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.
- __init__(st, groups=None)¶
- Parameters
groups (dict(int, int) or None) – Dictionary that maps atom indices onto “group IDs”. If
None
, use “GROUP_ID_PROP” to identify the “placeholder” atoms.
- property 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.
- __init__(filename, logger=None)¶
- schrodinger.structutils.markush_enumerate.read_scaffold(filename)¶
Reads scaffold from file.
- Parameters
filename (str) – File name.
- Returns
Scaffold instance.
- Return type
- Raises
ValueError on errors.
- class schrodinger.structutils.markush_enumerate.FragmentsIterator(sources, random=None)¶
Bases:
object
Iterator over Cartesian product of fragment collections.
- __init__(sources, random=None)¶
- Parameters
sources (list of list) – List of [iterable over fragments, id1, id2, …] lists (see
r_group_enumerate.parse_rgroups
).random (None or int) – If None, enumerate sequentially. If integer, enumerate randomly using
random
as a seed.
- class schrodinger.structutils.markush_enumerate.VirtualLibrary(scaffold, sources, random=None, logger=None)¶
Bases:
object
Implements common intended use case logic.
- __init__(scaffold, sources, random=None, logger=None)¶
- Parameters
scaffold (
Scaffold
) – Scaffold.sources (list of list) – List of [iterable over fragments, id1, id2, …] lists (see
r_group_enumerate.parse_rgroups
). Or list of [filename, id1, id2, …] lists.random (None or int) – If None, enumerate sequentially. If integer, enumerate randomly using
random
as a seed.