Liste al(Arbin a)//Parcours infixe inverse : d r g
{
Liste l=listenouv();
Listea tmp=listenouv_a();
Arbin atmp;
tmp=desd(a,tmp);
while(tailleliste_a(tmp)>0)
{
atmp=tete_a(tmp);
tmp=supt_a(tmp);
l=adjt(l,rac(atmp));
tmp=desd(ag(atmp),tmp);
}
freeListe_a(tmp);
return l;
}
int main(int argc, char *argv[])
{
int i;
int status = 0;
char command[MAXCHAR];
size_t copied_size;
amberhome = (char *) getenv("AMBERHOME");
if( amberhome == NULL ){
fprintf( stdout, "AMBERHOME is not set!\n" );
exit(1);
}
if (strcmp(COLORTEXT, "YES") == 0 || strcmp(COLORTEXT, "yes") == 0) {
if (argc == 2
&& (strcmp(argv[1], "-h") == 0
|| strcmp(argv[1], "-H") == 0)) {
printf("[31mUsage: respgen -i[0m input file name(ac)\n"
"[31m -o[0m output file name\n"
"[31m -l[0m maximum path length (default is -1, only recommand to use\n"
" when the program takes long time to finish or causes core dump.)\n"
" If applied, a value of 8 to 10 should good)\n"
"[31m -f[0m output file format (resp1 or resp2) \n"
"[32m resp0[0m - evaluation the current charges \n"
"[32m resp1[0m - first stage resp fitting \n"
"[32m resp2[0m - second stage resp fitting\n"
"[32m iresp0[0m - evaluation the current charges for polarizable model\n"
"[32m iresp1[0m- first stage of i_resp fitting \n"
"[32m iresp2[0m- second stage of i_resp fitting\n"
"[32m resp3[0m - one-stage resp fitting\n"
"[32m resp4[0m - calculating ESP from point charges\n"
"[32m resp5[0m - no-equalization\n"
"[31m -e[0m equalizing atomic charge, default is 1\n"
"[32m 0[0m not use \n"
"[32m 1[0m by atomic paths\n"
"[32m 2[0m by atomic paths and structural information, i.e. E/Z confirgurations\n"
"[31m -a[0m additional input data (predefined charges, atom groups etc).)\n"
"[31m -n[0m number of conformations (default is 1)\n"
"[31m -w[0m weight of charge constraint, in default, 0.0005 for resp1 and 0.001 fore resp2\n");
exit(1);
}
if (argc != 7 && argc != 9 && argc != 11 && argc != 13 && argc != 15 && argc != 17) {
printf("[31mUsage: respgen -i[0m input file name(ac)\n"
"[31m -o[0m output file name\n"
"[31m -l[0m maximum path length (default is -1, only recommand to use\n"
" when the program takes long time to finish or causes core dump.)\n"
" If applied, a value of 8 to 10 should good)\n"
"[31m -f[0m output file format (resp1 or resp2) \n"
"[32m resp0[0m - evaluation the current charges \n"
"[32m resp1[0m - first stage resp fitting \n"
"[32m resp2[0m - second stage resp fitting\n"
"[32m iresp0[0m - evaluation the current charges for polarizable model\n"
"[32m iresp1[0m- first stage of i_resp fitting \n"
"[32m iresp2[0m- second stage of i_resp fitting\n"
"[32m resp3[0m - one-stage resp fitting\n"
"[32m resp4[0m - calculating ESP from point charges\n"
"[32m resp5[0m - no-equalization\n"
"[31m -e[0m equalizing atomic charge, default is 1\n"
"[32m 0[0m not use \n"
"[32m 1[0m by atomic paths\n"
"[32m 2[0m by atomic paths and structural information, i.e. E/Z confirgurations\n"
"[31m -a[0m additional input data (predefined charges, atom groups etc).)\n"
"[31m -n[0m number of conformations (default is 1)\n"
"[31m -w[0m weight of charge constraint, in default, 0.0005 for resp1 and 0.001 fore resp2\n");
exit(1);
}
} else {
if (argc == 2
&& (strcmp(argv[1], "-h") == 0
|| strcmp(argv[1], "-H") == 0)) {
printf("Usage respgen -i input file name(ac)\n");
printf(" -o output file name\n");
printf(" -l maximum path length (default is -1, only recommand to use\n");
printf(" when the program takes long time to finish or causes core dump.)\n");
printf(" If applied, a value of 8 to 10 should good)\n");
printf(" -f output file format (resp1 or resp2)\n");
printf(" resp0 - evaluation the current charges \n");
printf(" resp1 - first stage resp fitting\n");
printf(" resp2 - second stage resp fitting \n");
printf(" iresp0 - evaluation the current charges for polarizable model \n");
printf(" iresp1- first stage of i_resp fitting\n");
printf(" iresp2- second stage of i_resp fitting \n");
printf(" resp3 - one-stage resp fitting\n");
printf(" resp4 - calculating ESP from point charges \n");
printf(" resp5 - no-equalization \n");
printf(" -e equalizing atomic charge, default is 1\n");
printf(" 0 not use \n");
printf(" 1 by atomic paths\n");
printf(" 2 by atomic paths and structural information, i.e. E/Z confirgurations\n");
printf(" -a additional input data (predefined charges, atom groups etc).)\n");
printf(" -n number of conformations (default is 1)\n");
printf(" -w weight of charge constraint, in default, 0.0005 for resp1 and 0.001 fore resp2\n");
exit(1);
}
if (argc != 7 && argc != 9 && argc != 11 && argc != 13 && argc != 15 && argc != 17) {
printf("Usage respgen -i input file name(ac)\n");
printf(" -o output file name\n");
printf(" -l maximum path length (default is -1, only recommand to use\n");
printf(" when the program takes long time to finish or causes core dump.)\n");
printf(" If applied, a value of 8 to 10 should good)\n");
printf(" -f output file format (resp1 or resp2)\n");
printf(" resp0 - evaluation the current charges \n");
printf(" resp1 - first stage resp fitting\n");
printf(" resp2 - second stage resp fitting \n");
printf(" iresp0 - evaluation the current charges for polarizable model \n");
printf(" iresp1- first stage of i_resp fitting\n");
printf(" iresp2- second stage of i_resp fitting \n");
printf(" resp3 - one-stage resp fitting\n");
printf(" resp4 - calculating ESP from point charges \n");
printf(" resp5 - no-equalization \n");
printf(" -e equalizing atomic charge, default is 1\n");
printf(" 0 not use \n");
printf(" 1 by atomic paths\n");
printf(" 2 by atomic paths and structural information, i.e. E/Z confirgurations\n");
printf(" -a additional input data (predefined charges, atom groups etc).)\n");
printf(" -w weight of charge constraint, in default, 0.0005 for resp1 and 0.001 fore resp2\n");
exit(1);
}
}
method = -1;
max_path_length = -1;
for (i = 1; i < argc; i += 2) {
if (strcmp(argv[i], "-i") == 0)
strcpy(ifilename, argv[i + 1]);
if (strcmp(argv[i], "-o") == 0)
strcpy(ofilename, argv[i + 1]);
if (strcmp(argv[i], "-a") == 0) {
strcpy(afilename, argv[i + 1]);
iaddinfo = 1;
}
if (strcmp(argv[i], "-n") == 0)
nconf = atoi(argv[i+1]);
if (strcmp(argv[i], "-l") == 0)
max_path_length = atoi(argv[i+1]);
if (strcmp(argv[i], "-f") == 0) {
if (strcmp("resp", argv[i + 1]) == 0)
method = -1;
if (strcmp("resp0", argv[i + 1]) == 0)
method = 0;
if (strcmp("resp1", argv[i + 1]) == 0) {
method = 1;
weight = 0.0005;
}
if (strcmp("resp2", argv[i + 1]) == 0) {
method = 2;
weight = 0.001;
}
if (strcmp("resp3", argv[i + 1]) == 0)
method = 3;
if (strcmp("iresp1", argv[i + 1]) == 0) {
method = 4;
weight = 0.0005;
}
if (strcmp("iresp2", argv[i + 1]) == 0) {
method = 5;
weight = 0.001;
}
if (strcmp("resp4", argv[i + 1]) == 0) {
method = 6;
weight = 0.000;
