cmp.search(ChemmineR)
cmp.search()所属R语言包：ChemmineR
Search a descriptor database for compounds similar to query compound
搜索查询化合物类似的化合物描述数据库
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Given descriptor of a query compound and a database of compound descriptors, search for compounds that are similar to the query compound. User can limit the output by supplying a cutoff similarity score or a cutoff that limits the number of returned compounds. The function can also return the scores together with the compounds.
鉴于查询化合物和复合描述，搜索查询化合物类似的化合物数据库的描述。通过提供一个截止的相似性得分或截止限制返回化合物的数量，用户可以限制输出。该功能也可以返回的分数，连同化合物。
用法----------Usage----------
cmp.search(db, query, type=1, cutoff = 0.5, return.score = FALSE, quiet = FALSE,
mode = 1, visualize=FALSE, visualize.browse=TRUE, visualize.query=NULL)
参数----------Arguments----------
参数：db
The compound descriptor database returned by 'cmp.parse'.
复合描述数据库返回cmp.parse“的。
参数：query
The query descriptor, which is usually returned by 'cmp.parse1'.
查询描述符，通常返回cmp.parse1的。
参数：type
Returns results in form of position indices (type=1), named vector with compound IDs (type=2) or data frame (type=3).
位置指数的形式返回结果（类型= 1），命名为复合标识（类型= 2）或数据框（类型= 3）的向量。
参数：cutoff
The cutoff similarity (when cutoff <= 1) or the number of maximum compounds to be returned (when cutoff > 1).
要返回截止相似（时截止<= 1）或数量最大的化合物（时截止> 1）。
参数：return.score
Whether to return similarity scores. If set to TRUE, a data frame will be returned; otherwise, only the compounds' indices in the database will be returned in the order of decreasing scores.
是否返回相似度。如果设置为TRUE，数据框将被退回，否则，只有化合物数据库中的指标将降低分数的顺序返回。
参数：quiet
Whether to disable progress information.
是否禁用进度信息。
参数：mode
Mode used when computing similarity scores. This value is passed to 'cmp.similarity'.
在计算相似度时模式下使用。这个值是通过“cmp.similarity”。
参数：visualize
Whether to visualize the search result in a webpage.
是否要在网页搜索结果的可视化。
参数：visualize.browse
Whether to open the browser automatically if you choose to visualize the search result.
是否自动打开浏览器，如果你选择可视化搜索结果。
参数：visualize.query
Filename/URL or a character string containing the SDF of the query structure if you also want to visualize the query in the search result visualization webpage.
文件名/ URL或一个字符串，包含查询结构的自卫队，如果你也想在搜索结果的可视化网页的可视化查询。
Details
详情----------Details----------
'cmp.search' will go through all the compound descriptors in the database and calculate the similarity between the query compound and compounds in the database. When cutoff similarity score is set, compounds having a similarity score higher than the cutoff will be returned. When maximum number of compounds to return is set to N via 'cutoff', the compounds having the highest N similarity scores will be returned.
，“cmp.search会通过在数据库中，所有的化合物描述计算在数据库中查询的化合物和化合物之间的相似性。截止相似性得分时，有一个相似性得分比截止较高的化合物将被退回。当返回的化合物的最大数量设置为N，通过“截止”的化合物，具有最高的列印相似度将被退回。
If 'visualize' is set to a TRUE value, sdf.visualize will be called to send the search results and the scores to ChemMine website. If 'visualize.browse' is set to a TRUE value, the browser will open to show the structures in the search result with their corresponding scores. Otherwise, a URL pointing to that webpage will be printed. By default, 'visualize.query' is not set, and the query structure will not be uploaded. If you want that to be included in the visualization webpage as well, you must set this argument to a character string containing the SDF of the query, or a filename pointing to a file containing the SDF of the query. If the character string or the file containing multiple SDFs, only the first will be considered as the SDF of the query.
如果“形象化”设置为TRUE值，sdf.visualize会被称为发送ChemMine网站的搜索结果和分数。如果visualize.browse“设置为TRUE值，浏览器将打开其相应的分数显示在搜索结果的结构。否则，指向该网页的URL将被打印。默认情况下，“visualize.query没有设置，将不被上传和查询结构。如果你想，可以在可视化的网页也包括在内，你必须将此参数设置为一个字符串，包含自卫队的查询，或文件名指向一个文件包含查询自卫队。如果字符串或文件，其中包含多个SDFS，只有第一个将被视为自卫队查询。
值----------Value----------
When 'return.score' is set to FALSE, a vector of matching compounds' indices in the database will be returned. Otherwise, a data frame will be returned:
当“return.score”设置为FALSE，在数据库中的匹配化合物的指数向量将被退回。否则，将返回一个数据框：
参数：ids
The indices of matching compounds in the database.
该指数的匹配数据库中的化合物。
参数：scores
The similarity scores between the matching compounds and the query compound
之间的匹配化合物和查询化合物的相似度
作者（S）----------Author(s)----------
Y. Eddie Cao, Li-Chang Cheng
参考文献----------References----------
in 2D fragment-based similarity searching: comparison of structural descriptors
参见----------See Also----------
cmp.parse1, cmp.parse, cmp.search, cmp.cluster,
cmp.parse1，cmp.parse，cmp.search，cmp.cluster
举例----------Examples----------
## Load sample SD file[＃负载样品的SD文件]
# data(sdfsample); sdfset <- sdfsample[数据（sdfsample）; sdfset < - sdfsample]
## Generate atom pair descriptor database for searching[＃生成原子对数据库搜索描述]
# apset <- sdf2ap(sdfset) [< - sdf2ap apset（sdfset）]
## Loads same atom pair sample data set provided by library[＃加载相同的原子对样本数据集，由图书馆提供]
data(apset)
db <- apset
query <- db[1]
## Ooptinally, save the db for future use[＃Ooptinally，保存以供将来使用的DB]
save(db, file="db.rda", compress=TRUE)
## Search for similar compounds using similarity cutoff[＃搜索使用相似度截止类似化合物]
cmp.search(db, query, cutoff=0.2, type=1) # returns index[回报指数]
cmp.search(db, query, cutoff=0.2, type=2) # returns named vector[命名为向量的回报]
cmp.search(db, query, cutoff=0.2, type=3) # returns data frame[返回的数据框]
# you may visualize the search result in ChemMine[你可以可视化的搜索结果在ChemMine]
## Not run: cmp.search(db, query, cutoff=10, visualize=TRUE, visualize.browse=FALSE, visualize.query=url)[＃无法运行：cmp.search（DB，查询，截止10日，形象化= TRUE，visualize.browse = FALSE visualize.query = URL）]
## in the next session, you may use load a saved db and do the search:[＃在下届会议上，您可以使用加载保存的数据库，做搜索：]
load("db.rda")
cmp.search(db, query, cutoff=3)
## you may also use the loaded db to do clustering:[＃你也可以使用载入的DB做聚类：]
cmp.cluster(db, cutoff=0.35)
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
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发表于 2012-2-25 14:42:31
