.conformer_generation.pruners#

    -

    Modules for pruning a group of conformers

    -
    -
    -class rdmc.conformer_generation.pruners.CRESTPruner(ethr: float = 0.15, rthr: float = 0.125, bthr: float = 0.01, ewin: float = 10000, track_stats: bool = False)#
    -

    Bases: ConfGenPruner

    -

    Prune conformers using CREST.

    -
    -
    Parameters:
    -
      -

    • ethr (float, optional) – Energy threshold. Defaults to 0.15.

      • -

    • rthr (float, optional) – RMSD threshold. Defaults to 0.125.

      • -

    • bthr (float, optional) – Bond threshold. Defaults to 0.01.

      • -

    • ewin (int, optional) – Energy window. Defaults to 10000.

      • -

    • track_stats (bool, optional) – Whether to track statistics. Defaults to False.

      • -
    -
    -
    -
    -
    -prune_conformers(current_mol_data: List[dict], unique_mol_data: List[dict] | None = None, sort_by_energy: bool = True, return_ids: bool = False)#
    -

    Prune conformers.

    -
    -
    Parameters:
    -
      -

    • current_mol_data (List[dict]) – conformer data of the current iteration.

      • -

    • unique_mol_data (List[dict], optional) – Unique conformer data of previous iterations. Defaults to None.

      • -

    • sort_by_energy (bool, optional) – Whether to sort conformers by energy. Defaults to True.

      • -

    • return_ids (bool, optional) – Whether to return conformer IDs. Defaults to False.

      • -
    -
    -
    Returns:
    -

    List[dict] – Updated conformer data.

    -
    -
    -
    - -
    - -
    -
    -class rdmc.conformer_generation.pruners.ConfGenPruner(track_stats: bool = False)#
    -

    Bases: object

    -

    Base class for conformer pruning.

    -
    -
    Parameters:
    -

    track_stats (bool, optional) – Whether to track statistics. Defaults to False.

    -
    -
    -
    -
    -prune_conformers(current_mol_data: List[dict], unique_mol_data: List[dict] | None = None, sort_by_energy: bool = True, return_ids: bool = False)#
    -

    Prune conformers.

    -
    -
    Parameters:
    -
      -

    • current_mol_data (List[dict]) – conformer data of the current iteration.

      • -

    • unique_mol_data (List[dict], optional) – Unique conformer data of previous iterations. Defaults to None.

      • -

    • sort_by_energy (bool, optional) – Whether to sort conformers by energy. Defaults to True.

      • -

    • return_ids (bool, optional) – Whether to return conformer IDs. Defaults to False.

      • -
    -
    -
    Raises:
    -

    NotImplementedError – This method should be implemented in the subclass.

    -
    -
    -
    - -
    - -
    -
    -class rdmc.conformer_generation.pruners.TorsionPruner(mean_chk_threshold: float = 10.0, max_chk_threshold: float = 20.0, track_stats: bool = False)#
    -

    Bases: ConfGenPruner

    -

    Prune conformers based on torsion angle criteria. -This method uses a mean and max criteria to prune conformers: -A conformer is considered unique if it satisfies either of the following criteria:

    -
      -

    • mean difference of all torsion angles > mean_chk_threshold

      • -

    • max difference of all torsion angles > max_chk_threshold

      • -
    -

    New conformers are compared to all conformers that have already been deemed unique.

    -
    -
    Parameters:
    -
      -

    • mean_chk_threshold (float, optional) – Mean difference threshold. Defaults to 10..

      • -

    • max_chk_threshold (float, optional) – Max difference threshold. Defaults to 20..

      • -

    • track_stats (bool, optional) – Whether to track statistics. Defaults to False.

      • -
    -
    -
    -
    -
    -calculate_torsions(mol_data: List[dict]) → List[dict]#
    -

    Calculate torsions for a list of conformers.

    -
    -
    Parameters:
    -

    mol_data (List[dict]) – conformer data.

    -
    -
    Returns:
    -

    List[dict] – Conformer data with values of torsions added.

    -
    -
    -
    - -
    -
    -initialize_torsions_list(smiles: str | None = None, torsions: list | None = None, excludeMethyl: bool = False)#
    -

    Initialize the list of torsions to be used for comparison and pruning.

    -
    -
    Parameters:
    -
      -

    • smiles (str, optional) – SMILES of the molecule. Defaults to None. This should be provided if -torsions is not provided.

      • -

    • torsions (list, optional) – List of torsions. Defaults to None, -in which case the torsions will be extracted from the molecule.

      • -

    • excludeMethyl (bool, optional) – Whether to exclude methyl groups. Defaults to False.

      • -
    -
    -
    -
    - -
    -
    -initialize_ts_torsions_list(rxn_smiles: str | None = None, torsions: list | None = None, excludeMethyl: bool = False)#
    -

    Initialize the list of torsions to be used for comparison and pruning for TS molecules.

    -
    -
    Parameters:
    -
      -

    • rxn_smiles (str, optional) – SMILES of the reaction. Defaults to None. This should be provided if -torsions is not provided.

      • -

    • torsions (list, optional) – List of torsions. Defaults to None, in which case the torsions will be -extracted according to the reactants and the products.

      • -

    • excludeMethyl (bool, optional) – Whether to exclude methyl groups. Defaults to False.

      • -
    -
    -
    -
    - -
    -
    -prune_conformers(current_mol_data: List[dict], unique_mol_data: List[dict] | None = None, sort_by_energy: bool = True, return_ids: bool = False)#
    -

    Prune conformers.

    -
    -
    Parameters:
    -
      -

    • current_mol_data (List[dict]) – conformer data of the current iteration.

      • -

    • unique_mol_data (List[dict], optional) – Unique conformer data of previous iterations. Defaults to None.

      • -

    • sort_by_energy (bool, optional) – Whether to sort conformers by energy. Defaults to True.

      • -

    • return_ids (bool, optional) – Whether to return conformer IDs. Defaults to False.

      • -
    -
    -
    Returns:
    -

    List[dict] – Updated conformer data.

    -
    -
    -
    - -
    -
    -static rad_angle_compare(x: float, y: float) → float#
    -

    Compare two angles in radians.

    -
    -
    Parameters:
    -
      -

    • x (float) – angle in degrees.

      • -

    • y (float) – angle in degrees.

      • -
    -
    -
    Returns:
    -

    float – Absolute difference between the two angles in radians.

    -
    -
    -
    - -
    -
    -static torsion_list_compare(c1_ts: List[float], c2_ts: List[float]) → List[float]#
    -

    Compare two lists of torsions in radians.

    -
    -
    Parameters:
    -
      -

    • c1_ts (list) – list of torsions in degrees.

      • -

    • c2_ts (list) – list of torsions in degress.

      • -
    -
    -
    Returns:
    -

    list – Absolute difference between the two lists of torsions in radians.

