schrodinger.livedesign.preprocessor module¶

schrodinger.livedesign.preprocessor.initialize_audit_log(verbose: bool)¶: Initialize global audit for logging purposes

class schrodinger.livedesign.preprocessor.ExplicitHydrogens(value)¶

Bases: enum.Enum

An enumeration.

REMOVE_ALL = 1¶

KEEP_WEDGED = 2¶

ADD_ALL = 3¶

AS_IS = 4¶

ON_HETERO_AND_KEEP_WEDGED = 5¶

class schrodinger.livedesign.preprocessor.GenerateCoordinates(value)¶

Bases: enum.Enum

An enumeration.

NONE = 1¶

FULL = 2¶

FULL_ALIGNED = 3¶

class schrodinger.livedesign.preprocessor.ChiralFlag0Meaning(value)¶

Bases: enum.Enum

An enumeration.

UNGROUPED_ARE_ABSOLUTE = 1¶

UNGROUPED_ARE_RACEMIC = 2¶

UNGROUPED_ARE_RELATIVE = 3¶

class schrodinger.livedesign.preprocessor.PreprocessorOptions(MAX_NUM_ATOMS: Optional[int] = None, KEEP_ONLY_LARGEST_STRUCTURE: bool = True, STRIP_SALTS: Optional[Tuple[str]] = None, NEUTRALIZE: bool = True, TRANSFORMATIONS: Optional[Tuple[str]] = ('[#7+0;v5:1]=[#8+0:2]>>[#7+:1]-[#8-:2]', '[#6:3][P+:1]([#6:4])([#6:5])[#6-:2]>>[#6:3][P-0:1]([#6:4])([#6:5])=[#6+0:2]', '[#6:3][P-:1]([#6:4])([#6:5])[#6+:2]>>[#6:3][P-0:1]([#6:4])([#6:5])=[#6+0:2]', '[#6:3][S+:1]([#6:4])-[#8-:2]>>[#6:3][S;X3+0:1]([#6:4])=[#8-0:2]', '[#6:3][P+:1]([#8;X2:4])([#8;X2:5])[#8-:2]>>[#6:3][P+0:1]([#8:4])([#8:5])=[#8-0:2]', '[#6:3][S+:1]([#6:4])([#8-:2])=[O:5]>>[#6:3][S+0:1]([#6:4])(=[#8-0:2])=[O:5]', '[#7;A;X2-:1][N;X2+:2]#[N;X1:3]>>[#7-0:1]=[N+:2]=[#7-:3]', '[#6;X3-:1][N;X2+:2]#[N;X1:3]>>[#6-0;A:1]=[N+:2]=[#7-:3]'), CHOOSE_CANONICAL_TAUTOMER: bool = False, RESOLVE_AMBIGUOUS_TAUTOMERS: bool = False, CHIRAL_FLAG_0_MEANING: schrodinger.livedesign.preprocessor.ChiralFlag0Meaning = ChiralFlag0Meaning.UNGROUPED_ARE_ABSOLUTE, STRIP_AND_GROUPS_ON_SINGLE_ATOM: bool = False, PRESERVE_ENHANCED_STEREO_GROUP_IDS: bool = False, REMOVE_PROPERTIES: bool = False, GENERATE_COORDINATES: schrodinger.livedesign.preprocessor.GenerateCoordinates = GenerateCoordinates.FULL_ALIGNED, EXPLICIT_HYDROGENS: schrodinger.livedesign.preprocessor.ExplicitHydrogens = ExplicitHydrogens.REMOVE_ALL, CLEAR_INVALID_WEDGE_BONDS: bool = True, WEDGE_TWO_BONDS_AROUND_CHIRAL_ATOMS: bool = False, HEAVY_HYDROGEN_DT: bool = False)¶

Bases: tuple

Options dictating preprocessor actions

Variables

KEEP_ONLY_LARGEST_STRUCTURE – whether additional discontiguous structures are removed
REMOVE_PROPERTIES – whether properties are removed
STRIP_SALTS – whether salts are removed
RESOLVE_AMBIGUOUS_TAUTOMERS – whether to guess tautomeric state for ambiguous input that would otherwise fail with a kekulization error
WEDGE_TWO_BONDS_AROUND_CHIRAL_ATOMS – whether to try to wedge/dash 2 bonds around chiral atoms which have 4 neighbors.

