Core::Core(const string& cLog, const string& cConfig)
: CoreObject("CORE", new ofstream(cLog), WorkPriority::WP_MAIN)
{
mLogger = mOutFileStream;
m_pRenderSystem = nullptr;
m_pInputSystem = nullptr;
m_pFileSystem = nullptr;
AddSystem(new FileSystem(mLogger), true);
ConfigFile* config = new ConfigFile(cConfig, mLogger);
for (auto it : config->Get())
{
if (it.first == "load_module")
{
LoadModule(it.second);
}
else if (it.first == "set_render_system")
{
if (it.second == "11.2")
{
ChangeSystem(SystemsType::SYSTEM_RENDER_DIRECTX_11_2);
}
else
{
DrawLine("Core: Íåâåðíûé ïàðàìåòîð! set_render_system");
}
}
else if (it.first == "set_input_system")
{
ChangeSystem(SystemsType::SYSTEM_INPUT_DX);
}
else if (it.first == "load_resource_folder")
{
m_pFileSystem->AddResourceFolder(it.second);
}
}
DrawLine("Core: Çàãðóçêà çàâåðøåíà!");
}
void Core::AddSystem(ISystem* s_ptr, bool set_def)
{
DrawLine("AddSystem(" + s_ptr->GetName() + ")");
_lSystemsByType::iterator it = m_lSystems.find(s_ptr->GetType());
if (it == m_lSystems.end()) {
m_lSystems.insert(_lSystemsByType::value_type(s_ptr->GetType(), s_ptr));
DrawLine("AddSystem: System " + s_ptr->GetName() + " loading");
}
else {
DrawLine("AddSystem: System " + s_ptr->GetName() + " is loaded", MessageTypes::MT_WARNING);
}
if (set_def) {
ChangeSystem(s_ptr->GetType());
}
}
int main (int argc, char **argv)
{
puts("Program starts");
/* Checking command line,
throw exception if not complete */
//printf("%s %s %s %s %s %s %s\n", argv[0], argv[1], argv[2], argv[3], argv[4], argv[5], argv[6]);
if (argc != 12)
{
printf("\nUsage: %s <input file 1.pdb> <input file 2.pdb> <output file> <chain1> <chain2> <start1> <end1> <start2> <end2> <file name for score> <is on server>", argv[0]);
printf("\nExample: %s 3hdd.pdb 1puf.pdb superpos_3hdd_1puf.pdb A B 5 60 zero inf max_score.txt 0\n\n", argv[0]);
exit (1);
} /* end if */
/* Done checking command line */
/* Reading command line arguments */
char *infile1, *infile2, *outfile, *max_score_filename;
char *start1, *end1, *start2, *end2;
char chain1, chain2;
unsigned int SERVER;
infile1 = (char *)malloc( sizeof(char)*(strlen(argv[1])+1) );
sscanf(argv[1],"%s", infile1);
infile2 = (char *)malloc( sizeof(char)*(strlen(argv[2])+1) );
sscanf(argv[2],"%s", infile2);
outfile = (char *)malloc( sizeof(char)*(strlen(argv[3])+1) );
sscanf(argv[3], "%s", outfile);
sscanf(argv[4], "%c", &chain1);
sscanf(argv[5], "%c", &chain2);
start1 = (char *)malloc( sizeof(char)*(strlen(argv[6])+1) );
end1 = (char *)malloc( sizeof(char)*(strlen(argv[7])+1) );
start2 = (char *)malloc( sizeof(char)*(strlen(argv[8])+1) );
end2 = (char *)malloc( sizeof(char)*(strlen(argv[9])+1) );
sscanf(argv[6], "%s", start1);
sscanf(argv[7], "%s", end1);
sscanf(argv[8], "%s", start2);
sscanf(argv[9], "%s", end2);
max_score_filename = (char *)malloc( sizeof(char)*(strlen(argv[10])+1) );
sscanf(argv[10], "%s", max_score_filename);
sscanf(argv[11], "%u", &SERVER);
/* Done reading arguments */
