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
- atom_map¶
Alias for field number 1
- score¶
Alias for field number 0
- schrodinger.application.jaguar.autots_rmsd.reform_barely_broken_bonds(st1: schrodinger.structure._structure.Structure, st2: schrodinger.structure._structure.Structure, fraction_different: float = 0.5, reform_always: bool = False) bool ¶
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 – the first structure
st2 – the second structure
fraction_different – 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
reform_always – If True, reform barely broken bonds even when doing so will not make the two structures into conformers. If False, only reform such bonds if doing so would render the two structures conformers.
- schrodinger.application.jaguar.autots_rmsd.molecule_lists_are_conformers(m1: List[schrodinger.structure._structure.Structure], m2: List[schrodinger.structure._structure.Structure], same_molecularity: bool = True, use_chirality: bool = False) bool ¶
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 – first list of molecules
m2 – first list of molecules
same_molecularity – if True, require that the two lists be the same length (i.e. number of molecules)
- Returns
whether the two lists of molecules are conformers
- schrodinger.application.jaguar.autots_rmsd.align_all_molecules(st1: schrodinger.structure._structure.Structure, st2: schrodinger.structure._structure.Structure, sort_rms: bool = True)¶
Inspects whether 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 – structure 1
st2 – structure 2
sort_rms – 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: List[schrodinger.structure._structure.Structure]) List[schrodinger.structure._structure.Structure] ¶
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 structures to be sorted
- Returns
sorted list
- schrodinger.application.jaguar.autots_rmsd.align_path_strs(path_strs: List[schrodinger.structure._structure.Structure])¶
Align the structures in a path.
- Parameters
path_strs – the structures along the path
- schrodinger.application.jaguar.autots_rmsd.order_atoms(reactant: schrodinger.structure._structure.Structure, product: List[schrodinger.structure._structure.Structure], debug: bool = False) Tuple[schrodinger.structure._structure.Structure, schrodinger.structure._structure.Structure] ¶
Renumber atoms in reactant and product in a consistent fashion.
- Parameters
reactant – reactant structure
product – reactant structure
debug – include debug printing
- Returns
renumbered reactant and product
- class schrodinger.application.jaguar.autots_rmsd.AutoTSAtomMapper(optimize_mapping: bool, use_chirality: bool, debug: bool = False)¶
Bases:
schrodinger.comparison.atom_mapper.BaseAtomMapper
Atom mapper used by AutoTS for reordering atoms of conformers. Uses element types and optionally chirality to equate atoms and all bonds are considered equivalent. Stereochemistry on atoms which are marked with the property “i_user_AutoTS_Atom_Class” are ignored when comparing stereochemistry. This property is used to mark the atoms in the reaction center.
Usage example: mapper = AutoTSAtomMapper(optimize_mapping=True, use_chirality=False) st1, st2 = mapper.reorder_atoms(st1, range(1, st1.atom_total + 1), st2, range(st2.atom_total + 1))
- RMSD_THRESH = 1e-08¶
- __init__(optimize_mapping: bool, use_chirality: bool, debug: bool = False)¶
- Parameters
optimize_mapping – if True search over all bijections to find the one with the lowest score
use_chirality – if True, in addition to element type use chirality (where defined) to equate atoms.
- initialize_atom_types(st: schrodinger.structure._structure.Structure, invert_stereocenters: bool = False)¶
Initialize the atom types
- Parameters
st – structure containing atoms
invert_stereocenters – whether R/S labels should be flipped
- reorder_structures(st1, atlist1, st2, atlist2)¶
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_mapping(st1: schrodinger.structure._structure.Structure, st2: schrodinger.structure._structure.Structure, atset: Set[int]) Tuple[int, int, int, int, float] ¶
Score a mapping over the atoms listed in atlist. This returns a number of chirality mis-alignments and the rms mis-alignments are neglected for atoms which are marked with atom property “i_user_AutoTS_Atom_Class”
- Parameters
st1 – first structure
st2 – second structure
atset – set of atoms that have been mapped (indexes refer to both structures)
- Returns
the negative of the number of active bonds, the number of misaligned atom-numbering stereocenters, the negative of the number of active atoms, the number of separate components, and the rmsd
- score_is_equivalent(score1: schrodinger.application.jaguar.autots_rmsd.MapScore, score2: schrodinger.application.jaguar.autots_rmsd.MapScore) bool ¶
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 discrepancies in the chosen map.