MAX_NUM_ATOMS: Optional[int]¶: Alias for field number 0

KEEP_ONLY_LARGEST_STRUCTURE: bool¶: Alias for field number 1

STRIP_SALTS: Optional[Tuple[str]]¶: Alias for field number 2

NEUTRALIZE: bool¶: Alias for field number 3

TRANSFORMATIONS: Optional[Tuple[str]]¶: Alias for field number 4

CHOOSE_CANONICAL_TAUTOMER: bool¶: Alias for field number 5

RESOLVE_AMBIGUOUS_TAUTOMERS: bool¶: Alias for field number 6

CHIRAL_FLAG_0_MEANING: schrodinger.livedesign.preprocessor.ChiralFlag0Meaning¶: Alias for field number 7

STRIP_AND_GROUPS_ON_SINGLE_ATOM: bool¶: Alias for field number 8

PRESERVE_ENHANCED_STEREO_GROUP_IDS: bool¶: Alias for field number 9

REMOVE_PROPERTIES: bool¶: Alias for field number 10

GENERATE_COORDINATES: schrodinger.livedesign.preprocessor.GenerateCoordinates¶: Alias for field number 11

EXPLICIT_HYDROGENS: schrodinger.livedesign.preprocessor.ExplicitHydrogens¶: Alias for field number 12

CLEAR_INVALID_WEDGE_BONDS: bool¶: Alias for field number 13

WEDGE_TWO_BONDS_AROUND_CHIRAL_ATOMS: bool¶: Alias for field number 14

HEAVY_HYDROGEN_DT: bool¶: Alias for field number 15

static fromConfig(config: dict)¶

Parameters

config – configuration from which to build options

Raises

KeyError – if an unknown key is present
ValueError – if an unknown value is present

toConfig() → dict¶

__contains__(key, /)¶: Return key in self.

__len__()¶: Return len(self).

count(value, /)¶: Return number of occurrences of value.

index(value, start=0, stop=9223372036854775807, /)¶

Return first index of value.

Raises ValueError if the value is not present.

schrodinger.livedesign.preprocessor.remove_invalid_config_options(config: dict) → Tuple[str]¶

Parameters: config – configuration from which to build options, from which all invalid keys and values will be stripped
Returns: tuple of errors encountered

schrodinger.livedesign.preprocessor.audit_changes(func: Callable, mol: rdkit.Chem.rdchem.Mol, *args)¶

When the global audit_changes_log is initialized, compares mol CXSMILES before and after the given function call, capturing information when the CXSMILES has been changed.

Parameters

func – transformation function
mol – molecule to apply transformation to

schrodinger.livedesign.preprocessor.getprop(getter: Callable, value: str, default: Optional[Any] = None) → Any¶

schrodinger.livedesign.preprocessor.is_wildcard(atom)¶: Is atom a wildcard?

schrodinger.livedesign.preprocessor.is_queryatom_exception(atom)¶

Normally we raise an exception if query atoms are in the molecule to be preprocessed, but we don’t want to do that if the atom is an attachment point

Parameters: atom – the atom to check
Returns: whether or not the atom is allowed in the preprocessor

schrodinger.livedesign.preprocessor.coords_all_zero(conf)¶: Returns whether or not all atom positions in a conformer are zero

schrodinger.livedesign.preprocessor.get_limited_sanitized_mol(mol: rdkit.Chem.rdchem.Mol) → rdkit.Chem.rdchem.Mol¶: Sanitize the molecule in a limited way as to avoid changing the molecule or throwing when valence errors are present. Specifically we turn off: SANITIZE_PROPERTIES: which otherwise checks valences SANITIZE_CLEANUP: which can change the shape of molecule SANITIZE_CLEANUPCHIRALITY: which can remove chirality markers SANITIZE_FINDRADICALS: which checks valences of radicals

schrodinger.livedesign.preprocessor.setup_mol(mol)¶

Setup on a molecule that is always done regardless of configuration.

