Mercurial > repos > guerler > springsuite
diff spring_package/pulchra/pulchra.c @ 17:c790d25086dc draft
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
| author | guerler |
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| date | Wed, 28 Oct 2020 05:11:56 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/spring_package/pulchra/pulchra.c Wed Oct 28 05:11:56 2020 +0000 @@ -0,0 +1,3212 @@ + +// +// PULCHRA +// Protein Chain Restoration Algorithm +// +// Version 3.04 +// July 2007 +// Contact: Piotr Rotkiewicz, piotr -at- pirx -dot- com +// +// to compile: +// cc -O3 pulchra.c pulchra_data.c -lm -o pulchra +// +// to use: +// ./pulchra file.pdb +// +// to display available options: +// ./pulchra +// + +#define COMPILE_BB +#define COMPILE_ROT + +#include <math.h> +#include <stdio.h> +#include <stdlib.h> +#include <string.h> +#include <sys/timeb.h> +#include <time.h> + +#define uchar unsigned char +#define uint unsigned int +#define real double + +#include "pulchra_common.h" + +#define PULCHRA_VERSION 3.04 +#define MAX_BUF_SIZE 1000 + +#define FILE_SUCCESS 0 +#define FILE_NOT_FOUND -1 +#define FILE_WARNING -2 + +#define FATAL_MAE -1 + +#define FLAG_BACKBONE 1 +#define FLAG_CALPHA 2 +#define FLAG_SIDECHAIN 4 +#define FLAG_SCM 8 + +#define FLAG_PROTEIN 1 +#define FLAG_DNA 2 +#define FLAG_RNA 4 +#define FLAG_CHYDRO 8 + +#define RADDEG 180./M_PI +#define DEGRAD M_PI/180. + +int _VERBOSE = 0; +int _BB_REARRANGE = 1; +int _BB_OPTIMIZE = 0; +int _CA_OPTIMIZE = 1; +int _CA_RANDOM = 0; +int _CA_ITER = 100; +int _CA_TRAJECTORY = 0; +int _CISPRO = 0; +int _CHIRAL = 1; +int _CENTER_CHAIN = 0; +int _REBUILD_BB = 1; +int _REBUILD_SC = 1; +int _REBUILD_H = 0; +int _PDB_SG = 0; +int _TIME_SEED = 0; +int _XVOLUME = 1; +int _XVOL_ITER = 3; +real _CA_START_DIST = 3.0; +real _CA_XVOL_DIST = 3.5; +real _SG_XVOL_DIST = 1.6; + +#define CALC_C_ALPHA +#define CALC_C_ALPHA_ANGLES +#define CALC_C_ALPHA_START +#define CALC_C_ALPHA_XVOL + +real CA_K=10.0; +real CA_ANGLE_K=20.0; +real CA_START_K=0.01; +real CA_XVOL_K=10.00; + +#define CA_DIST 3.8 +#define CA_DIST_TOL 0.1 +#define CA_DIST_CISPRO 2.9 +#define CA_DIST_CISPRO_TOL 0.1 +#define E_EPS 1e-10 + +// grid resolution (used for fast clash detection) +#define GRID_RES 6.0 + +int chain_length = 0; + +char AA_NAMES[21][4] = + { "GLY", "ALA", "SER", "CYS", "VAL", + "THR", "ILE", "PRO", "MET", "ASP", + "ASN", "LEU", "LYS", "GLU", "GLN", + "ARG", "HIS", "PHE", "TYR", "TRP", + "UNK" }; + +char SHORT_AA_NAMES[22] = { "GASCVTIPMDNLKEQRHFYWX" }; + +int AA_NUMS[256]; + +int nheavy[20] = { 0, 1, 2, 2, 3, 3, 4, 3, 4, 4, 4, 4, 5, 5, 5, 7, 6, 7, 8, 10}; + +char *backbone_atoms[4] = { "N ", "CA ", "C ", "O " }; + +char *heavy_atoms[200]= { +/* GLY */ NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, +/* ALA */ "CB ", NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, +/* SER */ "CB ", "OG ", NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, +/* CYS */ "CB ", "SG ", NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, +/* VAL */ "CB ", "CG1", "CG2", NULL, NULL, NULL, NULL, NULL, NULL, NULL, +/* THR */ "CB ", "OG1", "CG2", NULL, NULL, NULL, NULL, NULL, NULL, NULL, +/* ILE */ "CB ", "CG1", "CG2", "CD1", NULL, NULL, NULL, NULL, NULL, NULL, +/* PRO */ "CB ", "CG ", "CD ", NULL, NULL, NULL, NULL, NULL, NULL, NULL, +/* MET */ "CB ", "CG ", "SD ", "CE ", NULL, NULL, NULL, NULL, NULL, NULL, +/* ASP */ "CB ", "CG ", "OD1", "OD2", NULL, NULL, NULL, NULL, NULL, NULL, +/* ASN */ "CB ", "CG ", "OD1", "ND2", NULL, NULL, NULL, NULL, NULL, NULL, +/* LEU */ "CB ", "CG ", "CD1", "CD2", NULL, NULL, NULL, NULL, NULL, NULL, +/* LYS */ "CB ", "CG ", "CD ", "CE ", "NZ ", NULL, NULL, NULL, NULL, NULL, +/* GLU */ "CB ", "CG ", "CD ", "OE1", "OE2", NULL, NULL, NULL, NULL, NULL, +/* GLN */ "CB ", "CG ", "CD ", "OE1", "NE2", NULL, NULL, NULL, NULL, NULL, +/* ARG */ "CB ", "CG ", "CD ", "NE ", "CZ ", "NH1", "NH2", NULL, NULL, NULL, +/* HIS */ "CB ", "CG ", "ND1", "CD2", "CE1", "NE2", NULL, NULL, NULL, NULL, +/* PHE */ "CB ", "CG ", "CD1", "CD2", "CE1", "CE2", "CZ ", NULL, NULL, NULL, +/* TYR */ "CB ", "CG ", "CD1", "CD2", "CE1", "CE2", "CZ ", "OH ", NULL, NULL, +/* TRP */ "CB ", "CG ", "CD1", "CD2", "NE1", "CE2", "CE3", "CZ2", "CZ3", "CH2"}; + +/* reads full-atom pdb file */ + +struct _res_type; + +typedef struct _atom_type { + struct _atom_type *next; + real x, y, z; + char *name; + int num, locnum; + int flag; + char cispro; + int gx, gy, gz; + struct _res_type *res; + struct _atom_type *prev; +} atom_type; + +typedef struct _res_type { + struct _res_type *next; + atom_type *atoms; + int num, locnum, natoms; + int type; + char pdbsg; + char protein; + char *name; + char chain; + real sgx, sgy, sgz; + real cmx, cmy, cmz; + struct _res_type *prev; +} res_type; + +typedef struct _mol_type { + struct _mol_type *next; + res_type *residua; + int nres; + unsigned char *r14; + char *name; + uchar *seq; + char **contacts; + real **cutoffs; + struct _mol_type *prev; +} mol_type; + +#define MIN(a,b) (a<b?a:b) +#define MAX(a,b) (a>b?a:b) + +mol_type *chain = NULL; + + +real rnd(void) +{ + return 0.001*(real)(rand()%1000); +} + +atom_type *new_atom(void) +{ + atom_type *tmpatom; + + tmpatom = (atom_type*) calloc(sizeof(atom_type),1); + if (tmpatom) { + tmpatom->x=tmpatom->y=tmpatom->z=0.; + tmpatom->name=NULL; + tmpatom->num=tmpatom->locnum=tmpatom->flag=0; + tmpatom->next=tmpatom->prev=NULL; + } + + return tmpatom; +} + +res_type* new_res(void) +{ + res_type *tmpres; + + tmpres = (res_type*) calloc(sizeof(res_type),1); + if (tmpres) { + tmpres->num=0; + tmpres->name=NULL; + tmpres->atoms=NULL; + tmpres->chain=' '; + tmpres->next=tmpres->prev=NULL; + } + + return