schrodinger.structutils.markush_enumerate module

Support for “R-group” enumeration as in ENUM-108.

class schrodinger.structutils.markush_enumerate.PlaceHolder(group_id, atom, bonds)

Bases: tuple

atom

Alias for field number 1

bonds

Alias for field number 2

group_id

Alias for field number 0

schrodinger.structutils.markush_enumerate.get_placeholders(st, groups=None)

Gathers placeholders metadata.

Parameters:

• st (schrodinger.structure.Structure) – Structure.
• groups – Dictionary that maps placeholder atom indices onto their group IDs. If None, regard atoms that carry the “GROUP_ID_PROP” property as “placeholders”.

Returns:

List of the placeholders records.

Return type:

list(PlaceHolder)

Raises:

ValueError if something about st looks not right.

schrodinger.structutils.markush_enumerate.get_attachment_points(st)

Returns ordered list of attachment points in st. The order is either based upon atom labels (“ATTACHMENT_PROP”, if available) or decided by the bond order and the peer atom atomic number.

Returns:List of atoms. Return type:list(int)

class schrodinger.structutils.markush_enumerate.Scaffold(st, groups=None)

Bases: object

Holds reference to the “scaffold” structure. Knows how to join R-groups to the core.

fragmentIDs

Returns set of fragment IDs.

populate(fragments)

Replaces placeholders with fragments.

Parameters:fragments (dict(int, schrodinger.structure.Structure)) – Indexable that maps fragment IDs onto structures.

schrodinger.structutils.markush_enumerate.validate_fragment(st)

Parameters:st (schrodinger.structure.Structure) – Structure. Raises:ValueError if there is no attachment points.

schrodinger.structutils.markush_enumerate.validate_scaffold(st)

Parameters:st (schrodinger.structure.Structure) – Structure. Raises:ValueError if there is no placeholders.

schrodinger.structutils.markush_enumerate.convert_fragment_from_v3000(st)

Converts fragment metadata from MDL V3000 conventions to the ones expected by this module.

Parameters:st (schrodinger.structure.Structure) – Structure. Raises:ValueError if something goes wrong.

schrodinger.structutils.markush_enumerate.convert_scaffold_from_v3000(st)

Converts scaffold metadata from MDL V3000 conventions to the ones expected by this module.

Parameters:st (schrodinger.structure.Structure) – Structure.

class schrodinger.structutils.markush_enumerate.FragmentReader(filename, logger=None)

Bases: object

Reads structures from file, skips “invalid” (in context of ENUM-108) fragments.

schrodinger.structutils.markush_enumerate.read_scaffold(filename)

Reads scaffold from file.

Parameters:filename (str) – File name. Returns:Scaffold instance. Return type:Scaffold Raises:ValueError on errors.

class schrodinger.structutils.markush_enumerate.FragmentsIterator(sources, random=None)

Bases: object

Iterator over Cartesian product of fragment collections.

class schrodinger.structutils.markush_enumerate.VirtualLibrary(scaffold, sources, random=None, logger=None, max_failures=123)

Bases: object

Utility class that implements common intended use case logic.