CN110400607B - Method for expanding molecular library - Google Patents
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Abstract
The invention discloses an expansion method of a molecular library, wherein the self-contained molecular library and a newly-entered molecular library are both an already-held molecular library, the complete molecular formula and fingerprint of each molecule are stored in the self-contained molecular library, the newly-entered molecular library is a newly-uploaded molecular library and is composed of a plurality of sub-libraries, and the process of splicing a plurality of sub-libraries into the complete molecular library is time-consuming.
Description
Technical Field
The invention belongs to the technical field of molecular compound management, and particularly relates to an expansion method of a molecular library.
Background
In the management of molecular compounds, it is necessary to know the molecular formula in the database, and it is necessary to know whether each new chemical formula exists in its own molecular library, and in the production environment, the new chemical formula is generally given in the form of a plurality of sub-libraries, and each sub-library often has several thousands to several tens of thousands of molecular formulas. There is currently no optimization for this scenario.
Disclosure of Invention
The invention aims to provide an online extension method of a chemical molecular formula library, aiming at the defects of the prior art.
The purpose of the invention is realized by the following technical scheme: the method for expanding the molecular library comprises the steps that the self-contained molecular library and a new molecular library are used, the self-contained molecular library is composed of mol _ i { i ═ 1,2 and … n }, n is the number of chemical molecular formulas in the self-contained molecular library, the new molecular library is composed of BBlist _ j { j ═ 1,2 and … m }, m is the number of sub-libraries BBlist _ j in the new molecular library, and each sub-library BBlist _ j is composed of Mj chemical molecular formulas and is marked as BBlist _ j _ k { k ═ 1,2 and … Mj }. The expansion process comprises the following steps:
(1) the complete molecular formula mol _ i { i ═ 1,2, … n } and the fingerprint fp _ i { i ═ 1,2, … n } of each molecule, and the fingerprint fp _ all resulting from the or operation of all the fingerprints are stored in the own molecular library.
(2) And calculating fingerprints fp _ j _ k, j is 1,2, m, k is 1,2, … Mj of each molecular formula BBlist _ j _ k in each BBlist _ j for a new molecular library.
(3) Screening molecular formulas in BBlist: for each fingerprint fp _ j _ k, compared to the fingerprint fp _ all, if one bit (bit) in fp _ j _ k is not present in fp _ all, i.e. the one bit of fp _ j _ k is 1 and fp _ all is 0, BBlist _ j _ k and fp _ j _ k are removed and do not participate in the following calculation. In the screening process, if a certain fingerprint FP _ j _ K is not filtered, a set FP _ K containing fingerprints FP _ i of all parts of the fingerprint FP _ j _ K is recorded compared with each FP _ i.
(4) Carrying out one-step splicing on the molecular formula in the screened BBlist, and continuously screening in the splicing process, wherein the method specifically comprises the following steps: and (3) splicing two BBlist _ j, merging the two molecular formula sets FP _ K after each splicing to obtain a new FP _ K set of the spliced molecular formula, and screening in the new FP _ K set in the step (3).
(5) And (4) repeating the step (4) until a complete new molecule entering library and a set FP _ K in the self molecule library corresponding to each molecular formula in the new molecule library are obtained.
(6) Screening out the molecular formula which is completely the same as the molecular formula in the existing molecular library and adding the rest different molecular formulas into the existing molecular library to realize the expansion of the molecular formula library, wherein the screening process is as follows: searching whether a completely identical molecular formula exists in each molecular formula left in a newly-entered molecular formula library in a corresponding FP-K, firstly comparing whether the fingerprint of each molecular formula is completely identical to the fingerprint of a certain molecular formula in the FP-K, and accurately matching the two molecular formulas if the fingerprints are completely identical, or filtering the molecular formula; in the exact match process, the formula is filtered out if the match fails.
Further, in the step (4), the splicing can be performed only by using a formula labeled with the same site, the site in the formula is marked as [ i ], i is 0,1 … N, [ i ] corresponds to a certain reaction type and is obtained by performing a chemical reaction of the type by using a reagent molecule, and N is the total number of the reaction types.
Further, in the step (4), the step 3 of screening in the new FP _ K set specifically includes: and calculating a new fingerprint for the spliced molecular formula, comparing and screening the new fingerprint with FP _ all, and if the new fingerprint is not filtered, screening a set FP _ K _ sub containing the molecular formula of all parts of the new fingerprint in the new FP _ K set.
Further, in the step (6), the precise matching method adopts a smart pattern matching method.
The invention has the beneficial effects that: the method screens the newly uploaded new molecular library, and adds the rest molecular formulas into the self-owned molecular library after screening to realize the expansion of the molecular library. The newly entered molecular library is generally composed of a plurality of sub-libraries, the sub-libraries need to be spliced into a complete molecular library for screening, and the process of splicing a plurality of sub-libraries is time-consuming, so that the method for accelerating the process is realized.
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FIG. 1 is a flow chart of the method 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.