Parameters: mol – An unsanitized RDKit Mol
Returns: A partially sanitized RDKit mol, ready for the standardizer.

schrodinger.livedesign.preprocessor.check_kekulization(mol, options)¶

schrodinger.livedesign.preprocessor.assign_zero_coords_chirality(mol)¶: Molecules with all-zero coordinates need to have the “chirality tags” primed from the atom parity properties. Once these are in place, we remove the conformer, and leave the mol in a state equivalent to one that came from a SMILES input.

schrodinger.livedesign.preprocessor.correct_sgroup_coordinates(mol)¶: If coordinates are generated, make sure the FIELDDISP property in the Sgroups are using relative coordinates.

schrodinger.livedesign.preprocessor.preprocess_molblock(molblock: str, config: Optional[dict] = None) → str¶

Standardizes an MDL molblock

Parameters

molblock – input molblock
config – dict specifying preprocessor options

Returns

standardized molblock

schrodinger.livedesign.preprocessor.preprocess(mol: rdkit.Chem.rdchem.Mol, options: Optional[schrodinger.livedesign.preprocessor.PreprocessorOptions] = None, preserved_data_sgroups: Optional[List[str]] = None) → rdkit.Chem.rdchem.Mol¶

Standardizes an RDKit mol

Parameters

mol – input mol
options – preprocessor options

Returns

standardized mol

exception schrodinger.livedesign.preprocessor.BlindedCompoundError¶

Bases: ValueError

__init__(*args, **kwargs)¶

args¶

with_traceback()¶: Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

schrodinger.livedesign.preprocessor.assert_not_blinded(mol: rdkit.Chem.rdchem.Mol, max_num_atoms: Optional[int] = None)¶

Checks imcoming mol to confirm it has real atoms; if it doesn’t it may have been intentionally stripped by the caller. LiveDesign marks these structures as having been “blinded”, meaning a customer may have IP/legal restrictions, or there’s a delay in registering the structure despite having assay data available. Currently, LiveDesign handles these structures by keeping a row in the LiveReport, but without an associated SDF or image. This is different from other registration errors, which are simply archived.

Parameters

mol – RDKit Mol to consider
max_mol_wt – maximum allowed molecular weight

schrodinger.livedesign.preprocessor.assert_not_query(mol: rdkit.Chem.rdchem.Mol)¶

Checks incoming mol to confirm there are no query features present on atoms or bonds, which would otherwise make it not compatible with registration.

Parameters: mol – RDKit Mol to consider

schrodinger.livedesign.preprocessor.get_atoms_mapping(mol_atoms)¶

schrodinger.livedesign.preprocessor.get_bonds_mapping(mol, original_bond_mapping, atom_idx_mapping)¶

schrodinger.livedesign.preprocessor.tag_mol_indexes(mol)¶: Tag atoms with the initial indexes on the mol and create a bond mapping. Bonds are less stable than atoms, so we create an external mapping to the atoms they bind

schrodinger.livedesign.preprocessor.check_attachment_points_changed(sg, atom_idx_mapping)¶

schrodinger.livedesign.preprocessor.check_cstate_changed(sg, bond_idx_mapping)¶

schrodinger.livedesign.preprocessor.update_sgroup_indexes(sg, sg_atoms, sg_parent_atoms, sg_bonds, atom_idx_mapping, bond_idx_mapping)¶

schrodinger.livedesign.preprocessor.update_mol_groups(mol, stereo_groups, substance_groups, original_bond_mapping)¶: Update atoms and bonds in stereo and substance groups, dropping any atoms/groups that are no longer valid for the current state of the mol.

schrodinger.livedesign.preprocessor.update_sgroups(mol, substance_groups, atom_idx_mapping, bond_idx_mapping)¶: Update SGroups to reflect the transformations done on mol, updating with new atom and bond indexes, as well as atoms that might have been added or removed.

schrodinger.livedesign.preprocessor.update_stereo_groups(mol, stereo_groups, atom_idx_mapping)¶

schrodinger.livedesign.preprocessor.add_explicit_hydrogens(mol, only_on_hetero=False)¶

schrodinger.livedesign.preprocessor.remove_explicit_hydrogens(mol, sgroups, keep_wedged=False, keep_hetero=False)¶

schrodinger.livedesign.preprocessor.convert_to_molblock(mol, options=None)¶: Convert processed mol into a molblock and make necessary updates.

schrodinger.livedesign.preprocessor.convert_heavy_hydrogens(molblock)¶

NOTE that this operates on a molblock, not a molecule

The RDKit does not currently (v2020.03) support writing D or T to mol blocks, so we need to post-process the text. Fortunately it’s an easy regex in v3000 mol blocks. This does not work with V2000 mol blocks, so we throw a ValueError there. This doesn’t seem like a big deal since V2000 support is primarly being kept around for debugging purposes. If we need to eventually support V2000+HEAVY_HYDROGEN_DT, some not-completely-trivial code will need to be written.

