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this should have been added long ago
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Greg Landrum
199
Data/BaseFeatures.fdef
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199
Data/BaseFeatures.fdef
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# $Id$
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#
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# RDKit base fdef file.
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# Created by Greg Landrum
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#
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AtomType NDonor [N&!H0&v3,N&!H0&+1&v4,n&H1&+0]
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AtomType AmideN [$(N-C(=O))]
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AtomType SulfonamideN [$([N;H0]S(=O)(=O))]
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AtomType NDonor [$([Nv3](-C)(-C)-C)]
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AtomType NDonor [$(n[n;H1]),$(nc[n;H1])]
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AtomType ChalcDonor [O,S;H1;+0]
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DefineFeature SingleAtomDonor [{NDonor},{ChalcDonor}]
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Family Donor
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Weights 1
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EndFeature
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# aromatic N, but not indole or pyrole or fusing two rings
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AtomType NAcceptor [n;+0;!X3;!$([n;H1](cc)cc)]
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AtomType NAcceptor [$([N;H0]#[C&v4])]
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# tertiary nitrogen adjacent to aromatic carbon
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AtomType NAcceptor [N&v3;H0;$(Nc)]
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# removes thioether and nitro oxygen
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AtomType ChalcAcceptor [O;H0;v2;!$(O=N-*)]
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Atomtype ChalcAcceptor [O;-;!$(*-N=O)]
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# Removed aromatic sulfur from ChalcAcceptor definition
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Atomtype ChalcAcceptor [o;+0]
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# Hydroxyls and acids
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AtomType Hydroxyl [O;H1;v2]
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# F is an acceptor so long as the C has no other halogen neighbors. This is maybe
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# a bit too general, but the idea is to eliminate things like CF3
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AtomType HalogenAcceptor [F;$(F-[#6]);!$(FC[F,Cl,Br,I])]
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DefineFeature SingleAtomAcceptor [{Hydroxyl},{ChalcAcceptor},{NAcceptor},{HalogenAcceptor}]
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Family Acceptor
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Weights 1
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EndFeature
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# this one is delightfully easy:
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DefineFeature AcidicGroup [C,S](=[O,S,P])-[O;H1,H0&-1]
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Family NegIonizable
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Weights 1.0,1.0,1.0
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EndFeature
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AtomType Carbon_NotDouble [C;!$(C=*)]
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AtomType BasicNH2 [$([N;H2&+0][{Carbon_NotDouble}])]
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AtomType BasicNH1 [$([N;H1&+0]([{Carbon_NotDouble}])[{Carbon_NotDouble}])]
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AtomType PosNH3 [$([N;H3&+1][{Carbon_NotDouble}])]
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AtomType PosNH2 [$([N;H2&+1]([{Carbon_NotDouble}])[{Carbon_NotDouble}])]
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AtomType PosNH1 [$([N;H1&+1]([{Carbon_NotDouble}])([{Carbon_NotDouble}])[{Carbon_NotDouble}])]
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AtomType BasicNH0 [$([N;H0&+0]([{Carbon_NotDouble}])([{Carbon_NotDouble}])[{Carbon_NotDouble}])]
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AtomType QuatN [$([N;H0&+1]([{Carbon_NotDouble}])([{Carbon_NotDouble}])([{Carbon_NotDouble}])[{Carbon_NotDouble}])]
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DefineFeature BasicGroup [{BasicNH2},{BasicNH1},{BasicNH0};!$(N[a])]
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Family PosIonizable
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Weights 1.0
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EndFeature
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DefineFeature PosN [#7;+]
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Family PosIonizable
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Weights 1.0
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EndFeature
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# imidazole group can be positively charged (too promiscuous?)
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DefineFeature Imidazole c1ncnc1
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Family PosIonizable
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Weights 1.0,1.0,1.0,1.0,1.0
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EndFeature
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# guanidine group is positively charged (too promiscuous?)