tmpres; +} + +mol_type *new_mol(void) +{ + mol_type *tmpmol; + + tmpmol = (mol_type*) calloc(sizeof(mol_type),1); + if (tmpmol) { + tmpmol->name=NULL; + tmpmol->residua=NULL; + tmpmol->next=tmpmol->prev=NULL; + } + + return tmpmol; +} + +void add_atom(atom_type* atomlist, atom_type* newatom) +{ + atom_type *tmpatom; + + if (!atomlist) + atomlist=newatom; + else { + tmpatom=atomlist->next; + atomlist->next=newatom; + newatom->prev=atomlist; + newatom->next=tmpatom; + if (tmpatom) tmpatom->prev=newatom; + } +} + +void add_res(res_type* reslist, res_type* newres) +{ + res_type *tmpres; + + if (!reslist) + reslist=newres; + else { + tmpres=reslist->next; + reslist->next=newres; + newres->prev=reslist; + newres->next=tmpres; + if (tmpres) tmpres->prev=newres; + } +} + +void add_mol(mol_type* mollist, mol_type* newmol) +{ + mol_type *tmpmol; + + if (!mollist) + mollist=newmol; + else { + tmpmol=mollist->next; + mollist->next=newmol; + newmol->prev=mollist; + newmol->next=tmpmol; + if (tmpmol) tmpmol->prev=newmol; + } +} + +void delete_atom(atom_type* atom) +{ + atom_type *tmpatom; + + if (atom->prev) atom->prev->next=atom->next; + if (atom->next) atom->next->prev=atom->prev; + if (atom->name) free(atom->name); + free(atom); + atom=NULL; +} + +void delete_res(res_type* res) +{ + res_type *tmpres; + atom_type *tmpatom; + + if (res->prev) res->prev->next=res->next; + if (res->next) res->next->prev=res->prev; + if (res->name) free(res->name); + if (res->atoms) { + while (res->atoms) { + tmpatom = res->atoms->next; + delete_atom(res->atoms); + res->atoms=tmpatom; + } + } + free(res); + res=NULL; +} + +void delete_mol(mol_type* mol) +{ + mol_type *tmpmol; + res_type *tmpres; + int i; + + if (mol->prev) mol->prev->next=mol->next; + if (mol->next) mol->next->prev=mol->prev; + if (mol->name) free(mol->name); + if (mol->residua) { + while (mol->residua) { + tmpres = mol->residua->next; + delete_res(mol->residua); + mol->residua=tmpres; + } + } + if (mol->contacts) { + for (i=0; i<mol->nres; i++) free(mol->contacts[i]); + free(mol->contacts); + } + if (mol->cutoffs) { + for (i=0; i<mol->nres; i++) free(mol->cutoffs[i]); + free(mol->cutoffs); + } + free(mol); + mol=NULL; +} + + +atom_type* get_last_atom(atom_type* atom) +{ + while (atom->next) atom=atom->next; + + return atom; +} + +res_type* get_last_res(res_type* res) +{ + while (res->next) res=res->next; + + return res; +} + +mol_type *get_last_mol(mol_type* mol) +{ + while (mol->next) mol=mol->next; + + return mol; +} + +char setseq(char* aaname) +{ + int i; + + for (i=0; i<21; i++) { + if ((aaname[0]==AA_NAMES[i][0]) && + (aaname[1]==AA_NAMES[i][1]) && + (aaname[2]==AA_NAMES[i][2])) + break; + } + + if (i==21) { + if (!strcmp(aaname, "GLX")) + return 'E'; + if (!strcmp(aaname, "ASX")) + return 'D'; + if (!strcmp(aaname, "HID")) + return 