|
Molmodel
|
Ligands.h
Go to the documentation of this file.
00001 #include "molmodel/internal/common.h" 00002 #include "molmodel/internal/Compound.h" 00003 #include <iostream> 00004 #include <fstream> 00005 //#include <ios> 00006 00007 namespace SimTK 00008 { 00009 00010 // 00011 // This ligand is from 1UUI.pdb. Reference is: 00012 // 1. Davis, B. et al. Rational design of inhibitors of HIV-1 TAR RNA through the stabilisation of electrostatic "hot spots". J. Mol. Biol 336, 343-56(2004). 00013 // 00014 00015 class P12 : public Compound { 00016 public: 00017 //takes a DuMMForceFieldSubsystem as a reference argument so as to define all Biotypes, etc within the class. 00018 P12(DuMMForceFieldSubsystem &dumm) 00019 { 00020 00021 setBaseCompound("methyl", MethylGroup() ); 00022 bondAtom(BivalentAtom("OA1",Element::Oxygen(),109.5*Deg2Rad), "methyl/bond" ,.141);// third arg of bivalentatom is a bond angle in rads ;. angle betw bond1 and bond2. third argument of bondAtom is a distance. 00023 bondAtom(TrivalentAtom("C4", Element::Carbon()),"OA1/bond2",.141);//120*Deg2Rad); 00024 bondCompound("C3compound",AromaticSixMemberedCHGroup(),"C4/bond2",.141);//4th param is a distance. 00025 bondCompound("C5compound",AromaticSixMemberedCHGroup(),"C4/bond3",.141); 00026 bondCompound("C6compound",AromaticSixMemberedCHGroup(),"C5compound/C/bond2",.141); 00027 bondAtom(TrivalentAtom("C1", Element::Carbon()),"C6compound/C/bond2",.141); 00028 bondAtom(TrivalentAtom("C2", Element::Carbon()),"C3compound/C/bond2",.141); 00029 addRingClosingBond("C1/bond3", "C2/bond3", 0.1410); 00030 nameAtom("C5", "C5compound/C"); 00031 nameAtom("C6", "C6compound/C"); 00032 defineDihedralAngle("C4C3CC2C1","C4","C3compound/C","C2" ,"C1");//OA/bond2", "C1/bond2"); 00033 setDefaultDihedralAngle("C4C3CC2C1", 0.00*Deg2Rad); 00034 bondCompound("CAcompound",MethyleneGroup(),"C2/bond2" ,.141); 00035 nameAtom("CA", "CAcompound/C"); 00036 nameAtom("HA1", "CAcompound/H1"); 00037 nameAtom("HA2", "CAcompound/H2"); 00038 defineDihedralAngle("theta", "C4","C3compound/C","C2","CA");//OA/bond2", "C1/bond2"); 00039 setDefaultDihedralAngle("theta",140.0 *Deg2Rad); 00040 bondAtom(QuadrivalentAtom("NB",Element::Nitrogen()),"CAcompound/bond2",.141);// last param is distance; set to something more real // trivalent antom takes 2 bond angles, betw bond1 and bond2, and betw bond1 and bond3. //trivalents default to planar 00041 bondAtom( UnivalentAtom("HB",Element::Hydrogen()),"NB/bond4",.141);// last param is distance; set to something more real // trivalent antom takes 2 bond angles, betw bond1 and bond2, and betw bond1 and bond3. //trivalents default to planar 00042 defineDihedralAngle("omega", "C3compound/C","C2","CA","NB");//OA/bond2", "C1/bond2"); 00043 setDefaultDihedralAngle("omega", 40.0 *Deg2Rad); 00044 