CN110379467A - A kind of chemical molecular formula cutting method - Google Patents
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Abstract
The invention discloses a kind of chemical molecular formula cutting methods, cutting is realized on the basis of the graph structure of molecular formula, the a certain group of molecular formula is cut away with certain types of chemical reaction, cutting simulates a subprocess in chemical reaction, in true chemical reaction, the compound chemically reacted can be cut off a part, later in conjunction with other compounds, form new compound.The present invention atom, chemical bond graph structure on realize molecular formula cutting, operating flexibility is strong, and customizability is strong, suitable for the cutting for a variety of situations.Pass through the reaction type string in chemical formula to be slit with expression reaction type, and reaction type string indicates the atom map relationship between the reaction type string of translation type, finding which branch in chemical formula to be slit on which atom will cut off, which branch will retain, and realize correct cutting.
Description
Technical field
The invention belongs to compound synthesis technical field more particularly to a kind of chemical molecular formula cutting methods.
Background technique
In the process of compound synthesis, Deprotection, interreaction are carried out to the reagent molecule with blocking group
Obtain noval chemical compound.Chemically from the point of view of angle, the two steps are all chemical reactions；From the perspective of calculating, molecule is taken off
The chemical reaction of protecting group is molecule " site cutting ", obtains the site that (connection) can be reacted with other molecules, later mutually
Phase reaction is then intermolecular " site splicing ", and the site that can be chemically reacted is connected, noval chemical compound is obtained.
Current processing mode is that the molecule with site that the first step is obtained is recorded in calculating, and differential responses are obtained
The site separator arrived, the site-tag as reaction type 1 obtains is [R1], and the position, that is, molecule in site is sloughed in the reaction
Then the position of partial atom splices the molecule with same loci label, if two molecules all have [R1]
It can splice.
Current calculating chemical tools such as Openbabel, RdKit etc. are carried out by simulation true chemical reaction process
Cutting, that is, input compound to be reacted, the compound after being reacted.
Summary of the invention
In view of the above-mentioned deficiencies in the prior art, it is an object of the present invention to which the graph structure basis in molecular formula realizes a kind of cutting
Method, i.e., cut away a certain group of molecular formula with certain types of chemical reaction, and cutting simulates a son in chemical reaction
Process, true chemical reaction in, the compound chemically reacted can be cut off a part, later with other compound knots
It closes, forms new compound.Under the application scenarios for carrying out compound synthesis by a large amount of reagent molecules, molecular formula cutting is one
A intrinsic subring section, reagent molecule slough fixed group and first have to take off some group, could be in conjunction with other compounds.
The purpose of the present invention is achieved through the following technical solutions: a kind of chemical molecular formula cutting method, for one
It is a to be denoted as in the site in molecular formula [Ri], i=0,1 ... N with site or without the molecular formula smi in site, [Ri] corresponding Mr. Yu
One reaction type, N are the sum of reaction type；
To a kind of reaction type Reaction, a reaction type string smi_sub and translation type string smi_ are defined
Convert indicates that the substring is then partially converted to smi_convert if there is smi_sub substring in smi；smi_
Sub substring includes the site [Ri] that at least one connect with smi rest part, and smi_convert has identical in corresponding position
Site [Ri], smi_convert also include the atom to be cut off [*], and dicing process is as follows:
(1) smi and smi_sub is read in, graph structure mol and mol_sub are switched to, generates the atom map of mol_sub to mol
Relation table maplist2, if mol_sub minor structure is not present in mol, no longer progress cutting.If there are multiple in mol
Mol_sub minor structure then saves multiple mapping relations in maplist2.Consider whether the corresponding atom of connection site is full when mapping
Failure is mapped if being unsatisfactory for the restriction of [Ri] type in sufficient smi_sub.When reading in smi_sub, connection site is saved
The position of [Ri].
(2) smi_convert is read in, graph structure mol_convert is switched to, generates the original of mol_convert to mol_sub
Sub- mapping table maplist1 finds the position cut_idx of excision atom [*], finds the atom of excision atom [*] connection
Position cut_connect_idx.For each atom in mol_convert, the corresponding atomic time can not find in mol_sub,
The mapping atom site for indicating the atom with -1.
