System and method for identifying structures for a chemical compound
Embodiments of the present invention provide a system and method for determining the structures of a chemical compound. Generally, embodiments of the present invention can provide a computer executable program that, for a given compound, can derive any number of additional structures for the compound from an input structure. The additional structures can include all proto-stereomers, or any subset thereof, of the compound (i.e., all or a set of stereomers for all or a set of protomers). The proto-stereomers can be determined based on all the protomers for the compound, a plausible set of protomers or any subset of the protomers for the compound.
1 . Method for identifying structures of a chemical compound comprising:
identifying proto-centers of a structure from a representation of the structure, wherein the representation of the structure contains structural information for the structure;
identifying a set of protomers for further processing;
enumerating structural information for each protomer from the set of protomers for further processing;
identifying any invertible and proto-invertible centers for each protomer from structural information associated with each protomer; and
enumerating one or more proto-stereomers for each protomer identified for further processing based on the identified invertible and proto-invertible centers.
2 . The method of claim 1 , wherein identifying proto-centers further comprises identifying one or more acidic atoms.
3 . The method of claim 1 , wherein identifying proto-centers further comprises identifying one or more basic atoms.
4 . The method of claim 1 , wherein identifying proto-centers further comprises identifying one or more potential proton-donor/proton-acceptor pairs.
5 . The method of claim 1 , wherein identifying proto-centers further comprises identifying on ore or more true proton-donor/proton-acceptor pairs.
6 . The method of claim 1 , wherein identifying a set of protomers for further processing, comprises identifying one or more plausible protomers for further processing.
7 . The method of claim 6 , wherein identifying one or more plausible protomers for further processing comprises applying one or more plausibility rules.
8 . The method of claim 1 , wherein identifying proto-invertible centers further comprises identifying one or more proto-invertible chiral atoms.
9 . The method of claim 1 , wherein identifying proto-invertible centers further comprises identifying on or more proto-invertible chiral bonds.
10 . The method of claim 1 , wherein enumerating one or more proto-stereomers for each protomer further comprises, for each protomer:
enumerating the left hand state and right hand state for each proto-invertible chiral atom; and
enumerating E and Z state for each proto-invertible chiral bond.
11 . A computer program product for identifying structures of a chemical compound comprising a computer readable medium storing a set of computer instructions, wherein the set of computer instructions comprise instructions executable to:
identify proto-centers of a structure from a representation of the structure, wherein the representation of the structure contains structural information for the structure;
identify a set of protomers for further processing;
enumerate structural information for each protomer from the set of protomers for further processing;
identify any invertible and proto-invertible centers for each protomer from structural information associated with each protomer;
enumerate one or more proto-stereomers for each protomer identified for further processing based on the identified invertible and proto-invertible centers.
12 . The computer program product of claim 11 , wherein identifying proto-centers further comprises identifying one or more acidic atoms.
13 . The computer program product of claim 11 , wherein identifying proto-centers further comprises identifying one or more basic atoms.
14 . The computer program product of claim 11 , wherein identifying proto-centers further comprises identifying one or more potential proton-donor/proton-acceptor pairs.
15 . The computer program product of claim 11 , wherein identifying proto-centers further comprises identifying on ore or more true proton-donor/proton-acceptor pairs.
16 . The computer program product of claim 11 , wherein identifying a set of protomers for further processing, comprises identifying one or more plausible protomers for further processing.
17 . The computer program product of claim 16 , wherein identifying one or more plausible protomers for further processing comprises applying one or more plausibility rules.
18 . The computer program product of claim 11 , wherein identifying proto-invertible centers further comprises identifying one or more proto-invertible chiral atoms.
19 . The computer program product of claim 11 , wherein identifying proto-invertible centers further comprises identifying on or more proto-invertible chiral bonds.
20 . The computer program product of claim 11 , wherein enumerating one or more proto-stereomers for each protomer further comprises, for each protomer:
enumerating the left hand state and right hand state for each proto-invertible chiral atom; and
enumerating E and Z state for each proto-invertible chiral bond.
21 . A method of identifying structures of a chemical compound, comprising:
identifying a protomer for further processing based on structural information for an input structure;
identifying at least one invertible or proto-invertible center for the protomer from structural information associated with the protomer;
enumerating one or more stereomers for the protomer based on the at least one invertible or proto-invertible center for the protomer.
22 . The method of claim 21 , further comprising identifying at least one proto-center from the structural information for the input structure.
23 . The method of claim 21 , wherein the protomer is a plausible protomer based on one or plausibility rules.
24 . The method of claim 21 , wherein identifying the at least one invertible or proto-invertible center for the protomer comprises identifying an invertible or proto-invertible chiral atom.
25 . The method of claim 24 , wherein enumerating one or more stereomers further comprises:
enumerating a stereomer with a right hand (R) state for the invertible or proto-invertible chiral atom; and
enumerating a stereomer with a left hand (S) state for the invertible or proto-invertible chiral atom.
26 . The method of claim 25 , wherein enumerating the one or more stereomers for the protomer further comprises:
enumerating a stereomer with the proto-invertible chiral bond in a Z state; and
enumerating a stereomer with the proto-invertible chiral bond in an E state.
27 . A computer program product for identifying structures of a chemical compound comprising a set of computer instructions on a computer readable medium, wherein the set of computer instructions are executable to:
identify a protomer for further processing based on structural information for an input structure;
identify at least one invertible or proto-invertible center for the protomer from structural information associated with the protomer;
enumerate one or more proto-stereomers for the protomer based on the at least one invertible or proto-invertible center for the protomer.
28 . The computer program product of claim 27 , further comprising identifying at least one proto-center from the structural information for the input structure.
29 . The computer program product of claim 27 , wherein the protomer is a plausible protomer based on one or plausibility rules.
30 . The computer program product of claim 27 , wherein identifying the at least one invertible or proto-invertible center for the protomer comprises identifying an invertible or proto-invertible chiral atom.
31 . The computer program product of claim 30 , wherein enumerating on or more stereomers further comprises:
enumerating a stereomer with a right hand state for the invertible or proto-invertible chiral atom; and
enumerating a stereomer with a left hand state for the invertible or proto-invertible chiral atom.
32 . The computer program product of claim 27 , wherein identifying the at least one invertible or proto-invertible center for the protomer comprises identifying a invertible or proto-invertible chiral atom.
33 . The computer program product of claim 32 , wherein enumerating the one or more proto-stereomers for the protomer further comprises: enumerating a stereomer with the proto-invertible chiral bond in a Z state; and
enumerating a stereomer with the proto-invertible chiral bond in an E state.
34 . A method for identifying structures of a chemical compound comprising:
receiving structural information for an input structure of a chemical compound;
identifying one or more acidic/basic atoms from the structural information;
identifying one or more true proton-donor/proton-acceptor pairs;
determining a set of plausible protomers for the chemical compound based on the acidic/basic atoms and true proton-donor/proton-acceptor pairs identified and a set of plausibility rules;
enumerating structural information for the set of plausible protomers;
identifying any invertible centers and proto-invertible centers for each of the set of plausible protomers; and
enumerating one or more proto-stereomers for each protomer of the set of plausible protomers based on the identified invertible centers and proto-invertible centers.
35 . The method of claim 34 , wherein the one or more proto-invertible centers comprise proto-invertible chiral atoms.
36 . The method of claim 34 , wherein the one or more proto-invertible centers comprise proto-invertible chiral bonds.
37 . The method of claim 34 , further comprising enumerating the set of stereomers for the protomer based on the one or more proto-invertible centers identified for that protomer from the set of plausible protomers.