A new folder for further work

Author: y-popov

StructAlign/Makefile

@@ -0,0 +1,3 @@
+all: 
+	gcc algorithm.c pdb.c -o align -lm                     
+

StructAlign/algorithm.c

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+#include "pdb.h"
+#include <math.h>
+
+int main  (int argc, char **argv)
+{
+
+  /* Checking command line, 
+  throw exception if not complete */
+
+  if (argc != 4)
+  {
+    printf("\nUsage: %s <input file 1.pdb> <input file 2.pdb> <output file>", argv[0]);
+    printf("\nExample: %s 3hdd.pdb 1puf.pdb superpos_3hdd_1puf.pdb\n\n", argv[0]);
+    exit (1);
+  } /* end if */
+  
+  /* Done checking command line */
+
+  /* Reading command line arguments */
+
+  char *infile1, *infile2, *outfile;
+
+  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);
+
+  /* Done reading arguments */
+
+  /* DECLARATION AND ASSIGNMENT 
+  OF SOME VARIABLES */
+
+  struct atom *atoms_prot1 = NULL, *atoms_prot2 = NULL;
+  struct atom *atoms_dna1 = NULL, *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_i1 = NULL, *atoms_prot_i2 = NULL;
+  struct atom *atoms_prot_j1 = NULL, *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 m1=0, n1=0, w1=0, i, j, 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) );
+  
+  /* Reading PDB file */
+  
+  puts("Reading 1st PDB file...");
+  readerPDB(infile1, &m1, &n1, &w1, maxnumber, &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", m1, n1, w1);
+  SelectChain(atoms_prot1, n1, &atoms_prot1, &n1, prot_chains1[1]); 
+    // pdb.c function, select only first chain of protein from PDB file.
+  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, &m2, &n2, &w2, maxnumber, &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", m2, n2, w2);
+  SelectChain(atoms_prot2, n2, &atoms_prot2, &n2, prot_chains2[1]);
+  printf("Atoms in selected chain: %u\n\n", n2);
+
+  dna_chains1[0] = ' '; dna_chains2[0] = ' ';
+  printf("DNA1 chains: %s; DNA2 chains: %s\n", dna_chains1, dna_chains2);
+  /* Done reading */
+
+  /* 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_P2, *list_C12, *list_OP12, *list_OP22, *list_CA2;
+  unsigned int n_P1, n_C11, n_OP11, n_OP21, n_CA1, n_P2, n_C12, n_OP12, n_OP22, n_CA2;
+
+  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");
+  correctC1_P(atoms_dna1, &list_C11, &n_C11, list_P1, n_P1);
+    //corrects list_C1 to use rule list_P[i] and list_C1[i+1] are in the same nucleotide
+
+  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");
+  correctC1_P(atoms_dna2, &list_C12, &n_C12, list_P2, n_P2);
+
+  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
+	}
+  printf("Done atoms:\tP %u\tC1 %u\tOP1 %u\tOP2 %u\tCA %u\n",n_P1, n_C11, n_OP11, n_OP21, n_CA1);  
+  
+  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]]);
+	}
+  printf("Done atoms:\tP %u\tC1 %u\tOP1 %u\tOP2 %u\tCA %u\n",n_P2, n_C12, n_OP12, n_OP22, n_CA2);  
+
+  /* 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_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');
+	    BidirectionalHit(atoms_prot_i1, n_CA1, 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 compl1, compl2, n_first_chain, m_first_chain;
+  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);
+  find_compl(atoms_dna2, list_P2, list_C12, list_OP12, list_OP22, atoms_dna_P2, n_P2, &compl2, &m_first_chain);
+  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 */
+
+
+  struct atom *atoms_dna_i1 = 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, atoms_dna1[list_P1[i_max_measure]], atoms_dna1[list_C11[i_max_measure+1]], atoms_dna1[list_OP11[i_max_measure]], atoms_dna1[list_OP21[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, atoms_dna2[list_P2[j_max_measure]], atoms_dna2[list_C12[j_max_measure+1]], atoms_dna2[list_OP12[j_max_measure]], atoms_dna2[list_OP22[j_max_measure]], 'F');
+  ChangeSystem(atoms_dna1, m1, &atoms_dna_i1, atoms_dna1[list_P1[i_max_measure]], atoms_dna1[list_C11[i_max_measure+1]], atoms_dna1[list_OP11[i_max_measure]], atoms_dna1[list_OP21[i_max_measure]], 'C'); 
+  ChangeSystem(atoms_dna2, m2, &atoms_dna_j2, atoms_dna2[list_P2[j_max_measure]], atoms_dna2[list_C12[j_max_measure+1]], atoms_dna2[list_OP12[j_max_measure]], atoms_dna2[list_OP22[j_max_measure]], 'D');
+    
+  puts("\nFix 'nan' in pdb with this data:");
+  createPDB(outfile, outfile); 
+    // pdb.c function
+  writetoPDB(outfile, atoms_dna_i1, m1);
+  writetoPDB(outfile, 
+                atoms_prot_i1, n1); 
+    // pdb.c function. Write protein atoms to outfile
+
+  writetoPDB(outfile, 
+                atoms_prot_j2, n2);
+  writetoPDB(outfile, atoms_dna_j2, m2);
+  endPDB(outfile); 
+  
+  return 0;
+} 
+/* End main */