CN110379467B - Chemical molecular formula segmentation method - Google Patents
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Abstract
The invention discloses a chemical molecular formula segmentation method, which is implemented on the basis of a molecular formula graph structure, namely, a certain group of a molecular formula is cut off by using a specific type of chemical reaction, the segmentation simulates a sub-process in the chemical reaction, and in the real chemical reaction, a compound which has undergone the chemical reaction is cut off partially and then is combined with other compounds to form a new compound. The invention realizes the segmentation of molecular formula on the graph structure of atoms and chemical bonds, has strong operation flexibility and strong customizability, and is suitable for the segmentation of various situations. And finding out which branches on which atoms in the chemical formula to be split are to be split and which branches are to be reserved according to the reaction type string representing the reaction type in the chemical formula to be split and the atom mapping relation between the reaction type strings representing the conversion type in the chemical formula to be split, so as to realize correct splitting.
Description
Technical Field
The invention belongs to the technical field of compound synthesis, and particularly relates to a chemical molecular formula segmentation method.
Background
In the process of compound synthesis, reagent molecules with protecting groups are subjected to deprotection and mutual reaction to obtain a new compound. From a chemical point of view, both steps are chemical reactions; from the computational point of view, the chemical reaction of molecule deprotection is the "site cleavage" of the molecule, resulting in sites that can react (link) with other molecules, and then the reaction is the "site splicing" between molecules, linking the sites that can undergo chemical reaction, resulting in new compounds.
The current way of calculation is to record the molecules with sites obtained in the first step, to distinguish and label the sites obtained from different reactions, such as the site obtained from reaction type 1 is labeled as [ R1], the site position is the position of the atom of the molecule which is removed part of the reaction, then to splice the molecules with the same site label, such as two molecules with [ R1] can be spliced.
The current computational chemistry tools such as Openbabel, RdKit, etc. are segmented by simulating a real chemical reaction process, i.e. inputting a compound to be reacted to obtain the reacted compound.
Disclosure of Invention
The invention aims to overcome the defects of the prior art, and realizes a segmentation method on the basis of a graph structure of a molecular formula, namely, a certain group of the molecular formula is cut off by using a specific type of chemical reaction, the segmentation simulates a sub-process in the chemical reaction, and in the real chemical reaction, a compound which has undergone the chemical reaction is partially cut off and then is combined with other compounds to form a new compound. In the application scenario of compound synthesis through a large number of reagent molecules, molecular formula segmentation is an inherent sub-link, and reagent molecules are firstly bound with other compounds after a certain group is removed after the fixed group is removed.
The purpose of the invention is realized by the following technical scheme: a chemical molecular formula segmentation method is characterized in that for a molecular formula smi with or without sites, the sites in the molecular formula are marked as [ Ri ], i is 0,1 … N, [ Ri ] corresponds to a certain reaction type, and N is the total number of the reaction types;
for a Reaction type Reaction, defining a Reaction type string smi _ sub and a conversion type string smi _ convert, wherein if a substring of smi _ sub exists in smi, the substring is partially converted into the smi _ convert; the smi _ sub substring comprises at least one site [ Ri ] connected with the rest part of the smi, the smi _ covert comprises the same site [ Ri ] at the corresponding position, the smi _ covert also comprises atoms to be cut off, and the cutting process is as follows:
(1) and reading smi and smi _ sub, converting the smi and smi _ sub into a graph structure mol and a mol _ sub, generating an atom mapping relation table maplist2 from the mol _ sub to the mol, and if the mol _ sub substructure does not exist in the mol, not performing segmentation. If there are multiple mol _ sub substructures in mol, then multiple mappings are saved in maplist 2. And during mapping, whether the atom corresponding to the connecting site meets the limitation of the [ Ri ] type in the smi _ sub is considered, and if not, the mapping fails. The position of the attachment site [ Ri ] is saved when smi _ sub is read in.
(2) And reading smi _ convert, converting the smi _ convert into a graph structure mol _ convert, generating an atom mapping relation table maplist1 from mol _ convert to mol _ sub, finding the position cut _ idx of the cut atom [ ], and finding the position cut _ connect _ idx of the atom connected with the cut atom [ ]. For each atom in mol _ convert, when no corresponding atom can be found in mol _ sub, the mapping atom position of the atom is represented by-1.
(3) For each mapping relation in maplist2, a segmentation result is obtained:
(3.1) adding the mol and mol _ sub to obtain the updated mol.