/* DECLARATION AND ASSIGNMENT
OF SOME VARIABLES */
struct atom *atoms_prot1 = NULL, *atoms_prot2 = NULL;
struct atom *all_atoms_dna1 = NULL, *all_atoms_dna2 = NULL;
struct atom *atoms_wat1 = NULL, *atoms_wat2 = NULL;
struct atom *atoms_prot_CA1 = NULL, *atoms_prot_CA2 = NULL;
struct atom *atoms_prot_C1 = NULL, *atoms_prot_C2 = NULL;
struct atom *atoms_prot_i1 = NULL, *atoms_prot_i2 = NULL;
struct atom *atoms_prot_j1 = NULL, *atoms_prot_j2 = NULL;
struct atom *C_atoms_prot_i1 = NULL, *C_atoms_prot_j2 = NULL;
struct atomname *list1, *list2;
unsigned int maxnumber = 256; //primary number of atoms in each groups (DNA, protein, water)
FILE *flow_out;
unsigned int all_m1=0, n1=0, w1=0, i, j, all_m2=0, n2=0, w2=0;
/* m - number of DNA atoms
* n - number of protein atoms
* w - number of water atoms */
char *dna_chains1 = (char *)malloc( sizeof(char)*(2+1) );
char *prot_chains1 = (char *)malloc( sizeof(char)*(2+1) );
char *dna_chains2 = (char *)malloc( sizeof(char)*(2+1) );
char *prot_chains2 = (char *)malloc( sizeof(char)*(2+1) );
/*** For server ***/
FILE *max_score;
//printf("%s", max_score_filename);
max_score = fopen(max_score_filename, "w");
if (max_score == NULL) {
perror(max_score_filename);
exit(1);
}
/* Reading PDB file */
puts("Reading 1st PDB file...");
readerPDB(infile1, &all_m1, &n1, &w1, maxnumber, &all_atoms_dna1, &dna_chains1, &atoms_prot1, &prot_chains1, &atoms_wat1, &list1);
// pdb.c function, read PDB and put protein, DNA and water atoms in three different arrays
printf("...done; %d atoms of dna, %d atoms of protein, %d atoms of water\n", all_m1, n1, w1);
if (all_m1 == 0)
{fprintf(max_score, "Error\nFirst structure has no DNA!");
exit(1); }
if (chain1=='@')
chain1 = prot_chains1[1];
else
if ( inArray(chain1, prot_chains1)==0 )
{ fprintf(max_score, "Error\nChain %c is not a protein chain in first structure", chain1);
exit(1); }
SelectChain(atoms_prot1, n1, &atoms_prot1, &n1, chain1);
SelectRange(atoms_prot1, n1, &atoms_prot1, &n1, start1, end1);
// pdb.c function
printf("Atoms in selected chain: %u\n\n", n1);
// print to stdout number of protein atoms in selected chain
puts("Reading 2nd PDB file...");
readerPDB(infile2, &all_m2, &n2, &w2, maxnumber, &all_atoms_dna2, &dna_chains2, &atoms_prot2, &prot_chains2, &atoms_wat2, &list2);
printf("...done; %d atoms of dna, %d atoms of protein, %d atoms of water\n", all_m2, n2, w2);
if (all_m2 == 0)
{fprintf(max_score, "Error\nSecond structure has no DNA!");
exit(1); }
if (chain2=='@')
chain2 = prot_chains2[1];
else
if ( inArray(chain2, prot_chains2)==0 )
{ fprintf(max_score, "Error\nChain %c is not a protein chain in second structure!", chain2);
exit(1); }
SelectChain(atoms_prot2, n2, &atoms_prot2, &n2, chain2);
SelectRange(atoms_prot2, n2, &atoms_prot2, &n2, start2, end2);
printf("Atoms in selected chain: %u\n\n", n2);
dna_chains1[0] = ' '; dna_chains2[0] = ' ';
/*** For server ***/
char dna_chain1, dna_chain2;
//dna_chain2 = dna_chains2[1];