bondAtom(BivalentAtom("OA",Element::Oxygen(),109.5*Deg2Rad), "C1/bond2" ,.141); 00045 00046 bondCompound( "CBcompound",MethyleneGroup(),"OA/bond2" ,.141); 00047 nameAtom( "CB", "CBcompound/C"); 00048 nameAtom( "HB1","CBcompound/H1"); 00049 nameAtom( "HB2","CBcompound/H2"); 00050 00051 defineDihedralAngle("alpha", "C6compound/C","C1","OA","CB");//OA/bond2", "C1/bond2"); 00052 setDefaultDihedralAngle("alpha", 40.0 *Deg2Rad); 00053 00054 //bondAtom(QuadrivalentAtom("CG",Element::Carbon()), "CBcompound/bond2" ,.141); 00055 bondCompound("CGcompound",MethyleneGroup(),"CBcompound/bond2" ,.141); 00056 nameAtom("CG", "CGcompound/C"); 00057 nameAtom("HG1","CGcompound/H1"); 00058 nameAtom("HG2","CGcompound/H2"); 00059 //bondAtom(QuadrivalentAtom("CD",Element::Carbon()), "CGcompound/bond2" ,.141); 00060 bondCompound( "CDcompound",MethyleneGroup(),"CGcompound/bond2" ,.141); 00061 nameAtom("CD", "CDcompound/C"); 00062 nameAtom("HD1","CDcompound/H2"); 00063 nameAtom("HD2","CDcompound/H1"); 00064 defineDihedralAngle("zeta", "C1","OA","CB","CG");//OA/bond2", "C1/bond2"); 00065 setDefaultDihedralAngle("zeta" , 40.0 *Deg2Rad); 00066 //bondAtom(QuadrivalentAtom("NE",Element::Nitrogen()),"CDcompound/bond2",.141);// last param is distance; set to something more real // trivalent antom takes 2 bond angles, betw bond1 and bond2, and betw bond1 and bond3. //trivalents default to planar 00067 bondCompound("NEcompound",PrimaryAmineGroup(),"CDcompound/bond2" ,.141); 00068 nameAtom("NE", "NEcompound/N"); 00069 nameAtom("HE1","NEcompound/H1"); 00070 nameAtom("HE2","NEcompound/H2"); 00071 nameAtom("HE3","NEcompound/H3"); 00072 00073 defineDihedralAngle("gamma", "C3compound/C","C2","CA","NB");//OA/bond2", "C1/bond2"); 00074 setDefaultDihedralAngle("gamma", 140.0*Deg2Rad); 00075 //bondAtom(QuadrivalentAtom("CG1",Element::Carbon()), "NB/bond3" ,.141); 00076 bondCompound("CG1compound",MethyleneGroup(),"NB/bond2" ,.141); 00077 nameAtom("CG1", "CG1compound/C"); 00078 nameAtom("HG11","CG1compound/H2"); 00079 nameAtom("HG12","CG1compound/H1"); 00080 bondCompound("CG2compound",MethyleneGroup(),"NB/bond3" ,.141); 00081 nameAtom("CG2", "CG2compound/C"); 00082 nameAtom("HG21","CG2compound/H1"); 00083 nameAtom("HG22","CG2compound/H2"); 00084 bondCompound("CD1compound",MethyleneGroup(),"CG1compound/bond2" ,.141); 00085 nameAtom("CD1", "CD1compound/C"); 00086 nameAtom("HD11","CD1compound/H1"); 00087 nameAtom("HD12","CD1compound/H2"); 00088 bondCompound("CD2compound",MethyleneGroup(),"CG2compound/bond2" ,.141); 00089 nameAtom("CD2", "CD2compound/C"); 00090 nameAtom("HD21","CD2compound/H2"); 00091 nameAtom("HD22","CD2compound/H1"); 00092 00093 bondAtom(TrivalentAtom("NE1",Element::Nitrogen()),"CD1compound/bond2",.141); 00094 bondAtom( TrivalentAtom("CZ" ,Element::Carbon()), "NE1/bond2" ,.141); 00095 