(3) to each of maplist2 mapping relations, a cutting result is obtained:
(3.1) mol is added with mol_sub, obtains updated mol.
(3.2) cyclic structure for judging whether the mapping relations will lead in mol is cut open, if it is, skipping this
Mapping relations execute next mapping relations, otherwise, execute step 3.3.
(3.3) by the mapping relations, collect the position for being mapped to the atom not cut off in mol, i.e. in maplist1 > -1
The corresponding position of element, be stored in not_cut_idxs.
Collection is mapped to the position that the atom of atom [*] connection is cut off in mol, the i.e. corresponding original of cut_connect_idx
Son is stored in cut_connect_idxs.
Collect the position of complete resection atom being mapped in mol, i.e. the corresponding position of element for being -1 in maplist1,
It is stored in cut_idxs, for the atom of cut-off position, the atom in atom not in not_cut_idxs is abutted and deposited
It is put into cut_idxs.A cut_idxs list is safeguarded in each excision position, if the position can not find corresponding original in mol
Son, then the list of locations is sky.
Hydrogen atom in this position is cut off if it is sky to the cut_idxs of each excision position, if the position does not have
There is hydrogen atom, then skip the cutting of this mapping relations, executes next mapping relations.If being not sky, collect in this position
The atom to be cut off, atom and atom adjacent thereto but not in cut_connect_idxs, recurrence including the position are searched
Collect the adjacent atom of the position adjacent atom.
Collect the position of the atom to be cut off in mol, i.e. atom those of in cut_connect_idx, including the position
Atom and atom adjacent thereto but not in cut_connect_idx and cut_idx, these atoms have in new mol newly
Position, recurrence collects the adjacent atom of the position adjacent atom.
(3.4) it connects atom: cut_connect_idxs is connected with the correspondence atom in cut_idx with chemical bond.
(3.5) key attribute is copied: the key increased newly from duplicate key attribute in mol_sub into mol.New adatom is collected, i.e.,
The atom at the both ends of newly-increased key.
(3.6) update double bond and/space attribute: if in the space attribute structure of mol include the atom to be cut off,
It then needs to update space attribute.The atom for storing the atom at double bond both ends in double bond space attribute structure and being connected with them,
If both ends atom in double bond space attribute structure and having key between the new adatom of previous step, corresponding former in structure
Son replaces with new adatom.
(3.7) atom of collection to be cut off is cut off.
(3.8) molecule after exporting the cutting of a maplist2 mapping relations.
Further, according to each reaction type the characteristics of, to representated by the site [Ri] in reaction type string smi_sub
Atomic type makees some restrictions, i.e., makees some restrictions, including site to the type of [Ri] atom corresponded in molecular formula to be cut
[Ri] cannot be hydrogen atom (H), or be only C, N, O atom, or can be arbitrary atom, and restriction is standardized according to SMARTS.
Further, in the step (1), the molecular formula format of reading is Canonical SMILES, extended formatting
Input is converted to the format.
Further, consider whether the corresponding atom of connection site meets in smi_sub in the step (1), when mapping
Restriction to [Ri] type maps failure if being unsatisfactory for.
Further, in the step (3.2), judge whether the mapping relations will lead to the cyclic structure in mol and cut
The a part for the cyclic structure for judging whether mol_sub has been mapped to mol is opened, specifically: pass through the mapping in maplist2
Relationship finds the correspondence atom A in mol to enzyme site [Ri], if A has an adjacent atom A_neighbor to cut off
List in, and A_neighbor on ring, then ring can be cut open.
Further, in the step (3.5), the key increased newly from duplicate key attribute in mol_sub into mol is found
The atom at each key both ends in mol_sub finds corresponding two atoms in mol, by the key attribute between the two atoms
It is updated to the attribute value of corresponding keys in mol_sub.
The beneficial effects of the present invention are: the present invention atom, chemical bond graph structure on realize molecular formula cutting, operation
Strong flexibility, customizability is strong, suitable for the cutting for a variety of situations.By in chemical formula to be slit with indicate reaction type
Reaction type string and reaction type string indicate translation type reaction type string between atom map relationship, find to be cut
Which branch in chemical formula on which atom is divided to cut off, which branch will retain, and realize correct cutting.