printf("DNA1 chains: %s; DNA2 chains: %s\n", dna_chains1, dna_chains2);
/* Done reading */
/*** 3DNA block ***/
unsigned int *compl_list1, *compl_list2, n_pairs1, n_pairs2, pair1, pair2;
int **compl_pairs1, **compl_pairs2;
char **pairs1, **pairs2;
run_3dna(infile1, &compl_list1, &compl_pairs1, &pairs1, &n_pairs1, SERVER, max_score_filename);
run_3dna(infile2, &compl_list2, &compl_pairs2, &pairs2, &n_pairs2, SERVER, max_score_filename);
/*** 3DNA block end ***/
/*** MAIN FOR CYCLE ***/
struct atom *best_atoms_dna1 = NULL, *best_atoms_dna2 = NULL;
struct atom *best_dna1_chain1, *best_dna1_chain2, *best_dna2_chain1, *best_dna2_chain2;
unsigned int *best_list_P1, *best_list_C11, *best_list_OP11, *best_list_OP21, *best_list_P2, *best_list_C12, *best_list_OP12, *best_list_OP22;
unsigned int best_n_P1, best_n_P2;
unsigned int best_dna1_chain1_n, best_dna1_chain2_n, best_dna2_chain1_n, best_dna2_chain2_n;
unsigned int best_i_max_measure, best_j_max_measure;
unsigned int best_compl1, best_compl2;
unsigned int best_n_first_chain, best_m_first_chain;
unsigned int best_pair1, best_pair2;
double best_S_max = -1;
for (pair1=1; pair1<=n_pairs1; pair1++)
{
struct atom *atoms_dna1 = NULL, *dna1_chain1 = NULL, *dna1_chain2 = NULL;
unsigned int m1, dna1_chain1_n=0, dna1_chain2_n=0;
SelectChain(all_atoms_dna1, all_m1, &dna1_chain1, &dna1_chain1_n, pairs1[pair1][1]);
SelectChain(all_atoms_dna1, all_m1, &dna1_chain2, &dna1_chain2_n, pairs1[pair1][2]);
atomlistmerge(&atoms_dna1, &m1, dna1_chain1, dna1_chain1_n, dna1_chain2, dna1_chain2_n);
//printf("%u/%u\n", pair1, n_pairs1);
/* Make lists of P, C1', OP1 atoms
of dna and CA atoms of protein */
unsigned int *list_P1, *list_C11, *list_OP11, *list_OP21, *list_CA1, *list_C1;
unsigned int n_P1, n_C11, n_OP11, n_OP21, n_CA1, n_C1;
getAtomsNumbers(atoms_dna1, m1, &list_P1, &n_P1, "P");
// pdb.c function, get only indexes of atoms
getAtomsNumbers(atoms_dna1, m1, &list_C11, &n_C11, "C1'");
getAtomsNumbers(atoms_dna1, m1, &list_OP11, &n_OP11, "OP1");
getAtomsNumbers(atoms_dna1, m1, &list_OP21, &n_OP21, "OP2");
getAtomsNumbers(atoms_prot1, n1, &list_CA1, &n_CA1, "CA");
getAtomsNumbers(atoms_prot1, n1, &list_C1, &n_C1, "C");
correctC1_P(atoms_dna1, &list_C11, &n_C11, list_P1, &n_P1);
//for (i=1; i<=n_C11; i++) printf("%s.%c\n", atoms_dna1[list_C11[i]].ResNumber, atoms_dna1[list_C11[i]].Chain);
//corrects list_C1 to use rule list_P[i] and list_C1[i+1] are in the same nucleotide
atoms_prot_CA1 = (struct atom *)malloc( sizeof(struct atom)*(n_CA1+1) );
for (i=1; i<=n_CA1; i++) {
atomcpy(&atoms_prot_CA1[i], atoms_prot1[list_CA1[i]]);
//pdb.c function. Copy all properties of atom
}
atoms_prot_C1 = (struct atom *)malloc( sizeof(struct atom)*(n_C1+1) );
for (i=1; i<=n_C1; i++) {
atomcpy(&atoms_prot_C1[i], atoms_prot1[list_C1[i]]);
}
printf("Done atoms:\tP %u\tC1 %u\tOP1 %u\tOP2 %u\tCA %u\tC %u\n",n_P1, n_C11, n_OP11, n_OP21, n_CA1, n_C1);
for (pair2=1; pair2<=n_pairs2; pair2++)
{
//printf("%u/%u\n", pair2, n_pairs2);