(3.2) judging whether the mapping relation can cause the ring structure in the mol to be cut off, if so, skipping the mapping relation, and executing the next mapping relation, otherwise, executing the step 3.3.
(3.3) through the mapping relation, collecting the position mapped to the atom which is not cut off in mol, namely the position corresponding to the element of > -1 in maplist1, and storing the position in not _ cut _ idxs.
And collecting the atom which is mapped to the atom which is connected with the cut atom [ ] in the mol, namely the atom corresponding to cut _ connection _ idx, and storing the atom to cut _ connection _ idxs.
The positions of all the excised atoms mapped to mol, namely the positions corresponding to the elements with the value of-1 in maplist1 are collected and stored in cut _ idxs, and for the atoms at the positions of the cut points, the atoms which are not in the not _ cut _ idxs in the adjacent atoms are stored in the cut _ idxs. Each excision location maintains a cut _ idxs list, which is empty if the location cannot find the corresponding atom in mol.
And for cut _ idxs of each cutting position, if the position is empty, cutting a hydrogen atom on the position, and if the position does not have a hydrogen atom, skipping the cutting of the mapping relation and executing the next mapping relation. If not, atoms to be cut off at the position are collected, including the atom at the position and the atoms adjacent to the atom but not in cut _ connect _ idxs, and the adjacent atoms of the adjacent atoms at the position are recursively collected.
The positions of the atoms to be cut in mol, namely those atoms in cut _ connect _ idx, are collected, including the atom at the position and the atoms adjacent to the position but not in cut _ connect _ idx and cut _ idx, the atoms have new positions in new mol, and the adjacent atoms of the adjacent atoms at the position are collected recursively.
(3.4) linking atom: the corresponding atoms in cut _ connect _ idxs and cut _ idx are connected by chemical bonds.
(3.5) copy key attribute: copy bond attributes from mol _ sub to the newly added bond in mol. Newly added atoms, namely atoms at two ends of the newly added bond are collected.
(3.6) updating the \ and/or spatial attributes of the double bond: if mol contains the atom to be cut out in the spatial attribute structure, the spatial attribute needs to be updated. Atoms at two ends of the double bond and atoms connected with the atoms are stored in the double bond space attribute structure, and if bonds exist between the atoms at two ends in the double bond space attribute structure and the newly added atoms in the previous step, the corresponding atoms in the structure are replaced by the newly added atoms.
And (3.7) cutting the collected atoms to be cut off.
(3.8) outputting a sliced molecule of mapplist 2 mapping relation.
Further, according to the characteristics of each reaction type, some limitation is made on the atom type represented by the site [ Ri ] in the reaction type string smi _ sub, namely some limitation is made on the type of atom [ Ri ] corresponding to the molecular formula to be cut, including that the site [ Ri ] cannot be a hydrogen atom (H), or can only be C, N, O atoms, or can be any atom, and the limitation is in accordance with the SMARTS specification.
Further, in the step (1), the formula format read in is Canonical SMILES, and the input in other formats is converted into the format.
Further, in the step (1), whether the atom corresponding to the connecting site satisfies the limitation of the [ Ri ] type in smi _ sub is considered during mapping, and if not, the mapping fails.
Further, in the step (3.2), determining whether the mapping relationship may cause the ring structure in mol to be cut, that is, determining whether mol _ sub is mapped to a part of the ring structure in mol, specifically: the corresponding atom A of the to-be-cut site [ Ri ] in mol is found through the mapping relationship in maplist2, if A has an adjacent atom A _ neighbor not in the list to be cut off and A _ neighbor is on the ring, the ring will be cut.
Further, in the step (3.5), the bond attribute is copied from the mol _ sub to the newly added bond in the mol, that is, atoms at both ends of each bond in the mol _ sub are found, two corresponding atoms in the mol are found, and the bond attribute between the two atoms is updated to the attribute value of the corresponding bond in the mol _ sub.
The invention has the beneficial effects that: the invention realizes the segmentation of molecular formula on the graph structure of atoms and chemical bonds, has strong operation flexibility and strong customizability, and is suitable for the segmentation of various situations. And finding out which branches on which atoms in the chemical formula to be split are to be split and which branches are to be reserved according to the reaction type string representing the reaction type in the chemical formula to be split and the atom mapping relation between the reaction type strings representing the conversion type in the chemical formula to be split, so as to realize correct splitting.