}
if (strcmp("iresp0", argv[i + 1]) == 0)
method = 7;
if (strcmp("resp5", argv[i + 1]) == 0) {
method = 8;
weight = 0.0005;
}
}
if (strcmp(argv[i], "-w") == 0)
weight = atof(argv[i+1]);
if (strcmp(argv[i], "-e") == 0)
iequ = atoi(argv[i+1]);
}
if(nconf < 1) {
printf("\nNumber of conformations must be equal to or larger than 1");
exit(1);
}
if(iequ != 0 && iequ != 1 && iequ !=2)
iequ = 1;
default_cinfo(&cinfo);
default_minfo(&minfo);
atom = (ATOM *) malloc(sizeof(ATOM) * cinfo.maxatom);
if (atom == NULL) {
fprintf(stdout, "memory allocation error for *atom\n");
exit(1);
}
bond = (BOND *) malloc(sizeof(BOND) * cinfo.maxbond);
if (bond == NULL) {
fprintf(stdout, "memory allocation error for *bond\n");
exit(1);
}
for (i = 0; i < cinfo.maxbond; ++i) {
bond[i].jflag = -1; /* bond type has not been assigned */
}
overflow_flag =
rac(ifilename, &atomnum, atom, &bondnum, bond, &cinfo, &minfo);
if (overflow_flag) {
cinfo.maxatom = atomnum + 10;
cinfo.maxbond = bondnum + 10;
free(atom);
free(bond);
atom = (ATOM *) malloc(sizeof(ATOM) * cinfo.maxatom);
if (atom == NULL) {
fprintf(stdout, "memory allocation error for *atom\n");
exit(1);
}
bond = (BOND *) malloc(sizeof(BOND) * cinfo.maxbond);
if (bond == NULL) {
fprintf(stdout, "memory allocation error for *bond\n");
exit(1);
}
int i;
for (i = 0; i < cinfo.maxbond; ++i) {
bond[i].jflag = -1; /* bond type has not been assigned */
}
overflow_flag =
rac(ifilename, &atomnum, atom, &bondnum, bond, &cinfo, &minfo);
}
atomicnum(atomnum, atom);
adjustatomname(atomnum, atom, 1);
if(minfo.dcharge >= -9990) charge = minfo.dcharge;
equ_atom_id = (int *) malloc(sizeof(int) * atomnum);
if (equ_atom_id == NULL) {
fprintf(stdout, "memory allocation error for *equ_atom_id\n");
exit(1);
}
for (i = 0; i < atomnum; i++)
equ_atom_id[i] = -1;
if(method == 3) {
atqwt = (double *) malloc(sizeof(double) * atomnum);
if (atqwt == NULL) {
fprintf(stdout, "memory allocation error for *atqwt\n");
exit(1);
}
refcharge = (double *) malloc(sizeof(double) * atomnum);
if (refcharge == NULL) {
fprintf(stdout, "memory allocation error for *refcharge\n");
exit(1);
}
for(i=0;i<atomnum;i++) {
atqwt[i] = 0;
refcharge[i] = 0;
}
// now read in atomic weights and reference charge parameters
pfilename[0] = '\0';
strcpy(pfilename, amberhome);
strcat(pfilename, "/dat/antechamber/RESPPARM.DAT");
readparm(pfilename);
wac("ANTECHAMBER_RESP.AC", atomnum, atom, bondnum, bond, cinfo, minfo);
copied_size = build_exe_path(command,
"atomtype -i ANTECHAMBER_RESP.AC -o ANTECHAMBER_RESP_AT.AC -d ",
sizeof command, 1 );
dfilename[0] = '\0';
strcpy(dfilename, amberhome);
strcat(dfilename, "/dat/antechamber/ATOMTYPE_RESP.DEF");
strncat(command, dfilename, MAXCHAR - copied_size );
if (cinfo.intstatus == 2)
fprintf(stdout, "Running: %s\n", command);
status = system(command);
if(status != 0) {
fprintf(stdout, "Error: cannot run \"%s\" in respgen.c properly, exit\n", command);
exit(1);
}
assignparm("ANTECHAMBER_RESP_AT.AC");
}
if(iequ == 1)
identify_equatom(atomnum, atom, equ_atom_id, max_path_length, bondnum, bond, 0);
if(iequ == 2)
identify_equatom(atomnum, atom, equ_atom_id, max_path_length, bondnum, bond, 1);
icharge = (int *) malloc(sizeof(int) * atomnum);
if (icharge == NULL) {
fprintf(stdout, "memory allocation error for *icharge in respin()\n");
exit(1);
}
pcharge = (double *) malloc(sizeof(double) * atomnum);
if (pcharge == NULL) {
fprintf(stdout, "memory allocation error for *pcharge in respin()\n");
exit(1);
}
for(i=0;i<atomnum;i++) {
pcharge[i] = 0.0;
icharge[i] = 0;
}
if(iaddinfo == 1) {
if ((fpaddinfo = fopen(afilename, "r")) == NULL) {
fprintf(stdout, "Cannot open the additional file %s to read in main(), exit\n", afilename);
exit(1);
}
if ((fpcharge = fopen("QIN", "w")) == NULL) {
fprintf(stdout, "Cannot open file QIN, exit\n");
exit(1);
}
readinfo();
}
respin(method);
if(iaddinfo == 1) {
fclose(fpcharge);
fclose(fpaddinfo);
}
printf("\n");
/*
free(atom);
free(selectindex);
free(selectelement);
free(equ_atom_id);
free(pathnum);
free(pathatomnum);
for (i =0 ;i <atomnum; i++) free(pathscore[i]);
*/
return (0);
}
bool test(bool is_kernel_exact = true)
{
// types
typedef typename K::FT FT;
typedef typename K::Line_3 Line;
typedef typename K::Point_3 Point;
typedef typename K::Segment_3 Segment;
typedef typename K::Ray_3 Ray;
typedef typename K::Line_3 Line;
typedef typename K::Triangle_3 Triangle;
/* -------------------------------------
// Test data is something like that (in t supporting plane)
// Triangle is (p1,p2,p3)
//
// +E +1
// / \
// +C 6+ +8 +4 +B
// / 9++7 \
// 3+-------+5--+2
//
// +F +A
------------------------------------- */
Point p1(FT(1.), FT(0.), FT(0.));
Point p2(FT(0.), FT(1.), FT(0.));
Point p3(FT(0.), FT(0.), FT(1.));
Triangle t(p1,p2,p3);
// Edges of t
Segment s12(p1,p2);
Segment s21(p2,p1);
Segment s13(p1,p3);
Segment s23(p2,p3);
Segment s32(p3,p2);
Segment s31(p3,p1);
bool b = test_aux(is_kernel_exact,t,s12,"t-s12",s12);
b &= test_aux(is_kernel_exact,t,s21,"t-s21",s21);
b &= test_aux(is_kernel_exact,t,s13,"t-s13",s13);
b &= test_aux(is_kernel_exact,t,s23,"t-s23",s23);
// Inside points
Point p4(FT(0.5), FT(0.5), FT(0.));
Point p5(FT(0.), FT(0.75), FT(0.25));
Point p6(FT(0.5), FT(0.), FT(0.5));
Point p7(FT(0.25), FT(0.625), FT(0.125));
Point p8(FT(0.5), FT(0.25), FT(0.25));
Segment s14(p1,p4);
Segment s41(p4,p1);
Segment s24(p2,p4);
Segment s42(p4,p2);
Segment s15(p1,p5);
Segment s25(p2,p5);
Segment s34(p3,p4);
Segment s35(p3,p5);
Segment s36(p3,p6);
Segment s45(p4,p5);
Segment s16(p1,p6);
Segment s26(p2,p6);
Segment s62(p6,p2);
Segment s46(p4,p6);
Segment s48(p4,p8);
Segment s56(p5,p6);
Segment s65(p6,p5);
Segment s64(p6,p4);
Segment s17(p1,p7);
Segment s67(p6,p7);
Segment s68(p6,p8);
Segment s86(p8,p6);
Segment s78(p7,p8);
Segment s87(p8,p7);
b &= test_aux(is_kernel_exact,t,s14,"t-s14",s14);
b &= test_aux(is_kernel_exact,t,s41,"t-s41",s41);
b &= test_aux(is_kernel_exact,t,s24,"t-s24",s24);
b &= test_aux(is_kernel_exact,t,s42,"t-s42",s42);
b &= test_aux(is_kernel_exact,t,s15,"t-s15",s15);
b &= test_aux(is_kernel_exact,t,s25,"t-s25",s25);
b &= test_aux(is_kernel_exact,t,s34,"t-s34",s34);
b &= test_aux(is_kernel_exact,t,s35,"t-s35",s35);
b &= test_aux(is_kernel_exact,t,s36,"t-s36",s36);
b &= test_aux(is_kernel_exact,t,s45,"t-s45",s45);
b &= test_aux(is_kernel_exact,t,s16,"t-s16",s16);
b &= test_aux(is_kernel_exact,t,s26,"t-s26",s26);
b &= test_aux(is_kernel_exact,t,s62,"t-s62",s62);
b &= test_aux(is_kernel_exact,t,s46,"t-s46",s46);
b &= test_aux(is_kernel_exact,t,s65,"t-s65",s65);
b &= test_aux(is_kernel_exact,t,s64,"t-s64",s64);
b &= test_aux(is_kernel_exact,t,s48,"t-s48",s48);
b &= test_aux(is_kernel_exact,t,s56,"t-s56",s56);
b &= test_aux(is_kernel_exact,t,s17,"t-t17",s17);
b &= test_aux(is_kernel_exact,t,s67,"t-t67",s67);
