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View Code? Open in Web Editor NEWa fast and accurate physical energy function for predicting protein stability and protein-protein affinity changes upon amino-acid mutations
License: MIT License
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Non canonical amino acids
Hi,
Thanks for the excellent work. I was wondering whether it would be possible to support non-canonical amino acids in EvoEF such as phosphoserine.
Thanks a lot.
Mutating numbered antibody files
Hi,
When the antibody is numbered to a specific scheme, for example Chothia numbering scheme, you can expect the pdb to be numbered like this:
ATOM 24170 N ASN H 82A 219.106 150.023 123.621 1.00281.57 N
ATOM 24171 CA ASN H 82A 220.131 149.195 123.007 1.00281.57 C
ATOM 24172 C ASN H 82A 219.503 148.052 122.218 1.00281.57 C
ATOM 24173 O ASN H 82A 218.352 147.668 122.441 1.00281.57 O
ATOM 24174 CB ASN H 82A 221.083 148.644 124.070 1.00281.57 C
ATOM 24175 CG ASN H 82A 221.611 149.725 124.991 1.00281.57 C
ATOM 24176 OD1 ASN H 82A 222.071 150.772 124.537 1.00281.57 O
ATOM 24177 ND2 ASN H 82A 221.539 149.481 126.292 1.00281.57 N
ATOM 24178 N SER H 82B 220.287 147.507 121.288 1.00283.06 N
ATOM 24179 CA SER H 82B 219.867 146.405 120.422 1.00283.06 C
ATOM 24180 C SER H 82B 218.641 146.797 119.597 1.00283.06 C
ATOM 24181 O SER H 82B 217.557 146.224 119.719 1.00283.06 O
ATOM 24182 CB SER H 82B 219.599 145.137 121.234 1.00283.06 C
ATOM 24183 OG SER H 82B 218.292 145.162 121.777 1.00283.06 O
ATOM 24184 N LEU H 82C 218.839 147.806 118.753 1.00286.83 N
ATOM 24185 CA LEU H 82C 217.771 148.287 117.888 1.00286.83 C
ATOM 24186 C LEU H 82C 217.421 147.253 116.826 1.00286.83 C
ATOM 24187 O LEU H 82C 218.298 146.643 116.210 1.00286.83 O
ATOM 24188 CB LEU H 82C 218.186 149.603 117.236 1.00286.83 C
ATOM 24189 CG LEU H 82C 218.703 150.577 118.287 1.00286.83 C
ATOM 24190 CD1 LEU H 82C 219.295 151.821 117.674 1.00286.83 C
ATOM 24191 CD2 LEU H 82C 217.569 150.923 119.213 1.00286.83 C
After running EvoEF to build a mutant it removes the A, B, C and keeps the residue id:
ATOM 29502 N ASN H 82 219.106 150.023 123.621 1 N
ATOM 29503 H ASN H 82 218.521 149.543 124.273 1 H
ATOM 29504 CA ASN H 82 220.131 149.195 123.007 1 C
ATOM 29505 CB ASN H 82 221.083 148.644 124.070 1 C
ATOM 29506 CG ASN H 82 221.611 149.725 124.991 1 C
ATOM 29507 OD1 ASN H 82 222.071 150.772 124.537 1 O
ATOM 29508 ND2 ASN H 82 221.539 149.481 126.292 1 N
ATOM 29509 1HD2 ASN H 82 221.872 150.188 126.909 1 H
ATOM 29510 2HD2 ASN H 82 221.136 148.631 126.618 1 H
ATOM 29511 C ASN H 82 219.503 148.052 122.218 1 C
ATOM 29512 O ASN H 82 218.352 147.668 122.441 1 O
ATOM 29513 N SER H 82 220.287 147.507 121.288 1 N
ATOM 29514 H SER H 82 221.221 147.823 121.125 1 H
ATOM 29515 CA SER H 82 219.867 146.405 120.422 1 C
ATOM 29516 CB SER H 82 219.599 145.137 121.234 1 C
ATOM 29517 OG SER H 82 218.292 145.162 121.777 1 O
ATOM 29518 HG SER H 82 218.094 144.267 122.081 1 H
ATOM 29519 C SER H 82 218.641 146.797 119.597 1 C
ATOM 29520 O SER H 82 217.557 146.224 119.719 1 O
ATOM 29521 N LEU H 82 218.839 147.806 118.753 1 N
ATOM 29522 H LEU H 82 219.702 148.295 118.649 1 H
ATOM 29523 CA LEU H 82 217.771 148.287 117.888 1 C
ATOM 29524 CB LEU H 82 218.186 149.603 117.236 1 C
ATOM 29525 CG LEU H 82 218.703 150.577 118.287 1 C
ATOM 29526 CD1 LEU H 82 219.295 151.821 117.674 1 C
ATOM 29527 CD2 LEU H 82 217.569 150.923 119.213 1 C
ATOM 29528 C LEU H 82 217.421 147.253 116.826 1 C
ATOM 29529 O LEU H 82 218.298 146.643 116.210 1 O
I thought I'd bring this to your attention. We deal with the issue by renumbering the pdb from 1 and mapping all mutations back.
