#
#  All these atom types are used to define interactions with PN (normal lone pairs) of rings and other pi-groups
#  TODO: do they need to interact with aromatic carbons (A), too?
#  TODO: do planar atoms (Np, Op, etc) interact with each other? see 4BFQ.
#  
# 
#   - atom types are defined according to the SMARTS sequence
#   - atoms for which atom types are defined are specified in the second field
#   - for SMARTS atoms for which no atom type is defined, '*' is used
#
#   TODO:   maybe the indices are not necessary if null ('*') are used
#           re-consider oxygen types: there are a lot, not sure if all needed
#
#

[CH2X4][CH2X4][CH2X4][NHX3][CH0X3](=[NH2X3+,NHX2+0,N])[NH2X3]       guanidine;                          3,4,5,6;    *,*,*,Np,Cp,Np,Np

[*][CX3](=[OX1])[NX3H2]                                             amides;                             0,1,2,3;    *,Cp,Op,Np

[*][CX3](=[OX1])[OH0-,OH]                                           carboxylic/carboxylate;             0,1,2,3;    *,Cp,Op,Op

###  N-methylpyrrole, etc... (maybe superfluous? Np would be sufficient?)
[n;X3]                                                              N aromatic non-HBacc;               0;          Nr

### anyline
[N;X3]~[a]                                                          N aromatic amine non-HBacc;         0;          Np

### pyridine
[n;X2]                                                              N aromatic HBacc;                   0;          Nl

### aromatic hydroxyl/ether/cyclic carbonyl
[#8;!R]~[a]                                                         O aromatic OH HBacc;                0;          Op

[s]                                                                 S aromatic non-HBacc;               0;          Sr

[o]                                                                 O aromatic non-HBacc;               0;          Or

[NX4]                                                               N charged non-HBacc;                0;          N+

### nitro (NOTE: maybe Or instead of On, since both non HBacc?)
O~[N](~[O])-[a]                                                     aromatic nitro (all non-HBAcc);     0,1,2;      On,Np,On,*


### This might be superfluous? it has pseudo-atoms already...
[CH2X4][SX2][*]                                                     S cys/met;                          1;          *,Sp,*

[C]=[C]                                                             C aliphatic unsaturated;            0,1;        Cp,Cp
# TODO: sp1 (do they interact with aromatic? check literature)