printf("\nCYCLE %c:%c vs %c:%c\n", pairs1[pair1][1], pairs1[pair1][2], pairs2[pair2][1], pairs2[pair2][2]);
struct atom *atoms_dna2 = NULL, *dna2_chain1, *dna2_chain2;
unsigned int m2, dna2_chain1_n=0, dna2_chain2_n=0;
SelectChain(all_atoms_dna2, all_m2, &dna2_chain1, &dna2_chain1_n, pairs2[pair2][1]);
SelectChain(all_atoms_dna2, all_m2, &dna2_chain2, &dna2_chain2_n, pairs2[pair2][2]);
atomlistmerge(&atoms_dna2, &m2, dna2_chain1, dna2_chain1_n, dna2_chain2, dna2_chain2_n);
unsigned int *list_P2, *list_C12, *list_OP12, *list_OP22, *list_CA2, *list_C2;
unsigned int n_P2, n_C12, n_OP12, n_OP22, n_CA2, n_C2;
getAtomsNumbers(atoms_dna2, m2, &list_P2, &n_P2, "P");
getAtomsNumbers(atoms_dna2, m2, &list_C12, &n_C12, "C1'");
getAtomsNumbers(atoms_dna2, m2, &list_OP12, &n_OP12, "OP1");
getAtomsNumbers(atoms_dna2, m2, &list_OP22, &n_OP22, "OP2");
getAtomsNumbers(atoms_prot2, n2, &list_CA2, &n_CA2, "CA");
getAtomsNumbers(atoms_prot2, n2, &list_C2, &n_C2, "C");
correctC1_P(atoms_dna2, &list_C12, &n_C12, list_P2, &n_P2);
atoms_prot_CA2 = (struct atom *)malloc( sizeof(struct atom)*(n_CA2+1) );
for (i=1; i<=n_CA2; i++) {
atomcpy(&atoms_prot_CA2[i], atoms_prot2[list_CA2[i]]);
}
atoms_prot_C2 = (struct atom *)malloc( sizeof(struct atom)*(n_C2+1) );
for (i=1; i<=n_C2; i++) {
atomcpy(&atoms_prot_C2[i], atoms_prot2[list_C2[i]]);
}
printf("Done atoms:\tP %u\tC1 %u\tOP1 %u\tOP2 %u\tCA %u\tC %u\n",n_P2, n_C12, n_OP12, n_OP22, n_CA2, n_C2);
/* Done making lists */
/* Create array of measures for
all pairs of dna P atoms (list_measure).
dim(list_measure) = n_P2 x n_P1 */
double **list_measure;
unsigned int n_hit;
unsigned int **list_hit;
list_measure = (double **)malloc( (n_P2+1)*sizeof(double *)*(n_P1+1) );
for (i=1; i<=n_P1; i++) list_measure[i] = (double *)malloc( sizeof(double)*(n_P2+1) );
//for (i=1; i<=n_P1; i++) for (j=1; j<=n_P2;j++) list_measure[i][j] = (unsigned int *)malloc( sizeof(unsigned int) );
// Enable if measure function returns unsigned int
for (i=1; i<=n_P1; i++){
for (j=1; j<=n_P2; j++){
ChangeSystem(atoms_prot_CA1, n_CA1, &atoms_prot_i1, atoms_dna1[list_P1[i]], atoms_dna1[list_C11[i+1]], atoms_dna1[list_OP11[i]], atoms_dna1[list_OP21[i]], 'E');
// pdb.c function. Change the coordinate system of protein with given nucleotide
ChangeSystem(atoms_prot_C1, n_C1, &C_atoms_prot_i1, atoms_dna1[list_P1[i]], atoms_dna1[list_C11[i+1]], atoms_dna1[list_OP11[i]], atoms_dna1[list_OP21[i]], 'E');
ChangeSystem(atoms_prot_CA2, n_CA2, &atoms_prot_j2, atoms_dna2[list_P2[j]], atoms_dna2[list_C12[j+1]], atoms_dna2[list_OP12[j]], atoms_dna2[list_OP22[j]], 'F');
ChangeSystem(atoms_prot_C2, n_C2, &C_atoms_prot_j2, atoms_dna2[list_P2[j]], atoms_dna2[list_C12[j+1]], atoms_dna2[list_OP12[j]], atoms_dna2[list_OP22[j]], 'F');
BidirectionalHit(atoms_prot_i1, C_atoms_prot_i1, n_CA1, atoms_prot_j2, C_atoms_prot_j2, n_CA2, &list_hit, &n_hit);
// pdb.c function.
Measure2_p(&(list_measure[i][j]), list_hit, n_hit, atoms_prot_i1, atoms_prot_j2);
// pdb.c function.