Rotamer library
Is it possible to use a library with more rotamere and does this make the algorithm more accurate?
compile error
Hello, the compiler gives error below. What is possible problem for g++ 7.3.0? Thanks.
[root@loginnode evoef]# ./build.sh
src/Chain.cpp: In function ‘int ChainCreate(Chain*)’:
src/Chain.cpp:88:25: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
ChainSetName(pThis, "");
^
src/Getopt.cpp:88:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
#define EMSG ""
^
src/Getopt.cpp:97:22: note: in expansion of macro ‘EMSG’
static char *place = EMSG; /* option letter processing */
^~~~
src/Getopt.cpp: In function ‘int getopt_internal(int, char* const*, const char*, const option*, int*, int)’:
src/Getopt.cpp:88:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
#define EMSG ""
^
src/Getopt.cpp:330:21: note: in expansion of macro ‘EMSG’
place = EMSG;
^~~~
src/Getopt.cpp:88:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
#define EMSG ""
^
src/Getopt.cpp:349:21: note: in expansion of macro ‘EMSG’
place = EMSG; /* found non-option */
^~~~
src/Getopt.cpp:88:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
#define EMSG ""
^
src/Getopt.cpp:387:21: note: in expansion of macro ‘EMSG’
place = EMSG;
^~~~
src/Getopt.cpp:88:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
#define EMSG ""
^
src/Getopt.cpp:419:21: note: in expansion of macro ‘EMSG’
place = EMSG;
^~~~
src/Getopt.cpp:88:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
#define EMSG ""
^
src/Getopt.cpp:446:21: note: in expansion of macro ‘EMSG’
place = EMSG;
^~~~
src/Getopt.cpp:88:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
#define EMSG ""
^
src/Getopt.cpp:455:17: note: in expansion of macro ‘EMSG’
place = EMSG;
^~~~
src/Getopt.cpp:88:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
#define EMSG ""
^
src/Getopt.cpp:468:25: note: in expansion of macro ‘EMSG’
place = EMSG;
^~~~
src/Getopt.cpp:88:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
#define EMSG ""
^
src/Getopt.cpp:484:17: note: in expansion of macro ‘EMSG’
place = EMSG;
^~~~
src/Main.cpp: In function ‘int main(int, char**)’:
src/Main.cpp:82:19: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
char *cmdname = "ComputeResiEnergy";
^~~~~~~~~~~~~~~~~~~
src/ProgramFunction.cpp: In function ‘char CheckCommandName(char*)’:
src/ProgramFunction.cpp:89:3: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
};
^
src/ProgramFunction.cpp:89:3: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
src/ProgramFunction.cpp:89:3: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
src/ProgramFunction.cpp:89:3: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
src/ProgramFunction.cpp:89:3: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
src/ProgramFunction.cpp:89:3: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
src/ProgramFunction.cpp:89:3: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
src/ProgramFunction.cpp:89:3: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
src/ProgramFunction.cpp: In function ‘int EvoEF_BuildMutant(Structure*, char*, RotamerLib*, AtomParamsSet*, ResiTopoSet*, char*)’:
src/ProgramFunction.cpp:672:82: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designType, mutaatype); StringArrayAppend(&patchType, "");
^
src/ProgramFunction.cpp:673:56: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if(aa2=='H'){StringArrayAppend(&designType, "HSE"); StringArrayAppend(&patchType, "");}
^
src/ProgramFunction.cpp:673:91: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if(aa2=='H'){StringArrayAppend(&designType, "HSE"); StringArrayAppend(&patchType, "");}
^
src/Residue.cpp: In function ‘int ResidueReadXYZFromPDB(Residue*, FileReader*, AtomParamsSet*, ResiTopoSet*)’:
src/Residue.cpp:333:57: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
AtomCopy(&atomOXT, ResidueGetAtomByName(pThis, "O"));
^
src/Residue.cpp:338:38: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
ResidueGetAtomByName(pThis, "O")->CHARMM_charge = -0.55;
^
src/Residue.cpp:339:38: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
ResidueGetAtomByName(pThis, "C")->CHARMM_charge = 0.1;
^
src/Residue.cpp: In function ‘int ResiduePatchCTER(Residue*, char*, AtomParamsSet*, ResiTopoSet*)’:
src/Residue.cpp:434:61: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
int result = ResiTopoSetGet(pTopos, "CTER", &patchResiTopo);
^
src/Residue.cpp: In function ‘int ResiduePatchNTERorCTER(Residue*, char*, AtomParamsSet*, ResiTopoSet*)’:
src/Residue.cpp:502:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
result = ResiduePatch(pThis, "GLYP", pAtomParam, pTopos);
^
src/Residue.cpp:505:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
result = ResiduePatch(pThis, "PROP", pAtomParam, pTopos);
^
