Add phosphorus atom types

documentation/source/reference/molecule/atomtype.rst

@@ -86,6 +86,28 @@ Atom type       Description
 ``Sit``         silicon atom with one triple bond and one single bond
 ``Sib``         silicon atom with two benzene bonds and one single bond
 ``Sibf``        silicon atom with three benzene bonds
+*Phosphorus atom types*
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+``P``           phosphorus atom with any local bond structure
+``P0sc``        charged phosphorus atom with three lone pairs (valence 0) and up to 1 single bond
+``P1s``         phosphorus atom with two lone pairs (valence 1) and up to 1 single bond
+``P1sc``        charged phosphorus atom with two lone pairs (valence 1) and up to 2 single bonds
+``P1dc``        charged phosphorus atom with two lone pairs (valence 1) and 1 double bond
+``P3s``         phosphorus atom with one lone pair (valence 3) and up to 3 single bonds
+``P3d``         phosphorus atom with one lone pair (valence 3), 1 double bond and up to 1 single bond
+``P3t``         phosphorus atom with one lone pair (valence 3) and 1 triple bond
+``P3b``         phosphorus atom with one lone pair (valence 3) and 2 benzene bonds
+``P5s``         phosphorus atom with no lone pairs (valence 5) and up to 5 single bonds
+``P5sc``        charged phosphorus atom with no lone pairs (valence 5) and up to 6 single bonds
+``P5d``         phosphorus atom with no lone pairs (valence 5), 1 double bond and up to 3 single bonds
+``P5dd``        phosphorus atom with no lone pairs (valence 5), 2 double bonds and up to 1 single bond
+``P5dc``        charged phosphorus atom with no lone pairs (valence 5), 1 double bond and up to 2 single bonds
+``P5ddc``       charged phosphorus atom with no lone pairs (valence 5) and 2 double bonds
+``P5t``         phosphorus atom with no lone pairs (valence 5), 1 triple bond and up to 2 single bonds
+``P5td``        phosphorus atom with no lone pairs (valence 5), 1 triple bond and 1 double bond
+``P5tc``        charged phosphorus atom with no lone pairs (valence 5), 1 triple bond and up to 1 single bond
+``P5b``         phosphorus atom with no lone pairs (valence 5), 2 benzene bonds and up to 1 single bond
+``P5bd``        phosphorus atom with no lone pairs (valence 5), 2 benzene bonds and 1 double bond
 *Sulfur atom types*
 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
 ``S``           sulfur atom with any local bond structure

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

@@ -135,6 +135,46 @@ table below shows all atoms types in RMG.
 +----------+-------------------+------------------------------------------------------------------------------------------------------------------+
 |Sibf      |Silicon            |Three benzene bonds (fused aromatics)                                                                             |
 +----------+-------------------+------------------------------------------------------------------------------------------------------------------+
+|P         |Phosphorus         |No requirements                                                                                                   |
++----------+-------------------+------------------------------------------------------------------------------------------------------------------+
+|P0sc      |Phosphorus         |Three lone pairs, up to one single bond, charged -2                                                               |
++----------+-------------------+------------------------------------------------------------------------------------------------------------------+
+|P1s       |Phosphorus         |Two lone pairs, up to one single bond                                                                             |
++----------+-------------------+------------------------------------------------------------------------------------------------------------------+
+|P1sc      |Phosphorus         |Two lone pairs, up to two single bonds, charged -1                                                                |
++----------+-------------------+------------------------------------------------------------------------------------------------------------------+
+|P1dc      |Phosphorus         |Two lone pairs, one double bond, charged -1                                                                       |
++----------+-------------------+------------------------------------------------------------------------------------------------------------------+
+|P3s       |Phosphorus         |One lone pair, up to three single bonds                                                                           |
++----------+-------------------+------------------------------------------------------------------------------------------------------------------+
+|P3d       |Phosphorus         |One lone pair, one double bond, up to one single bond                                                             |
++----------+-------------------+------------------------------------------------------------------------------------------------------------------+
+|P3t       |Phosphorus         |One lone pair, one triple bond                                                                                    |
++----------+-------------------+------------------------------------------------------------------------------------------------------------------+
+|P3b       |Phosphorus         |One lone pair, two aromatic bonds                                                                                 |
++----------+-------------------+------------------------------------------------------------------------------------------------------------------+
+|P5s       |Phosphorus         |No lone pairs, up to five single bonds                                                                            |
++----------+-------------------+------------------------------------------------------------------------------------------------------------------+
+|P5sc      |Phosphorus         |No lone pairs, up to six single bonds, charged -1/+1/+2                                                           |
++----------+-------------------+------------------------------------------------------------------------------------------------------------------+
+|P5d       |Phosphorus         |No lone pairs, one double bond, up to three single bonds                                                          |
++----------+-------------------+------------------------------------------------------------------------------------------------------------------+
+|P5dd      |Phosphorus         |No lone pairs, two double bonds, up to one single bond                                                            |
++----------+-------------------+------------------------------------------------------------------------------------------------------------------+
+|P5dc      |Phosphorus         |No lone pairs, one double bond, up to two single bonds, charged +1                                                |
++----------+-------------------+------------------------------------------------------------------------------------------------------------------+
+|P5ddc     |Phosphorus         |No lone pairs, two double bonds, charged +1                                                                       |
++----------+-------------------+------------------------------------------------------------------------------------------------------------------+
+|P5t       |Phosphorus         |No lone pairs, one triple bond, up to two single bonds                                                            |
++----------+-------------------+------------------------------------------------------------------------------------------------------------------+
+|P5td      |Phosphorus         |No lone pairs, one triple bond, one double bond                                                                   |
++----------+-------------------+------------------------------------------------------------------------------------------------------------------+
+|P5tc      |Phosphorus         |No lone pairs, one triple bond, up to one single bond, charged +1                                                 |
++----------+-------------------+------------------------------------------------------------------------------------------------------------------+
+|P5b       |Phosphorus         |No lone pairs, two aromatic bonds, up to one single bond, charged 0/+1                                            |
++----------+-------------------+------------------------------------------------------------------------------------------------------------------+
+|P5bd      |Phosphorus         |No lone pairs, two aromatic bonds, one double bond                                                                |
++----------+-------------------+------------------------------------------------------------------------------------------------------------------+
 |S         |Sulfur             |No requirements                                                                                                   |
 +----------+-------------------+------------------------------------------------------------------------------------------------------------------+
 |Sa        |Sulfur             |Atomic sulfur with three lone pairs and no bonds                                                                  |