b &= test_aux(is_kernel_exact,t,s68,"t-s68",s68);
b &= test_aux(is_kernel_exact,t,s86,"t-s86",s86);
b &= test_aux(is_kernel_exact,t,s78,"t-t78",s78);
b &= test_aux(is_kernel_exact,t,s87,"t-t87",s87);
// Outside points (in triangle plane)
Point pA(FT(-0.5), FT(1.), FT(0.5));
Point pB(FT(0.5), FT(1.), FT(-0.5));
Point pC(FT(0.5), FT(-0.5), FT(1.));
Point pE(FT(1.), FT(-1.), FT(1.));
Point pF(FT(-1.), FT(0.), FT(2.));
Segment sAB(pA,pB);
Segment sBC(pB,pC);
Segment s2E(p2,pE);
Segment sE2(pE,p2);
Segment s2A(p2,pA);
Segment s6E(p6,pE);
Segment sB8(pB,p8);
Segment sC8(pC,p8);
Segment s8C(p8,pC);
Segment s1F(p1,pF);
Segment sF6(pF,p6);
b &= test_aux(is_kernel_exact,t,sAB,"t-sAB",p2);
b &= test_aux(is_kernel_exact,t,sBC,"t-sBC",s46);
b &= test_aux(is_kernel_exact,t,s2E,"t-s2E",s26);
b &= test_aux(is_kernel_exact,t,sE2,"t-sE2",s62);
b &= test_aux(is_kernel_exact,t,s2A,"t-s2A",p2);
b &= test_aux(is_kernel_exact,t,s6E,"t-s6E",p6);
b &= test_aux(is_kernel_exact,t,sB8,"t-sB8",s48);
b &= test_aux(is_kernel_exact,t,sC8,"t-sC8",s68);
b &= test_aux(is_kernel_exact,t,s8C,"t-s8C",s86);
b &= test_aux(is_kernel_exact,t,s1F,"t-s1F",s13);
b &= test_aux(is_kernel_exact,t,sF6,"t-sF6",s36);
// Outside triangle plane
Point pa(FT(0.), FT(0.), FT(0.));
Point pb(FT(2.), FT(0.), FT(0.));
Point pc(FT(1.), FT(0.), FT(1.));
Point pe(FT(1.), FT(0.5), FT(0.5));
Segment sab(pa,pb);
Segment sac(pa,pc);
Segment sae(pa,pe);
Segment sa8(pa,p8);
Segment sb2(pb,p2);
b &= test_aux(is_kernel_exact,t,sab,"t-sab",p1);
b &= test_aux(is_kernel_exact,t,sac,"t-sac",p6);
b &= test_aux(is_kernel_exact,t,sae,"t-sae",p8);
b &= test_aux(is_kernel_exact,t,sa8,"t-sa8",p8);
b &= test_aux(is_kernel_exact,t,sb2,"t-sb2",p2);
// -----------------------------------
// ray queries
// -----------------------------------
// Edges of t
Ray r12(p1,p2);
Ray r21(p2,p1);
Ray r13(p1,p3);
Ray r23(p2,p3);
b &= test_aux(is_kernel_exact,t,r12,"t-r12",s12);
b &= test_aux(is_kernel_exact,t,r21,"t-r21",s21);
b &= test_aux(is_kernel_exact,t,r13,"t-r13",s13);
b &= test_aux(is_kernel_exact,t,r23,"t-r23",s23);
// In triangle
Point p9_(FT(0.), FT(0.5), FT(0.5));
Point p9(FT(0.25), FT(0.375), FT(0.375));
Ray r14(p1,p4);
Ray r41(p4,p1);
Ray r24(p2,p4);
Ray r42(p4,p2);
Ray r15(p1,p5);
Ray r25(p2,p5);
Ray r34(p3,p4);
Ray r35(p3,p5);
Ray r36(p3,p6);
Ray r45(p4,p5);
Ray r16(p1,p6);
Ray r26(p2,p6);
Ray r62(p6,p2);
Ray r46(p4,p6);
Ray r48(p4,p8);
Ray r56(p5,p6);
Ray r47(p4,p7);
Ray r89(p8,p9);
Ray r86(p8,p6);
Ray r68(p6,p8);
Segment r89_res(p8,p9_);
b &= test_aux(is_kernel_exact,t,r14,"t-r14",s12);
b &= test_aux(is_kernel_exact,t,r41,"t-r41",s41);
b &= test_aux(is_kernel_exact,t,r24,"t-r24",s21);
b &= test_aux(is_kernel_exact,t,r42,"t-r42",s42);
b &= test_aux(is_kernel_exact,t,r15,"t-r15",s15);
b &= test_aux(is_kernel_exact,t,r25,"t-r25",s23);
b &= test_aux(is_kernel_exact,t,r34,"t-r34",s34);
b &= test_aux(is_kernel_exact,t,r35,"t-r35",s32);
b &= test_aux(is_kernel_exact,t,r36,"t-r36",s31);
b &= test_aux(is_kernel_exact,t,r45,"t-r45",s45);
b &= test_aux(is_kernel_exact,t,r16,"t-r16",s13);
b &= test_aux(is_kernel_exact,t,r26,"t-r26",s26);
b &= test_aux(is_kernel_exact,t,r62,"t-r62",s62);
b &= test_aux(is_kernel_exact,t,r46,"t-r46",s46);
b &= test_aux(is_kernel_exact,t,r48,"t-r48",s46);
b &= test_aux(is_kernel_exact,t,r56,"t-r56",s56);
b &= test_aux(is_kernel_exact,t,r47,"t-r47",s45);
b &= test_aux(is_kernel_exact,t,r89,"t-t89",r89_res);
b &= test_aux(is_kernel_exact,t,r68,"t-r68",s64);
b &= test_aux(is_kernel_exact,t,r86,"t-r86",s86);
// Outside points (in triangre prane)
Ray rAB(pA,pB);
Ray rBC(pB,pC);
Ray r2E(p2,pE);
Ray rE2(pE,p2);
Ray r2A(p2,pA);
Ray r6E(p6,pE);
Ray rB8(pB,p8);
Ray rC8(pC,p8);
Ray r8C(p8,pC);
Ray r1F(p1,pF);
Ray rF6(pF,p6);
b &= test_aux(is_kernel_exact,t,rAB,"t-rAB",p2);
b &= test_aux(is_kernel_exact,t,rBC,"t-rBC",s46);
b &= test_aux(is_kernel_exact,t,r2E,"t-r2E",s26);
b &= test_aux(is_kernel_exact,t,rE2,"t-rE2",s62);
b &= test_aux(is_kernel_exact,t,r2A,"t-r2A",p2);
b &= test_aux(is_kernel_exact,t,r6E,"t-r6E",p6);
b &= test_aux(is_kernel_exact,t,rB8,"t-rB8",s46);
b &= test_aux(is_kernel_exact,t,rC8,"t-rC8",s64);
b &= test_aux(is_kernel_exact,t,r8C,"t-r8C",s86);
b &= test_aux(is_kernel_exact,t,r1F,"t-r1F",s13);
b &= test_aux(is_kernel_exact,t,rF6,"t-rF6",s31);
// Outside triangle plane
Ray rab(pa,pb);
Ray rac(pa,pc);
Ray rae(pa,pe);
Ray ra8(pa,p8);
Ray rb2(pb,p2);
b &= test_aux(is_kernel_exact,t,rab,"t-rab",p1);
b &= test_aux(is_kernel_exact,t,rac,"t-rac",p6);
b &= test_aux(is_kernel_exact,t,rae,"t-rae",p8);
b &= test_aux(is_kernel_exact,t,ra8,"t-ra8",p8);
b &= test_aux(is_kernel_exact,t,rb2,"t-rb2",p2);
// -----------------------------------
// Line queries
// -----------------------------------
// Edges of t
Line l12(p1,p2);
Line l21(p2,p1);
Line l13(p1,p3);
Line l23(p2,p3);
b &= test_aux(is_kernel_exact,t,l12,"t-l12",s12);
b &= test_aux(is_kernel_exact,t,l21,"t-l21",s21);
b &= test_aux(is_kernel_exact,t,l13,"t-l13",s13);
b &= test_aux(is_kernel_exact,t,l23,"t-l23",s23);
// In triangle
Line l14(p1,p4);
Line l41(p4,p1);
Line l24(p2,p4);
Line l42(p4,p2);
Line l15(p1,p5);
Line l25(p2,p5);
Line l34(p3,p4);
Line l35(p3,p5);
Line l36(p3,p6);
Line l45(p4,p5);
Line l16(p1,p6);
Line l26(p2,p6);
Line l62(p6,p2);
Line l46(p4,p6);
Line l48(p4,p8);
Line l56(p5,p6);
Line l47(p4,p7);
Line l89(p8,p9);
Line l86(p8,p6);
Line l68(p6,p8);
Segment l89_res(p1,p9_);
b &= test_aux(is_kernel_exact,t,l14,"t-l14",s12);
b &= test_aux(is_kernel_exact,t,l41,"t-l41",s21);
b &= test_aux(is_kernel_exact,t,l24,"t-l24",s21);
b &= test_aux(is_kernel_exact,t,l42,"t-l42",s12);
b &= test_aux(is_kernel_exact,t,l15,"t-l15",s15);
b &= test_aux(is_kernel_exact,t,l25,"t-l25",s23);
b &= test_aux(is_kernel_exact,t,l34,"t-l34",s34);
b &= test_aux(is_kernel_exact,t,l35,"t-l35",s32);
b &= test_aux(is_kernel_exact,t,l36,"t-l36",s31);
b &= test_aux(is_kernel_exact,t,l45,"t-l45",s45);
b &= test_aux(is_kernel_exact,t,l16,"t-l16",s13);
b &= test_aux(is_kernel_exact,t,l26,"t-l26",s26);
b &= test_aux(is_kernel_exact,t,l62,"t-l62",s62);
b &= test_aux(is_kernel_exact,t,l46,"t-l46",s46);
b &= test_aux(is_kernel_exact,t,l48,"t-l48",s46);
b &= test_aux(is_kernel_exact,t,l56,"t-l56",s56);
b &= test_aux(is_kernel_exact,t,l47,"t-l47",s45);
b &= test_aux(is_kernel_exact,t,l89,"t-t89",l89_res);
b &= test_aux(is_kernel_exact,t,l68,"t-l68",s64);
b &= test_aux(is_kernel_exact,t,l86,"t-l86",s46);
// Outside points (in triangle plane)
Line lAB(pA,pB);
Line lBC(pB,pC);
Line l2E(p2,pE);
Line lE2(pE,p2);
Line l2A(p2,pA);
Line l6E(p6,pE);
Line lB8(pB,p8);
Line lC8(pC,p8);
Line l8C(p8,pC);
Line l1F(p1,pF);
Line lF6(pF,p6);
b &= test_aux(is_kernel_exact,t,lAB,"t-lAB",p2);
b &= test_aux(is_kernel_exact,t,lBC,"t-lBC",s46);