src/Residue.cpp:508:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
result = ResiduePatch(pThis, "NTER", pAtomParam, pTopos);
^
src/Residue.cpp:513:60: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
result = ResiduePatch(pThis, "CTER", pAtomParam, pTopos);
^
src/Rotamer.cpp: In function ‘int RotamerShow(Rotamer*)’:
src/Rotamer.cpp:272:80: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
AtomArrayShowInPDBFormat(&pThis->atoms,"ATOM",pThis->type," ",0,0,TRUE,NULL);
^
src/Rotamer.cpp:272:80: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
src/Rotamer.cpp: In function ‘int RotamerOfProteinInitAtomsAndBonds_Charmm22(Rotamer*, Residue*, AtomParamsSet*, ResiTopoSet*)’:
src/Rotamer.cpp:394:46: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
AtomArrayRemoveByName(&pThis->atoms,"HA1");
^
src/Rotamer.cpp:395:46: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
AtomArrayRemoveByName(&pThis->atoms,"HA2");
^
src/Rotamer.cpp:397:45: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
AtomArrayRemoveByName(&pThis->atoms,"HA");
^
src/Rotamer.cpp:398:45: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
AtomArrayRemoveByName(&pThis->atoms,"CB");
^
src/Rotamer.cpp:422:87: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
AtomParamsSetGetAtomParamByName(atomParams,RotamerGetType(pThis),"HN",&rotamerAtom);
^
src/Rotamer.cpp:423:42: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
ResidueGetAtomXYZ(pResi, "CD", &xyzCD);
^
src/Rotamer.cpp:424:40: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
ResidueGetAtomXYZ(pResi, "N", &xyzN);
^
src/Rotamer.cpp:437:72: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
AtomParamsSetGetAtomParamByName(atomParams,"GLY","HA1",&rotamerAtom);
^
src/Rotamer.cpp:437:72: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
src/Rotamer.cpp:441:72: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
AtomParamsSetGetAtomParamByName(atomParams,"GLY","HA2",&rotamerAtom);
^
src/Rotamer.cpp:441:72: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
src/Rotamer.cpp:448:87: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
AtomParamsSetGetAtomParamByName(atomParams,RotamerGetType(pThis),"CB",&rotamerAtom);
^
src/Rotamer.cpp:458:58: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
ResidueTopologyFindCharmmIC(&rotamerTopo, "CB", &ic);
^
src/Rotamer.cpp:459:53: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
GetFourthAtom(&RotamerGetAtomByName(pThis, "N")->xyz,&RotamerGetAtomByName(pThis, "C")->xyz,&RotamerGetAtomByName(pThis, "CA")->xyz,ic.icParam,&xyz);
^
src/Rotamer.cpp:459:92: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
GetFourthAtom(&RotamerGetAtomByName(pThis, "N")->xyz,&RotamerGetAtomByName(pThis, "C")->xyz,&RotamerGetAtomByName(pThis, "CA")->xyz,ic.icParam,&xyz);
^
src/Rotamer.cpp:459:132: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
GetFourthAtom(&RotamerGetAtomByName(pThis, "N")->xyz,&RotamerGetAtomByName(pThis, "C")->xyz,&RotamerGetAtomByName(pThis, "CA")->xyz,ic.icParam,&xyz);
^
src/Rotamer.cpp:464:49: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
result = ResidueGetAtomXYZ(pResi,"CB",&xyz);
^
src/Rotamer.cpp:470:87: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
AtomParamsSetGetAtomParamByName(atomParams,RotamerGetType(pThis),"HA",&rotamerAtom);
^
src/Rotamer.cpp:529:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
BondSetAdd(&newBonds,"CA","HA",Type_Bond_Single);
^
src/Rotamer.cpp:529:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
src/Rotamer.cpp:532:53: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
BondSetAdd(&newBonds,"CA","HA1",Type_Bond_Single);
^
src/Rotamer.cpp:532:53: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
src/Rotamer.cpp:533:53: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
BondSetAdd(&newBonds,"CA","HA2",Type_Bond_Single);
^
src/Rotamer.cpp:533:53: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
src/Rotamer.cpp: In function ‘int RotamerOfProteinInitAtomsAndBonds_Charmm19(Rotamer*, Residue*, AtomParamsSet*, ResiTopoSet*)’:
src/Rotamer.cpp:588:44: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&hydrogens, "HT1");
^
src/Rotamer.cpp:589:44: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&hydrogens, "HT2");
^
src/Rotamer.cpp:590:44: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&hydrogens, "HT3");
^
src/Rotamer.cpp:592:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
ResiTopoSetGet(resiTopos, "NTER", &nterTopo);
^
src/Rotamer.cpp:596:85: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
AtomParamsSetGetAtomParamByName(atomParams, "NTER", atomName, &rotamerAtom);
^
src/Rotamer.cpp:613:65: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
AtomCopy(&rotamerAtom, ResidueGetAtomByName(pResi, "HT1"));
^
src/Rotamer.cpp:616:65: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
