# Please go to the end to see rules of defining an atom ============================================================================================ Defination begin ============================================================================================ -------------------------------------------------------------------------------------------- WILDATOM XX C N O S P WILDATOM XA O S WILDATOM XB N P WILDATOM XC F Cl Br I -------------------------------------------------------------------------------------------- f1 f2 f3 f4 f5 f6 f7 f8 f9 f10 -------------------------------------------------------------------------------------------- ATD CT * 6 4 & ATD C * 6 3 * * * (XA1) & ATD CN * 6 3 * * [RG5,RG6,AR1.AR2.AR3] (C3,C3,N3(H)) & ATD CB * 6 3 * * [RG5,RG6,AR1.AR2.AR3] & ATD CR * 6 3 * * [RG5,AR1.AR2.AR3] (N3,N3) & ATD CR * 6 3 * * [RG5,AR1.AR2.AR3] (N2,N3(H)) & ATD CK * 6 3 * * [RG5,AR1.AR2.AR3] (N2,N3) & ATD CC * 6 3 0 * [RG5,AR1.AR2.AR3] (C3,N3(C3,H)) & ATD CC * 6 3 0 * [RG5,AR1.AR2.AR3] (C3,N2(C3)) & ATD CW * 6 3 * * [RG5,AR1.AR2.AR3] (C3,N3(H)) & ATD CV * 6 3 * * [RG5,AR1.AR2.AR3] (C3,N2) & ATD C* * 6 3 * * [RG5,AR1.AR2.AR3] (C3,C3) & ATD CQ * 6 3 * * [RG6,AR1.AR2.AR3] (N2,N2) & ATD CM * 6 3 * * [RG6,AR1.AR2.AR3] (C3,C3(N2(C3(N3(C3))))) & ATD CM * 6 3 * * [RG6,AR1.AR2.AR3] (C3,C3(N3(C3(N3(C3))))) & ATD CM * 6 3 * * [RG6,AR1.AR2.AR3] (C3,N3(C3(N2(C3(C3))))) & ATD CM * 6 3 * * [RG6,AR1.AR2.AR3] (N3,C3(C3(N3(C3(N3))))) & ATD CA * 6 3 * * [AR1.AR2.AR3] & ATD CD * 6 3 * * * (C3,C3) & ATD CM * 6 3 & ATD CZ * 6 2 & ATD H * 1 1 * * * (N) & ATD HO * 1 1 * * * (O) & ATD HS * 1 1 * * * (S) & ATD HP * 1 1 * * * (C(N4)) & ATD HW * 1 1 * * * (O(H1)) & ATD H3 * 1 1 * 3 * (C4) & ATD H2 * 1 1 * 2 * (C4) & ATD H1 * 1 1 * 1 * (C4) & ATD HC * 1 1 * * * (C4) & ATD H5 * 1 1 * 2 * (XX[AR1.AR2.AR3]) & ATD H4 * 1 1 * 1 * (XX[AR1.AR2.AR3]) & ATD HA * 1 1 * * * (XX[AR1.AR2.AR3]) & ATD HA * 1 1 & ATD F * 9 1 & ATD Cl * 17 1 & ATD Br * 35 1 & ATD F * 53 1 & ATD P * 15 & ATD N1 * 7 1 & ATD NB * 7 2 * * [RG5,AR1.AR2.AR3] & ATD NC * 7 2 * * [RG6,AR1.AR2.AR3] & ATD N2 * 7 * * * * (C3(N3,N3)) & ATD N2 * 7 * * * * (C3(N3,N3)) & ATD NO * 7 3 * * * (O1,O1) & ATD NA * 7 3 1 * [RG5.RG6,AR1.AR2.AR3] & ATD N2 * 7 3 * * [NR] (XX[AR1.AR2.AR3]) & ATD N* * 7 3 * * [AR1.AR2.AR3] & ATD N * 7 3 * * * (C3(XA1)) & ATD NT * 7 3 & ATD N3 * 7 4 & ATD O2 * 8 1 * * * (C(O1)) & ATD O2 * 8 1 * * * (P) & ATD O * 8 1 * * * (C) & ATD O * 8 1 * * * (S) & ATD OH * 8 2 1 & ATD OW * 8 2 2 & ATD OS * 8 2 & ATD SH * 16 2 1 & ATD SH * 16 2 2 & ATD S * 16 2 & ATD SO * 16 4 & ATD LP * 0 & ATD DU & -------------------------------------------------------------------------------------------- ============================================================================================ ============================================================================================ Field descriptions ============================================================================================ (1) ATD, which stands for atom type defination, ATD should always in the first three columns (2) Atom type name, can be letters or numbers (3) Residue names, which means this description is only applied to atoms in special residues (4) Atomic number (5) Number of attached atoms (6) Number of attached hydrogen atoms (7) For hydrogen, number of the electron-withdrawal atoms connected to the atom that the hydrogen attached (8) atomic property (9) Chemical enviornment definations ============================================================================================ Specific symbols ============================================================================================ * Ignore this field & End of defination . "or" operation in the ring and aromatity descriptions ============================================================================================ Predefined words ============================================================================================ EW Electron-withdraw atom AA Amino acid residue NA Nucleric acid BIO AA + NA AR1 Pure aromatic atom (benzene and pyridine) AR2 Atom in a planar ring, usually the ring has two continous single bonds AR3 Atom in a planar ring, which has one or several double bonds formed between outside atoms and 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 NG non-ring atom SB Single bond DB Double bond TB Triple bond AB Aromatic bond sb Single bond, including aromatic single db Double bond, including aromatic double tb Triple bond ============================================================================================ Miscellaneous ============================================================================================ 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 defination order is crucial, special atom types should defined before the more general ones 6. Bonds in COO- and -NO2 are considered as double bonds