schrodinger.application.jaguar.autots_rmsd module

methods for comparison of structures using rmsd

class schrodinger.application.jaguar.autots_rmsd.MapScore(score, atom_map)

Bases: tuple

__contains__

Return key in self.

__init__

Initialize self. See help(type(self)) for accurate signature.

__len__

Return len(self).

atom_map

Alias for field number 1

count(value) → integer -- return number of occurrences of value
index(value[, start[, stop]]) → integer -- return first index of value.

Raises ValueError if the value is not present.

score

Alias for field number 0

schrodinger.application.jaguar.autots_rmsd.reform_barely_broken_bonds(st1, st2, fraction_different=0.5)

Given two structures that have consistently ordered atoms, reform bonds that have not broken very much (stretched by less than fraction_different*d0). Return False if not all broken bonds can be reformed. Structures are run through mmlewis to get new bond orders and formal charges.

Parameters:
  • st1 (Structure) – the first structure
  • st2 (Structure) – the second structure
  • fraction_different (float) – if a bond breaks then it is also required that the bond distance increases by a factor of fraction_different*d0 where d0 is the bond distance before breaking
schrodinger.application.jaguar.autots_rmsd.molecule_lists_are_conformers(m1, m2, same_molecularity=True)

Compare two non-empty lists of structures and return True if matching pairs of conformers can be found. The structures in m1 and m2 are assumed to be fully connected (molecules) if same_molecularity==True.

Returns False if the number of molecules differs and same_molecularity==True.

Parameters:
  • m1 (list of structures) – first list of molecules
  • m2 (list of structures) – first list of molecules
  • same_molecularity (bool) – if True, require that the two lists be the same length (i.e. number of molecules)
Return type:

bool
Returns:

whether or not the two lists of molecules are conformers
schrodinger.application.jaguar.autots_rmsd.align_all_molecules(st1, st2, sort_rms=True)

Inspects whether or not all the molecules in reactant are conformers of those in product. If they are, each molecule in product is superimposed onto the corresponding reactant molecule.

Parameters:
  • st1 (schrodinger.structure.Structure instance) – structure 1
  • st2 (schrodinger.structure.Structure instance) – structure 2
  • sort_rms (boolean) – If True the structure in which the inter-molecule distances are larger is superimposes onto the smaller, see sort_by_centroid_distance, which does the sorting.
schrodinger.application.jaguar.autots_rmsd.sort_by_centroid_distance(strs)

Given a list of structures sort the list in non-decreasing order using the rms distance between molecules in the structures. e.g. for two structures which are each water dimers, the water dimer with the smaller

intermolecular distance would appear first in the list
Parameters:strs (list of schrodinger.structure.Structure instances) – list of structures to be sorted
Return type:list of schrodinger.structure.Structure instances
Returns:sorted list
schrodinger.application.jaguar.autots_rmsd.align_path_strs(path_strs)

Align the structures in a path.

Parameters:path_strs (list of structures) – the structures along the path
schrodinger.application.jaguar.autots_rmsd.order_atoms(reactant, product, debug=False)

Renumber atoms in reactant and product in a consistent fashion.

Parameters:
  • reactant (schrodinger.structure.Structure) – reactant structure
  • product (schrodinger.structure.Structure) – reactant structure
Return type:

tuple of two structures
Returns:

renumbered reactant and product
class schrodinger.application.jaguar.autots_rmsd.AutoTSAtomMapper(optimize_mapping, use_chirality, debug=False)

Bases: schrodinger.comparison.atom_mapper.BaseAtomMapper

RMSD_THRESH = 1e-08
__init__(optimize_mapping, use_chirality, debug=False)
Parameters:
  • optimize_mapping (boolean) – if True search over all bijections to find the one with lowest score
  • use_chirality (boolean) – if True, in addition to element type use chirality (where defined) to equate atoms.
initialize_atom_types(st, invert_stereocenters=False)

Initialize the atom types

Parameters:
  • st (Structure) – structure containing atoms
  • invert_stereocenters (boolean) – whether or not R/S labels should be flipped
score_mapping(st1, st2, atset)

Scores a particular atom reordering.