// printf("Measure: %f i: %u j: %u n_P1: %u n_P2: %u \n",(list_measure[i][j]), i,j, n_P1, n_P2);
// Enable in test mode
}
}
/* Done creation of array of measures */
/* Start working with diagonals */
unsigned int i_max, j_max, i_start, j_start, i_max_measure, j_max_measure;
unsigned int n_first_chain, m_first_chain;
unsigned int compl1, compl2;
double S_max;
struct atom *atoms_dna_P1 = NULL;
struct atom *atoms_dna_P2 = NULL;
// print measure-table
/*printf(" ");
for (j=1; j<=n_P2; j++) printf("%4d", j);
puts("");
for (i=n_P1; i>=1; i--){
printf("%2d", i);
for (j=1; j<=n_P2; j++){
printf("%4.0f", list_measure[i][j]>0 ? list_measure[i][j] : 0);
}
puts("");
}
printf(" ");
for (j=1; j<=n_P2; j++) printf("%4d", j);
puts(""); */
i_max_measure=0;
j_max_measure=0;
atoms_dna_P1 = (struct atom *)malloc( sizeof(struct atom)*(n_P1+1) );
for (i=1; i<=n_P1; i++) {
atomcpy(&atoms_dna_P1[i], atoms_dna1[list_P1[i]]);
}
atoms_dna_P2 = (struct atom *)malloc( sizeof(struct atom)*(n_P2+1) );
for (i=1; i<=n_P2; i++) {
atomcpy(&atoms_dna_P2[i], atoms_dna2[list_P2[i]]);
}
//find_compl(atoms_dna1, list_P1, list_C11, list_OP11, list_OP21, atoms_dna_P1, n_P1, &compl1, &n_first_chain, max_score);
run_find_compl(atoms_dna_P1, n_P1, &compl1, &n_first_chain, compl_pairs1[pair1]);
//find_compl(atoms_dna2, list_P2, list_C12, list_OP12, list_OP22, atoms_dna_P2, n_P2, &compl2, &m_first_chain, max_score);
run_find_compl(atoms_dna_P2, n_P2, &compl2, &m_first_chain, compl_pairs2[pair2]);
BestDiag(list_measure, n_P1, n_P2, &S_max, &i_max, &j_max, &i_start, &j_start, &i_max_measure, &j_max_measure,
atoms_dna1, list_P1, atoms_dna2, list_P2, compl1, compl2, n_first_chain, m_first_chain);
// pdb.c function
/* Done diagonal search */
if (S_max > best_S_max)
{
best_S_max = S_max;
atomlistcpy(&best_dna1_chain1, dna1_chain1, dna1_chain1_n);
best_dna1_chain1_n = dna1_chain1_n;
atomlistcpy(&best_dna1_chain2, dna1_chain2, dna1_chain2_n);
best_dna1_chain2_n = dna1_chain2_n;
atomlistcpy(&best_dna2_chain1, dna2_chain1, dna2_chain1_n);
best_dna2_chain1_n = dna2_chain1_n;
atomlistcpy(&best_dna2_chain2, dna2_chain2, dna2_chain2_n);
best_dna2_chain2_n = dna2_chain2_n;
best_n_P1 = n_P1;
best_n_P2 = n_P2;
atomlistcpy(&best_atoms_dna1, atoms_dna1, m1);
best_list_P1 = (unsigned int *)malloc(sizeof(unsigned int)*(n_P1+1));
best_list_C11 = (unsigned int *)malloc(sizeof(unsigned int)*(n_C11+1));
best_list_OP11 = (unsigned int *)malloc(sizeof(unsigned int)*(n_OP11+1));
best_list_OP21 = (unsigned int *)malloc(sizeof(unsigned int)*(n_OP21+1));
memcpy(best_list_P1, list_P1, sizeof(unsigned int)*(n_P1+1));
memcpy(best_list_C11, list_C11, sizeof(unsigned int)*(n_C11+1));
memcpy(best_list_OP11, list_OP11, sizeof(unsigned int)*(n_OP11+1));
memcpy(best_list_OP21, list_OP21, sizeof(unsigned int)*(n_OP21+1));
atomlistcpy(&best_atoms_dna2, atoms_dna2, m2);
best_list_P2 = (unsigned int *)malloc(sizeof(unsigned int)*(n_P2+1));
best_list_C12 = (unsigned int *)malloc(sizeof(unsigned int)*(n_C12+1));
best_list_OP12 = (unsigned int *)malloc(sizeof(unsigned int)*(n_OP12+1));
best_list_OP22 = (unsigned int *)malloc(sizeof(unsigned int)*(n_OP22+1));
