# Please go to the end to see rules of defining an atom

============================================================================================
                        Definition begin
============================================================================================
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WILDATOM XX C N O S P
WILDATOM XA O S
WILDATOM XB N P
WILDATOM XC F Cl Br I
WILDATOM XD S P
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 f1  f2    f3  f4  f5  f6  f7  f8      		f9
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ATD  C.3   *   6   4   &
ATD  C.cat *   6   3   *   *   *  		(N3,N3,N3)  &
ATD  C.ar  *   6   3   *   *   [AR1]    &
ATD  C.2   *   6   3   &
ATD  C.1   *   6   2   &
ATD  C.1   *   6   1   &
ATD  H     *   1   &
ATD  F     *   9   &
ATD  Cl    *   17  &
ATD  Br    *   35  &
ATD  I     *   53  &
ATD  P.3   *   15  &
ATD  N.4   *   7   4   &
ATD  N.am  *   7   3   *   *   *                (C3(XA1))       &
ATD  N.pl3 *   7   3   *   *   *       		(O1,O1)		&
ATD  N.pl3 *   7   3   *   *   [AR1.AR2.AR3]    &
ATD  N.3   *   7   3   &
ATD  N.ar  *   7   2   *   *   [AR1]    &
ATD  N.2   *   7   2   &
ATD  N.1   *   7   1   &
ATD  O.co2 *   8   1   *   *   *       		(C3(O1))	&
ATD  O.co2 *   8   1   *   *   *       		(P(O1))		&
ATD  O.2   *   8   1   &
ATD  O.3   *   8   2   &
ATD  S.2   *   16  1   &
ATD  S.3   *   16  2   &
ATD  S.o   *   16  3   *   *   *       		(O1[DB'])  	&
ATD  S.o2  *   16  4   *   *   *       		(O1[DB'],O1[DB'])  	&
ATD  S.3   *   16  &
ATD  Li    *   3   &
ATD  Be    *   4   &
ATD  B     *   5   &
ATD  Na    *   11  &
ATD  Mg    *   12  &
ATD  Al    *   13  &
ATD  Si    *   14  &
ATD  K     *   19  &
ATD  Ca    *   20  &
ATD  Sr    *   38  &
ATD  Ba    *   56  &
ATD  Sc    *   21  &
ATD  Ti    *   22  &
ATD  V     *   23  &
ATD  Cr    *   24  &
ATD  Mn    *   25  &
ATD  Fe    *   26  &
ATD  Co    *   27  &
ATD  Ni    *   28  &
ATD  Cu    *   29  &
ATD  Zn    *   30  &
ATD  Ga    *   31  &
ATD  Ge    *   32  &
ATD  As    *   33  &
ATD  Se    *   34  &
ATD  Ru    *   44  &
ATD  Rh    *   45  &
ATD  Pd    *   46  &
ATD  Ag    *   47  &
ATD  Cd    *   48  &
ATD  Pt    *   78  &
ATD  Au    *   79  &
ATD  Hg    *   80  &
ATD  Tl    *   81  &
ATD  Pb    *   82  &
ATD  lp    *   0   1   &
ATD  ANY   &
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============================================================================================
			Field descriptions
============================================================================================
f1  ATD, which stands for atom type definition, ATD should always in the first three columns
f2  Atom type name, can be letters or numbers
f3  Residue names, which means this description is only applied to atoms in special residues
f4  Atomic number
f5  Number of attached atoms
f6  Number of attached hydrogen atoms
f7  For hydrogen, number of the electron-withdrawal atoms connected to the atom that the
    hydrogen attached
f8  atomic property
f9  Chemical environment definitions


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			Specific symbols
============================================================================================
*  Ignore this field
&  End of definition
.  "or" operation in the ring and aromatity descriptions


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			Predefined words
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EW   Electron-withdraw atom
AA   Amino acid residue
NA   Nucleic acid
BIO  AA + NA

AR1  Pure aromatic atom (such as benzene and pyridine)
AR2  Atom in a planar ring, usually the ring has two continuous single bonds and at least two
     double bonds
AR3  Atom in a planar ring, which has one or several double bonds formed between non-ring atoms
     and the ring atoms
AR4  Atom other than AR1, AR2, AR3 and AR5.
AR5  Pure aliphatic atom in a ring, which is made of sp3 carbon

RG   Ring (from 3-membered to nine-membered)
RG3  3-membered ring
RG4  4-membered ring
RG5  5-membered ring
RG6  6-membered ring
RG7  7-membered ring
RG8  8-membered ring
RG9  9-membered ring
NR   non-ring atom

SB   Single bond
DB   Double bond
TB   Triple bond
AB   Aromatic bond
DL   Delocalized bond (9 in AM1-BCC)
sb   Single bond, including aromatic single, delocalized bond (9 in AM1-BCC)
db   Double bond, including aromatic double
tb   Triple bond

'    Bond type (SB sb etc) followed by ' means the current atom forms this kind of bond with the
     immediate predecessor in a chain of atoms
     For example, (XD3[SB',db]) means the current atom XD3 has a double bond with the atom in
     definition
''   Bond type (SB sb etc) followed by '' means the current atom does not form this kind of bond
     with the immediate predecessor in a chain of atoms
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			Miscellaneous
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1. maximum line length is 500 characters
2. no space in the atomic property string
3. no space in the chemical environment string
4. no filed missing before &
5. the definition order is crucial, special atom types should defined before the more general
   ones
