schrodinger.structutils.ccd module

This module contains API for assigning bond orders and formal charges to structures based on the CCD database. Residues and atoms are identified by their PDB residue names and PDB atom names, or by SMILES.

class schrodinger.structutils.ccd.CCDAtomMapper(use_chirality: bool)

Bases: schrodinger.comparison.atom_mapper.ConnectivityAtomMapper

Class for determining most ideal mapping of a CCD SMILES structure to a 3D ligand conformation.

score_mapping(ccd_st, st, atset)

This method is called to “score” a given mapping. Here, both input structures have been re-ordered to have the same atom ordering, and <atset> is a set of atoms that are “shared” between the 2 structures.

ATOM_TYPE = 's_m_custom_atom_type'
MAPPER_INDEX = 'i_m_atom_mapper_index'
__init__(use_chirality: bool)
Parameters

use_chirality – if True, in addition to element type use chirality (where defined) to equate atoms.

are_conformers(st1: schrodinger.structure._structure.Structure, atlist1: List[int], st2: schrodinger.structure._structure.Structure, atlist2: List[int]) → bool

Determine if the two substructures, as defined by the atom lists, are conformers but do not explore isomorphisms.

Parameters

  • st1 – the first structure

  • atlist1 – list of atom indexes defining the first substructure

  • st2 – the second structure

  • atlist2 – list of atom indexes defining the second substructure

Returns

boolean indicating whether or not the two structures are conformers

are_consistently_ordered_conformers(st1: schrodinger.structure._structure.Structure, st2: schrodinger.structure._structure.Structure, atlist: List[int]) → bool

Determine if two substructures are consistently ordered conformers. That is, they have the same atom numbering and bonding

Parameters

  • st1 – the first structure

  • st2 – the second structure

  • atlist – list of atom indexes defining the substructure

Returns

boolean indicating whether or not the two structures are ordered conformers

are_enantiomers(st1: schrodinger.structure._structure.Structure, atlist1: List[int], st2: schrodinger.structure._structure.Structure, atlist2: List[int]) → bool

Determine if the two substructures, as defined by the atom lists, are enantiomers but do not explore isomorphisms.

Parameters

  • st1 – the first structure

  • atlist1 – list of atom indexes defining the first substructure

  • st2 – the second structure

  • atlist2 – list of atom indexes defining the second substructure

Returns

boolean indicating whether or not the two structures are conformers

comparator(d1: Dict, d2: Dict) → bool

Comparison function to be used to determine if two nodes on graph are equivalent.

If this method is not used when constructing a GraphMatcher, node attributes will not be considered for the purpose of determining isomorphism.

Parameters

  • d1 (dict) – key=value dictionary from graph returned from st_to_graph which represents node 1

  • d1 – key=value dictionary from graph returned from st_to_graph which represents node 2

Returns

boolean indicating equilvalence

early_stop(score: float) → bool

Check if score is such that we should abort the atom_mapper early.

Parameters

score – score to check for early stopping condition

Returns

If True, AtomMapper should stop early. By default, we will not have an early stopping condition

get_atom_type(at: schrodinger.structure._structure._StructureAtom) → str

This value is used as an atom property

Parameters

at – atom we wish to obtain a type for

Returns

string which identifies atom type

initialize_atom_types(st: schrodinger.structure._structure.Structure, invert_stereocenters: bool = False)

Initialize the atom types

Parameters

  • st – structure containing atoms

  • invert_stereocenters – whether or not R/S labels should be flipped

invert_chirality(ch_list: List[str])

Invert the chirality (R/S) of an input list of chiralities.

Parameters

ch_list – list of chirality labels for a structure

isomeric_atom_sets(st1: schrodinger.structure._structure.Structure, atset1: Set[int], st2: schrodinger.structure._structure.Structure, atset2: Set[int]) → bool

Check that the atom types in atset1 are the same as those in atset2. If not, the two structures cannot be conformers.

