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Merge pull request #2037 from ReactionMechanismGenerator/add_Phosphorus_atomType
Add phosphorus atom types
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‎documentation/source/reference/molecule/atomtype.rst‎

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``Sit`` silicon atom with one triple bond and one single bond
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``Sib`` silicon atom with two benzene bonds and one single bond
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``Sibf`` silicon atom with three benzene bonds
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*Phosphorus atom types*
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``P`` phosphorus atom with any local bond structure
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``P0sc`` charged phosphorus atom with three lone pairs (valence 0) and up to 1 single bond
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``P1s`` phosphorus atom with two lone pairs (valence 1) and up to 1 single bond
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``P1sc`` charged phosphorus atom with two lone pairs (valence 1) and up to 2 single bonds
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``P1dc`` charged phosphorus atom with two lone pairs (valence 1) and 1 double bond
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``P3s`` phosphorus atom with one lone pair (valence 3) and up to 3 single bonds
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``P3d`` phosphorus atom with one lone pair (valence 3), 1 double bond and up to 1 single bond
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``P3t`` phosphorus atom with one lone pair (valence 3) and 1 triple bond
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``P3b`` phosphorus atom with one lone pair (valence 3) and 2 benzene bonds
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``P5s`` phosphorus atom with no lone pairs (valence 5) and up to 5 single bonds
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``P5sc`` charged phosphorus atom with no lone pairs (valence 5) and up to 6 single bonds
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``P5d`` phosphorus atom with no lone pairs (valence 5), 1 double bond and up to 3 single bonds
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``P5dd`` phosphorus atom with no lone pairs (valence 5), 2 double bonds and up to 1 single bond
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``P5dc`` charged phosphorus atom with no lone pairs (valence 5), 1 double bond and up to 2 single bonds
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``P5ddc`` charged phosphorus atom with no lone pairs (valence 5) and 2 double bonds
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``P5t`` phosphorus atom with no lone pairs (valence 5), 1 triple bond and up to 2 single bonds
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``P5td`` phosphorus atom with no lone pairs (valence 5), 1 triple bond and 1 double bond
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``P5tc`` charged phosphorus atom with no lone pairs (valence 5), 1 triple bond and up to 1 single bond
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``P5b`` phosphorus atom with no lone pairs (valence 5), 2 benzene bonds and up to 1 single bond
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``P5bd`` phosphorus atom with no lone pairs (valence 5), 2 benzene bonds and 1 double bond
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*Sulfur atom types*
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``S`` sulfur atom with any local bond structure

‎documentation/source/users/rmg/database/introduction.rst‎

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+----------+-------------------+------------------------------------------------------------------------------------------------------------------+
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|Sibf |Silicon |Three benzene bonds (fused aromatics) |
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+----------+-------------------+------------------------------------------------------------------------------------------------------------------+
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|P |Phosphorus |No requirements |
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+----------+-------------------+------------------------------------------------------------------------------------------------------------------+
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|P0sc |Phosphorus |Three lone pairs, up to one single bond, charged -2 |
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+----------+-------------------+------------------------------------------------------------------------------------------------------------------+
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|P1s |Phosphorus |Two lone pairs, up to one single bond |
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+----------+-------------------+------------------------------------------------------------------------------------------------------------------+
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|P1sc |Phosphorus |Two lone pairs, up to two single bonds, charged -1 |
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+----------+-------------------+------------------------------------------------------------------------------------------------------------------+
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|P1dc |Phosphorus |Two lone pairs, one double bond, charged -1 |
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+----------+-------------------+------------------------------------------------------------------------------------------------------------------+
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|P3s |Phosphorus |One lone pair, up to three single bonds |
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+----------+-------------------+------------------------------------------------------------------------------------------------------------------+
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|P3d |Phosphorus |One lone pair, one double bond, up to one single bond |
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+----------+-------------------+------------------------------------------------------------------------------------------------------------------+
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|P3t |Phosphorus |One lone pair, one triple bond |
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+----------+-------------------+------------------------------------------------------------------------------------------------------------------+
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|P3b |Phosphorus |One lone pair, two aromatic bonds |
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+----------+-------------------+------------------------------------------------------------------------------------------------------------------+
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|P5s |Phosphorus |No lone pairs, up to five single bonds |
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+----------+-------------------+------------------------------------------------------------------------------------------------------------------+
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|P5sc |Phosphorus |No lone pairs, up to six single bonds, charged -1/+1/+2 |
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+----------+-------------------+------------------------------------------------------------------------------------------------------------------+
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|P5d |Phosphorus |No lone pairs, one double bond, up to three single bonds |
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+----------+-------------------+------------------------------------------------------------------------------------------------------------------+
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|P5dd |Phosphorus |No lone pairs, two double bonds, up to one single bond |
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+----------+-------------------+------------------------------------------------------------------------------------------------------------------+
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|P5dc |Phosphorus |No lone pairs, one double bond, up to two single bonds, charged +1 |
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+----------+-------------------+------------------------------------------------------------------------------------------------------------------+
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|P5ddc |Phosphorus |No lone pairs, two double bonds, charged +1 |
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+----------+-------------------+------------------------------------------------------------------------------------------------------------------+
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|P5t |Phosphorus |No lone pairs, one triple bond, up to two single bonds |
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+----------+-------------------+------------------------------------------------------------------------------------------------------------------+
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|P5td |Phosphorus |No lone pairs, one triple bond, one double bond |
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+----------+-------------------+------------------------------------------------------------------------------------------------------------------+
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|P5tc |Phosphorus |No lone pairs, one triple bond, up to one single bond, charged +1 |
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+----------+-------------------+------------------------------------------------------------------------------------------------------------------+
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|P5b |Phosphorus |No lone pairs, two aromatic bonds, up to one single bond, charged 0/+1 |
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+----------+-------------------+------------------------------------------------------------------------------------------------------------------+
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|P5bd |Phosphorus |No lone pairs, two aromatic bonds, one double bond |
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+----------+-------------------+------------------------------------------------------------------------------------------------------------------+
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|S |Sulfur |No requirements |
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+----------+-------------------+------------------------------------------------------------------------------------------------------------------+
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|Sa |Sulfur |Atomic sulfur with three lone pairs and no bonds |

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