schrodinger.livedesign.preprocessor.neutralize(mol, checkForProblematicHs=False)¶

schrodinger.livedesign.preprocessor.unicode_to_str(unicode_str)¶

Takes a unicode object and converts it to a str (utf-8). If the arg is already a str, returns unicode_str (i.e. if run with python 3). Needed to support python 2/3 with unicode_literals.

py2: type<unicode> -> type<str utf-8> py3: type<str utf-8> (no unicode type exists)

Parameters: unicode_str (unicode (py2) or str (py3)) – the unicode that potentially needs converting (i.e. if run with python 2)
Returns: str

schrodinger.livedesign.preprocessor.transform(mol, transformation)¶

apply the transformation to the molecule repeatedly until it no longer applies.

the maxTransformations argument is just there to prevent us from ending up in an infinite loop due to a bogus transformation

Please note that running transformations may alter the stereochemistry of mol, so a stereo recalculation from coordinates might be required.

schrodinger.livedesign.preprocessor.in_xy_plane(mol)¶

schrodinger.livedesign.preprocessor.generate_coordinates(mol, align=False)¶

schrodinger.livedesign.preprocessor.is_polymer(s_group)¶

schrodinger.livedesign.preprocessor.clean_up_polymer_brackets(mol, revert_to_mol=None, keep_existing_brackets=False)¶

Add polymer brackets back to mol.

Parameters

mol – RDKit mol to add polymer brackets to
revert_to_mol – RDKit mol to revert to if polymer brackets cannot be added correctly to provided mol. This will occur when brackets cross more than one bond.
keep_existing_brackets – whether to recalculate the positions of brackets that are already present

Returns

RDKit mol with polymer brackets

schrodinger.livedesign.preprocessor.copy_lewis_structure_and_hydrogens(st, mol)¶

Applies bond orders and charges from st to mol. Updates #implicitH to match

Assumes st includes all hydrogens. Adds implicit and explicit hydrogens to the mol, but does not add any graph hydrogens. May remove graph hydrogens.

schrodinger.livedesign.preprocessor.generate_canonical_tautomer(mol)¶

schrodinger.livedesign.preprocessor.clear_wedge_bonds_from_achiral_centers(mol)¶

schrodinger.livedesign.preprocessor.calculate_enhanced_stereo(mol, enh_stereo_default_grouping, initial_chiral_flag)¶

schrodinger.livedesign.preprocessor.strip_stereo_and(input_mol)¶

Removes any Stereo AND groups with only one center and flattens the bonds around it

Parameters: input_mol – The original molecule to consider
Returns: post-processed molecule, if the input molecule was modified

schrodinger.livedesign.preprocessor.frag_is_smaller(atoms, largest_atoms, weight, largest_weight, smiles, largest_smiles)¶: A fragment is considered larger if its atoms/weight are larger, the length of the smiles string is larger, or the smiles string is lexicographically smaller if they are equal length. ie, ‘AAA’ is larger than ‘AAB’.. hence the final smiles > largest_smiles check here to reject

schrodinger.livedesign.preprocessor.connect_variable_attachment_points(mol)¶

forms zero-order bonds between one of the atoms of a bond with an ATTACH property to the “main” molecule in order to have the molecule+variable attachment point treated as a single fragment

returns a 2-tuple with:

the modified molecule
whether or not the molecule was modified

schrodinger.livedesign.preprocessor.remove_fragments(mol, substance_groups)¶

Fragments are not removed if the molecule contains any SGroups which are associated with polymers

Use the following criteria to remove unwanted fragments from mol:

keep only the fragment which has the most number of atoms
break ties by keeping only fragments with the greatest molecular weight
break ties with the longest smiles string
break additional ties by keeping the fragment with the earliest alpha sorted SMILES string

If two or more identical fragments remain after 1-4, we will throw a fatal error.

schrodinger.livedesign.preprocessor.remove_properties(mol)¶

schrodinger.livedesign.preprocessor.strip_salts(mol, salt_list)¶

schrodinger.livedesign.preprocessor.apply_transformations(mol, transformations)¶: Apply the given list of transformations, and recalculate stereo if at least one transformation applies.

schrodinger.livedesign.preprocessor.add_chiral_hs(mol)¶

schrodinger.livedesign.preprocessor.wedge_clean(mol, wedge_2_bonds_if_possible)¶

schrodinger.livedesign.preprocessor.remove_wiggly_bonds_around_double_bonds(mol)¶