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Added a docstring describing the atomType naming convention
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alongd committed Jun 28, 2017
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9 changes: 9 additions & 0 deletions rmgpy/molecule/atomtype.py
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Expand Up @@ -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:
<element> <valence> <characteristic bonds> <charge(optional)>
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 = {}
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