memcpy(best_list_P2, list_P2, sizeof(unsigned int)*(n_P2+1));
memcpy(best_list_C12, list_C12, sizeof(unsigned int)*(n_C12+1));
memcpy(best_list_OP12, list_OP12, sizeof(unsigned int)*(n_OP12+1));
memcpy(best_list_OP22, list_OP22, sizeof(unsigned int)*(n_OP22+1));
best_i_max_measure = i_max_measure;
best_j_max_measure = j_max_measure;
best_compl1 = compl1;
best_compl2 = compl2;
best_n_first_chain = n_first_chain;
best_m_first_chain = m_first_chain;
best_pair1 = pair1;
best_pair2 = pair2;
}
//free array's memory after cycle
/*free(list_P2);
free(list_C12);
free(list_OP12);
free(list_OP22);
free(list_CA2);
free(list_C2);
free(atoms_prot_CA2);
free(atoms_prot_C2);
for (i=1; i<=n_P1; i++) free(list_measure[i]);
free(list_measure);
free(atoms_dna_P1);
free(atoms_dna_P2);
free(atoms_dna2);
free(dna2_chain1);
free(dna2_chain2);
free(atoms_prot_i1);
free(C_atoms_prot_i1);
free(atoms_prot_j2);
free(C_atoms_prot_j2);*/
}
/*free(list_P1);
free(list_C11);
free(list_OP11);
free(list_OP21);
free(list_CA1);
free(list_C1);
free(atoms_prot_CA1);
free(atoms_prot_C1);
free(atoms_dna1);
free(dna1_chain1);
free(dna1_chain2);*/
}
/*** END OF MAIN CYCLE ***/
/****reading DNA sequences ***/
unsigned int dna_n11, dna_n12, dna_n21, dna_n22; //sequence length
char *dna_seq11, *dna_seq12, *dna_seq21, *dna_seq22;
char *dna_num_seq11, *dna_num_seq12, *dna_num_seq21, *dna_num_seq22;
int dna1_chain1_start, dna1_chain2_start, dna2_chain1_start, dna2_chain2_start;
//SelectChain(atoms_dna1, m1, &dna1_chain1, &dna1_chain1_n, dna_chains1[1]);
Seq(best_dna1_chain1, best_dna1_chain1_n, &dna_seq11, &dna_num_seq11, &dna_n11, max_score);
sscanf(best_dna1_chain1[1].ResNumber, "%d", &dna1_chain1_start);
Seq(best_dna1_chain2, best_dna1_chain2_n, &dna_seq12, &dna_num_seq12, &dna_n12, max_score);
sscanf(best_dna1_chain2[1].ResNumber, "%d", &dna1_chain2_start);
Seq(best_dna2_chain1, best_dna2_chain1_n, &dna_seq21, &dna_num_seq21, &dna_n21, max_score);
sscanf(best_dna2_chain1[1].ResNumber, "%d", &dna2_chain1_start);
Seq(best_dna2_chain2, best_dna2_chain2_n, &dna_seq22, &dna_num_seq22, &dna_n22, max_score);
sscanf(best_dna2_chain2[1].ResNumber, "%d", &dna2_chain2_start);
//printf("%c %c %c %c %c %c\n%lg\n%s\n%s", chain1, chain2, dna_chains1[1], dna_chains1[2], dna_chains2[1], dna_chains2[2], S_max, dna_string1, dna_string2);
/*** For server work - DNA alignment making ***/
if (best_S_max == 0)
fprintf(max_score, "Warning! The score is zero! It seems you have specified wrong parameters.\n");
unsigned int i_max_measure_compl, j_max_measure_compl;
unsigned int is_reverse1, is_reverse2;
//printf("n_first_chain=%u i_max_measure=%u best_compl1=%u\n", best_n_first_chain, best_i_max_measure, best_compl1);
is_reverse1 = ((best_i_max_measure > best_n_first_chain) ? 1 : 0);
is_reverse2 = ((best_j_max_measure > best_m_first_chain) ? 1 : 0);
i_max_measure_compl = ((best_i_max_measure > best_n_first_chain) ? best_compl1-best_i_max_measure+1 : best_compl1-best_i_max_measure+1);
j_max_measure_compl = ((best_j_max_measure > best_m_first_chain) ? best_compl2-best_j_max_measure+1 : best_compl2-best_j_max_measure+1);
