rings(ChemmineR)
rings()所属R语言包：ChemmineR
Ring and Aromaticity Perception
环和芳香知觉
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Identifies all possible rings in molecules using the exhaustive ring perception algorithm from Hanser et al (1996). In addition, the function can return all smallest possible rings as well as aromaticity information for each ring.
标识所有可能在使用详尽环从感知器算法，Hanser等（1996）的分子环。此外，该函数可以返回所有可能最小的戒指，以及为每个环的芳香信息。
用法----------Usage----------
rings(x, upper = Inf, type = "all", arom = FALSE, inner = FALSE)
参数----------Arguments----------
参数：x
SDF or SDFset containers
SDF或SDFset容器
参数：upper
allows to specify an upper length limit for ring predictions. The default setting upper=Inf will return all possible rings. Smaller length limits will reduce the search space resulting in shortened compute times.
允许指定环预测的上限长度的限制。默认设置upper=Inf将返回所有可能的戒指。规模较小的长度的限制，将减少搜索空间，缩短计算时间。
参数：type
if type="all", the function returns each ring of a compound as character vector of atom symbols that are numbered by their position in the atom block of an SDF/SDFset object. Note: the example below shows how to plot structures with the same numbering information for visual inspection. If type="arom", only aromatic rings are returned, while type="count" returns the ring and/or aromaticity counts for each compound in a matrix.
如果type="all"，该函数返回每个环的化合物作为其在SDF/SDFset对象的原子块的位置编号的原子符号矢量字符。注意：下面的例子演示了如何绘制结构具有相同编号目测信息。如果type="arom"，只有芳香环返回，而type="count"返回矩阵中每个化合物的环和/或芳香计数。
参数：arom
if arom="TRUE", ring aromaticity information will be computed. If type="all", the output is a logical vector where 'TRUE' values indicate aromatic rings in the associated ring list. If type="arom", then the function returns only aromatic rings. A ring is considered aromatic if it meets the following requirements: (i) all atoms in the ring need to be sp2 hybridized. This means each atom has to have a double bond or at least one lone electron pair and it needs to be attached to an sp2 hybridized atom. (ii) In addition, Hueckel's rule '4n + 2' needs to be true, where 'n' is either zero or any positive integer.
如果arom="TRUE"，环芳香的信息将被计算。如果type="all"，输出是一个逻辑向量，其中“TRUE”值表示相关的环列表中的芳香环。如果type="arom"，那么该函数只返回芳香环。被认为是A环芳香，它是否符合以下要求：（一）中环所有原子需要sp2杂。这意味着每个原子都必须有一个双键或至少有一个孤电子对，它需要连接到一个sp2杂原子。 （ii）此外，Hueckel的规则4列印+ 2“的需求是真实的，其中”n“是零或正整数。
参数：inner
if inner="TRUE", only inner (smallest possible) rings will be returned. They are identified by first computing all possible rings and then selecting only the inner rings. Note: this requires the setting upper=Inf. If only rings below a certain size limit (e.g. 6) are of interest, then it will be more time efficient to set this limmit under the upper argument than identifying all smallest rings.
如果inner="TRUE"，只有内（最小）环将被退回。他们首先计算所有可能的环和内圈，然后选择确定。注：这需要设置upper=Inf。如果低于一定规模的限制（如6）只戒指的兴趣，那么这将是有效的设置确定所有最小环比upper参数下limmit更多的时间。
Details
详情----------Details----------
...
...
值----------Value----------
The settings type="all" and type="arom" return lists, and type="count" returns a matrix.
设置type="all"和type="arom"回报lists，type="count"返回一个matrix。
作者（S）----------Author(s)----------
Thomas Girke
参考文献----------References----------
Journal of Chemical Information and Computer Sciences, 36: 1146-1152. URL: http://pubs.acs.org/doi/abs/10.1021/ci960322f
参见----------See Also----------
...
...
举例----------Examples----------
## Instances of SDFset class[＃实例SDFset类，]
data(sdfsample)
sdfset <- sdfsample
## Return all possible rings for a single compound [＃返回一个单一的化合物所有可能的环]
rings(sdfset[1], upper=Inf, type="all", arom=FALSE, inner=FALSE)
plot(sdfset[1], print=FALSE, atomnum=TRUE, no_print_atoms="H")
## Return all possible rings for several compounds plus their [＃几种化合物，加上他们返回的所有可能的环]
## aromaticity information[＃芳香信息]
rings(sdfset[1:4], upper=Inf, type="all", arom=TRUE, inner=FALSE)
## Return rings with no more than 6 atoms[＃返回不超过6个原子的环]
rings(sdfset[1:4], upper=6, type="all", arom=TRUE, inner=FALSE)
## Return rings with no more than 6 atoms that are also armomatic[＃返回不超过6原子环，也armomatic]
rings(sdfset[1:4], upper=6, type="arom", arom=TRUE, inner=FALSE)
## Return shortest possible rings (no complex rings)[＃返回最短可能环（没有复杂的环）]
rings(sdfset[1:4], upper=Inf, type="all", arom=TRUE, inner=TRUE)
## Count shortest possible rings[＃计数最短的戒指]
rings(sdfset[1:4], upper=Inf, type="count", arom=TRUE, inner=TRUE)
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。
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发表于 2012-2-25 14:44:35