AtomCopy(&rotamerAtom, ResidueGetAtomByName(pResi, "HT2"));
^
src/Rotamer.cpp:625:90: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
AtomParamsSetGetAtomParamByName(atomParams,RotamerGetType(pThis),"H",&rotamerAtom);
^
src/Rotamer.cpp:626:46: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
ResidueGetAtomXYZ(pResi, "CD", &xyzCD);
^
src/Rotamer.cpp:627:44: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
ResidueGetAtomXYZ(pResi, "N", &xyzN);
^
src/Rotamer.cpp:644:65: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
AtomCopy(&rotamerAtom, ResidueGetAtomByName(pResi, "HT1"));
^
src/Rotamer.cpp:647:65: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
AtomCopy(&rotamerAtom, ResidueGetAtomByName(pResi, "HT2"));
^
src/Rotamer.cpp:650:65: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
AtomCopy(&rotamerAtom, ResidueGetAtomByName(pResi, "HT3"));
^
src/Rotamer.cpp:655:64: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
RotamerOfProteinPatch(pThis,"PROP",atomParams,resiTopos);
^
src/Rotamer.cpp:661:63: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
AtomCopy(&rotamerAtom, ResidueGetAtomByName(pResi, "H"));
^
src/Rotamer.cpp:682:58: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
ResidueTopologyFindCharmmIC(&rotamerTopo, "CB", &ic);
^
src/Rotamer.cpp:683:53: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
GetFourthAtom(&RotamerGetAtomByName(pThis, "N")->xyz,&RotamerGetAtomByName(pThis, "C")->xyz,&RotamerGetAtomByName(pThis, "CA")->xyz,ic.icParam,&AtomArrayGetByName(&pThis->atoms, "CB")->xyz);
^
src/Rotamer.cpp:683:92: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
GetFourthAtom(&RotamerGetAtomByName(pThis, "N")->xyz,&RotamerGetAtomByName(pThis, "C")->xyz,&RotamerGetAtomByName(pThis, "CA")->xyz,ic.icParam,&AtomArrayGetByName(&pThis->atoms, "CB")->xyz);
^
src/Rotamer.cpp:683:132: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
GetFourthAtom(&RotamerGetAtomByName(pThis, "N")->xyz,&RotamerGetAtomByName(pThis, "C")->xyz,&RotamerGetAtomByName(pThis, "CA")->xyz,ic.icParam,&AtomArrayGetByName(&pThis->atoms, "CB")->xyz);
^
src/Rotamer.cpp:683:189: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
, "N")->xyz,&RotamerGetAtomByName(pThis, "C")->xyz,&RotamerGetAtomByName(pThis, "CA")->xyz,ic.icParam,&AtomArrayGetByName(&pThis->atoms, "CB")->xyz);
^
src/Rotamer.cpp:684:45: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
AtomArrayGetByName(&pThis->atoms, "CB")->isXyzValid = TRUE;
^
src/Rotamer.cpp:694:61: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
Atom *pAtomCB = AtomArrayGetByName(&pThis->atoms, "CB");
^
src/Rotamer.cpp:695:54: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
pAtomCB->xyz = ResidueGetAtomByName(pResi, "CB")->xyz;
^
src/Rotamer.cpp:760:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
BondSetAdd(&newBonds,"N","CD",Type_Bond_Single);
^
src/Rotamer.cpp:760:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
src/Rotamer.cpp:763:56: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
BondSetAdd(&newBonds,"HT3","N",Type_Bond_Single);
^
src/Rotamer.cpp:763:56: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
src/Rotamer.cpp:768:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
BondSetAdd(&newBonds,"N","CD",Type_Bond_Single);
^
src/Rotamer.cpp:768:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
src/Rotamer.cpp:771:54: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
BondSetAdd(&newBonds,"N","H",Type_Bond_Single);
^
src/Rotamer.cpp:771:54: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
src/Rotamer.cpp:777:53: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
BondSetAdd(&newBonds,"N","CD",Type_Bond_Single);
^
src/Rotamer.cpp:777:53: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
src/Rotamer.cpp: In function ‘int RotamerOfProteinCalcXYZ(Rotamer*, Residue*, char*, DoubleArray*, ResiTopoSet*)’:
src/Rotamer.cpp:896:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
Atom *pAtomCA = RotamerGetAtomByName(pThis, "CA");
^
src/Rotamer.cpp:897:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
Atom *pAtomCD = RotamerGetAtomByName(pThis, "CD");
^
src/Rotamer.cpp:898:53: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
Atom *pAtomN = RotamerGetAtomByName(pThis, "N");
^
src/Rotamer.cpp:899:57: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
Atom *pAtomHT1 = RotamerGetAtomByName(pThis, "HT1");
^
src/Rotamer.cpp:900:57: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
Atom *pAtomHT2 = RotamerGetAtomByName(pThis, "HT2");
^
src/Rotamer.cpp:925:82: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
AtomArrayShowInPDBFormat(&pThis->atoms,"ATOM",pThis->type," ",0,0,TRUE,NULL);
^
src/Rotamer.cpp:925:82: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
