Module rxn_channel

Process the seed to the random number generator.

Parameters:

• random_seed (None or int) - the seed for the random number generator
• logger (logging.Logger) - output logger

Returns: int

final random seed

Return two SMILES patterns of the two molecule fragments that would result from breaking the bond specified by the given two atoms or return the SMILES pattern of the molecule containing idx1 if idx2 is None.

Parameters:

• astructure (schrodinger.structure.Structure) - the structure containing the molecule for which fragment SMILES are wanted
• idx1 (int) - an atom index
• idx2 (int) - the atom index for the target bond formed with idx1 or None

Returns: str, str or str, None

either two strings one for each of two fragments or a single string for the molecule containing idx1 and None

Return a list of atom indicies obtained by collecting all atoms that are connected, in the bond traversal sense, to the given start atom by a number of bonds that is less than or equal to that given by the provided depth parameter. The start atom is included in the returned list. One can set a direction for the traversal by specifying exclusion atoms that are bound to the given start atom; the traversal will be done away from these atoms. Useful for doing SMARTS analysis from a central atom and proceeding outwards from that atom, as in nearest-neighbor, next-nearest-neighbor, etc., i. e. shells. Also useful for splitting a molecule into fragments about a given bond.

Parameters:

• astructure (schrodinger.structure.Structure) - the structure containing all atoms
• start_atom_index (int) - the atom index from which to start the traversal
• exclude_atom_indicies (list of int) - atom indicies to exclude from the bond traversal which basically sets the direction of the bond traversal, for example in the direction of a certain bond
• depth (int) - the maximum depth that the traversal is allowed to traverse in terms of the number of bonds from the starting atom

Returns: list of ints @return indicies, atom indicies connected to the start atom by up to the specified bond depth

If the given structure has a zero-order bond for the given atom indicies then make this bond a single-order bond.

Parameters:

• astructure (schrodinger.structure.Structure) - the structure for which the bond order may be changed
• atom_one (int) - the first atom index of the bond whose order needs changing
• atom_two (int) - the second atom index of the bond whose order needs changing

A wrapper that corrects the atom reorder map returned from build.attach_structure to account for deleted fragment atoms and wraps the case where the active bonds may be of zero-order.

Parameters:

• mol_one_st (schrodinger.structure.Structure) - the base structure to which the fragment will be added
• mol_one_from_atom (int) - defines the point at which the fragment structure will be added to the base structure
• mol_one_to_atom (int) - this atom defines the part of the base structure that will be replaced by the fragment
• mol_two_st (schrodinger.structure.Structure) - the fragment structure to be added to the base structure
• mol_two_from_atom (int) - defines the point at which the base structure will be added to the fragment structure
• mol_two_to_atom (int) - this atom defines the part of the fragment structure that will be replaced by the base

Returns: dict, dict, dict

three mapping dictionaries, (1) original_map, which is the original map returned from build.attach_structure, (2) orig_to_new_map, which is the corrected version of (1), and (3) new_to_orig_map, the reverse of (2).

Return the dictionary obtained from the input dictionary by deleting an entry with the specified key and then decrementing all keys larger than the specified key. Leave the values unchanged.

Parameters:

• indict (dict) - dictionary with integer keys and values from which to remove and decrement the specified key
• key_to_delete (int) - the key to delete from the input dictionary

Returns: dict

Return the number of open bonding sites available for the provided atom in the given structure. This number is the same as the number of unpaired electrons for the atom in its current state in the given structure.

Parameters:

• astructure (schrodinger.structure.Structure) - the structure that contains the provided atom
• atom_index (int) - the index of the atom for which the number of open bonding sites will be reported

Returns: int

atom_open_val, the number of open bonding sites for the provided atom

Perform a geometry minimization on the provided structure.

Parameters:

• astructure (schrodinger.structure.Structure) - the structure object needing minimization

Returns: bool

False if the minimization was successful, True otherwise

This is a convenience function to get a list of bond objects from a molecule object, since no such function exists in our Python API.

Parameters:

• amolecule (schrodinger.structure._Molecule) - the molecule object from which bonds will be defined

Returns: list of schrodinger.structure._StructureBond

bonds, list of bond objects for bonds in the specified molecule

Log the list of allowed adsorption sites.

Parameters:

• allow_adsorption_onto (list) - SMARTS patterns of arbitrary adsorption sites to support
• logger (logging.getLogger) - output logger

Return a single structure object containing the given molecules but such that the atom ordering per molecule is contiguous.

Parameters:

• molecules (list of schrodinger.structure._Molecule) - molecules that need to be contiguously assembled into a single structure

Returns: schrodinger.structure.Structure and two dicts

mols_st, single structure containing all molecules in contiguous form, and mols_new_to_old and mols_old_to_new, two reordering dictionaries

__doc__

Value:

""" Classes and functions for building reaction channels. Copyright Schrodinger, LLC. All rights reserved."""