Classes and functions for building reaction channels.
Copyright Schrodinger, LLC. All rights reserved.
int
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init_random_seed(random_seed,
logger)
Process the seed to the random number generator. |
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str, str or str, None
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get_fragment_smiles(astructure,
idx1,
idx2)
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. |
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list of ints @return indicies, atom indicies connected to the start
atom by up to the specified bond depth
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indicies_from_bonds_deep(astructure,
start_atom_index,
exclude_atom_indicies=None,
depth=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. |
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set_zob_to_sob(astructure,
atom_one,
atom_two)
If the given structure has a zero-order bond for the given atom
indicies then make this bond a single-order bond. |
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dict, dict, dict
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wrapper_build_attach_structure(mol_one_st,
mol_one_from_atom,
mol_one_to_atom,
mol_two_st,
mol_two_from_atom,
mol_two_to_atom)
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. |
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dict
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dict_delete_and_decrement_keys(indict,
key_to_delete)
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. |
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int
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open_bonding_sites(astructure,
atom_index)
Return the number of open bonding sites available for the provided
atom in the given structure. |
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bool
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minimize_geometry(astructure)
Perform a geometry minimization on the provided structure. |
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list of schrodinger.structure._StructureBond
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get_bonds_in_molecule(amolecule)
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. |
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schrodinger.structure.Structure and two dicts
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canonical_conformation(input_ct,
raise_on_failure=False)
Convert a ct to a canonical conformation using the same method as the
FFLD16 force field structure in ct IS modified If the input structure
contains more than one molecule then simply return the original
structure if raise_on_failure {boolean} is False and raise a
TypeError if True |
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schrodinger.structure.Structure
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eliminate_spears(speared_st)
Return the given structure with any intra-molecular ring spears
eliminated. |
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