src/Structure.cpp: In function ‘int StructureShowInPDBFormat(Structure*, char, FILE*)’:
src/Structure.cpp:143:132: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
ResidueShowInPDBFormat(pResi, "ATOM", ResidueGetChainName(pResi), atomIndex, ResidueGetPosInChain(pResi), showHydrogen, pFile);
^
src/Structure.cpp: In function ‘int StructureInitialize(Structure*, char*, AtomParamsSet*, ResiTopoSet*)’:
src/Structure.cpp:247:71: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
ResiduePatchNTERorCTER(&newResi, "NTER", pAtomParams, pTopos);
^
src/Structure.cpp:274:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if(ResidueGetAtomByName(pFirsResidueInChain, "HT1") != NULL || ResidueGetAtomByName(pFirsResidueInChain, "HN1") !=NULL){
^
src/Structure.cpp:274:115: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if(ResidueGetAtomByName(pFirsResidueInChain, "HT1") != NULL || ResidueGetAtomByName(pFirsResidueInChain, "HN1") !=NULL){
^
src/Structure.cpp:276:72: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
ResiduePatchCTER(pLastResidueInChain, "CTER", pAtomParams, pTopos);
^
src/Structure.cpp: In function ‘int ChainComputeResiduePosition(Structure*, int)’:
src/Structure.cpp:302:60: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
Atom *pAtomCAorCB1 = ResidueGetAtomByName(pResiIR, "CB");
^
src/Structure.cpp:303:79: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if(pAtomCAorCB1 == NULL) pAtomCAorCB1 = ResidueGetAtomByName(pResiIR, "CA");
^
src/Structure.cpp:306:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
Atom *pAtomCAorCB2 = ResidueGetAtomByName(pResiIS, "CB");
^
src/Structure.cpp:307:81: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if(pAtomCAorCB2 == NULL) pAtomCAorCB2 = ResidueGetAtomByName(pResiIS, "CA");
^
src/Structure.cpp: In function ‘int StructureComputeResiduePosition(Structure*)’:
src/Structure.cpp:332:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
Atom *pAtomCAorCB1 = ResidueGetAtomByName(pResiIR, "CB");
^
src/Structure.cpp:333:79: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if(pAtomCAorCB1==NULL) pAtomCAorCB1 = ResidueGetAtomByName(pResiIR, "CA");
^
src/Structure.cpp:336:64: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
Atom *pAtomCAorCB2 = ResidueGetAtomByName(pResiIS, "CB");
^
src/Structure.cpp:337:81: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if(pAtomCAorCB2==NULL) pAtomCAorCB2 = ResidueGetAtomByName(pResiIS, "CA");
^
src/Structure.cpp:348:81: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
Atom *pAtomCAorCB2 = pAtomCAorCB2 = ResidueGetAtomByName(pResiKS, "CB");
^
src/Structure.cpp:349:83: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if(pAtomCAorCB2==NULL) pAtomCAorCB2 = ResidueGetAtomByName(pResiKS, "CA");
^
src/Structure.cpp: In function ‘int ProteinSiteBuildAllRotamers(Structure*, int, int, RotamerLib*, AtomParamsSet*, ResiTopoSet*)’:
src/Structure.cpp:544:40: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "ALA"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:544:76: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "ALA"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:545:40: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "ARG"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:545:76: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "ARG"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:546:40: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "ASN"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:546:76: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "ASN"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:547:40: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "ASP"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:547:76: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "ASP"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:548:40: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "CYS"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:548:76: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "CYS"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:549:40: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "GLN"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:549:76: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "GLN"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:550:40: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "GLU"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:550:76: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "GLU"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:551:40: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "GLY"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:551:76: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "GLY"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