Parameters:
@pararm atset: the atoms which have been mapped. This may be a subset
of the atoms in the two structures as we test partial as well as full maps.
Returns:any metric which measures the goodness of a particular relative atom ordering in st1 and st2. Can be any type that has the less than operator implemented.
score_is_equivalent(score1, score2)

Here we declare 2 scores equivalent if the same number of chirality mismatches are present and the rmsd difference is within RMSD_THRESH. This resolves machine dependent descrepancies in the chosen map.

Parameters:
  • score1 (tuple) – the first score (chirality mismatches, active atoms, rms)
  • score2 (tuple) – the first score (chirality mismatches, active atoms, rms)

:return boolean indicating if the score is the same or different

ATOM_TYPE = 's_m_custom_atom_type'
MAPPER_INDEX = 'i_m_atom_mapper_index'
are_conformers(st1, atlist1, st2, atlist2)

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

Parameters:
  • st1 (Structure) – the first structure
  • atlist1 (list of ints) – list of atom indexes defining the first substructure
  • st2 (Structure) – the second structure
  • atlist2 (list of ints) – list of atom indexes defining the second substructure
Returns:

boolean indicating whether or not the two structures are conformers
are_consistently_ordered_conformers(st1, st2, atlist)

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

Parameters:
  • st1 (Structure) – the first structure
  • st2 (Structure) – the second structure
  • atlist (list of ints) – list of atom indexes defining the substructure
Returns:

boolean indicating whether or not the two structures are ordered conformers
are_enantiomers(st1, atlist1, st2, atlist2)

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

Parameters:
  • st1 (Structure) – the first structure
  • atlist1 (list of ints) – list of atom indexes defining the first substructure
  • st2 (Structure) – the second structure
  • atlist2 (list of ints) – list of atom indexes defining the second substructure
Returns:

boolean indicating whether or not the two structures are conformers
comparator(d1, d2)

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
get_atom_type(at)

This value is used as an atom property

Parameters:at (_StructureAtom) – atom we wish to obtain a type for
Returns:string which identifies atom type
invert_chirality(ch_list)

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

Parameters:ch_list (list of strings) – list of chirality labels for a structure
isomeric_atom_sets(st1, atset1, st2, atset2)

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

Parameters:
  • st1 (Structure) – the first structure
  • atset1 (set of ints) – set of atom indexes defining the first substructure
  • st2 (Structure) – the second structure
  • atset2 (set of ints) – set of atom indexes defining the second substructure
Returns:

a boolean indicating if these atom lists are isomeric
reorder_structures(st1, atlist1, st2, atlist2, invert_stereocenters=False)

Reorder the atoms in the two structures.

Parameters:
  • st1 (Structure) – the first structure
  • atlist1 (list of ints) – list of atom indexes defining the first substructure
  • st2 (Structure) – the second structure
  • atlist2 (list of ints) – list of atom indexes defining the second substructure
Returns:

the two structures with structure 2 having had atoms reordered
set_atom_type(at, value)

Set the value of the atom type

Parameters:
  • at (_StructureAtom) – atom we wish to set type for
  • value (string) – set the type of atom to this
st_to_graph(st, atset)

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

Parameters:
  • st (Structure) – the structure to convert
  • atset (set of ints) – a set of atoms to use to create the graph
Returns:

networkx Graph
unique_job_name(base_name)

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

Parameters:base_name (str) – base job name
class schrodinger.application.jaguar.autots_rmsd.AutoTSTemplateAtomMapper(optimize_mapping, use_chirality, debug=False)

Bases: schrodinger.application.jaguar.autots_rmsd.AutoTSAtomMapper

RMSD_THRESH = 1e-08
initialize_atom_types(st, active_ats, invert_stereocenters=False)

Initialize the atom types

Parameters:
  • st (Structure) – structure containing atoms
  • active_ats (list of ints) – atom indices of the reaction center
  • invert_stereocenters (boolean) – whether or not R/S labels should be flipped
choose_template_map(reactant, product, input_indexes, r_template, p_template, template_indexes)

Determine the optimal map from the input reactant and product structures to the template reactant and product structures.