'H'; + if (!strcmp(aaname, "MSE")) + return 'M'; + if (!strcmp(aaname, "SEP")) + return 'S'; + if (!strcmp(aaname, "TPO")) + return 'T'; + if (!strcmp(aaname, "PTR")) + return 'Y'; + i--; + } + + return SHORT_AA_NAMES[i]; +} + +int orient(res_type *res1, res_type *res2) +{ + real x1, y1, z1; + real x2, y2, z2; + real cax, cay, caz; + real len, vect, angle; + atom_type *atom; + + if (!res1 || !res2) return 0; + + atom=res1->atoms; + cax=cay=caz=0.; + while (atom) { + if (!strncmp(atom->name,"CA",2)) { + cax=atom->x; cay=atom->y; caz=atom->z; + } + atom=atom->next; + } + x1=res1->sgx-cax; y1=res1->sgy-cay; z1=res1->sgz-caz; + if (x1==0. && y1==0. && z1==0.) x1+=1.0; + + atom=res2->atoms; + cax=cay=caz=0.; + while (atom) { + if (!strncmp(atom->name,"CA",2)) { + cax=atom->x; cay=atom->y; caz=atom->z; + } + atom=atom->next; + } + x2=res2->sgx-cax; y2=res2->sgy-cay; z2=res2->sgz-caz; + if (x2==0. && y2==0. && z2==0.) x2+=1.0; + + vect = x1*x2+y1*y2+z1*z2; + len = sqrt(x1*x1+y1*y1+z1*z1)*sqrt(x2*x2+y2*y2+z2*z2); + if (len) vect /= len; + + angle=RADDEG*acos(vect); + + if (angle>120.) return 1; /*anti*/ + if (angle>60.) return 2; /*mid*/ + + return 3; /*par*/ +} + +int res_contact(res_type *res1, res_type *res2) { + atom_type *atoms1, *atoms2; + real dx, dy, dz; + + atoms1 = res1->atoms; + while (atoms1) { + atoms2 = res2->atoms; + while (atoms2) { + dx=atoms1->x-atoms2->x; + dy=atoms1->y-atoms2->y; + dz=atoms1->z-atoms2->z; + if ((atoms1->flag & FLAG_SIDECHAIN) && (atoms2->flag & FLAG_SIDECHAIN) && (dx*dx+dy*dy+dz*dz<20.25)) { + return 1; + } + atoms2=atoms2->next; + } + atoms1=atoms1->next; + } + + return 0; +} + +int read_pdb_file(char* filename, mol_type* molecules, char *realname) +{ + FILE *inp; + char buffer[1000]; + char atmname[10]; + char resname[10]; + char version; + int prevresnum, resnum, atmnum, locatmnum, num, locnum=0, i, j; + atom_type *prevatom1, *prevatom2, *prevatom3, *prevatom4; + int sgnum, cc, nres, ok, natom; + real sgx, sgy, sgz; + res_type *res, *test1, *test2; + atom_type *atom; + real x, y, z; + real dist; + unsigned char bin; + int warn=0; + real cutoff; + + if (_VERBOSE) printf("Reading input file %s...\n", filename); + + inp = fopen(filename, "r"); + if (!inp) { + if (_VERBOSE) printf("ERROR: can't open %s !!!\n", filename); + return FILE_NOT_FOUND; + } + + molecules->nres=0; + molecules->name=(char*)calloc(strlen(realname)+1,1); + strcpy(molecules->name, realname); + + atmname[3]=0; + resname[3]=0; + prevresnum=-666; + locatmnum=0; + sgnum=0; + sgx=sgy=sgz=0.; + res=NULL; + while (!feof(inp)) { + if (fgets(buffer, 1000, inp)!=buffer) break; + if (!strncmp(buffer, "END", 3) || !strncmp(buffer, "TER", 3)) break; // end of file; only single molecule read + if (!strncmp(buffer, "ATOM", 4) || !strncmp(buffer, "HETATM", 6)) { + if (buffer[16]!=' ' && buffer[16]!