:552:40: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "HSD"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:552:76: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "HSD"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:553:40: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "HSE"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:553:76: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "HSE"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:554:40: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "ILE"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:554:76: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "ILE"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:555:40: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "LEU"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:555:76: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "LEU"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:556:40: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "LYS"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:556:76: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "LYS"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:557:40: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "MET"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:557:76: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "MET"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:558:40: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "PHE"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:558:76: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "PHE"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:559:40: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "PRO"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:559:76: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "PRO"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:560:40: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "SER"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:560:76: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "SER"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:561:40: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "THR"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:561:76: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "THR"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:562:40: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "TRP"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:562:76: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "TRP"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:563:40: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "TYR"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:563:76: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "TYR"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:564:40: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "VAL"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:564:76: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "VAL"); StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp: In function ‘int ProteinSiteBuildWildtypeRotamers(Structure*, int, int, RotamerLib*, AtomParamsSet*, ResiTopoSet*)’:
src/Structure.cpp:620:36: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:622:42: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "HSE");
^
src/Structure.cpp:623:38: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp:626:42: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&designTypes, "HSD");
^
src/Structure.cpp:627:38: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
StringArrayAppend(&patchTypes, "");
^
src/Structure.cpp: In function ‘int ProteinSiteWriteRotamers(Structure*, int, int, const char*)’:
src/Structure.cpp:648:93: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
RotamerShowInPDBFormat(pRotamer, "ATOM", RotamerGetChainName(pRotamer),1, i, FALSE, pOut);
^
src/Structure.cpp: In function ‘int ProteinSiteAddCrystalRotamer(Structure*, int, int, ResiTopoSet*)’:
src/Structure.cpp:711:76: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if((pRotamerRepresentative = RotamerSetGetRepresentative(pSetI, "HSE")) != NULL){
^
src/Structure.cpp:714:39: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
ResidueSetName(&newResi, "HSE");
^
src/Structure.cpp:727:42: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
RotamerSetType(&tempRotamer,"HSE");
^
src/Structure.cpp:749:76: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if((pRotamerRepresentative = RotamerSetGetRepresentative(pSetI, "HSD")) != NULL){
^
src/Structure.cpp:752:39: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
ResidueSetName(&newResi, "HSD");
^
src/Structure.cpp:765:42: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