- Parameters
score1 – the first score (chirality mismatches, active atoms, rms)
score2 – the first score (chirality mismatches, active atoms, rms)
- Returns
boolean indicating if the score is the same or different
- determine_active_bonds_info(st1: schrodinger.structure._structure.Structure, st2: schrodinger.structure._structure.Structure, atlist: List[int]) Tuple[int, int] ¶
Determine the number of active bonds after numbering and the number of components.
It is possible for the numbering code to “deactivate” an active bond and such numbering should be considered invalid. The way this might happen is for the numbering to lead to two active bonds to be numbered equivalently. Say you have a reactant water with an O-H active and a product water with an O-H active (for example, in a water wire). The numbering code could decide to number both of these O’s the same and both H’s the same. Thus, the code thinks it has both O-H’s active but, in reality, now neither are because the equivalently numbered atoms have bonds in both reactant and product.
The active bonds have been stored as a binary vector (i.e. an int). An active bond destroying numbering will have the same two atom numbers as the endpoint of more than one active bond.
We define the number of ‘components’ as the number of disjoint sets of molecules that are involved in active bonds. That is, if all active bonds in reactants and products were drawn in one structure, how many “molecules” would there be? For example, it is possible to number a set of bonds in the reaction A+B+C+D -> E+F, where A+B->E and C+D->F or one in which atoms from all 4 reactant molecules appear among all 2 of the products. The former case is a 2-component reaction (consisting of (A, B, E) and (C, D, F)) and the latter is a 1-component reaction (A, B, C, D, E ,F). We assume that the user put in an irreducible reaction, and hence fewer component renumbered solutions are to be preferred.
- Parameters
st1 – first structure
st2 – second structure
atlist – list of atoms that have been mapped (indexes refer to both structures)
- Returns
number of active bonds from this numbering, number of components
- class schrodinger.application.jaguar.autots_rmsd.AutoTSTemplateAtomMapper(optimize_mapping: bool, use_chirality: bool, debug: bool = False)¶
Bases:
schrodinger.application.jaguar.autots_rmsd.AutoTSAtomMapper
Atom mapper used by AutoTS’s template code for reordering atoms to align template and input. Uses element types to equate atoms and all bonds are considered equivalent. Stereochemistry on atoms which are marked with the property “i_user_AutoTS_Atom_Class” are ignored when comparing stereochemistry.
This differs from the AutoTSAtomMapper in that it simultaneously renumbers 4 structures instead of 2, assuming two pairs of those structures are already consistently numbered. Moreover, the return value of this class is the optimal map that accomplishes the renumbering, as opposed to the renumbered Structures themselves.
Usage example: mapper = AutoTSTemplateAtomMapper(optimize_mapping=True, use_chirality=False) map = mapper.choose_template_map(reactant, product, input_indexes, r_template, p_template, template_indexes)
- RMSD_THRESH = 1e-08¶
- initialize_atom_types(st: schrodinger.structure._structure.Structure, active_ats: List[int], invert_stereocenters: bool = False)¶
Initialize the atom types
- Parameters
st – structure containing atoms
active_ats – atom indices of the reaction center
invert_stereocenters – whether R/S labels should be flipped
- score_mapping(st1: schrodinger.structure._structure.Structure, st2: schrodinger.structure._structure.Structure, st3: schrodinger.structure._structure.Structure, st4: schrodinger.structure._structure.Structure, atset: Set[int]) Tuple[int, int, int, int, float] ¶
Score a mapping over the atoms listed in atlist. This returns a number of chirality mis-alignments and the rms mis-alignments are neglected for atoms which are marked with atom property “i_user_AutoTS_Atom_Class”
- Parameters
st1 – first structure (reactant)
st2 – second structure (reactant)
st3 – first structure (product)
st4 – second structure (product)
atset – set of atoms that have been mapped (indexes refer to both structures)
- Returns
the negative of the number of active bonds, the number of misaligned atom-numbering stereocenters, the negative of the number of active atoms, the number of separate components, and the rmsd
- choose_template_map(reactant: schrodinger.structure._structure.Structure, product: schrodinger.structure._structure.Structure, input_indexes, r_template: schrodinger.structure._structure.Structure, p_template: schrodinger.structure._structure.Structure, template_indexes) dict ¶
Determine the optimal map from the input reactant and product structures to the template reactant and product structures.
- Parameters
reactant – input reactant structure
product – input product structure
input_indexes (RxnIndxDecomp instance) – breakdown of input atom indexes into core, reaction center
r_template – template reactant structure
p_template – template product structure
template_indexes (RxnIndxDecomp instance) – breakdown of template atom indexes into core, reaction center
- Returns
mapping from input number to template numbering