Drawings
FIG. 1 is a flow chart of the method of the present invention;
fig. 2 is a slicing example of the present invention.
Detailed Description
In order to make the objects, technical solutions and advantages of the present invention more apparent, the present invention is described in further detail below with reference to the accompanying drawings and embodiments. It should be understood that the specific embodiments described herein are merely illustrative of the invention and are not intended to limit the invention.
The invention provides a chemical molecular formula segmentation method which comprises the following specific steps:
for a molecular formula smi with or without a site (assuming that the input format is Canonical SMILES, other formats of inputs can be converted into the format), the site in the molecular formula is marked as [ Ri ], i is 0,1 … N, [ Ri ] corresponds to a certain reaction type and is obtained by carrying out a chemical reaction of the reaction type by using reagent molecules, and N is the total number of the reaction types;
for a Reaction type Reaction, defining a Reaction type string smi _ sub and a conversion type string smi _ convert, wherein if a substring of smi _ sub exists in smi, the substring is partially converted into the smi _ convert. The smi _ sub substring comprises at least one site [ Ri ] connected with the rest of the smi, the smi _ convert has the same site [ Ri ] at the corresponding position, and the smi _ convert also comprises atoms [ star ] to be cut. In particular, according to the characteristics of each reaction type, some limitations are made on the type of atom represented by the site [ Ri ] in the reaction type string smi _ sub, i.e. the type of atom [ Ri ] corresponding to the formula to be cut is limited, for example, the site [ Ri ] cannot be a hydrogen atom (H), or can only be C, N, O atoms, or can be any atom, and the specific limitation treatment is mainly in accordance with the smart specification. The cutting process is as follows:
1. and reading in smi and smi _ sub, converting the smi and smi _ sub into a graph structure mol and mol _ sub, generating an atom mapping relation table maplist2 from mol _ sub to mol, and if the mol _ sub substructure does not exist in the mol, not cutting the molecular formula smi, so that the molecular formula smi can not generate the chemical Reaction of the Reaction type Reaction. If there are more than one mol _ sub-structure in mol, then there are more than one mapping in maplist2, indicating that there are more than one group of formula smi that can undergo this type of chemical reaction. And during mapping, whether the atom corresponding to the connecting site meets the limitation of the [ Ri ] type in smi _ sub is considered, and if not, the mapping fails.
The position of the attachment site [ Ri ] is saved when smi _ sub is read in.
2. Reading smi _ convert, converting into a graph structure mol _ convert, generating an atom mapping relation table maplist1 from mol _ convert to mol _ sub, finding the position cut _ idx of the cut atom [ ] and finding the position cut _ connect _ idx of the atom connected with the cut atom [ ]. For each atom in mol _ convert, the mapped atom position of the atom is represented by-1 when the corresponding atom cannot be found in mol _ sub due to being cut out or replaced by a longer substring in maplist 1.
3. For each mapping relation in maplist2, a segmentation result is obtained:
3.1. and adding the mol and the mol _ sub, namely stacking the data structures of the mol and the mol _ sub to obtain the updated mol.
3.2. Judging whether the mapping relation can cause the ring structure in the mol to be cut off, if so, skipping the mapping relation, and executing the next mapping relation, otherwise, executing the step 3.3; judging whether the mapping relation can cause the ring structure in mol to be cut, that is, judging whether mol _ sub is mapped to a part of the ring structure in mol, specifically: the corresponding atom A of the to-be-cut site [ Ri ] in mol is found through the mapping relationship in maplist2, if A has an adjacent atom A _ neighbor not in the list to be cut off and A _ neighbor is on the ring, the ring will be cut.
3.3. Through the mapping relation, the position of the atom which is mapped to the non-excision in the mol, namely the position corresponding to the element of > -1 in maplist1 is collected and stored in the not _ cut _ idxs.
And collecting the atom which is mapped to the atom which is connected with the cut atom [ ] in the mol, namely the atom corresponding to cut _ connection _ idx, and storing the atom to cut _ connection _ idxs.
The positions of all the excised atoms mapped to mol, namely the positions corresponding to the elements of-1 in maplist1, are collected and stored to cut _ idxs, and for the atoms at the positions of the cut points, the atoms which are not in not _ cut _ idxs in the adjacent atoms are stored to cut _ idxs, and the atoms are also to be excised because the atoms do not exist in the conversion string. Each excision location maintains a cut _ idxs list, which is empty if the location cannot find the corresponding atom in mol.