    -
    -
    -
    - -
    - +
    +

    rdmc.conformer_generation.pruners#

    @@ -698,32 +505,6 @@
    -
    -
    - On this page -
    -
    -
    diff --git a/reference/conformer_generation/postprocessing/solvation.html b/reference/conformer_generation/postprocessing/solvation.html index 860f90b2..6288786d 100644 --- a/reference/conformer_generation/postprocessing/solvation.html +++ b/reference/conformer_generation/postprocessing/solvation.html @@ -464,67 +464,8 @@
    -
    -

    rdmc.conformer_generation.solvation#

    -

    Modules for including computing solvation corrections.

    -
    -
    -class rdmc.conformer_generation.solvation.ConfSolv(trained_model_dir: str, track_stats: bool | None = False)#
    -

    Bases: Estimator

    -

    Class for estimating conformer energies in solution with neural networks.

    -
    -
    Parameters:
    -
      -

    • trained_model_dir (str) – The path to the directory storing the trained ConfSolv model.

      • -

    • track_stats (bool, optional) – Whether to track timing stats. Defaults to False.

      • -
    -
    -
    -
    -
    -predict_energies(mol_data: List[dict], **kwargs) → List[dict]#
    -

    Predict conformer free energies in a given solvent.

    -
    -
    Parameters:
    -

    mol_data (List[dict]) – A list of molecule dictionaries.

    -
    -
    Returns:
    -

    mol_data (List[dict]) – A list of molecule dictionaries with energy values updated.

    -
    -
    -
    - -
    - -
    -
    -class rdmc.conformer_generation.solvation.Estimator(track_stats: bool | None = False)#
    -

    Bases: object

    -

    The abstract class for energy estimator.

    -
    -
    Parameters:
    -

    track_stats (bool, optional) – Whether to track timing stats. Defaults to False.

    -
    -
    -
    -
    -predict_energies(mol_data: List[dict], **kwargs)#
    -

    The abstract method for predicting energies. It will be implemented in actual classes. -The method needs to take mol_data which is a dictionary containing info about the -conformers of the molecules. It will return the molecule as the same mol_data object -with the energy values altered.

    -
    -
    Parameters:
    -

    mol_data (List[dict]) – A list of molecule dictionaries.

    -
    -
    Returns:
    -

    mol_data (List[dict]) – A list of molecule dictionaries with energy values updated.

    -
    -
    -
    - -
    - +
    +

    rdmc.conformer_generation.solvation#

    @@ -564,23 +505,6 @@
    -
    -
    - On this page -
    -
    -
    diff --git a/reference/conformer_generation/postprocessing/ts_verifiers.html b/reference/conformer_generation/postprocessing/ts_verifiers.html index e0d6f03e..37794a67 100644 --- a/reference/conformer_generation/postprocessing/ts_verifiers.html +++ b/reference/conformer_generation/postprocessing/ts_verifiers.html @@ -464,220 +464,8 @@
    -
    -

    rdmc.conformer_generation.ts_verifiers#

    -

    Modules for verifying optimized ts

    -
    -
    -class rdmc.conformer_generation.ts_verifiers.GaussianIRCVerifier(method: str = 'GFN2-xTB', nprocs: int = 1, memory: int = 1, fc_kw: str = 'calcall', track_stats: bool = False)#
    -

    Bases: TSVerifier

    -

    The class for verifying the TS by calculating and checking its IRC analysis using Gaussian.

    -
    -
    Parameters:
    -
      -

    • method (str, optional) – The method to be used for TS optimization. you can use the level of theory available in Gaussian. -We provided a script to run XTB using Gaussian, but there are some extra steps to do. -Defaults to "GFN2-xTB".

      • -

    • nprocs (int, optional) – The number of processors to use. Defaults to 1.

      • -

    • memory (int, optional) – Memory in GB used by Gaussian. Defaults to 1.

      • -

    • fc_kw (str, optional) – Keyword specifying how often to compute force constants Defaults to "calcall".

      • -

    • track_stats (bool, optional) – Whether to track the status. Defaults to False.

      • -
    -
    -
    -
    -
    -verify_ts_guesses(ts_mol: RDKitMol, multiplicity: int = 1, save_dir: str | None = None, **kwargs) → RDKitMol#
    -

    Verifying TS guesses (or optimized TS geometries).

    -
    -
    Parameters:
    -
      -

    • ts_mol ('RDKitMol') – The TS in RDKitMol object with 3D geometries embedded.

      • -

    • multiplicity (int, optional) – The spin multiplicity of the TS. Defaults to 1.

      • -

    • save_dir (str, optional) – The directory path to save the results. Defaults to None.

      • -
    -
    -
    Returns:
    -

    RDKitMol – The molecule in RDKitMol object with verification results stored in KeepIDs.

    -
    -
    -
    - -
    - -
    -
    -class rdmc.conformer_generation.ts_verifiers.OrcaIRCVerifier(method: str = 'XTB2', nprocs: int = 1, track_stats: bool = False)#
    -

    Bases: TSVerifier

    -

    The class for verifying the TS by calculating and checking its IRC analysis using Orca.

    -
    -
    Parameters:
    -
      -

    • method (str, optional) – The method to be used for TS optimization. you can use the level of theory available in Orca. -If you want to use XTB methods, you need to put the xtb binary into the Orca directory. -Defaults to "XTB2".

      • -

    • nprocs (int, optional) – The number of processors to use. Defaults to 1.

      • -

    • track_stats (bool, optional) – Whether to track the status. Defaults to False.

      • -
    -
    -
    -
    -
    -verify_ts_guesses(ts_mol: RDKitMol, multiplicity: int = 1, save_dir: str | None = None, **kwargs) → RDKitMol#
    -

    Verifying TS guesses (or optimized TS geometries).

    -
    -
    Parameters:
    -
      -

    • ts_mol (RDKitMol) – The TS in RDKitMol object with 3D geometries embedded.

      • -

    • multiplicity (int, optional) – The spin multiplicity of the TS. Defaults to 1.

      • -

    • save_dir (str, optional) – The directory path to save the results. Defaults to None.

      • -
    -
    -
    Returns:
    -

    RDKitMol – The molecule in RDKitMol object with verification results stored in KeepIDs.

    -
    -
    -
    - -
    - -
    -
    -class rdmc.conformer_generation.ts_verifiers.QChemIRCVerifier(method: str = 'wB97x-d3', basis: str = 'def2-tzvp', nprocs: int = 1, track_stats: bool = False)#
    -

    Bases: TSVerifier

    -

    The class for verifying the TS by calculating and checking its IRC analysis using QChem.

    -
    -
    Parameters:
    -
      -

    • method (str, optional) – The method to be used for TS optimization. you can use the method available in QChem. -Defaults to "wB97x-d3".