Detailed description of the invention
Fig. 1 is the method for the present invention flow chart；
Fig. 2 is a cutting example of the invention.
Specific embodiment
In order to make the objectives, technical solutions, and advantages of the present invention clearer, with reference to the accompanying drawings and embodiments, right
The present invention is further elaborated.It should be appreciated that the specific embodiments described herein are merely illustrative of the present invention, and
It is not used in the restriction present invention.
A kind of chemical molecular formula cutting method provided by the invention, specific as follows:
For one with site or without site molecular formula smi (assuming that input format be Canonical SMILES,
The input of his format also can be exchanged into the format), the site in molecular formula is denoted as [Ri], i=0,1 ... N, [Ri] corresponding Mr. Yu
One reaction type is that the chemical reaction for carrying out the type with reagent molecule obtains, and N is the sum of reaction type；
To a kind of reaction type Reaction, a reaction type string smi_sub and translation type string smi_ are defined
Convert indicates that the substring is then partially converted to smi_convert if there is smi_sub substring in smi.smi_
Sub substring includes the site [Ri] that at least one connect with smi rest part, and smi_convert has identical in corresponding position
Site [Ri], smi_convert also include the atom to be cut off [*].Particularly, according to each reaction type the characteristics of, to reaction
Atomic type representated by site [Ri] in type string smi_sub makees some restrictions, i.e., corresponds to molecular formula to be cut to [Ri]
In the type of atom make some restrictions, if site [Ri] cannot be hydrogen atom (H), or be only C, N, O atom, or can be
Arbitrary atom, it is specific to limit processing essentially according to SMARTS specification.Dicing process is as follows:
1. reading in smi and smi_sub, switch to graph structure mol and mol_sub, generates the atom map of mol_sub to mol
Relation table maplist2, if mol_sub minor structure is not present in mol, no longer progress cutting illustrates that molecular formula smi cannot
The chemical reaction of the type that reacts Reaction.If protected in maplist2 there are multiple mol_sub minor structures in mol
Multiple mapping relations are deposited, illustrate the chemical reaction that molecular formula smi there are multiple groups that the type can occur at this time.Consider when mapping
Whether the corresponding atom of connection site, which meets the restriction in smi_sub to [Ri] type, maps failure if being unsatisfactory for.
When reading in smi_sub, the position of connection site [Ri] is saved.
2. reading in smi_convert, switch to graph structure mol_convert, generates the original of mol_convert to mol_sub
Sub- mapping table maplist1 finds the position cut_idx of excision atom [*], finds the atom of excision atom [*] connection
Position cut_connect_idx.For each atom in mol_convert, due to being removed or replacing in maplist1
Longer substring causes to can not find the corresponding atomic time in mol_sub, the mapping atom site for indicating the atom with -1.
3. each of couple maplist2 mapping relations obtain a cutting result:
3.1. mol is added with mol_sub, i.e., the data structure of the two is stacked, obtains updated mol.
3.2. the cyclic structure for judging whether the mapping relations will lead in mol is cut open, and is reflected if it is, skipping this
Relationship is penetrated, next mapping relations are executed, otherwise, executes step 3.3；Judge whether the mapping relations will lead to the ring in mol
Shape structure is cut open a part for the cyclic structure for judging whether mol_sub has been mapped to mol, specifically: pass through
Mapping relations in maplist2 find the correspondence atom A in mol to enzyme site [Ri], if A has an adjacent atom A_
Neighbor is not in the list to be cut off, and A_neighbor on ring, then ring can be cut open.
3.3. by the mapping relations, collect the position for being mapped to the atom not cut off in mol, i.e. in maplist1 > -1
The corresponding position of element, be stored in not_cut_idxs.
Collection is mapped to the position that the atom of atom [*] connection is cut off in mol, the i.e. corresponding original of cut_connect_idx
Son is stored in cut_connect_idxs.
Collect the position of complete resection atom being mapped in mol, i.e. the corresponding position of element for being -1 in maplist1,
It is stored in cut_idxs, for the atom of cut-off position, the atom in atom not in not_cut_idxs is abutted and deposited
It is put into cut_idxs, due to being not present in conversion string, so these atoms are also intended to excision.Each excision location dimension
A cut_idxs list is protected, if the position can not find corresponding atom in mol, which is sky.
