From owner-chemistry@ccl.net Wed Dec 8 09:23:00 2010 From: "Michel Petitjean petitjean.chiral[]gmail.com" To: CCL Subject: CCL: multiple conformations analysis free\open source\academic free software Message-Id: <-43300-101208091522-18497-0NrimKqTNnRhLZi9CperXA=server.ccl.net> X-Original-From: Michel Petitjean Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 8 Dec 2010 15:15:11 +0100 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral|gmail.com] Dear Andrew, I assume that it is a 3D linearity coefficient rather than a graph index. You could think that linearity can be evaluated from the eigenvalues L1>L2>L3 of the variance matrix of the atomic centers: a linear shape should be such that L2 is very small compared to L1. In other words, the percentage of inertia associated to the first eigenvalue (perform an ACP, centered, but not reduced) should be close to 100%. There are other variants, but the latter should be computable with many freewares such as R). An other index could be derived from the computation of the minimal enclosing rectangular box, of size L1>L2>L3, then consider L1/(L1+L2+L3). Etc., etc. Best, Michel. Michel Petitjean MTi, INSERM UMR-S 973, University Paris 7 CNRS SNC 9079 35 rue Helene Brion, 75205 Paris Cedex 13, France. Phone: +331 5727 8434; Fax: +331 5727 8372 E-mail: petitjean.chiral+*+gmail.com, michel.petitjean+*+univ-paris-diderot.fr http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html 2010/12/7 Andrew Voronkov drugdesign=yandex.ru : > > Sent to CCL by: Andrew Voronkov [drugdesign * yandex.ru] > Thank you very much for the answer. Can also anyone recommend me some way to describe the linearity of the molecule? Let's say that I have 50 conformations for each compound and want to measure the degree of linearity of the molecules. How is possible to do that? > > > Best regards, > Andrew