      • -

    • basis (str, optional) – The method to be used for TS optimization. you can use the basis available in QChem. -Defaults to "def2-tzvp".

      • -

    • nprocs (int, optional) – The number of processors to use. Defaults to 1.

      • -

    • track_stats (bool, optional) – Whether to track the status. Defaults to False.

      • -
    -
    -
    -
    -
    -verify_ts_guesses(ts_mol: RDKitMol, multiplicity: int = 1, save_dir: str | None = None, **kwargs)#
    -

    Verifying TS guesses (or optimized TS geometries).

    -
    -
    Parameters:
    -
      -

    • ts_mol ('RDKitMol') – The TS in RDKitMol object with 3D geometries embedded.

      • -

    • multiplicity (int, optional) – The spin multiplicity of the TS. Defaults to 1.

      • -

    • save_dir (_type_, optional) – The directory path to save the results. Defaults to None.

      • -
    -
    -
    Returns:
    -

    RDKitMol – The molecule in RDKitMol object with verification results stored in KeepIDs.

    -
    -
    -
    - -
    - -
    -
    -class rdmc.conformer_generation.ts_verifiers.TSScreener(trained_model_dir: str, threshold: float = 0.95, track_stats: bool | None = False)#
    -

    Bases: TSVerifier

    -

    The class for screening TS guesses using graph neural networks.

    -
    -
    Parameters:
    -
      -

    • trained_model_dir (str) – The path to the directory storing the trained TS-Screener model.

      • -

    • threshold (float) – Threshold prediction at which we classify a failure/success. Defaults to 0.95.

      • -

    • track_stats (bool, optional) – Whether to track timing stats. Defaults to False.

      • -
    -
    -
    -
    -
    -verify_ts_guesses(ts_mol: RDKitMol, multiplicity: int = 1, save_dir: str | None = None, **kwargs) → RDKitMol#
    -

    Screen poor TS guesses by using reacting mode from frequency calculation.

    -
    -
    Parameters:
    -
      -

    • ts_mol ('RDKitMol') – The TS in RDKitMol object with 3D geometries embedded.

      • -

    • multiplicity (int, optional) – The spin multiplicity of the TS. Defaults to 1.

      • -

    • save_dir (str, optional) – The directory path to save the results. Defaults to None.

      • -
    -
    -
    Returns:
    -

    RDKitMol – The molecule in RDKitMol object with verification results stored in KeepIDs.

    -
    -
    -
    - -
    - -
    -
    -class rdmc.conformer_generation.ts_verifiers.TSVerifier(track_stats: bool = False)#
    -

    Bases: object

    -

    The abstract class for TS verifiers.

    -
    -
    Parameters:
    -

    track_stats (bool, optional) – Whether to track status. Defaults to False.

    -
    -
    -
    -
    -verify_ts_guesses(ts_mol: RDKitMol, multiplicity: int = 1, save_dir: str | None = None, **kwargs)#
    -

    The abstract method for verifying TS guesses (or optimized TS geometries). The method need to take -ts_mol in RDKitMol, keep_ids in list, multiplicity in int, and save_dir in str.

    -
    -
    Parameters:
    -
      -

    • ts_mol ('RDKitMol') – The TS in RDKitMol object with 3D geometries embedded.

      • -

    • multiplicity (int, optional) – The spin multiplicity of the TS. Defaults to 1.

      • -

    • save_dir (str, optional) – The directory path to save the results. Defaults to None.

      • -
    -
    -
    Raises:
    -

    NotImplementedError – This method needs to be implemented in the subclass.

    -
    -
    -
    - -
    - -
    -
    -class rdmc.conformer_generation.ts_verifiers.XTBFrequencyVerifier(cutoff_frequency: float = -100.0, track_stats: bool = False)#
    -

    Bases: TSVerifier

    -

    The class for verifying the TS by calculating and checking its frequencies using XTB.

    -
    -
    Parameters:
    -
      -

    • cutoff_frequency (float, optional) – Cutoff frequency above which a frequency does not correspond to a TS -imaginary frequency to avoid small magnitude frequencies which correspond to internal bond rotations -Defaults to -100. cm-1

      • -

    • track_stats (bool, optional) – Whether to track stats. Defaults to False.

      • -
    -
    -
    -
    -
    -verify_ts_guesses(ts_mol: RDKitMol, multiplicity: int = 1, save_dir: str | None = None, **kwargs) → RDKitMol#
    -

    Verifying TS guesses (or optimized TS geometries).

    -
    -
    Parameters:
    -
      -

    • ts_mol ('RDKitMol') – The TS in RDKitMol object with 3D geometries embedded.

      • -

    • multiplicity (int, optional) – The spin multiplicity of the TS. Defaults to 1.

      • -

    • save_dir (str, optional) – The directory path to save the results. Defaults to None.

      • -
    -
    -
    Returns:
    -

    RDKitMol – The molecule in RDKitMol object with verification results stored in KeepIDs.

    -
    -
    -
    - -
    - +
    +

    rdmc.conformer_generation.ts_verifiers#

    @@ -717,39 +505,6 @@
    -
    -
    - On this page -
    -
    -
    diff --git a/reference/conformer_generation/postprocessing/verifiers.html b/reference/conformer_generation/postprocessing/verifiers.html index ada566a0..edcd42e2 100644 --- a/reference/conformer_generation/postprocessing/verifiers.html +++ b/reference/conformer_generation/postprocessing/verifiers.html @@ -464,76 +464,8 @@
    -
    -

    rdmc.conformer_generation.verifiers#

    -

    Modules for verifying optimized stable species

    -
    -
    -class rdmc.conformer_generation.verifiers.Verifier(track_stats: bool = False)#
    -

    Bases: object

    -

    The abstract class for verifiers.

    -
    -
    Parameters:
    -

    track_stats (bool, optional) – Whether to track status. Defaults to False.

    -
    -
    -
    -
    -verify_guesses(mol: RDKitMol, multiplicity: int = 1, save_dir: str | None = None, **kwargs)#
    -

    The abstract method for verifying guesses (or optimized stable species geometries). The method need to take -mol in RDKitMol, keep_ids in list, multiplicity in int, and save_dir in str, and returns -a list indicating the ones passing the check.

    -
    -
    Parameters:
    -
      -

    • mol ('RDKitMol') – The stable species in RDKitMol object with 3D geometries embedded.

      • -

    • multiplicity (int, optional) – The spin multiplicity of the stable species. Defaults to 1.

      • -

    • save_dir (_type_, optional) – The directory path to save the results. Defaults to None.

      • -
    -
    -
    Raises:
    -

    NotImplementedError –

    -
    -
    -
    - -
    - -
    -
    -class rdmc.conformer_generation.verifiers.XTBFrequencyVerifier(cutoff_frequency: float = -100.0, track_stats: bool = False)#
    -

    Bases: Verifier

    -

    The class for verifying the stable species by calculating and checking its frequencies using XTB.