//printf("i_max_measure=%u i_max_measure_compl=%u\n", best_i_max_measure, i_max_measure_compl);
//printf("i_max_measure=%s\n", best_atoms_dna1[best_list_P1[best_i_max_measure]].ResNumber);
//printf("i_max_measure_compl=%s\n", best_atoms_dna1[best_list_P1[i_max_measure_compl]].ResNumber);
//puts("OK1");
if (i_max_measure_compl > best_n_P1)
{
//printf("i_compl=%u n11=%u n12=%u\n", i_max_measure_compl, dna_n11, dna_n12);
j_max_measure_compl = j_max_measure_compl-(i_max_measure_compl-best_n_P1);
i_max_measure_compl = best_n_P1;
//printf("i_compl=%u n11=%u n12=%u\n", i_max_measure_compl, dna_n11, dna_n12);
}
if (j_max_measure_compl > best_n_P2)
{
//printf("j_compl=%u n21=%u n22=%u\n", j_max_measure_compl, dna_n21, dna_n22);
i_max_measure_compl = i_max_measure_compl-(j_max_measure_compl-best_n_P2);
j_max_measure_compl = best_n_P2;
//printf("j_compl=%u n21=%u n22=%u\n", j_max_measure_compl, dna_n21, dna_n22);
}
//puts("OK2");
//if max_compl = 0 or less
if (i_max_measure_compl < 1)
{
i_max_measure_compl = 1;
j_max_measure_compl = j_max_measure_compl + 1 - i_max_measure_compl;
}
if (j_max_measure_compl < 1)
{
j_max_measure_compl = 1;
i_max_measure_compl = i_max_measure_compl + 1 - j_max_measure_compl;
}
//puts("OK3");
int i_max_measure_compl_num, j_max_measure_compl_num;
char *i_max_measure_compl_str, *j_max_measure_compl_str;
i_max_measure_compl_str = (char *)malloc( sizeof(char)*7 );
j_max_measure_compl_str = (char *)malloc( sizeof(char)*7 );
sscanf(best_atoms_dna1[best_list_P1[i_max_measure_compl]].ResNumber, "%d", &i_max_measure_compl_num);
sscanf(best_atoms_dna2[best_list_P2[j_max_measure_compl]].ResNumber, "%d", &j_max_measure_compl_num);
if (i_max_measure_compl==best_i_max_measure)
{
sscanf(best_atoms_dna1[best_list_P1[i_max_measure_compl+1]].ResNumber, "%d", &i_max_measure_compl_num);
i_max_measure_compl_num = i_max_measure_compl_num - 1;
//puts("Here1");
}
if (j_max_measure_compl==best_j_max_measure)
{
sscanf(best_atoms_dna2[best_list_P2[j_max_measure_compl+1]].ResNumber, "%d", &j_max_measure_compl_num);
j_max_measure_compl_num = j_max_measure_compl_num - 1;
//puts("Here2");
}
//printf("%d\n", j_max_measure_compl_num);
//puts("OK4");
int start, i_start;
start = (is_reverse1 == 1) ? dna1_chain1_start : dna1_chain2_start;
i_start = (is_reverse1 == 1) ? 1 : dna_n11+1;
if (i_max_measure_compl_num < start && i_max_measure_compl < i_start)
{
//printf("ires_compl=%d start=%d\n", i_max_measure_compl_num, start);
j_max_measure_compl_num = j_max_measure_compl_num + start - i_max_measure_compl_num;
i_max_measure_compl_num = start;
//printf("ires_compl=%d start=%d\n", i_max_measure_compl_num, start);
}
start = (is_reverse2 == 1) ? dna2_chain1_start : dna2_chain2_start;
i_start = (is_reverse2 == 1) ? 1 : dna_n21+1;
if (j_max_measure_compl_num < start && j_max_measure_compl < i_start)
{
//printf("jres_compl=%d start=%d\n", j_max_measure_compl_num, start);
i_max_measure_compl = i_max_measure_compl_num + start - j_max_measure_compl_num;
j_max_measure_compl = start;
//printf("jres_compl=%d start=%d\n", j_max_measure_compl_num, start);
}
//printf("%d\n", j_max_measure_compl_num);