addRingClosingBond("CD2compound/bond2", "NE1/bond3", 0.1410); 00096 bondAtom(TrivalentAtom("NH1",Element::Nitrogen()), "CZ/bond2",.141); 00097 bondAtom(UnivalentAtom("HH11",Element::Hydrogen()),"NH1/bond2",.141); 00098 bondAtom(UnivalentAtom("HH12",Element::Hydrogen()),"NH1/bond3",.141); 00099 bondAtom(TrivalentAtom("NH2",Element::Nitrogen()), "CZ/bond3",.141); 00100 bondAtom(UnivalentAtom("HH21",Element::Hydrogen()),"NH2/bond2",.141); 00101 bondAtom(UnivalentAtom("HH22",Element::Hydrogen()),"NH2/bond3",.141); 00102 00103 defineDihedralAngle("delta", "NH1" ,"CZ","NE1","CD1");//OA/bond2", "C1/bond2"); 00104 setDefaultDihedralAngle("delta", 70.00*Deg2Rad); 00105 00106 defineDihedralAngle("beta" , "C1","OA","CB","CG");//OA/bond2", "C1/bond2"); 00107 setDefaultDihedralAngle("beta" , 40.0 *Deg2Rad); 00108 00109 00110 00111 00112 nameAtom("CB1", "methyl/C");// just an alias or shorthand 00113 nameAtom("HB11", "methyl/H1"); 00114 nameAtom("HB12", "methyl/H2"); 00115 nameAtom("HB13", "methyl/H3"); 00116 nameAtom("C3", "C3compound/C"); 00117 nameAtom("H3", "C3compound/H"); 00118 nameAtom("H5", "C5compound/H"); 00119 nameAtom("H6", "C6compound/H"); 00120 // nameAtom("O", "OA1"); 00121 00122 00123 00124 00125 setAtomBiotype("CB1" ,"P12","CB1" ); 00126 setAtomBiotype("HB11","P12","HB11"); 00127 setAtomBiotype("HB12","P12","HB11"); 00128 setAtomBiotype("HB13","P12","HB11"); 00129 setAtomBiotype("HA1" ,"P12","HC" ); 00130 setAtomBiotype("HA2" ,"P12","HC" ); 00131 setAtomBiotype("HB1" ,"P12","HC" ); 00132 setAtomBiotype("HB2" ,"P12","HC" ); 00133 //setBiotypeIndex( "HD1", Biotype::get("P12", "HC").getIndex() ); 00134 setAtomBiotype("HD1" ,"P12","HC" ); 00135 //setBiotypeIndex( "HD2", Biotype::get("P12", "HC").getIndex() ); 00136 setAtomBiotype("HD2" ,"P12","HC" ); 00137 //setBiotypeIndex( "HG1", Biotype::get("P12", "HC").getIndex() ); 00138 setAtomBiotype("HG1" ,"P12","HC" ); 00139 //setBiotypeIndex( "HG2", Biotype::get("P12", "HC").getIndex() ); 00140 setAtomBiotype("HG2" ,"P12","HC" ); 00141 //setBiotypeIndex("HG11", Biotype::get("P12", "HC").getIndex() ); 00142 setAtomBiotype("HG11","P12","HC" ); 00143 //setBiotypeIndex("HG12", Biotype::get("P12", "HC").getIndex() ); 00144 setAtomBiotype("HG12","P12","HC" ); 00145 //setBiotypeIndex("HG21", Biotype::get("P12", "HC").getIndex() ); 00146 setAtomBiotype("HG21","P12","HC" ); 00147 //setBiotypeIndex("HG22", Biotype::get("P12", "HC").getIndex() ); 00148 setAtomBiotype("HG22","P12","HC" ); 00149 //setBiotypeIndex("HD11", Biotype::get("P12", "HC").getIndex() ); 00150 setAtomBiotype("HD11","P12","HC" ); 00151 //setBiotypeIndex("HD12", Biotype::get("P12", "HC").getIndex() ); 00152 setAtomBiotype("HD12","P12","HC" ); 00153 //setBiotypeIndex("HD21", Biotype::get("P12", "HC").getIndex() ); 00154 setAtomBiotype("HD21","P12","HC" ); 