    -
    -
    Parameters:
    -
      -

    • cutoff_frequency (float, optional) – Cutoff frequency above which a frequency does not correspond to a TS -imaginary frequency to avoid small magnitude frequencies which correspond to internal bond rotations -Defaults to -100. cm-1.

      • -

    • track_stats (bool, optional) – Whether to track stats. Defaults to False.

      • -
    -
    -
    -
    -
    -verify_guesses(mol: RDKitMol, multiplicity: int = 1, save_dir: str | None = None, **kwargs)#
    -

    Verifying stable species guesses (or optimized stable species geometries).

    -
    -
    Parameters:
    -
      -

    • mol ('RDKitMol') – The stable species in RDKitMol object with 3D geometries embedded.

      • -

    • multiplicity (int, optional) – The spin multiplicity of the stable species. Defaults to 1.

      • -

    • save_dir (_type_, optional) – The directory path to save the results. Defaults to None.

      • -
    -
    -
    Returns:
    -

    RDKitMol – The molecule in RDKitMol object with verification results stored in KeepIDs.

    -
    -
    -
    - -
    - +
    +

    rdmc.conformer_generation.verifiers#

    @@ -573,23 +505,6 @@
    -
    -
    - On this page -
    -
    -
    diff --git a/reference/conformer_generation/utils.html b/reference/conformer_generation/utils.html index 082f5566..7249a1ec 100644 --- a/reference/conformer_generation/utils.html +++ b/reference/conformer_generation/utils.html @@ -459,140 +459,8 @@
    -
    -

    Utils#

    -

    Utilities for conformer generation modules.

    -
    -
    -rdmc.conformer_generation.utils.cluster_confs(mol: RDKitMol, cutoff: float = 1.0) → RDKitMol#
    -

    Cluster conformers of a molecule based on RMSD.

    -
    -
    Parameters:
    -
      -

    • mol ('RDKitMol') – An RDKitMol object.

      • -

    • cutoff (float, optional) – The cutoff for clustering. Defaults to 1.0.

      • -
    -
    -
    Returns:
    -

    mol (‘RDKitMol’) – An RDKitMol object with clustered conformers.

    -
    -
    -
    - -
    -
    -rdmc.conformer_generation.utils.convert_log_to_mol(log_path: str, amplitude: float = 1.0, num_frames: int = 10, weights: bool | array = False) → None | RDKitMol#
    -

    Convert a TS optimization log file to an RDKitMol object with conformers.

    -
    -
    Parameters:
    -
      -

    • log_path (str) – The path to the log file.

      • -

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

      • -

    • num_frames (int) – The number of frames in each direction (forward and reverse). Defaults to 10.

      • -

    • 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.

      • -
    -
    -
    Returns:
    -

    mol (‘RDKitMol’) – An RDKitMol object.

    -
    -
    -
    - -
    -
    -rdmc.conformer_generation.utils.dict_to_mol(mol_data: List[dict], conf_copy_attrs: list | None = None)#
    -

    Convert a dictionary that stores its conformers object, atom coordinates, -and conformer-level attributes to an RDKitMol. The method assumes that the -first conformer’s owning mol contains the conformer-level attributes, which -are extracted through the Copy function (this should be the case if the -dictionary was generated with the mol_to_dict function).

    -
    -
    Parameters:
    -
      -

    • mol_data (list) – A list containing dictionaries of data entries for each conformer.

      • -

    • conf_copy_attrs (list, optional) – Conformer-level attributes to copy to the mol. -Defaults to None, which means no attributes will be copied.

      • -
    -
    -
    Returns:
    -

    mol (‘RDKitMol’) – An RDKitMol object.

    -
    -
    -
    - -
    -
    -rdmc.conformer_generation.utils.get_conf_failure_mode(rxn_dir: str, pruner: bool = True) → dict#
    -

    Parse a reaction directory for a TS generation run and extract failure modes (which conformer failed the -full workflow and for what reason).

    -
    -
    Parameters:
    -
      -

    • rxn_dir (str) –

      • -

    • (bool (pruner) – Optional) Whether or not pruner was used during workflow. Defaults to True.

      • -
    -
    -
    Returns:
    -

    failure_dict (‘dict’) – Dictionary of conformer ids mapped to the corresponding failure mode. -the failure_mode can be one of the following: -opt, prune, freq, irc, workflow, none.

    -
    -
    -
    - -
    -
    -rdmc.conformer_generation.utils.get_frames_from_freq(log: ~rdmc.external.logparser.gaussian.GaussianLog, amplitude: float = 1.0, num_frames: int = 10, weights: bool | ~numpy.array = False) -> (<built-in function array>, <built-in function array>)#
    -

    Get the reaction mode as frames from a TS optimization log file.

    -
    -
    Parameters:
    -
      -

    • log (GaussianLog) – A gaussian log object with vibrational freq calculated.

      • -

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

      • -

    • num_frames (int) – The number of frames in each direction (forward and reverse). Defaults to 10.

      • -

    • 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.

      • -
    -
    -
    Returns:
    -
      -

    • np.array – The atomic numbers as an 1D array

      • -

    • np.array – The 3D geometries at each frame as a 3D array (number of frames x 2 + 1, number of atoms, 3)

      • -
    -
    -
    -
    - -
    -
    -rdmc.conformer_generation.utils.mol_to_dict(mol: RDKitMol, copy: bool = True, iter: int | None = None, conf_copy_attrs: list | None = None) → List[dict]#
    -

    Convert a molecule to a dictionary that stores its conformers object, atom coordinates, -and iteration numbers for a certain calculation (optional).

    -
    -
    Parameters:
    -
      -

    • mol ('RDKitMol') – An RDKitMol object.

      • -

    • copy (bool, optional) – Use a copy of the molecule to process data. Defaults to True.

      • -

    • iter (int, optional) – Number of iterations. Defaults to None.

      • -

    • conf_copy_attrs (list, optional) – Conformer-level attributes to copy to the dictionary. -Defaults to None, which means no attributes will be copied.

      • -
    -
    -
    Returns:
    -

    list – mol data as a list of dict; each dict corresponds to a conformer.