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DefineFeature Guanidine NC(=N)N
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Family PosIonizable
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Weights 1.0,1.0,1.0,1.0
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EndFeature
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# the LigZn binder features were adapted from combichem.fdl
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DefineFeature ZnBinder1 [S;D1]-[#6]
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Family ZnBinder
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Weights 1,0
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EndFeature
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DefineFeature ZnBinder2 [#6]-C(=O)-C-[S;D1]
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Family ZnBinder
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Weights 0,0,1,0,1
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EndFeature
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DefineFeature ZnBinder3 [#6]-C(=O)-C-C-[S;D1]
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Family ZnBinder
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Weights 0,0,1,0,0,1
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EndFeature
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DefineFeature ZnBinder4 [#6]-C(=O)-N-[O;D1]
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Family ZnBinder
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Weights 0,0,1,0,1
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EndFeature
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DefineFeature ZnBinder5 [#6]-C(=O)-[O;D1]
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Family ZnBinder
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Weights 0,0,1,1
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EndFeature
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DefineFeature ZnBinder6 [#6]-P(=O)(-O)-[C,O,N]-[C,H]
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Family ZnBinder
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Weights 0,0,1,1,0,0
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EndFeature
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# aromatic rings of various sizes:
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#
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# Note that with the aromatics, it's important to include the ring-size queries (;rN) along with
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# the aromaticity query for two reasons:
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# 1) Much of the current feature-location code assumes that the feature point is
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# equidistant from the atoms defining it. Larger definitions like: a1aaaaaaaa1 will actually
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# match things like 'o1c2cccc2ccc1', which have an aromatic unit spread across multiple simple
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# rings and so don't fit that requirement.
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# 2) It's *way* faster.
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#
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DefineFeature Arom4 [a;r4]1[a;r4][a;r4][a;r4]1
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Family Aromatic
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Weights 1.0,1.0,1.0,1.0
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EndFeature
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DefineFeature Arom5 [a;r5]1[a;r5][a;r5][a;r5][a;r5]1
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Family Aromatic
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Weights 1.0,1.0,1.0,1.0,1.0
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EndFeature
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DefineFeature Arom6 [a;r6]1[a;r6][a;r6][a;r6][a;r6][a;r6]1
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Family Aromatic
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Weights 1.0,1.0,1.0,1.0,1.0,1.0
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EndFeature
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DefineFeature Arom7 [a;r7]1[a;r7][a;r7][a;r7][a;r7][a;r7][a;r7]1
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Family Aromatic
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Weights 1.0,1.0,1.0,1.0,1.0,1.0,1.0
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EndFeature
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DefineFeature Arom8 [a;r8]1[a;r8][a;r8][a;r8][a;r8][a;r8][a;r8][a;r8]1
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Family Aromatic
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Weights 1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0
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EndFeature
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# hydrophobic features
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# any carbon that is not bonded to a polar atom is considered a hydrophobe
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#
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# generic non-polar carbon atom
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AtomType Carbon_Polar [$([#6][#7,#8,#9])]
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AtomType Carbon_NonPolar [#6;!{Carbon_Polar}]
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DefineFeature ThreeWayAttach [D3,D4;{Carbon_NonPolar}]
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Family Hydrophobe
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Weights 1.0
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EndFeature
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DefineFeature ChainTwoWayAttach [R0;D2;{Carbon_NonPolar}]
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Family Hydrophobe
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Weights 1.0
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EndFeature
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# hydrophobic atom
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AtomType Hphobe [c,s,S&H0&v2,Br,I,{Carbon_NonPolar}]
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AtomType RingHphobe [R;{Hphobe}]
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# nitro groups in the RD code are always: *-[N+](=O)[O-]
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DefineFeature Nitro2 [N;D3;+](=O)[O-]
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Family LumpedHydrophobe
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Weights 1.0,1.0,1.0
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EndFeature
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DefineFeature RH6_6 [r6;{RingHphobe}]1[r6;{RingHphobe}][r6;{RingHphobe}][r6;{RingHphobe}][r6;{RingHphobe}][r6;{RingHphobe}]1
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Family LumpedHydrophobe
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Weights 1.0,1.0,1.0,1.0,1.0,1.0
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EndFeature
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DefineFeature RH5_5 [r5;{RingHphobe}]1[r5;{RingHphobe}][r5;{RingHphobe}][r5;{RingHphobe}][r5;{RingHphobe}]1
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Family LumpedHydrophobe
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Weights 1.0,1.0,1.0,1.0,1.0
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EndFeature
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DefineFeature RH4_4 [r4;{RingHphobe}]1[r4;{RingHphobe}][r4;{RingHphobe}][r4;{RingHphobe}]1
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Family LumpedHydrophobe
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Weights 1.0,1.0,1.0,1.0
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EndFeature
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DefineFeature RH3_3 [r3;{RingHphobe}]1[r3;{RingHphobe}][r3;{RingHphobe}]1
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Family LumpedHydrophobe
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Weights 1.0,1.0,1.0
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EndFeature
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DefineFeature tButyl [C;!R](-[CH3])(-[CH3])-[CH3]
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Family LumpedHydrophobe
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Weights 1.0,0.0,0.0,0.0
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EndFeature
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DefineFeature iPropyl [CH;!R](-[CH3])-[CH3]
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Family LumpedHydrophobe
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Weights 1.0,1.0,1.0
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EndFeature
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