00155 //setBiotypeIndex("HD22", Biotype::get("P12", "HC").getIndex() ); 00156 setAtomBiotype("HD22","P12","HC" ); 00157 setAtomBiotype("HE1" ,"P12", "HE1"); 00158 //setBiotypeIndex("HE1" , Biotype::get("P12", "HE1").getIndex() ); 00159 //setBiotypeIndex("HE2" , Biotype::get("P12", "HE1").getIndex() ); 00160 setAtomBiotype("HE2" ,"P12","HE1" ); 00161 //setBiotypeIndex("HE3" , Biotype::get("P12", "HE1").getIndex() ); 00162 setAtomBiotype("HE3" ,"P12","HE1" ); 00163 setAtomBiotype("HA1" ,"P12","HC" ); 00164 //setBiotypeIndex("HH11", Biotype::get("P12", "HH11").getIndex() ); 00165 setAtomBiotype("HH11","P12","HH11"); 00166 //setBiotypeIndex("HH12", Biotype::get("P12", "HH11").getIndex() ); 00167 setAtomBiotype("HH12","P12","HH11"); 00168 //setBiotypeIndex("HH21", Biotype::get("P12", "HH11").getIndex() ); 00169 setAtomBiotype("HH21","P12","HH11"); 00170 //setBiotypeIndex("HH22", Biotype::get("P12", "HH11").getIndex() ); 00171 setAtomBiotype("HH22","P12","HH11"); 00172 //setBiotypeIndex( "OA1", Biotype::get("P12", "OA1").getIndex() ); 00173 setAtomBiotype("OA1" ,"P12","OA1" ); 00174 //cout<<"check OA"<<endl; 00175 //setBiotypeIndex( "OA", Biotype::get("P12", "OA1").getIndex() ); 00176 setAtomBiotype("OA" ,"P12","OA1" ); 00177 //setBiotypeIndex( "NE", Biotype::get("P12", "NE").getIndex() );//this can only be called for an existing atom. 00178 setAtomBiotype("NE" ,"P12", "NE" ); 00179 //setBiotypeIndex( "NE1", Biotype::get("P12", "NE1").getIndex() );//this can only be called for an existing atom. 00180 setAtomBiotype("NE1" ,"P12", "NE1" ); 00181 //setBiotypeIndex( "NH1", Biotype::get("P12", "NH1").getIndex() );//this can only be called for an existing atom. 00182 setAtomBiotype("NH1" ,"P12", "NH1"); 00183 //setBiotypeIndex( "NH2", Biotype::get("P12", "NH1").getIndex() );//this can only be called for an existing atom. 00184 setAtomBiotype("NH2" ,"P12","NH1" ); 00185 //setAtomBiotype("NE" ,"P12", "NE" ); 00186 //setBiotypeIndex( "NB", Biotype::get("P12", "NE").getIndex() );//this can only be called for an existing atom. 00187 setAtomBiotype("NB" ,"P12","NE" ); 00188 //setBiotypeIndex( "C4", Biotype::get("P12", "C4").getIndex() );//FIRST argument is atom name within the particular compound 00189 setAtomBiotype("C4" ,"P12","C4" ); 00190 //setBiotypeIndex( "C1", Biotype::get("P12", "C4").getIndex() );//FIRST argument is atom name within the particular compound 00191 //setBiotypeIndex( "C1","P12", "C4"); 00192 setAtomBiotype("C1" ,"P12","C4" ); 00193 setAtomBiotype("C3" ,"P12", "C3" ); 00194 setAtomBiotype("H3" ,"P12", "H3" ); 00195 //setBiotypeIndex( "C5", Biotype::get("P12", "C3").getIndex() );//FIRST argument is atom name within the particular compound 00196 setAtomBiotype("C5" ,"P12","C3" ); 00197 //setBiotypeIndex( "H5", Biotype::get("P12", "H3").getIndex() );//FIRST