    -
    -
    -
    - +
    +

    Utils#

    @@ -632,21 +500,6 @@
    -
    -
    - On this page -
    -
    -
    diff --git a/reference/conformer_generation/workflow/generators.html b/reference/conformer_generation/workflow/generators.html index ff99c908..e64c5bc2 100644 --- a/reference/conformer_generation/workflow/generators.html +++ b/reference/conformer_generation/workflow/generators.html @@ -464,143 +464,8 @@
    -
    -

    rdmc.conformer_generation.generators#

    -

    Modules for conformer generation workflows

    -
    -
    -class rdmc.conformer_generation.generators.ConformerGenerator(smiles: str, multiplicity: int | None = None, optimizer: ConfGenOptimizer | None = None, pruner: ConfGenPruner | None = None, verifiers: Verifier | List[Verifier] | None = None, sampler: TorisonalSampler | None = None, final_modules: ConfGenOptimizer | Verifier | None = None, save_dir: str | None = None)#
    -

    Bases: object

    -

    A module for conformer generation. The workflow follows an embed -> optimize -> prune cycle with -custom stopping criteria. Additional final modules can be added at the user’s discretion.

    -
    -
    Parameters:
    -
    -
    -
    -
    -
    -embed_stable_species(smiles: str, n_conformers: int = 20) → RDKitMol#
    -

    Embed the well conformer according to the SMILES provided.

    -
    -
    Parameters:
    -
      -

    • smiles (str) – The well conformer SMILES.

      • -

    • n_conformers (int, optional) – The maximum number of conformers to be generated. Defaults to 20.

      • -
    -
    -
    Returns:
    -

    An RDKitMol of the well conformer with 3D geometry embedded.

    -
    -
    -
    - -
    -
    -set_filter(mol: RDKitMol, n_conformers: int) → list#
    -

    Assign the indices of conformers to track whether the conformers are passed to the following steps.

    -
    -
    Parameters:
    -
      -

    • mol ('RDKitMol') – The stable species in RDKitMol object with 3D geometries embedded.

      • -

    • n_conformers (int) – The maximum number of conformers to be passed to the following steps.

      • -
    -
    -
    Returns:
    -

    RDKitMol – with KeepIDs as a list of True and False indicating whether a conformer passes the check.

    -
    -
    -
    - -
    - -
    -
    -class rdmc.conformer_generation.generators.StochasticConformerGenerator(smiles, embedder: ConfGenEmbedder | None = None, optimizer: ConfGenOptimizer | None = None, estimator: Estimator | None = None, pruner: ConfGenPruner | None = None, metric: SCGMetric | None = None, min_iters: int | None = None, max_iters: int | None = None, final_modules: list | None = None, config: dict | None = None, track_stats: bool = False)#
    -

    Bases: object

    -

    A module for stochastic conformer generation. The workflow follows an embed -> optimize -> prune cycle with -custom stopping criteria. Additional final modules can be added at the user’s discretion.

    -
    -
    Parameters:
    -
    -
    -
    -
    -
    -set_config(config: str, embedder: ConfGenEmbedder | None = None, optimizer: ConfGenOptimizer | None = None, pruner: ConfGenPruner | None = None, metric: SCGMetric | None = None, min_iters: int | None = None, max_iters: int | None = None, final_modules: list | None = None)#
    -

    Set the configuration for the conformer generator with pre-defined options: "loose" and "normal".

    -
    -
    Parameters:
    -
      -

    • embedder (ConfGenEmbedder, optional) – Instance of a ConfGenEmbedder. -Available options are ETKDGEmbedder, -GeoMolEmbedder, and -RandomEmbedder. -Defaults to ETKDGEmbedder.

      • -

    • optimizer (ConfGenOptimizer, optional) – Instance of a ConfGenOptimizer. -Available options are XTBOptimizer, -GaussianOptimizer, and -MMFFOptimizer. Defaults to -XTBOptimizer with "gff" method.

      • -

    • pruner (ConfGenPruner, optional) – Instance of a ConfGenPruner. Available options are -CRESTPruner and -TorsionPruner. By default, -"loose" utilizes TorsionPruner with -mean_chk_threshold=20 and max_chk_threshold=30, and "normal" utilizes -CRESTPruner.

      • -

    • metric (SCGMetric, optional) – The available option is SCGMetric <rdmc.conformer_generation.metrics.SCGMetric>. -By default, both modes use "entropy" metric, while "loose" with window=3 and threshold=0.05, -and "normal" with window=5 and threshold=0.01.

      • -

    • min_iters (int, optional) – Minimum number of iterations for which to run the module. Defaults to 3 for "loose" and 5 for "normal".

      • -

    • (int (max_iters) – Maximum number of iterations for which to run the module. Defaults to 20 for "loose" and 100 for "normal".

      • -

    • optional} – Maximum number of iterations for which to run the module. Defaults to 20 for "loose" and 100 for "normal".

      • -

    • final_modules (list) – List of instances of optimizer/pruner to run after initial cycles complete. By default, no final modules are used for "loose". -For "normal", two CRESTPruner with ewin=12 and ewin=6, are introduced -before and after a XTBOptimizer with "gfn2" method -and "vtight" level.

      • -
    -
    -
    -
    - -
    - +
    +

    rdmc.conformer_generation.generators#

    @@ -640,24 +505,6 @@
    -
    -
    - On this page -
    -
    -
    diff --git a/reference/conformer_generation/workflow/index.html b/reference/conformer_generation/workflow/index.html index 3f146684..2d2c2fad 100644 --- a/reference/conformer_generation/workflow/index.html +++ b/reference/conformer_generation/workflow/index.html @@ -463,27 +463,10 @@

    Workflow#

    diff --git a/reference/conformer_generation/workflow/metrics.html b/reference/conformer_generation/workflow/metrics.html index e6087702..40303ee9 100644 --- a/reference/conformer_generation/workflow/metrics.html +++ b/reference/conformer_generation/workflow/metrics.html @@ -464,73 +464,8 @@
    -
    -

    rdmc.conformer_generation.metrics#

    -

    Modules for computing metrics to decide when to stop generating conformers

    -
    -
    -class rdmc.conformer_generation.metrics.SCGMetric(metric: str | None = 'entropy', window: int | None = 5, threshold: float | None = 0.01, T: float | None = 298)#
    -

    Bases: object

    -

    A class to calculate and track the given metric (“entropy”, “partition function”, or “total conformers”) for a molecule over time.

    -
    -
    Parameters:
    -
      -

    • metric (str, optional) – Metric to be calculated. Options are "entropy", "partition function", or "total conformers". -Defaults to "entropy".

      • -

    • window (int, optional) – Window size to compute the change in metric (doesn’t work when the metric is “total conformers”). -Defaults to 5.

      • -

    • threshold (float, optional) – Threshold for the change in metric to decide when to stop generating conformers. -Defaults to 0.01.

      • -

    • T (float, optional) – Temperature for entropy or partition function calculations. Defaults to 298 K.

      • -
    -
    -
    -
    -
    -calculate_entropy(mol_data: List[dict])#
    -

    Calculate the entropy of a molecule.

    -
    -
    Parameters:
    -

    mol_data (List[dict]) – A list of dictionaries with molecule conformers.

    -
    -
    -
    - -
    -
    -calculate_metric(mol_data: List[dict])#
    -

    Calculate the metric for a given molecule. The calculated value will be appended to the metric_history list.