Hydrogen atom in this position is cut off if it is sky to the cut_idxs of each excision position, if the position does not have
There is hydrogen atom, then skip the cutting of this mapping relations, executes next mapping relations.If being not sky, collect in this position
The atom to be cut off, atom and atom adjacent thereto but not in cut_connect_idxs, recurrence including the position are searched
Collect the adjacent atom of the position adjacent atom.
Collect the position of the atom to be cut off in mol, i.e. atom those of in cut_connect_idx, including the position
Atom and atom adjacent thereto but not in cut_connect_idx and cut_idx, these atoms have in new mol newly
Position, recurrence collects the adjacent atom of the position adjacent atom.
3.4. it connects atom: cut_connect_idxs is connected with the correspondence atom in cut_idx with chemical bond.
3.5. copy key attribute: the key increased newly from duplicate key attribute in mol_sub into mol is found every in mol_sub
The atom at a key both ends finds corresponding two atoms in mol, the key attribute between the two atoms is updated to mol_
The attribute value of corresponding keys in sub.Collect new adatom, i.e., the atom at the both ends of newly-increased key.
3.6. update double bond and/space attribute: since space attribute individually stores, need individually to handle, if
Include the atom to be cut off in the space attribute structure of mol, then needs to update space attribute.It is stored in double bond space attribute structure
The atom at double bond both ends and the atom being connected with them, if both ends atom and previous step in double bond space attribute structure
There is key between new adatom, then the correspondence atom in structure is replaced with new adatom.
3.7. the atom of collection to be cut off is cut off.
Mol, i.e., be converted to Canonical by the molecule after 3.8. exporting the cutting of a maplist2 mapping relations
SMILES format.
Cutting example is as follows: as shown in Fig. 2, (a), (b), (c), (d) are successively are as follows: reaction type, translation type, to be slit
Minor, cutting final result, wherein Xx be [*] atom, S be [R] atom；Corresponding chemical formula is successively are as follows:
[S] C=C
[S]C([*])C[*]
CCOC (=O)/C=C/C (O)=O
CCOC (=O) C (C (C (=O) O) [*]) [*]
Mol_convert (the 2nd chemical formula) arrives the atom map relation table of mol_sub (the 1st chemical formula)
Maplist1 is { 0,1, -1,2, -1 }.
It is to be understood that the content of present invention and specific embodiment are intended to prove the reality of technical solution provided by the present invention
Border application, should not be construed as limiting the scope of the present invention.Within the spirit of the invention and the scope of protection of the claims,
To any modifications and changes that the present invention makes, protection scope of the present invention is both fallen within.
Claims (6)
1. a kind of chemical molecular formula cutting method, which is characterized in that for one with site or without the molecular formula smi in site,
Site in molecular formula is denoted as [Ri], i=0,1 ... N, [Ri] corresponds to a certain reaction type, and N is the sum of reaction type；
To a kind of reaction type Reaction, a reaction type string smi_sub and translation type string smi_convert are defined,
It indicates that the substring is then partially converted to smi_convert if there is smi_sub substring in smi；Smi_sub substring packet
The site [Ri] connecting containing at least one with smi rest part, smi_convert have identical site [Ri] in corresponding position,
Smi_convert also includes the atom to be cut off [*], and dicing process is as follows:
(1) smi and smi_sub is read in, graph structure mol and mol_sub are switched to, generates the atom map relationship of mol_sub to mol
Table maplist2, if mol_sub minor structure is not present in mol, no longer progress cutting.If there are multiple mol_ in mol
Sub minor structure then saves multiple mapping relations in maplist2.Consider whether the corresponding atom of connection site meets when mapping
Failure is mapped if being unsatisfactory for the restriction of [Ri] type in smi_sub.When reading in smi_sub, save connection site [Ri]
Position.
(2) smi_convert is read in, graph structure mol_convert is switched to, the atom for generating mol_convert to mol_sub reflects
Relation table maplist1 is penetrated, the position cut_idx of excision atom [*] is found, finds the position of the atom of excision atom [*] connection
cut_connect_idx.For each atom in mol_convert, the corresponding atomic time can not find in mol_sub, with -1
Indicate the mapping atom site of the atom.