argument is atom name within the particular compound 00198 setAtomBiotype("H5" ,"P12","H3" ); 00199 //setBiotypeIndex( "C6", Biotype::get("P12", "C3").getIndex() );//FIRST argument is atom name within the particular compound 00200 setAtomBiotype("C6" ,"P12","C3" ); 00201 //setBiotypeIndex( "H6", Biotype::get("P12", "H3").getIndex() );//FIRST argument is atom name within the particular compound 00202 setAtomBiotype("H6" ,"P12","H3" ); 00203 //setBiotypeIndex( "C2", Biotype::get("P12", "C2").getIndex() );//FIRST argument is atom name within the particular compound 00204 setAtomBiotype("C2" ,"P12", "C3" ); 00205 setAtomBiotype("CB" ,"P12", "CD" );//setBiotypeIndex( "CB", Biotype::get("P12", "CD").getIndex() );//FIRST argument is atom name within the particular compound 00206 setAtomBiotype("CD" ,"P12", "CD" ); 00207 //setBiotypeIndex( "CG", Biotype::get("P12", "CD").getIndex() );//FIRST argument is atom name within the particular compound 00208 setAtomBiotype("CG" ,"P12","CD" ); 00209 //setBiotypeIndex( "CD", Biotype::get("P12", "CD").getIndex() );//FIRST argument is atom name within the particular compound 00210 setAtomBiotype("CD" ,"P12","CD" ); 00211 setAtomBiotype("CA" ,"P12","CD" ); 00212 setAtomBiotype("CG1" ,"P12","CD" ); 00213 setAtomBiotype("CG2" ,"P12","CD" ); 00214 setAtomBiotype("CD1","P12","CD");//setBiotypeIndex("CD1", Biotype::get("P12", "CD").getIndex() );//FIRST argument is atom name within the particular compound 00215 setAtomBiotype("CD2" ,"P12","CD" ); 00216 setAtomBiotype("CZ" ,"P12", "CZ" ); 00217 setAtomBiotype("C4" ,"P12","C4" ); 00218 00219 /* 00220 DuMM::AtomClassIndex amber1CTAtomClassIndex(1); 00221 DuMM::AtomClassIndex amber3CAAtomClassIndex(1); 00222 DuMM::AtomClassIndex amber9CBAtomClassIndex(1); 00223 DuMM::AtomClassIndex amber19N2AtomClassIndex(1); 00224 DuMM::AtomClassIndex amber23OSAtomClassIndex(1); 00225 DuMM::AtomClassIndex amber29H1AtomClassIndex(1); 00226 DuMM::AtomClassIndex amber33HAAtomClassIndex(1); 00227 DuMM::AtomClassIndex amber34HCAtomClassIndex(1); 00228 */ 00229 00230 dumm.setBiotypeChargedAtomType(DuMM::ChargedAtomTypeIndex(37),Biotype::get("P12","CB1").getIndex()); 00231 dumm.setBiotypeChargedAtomType(DuMM::ChargedAtomTypeIndex(38),Biotype::get("P12","HB11").getIndex()); 00232 dumm.setBiotypeChargedAtomType(DuMM::ChargedAtomTypeIndex(34),Biotype::get("P12","HC").getIndex()); 00233 dumm.setBiotypeChargedAtomType(DuMM::ChargedAtomTypeIndex(371),Biotype::get("P12","HE1").getIndex()); 00234 cout << "setting parameters for P12 HB"<<endl; 00235 setAtomBiotype("HB","P12","HB"); 00236 if (! dumm.hasChargedAtomType(DuMM::ChargedAtomTypeIndex(4000))) 00237 { 00238 dumm.defineChargedAtomType(DuMM::ChargedAtomTypeIndex(4000),"P12 HB",DuMM::AtomClassIndex(29),.6); 00239 dumm.setBiotypeChargedAtomType(DuMM::ChargedAtomTypeIndex(4000),Biotype::get("P12","HB").getIndex()); 00240 00241 } 00242 /*dumm.setBiotypeChargedAtomType(DuMM::ChargedAtomTypeIndex(303),Biotype::get("P12","HB").getIndex()); 00243 if (! Biotype::exists("P12", "HB" ) ) 00244 { 00245 cout<<"apparently biotype P12 HB doesn't exist.."