RotamerSetType(&tempRotamer,"HSD");
^
src/Structure.cpp: In function ‘int ProteinSiteBuildFlippedCrystalRotamer(Structure*, int, int, ResiTopoSet*)’:
src/Structure.cpp:813:51: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
RotamerFindAtom(&tempRotamer,"ND2",&index1);
^
src/Structure.cpp:814:51: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
RotamerFindAtom(&tempRotamer,"OD1",&index2);
^
src/Structure.cpp:825:50: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
ResiTopoSetGet(pResiTopos,"ASN",&resiTopo);
^
src/Structure.cpp:826:57: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
ResidueTopologyFindCharmmIC(&resiTopo,"HD21",&ic);
^
src/Structure.cpp:832:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
RotamerFindAtom(&tempRotamer,"HD21",&index1);
^
src/Structure.cpp:835:57: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
ResidueTopologyFindCharmmIC(&resiTopo,"HD22",&ic);
^
src/Structure.cpp:841:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
RotamerFindAtom(&tempRotamer,"HD22",&index1);
^
src/Structure.cpp:849:51: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
RotamerFindAtom(&tempRotamer,"NE2",&index1);
^
src/Structure.cpp:850:51: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
RotamerFindAtom(&tempRotamer,"OE1",&index2);
^
src/Structure.cpp:861:50: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
ResiTopoSetGet(pResiTopos,"GLN",&resiTopo);
^
src/Structure.cpp:862:57: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
ResidueTopologyFindCharmmIC(&resiTopo,"HE21",&ic);
^
src/Structure.cpp:868:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
RotamerFindAtom(&tempRotamer,"HE21",&index1);
^
src/Structure.cpp:871:57: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
ResidueTopologyFindCharmmIC(&resiTopo,"HE22",&ic);
^
src/Structure.cpp:877:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
RotamerFindAtom(&tempRotamer,"HE22",&index1);
^
src/Structure.cpp:885:51: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
RotamerFindAtom(&tempRotamer,"CD2",&index1);
^
src/Structure.cpp:886:51: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
RotamerFindAtom(&tempRotamer,"ND1",&index2);
^
src/Structure.cpp:893:51: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
RotamerFindAtom(&tempRotamer,"NE2",&index1);
^
src/Structure.cpp:894:51: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
RotamerFindAtom(&tempRotamer,"CE1",&index2);
^
src/Structure.cpp:905:50: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
ResiTopoSetGet(pResiTopos,"HSD",&resiTopo);
^
src/Structure.cpp:906:56: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
ResidueTopologyFindCharmmIC(&resiTopo,"HD1",&ic);
^
src/Structure.cpp:912:51: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
RotamerFindAtom(&tempRotamer,"HD1",&index1);
^
src/Structure.cpp:920:51: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
RotamerFindAtom(&tempRotamer,"CD2",&index1);
^
src/Structure.cpp:921:51: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
RotamerFindAtom(&tempRotamer,"ND1",&index2);
^
src/Structure.cpp:928:51: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
RotamerFindAtom(&tempRotamer,"NE2",&index1);
^
src/Structure.cpp:929:51: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
RotamerFindAtom(&tempRotamer,"CE1",&index2);
^
src/Structure.cpp:940:50: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
ResiTopoSetGet(pResiTopos,"HSE",&resiTopo);
^
src/Structure.cpp:941:56: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
ResidueTopologyFindCharmmIC(&resiTopo,"HE2",&ic);
^
src/Structure.cpp:947:51: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
RotamerFindAtom(&tempRotamer,"HE2",&index1);
^
src/Structure.cpp: In function ‘int ProteinSiteExpandHydroxylRotamers(Structure*, int, int, ResiTopoSet*)’:
src/Structure.cpp:972:54: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if(RotamerSetGetRepresentative(pRotamerSet, "SER") != NULL ){
^
src/Structure.cpp:973:42: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
ResiTopoSetGet(pTopos, "SER", &tops);
^
src/Structure.cpp:974:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
ResidueTopologyFindCharmmIC(&tops, "HG", &ics);
^
src/Structure.cpp:984:53: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
RotamerFindAtom(pRotamer, "HG", &atomIndex);
^
src/Structure.cpp:991:63: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
GetFourthAtom(&RotamerGetAtomByName(&tempRot, "CA")->xyz,&RotamerGetAtomByName(&tempRot, "CB")->xyz,&RotamerGetAtomByName(&tempRot, "OG")->xyz,ics.icParam,&RotamerGetAtomByName(&tempRot, "HG")->xyz);
^
src/Structure.cpp:991:106: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