As shown in fig. 1, the method for expanding a molecular library provided by the present invention specifically includes the following steps:
for two molecule libraries (a large number of chemical molecular formulas are stored in the molecule libraries), an own molecule library and a new molecule library are provided, the own molecule library is composed of mol _ i { i ═ 1,2 and … n }, n is the number of the chemical molecular formulas in the own molecule library, the new molecule library is composed of BBlist _ j { j ═ 1,2 and … m }, m is the number of the sub-libraries BBlist _ j in the new molecule library, each sub-library BBlist _ j is composed of Mj chemical molecular formulas, and each molecular formula is a building block, namely BBlist _ j _ k ═ 1,2 and … Mj }. In the actual online service, the self-contained molecular library is an already-held molecular library, the complete molecular formula and the fingerprint (finger print) of each molecule are stored in the self-contained molecular library, the newly-entered molecular library is a newly-uploaded molecular library and is composed of a plurality of sub-libraries BBlist _ j, the process of splicing a plurality of BBlist _ j into the complete molecular library is time-consuming, only the molecular formula which needs to be spliced is taken when the self-contained molecular library and the newly-entered molecular library are compared, the molecular formula which is not spliced can be obtained by filtering, the molecular formula which is the same as the self-contained molecular library is found, the rest different molecular formulas are added into the self-contained molecular library, and the expansion process of the molecular formula library is realized and comprises the following steps:
1. the complete molecular formula mol _ i { i ═ 1,2, … n } and the fingerprint fp _ i { i ═ 1,2, … n } of each molecule, and the fingerprint fp _ all resulting from the or operation of all the fingerprints are stored in the own molecular library.
2. For a new entry molecular library, a fingerprint (fingerprint) fp _ j _ k of each molecular formula BBlist _ j _ k in each BBlist _ j is calculated, wherein j is 1,2, m, k is 1,2, … Mj.
3. Screening molecular formulas in BBlist: for each fingerprint fp _ j _ k, compared to the fingerprint fp _ all, if one bit (bit) in fp _ j _ k is not present in fp _ all, i.e. the one bit of fp _ j _ k is 1 and fp _ all is 0, BBlist _ j _ k and fp _ j _ k are removed and do not participate in the following calculation. Since a bit of the fingerprint is 1, which indicates that the molecule has a specific atomic sequence or property, for a specific bit, fp _ j _ k is 1 and fp _ all is 0, which indicates that fp _ j _ k has an atomic sequence or property that fp _ all does not have, i.e., there is no atomic sequence or property in the own molecular library, i.e., fp _ j _ k cannot be identical to a certain mol _ i.
In the screening process, if a certain fingerprint FP _ j _ K is not filtered, a set FP _ K containing fingerprints FP _ i of all parts of the fingerprint FP _ j _ K is recorded compared with each FP _ i.
4. And (3) carrying out one-step splicing on the molecular formula in the screened BBlist, and continuously screening in the splicing process:
the complete molecular formula is obtained by splicing all the BBlist _ j { j ═ 1,2 and m }, namely splicing each molecular formula in the BBlist _1 with all the spliceable molecular formulas in the BBlist _2 to obtain the BBlist _1_2, and then splicing each molecular formula in the BBlist _1_2 with all the spliceable molecular formulas in the BBlist _3 to obtain the BBlist _1_2_ 3. The sites in the formula are marked as [ i ], i is 0,1 … N, and [ i ] corresponds to a certain reaction type and is obtained by carrying out chemical reaction of the type by using reagent molecules, and N is the total number of the reaction types; the molecular formula with the same site mark can be spliced, for example, the molecule [1] C ═ O in BBlist _1 and [2] CCO [1] in BBlist _2 have the same site mark [1] which can be spliced, but can not be spliced with [2] CCO [3 ].
In this step, two BBlist _ j are spliced, for example, BBlist _1 and BBlist _2 are spliced. The splicing sequence for forming the complete molecular library is assumed to be 1,2 and … m, namely 1 and 2 are spliced firstly, and the result is spliced with 3 again until the m-th BBlist is spliced to obtain the complete molecular library.
Merging the two molecular formula sets FP _ K after each splicing to obtain a new FP _ K set of the spliced molecular formula, and carrying out the step 3 screening in the new FP _ K set: and calculating a new fingerprint for the spliced molecular formula, comparing the new fingerprint with FP _ all for screening, and if the new fingerprint is not filtered, screening a set FP _ K _ sub containing the molecular formula of all parts of the new fingerprint in a new FP _ K set.
5. And (4) repeating the step (4) until a complete new molecule entering library and a set FP _ K in the self molecule library corresponding to each molecular formula in the new molecule library are obtained.
6. Screening out the molecular formula which is completely the same as the molecular formula in the existing molecular library and adding the rest different molecular formulas into the existing molecular library to realize the expansion of the molecular formula library, wherein the screening process is as follows: and searching whether the completely same molecular formula exists in the corresponding FP-K for each molecular formula left in the newly-entered molecular library, firstly comparing whether the fingerprint of each molecular formula is completely the same as the fingerprint of a certain molecular formula in the FP-K, and accurately matching the two molecular formulas if the fingerprints are completely the same, otherwise, filtering out the molecular formula. In the exact match process, the formula is filtered out if the match fails. The exact matching method may employ a smart pattern matching method.