<<endl; 00246 //setAtomBiotype("HB","P12","HB"); 00247 Biotype::defineBiotype(Element::Hydrogen(),1,"P12","HB"); 00248 dumm.defineChargedAtomType(DuMM::ChargedAtomTypeIndex(4000),"P12 HB",DuMM::AtomClassIndex(29),.6); 00249 dumm.setBiotypeChargedAtomType(DuMM::ChargedAtomTypeIndex(4000),Biotype::get("P12","HB").getIndex()); 00250 } else 00251 cout << "Biotype P12 HB exists"<<endl; 00252 */ 00253 dumm.setBiotypeChargedAtomType(DuMM::ChargedAtomTypeIndex(303),Biotype::get("P12","HH11").getIndex()); 00254 dumm.setBiotypeChargedAtomType(DuMM::ChargedAtomTypeIndex(1068),Biotype::get("P12","OA1").getIndex()); 00255 dumm.setBiotypeChargedAtomType(DuMM::ChargedAtomTypeIndex(368),Biotype::get("P12","NE").getIndex()); 00256 dumm.setBiotypeChargedAtomType(DuMM::ChargedAtomTypeIndex(1078),Biotype::get("P12","NE1").getIndex()); 00257 dumm.setBiotypeChargedAtomType(DuMM::ChargedAtomTypeIndex(302),Biotype::get("P12","NH1").getIndex()); 00258 dumm.setBiotypeChargedAtomType(DuMM::ChargedAtomTypeIndex(130),Biotype::get("P12","C4").getIndex()); 00259 dumm.setBiotypeChargedAtomType(DuMM::ChargedAtomTypeIndex(133),Biotype::get("P12","C3").getIndex()); 00260 dumm.setBiotypeChargedAtomType(DuMM::ChargedAtomTypeIndex(134),Biotype::get("P12","H3").getIndex()); 00261 //dumm.setBiotypeChargedAtomType(DuMM::ChargedAtomTypeIndex(1049),Biotype::get("P12","C2").getIndex()); 00262 dumm.setBiotypeChargedAtomType(DuMM::ChargedAtomTypeIndex(33),Biotype::get("P12","CD").getIndex()); 00263 dumm.setBiotypeChargedAtomType(DuMM::ChargedAtomTypeIndex(301),Biotype::get("P12","CZ").getIndex()); 00264 00265 for (int r =0 ; r<getNumBonds(); r++) //)//(Compound::Index(q)). 00266 { 00267 setBondMobility(BondMobility::Free ,Compound::BondIndex(r)); 00268 } 00269 00270 setPdbResidueNumber(1046); 00271 setPdbResidueName("P12") ; 00272 setPdbChainId('B'); 00273 00274 std::ifstream inFileStream("1UUI.pdb",std::ifstream::in); 00275 //assert(inFileStream.good()); 00276 //assert(inFileStream.bad()); 00277 //assert(0); 00278 PdbStructure pdbStructure(inFileStream); 00279 Compound::AtomTargetLocations atomTargets = createAtomTargets(pdbStructure); 00280 std::cout<<"atomtargest.szie "<<atomTargets.size()<<std::endl; 00281 matchDefaultBondLengths(atomTargets); 00282 matchDefaultBondAngles(atomTargets); 00283 matchDefaultAtomChirality(atomTargets); 00284 matchDefaultDihedralAngles(atomTargets); 00285 matchDefaultTopLevelTransform(atomTargets); 00286 //int mpResidueNumber = 1046; 00287 } 00288 /* 00289 */ 00290 00291 }; 00292 }
