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clarify exactly what is used to identify reaction site

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thanks to Øystein Gullbrekken for the suggestion
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jrgissing
2020-10-24 13:46:28 -04:00
parent c29474c533
commit c2a852ddef
1 changed files with 6 additions and 4 deletions
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10
doc/src/fix_bond_react.rst
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@ -174,10 +174,12 @@ integer.
Three physical conditions must be met for a reaction to occur. First,
a bonding atom pair must be identified within the reaction distance
cutoffs. Second, the topology surrounding the bonding atom pair must
match the topology of the pre-reaction template. Finally, any reaction
constraints listed in the map file (see below) must be satisfied. If
all of these conditions are met, the reaction site is eligible to be
modified to match the post-reaction template.
match the topology of the pre-reaction template. Only atom types and
bond connectivity are used to identify a valid reaction site (not bond
types, etc.). Finally, any reaction constraints listed in the map file
(see below) must be satisfied. If all of these conditions are met, the
reaction site is eligible to be modified to match the post-reaction
template.
A bonding atom pair will be identified if several conditions are met.
First, a pair of atoms I,J within the specified react-group-ID of type