And for cut _ idxs of each cutting position, if the position is empty, cutting a hydrogen atom on the position, and if the position does not have a hydrogen atom, skipping the cutting of the mapping relation and executing the next mapping relation. If not, atoms to be cut off at the position are collected, including the atom at the position and the atoms adjacent to the atom and not in cut _ connect _ idxs, and the adjacent atoms of the adjacent atoms at the position are recursively collected.
Positions of atoms to be cut out in mol, namely those atoms in cut _ connect _ idx, are collected, the atoms of the positions are included and atoms adjacent to the positions but not in cut _ connect _ idx and cut _ idx, the atoms have new positions in new mol, and adjacent atoms of the positions are recursively collected.
3.4. A linking atom: the corresponding atoms in cut _ connect _ idxs and cut _ idx are connected by chemical bonds.
3.5. Copy key attribute: and copying the bond attribute from the mol _ sub to the newly added bond in the mol, namely finding atoms at two ends of each bond in the mol _ sub, finding two corresponding atoms in the mol, and updating the bond attribute between the two atoms into the attribute value of the corresponding bond in the mol _ sub. Newly added atoms are collected, namely atoms at two ends of the newly added bond.
3.6. Updating \ and/or spatial attributes of the double bonds: since the spatial attributes are stored separately, separate processing is required, and if the spatial attribute structure of mol contains atoms to be cut, the spatial attributes need to be updated. Atoms at two ends of the double bond and atoms connected with the atoms are stored in the double bond space attribute structure, and if bonds exist between the atoms at two ends in the double bond space attribute structure and the newly added atoms in the previous step, the corresponding atoms in the structure are replaced by the newly added atoms.
3.7. And cutting the collected atoms to be cut off.
3.8. And outputting a sliced molecule of the maplist2 mapping relation, namely converting mol into the Canonical SMILES format.
An example of the segmentation is as follows: as shown in FIG. 2, (a), (b), (c) and (d) are sequentially as follows: reaction type, conversion type, molecular formula to be cut and final result of cutting, wherein Xx is [. multidot. ] atom, and S is [ R ] atom; the corresponding chemical formula is as follows:
[S]C＝C
[S]C([*])C[*]
CCOC(＝O)/C＝C/C(O)＝O
CCOC(＝O)C(C(C(＝O)O)[*])[*]
the atom mapping table maplist1 of mol _ convert (2 nd formula) to mol _ sub (1 st formula) is {0,1, -1,2, -1 }.
It should be noted that the summary and the detailed description of the invention are intended to demonstrate the practical application of the technical solutions provided by the present invention, and should not be construed as limiting the scope of the present invention. Any modifications and variations of the present invention, which fall within the spirit of the present invention and the scope of the appended claims, are also included.
Claims (6)
1. A chemical molecular formula splitting method is characterized in that for a molecular formula smi with or without sites, the sites in the molecular formula are marked as [ Ri ], i is 0,1 … N, [ Ri ] corresponds to a certain reaction type, and N is the total number of the reaction types;
for a Reaction type Reaction, defining a Reaction type string smi _ sub and a conversion type string smi _ convert, wherein if a substring of smi _ sub exists in smi, the substring is partially converted into the smi _ convert; the smi _ sub substring comprises at least one site [ Ri ] connected with the rest part of the smi, the smi _ covert comprises the same site [ Ri ] at the corresponding position, the smi _ covert also comprises atoms to be cut off, and the cutting process is as follows:
(1) reading smi and smi _ sub, converting the smi _ sub into a graph structure mol and a graph structure mol _ sub, generating an atom mapping relation table maplist2 from the mol _ sub to the mol, and if the mol _ sub substructure does not exist in the mol, not performing segmentation; if a plurality of mol _ sub substructures exist in the mol, a plurality of mapping relations are stored in the maplist 2; whether atoms corresponding to the connection sites meet the limitation of the [ Ri ] type in the smi _ sub is considered during mapping, and if not, the mapping fails; when smi _ sub is read in, the position of the connection site [ Ri ] is saved;
(2) reading smi _ convert, converting the smi _ convert into a graph structure mol _ convert, generating an atom mapping relation table maplist1 from mol _ convert to mol _ sub, finding the position cut _ idx of the cut atom [ ], and finding the position cut _ connect _ idx of the atom connected with the cut atom [ ]; for each atom in mol _ convert, when the corresponding atom cannot be found in mol _ sub, representing the mapping atom position of the atom by-1;