b &= test_aux(is_kernel_exact,t,l2E,"t-l2E",s26);
b &= test_aux(is_kernel_exact,t,lE2,"t-lE2",s62);
b &= test_aux(is_kernel_exact,t,l2A,"t-l2A",p2);
b &= test_aux(is_kernel_exact,t,l6E,"t-l6E",s26);
b &= test_aux(is_kernel_exact,t,lB8,"t-lB8",s46);
b &= test_aux(is_kernel_exact,t,lC8,"t-lC8",s64);
b &= test_aux(is_kernel_exact,t,l8C,"t-l8C",s46);
b &= test_aux(is_kernel_exact,t,l1F,"t-l1F",s13);
b &= test_aux(is_kernel_exact,t,lF6,"t-lF6",s31);
// Outside triangle plane
Line lab(pa,pb);
Line lac(pa,pc);
Line lae(pa,pe);
Line la8(pa,p8);
Line lb2(pb,p2);
b &= test_aux(is_kernel_exact,t,lab,"t-lab",p1);
b &= test_aux(is_kernel_exact,t,lac,"t-lac",p6);
b &= test_aux(is_kernel_exact,t,lae,"t-lae",p8);
b &= test_aux(is_kernel_exact,t,la8,"t-la8",p8);
b &= test_aux(is_kernel_exact,t,lb2,"t-lb2",p2);
return b;
}
int main(int argc, char *argv[])
{
int i,j;
int index;
int num_sep_bond_type1 = 0;
int num_sep_bond_type2 = 0;
int overflow_flag = 0; /*if overflow_flag ==1, reallocate memory */
amberhome = (char *) getenv("AMBERHOME");
if( amberhome == NULL ){
fprintf( stdout, "AMBERHOME is not set!\n" );
exit(1);
}
if (strcmp(COLORTEXT, "YES") == 0 || strcmp(COLORTEXT, "yes") == 0) {
if (argc == 2
&& (strcmp(argv[1], "-h") == 0
|| strcmp(argv[1], "-H") == 0)) {
printf("[31mUsage: residuegen [0m input_file \n");
exit(1);
}
if (argc != 2) {
printf("[31mUsage: residuegen [0m input_file \n");
exit(1);
}
} else {
if (argc == 2
&& (strcmp(argv[1], "-h") == 0
|| strcmp(argv[1], "-H") == 0)) {
printf("Usage residuegen input_file\n");
exit(1);
}
if (argc != 2) {
printf("Usage residuegen input_file\n");
exit(1);
}
}
if ((fpin = fopen(argv[1], "r")) == NULL) {
fprintf(stdout, "Cannot open input file: %s, exit\n", argv[1]);
exit(1);
}
for(i=0; i<MAXSEPBOND; i++)
sepbond[i].type = 0;
for (;;) {
if (fgets(line, MAXCHAR, fpin) == NULL) break;
if (strncmp("ESP_FILE", line, 8) == 0) {
sscanf(&line[9], "%s", espfile);
continue;
}
if (strncmp("INPUT_FILE", line, 10) == 0) {
sscanf(&line[11], "%s", inputfile);
continue;
}
if (strncmp("CONF_NUM", line, 8) == 0) {
sscanf(&line[9], "%d", &confnum);
continue;
}
if (strncmp("SEP_BOND", line, 8) == 0) {
sscanf(&line[9], "%s%s%d", sepbond[sepbondnum].resat, sepbond[sepbondnum].capat, &sepbond[sepbondnum].type);
sepbondnum++;
continue;
}
if (strncmp("PSEUDO_HEAD_ATOM", line, 16) == 0) {
sscanf(&line[17], "%s", pseudo_head_name);
continue;
}
if (strncmp("PSEUDO_TAIL_ATOM", line, 16) == 0) {
sscanf(&line[17], "%s", pseudo_tail_name);
continue;
}
if (strncmp("NET_CHARGE", line, 10) == 0) {
sscanf(&line[11], "%lf", &netcharge);
continue;
}
if (strncmp("PREP_FILE", line, 9) == 0) {
sscanf(&line[10], "%s", prepfile);
continue;
}
if (strncmp("RESIDUE_FILE_NAME", line, 17) == 0) {
sscanf(&line[18], "%s", residue_file_name);
continue;
}
if (strncmp("RESIDUE_SYMBOL", line, 14) == 0) {
sscanf(&line[15], "%s", residue_symbol);
continue;
}
if (strncmp("ATOM_CHARGE", line, 11) == 0) {
if ( chargenum >= MAXCHARGE ) {
fprintf(stdout, "Error: MAXCHARGE is too small in residuegen.c\n"
" Increase MAXCHARGE and reinstall antechamber\n"
);
exit(1);
}
sscanf(&line[12], "%s%lf", charge[chargenum].name, &charge[chargenum].charge);
chargenum++;
continue;
}
}
fclose(fpin);
printf("\nINPUT_FILE:\t\t%s", inputfile);
printf("\nESP_FILE:\t\t%s", espfile);
printf("\nCONF_NUM:\t\t%d", confnum);
printf("\nNET_CHARGE:\t\t%-9.5lf", netcharge);
if(strcmp(pseudo_head_name, "PSEUDO_HEAD") != 0)
printf("\nPSEUDO_HEAD_NAME:\t\t%s", pseudo_head_name);
if(strcmp(pseudo_tail_name, "PSEUDO_TAIL") != 0)
printf("\nPSEUDO_TAIL_NAME:\t\t%s", pseudo_tail_name);
printf("\nThere are %d separating bonds", sepbondnum);
for(i=0;i<sepbondnum;i++)
printf("\nSEPBOND\t\t\t%d\t%s\t%s\t%d", i+1, sepbond[i].resat, sepbond[i].capat, sepbond[i].type);
printf("\nThere are %d predefined charges", chargenum);
for(i=0;i<chargenum;i++)
printf("\nATOM_CHARGE\t\t%d\t%s\t%9.5lf", i+1, charge[i].name, charge[i].charge);
printf("\nPREP_FILE: %s", prepfile);
/* read molecule information */
default_cinfo(&cinfo);
default_minfo(&minfo);
atom = (ATOM *) malloc(sizeof(ATOM) * cinfo.maxatom);
if (atom == NULL) {
fprintf(stdout, "memory allocation error for *atom\n");
exit(1);
}
bond = (BOND *) malloc(sizeof(BOND) * cinfo.maxbond);
if (bond == NULL) {
fprintf(stdout, "memory allocation error for *bond\n");
exit(1);
}
for (i = 0; i < cinfo.maxbond; ++i) {
bond[i].jflag = -1; /* bond type has not been assigned */
}
overflow_flag =
rac(inputfile, &atomnum, atom, &bondnum, bond, &cinfo, &minfo);
if (overflow_flag) {
cinfo.maxatom = atomnum + 10;
cinfo.maxbond = bondnum + 10;
free(atom);
free(bond);
atom = (ATOM *) malloc(sizeof(ATOM) * cinfo.maxatom);
if (atom == NULL) {
fprintf(stdout, "memory allocation error for *atom\n");
exit(1);
}
bond = (BOND *) malloc(sizeof(BOND) * cinfo.maxbond);
if (bond == NULL) {
fprintf(stdout, "memory allocation error for *bond\n");
exit(1);
}
int i;
for (i = 0; i < cinfo.maxbond; ++i) {
bond[i].jflag = -1; /* bond type has not been assigned */
}
overflow_flag =
rac(ifilename, &atomnum, atom, &bondnum, bond, &cinfo, &minfo);
}
atomicnum(atomnum, atom);
/* allocate memory*/
selectelement = (int *) malloc(sizeof(int) * atomnum);
if (selectelement == NULL) {
fprintf(stdout, "memory allocation error for *selectelement\n");
exit(1);
}
selectelement2 = (int *) malloc(sizeof(int) * atomnum);
if (selectelement2 == NULL) {
fprintf(stdout, "memory allocation error for *selectelement2\n");
exit(1);
}
flag = (int *) malloc(sizeof(int) * atomnum);
if (flag == NULL) {
fprintf(stdout, "memory allocation error for *flag\n");
exit(1);
}
/* find atom ids for predefined charges*/
for(i =0; i< chargenum; i++) {
charge[i].id = -1;
index = 0;
length = strlen(charge[i].name);
for(j =0; j< atomnum; j++)
if(strncmp(atom[j].name, charge[i].name,length) == 0) {
charge[i].id = j;
index = 1;
break;
}
if(index == 0) {
fprintf(stdout, "Error: the charge name, %s does not show up in the molecule\n", charge[i].name);
exit(1);
}
}
/* find atom ids for separted bonds*/
for(i =0; i<sepbondnum; i++) {
sepbond[i].resid = -1;
sepbond[i].capid = -1;
for(j =0; j< atomnum; j++) {
length = strlen(sepbond[i].resat);
if(strncmp(atom[j].name, sepbond[i].resat, length) == 0) {
sepbond[i].resid = j;
continue;
}
length = strlen(sepbond[i].capat);
if(strncmp(atom[j].name, sepbond[i].capat, length) == 0) {
sepbond[i].capid = j;
continue;
}
if(sepbond[i].resid != -1 && sepbond[i].capid != -1) break;
}
if(sepbond[i].resid == -1) {
fprintf(stdout, "Error: the ATOM_NAME1 %s of %d does not show up in the molecule\n", sepbond[i].resat, i+1);
exit(1);
}
if(sepbond[i].capid == -1) {
fprintf(stdout, "Error: the ATOM_NAME2 %s of %d does not show up in the molecule\n", sepbond[i].capat, i+1);
exit(1);
}
if(sepbond[i].type == 1) {