Parameters

  • st1 – the first structure

  • atset1 – set of atom indexes defining the first substructure

  • st2 – the second structure

  • atset2 – set of atom indexes defining the second substructure

Returns

a boolean indicating if these atom lists are isomeric

reorder_structures(st1: schrodinger.structure._structure.Structure, atlist1: List[int], st2: schrodinger.structure._structure.Structure, atlist2: List[int], invert_stereocenters: bool = False) → Tuple[schrodinger.structure._structure.Structure, schrodinger.structure._structure.Structure]

Reorder the atoms in the two structures.

Parameters

  • st1 – the first structure

  • atlist1 – list of atom indexes defining the first substructure

  • st2 – the second structure

  • atlist2 – list of atom indexes defining the second substructure

  • invert_stereocenters – If True, flip all R<->S, used for are_enantiomers

Returns

the two structures with structure 2 having had atoms reordered

score_is_equivalent(score1: float, score2: float) → bool

determines if score should be considered equivalent

Parameters

  • score1 – the first score

  • score2 – the second score

set_atom_type(at: schrodinger.structure._structure._StructureAtom, value: str)

Set the value of the atom type

Parameters

  • at – atom we wish to set type for

  • value – set the type of atom to this

st_to_graph(st: schrodinger.structure._structure.Structure, atset: Set[int]) → networkx.classes.graph.Graph

Convert Structure instance to a networkx Graph using _StructureAtom instances as nodes and adding an atom type property

Parameters

  • st – the structure to convert

  • atset – a set of atoms to use to create the graph

Returns

networkx Graph

unique_job_name(base_name: str) → str

Add an integer to the end of the base_name to get a unique name.

Parameters

base_name – base job name

Returns

unique name

exception schrodinger.structutils.ccd.CCDStructureMismatchError

Bases: RuntimeError

raise this error when structure in CCD template doesn’t match HET

__init__(*args, **kwargs)
args
with_traceback()

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

exception schrodinger.structutils.ccd.SmilesGenerateError

Bases: RuntimeError

raise this error when RDKit fails to generate SMILES

__init__(*args, **kwargs)
args
with_traceback()

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

schrodinger.structutils.ccd.read_ccd_structures(pdbres_iter: Iterable[str]) → Dict[str, List[schrodinger.structure._structure.Structure]]

Read in CCD entries as structures.

Returns

Dictionary that maps a pdbres to reference CCD structures

schrodinger.structutils.ccd.build_ref_charges_and_bonds_cache(st: schrodinger.structure._structure.Structure)

Given a structure extract all CCD reference charges and bonds for each unique residue.

Populates the module level CCD_CHARGES_AND_BONDS_CACHE dict.

schrodinger.structutils.ccd.determine_ccd_pdbres(res: schrodinger.structure._structure._Residue) → str

Determine the CCD state that is consistent with the information present in the residue. For now only histidine is checked.

schrodinger.structutils.ccd.determine_his_ccd_pdbres(his: schrodinger.structure._structure._Residue) → str

Given a HIS residue, determine its protonation state based on PDB names and bond orders, and return the PDB residue name for the state.

schrodinger.structutils.ccd.ccd_assign_by_names_and_bonds(res: schrodinger.structure._structure._Residue) → Tuple[List[Tuple[int, int]], List[Tuple[int, int, int]]]

Assign bond orders and charges to residue based on CCD entry. A target residue matches with the reference if the atom names and all intra-residue bonds are a subset of the reference atom names and intra-residue bonds.

The CCD typically contains the most protonated form, which is not desirable for residues that are not handled by Epik, typically standard residues, e.g. it contains the neutral form of GLU. In that case the CCD is overwritten.

Returns

Tuple with list of atom indices and assigned charges, and list of assigned bond orders.

schrodinger.structutils.ccd.attempt_ccd_assignment(res: schrodinger.structure._structure._Residue, res_assign_atoms: Optional[List[int]] = None, _logger: Optional[logging.Logger] = None) → Tuple[List[Tuple[int, int]], List[Tuple[int, int, int]]]

Attempt to use the CCD record to assign the bond orders. Returns list of bonds that were assigned. Returns empty list if assignment was not successful.

Parameters

  • res – Residue for the het to assign orders to.

  • res_assign_atoms – List of atoms (substructure from the residue) to assign bond orders to. By default all residue atoms are assigned.

  • _logger – Logger

Returns

List of assigned charges and bonds