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 modification and variation of the present invention within the spirit of the present invention and the scope of the claims will fall within the scope of the present invention.
Claims (4)
1. The method for expanding the molecular library is characterized in that for an own molecular library and a new molecular library, the own molecular library is composed of mol _ i { i ═ 1,2, … n }, n is the number of chemical molecular formulas in the own molecular library, the new molecular library is composed of BBlist _ j { j ═ 1,2, … m }, m is the number of sub-libraries BBlist _ j in the new molecular library, each sub-library BBlist _ j is composed of Mj chemical molecular formulas, and the number is marked as BBlist _ j _ k { k ═ 1,2, … Mj }; the expansion process comprises the following steps:
(1) the complete molecular formula mol _ i { i ═ 1,2, … n } and the fingerprint fp _ i { i ═ 1,2, … n } of each molecule, and the fingerprint fp _ all obtained by OR operation of all the fingerprints are stored in an own molecular library;
(2) calculating fingerprints fp _ j _ k, j is 1,2, m, k is 1,2, … Mj of each molecular formula BBlist _ j _ k in each BBlist _ j;
(3) screening molecular formulas in BBlist _ j: for each fingerprint fp _ j _ k, comparing with the fingerprint fp _ all, if one bit (bit) in fp _ j _ k is not available to fp _ all, namely the bit of fp _ j _ k is 1 and fp _ all is 0, removing BBlist _ j _ k and fp _ j _ k, and not participating in the later calculation; in the screening process, if a certain fingerprint FP _ j _ K is not filtered, comparing the certain fingerprint FP _ j _ K with each FP _ i, and recording a set FP _ K of fingerprints FP _ i containing all parts of the fingerprint FP _ j _ K;
(4) carrying out one-step splicing on the screened molecular formula in the BBlist _ j, and continuously screening in the splicing process, wherein the method specifically comprises the following steps: splicing two BBlist _ j, merging the two molecular formula sets FP _ K after each splicing to obtain a new FP _ K set of the spliced molecular formula, and screening in the step (3) in the new FP _ K set;
(5) repeating the step (4) until a complete new molecule entering library and a set FP _ K in the self molecule library corresponding to each molecular formula in the new molecule library are obtained;
(6) screening out the molecular formula which is completely the same as the molecular formula in the existing molecular library and adding the rest different molecular formulas into the existing molecular library to realize the expansion of the molecular formula library, wherein the screening process is as follows: searching whether a completely identical molecular formula exists in each molecular formula left in a newly-entered molecular formula library in a corresponding FP-K, firstly comparing whether the fingerprint of each molecular formula is completely identical to the fingerprint of a certain molecular formula in the FP-K, and accurately matching the two molecular formulas if the fingerprints are completely identical, or filtering the molecular formula; in the exact match process, the formula is filtered out if the match fails.
2. The method for expanding a library of molecules according to claim 1, wherein in step (4), the same site-labeled formula is used for splicing, the sites in the formula are represented by [ i ], i is 0,1 … N, and [ i ] corresponds to a certain reaction type and is obtained by performing a chemical reaction of the reaction type with a reagent molecule, and N is the total number of the reaction types.
3. The method for extending a molecular library according to claim 1, wherein in the step (4), the screening in the step (3) in the new FP _ K set is specifically: and calculating a new fingerprint for the spliced molecular formula, comparing and screening the new fingerprint with FP _ all, and if the new fingerprint is not filtered, screening a set FP _ K _ sub containing the molecular formula of all parts of the new fingerprint in the new FP _ K set.
4. The method for extending a molecular library according to claim 1, wherein in the step (6), the exact matching method is a smart pattern matching method.
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| CN108149325A (en) * | 2016-12-02 | 2018-06-12 | 杭州阿诺生物医药科技股份有限公司 | The synthesis of DNA encoding dynamic library of molecules and screening technique |
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| CN104750761B (en) * | 2013-12-31 | 2018-06-22 | 上海致化化学科技有限公司 | The method for building up and searching method of Molecular structure database |
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| CN108149325A (en) * | 2016-12-02 | 2018-06-12 | 杭州阿诺生物医药科技股份有限公司 | The synthesis of DNA encoding dynamic library of molecules and screening technique |
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Address after: 7 / F, building B, 482 Qianmo Road, Xixing street, Binjiang District, Hangzhou City, Zhejiang Province 310000 Patentee after: Huoshi Creation Technology Co.,Ltd. Address before: 7 / F, building B, 482 Qianmo Road, Xixing street, Binjiang District, Hangzhou City, Zhejiang Province 310000 Patentee before: HANGZHOU FIRESTONE TECHNOLOGY Co.,Ltd. |