head_id = sepbond[i].resid;
pre_head_id = sepbond[i].capid;
num_sep_bond_type1 ++;
}
if(sepbond[i].type ==-1) {
tail_id = sepbond[i].resid;
post_tail_id = sepbond[i].capid;
num_sep_bond_type2 ++;
}
}
if(num_sep_bond_type1 > 1) {
fprintf(stdout, "Error: only one or none SEP_BOND has a type of '1'\n");
exit(1);
}
if(num_sep_bond_type2 > 1) {
fprintf(stdout, "Error: only one or none SEP_BOND has a type of '-1'\n");
exit(1);
}
/* find atom ids for terminal atoms */
num_terminal_atom = 0;
if(num_sep_bond_type1 == 1) num_terminal_atom ++;
if(num_sep_bond_type2 == 1) num_terminal_atom ++;
if(head_id == -1 && strcmp(pseudo_head_name, "PSEUDO_HEAD") != 0) {
for(i=0;i<atomnum;i++)
if(strcmp(atom[i].name, pseudo_head_name) == 0) {
head_id = i;
num_terminal_atom ++;
break;
}
}
if(tail_id == -1 && strcmp(pseudo_tail_name, "PSEUDO_TAIL") != 0) {
for(i=0;i<atomnum;i++)
if(strcmp(atom[i].name, pseudo_tail_name) == 0) {
tail_id = i;
num_terminal_atom ++;
break;
}
}
/* Now we allow a residue only has one cap (either the N or C-terminal) */
/*
if(num_terminal_atom != 0 && num_terminal_atom != 2) {
fprintf(stdout, "Error, the total number of terminal atoms must be zero or 2 (HEAD_ATOM / PSEUDO_HEAD_ATOM + TAIL_ATOM / PSEUDO_TAIL_ATOM)\n");
exit(0);
}
*/
/* find cap atoms and residue atoms*/
if(sepbondnum > 0) {
for(i=0;i<sepbondnum;i++) {
printf("\n\nCap Atoms for #%d separating bond (%s - %s) with a type of %d", i+1, sepbond[i].capat, sepbond[i].resat, sepbond[i].type);
group_atom1(i);
for (j = 0; j<atomnum; j++)
if(flag[j] == 1)
printf("\nATOM\t %d\t%s", j+1, atom[j].name);
}
printf("\n\nResidue Atoms");
group_atom2();
residueatnum = 0;
for (i = 0; i<atomnum; i++)
if(flag[i] == 1) {
residueatnum ++;
printf("\nATOM\t %d\t%s", i+1, atom[i].name);
}
}
else {
for (i = 0; i<atomnum; i++)
flag[i] = 1;
}
/* find main chain atoms when num_terminal_atom is 2, otherwise no main chain atoms are determined*/
if(num_terminal_atom == 2) {
printf("\n\n(PSEUDO) HEAD ATOM: %s", atom[head_id].name);
printf("\n\n(PSEUDO) TAIL ATOM: %s", atom[tail_id].name);
selectnum = 0;
for (i = 0; i<atomnum; i++) {
selectelement[i] = -1;
selectelement2[i] = -1;
}
findpath(atom, 0, head_id);
printf("\n\nMain Chain Atoms");
for (j = 0; j < selectnum2 ; j++)
printf("\nATOM\t%d\t%s", j+1, atom[selectelement2[j]].name);
}
/* generate charge input file for respgen */
printf("\nGenerate charge input file for respgen ... \n");
if ((fpout = fopen("RESIDUE_GEN_RESPGEN.DAT", "w")) == NULL) {
fprintf(stdout, "Cannot open input file RESIDUE_GEN_RESPGEN.DAT, exit\n");
exit(1);
}
fprintf(fpout, "//predefined charges in a format of (CHARGE partical_charge atom_ID atom_name)");
for(i=0;i<chargenum;i++)
fprintf(fpout, "\nCHARGE %9.6lf\t%d\t%s", charge[i].charge, charge[i].id + 1, charge[i].name);
fprintf(fpout, "\n//charge groups in a format of (GROUP num_atom net_charge)");
fprintf(fpout, "\nGROUP\t%d\t%9.5lf\n", residueatnum, netcharge);
fprintf(fpout, "//atoms in the group in a format of (ATOM atom_ID atom_name)");
for (i = 0; i<atomnum; i++)
if(flag[i] == 1)
fprintf(fpout, "\nATOM\t%d\t%s", i+1, atom[i].name);
fclose(fpout);
/* generate main chain file for prepgen */
printf("\nGenerate main chain atom file for prepgen ... \n");
if ((fpout = fopen("RESIDUE_GEN_MAINCHAIN.DAT", "w")) == NULL) {
fprintf(stdout, "Cannot open input file RESIDUE_GEN_MAINCHAIN.DAT, exit\n");
exit(1);
}
if(head_id != -1 && pre_head_id != -1)
fprintf(fpout, "HEAD_NAME\t%s\n", atom[head_id].name);
if(tail_id != -1 && post_tail_id != -1)
fprintf(fpout, "TAIL_NAME\t%s\n", atom[tail_id].name);
for (i = 0; i < selectnum2 ; i++) {
if(head_id != -1 && pre_head_id != -1) {
length = strlen(atom[head_id].name);
if(strncmp(atom[selectelement2[i]].name, atom[head_id].name, length) == 0)
continue;
}
if(tail_id != -1 && post_tail_id != -1) {
length = strlen(atom[tail_id].name);
if(strncmp(atom[selectelement2[i]].name, atom[tail_id].name, length) == 0)
continue;
}
fprintf(fpout, "MAIN_CHAIN\t%s\n", atom[selectelement2[i]].name);
}
for (i = 0; i<atomnum; i++)
if(flag[i] == 1)
continue;
else
fprintf(fpout, "OMIT_NAME\t%s\n", atom[i].name);
if(pre_head_id != -1)
fprintf(fpout, "PRE_HEAD_TYPE\t%s\n", atom[pre_head_id].ambername);
if(post_tail_id != -1)
fprintf(fpout, "POST_TAIL_TYPE\t%s\n", atom[post_tail_id].ambername);
fprintf(fpout, "CHARGE\t%9.5lf\n", netcharge);
fflush(stdout);
fclose(fpout);
proceed();
printf("\n");
return (0);
}
int main(int argc, char *argv[]) {
int i,j,k;
int overflow_flag = 0;
int count;
int atid1, atid2;
int resid1, resid2;
int oldresid;
int suc;
double sum;
double x,y,z;
char line[MAXCHAR];
char defstr[MAXCHAR];
char atomname[MAXCHAR];
amberhome = (char *) getenv("AMBERHOME");
if( amberhome == NULL ){
fprintf( stdout, "AMBERHOME is not set!\n" );
exit(1);
}
if (strcmp(COLORTEXT, "YES") == 0 || strcmp(COLORTEXT, "yes") == 0) {
if (argc == 2
&& (strcmp(argv[1], "-h") == 0
|| strcmp(argv[1], "-H") == 0)) {
printf
("[31mUsage: match -i [0m input file name \n"
"[31m -r [0m reference file name \n"
"[31m -f [0m format: 1-pdb (the default), 2-ac, 3-mol2, 4-sdf, 5-crd/rst\n"
"[31m -o [0m output file name\n"
"[31m -l [0m run log file name, default is \"match.log\"\n"
"[31m -s [0m selection mode\n"
"[34m 0:[0m use all atoms (the default)\n"
"[34m 1:[0m specify atom names\n"
"[34m 2:[0m use atom defination file\n"
"[34m 3:[0m use residue defination file - original residue IDs\n"
"[34m 4:[0m use residue defination file - renumbered residue IDs\n"
"[31m -ds [0mdefinition string if selection modes of '1' or '3' or '4'\n"
"[31m [0me.g. 'C,N,O,CA', or 'HET' which stands for heavy atoms for '-ds 1')\n"
"[31m -df [0mdefinition file if selection mode of '2' or '3' or '4'\n"
"[31m [0mrecords take a form of 'ATOM atom_id_input atom_id_reference'\n"
"[31m [0mor 'RES res_id_input res_id_reference'\n"
"[31m -n [0m number of atoms participating ls-fitting,\n"
"[31m [0m default is -1, which implies to use all the selected atoms\n"
"[31m -m [0m matrix file, default is \"match.matrix\"\n"
"[31m -t [0m job type:\n"
"[35m 0:[0m calculate rms only, need -i and -r\n"
"[35m 1:[0m lsfit, need -i, -r and -o the default\n"
"[35m 2:[0m translation/rotation, need -i, -o and -m\n");
exit(0);
}
if (argc != 23 && argc != 21 && argc != 19 && argc != 17 && argc != 15 && argc != 13 && argc != 11 && argc !=9 && argc !=7 && argc !=5) {
printf
("[31mUsage: match -i [0m input file name \n"
"[31m -r [0m reference file name \n"
"[31m -f [0m format: 1-pdb (the default), 2-ac, 3-mol2, 4-sdf, 5-crd/rst\n"
"[31m -o [0m output file name\n"
"[31m -l [0m run log file name, default is \"match.log\"\n"
"[31m -s [0m selection mode\n"
"[34m 0:[0m use all atoms (the default)\n"
"[34m 1:[0m specify atom names\n"
"[34m 2:[0m use atom defination file\n"