(3) to each of maplist2 mapping relations, a cutting result is obtained:
(3.1) mol is added with mol_sub, obtains updated mol.
(3.2) cyclic structure for judging whether the mapping relations will lead in mol is cut open, if it is, skipping this mapping
Relationship executes next mapping relations, otherwise, executes step 3.3.
(3.3) by the mapping relations, collect the position for being mapped to the atom not cut off in mol, i.e. in maplist1 > -1 member
The corresponding position of element, is stored in not_cut_idxs.
Collection is mapped to the position that the atom of atom [*] connection is cut off in mol, i.e. the corresponding atom of cut_connect_idx is deposited
It is put into cut_connect_idxs.
Collect the position for the complete resection atom being mapped in mol, the i.e. corresponding position of element for being -1 in maplist1, storage
To cut_idxs, for the atom of cut-off position, is abutted the atom in atom not in not_cut_idxs and be stored in
cut_idxs.A cut_idxs list is safeguarded in each excision position, if the position can not find corresponding atom in mol,
The list of locations is sky.
Hydrogen atom in this position is cut off if it is sky to the cut_idxs of each excision position, if the position does not have hydrogen
Atom then skips the cutting of this mapping relations, executes next mapping relations.If being not sky, collection will be cut in this position
The atom removed, atom and atom adjacent thereto but not in cut_connect_idxs including the position, recurrence is collected should
The adjacent atom of position adjacent atom.
Collect the position of the atom to be cut off in mol, i.e. atom those of in cut_connect_idx, the original including the position
Atom and adjacent thereto but not in cut_connect_idx and cut_idx, these atoms have new position in new mol
It sets, recurrence collects the adjacent atom of the position adjacent atom.
(3.4) it connects atom: cut_connect_idxs is connected with the correspondence atom in cut_idx with chemical bond.
(3.5) key attribute is copied: the key increased newly from duplicate key attribute in mol_sub into mol.Collect new adatom, i.e., it is newly-increased
The atom at the both ends of key.
(3.6) update double bond and/space attribute: if in the space attribute structure of mol include the atom to be cut off, need
Update space attribute.The atom for storing the atom at double bond both ends in double bond space attribute structure and being connected with them, if
Both ends atom in double bond space attribute structure and there is key between the new adatom of previous step, then the correspondence atom in structure is replaced
It is changed to new adatom.
(3.7) atom of collection to be cut off is cut off.
(3.8) molecule after exporting the cutting of a maplist2 mapping relations.
2. a kind of chemical molecular formula cutting method according to claim 1, which is characterized in that according to the spy of each reaction type
Point makees some restrictions to atomic type representated by the site [Ri] in reaction type string smi_sub, i.e., to [Ri] correspond to
The type of atom in cutting minor makees some restrictions, including site [Ri] cannot be hydrogen atom (H), or be only C, N, O original
Son, or can be arbitrary atom, restriction is standardized according to SMARTS.
3. a kind of chemical molecular formula cutting method according to claim 1, which is characterized in that in the step (1), read in
Molecular formula format be Canonical SMILES, the input of extended formatting is converted to the format.
4. a kind of chemical molecular formula cutting method according to claim 1, which is characterized in that in the step (1), mapping
When consider whether the corresponding atom of connection site meets the restriction in smi_sub to [Ri] type and map failure if being unsatisfactory for.
5. a kind of chemical molecular formula cutting method according to claim 1, which is characterized in that in the step (3.2), sentence
Whether the mapping relations of breaking will lead to the cyclic structure in mol and are cut open the ring-type for judging whether mol_sub has been mapped to mol
A part of structure, specifically: the correspondence atom A in mol to enzyme site [Ri] is found by the mapping relations in maplist2,
If A has an adjacent atom A_neighbor not in the list to be cut off, and A_neighbor on ring, then ring can be cut
It opens.
6. a kind of chemical molecular formula cutting method according to claim 1, which is characterized in that in the step (3.5), from
The key that duplicate key attribute increases newly into mol in mol_sub, that is, find the atom at each key both ends in mol_sub, find in mol
In corresponding two atoms, the key attribute between the two atoms is updated to the attribute value of corresponding keys in mol_sub.
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