    -
    -
    Parameters:
    -

    mol_data (List[dict]) – A list of dictionaries with molecule conformers.

    -
    -
    -
    - -
    -
    -calculate_partition_function(mol_data: List[dict])#
    -

    Calculate the partition function of a molecule.

    -
    -
    Parameters:
    -

    mol_data (List[dict]) – A list of dictionaries with molecule conformers.

    -
    -
    -
    - -
    -
    -check_metric()#
    -

    Check if the change in metric is below the threshold.

    -
    -
    Returns:
    -

    bool – True if the change in metric is below the threshold, False otherwise.

    -
    -
    -
    - -
    - +
    +

    rdmc.conformer_generation.metrics#

    @@ -570,22 +505,6 @@
    -
    -
    - On this page -
    -
    -
    diff --git a/reference/conformer_generation/workflow/sampler.html b/reference/conformer_generation/workflow/sampler.html index fc6a5413..5e6462fa 100644 --- a/reference/conformer_generation/workflow/sampler.html +++ b/reference/conformer_generation/workflow/sampler.html @@ -464,142 +464,8 @@
    -
    -

    rdmc.conformer_generation.sampler#

    -

    Modules for torsional sampling

    -
    -
    -class rdmc.conformer_generation.sampler.TorsionalSampler(method: str = 'GFN2-xTB', nprocs: int = 1, memory: int = 1, n_point_each_torsion: int = 45, n_dimension: int = 2, optimizer: ConfGenOptimizer | TSOptimizer | None = None, pruner: ConfGenPruner | None = None, verifiers: TSVerifier | Verifier | List[TSVerifier] | List[Verifier] | None = None)#
    -

    Bases: object

    -

    A class to find possible conformers by sampling the PES for each torsional pair. -You have to have the Sparrow and xtb-python packages installed to run this workflow.

    -
    -
    Parameters:
    -
      -

    • method (str, optional) – The method to be used for automated conformer search. Only the methods available in Spharrow and xtb-python can be used. -Defaults to "GFN2-xTB".

      • -

    • nprocs (int, optional) – The number of processors to use. Defaults to 1.

      • -

    • memory (int, optional) – Memory in GB used by Gaussian. Defaults to 1.

      • -

    • n_point_each_torsion (float, optional) – Number of points to be sampled along each rotational mode. Defaults to 45..

      • -

    • n_dimension (int, optional) – Number of dimensions. Defaults to 2. If -1 is assigned, the number of dimension would be the number of rotatable bonds.

      • -

    • optimizer (ConfGenOptimizer or TSOptimizer, optional) – The optimizer used to optimize TS or stable specials geometries. Available options for -TSOptimizer <rdmc.conformer_generation.ts_optimizers.TSOptimizer> -are SellaOptimizer, -OrcaOptimizer, -and GaussianOptimizer.

      • -

    • pruner (ConfGenPruner, optional) – The pruner used to prune conformers based on geometric similarity after optimization. Available options are -CRESTPruner and -TorsionPruner.

      • -

    • verifiers (TSVerifier, Verifier, list of TSVerifiers or list of Verifiers, optional) – The verifier or a list of verifiers used to verify the obtained conformer. Available -options are -GaussianIRCVerifier, -OrcaIRCVerifier, and -XTBFrequencyVerifier.

      • -
    -
    -
    -
    -
    -get_conformers_by_change_torsions(mol: RDKitMol, id: int = 0, torsions: list | None = None, exclude_methyl: bool = True, on_the_fly_check: bool = True) → List[RDKitMol]#
    -

    Generate conformers by rotating the angles of the torsions. A on-the-fly check -can be applied, which identifies the conformers with colliding atoms.

    -
    -
    Parameters:
    -
      -

    • mol (RDKitMol) – A RDKitMol molecule object.

      • -

    • id (int) – The ID of the conformer to be obtained. Defaults to 0.

      • -

    • torsions (list) – A list of four-atom-index lists indicating the torsional modes. Defaults to None, -which means all the rotatable bonds will be used.

      • -

    • exclude_methyl (bool) – Whether exclude the torsions with methyl groups. Defaults to False. -Only valid if torsions is not provided.

      • -

    • on_the_fly_filter (bool) – Whether to check colliding atoms on the fly. Defaults to True.

      • -
    -
    -
    Returns:
    -

    lis – A list of RDKitMol of sampled 3D geometries for each torsional mode.

    -
    -
    -
    - -
    - -
    -
    -rdmc.conformer_generation.sampler.get_energy(mol: RDKitMol, confId: int = 0, method: str = 'GFN2-xTB') → float#
    -

    Calculate the energy of the RDKitMol with given confId. The unit is in kcal/mol. -Only support methods already supported either in sparrow or xtb-python.

    -
    -
    Parameters:
    -
      -

    • mol (RDKitMol) – A RDKitMol molecule object.

      • -

    • confId (int) – The ID of the conformer for calculating energy. Defaults to 0.

      • -

    • method (str) – Which semi-empirical method to be used in running energy calculation. Defaults to "GFN2-xTB".

      • -
    -
    -
    Returns:
    -

    The energy of the conformer.

    -
    -
    -
    - -
    -
    -rdmc.conformer_generation.sampler.get_separable_angle_list(samplings: List | Tuple, from_angles: List | Tuple | None = None) → List[List]#
    -

    Get a angle list for each input dimension. For each dimension -The input can be a int indicating the angles will be evenly sampled; -or a list indicating the angles to be sampled;

    -
    -
    Parameters:
    -
      -

    • samplings (Union[List, Tuple]) – An array of sampling information. -For each element, it can be either list or int.

      • -

    • from_angles (Union[List, Tuple]) – An array of initial angles. -If not set, all angles will begin at zeros.

      • -
    -
    -
    Returns:
    -

    list – A list of sampled angles sets.

    -
    -
    -

    Examples

    -
    get_separable_angle_list([[120, 240,], 4, 0])
->>> [[120, 240], [0, 90, 180, 270], [0]]
-
    -
    -
    - -
    -
    -rdmc.conformer_generation.sampler.plot_heat_map(energies: ndarray, minimum_points: List[Tuple], save_path: str, mask: ndarray | None = None, detailed_view: bool = False, title: str | None = None)#
    -

    Plot and save the heat map of a given PES.

    -
    -
    Parameters:
    -
      -

    • energies (np.ndarray) – A np.ndarray containing the energies for each sampled point.

      • -

    • minimum_points (List[Tuple]) – A list of tuples containing the indices of the minimum points.

      • -

    • save_path (str) – The path to save the plot.

      • -

    • mask (np.ndarray, optional) – A np.ndarray containing the mask for the energies.

      • -

    • detailed_view (bool) – Whether to plot the detailed view of the PES. Defaults to False.