"[34m 3:[0m use residue defination file - original residue IDs\n"
"[34m 4:[0m use residue defination file - renumbered residue IDs\n"
"[31m -ds [0mdefinition string if selection modes of '1' or '3' or '4'\n"
"[31m [0me.g. 'C,N,O,CA', or 'HET' which stands for heavy atoms for '-ds 1')\n"
"[31m -df [0mdefinition file if selection mode of '2' or '3' or '4'\n"
"[31m [0mrecords take a form of 'ATOM atom_id_input atom_id_reference'\n"
"[31m [0mor 'RES res_id_input res_id_reference'\n"
"[31m -n [0m number of atoms participating ls-fitting,\n"
"[31m [0m default is -1, which implies to use all the selected atoms\n"
"[31m -m [0m matrix file, default is \"match.matrix\"\n"
"[31m -t [0m job type:\n"
"[35m 0:[0m calculate rms only, need -i and -r\n"
"[35m 1:[0m lsfit, need -i, -r and -o the default\n"
"[35m 2:[0m translation/rotation, need -i, -o and -m\n");
exit(0);
}
} else {
if (argc == 2
&& (strcmp(argv[1], "-h") == 0
|| strcmp(argv[1], "-H") == 0)) {
printf
("Usage: match -i input file name \n"
" -r reference file name \n"
" -f format: 1-pdb (the default), 2-ac, 3-mol2, 4-sdf, 5-crd/rst\n"
" -o output file name\n"
" -l run log file name, default is \"match.log\"\n"
" -s selection mode\n"
" 0: use all atoms (the default)\n"
" 1: specify atom names\n"
" 2: use atom defination file\n"
" 3: use residue defination file - original residue IDs\n"
" 4: use residue defination file - renumbered residue IDs\n"
" -ds definition string if selection modes of '1' or '3' or '4'\n"
" e.g. 'C,N,O,CA', or 'HET' which stands for heavy atoms for '-ds 1')\n"
" -df definition file if selection mode of '2' or '3' or '4'\n"
" records take a form of 'ATOM atom_id_input atom_id_reference'\n"
" or 'RES res_id_input res_id_reference'\n"
" -n number of atoms participating ls-fitting,\n"
" default is -1, which implies to use all the selected atoms\n"
" -m matrix file, default is \"match.matrix\"\n"
" -t job type:\n"
" 0: calculate rms only, need -i and -r\n"
" 1: lsfit, need -i, -r and -o the default\n"
" 2: translation/rotation, need -i, -o and -m\n");
exit(0);
}
if (argc != 23 && argc != 21 && argc != 19 && argc != 17 && argc != 15 && argc != 13 && argc != 11 && argc !=9 && argc !=7 && argc !=5) {
printf
("Usage: match -i input file name \n"
" -r reference file name \n"
" -f format: 1-pdb (the default), 2-ac, 3-mol2, 4-sdf, 5-crd/rst\n"
" -o output file name\n"
" -l run log file name, default is \"match.log\"\n"
" -s selection mode\n"
" 0: use all atoms (the default)\n"
" 1: specify atom names\n"
" 2: use atom defination file\n"
" 3: use residue defination file - original residue IDs\n"
" 4: use residue defination file - renumbered residue IDs\n"
" -ds definition string if selection modes of '1' or '3' or '4'\n"
" e.g. 'C,N,O,CA', or 'HET' which stands for heavy atoms for '-ds 1')\n"
" -df definition file if selection mode of '2' or '3' or '4'\n"
" records take a form of 'ATOM atom_id_input atom_id_reference'\n"
" or 'RES res_id_input res_id_reference'\n"
" -n number of atoms participating ls-fitting,\n"
" default is -1, which implies to use all the selected atoms\n"
" -m matrix file, default is \"match.matrix\"\n"
" -t job type:\n"
" 0: calculate rms only, need -i and -r\n"
" 1: lsfit, need -i, -r and -o the default\n"
" 2: translation/rotation, need -i, -o and -m\n");
exit(0);
}
}
for (i = 1; i < argc; i += 2) {
if (strcmp(argv[i], "-i") == 0) {
strcpy(ifilename, argv[i + 1]);
iinput = 1;
}
if (strcmp(argv[i], "-f") == 0)
format=atoi(argv[i+1]);
if (strcmp(argv[i], "-o") == 0) {
strcpy(ofilename, argv[i + 1]);
ioutput = 1;
}
if (strcmp(argv[i], "-r") == 0) {
strcpy(rfilename, argv[i + 1]);
iref = 1;
}
if (strcmp(argv[i], "-s") == 0)
stype = atoi(argv[i+1]);
if (strcmp(argv[i], "-ds") == 0)
strcpy(def_atomname_str, argv[i + 1]);
if (strcmp(argv[i], "-df") == 0)
strcpy(def_filename, argv[i + 1]);
if (strcmp(argv[i], "-m") == 0) {
strcpy(mfilename, argv[i + 1]);
imatrix = 1;
}
if (strcmp(argv[i], "-t") == 0)
jobtype = atoi(argv[i+1]);
if (strcmp(argv[i], "-n") == 0)
nsel = atoi(argv[i+1]);
if (strcmp(argv[i], "-l") == 0)
strcpy(lfilename, argv[i + 1]);
}
if(jobtype !=0 && jobtype != 1 && jobtype != 2) jobtype = 1;
if(format != 1 && format != 2 && format != 3 && format != 4 && format != 5) format = 1;
if(jobtype == 0)
if(iinput == 0 || iref == 0) {
fprintf(stderr, "RMS calculation needs an input and a reference files, exit\n");
exit(0);
}
if(jobtype == 1)
if(iinput == 0 || ioutput == 0 || iref == 0) {
fprintf(stderr, "The least-square fitting calculation needs an input, an output and a reference files, exit\n");
exit(0);
}
if(jobtype == 2)
if(iinput == 0 || ioutput == 0) {
fprintf(stderr, "The translation/rotation job needs an input and an output files, exit\n");
exit(0);
}
if(jobtype == 0 || jobtype == 1) {
if ((fplog = fopen(lfilename, "w")) == NULL) {
fprintf(stderr, "Cannot open log file %s to write, exit\n", lfilename);
exit(1);
}
}
/* read in input files*/
memory(0, MAXATOM, MAXBOND, MAXRING);
if(format == 1) {
overflow_flag = rpdb(ifilename, &atomnum, atom, cinfo, minfo, 0);
if (overflow_flag) {
cinfo.maxatom = atomnum + 10;
cinfo.maxbond = bondnum + 10;
memory(7, cinfo.maxatom, cinfo.maxbond, cinfo.maxring);
overflow_flag = rpdb(ifilename, &atomnum, atom, cinfo, minfo, 0);
}
}
if(format == 2) {
overflow_flag = rac(ifilename, &atomnum, atom, &bondnum, bond, &cinfo, &minfo);
if (overflow_flag) {
cinfo.maxatom = atomnum + 10;
cinfo.maxbond = bondnum + 10;
memory(7, cinfo.maxatom, cinfo.maxbond, cinfo.maxring);
overflow_flag = rac(ifilename, &atomnum, atom, &bondnum, bond, &cinfo, &minfo);
}
}
if(format == 3) {
overflow_flag = rmol2(ifilename, &atomnum, atom, &bondnum, bond, &cinfo, &minfo, 0);
if (overflow_flag) {
cinfo.maxatom = atomnum + 10;
cinfo.maxbond = bondnum + 10;
memory(7, cinfo.maxatom, cinfo.maxbond, cinfo.maxring);
overflow_flag =
rmol2(ifilename, &atomnum, atom, &bondnum, bond, &cinfo, &minfo, 0);
}
}
if(format == 4) {
overflow_flag = rmdl(ifilename, &atomnum, atom, &bondnum, bond, cinfo, minfo);
if (overflow_flag) {
cinfo.maxatom = atomnum + 10;
cinfo.maxbond = bondnum + 10;
memory(7, cinfo.maxatom, cinfo.maxbond, cinfo.maxring);
overflow_flag = rmdl(ifilename, &atomnum, atom, &bondnum, bond, cinfo, minfo);
}
}
if(format == 5) {
overflow_flag = rrst(ifilename, &atomnum, atom, cinfo);
if (overflow_flag) {
cinfo.maxatom = atomnum + 10;
memory(7, cinfo.maxatom, cinfo.maxbond, cinfo.maxring);
overflow_flag = rrst(ifilename, &atomnum, atom, cinfo);
}
}
free(bond);
free(ring);
free(arom);
cinfo.maxatom = MAXATOM;
cinfo.maxbond = MAXBOND;
cinfo.maxring = MAXRING;
ref_memory(0, MAXATOM, MAXBOND, MAXRING);
if(format == 1) {
overflow_flag = rpdb(rfilename, &refatomnum, refatom, cinfo, minfo, 0);
if (overflow_flag) {
cinfo.maxatom = refatomnum + 10;