(3) for each mapping relation in maplist2, a segmentation result is obtained:
(3.1) adding the mol and the mol _ sub to obtain updated mol;
(3.2) judging whether the mapping relation can cause the ring structure in the mol to be cut, if so, skipping the mapping relation, and executing the next mapping relation, otherwise, executing the step 3.3;
(3.3) collecting the positions of atoms which are mapped to the non-excision in the mol, namely the positions corresponding to the elements of > -1 in maplist1, and storing the positions to the not _ cut _ idxs through the mapping relation;
collecting and mapping the position of the atom connected with the cut atom [ ] in the mol, namely the atom corresponding to cut _ connect _ idx, and storing the atom to cut _ connect _ idxs;
collecting positions of all cut atoms mapped to mol, namely positions corresponding to elements which are-1 in maplist1, and storing the cut atoms to cut _ idxs, and storing atoms which are not in the not _ cut _ idxs in adjacent atoms to the cut points to cut _ idxs; maintaining a cut _ idxs list at each excision position, and if the corresponding atom in the mol cannot be found at the position, the position list is empty;
for cut _ idxs of each cutting position, if the cut _ idxs is empty, cutting a hydrogen atom on the position, and if the position does not have the hydrogen atom, skipping the cutting of the mapping relation and executing the next mapping relation; if not, collecting atoms to be cut off at the position, including the atom at the position and the atoms adjacent to the atom and not in cut _ connect _ idxs, and recursively collecting adjacent atoms of the adjacent atoms at the position;
collecting the positions of atoms to be cut in mol, namely those atoms in cut _ connect _ idx, including the atoms of the positions and the atoms adjacent to the positions but not in cut _ connect _ idx and cut _ idx, wherein the atoms have new positions in new mol, and recursively collecting the adjacent atoms of the positions;
(3.4) linking atom: connecting cut _ connect _ idxs with corresponding atoms in cut _ idx by chemical bonds;
(3.5) copy key attribute: copying bond attributes from the mol _ sub to newly added bonds in the mol; newly added atoms are collected, namely atoms at two ends of a newly added bond;
(3.6) updating the \ and/or spatial attributes of the double bond: if the mol spatial attribute structure contains atoms to be cut, the spatial attribute needs to be updated; atoms at two ends of the double bond and atoms connected with the atoms are stored in the double bond space attribute structure, if bonds exist between the atoms at two ends in the double bond space attribute structure and the newly added atoms in the previous step, the corresponding atoms in the structure are replaced by the newly added atoms;
(3.7) cutting the collected atoms to be cut off;
(3.8) outputting a sliced molecule of mapplist 2 mapping relation.
2. The method for chemical formula splitting according to claim 1, characterized in that, according to the characteristics of each reaction type, the atom type represented by the site [ Ri ] in the reaction type string smi _ sub is defined, i.e. the type of atom [ Ri ] corresponding to the formula to be split is defined, including the site [ Ri ] being not hydrogen (H), only C, N, O atom, or being any atom, defined according to the smart specification.
3. The method according to claim 1, wherein in step (1), the formula is read in a format of Canonical SMILES, and the other format of the input is converted into the format.
4. The method for splitting chemical formula according to claim 1, wherein in step (1), the mapping is performed by considering whether the atoms corresponding to the connecting sites satisfy the restriction on the type of [ Ri ] in smi _ sub, and if not, the mapping fails.
5. The method for splitting chemical molecular formula according to claim 1, wherein in the step (3.2), it is determined whether the mapping relationship would result in the ring structure in mol being split, that is, it is determined whether mol _ sub maps to a part of the ring structure in mol, specifically: the corresponding atom A of the to-be-cut site [ Ri ] in mol is found through the mapping relationship in maplist2, if A has an adjacent atom A _ neighbor not in the list to be cut off and A _ neighbor is on the ring, the ring will be cut.
6. The method for splitting chemical formulas according to claim 1, wherein in the step (3.5), the bond attributes are copied from mosub to newly added bonds in mol, that is, atoms at two ends of each bond in mosub are found, two atoms corresponding to mol are found, and the bond attribute between the two atoms is updated to the attribute value of the corresponding bond in mosub.
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