      • -

    • title (str, optional) – The title of the plot.

      • -
    -
    -
    -
    - -
    -
    -rdmc.conformer_generation.sampler.preprocess_energies(energies: ndarray) → Tuple[ndarray, ndarray]#
    -

    Rescale the energy based on the lowest energy.

    -
    -
    Parameters:
    -

    energies (np.ndarray) – A np.ndarray containing the energies for each sampled point.

    -
    -
    Returns:
    -

    tuple – The rescaled energies and the mask pointing out positions having values

    -
    -
    -
    - +
    +

    rdmc.conformer_generation.sampler#

    @@ -639,23 +505,6 @@
    -
    -
    - On this page -
    -
    -
    diff --git a/reference/conformer_generation/workflow/ts_generators.html b/reference/conformer_generation/workflow/ts_generators.html index fe2c63fe..a2fd4a67 100644 --- a/reference/conformer_generation/workflow/ts_generators.html +++ b/reference/conformer_generation/workflow/ts_generators.html @@ -464,105 +464,8 @@
    -
    -

    rdmc.conformer_generation.ts_generators#

    -

    Modules for TS conformer generation workflows.

    -
    -
    -class rdmc.conformer_generation.ts_generators.TSConformerGenerator(rxn_smiles: str, multiplicity: int | None = None, use_smaller_multiplicity: bool = True, embedder: TSInitialGuesser | None = None, optimizer: TSOptimizer | None = None, pruner: ConfGenPruner | None = None, verifiers: TSVerifier | List[TSVerifier] | None = None, sampler: TorisonalSampler | None = None, final_modules: TSOptimizer | TSVerifier | List[TSVerifier] | None = None, save_dir: str | None = None)#
    -

    Bases: object

    -

    The class used to define a workflow for generating a set of TS conformers.

    -
    -
    Parameters:
    -
      -

    • rxn_smiles (str) – The SMILES of the reaction. The SMILES should be formatted similar to "reactant1.reactant2>>product1.product2.".

      • -

    • multiplicity (int, optional) – The spin multiplicity of the reaction. The spin multiplicity will be interpreted from the reaction smiles if this -is not given by the user.

      • -

    • use_smaller_multiplicity (bool, optional) – Whether to use the smaller multiplicity when the interpreted multiplicity from the reaction smiles is -inconsistent between reactants and products. Defaults to True.

      • -

    • embedder (TSInitialGuesser, optional) – Instance of a TSInitialGuesser. Available options are -TSEGNNGuesser, -TSGCNGuesser, -AutoNEBGuesser, -RMSDPPGuesser, and -DEGSMGuesser.

      • -

    • optimizer (TSOptimizer, optional) – Instance of a TSOptimizer. Available options are -SellaOptimizer, -OrcaOptimizer, -GaussianOptimizer, and -QChemOptimizer.

      • -

    • pruner (ConfGenPruner, optional) – The pruner used to prune conformers based on geometric similarity after optimization. -Instance of a ConfGenPruner. Available options are -CRESTPruner and -TorsionPruner.

      • -

    • verifiers (TSVerifier or list of TSVerifiers, optional) – The verifier or a list of verifiers used to verify the obtained TS conformer. -Instance of a TSVerifier. -Available options are -XTBFrequencyVerifier, -GaussianIRCVerifier, -OrcaIRCVerifier, -QChemIRCVerifier, and -TSScreener.

      • -

    • sampler (TorisonalSampler, optional) – The sampler used to do automated conformer search for the obtained TS conformer. You can use -TorsionalSampler to define your own sampler.

      • -

    • final_modules (TSOptimizer, TSVerifier or list of TSVerifiers, optional) – The final modules can include optimizer in different LoT than previous -one and verifier(s) used to verify the obtained TS conformer.

      • -

    • save_dir (str or Pathlike object, optional) – The path to save the intermediate files and outputs generated during the generation. Defaults to None.

      • -
    -
    -
    -
    -
    -embed_stable_species(smiles: str) → rdmc.RDKitMol#
    -

    Embed the reactant and product complex according to the SMILES provided.

    -
    -
    Parameters:
    -

    smiles (str) – The reactant or product complex in SMILES. if multiple molecules involve, -use "." to separate them.

    -
    -
    Returns:
    -

    RDKitMol – An RDKitMol of the reactant or product complex with 3D geometry embedded.

    -
    -
    -
    - -
    -
    -generate_seed_mols(rxn_smiles: str, n_conformers: int = 20, shuffle: bool = False) → list#
    -

    Genereate seeds of reactant/product pairs to be passed to the following steps.

    -
    -
    Parameters:
    -
      -

    • rxn_smiles (str) – The reaction smiles of the reaction.

      • -

    • n_conformers (int, optional) – The maximum number of conformers to be generated. Defaults to 20.

      • -

    • shuffle (bool, optional) – Whether or not to shuffle the embedded mols. Defaults to False.

      • -
    -
    -
    Returns:
    -

    list – A list of reactant/product pairs in RDKitMol.

    -
    -
    -
    - -
    -
    -set_filter(ts_mol: RDKitMol, n_conformers: int) → RDKitMol#
    -

    Assign the indices of reactions to track whether the conformers are passed to the following steps.

    -
    -
    Parameters:
    -
      -

    • ts_mol ('RDKitMol') – The TS in RDKitMol object with 3D geometries embedded.

      • -

    • n_conformers (int) – The maximum number of conformers to be passed to the following steps.

      • -
    -
    -
    Returns:
    -

    RDKitMol – with KeepIDs as a list of True and False indicating whether a conformer passes the check.

    -
    -
    -
    - -
    - +
    +

    rdmc.conformer_generation.ts_generators#

    @@ -602,21 +505,6 @@
    -
    -
    - On this page -
    -
    -
    diff --git a/reference/external/index.html b/reference/external/index.html index 1bbe0cc4..49a24857 100644 --- a/reference/external/index.html +++ b/reference/external/index.html @@ -496,91 +496,11 @@
  • 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