cinfo.maxbond = refbondnum + 10;
ref_memory(7, cinfo.maxatom, cinfo.maxbond, cinfo.maxring);
overflow_flag = rpdb(rfilename, &refatomnum, refatom, cinfo, minfo, 0);
}
}
if(format == 2) {
overflow_flag = rac(rfilename, &refatomnum, refatom, &refbondnum, refbond, &cinfo, &minfo);
if (overflow_flag) {
cinfo.maxatom = refatomnum + 10;
cinfo.maxbond = refbondnum + 10;
ref_memory(7, cinfo.maxatom, cinfo.maxbond, cinfo.maxring);
overflow_flag = rac(rfilename, &refatomnum, refatom, &refbondnum, refbond, &cinfo, &minfo);
}
}
if(format == 3) {
overflow_flag = rmol2(rfilename, &refatomnum, refatom, &refbondnum, refbond, &cinfo, &minfo, 0);
if (overflow_flag) {
cinfo.maxatom = refatomnum + 10;
cinfo.maxbond = refbondnum + 10;
ref_memory(7, cinfo.maxatom, cinfo.maxbond, cinfo.maxring);
overflow_flag = rmol2(rfilename, &refatomnum, refatom, &refbondnum, refbond, &cinfo, &minfo, 0);
}
}
if(format == 4) {
overflow_flag = rmdl(rfilename, &refatomnum, refatom, &refbondnum, refbond, cinfo, minfo);
if (overflow_flag) {
cinfo.maxatom = refatomnum + 10;
cinfo.maxbond = refbondnum + 10;
ref_memory(7, cinfo.maxatom, cinfo.maxbond, cinfo.maxring);
overflow_flag = rmdl(rfilename, &refatomnum, refatom, &refbondnum, refbond, cinfo, minfo);
}
}
if(format == 5) {
overflow_flag = rrst(rfilename, &refatomnum, refatom, cinfo);
if (overflow_flag) {
cinfo.maxatom = refatomnum + 10;
ref_memory(7, cinfo.maxatom, cinfo.maxbond, cinfo.maxring);
overflow_flag = rrst(rfilename, &refatomnum, refatom, cinfo);
}
}
free(refbond);
free(refring);
free(refarom);
if(debug == 1) {
for(i=0;i<atomnum;i++)
printf("ATOM %5d %5s %5s %5d %8.3lf %8.3lf %8.3lf\n", i+1, atom[i].name, atom[i].aa, atom[i].resno, atom[i].x, atom[i].y, atom[i].z);
for(i=0;i<refatomnum;i++)
printf("ATOM %5d %5s %5s %5d %8.3lf %8.3lf %8.3lf\n", i+1, refatom[i].name, refatom[i].aa, refatom[i].resno, refatom[i].x, refatom[i].y, refatom[i].z);
}
if(jobtype == 0 || jobtype == 1) {
fit_atom = (FITATOM *) malloc(sizeof(FITATOM) * atomnum);
if (fit_atom == NULL) {
fprintf(stderr, "memory allocation error for *fit_atom\n");
exit(1);
}
fit_refatom = (FITATOM *) malloc(sizeof(FITATOM) * refatomnum);
if (fit_refatom == NULL) {
fprintf(stderr, "memory allocation error for *fit_refatom\n");
exit(1);
}
if(stype == 0) {
for(i=0;i<atomnum;i++) {
fit_atom[i].x=atom[i].x;
fit_atom[i].y=atom[i].y;
fit_atom[i].z=atom[i].z;
}
for(i=0;i<refatomnum;i++) {
fit_refatom[i].x=refatom[i].x;
fit_refatom[i].y=refatom[i].y;
fit_refatom[i].z=refatom[i].z;
}
fit_atomnum = atomnum;
fit_refatomnum = refatomnum;
}
if(stype == 1) {
count = 0;
for(i=0;i <= strlen(def_atomname_str);i++) {
if(def_atomname_str[i]==' ') continue;
if(def_atomname_str[i]==',') def_atomname_str[i] = ' ';
defstr[count] = def_atomname_str[i];
count++;
}
sscanf(defstr, "%s", atomname);
strcpy(def_atomname[ndef_atomname].str, atomname);
ndef_atomname++;
for(i=1;i<strlen(defstr);i++)
if(defstr[i] == ' ') {
sscanf(&defstr[i], "%s", atomname);
strcpy(def_atomname[ndef_atomname].str, atomname);
ndef_atomname++;
}
for(i=0;i<atomnum;i++) {
suc = 0;
for(j=0;j<ndef_atomname;j++) {
if(strcmp(def_atomname[j].str, atom[i].name) == 0) {
suc = 1;
break;
}
if(strcmp(def_atomname[j].str, "HET") == 0)
if(atom[i].name[0] != 'H') {
suc = 1;
break;
}
}
if(suc == 1) {
fit_atom[fit_atomnum].x=atom[i].x;
fit_atom[fit_atomnum].y=atom[i].y;
fit_atom[fit_atomnum].z=atom[i].z;
fit_atomnum++;
}
}
for(i=0;i<refatomnum;i++) {
suc = 0;
for(j=0;j<ndef_atomname;j++) {
if(strcmp(def_atomname[j].str, refatom[i].name) == 0) {
suc = 1;
break;
}
if(strcmp(def_atomname[j].str, "HET") == 0)
if(refatom[i].name[0] != 'H') {
suc = 1;
break;
}
}
if(suc == 1) {
fit_refatom[fit_refatomnum].x=refatom[i].x;
fit_refatom[fit_refatomnum].y=refatom[i].y;
fit_refatom[fit_refatomnum].z=refatom[i].z;
fit_refatomnum++;
}
}
}
if(stype == 2) {
if ((fpdef = fopen(def_filename, "r")) == NULL) {
fprintf(stderr, "Cannot open file %s, exit\n", def_filename);
exit(1);
}
count = 0;
for(;;) {
if (fgets(line, MAXCHAR, fpdef) == NULL) break;
if(strncmp(line, "ATOM", 4) == 0) {
sscanf(&line[4], "%d%d", &atid1, &atid2);
atid1--;
atid2--;
fit_atom[count].x=atom[atid1].x;
fit_atom[count].y=atom[atid1].y;
fit_atom[count].z=atom[atid1].z;
fit_refatom[count].x=refatom[atid2].x;
fit_refatom[count].y=refatom[atid2].y;
fit_refatom[count].z=refatom[atid2].z;
count++;
}
}
fit_atomnum = count;
fit_refatomnum = count;
fclose(fpdef);
}
if(stype == 3 || stype == 4) {
/*first of all, read in atom name definition strings*/
count = 0;
for(i=0;i <= strlen(def_atomname_str);i++) {
if(def_atomname_str[i]==' ') continue;
if(def_atomname_str[i]==',') def_atomname_str[i] = ' ';
defstr[count] = def_atomname_str[i];
count++;
}
sscanf(defstr, "%s", atomname);
strcpy(def_atomname[ndef_atomname].str, atomname);
ndef_atomname++;
for(i=1;i<strlen(defstr);i++)
if(defstr[i] == ' ') {
sscanf(&defstr[i], "%s", atomname);
if(strcmp(atomname, "HET") == 0) {
fprintf(stderr, "Warning: HET cannot be defined with -s of 3\n");
continue;
}
strcpy(def_atomname[ndef_atomname].str, atomname);
ndef_atomname++;
}
if(debug == 1) {
for(i=0;i<ndef_atomname;i++)
printf("DEF %5d %5s\n", i+1, def_atomname[i].str);
}
if(stype == 4) {
count = 0;
oldresid = -99999;
for(i=0;i<atomnum;i++) {
if(atom[i].resno != oldresid) {
oldresid = atom[i].resno;
count++;
}
atom[i].resno = count;
}
count = 0;
oldresid = -99999;
for(i=0;i<refatomnum;i++) {
if(refatom[i].resno != oldresid) {
oldresid = refatom[i].resno;
count++;
}
refatom[i].resno = count;
}
}
/* now working on residue definition file */
if ((fpdef = fopen(def_filename, "r")) == NULL) {
fprintf(stderr, "Cannot open file %s, exit\n", def_filename);
exit(1);
}
count = 0;
for(;;) {
if (fgets(line, MAXCHAR, fpdef) == NULL) break;
if(strncmp(line, "RES", 3) == 0) {
sscanf(&line[3], "%d%d", &resid1, &resid2);
if(debug == 1)
printf("RES %5d %5d\n", resid1, resid2);
for(i=0; i< ndef_atomname; i++) {
atid1 = -1;
atid2 = -1;
for(j=0;j<atomnum;j++)
if(strcmp(def_atomname[i].str, atom[j].name) == 0 && atom[j].resno == resid1) {
atid1 = j;
break;
}
for(j=0;j<refatomnum;j++)
if(strcmp(def_atomname[i].str, refatom[j].name) == 0 && refatom[j].resno == resid2) {
atid2 = j;
break;
}
if(atid1 >= 0 && atid2 >= 0) {
fit_atom[count].x=atom[atid1].x;
fit_atom[count].y=atom[atid1].y;
fit_atom[count].z=atom[atid1].z;
fit_refatom[count].x=refatom[atid2].x;
fit_refatom[count].y=refatom[atid2].y;
fit_refatom[count].z=refatom[atid2].z;
count++;
}
}
}
}
fit_atomnum = count;
fit_refatomnum = count;
fclose(fpdef);
}
if(fit_atomnum != fit_refatomnum || fit_atomnum <=0) {
fprintf(stderr, "\nThe numumber of fitting atoms in input file (%d) is different from the number of fitting atoms in ref file (%d)", fit_atomnum, fit_refatomnum);
exit(0);
}
if(nsel > 0 && fit_atomnum > nsel) fit_atomnum = nsel;
