schrodinger.comparison.comparison module¶
Answers to the question of ‘are these two structures the same?’ using various definitions of ‘the same’
- schrodinger.comparison.comparison.are_isomers(st1, st2)[source]¶
Determines if the two structures are isomers (same number of each type of element)
- schrodinger.comparison.comparison.are_conformers(st1, st2, use_lewis_structure=True, use_stereo=False)[source]¶
Determines if the two structures are conformers (atom order independent). This does not make any assumptions about atom ordering being initially correct and, if that is your case this may not be the appropriate tool.
- Parameters
st1 (Structure) – the first structure
st2 (Structure) – the second structure
use_lewis_structure (bool) – if True, use atomic symbol, formal charge and bond orders to define equivalence of atoms, else use only atomic symbol. The former definition is more traditional whereas the latter only requires consistent connectivity
use_stereo (bool) – if True also use atomic stereochemical labels generated by mmstereo to equate atoms. This includes E/Z labels but excludes the labels ANR, ANS. i.e. answer the question of whether these structures are stereoisomers
- Returns
bool
- schrodinger.comparison.comparison.are_tautomers(st1, st2, use_stereo=False)[source]¶
Determines if the two structures are tautomers by inspecting if the heavy atom connectivity is the same. Here, the definition of the same uses connectivity only, it is not assumed bond orders are the same. This does not make any assumptions about atom ordering being initially correct and, if that is your case this may not be the appropriate tool.
We remove hydrogens that are connected to atoms that are not chiral centers. This is to avoid hydrogen atoms, which are ignored in this procedure, from causing symmetry-breaking at remote heavy atom sites. We leave H’s directly attached to chiral centers effectively as dummy atoms to ensure that chirality of the remaining three substituents is computed.
- schrodinger.comparison.comparison.are_heavy_atom_conformers(st1, st2, use_stereo=False)[source]¶
Determines if the two structures are heavy-atom conformers (i.e. if, ignoring hydrogens, they are conformers) by inspecting if the heavy atom connectivity is the same. We do not check that the strucutres are isomers, so differently protonated forms (e.g. H2O and -OH and H3O+ would all be considered heavy-atom conformers). Here, the definition of the same uses connectivity only, it is not assumed bond orders are the same. This does not make any assumptions about atom ordering being initially correct and, if that is your case this may not be the appropriate tool.
We remove hydrogens that are connected to atoms that are not chiral centers. This is to avoid hydrogen atoms, which are ignored in this procedure, from causing symmetry-breaking at remote heavy atom sites. We leave H’s directly attached to chiral centers effectively as dummy atoms to ensure that chirality of the remaining three substituents is computed.
- schrodinger.comparison.comparison.are_stereoisomers(st1, st2, use_lewis_structure=True)[source]¶
Determines if the two structures are stereoisomers (atom order independent). A molecule is not a stereoisomer of itself, i.e. are_stereoisomers(st, st)==False This does not make any assumptions about atom ordering being initially correct and, if that is your case this may not be the appropriate tool.
- Parameters
st1 (Structure) – the first structure
st2 (Structure) – the second structure
use_lewis_structure (bool) – if True, use atomic symbol, formal charge and bond orders to define equivalence of atoms, else use only atomic symbol. The former definition is more traditional whereas the latter only requires consistent connectivity
- Returns
bool
- schrodinger.comparison.comparison.are_enantiomers(st1, st2, use_lewis_structure=True)[source]¶
Determines if the two structures are enantiomers (atom order independent). This does not make any assumptions about atom ordering being initially correct and, if that is your case this may not be the appropriate tool.
- Parameters
st1 (Structure) – the first structure
st2 (Structure) – the second structure
use_lewis_structure (bool) – if True, use atomic symbol, formal charge and bond orders to define equivalence of atoms, else use only atomic symbol. The former definition is more traditional whereas the latter only requires consistent connectivity
- Returns
bool
- schrodinger.comparison.comparison.are_diastereomers(st1, st2, use_lewis_structure=True)[source]¶
Determines if the two structures are diastereomers (atom order independent). This does not make any assumptions about atom ordering being initially correct and, if that is your case this may not be the appropriate tool.
- Parameters
st1 (Structure) – the first structure
st2 (Structure) – the second structure
use_lewis_structure (bool) – if True, use atomic symbol, formal charge and bond orders to define equivalence of atoms, else use only atomic symbol. The former definition is more traditional whereas the latter only requires consistent connectivity
- Returns
bool
- schrodinger.comparison.comparison.are_same_geometry(st1, st2, rms_thresh=0.25)[source]¶
Determines if two structures are conformers with the same geometry. Assumes that structures are already consistently numbered.
- Parameters
st1 (Structure) – the first structure
st2 (Structure) – the second structure
use_lewis_structure (bool) – if True, use atomic symbol, formal charge and bond orders to define equivalence of atoms, else use only atomic symbol. The former definition is more traditional whereas the latter only requires consistent connectivity
rms_thresh – Threshold for RMSD to be considered the same geometry
- Returns
bool