    -
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    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 -
    -
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"rdmc.conformer_generation.ts_generators": [[21, "module-rdmc.conformer_generation.ts_generators"]], "set_filter() (rdmc.conformer_generation.ts_generators.tsconformergenerator method)": [[21, "rdmc.conformer_generation.ts_generators.TSConformerGenerator.set_filter"]], "rdmc.external": [[23, "module-rdmc.external"]], "rdmc.external.inpwriter.gaussian": [[24, "module-rdmc.external.inpwriter.gaussian"]], "write_gaussian_config() (in module rdmc.external.inpwriter.gaussian)": [[24, "rdmc.external.inpwriter.gaussian.write_gaussian_config"]], "write_gaussian_freq() (in module rdmc.external.inpwriter.gaussian)": [[24, "rdmc.external.inpwriter.gaussian.write_gaussian_freq"]], "write_gaussian_gsm() (in module rdmc.external.inpwriter.gaussian)": [[24, "rdmc.external.inpwriter.gaussian.write_gaussian_gsm"]], "write_gaussian_inp() (in module rdmc.external.inpwriter.gaussian)": [[24, "rdmc.external.inpwriter.gaussian.write_gaussian_inp"]], "write_gaussian_irc() (in module rdmc.external.inpwriter.gaussian)": [[24, "rdmc.external.inpwriter.gaussian.write_gaussian_irc"]], "write_gaussian_opt() (in module rdmc.external.inpwriter.gaussian)": [[24, "rdmc.external.inpwriter.gaussian.write_gaussian_opt"]], "rdmc.external.inpwriter": [[25, "module-rdmc.external.inpwriter"]], "rdmc.external.inpwriter.orca": [[26, "module-rdmc.external.inpwriter.orca"]], "write_orca_freq() (in module rdmc.external.inpwriter.orca)": [[26, "rdmc.external.inpwriter.orca.write_orca_freq"]], "write_orca_gsm() (in module rdmc.external.inpwriter.orca)": [[26, "rdmc.external.inpwriter.orca.write_orca_gsm"]], "write_orca_irc() (in module rdmc.external.inpwriter.orca)": [[26, "rdmc.external.inpwriter.orca.write_orca_irc"]], "write_orca_opt() (in module rdmc.external.inpwriter.orca)": [[26, "rdmc.external.inpwriter.orca.write_orca_opt"]], "rdmc.external.inpwriter.qchem": [[27, "module-rdmc.external.inpwriter.qchem"]], "write_qchem_freq() (in module rdmc.external.inpwriter.qchem)": [[27, "rdmc.external.inpwriter.qchem.write_qchem_freq"]], "write_qchem_irc() (in module rdmc.external.inpwriter.qchem)": [[27, "rdmc.external.inpwriter.qchem.write_qchem_irc"]], "write_qchem_opt() (in module rdmc.external.inpwriter.qchem)": [[27, "rdmc.external.inpwriter.qchem.write_qchem_opt"]], "rdmc.external.inpwriter.utils": [[28, "module-rdmc.external.inpwriter.utils"]], "baselog (class in rdmc.external.logparser.base)": [[29, "rdmc.external.logparser.base.BaseLog"]], "ccliblog (class in rdmc.external.logparser.base)": [[29, "rdmc.external.logparser.base.CclibLog"]], "all_geometries (rdmc.external.logparser.base.ccliblog property)": [[29, "rdmc.external.logparser.base.CclibLog.all_geometries"]], "auto_update_prop() (rdmc.external.logparser.base.baselog method)": [[29, "rdmc.external.logparser.base.BaseLog.auto_update_prop"]], "cclib_results (rdmc.external.logparser.base.ccliblog property)": [[29, "rdmc.external.logparser.base.CclibLog.cclib_results"]], "charge (rdmc.external.logparser.base.ccliblog property)": [[29, "rdmc.external.logparser.base.CclibLog.charge"]], "converged_geometries (rdmc.external.logparser.base.ccliblog property)": [[29, "rdmc.external.logparser.base.CclibLog.converged_geometries"]], "finished (rdmc.external.logparser.base.baselog property)": [[29, "rdmc.external.logparser.base.BaseLog.finished"]], "freqs (rdmc.external.logparser.base.ccliblog property)": [[29, "rdmc.external.logparser.base.CclibLog.freqs"]], "get_best_opt_geom() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.get_best_opt_geom"]], "get_converged_geom_idx() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.get_converged_geom_idx"]], "get_irc_midpoint() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.get_irc_midpoint"]], "get_lowest_e_geometry() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.get_lowest_e_geometry"]], "get_mol() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.get_mol"]], "get_scannames() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.get_scannames"]], "get_scanparams() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.get_scanparams"]], "get_scf_energies() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.get_scf_energies"]], "get_xyzs() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.get_xyzs"]], "guess_rxn_from_irc() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.guess_rxn_from_irc"]], "guess_rxn_from_normal_mode() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.guess_rxn_from_normal_mode"]], "initial_geometry (rdmc.external.logparser.base.ccliblog property)": [[29, "rdmc.external.logparser.base.CclibLog.initial_geometry"]], "interact_freq() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.interact_freq"]], "interact_irc() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.interact_irc"]], "interact_opt() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.interact_opt"]], "interact_scan() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.interact_scan"]], "is_ts (rdmc.external.logparser.base.baselog property)": [[29, "rdmc.external.logparser.base.BaseLog.is_ts"]], "job_type (rdmc.external.logparser.base.baselog property)": [[29, "rdmc.external.logparser.base.BaseLog.job_type"]], "multiplicity (rdmc.external.logparser.base.ccliblog property)": [[29, "rdmc.external.logparser.base.CclibLog.multiplicity"]], "neg_freqs (rdmc.external.logparser.base.ccliblog property)": [[29, "rdmc.external.logparser.base.CclibLog.neg_freqs"]], "num_all_geoms (rdmc.external.logparser.base.ccliblog property)": [[29, "rdmc.external.logparser.base.CclibLog.num_all_geoms"]], "num_converged_geoms (rdmc.external.logparser.base.ccliblog property)": [[29, "rdmc.external.logparser.base.CclibLog.num_converged_geoms"]], "num_neg_freqs (rdmc.external.logparser.base.ccliblog property)": [[29, "rdmc.external.logparser.base.CclibLog.num_neg_freqs"]], "opt_convergence (rdmc.external.logparser.base.ccliblog property)": [[29, "rdmc.external.logparser.base.CclibLog.opt_convergence"]], "opt_criteria (rdmc.external.logparser.base.baselog attribute)": [[29, "rdmc.external.logparser.base.BaseLog.opt_criteria"]], "optstatus (rdmc.external.logparser.base.ccliblog property)": [[29, "rdmc.external.logparser.base.CclibLog.optstatus"]], "plot_irc_energies() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.plot_irc_energies"]], "plot_opt_convergence() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.plot_opt_convergence"]], "plot_scan_energies() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.plot_scan_energies"]], "rdmc.external.logparser.base": [[29, "module-rdmc.external.logparser.base"]], "require_job_type() (rdmc.external.logparser.base.baselog method)": [[29, "rdmc.external.logparser.base.BaseLog.require_job_type"]], "require_ts() (rdmc.external.logparser.base.baselog method)": [[29, "rdmc.external.logparser.base.BaseLog.require_ts"]], "schemes (rdmc.external.logparser.base.baselog property)": [[29, "rdmc.external.logparser.base.BaseLog.schemes"]], "success (rdmc.external.logparser.base.baselog property)": [[29, "rdmc.external.logparser.base.BaseLog.success"]], "termination_time (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 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