if(fit_atomnum <= 0) {
fprintf(stderr, "\nThe number of fitting atoms is smaller than or equal to zero, exit!");
exit(1);
}
sum = 0;
for(i=0;i<fit_atomnum;i++) {
sum+=(fit_atom[i].x-fit_refatom[i].x) * (fit_atom[i].x-fit_refatom[i].x);
sum+=(fit_atom[i].y-fit_refatom[i].y) * (fit_atom[i].y-fit_refatom[i].y);
sum+=(fit_atom[i].z-fit_refatom[i].z) * (fit_atom[i].z-fit_refatom[i].z);
}
rms = sqrt(sum/fit_atomnum);
fprintf(fplog, "The rmsd before least-square fitting is %9.4lf\n", rms);
fprintf(fplog, "Number of atoms participate least-square fitting is %9d\n", fit_atomnum);
fprintf(stdout, "\nThe rmsd before least-square fitting is %9.4lf", rms);
fprintf(stdout, "\nNumber of atoms participate least-square fitting is %9d", fit_atomnum);
if(jobtype == 0) {
fclose(fplog);
return 0;
}
if ((fpmatrix = fopen(mfilename, "w")) == NULL) {
fprintf(stderr, "Cannot open file %s, exit\n", mfilename);
exit(1);
}
rms = lsfit(fit_refatom, fit_atom, fit_atomnum) ;
for(i=0;i<fit_atomnum;i++) {
x=CG0[0]+ROT[0][0]*(fit_atom[i].x-CG1[0])+ ROT[0][1]*(fit_atom[i].y-CG1[1])+ ROT[0][2]*(fit_atom[i].z-CG1[2]);
y=CG0[1]+ROT[1][0]*(fit_atom[i].x-CG1[0])+ ROT[1][1]*(fit_atom[i].y-CG1[1])+ ROT[1][2]*(fit_atom[i].z-CG1[2]);
z=CG0[2]+ROT[2][0]*(fit_atom[i].x-CG1[0])+ ROT[2][1]*(fit_atom[i].y-CG1[1])+ ROT[2][2]*(fit_atom[i].z-CG1[2]);
sum =(x-fit_refatom[i].x) * (x-fit_refatom[i].x);
sum+=(y-fit_refatom[i].y) * (y-fit_refatom[i].y);
sum+=(z-fit_refatom[i].z) * (z-fit_refatom[i].z);
sum = sqrt(sum);
fprintf(fplog, "ATOM %5d %9.3lf %9.3lf %9.3lf ", i+1, fit_atom[i].x, fit_atom[i].y, fit_atom[i].z);
fprintf(fplog, "REFATOM %9.3lf %9.3lf %9.3lf %9.3lf\n", fit_refatom[i].x, fit_refatom[i].y, fit_refatom[i].z, sum);
}
fclose(fpmatrix);
fprintf(fplog, "\nThe rmsd after least-square fitting is %9.4lf\n", rms);
fprintf(stdout, "\nThe rmsd after least-square fitting is %9.4lf\n", rms);
fclose(fplog);
}
if(jobtype == 2)
rmatrix(mfilename);
if(jobtype == 1 || jobtype == 2) {
for(i=0;i<atomnum;i++) {
x=CG0[0]+ROT[0][0]*(atom[i].x-CG1[0])+ ROT[0][1]*(atom[i].y-CG1[1])+ ROT[0][2]*(atom[i].z-CG1[2]);
y=CG0[1]+ROT[1][0]*(atom[i].x-CG1[0])+ ROT[1][1]*(atom[i].y-CG1[1])+ ROT[1][2]*(atom[i].z-CG1[2]);
z=CG0[2]+ROT[2][0]*(atom[i].x-CG1[0])+ ROT[2][1]*(atom[i].y-CG1[1])+ ROT[2][2]*(atom[i].z-CG1[2]);
atom[i].x = x;
atom[i].y = y;
atom[i].z = z;
}
if(format == 1) wpdb(ofilename, atomnum, atom);
if(format == 2) wac(ofilename, atomnum, atom, bondnum, bond, cinfo, minfo);
if(format == 3) wmol2(ofilename, atomnum, atom, bondnum, bond, arom, cinfo, minfo);
if(format == 4) wmdl(ofilename, atomnum, atom, bondnum, bond, cinfo);
if(format == 5) wrst(ofilename, atomnum, atom);
}
return 0;
}
int main(int argc, char *argv[])
{
if (strcmp(COLORTEXT, "YES") == 0 || strcmp(COLORTEXT, "yes") == 0) {
if (argc == 2
&& (strcmp(argv[1], "-h") == 0
|| strcmp(argv[1], "-H") == 0)) {
printf("[31mUsage: respgen -i[0m input file name(ac)\n"
"[31m -o[0m output file name\n"
"[31m -f[0m output file format (resp1 or resp2) \n"
"[32m resp1[0m - first stage resp fitting \n"
"[32m resp2[0m - second stage resp fitting\n");
exit(0);
}
if (argc != 7) {
printf("[31mUsage: respgen -i[0m input file name(ac)\n"
"[31m -o[0m output file name\n"
"[31m -f[0m output file format (resp1 or resp2) \n"
"[32m resp1[0m - first stage resp fitting \n"
"[32m resp2[0m - second stage resp fitting\n");
exit(0);
}
} else {
if (argc == 2
&& (strcmp(argv[1], "-h") == 0
|| strcmp(argv[1], "-H") == 0)) {
printf("Usage respgen -i input file name(ac)\n");
printf(" -o output file name\n");
printf(" -f output file format (resp1 or resp2)\n");
printf(" resp1 - first stage resp fitting\n");
printf
(" resp2 - second stage resp fitting \n");
exit(0);
}
if (argc != 7) {
printf("Usage respgen -i input file name(ac)\n");
printf(" -o output file name\n");
printf(" -f output file format (resp1 or resp2)\n");
printf(" resp1 - first stage resp fitting\n");
printf
(" resp2 - second stage resp fitting \n");
exit(0);
}
}
method = 0;
for (i = 1; i < argc; i += 2) {
if (strcmp(argv[i], "-i") == 0)
strcpy(ifilename, argv[i + 1]);
if (strcmp(argv[i], "-o") == 0)
strcpy(ofilename, argv[i + 1]);
if (strcmp(argv[i], "-f") == 0) {
if (strcmp("resp", argv[i + 1]) == 0)
method = 0;
if (strcmp("resp1", argv[i + 1]) == 0)
method = 1;
if (strcmp("resp2", argv[i + 1]) == 0)
method = 2;
}
}
default_minfo(&minfo);
default_cinfo(&cinfo);
atom = (ATOM *) malloc(sizeof(ATOM) * cinfo.maxatom);
if (atom == NULL) {
fprintf(stderr, "memory allocation error for *atom\n");
exit(0);
}
bond = (BOND *) malloc(sizeof(BOND) * cinfo.maxbond);
if (bond == NULL) {
fprintf(stderr, "memory allocation error for *bond\n");
exit(0);
}
overflow_flag =
rac(ifilename, &atomnum, atom, &bondnum, bond, &cinfo, &minfo);
if (overflow_flag) {
cinfo.maxatom = atomnum + 10;
cinfo.maxbond = bondnum + 10;
free(atom);
free(bond);
atom = (ATOM *) malloc(sizeof(ATOM) * cinfo.maxatom);
if (atom == NULL) {
fprintf(stderr, "memory allocation error for *atom\n");
exit(0);
}
bond = (BOND *) malloc(sizeof(BOND) * cinfo.maxbond);
if (bond == NULL) {
fprintf(stderr, "memory allocation error for *bond\n");
exit(0);
}
overflow_flag =
rac(ifilename, &atomnum, atom, &bondnum, bond, &cinfo, &minfo);
}
atomicnum(atomnum, atom);
adjustatomname(atomnum, atom, 1);
if(minfo.dcharge >= -9990) charge = minfo.dcharge;
selectindex = (int *) malloc(sizeof(int) * atomnum);
if (selectindex == NULL) {
fprintf(stderr, "memory allocation error for *selectindex\n");
exit(0);
}
equatomno = (int *) malloc(sizeof(int) * atomnum);
if (equatomno == NULL) {
fprintf(stderr, "memory allocation error for *equatomno\n");
exit(0);
}
pathnum = (int *) malloc(sizeof(int) * atomnum);
if (pathnum == NULL) {
fprintf(stderr, "memory allocation error for *pathnum\n");
exit(0);
}
selectelement = (int *) malloc(sizeof(int) * atomnum);
if (selectelement == NULL) {
fprintf(stderr, "memory allocation error for *selectelement\n");
exit(0);
}
pathatomnum = (int *) malloc(sizeof(int) * atomnum);
if (pathatomnum == NULL) {
fprintf(stderr, "memory allocation error for *pathatomnum\n");
exit(0);
}
if(atomnum > MAX_RESP_ATOM) {
fprintf(stderr, "The number of atoms (%d) exceed the MAX_RESP_ATOM (%d) defined in respgen.c, extend MAX_RESP_ATOM and recompile the program\n, atomnum, MAX_RESP_ATOM");
exit(0);
}
for (i = 0; i < atomnum; i++) {
pathatomnum[i] = MAXPATHATOMNUM;
pathscore[i] = (double *) calloc(pathatomnum[i], sizeof(double));
if (pathscore == NULL) {
fprintf(stderr, "memory allocation error for *pathscore[%d]\n",
i + 1);
exit(0);
}
}
equatom();
respin(method);
printf("\n");
/*
free(atom);
free(selectindex);
free(selectelement);
free(equatomno);
free(pathnum);
free(pathatomnum);
for (i =0 ;i <atomnum; i++) free(pathscore[i]);
*/
return (0);
}