Parameters:
  • reactant (Structure instance) – input reactant structure
  • product (Structure instance) – input product structure
  • input_indexes (RxnIndxDecomp instance) – breakdown of input atom indexes into core, reaction center
  • r_template (Structure instance) – template reactant structure
  • p_template (Structure instance) – template product structure
  • template_indexes (RxnIndxDecomp instance) – breakdown of template atom indexes into core, reaction center
Return type:

dict
Returns:

mapping from input number to template numbering
ATOM_TYPE = 's_m_custom_atom_type'
MAPPER_INDEX = 'i_m_atom_mapper_index'
__init__(optimize_mapping, use_chirality, debug=False)
Parameters:
  • optimize_mapping (boolean) – if True search over all bijections to find the one with lowest score
  • use_chirality (boolean) – if True, in addition to element type use chirality (where defined) to equate atoms.
are_conformers(st1, atlist1, st2, atlist2)

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

Parameters:
  • st1 (Structure) – the first structure
  • atlist1 (list of ints) – list of atom indexes defining the first substructure
  • st2 (Structure) – the second structure
  • atlist2 (list of ints) – list of atom indexes defining the second substructure
Returns:

boolean indicating whether or not the two structures are conformers
are_consistently_ordered_conformers(st1, st2, atlist)

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

Parameters:
  • st1 (Structure) – the first structure
  • st2 (Structure) – the second structure
  • atlist (list of ints) – list of atom indexes defining the substructure
Returns:

boolean indicating whether or not the two structures are ordered conformers
are_enantiomers(st1, atlist1, st2, atlist2)

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

Parameters:
  • st1 (Structure) – the first structure
  • atlist1 (list of ints) – list of atom indexes defining the first substructure
  • st2 (Structure) – the second structure
  • atlist2 (list of ints) – list of atom indexes defining the second substructure
Returns:

boolean indicating whether or not the two structures are conformers
comparator(d1, d2)

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
get_atom_type(at)

This value is used as an atom property

Parameters:at (_StructureAtom) – atom we wish to obtain a type for
Returns:string which identifies atom type
invert_chirality(ch_list)

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

Parameters:ch_list (list of strings) – list of chirality labels for a structure
isomeric_atom_sets(st1, atset1, st2, atset2)

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

Parameters:
  • st1 (Structure) – the first structure
  • atset1 (set of ints) – set of atom indexes defining the first substructure
  • st2 (Structure) – the second structure
  • atset2 (set of ints) – set of atom indexes defining the second substructure
Returns:

a boolean indicating if these atom lists are isomeric
reorder_structures(st1, atlist1, st2, atlist2, invert_stereocenters=False)

Reorder the atoms in the two structures.

Parameters:
  • st1 (Structure) – the first structure
  • atlist1 (list of ints) – list of atom indexes defining the first substructure
  • st2 (Structure) – the second structure
  • atlist2 (list of ints) – list of atom indexes defining the second substructure
Returns:

the two structures with structure 2 having had atoms reordered
score_is_equivalent(score1, score2)

Here we declare 2 scores equivalent if the same number of chirality mismatches are present and the rmsd difference is within RMSD_THRESH. This resolves machine dependent descrepancies in the chosen map.

Parameters:
  • score1 (tuple) – the first score (chirality mismatches, active atoms, rms)
  • score2 (tuple) – the first score (chirality mismatches, active atoms, rms)

:return boolean indicating if the score is the same or different

score_mapping(st1, st2, atset)

Scores a particular atom reordering.

Parameters:
@pararm atset: the atoms which have been mapped. This may be a subset
of the atoms in the two structures as we test partial as well as full maps.
Returns:any metric which measures the goodness of a particular relative atom ordering in st1 and st2. Can be any type that has the less than operator implemented.
set_atom_type(at, value)

Set the value of the atom type

Parameters:
  • at (_StructureAtom) – atom we wish to set type for
  • value (string) – set the type of atom to this
st_to_graph(st, atset)

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

Parameters:
  • st (Structure) – the structure to convert
  • atset (set of ints) – a set of atoms to use to create the graph
Returns:

networkx Graph
unique_job_name(base_name)

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

Parameters:base_name (str) – base job name