sprintf(i_max_measure_compl_str, "%d", i_max_measure_compl_num);
sprintf(j_max_measure_compl_str, "%d", j_max_measure_compl_num);
//printf("%d\n", j_max_measure_compl_num);
//puts("OK5");
fprintf(max_score, "%c %c %c %c %c %c %s %s %s %s %u %u\n%lg\n%s %s\n%s %s\n%s %s\n%s %s", chain1, chain2, pairs1[best_pair1][1], pairs1[best_pair1][2], pairs2[best_pair2][1], pairs2[best_pair2][2], best_atoms_dna1[best_list_P1[best_i_max_measure]].ResNumber, best_atoms_dna2[best_list_P2[best_j_max_measure]].ResNumber, i_max_measure_compl_str, j_max_measure_compl_str, is_reverse1, is_reverse2, best_S_max, dna_seq11, dna_num_seq11, dna_seq12, dna_num_seq12, dna_seq21, dna_num_seq21, dna_seq22, dna_num_seq22);
fclose(max_score);
struct atom *atoms_dna_i1 = NULL;
struct atom *atoms_dna_i2 = NULL;
struct atom *atoms_dna_j1 = NULL;
struct atom *atoms_dna_j2 = NULL;
/* Change the system to i and j coordinates, write the alignment to file */
ChangeSystem(atoms_prot1, n1, &atoms_prot_i1, best_atoms_dna1[best_list_P1[best_i_max_measure]], best_atoms_dna1[best_list_C11[best_i_max_measure+1]], best_atoms_dna1[best_list_OP11[best_i_max_measure]], best_atoms_dna1[best_list_OP21[best_i_max_measure]], 'E');
// Note that names of chains will be changed to 'E' and 'F' by default! Modify if required.
ChangeSystem(atoms_prot2, n2, &atoms_prot_j2, best_atoms_dna2[best_list_P2[best_j_max_measure]], best_atoms_dna2[best_list_C12[best_j_max_measure+1]], best_atoms_dna2[best_list_OP12[best_j_max_measure]], best_atoms_dna2[best_list_OP22[best_j_max_measure]], 'F');
ChangeSystem(best_dna1_chain1, best_dna1_chain1_n, &atoms_dna_i1, best_atoms_dna1[best_list_P1[best_i_max_measure]], best_atoms_dna1[best_list_C11[best_i_max_measure+1]], best_atoms_dna1[best_list_OP11[best_i_max_measure]], best_atoms_dna1[best_list_OP21[best_i_max_measure]], 'A');
ChangeSystem(best_dna1_chain2, best_dna1_chain2_n, &atoms_dna_i2, best_atoms_dna1[best_list_P1[best_i_max_measure]], best_atoms_dna1[best_list_C11[best_i_max_measure+1]], best_atoms_dna1[best_list_OP11[best_i_max_measure]], best_atoms_dna1[best_list_OP21[best_i_max_measure]], 'B');
ChangeSystem(best_dna2_chain1, best_dna2_chain1_n, &atoms_dna_j1, best_atoms_dna2[best_list_P2[best_j_max_measure]], best_atoms_dna2[best_list_C12[best_j_max_measure+1]], best_atoms_dna2[best_list_OP12[best_j_max_measure]], best_atoms_dna2[best_list_OP22[best_j_max_measure]], 'C');
ChangeSystem(best_dna2_chain2, best_dna2_chain2_n, &atoms_dna_j2, best_atoms_dna2[best_list_P2[best_j_max_measure]], best_atoms_dna2[best_list_C12[best_j_max_measure+1]], best_atoms_dna2[best_list_OP12[best_j_max_measure]], best_atoms_dna2[best_list_OP22[best_j_max_measure]], 'D');
//puts("\nFix 'nan' in pdb with this data:");
createPDB(outfile, outfile);
// pdb.c function
writetoPDB(outfile, atoms_dna_i1, best_dna1_chain1_n);
writetoPDB(outfile, atoms_dna_i2, best_dna1_chain2_n);
writetoPDB(outfile,
atoms_prot_i1, n1);
// pdb.c function. Write protein atoms to outfile
writetoPDB(outfile,
atoms_prot_j2, n2);
writetoPDB(outfile, atoms_dna_j1, best_dna2_chain1_n);
writetoPDB(outfile, atoms_dna_j2, best_dna2_chain2_n);
endPDB(outfile);
return 0;
}
