From ad188bcee1df2db3795561aab21e4b9f33e83804 Mon Sep 17 00:00:00 2001 From: Alon Grinberg Dana Date: Wed, 28 Jun 2017 12:01:41 -0400 Subject: [PATCH] Added a docstring describing the atomType naming convention --- rmgpy/molecule/atomtype.py | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/rmgpy/molecule/atomtype.py b/rmgpy/molecule/atomtype.py index d10c984c96f..2b58992693b 100644 --- a/rmgpy/molecule/atomtype.py +++ b/rmgpy/molecule/atomtype.py @@ -223,6 +223,15 @@ def getFeatures(self): For making sample atoms, we use the first atomtype under specific, therefore the first one in the list should always be an element. + +The atomTypes naming convention is: + +For example: +- N3d is nitrogen with valence=3 (i.e., 3 electronce are able to form bonds or remain as radicals) with one double bond +- S4tc is sulfur with valence=4 with one triple bond and charged +- S2sp is sulfur with valence=2 with only single bonds and charged positively +- S2sn is similar to S2sp, only charged negatively +- Oa is atomic oxygen, i.e., a closed shell atom """ atomTypes = {}