GetFourthAtom(&RotamerGetAtomByName(&tempRot, "CA")->xyz,&RotamerGetAtomByName(&tempRot, "CB")->xyz,&RotamerGetAtomByName(&tempRot, "OG")->xyz,ics.icParam,&RotamerGetAtomByName(&tempRot, "HG")->xyz);
^
src/Structure.cpp:991:149: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
GetFourthAtom(&RotamerGetAtomByName(&tempRot, "CA")->xyz,&RotamerGetAtomByName(&tempRot, "CB")->xyz,&RotamerGetAtomByName(&tempRot, "OG")->xyz,ics.icParam,&RotamerGetAtomByName(&tempRot, "HG")->xyz);
^
src/Structure.cpp:991:204: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
)->xyz,&RotamerGetAtomByName(&tempRot, "CB")->xyz,&RotamerGetAtomByName(&tempRot, "OG")->xyz,ics.icParam,&RotamerGetAtomByName(&tempRot, "HG")->xyz);
^
src/Structure.cpp:992:87: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
XYZArraySet(&tempRot.xyzs, atomIndex, &RotamerGetAtomByName(&tempRot, "HG")->xyz);
^
src/Structure.cpp:1023:54: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if(RotamerSetGetRepresentative(pRotamerSet, "THR") != NULL ){
^
src/Structure.cpp:1024:42: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
ResiTopoSetGet(pTopos, "THR", &tops);
^
src/Structure.cpp:1025:53: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
ResidueTopologyFindCharmmIC(&tops, "HG1", &ics);
^
src/Structure.cpp:1035:54: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
RotamerFindAtom(pRotamer, "HG1", &atomIndex);
^
src/Structure.cpp:1042:63: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
GetFourthAtom(&RotamerGetAtomByName(&tempRot, "CA")->xyz,&RotamerGetAtomByName(&tempRot, "CB")->xyz,&RotamerGetAtomByName(&tempRot, "OG1")->xyz,ics.icParam,&RotamerGetAtomByName(&tempRot, "HG1")->xyz);
^
src/Structure.cpp:1042:106: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
GetFourthAtom(&RotamerGetAtomByName(&tempRot, "CA")->xyz,&RotamerGetAtomByName(&tempRot, "CB")->xyz,&RotamerGetAtomByName(&tempRot, "OG1")->xyz,ics.icParam,&RotamerGetAtomByName(&tempRot, "HG1")->xyz);
^
src/Structure.cpp:1042:150: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
GetFourthAtom(&RotamerGetAtomByName(&tempRot, "CA")->xyz,&RotamerGetAtomByName(&tempRot, "CB")->xyz,&RotamerGetAtomByName(&tempRot, "OG1")->xyz,ics.icParam,&RotamerGetAtomByName(&tempRot, "HG1")->xyz);
^
src/Structure.cpp:1042:206: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
>xyz,&RotamerGetAtomByName(&tempRot, "CB")->xyz,&RotamerGetAtomByName(&tempRot, "OG1")->xyz,ics.icParam,&RotamerGetAtomByName(&tempRot, "HG1")->xyz);
^
src/Structure.cpp:1043:88: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
XYZArraySet(&tempRot.xyzs, atomIndex, &RotamerGetAtomByName(&tempRot, "HG1")->xyz);
^
src/Structure.cpp:1074:54: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if(RotamerSetGetRepresentative(pRotamerSet, "TYR") != NULL ){
^
src/Structure.cpp:1075:42: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
ResiTopoSetGet(pTopos, "TYR", &tops);
^
src/Structure.cpp:1076:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
ResidueTopologyFindCharmmIC(&tops, "HH", &ics);
^
src/Structure.cpp:1086:53: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
RotamerFindAtom(pRotamer, "HH", &atomIndex);
^
src/Structure.cpp:1092:64: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
GetFourthAtom(&RotamerGetAtomByName(&tempRot, "CE1")->xyz,&RotamerGetAtomByName(&tempRot, "CZ")->xyz,&RotamerGetAtomByName(&tempRot, "OH")->xyz,ics.icParam,&RotamerGetAtomByName(&tempRot, "HH")->xyz);
^
src/Structure.cpp:1092:107: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
GetFourthAtom(&RotamerGetAtomByName(&tempRot, "CE1")->xyz,&RotamerGetAtomByName(&tempRot, "CZ")->xyz,&RotamerGetAtomByName(&tempRot, "OH")->xyz,ics.icParam,&RotamerGetAtomByName(&tempRot, "HH")->xyz);
^
src/Structure.cpp:1092:150: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
GetFourthAtom(&RotamerGetAtomByName(&tempRot, "CE1")->xyz,&RotamerGetAtomByName(&tempRot, "CZ")->xyz,&RotamerGetAtomByName(&tempRot, "OH")->xyz,ics.icParam,&RotamerGetAtomByName(&tempRot, "HH")->xyz);
^
src/Structure.cpp:1092:205: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
)->xyz,&RotamerGetAtomByName(&tempRot, "CZ")->xyz,&RotamerGetAtomByName(&tempRot, "OH")->xyz,ics.icParam,&RotamerGetAtomByName(&tempRot, "HH")->xyz);
^
src/Structure.cpp:1093:87: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
XYZArraySet(&tempRot.xyzs, atomIndex, &RotamerGetAtomByName(&tempRot, "HH")->xyz);
^
[root@loginnode evoef]#
```
Buffer overflow error during BuildMutant
I'm getting *** buffer overflow detected ***: terminated error when I'm trying to used following command with more than 1 mutation in individual_list.txt file:
./EvoEF/EvoEF --command=BuildMutant --pdb=wt_Repair.pdb --mutant_file=individual_list.txt
It works correctly with only 1 mutation in the individual_list.txt file.
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