='A') continue; + sscanf(&buffer[22], "%d", &resnum); + strncpy(resname, &buffer[17], 3); + strncpy(atmname, &buffer[13], 3); + if (resnum==prevresnum && !strncmp(atmname, "N ", 2)) { + if (_VERBOSE) printf("WARNING: fault in numeration at residuum %s[%d]\n", resname, resnum); + warn=1; + } + if (atmname[0]=='H') continue; + if (resnum!=prevresnum || !strncmp(atmname, "N ", 2)) { + prevresnum=resnum; + if (res) { + if (sgnum) { + res->sgx=sgx/(real)sgnum; + res->sgy=sgy/(real)sgnum; + res->sgz=sgz/(real)sgnum; + } else { + res->sgx=res->sgy=res->sgz=0.; + } + } + locatmnum=0; + version=' '; + res = new_res(); + sgnum=0; + sgx=sgy=sgz=0.; + molecules->nres++; + res->name = calloc(strlen(resname)+1, 1); + res->type = AA_NUMS[setseq(resname)]; + res->locnum=locnum++; + res->num = resnum; + res->natoms=0; + res->chain = buffer[21]; + strcpy(res->name, resname); + if (molecules->residua) { + add_res(get_last_res(molecules->residua), res); + } else { + molecules->residua = res; + } + } + atom = new_atom(); + atom->res = res; + res->natoms++; + locatmnum++; + sscanf(&buffer[7], "%d", &atmnum); + sscanf(&buffer[30], "%lf", &x); + sscanf(&buffer[38], "%lf", &y); + sscanf(&buffer[46], "%lf", &z); + version = buffer[16]; + atom->name = calloc(strlen(atmname)+1,1); + strcpy(atom->name, atmname); + atom->x=x; atom->y=y; atom->z=z; + atom->num = atmnum; + atom->locnum = locatmnum; + if ((atmname[0]=='S' && atmname[1]=='C')||(atmname[0]=='C' && atmname[1]=='M')) { + res->cmx = x; + res->cmy = y; + res->cmz = z; + res->pdbsg=1; + if (res->type<20) { + res->protein=1; + } + } else + if (!( ((atmname[0]=='C' || atmname[0]=='N' || atmname[0]=='O') && atmname[1]==' ') || + (atmname[0]=='H') || + (atmname[0]=='C' && atmname[1]=='A') || + (atmname[0]=='O' && atmname[1]=='X' && atmname[2]=='T') ) ) { + sgx+=x; + sgy+=y; + sgz+=z; + sgnum++; + atom->flag |= FLAG_SIDECHAIN; + } else + atom->flag |= FLAG_BACKBONE; + if (atmname[0]=='C' && atmname[1]=='A') { + atom->flag |= FLAG_BACKBONE; + if (res->type<20) { + res->protein=1; + } + if (!res->pdbsg) { + res->cmx = x; + res->cmy = y; + res->cmz = z; + } + } + if (atmname[0]=='C' && atmname[1]=='M') { + atom->flag |= FLAG_SCM; + } + if (atmname[0]=='S' && atmname[1]=='C') { + atom->flag |= FLAG_SCM; + } + if (res->atoms) { + add_atom(get_last_atom(res->atoms), atom); + } else { + res->atoms = atom; + } + } + } + + if (res) { + if (sgnum) { + res->sgx=sgx/(real)sgnum; + res->sgy=sgy/(real)sgnum; + res->sgz=sgz/(real)sgnum; + } else { + res->sgx=res->sgy=res->sgz=0.; + } + } + fclose(inp); + + molecules->seq = (uchar*)calloc(sizeof(uchar)*molecules->nres+1,1); + res=molecules->residua; i=0; + while (res) { + molecules->seq[i++]=(uchar)AA_NUMS[(int)setseq(res->name)]; + res=res->next; + } + + if (!warn) return FILE_SUCCESS; else return FILE_WARNING; +} + +#define bool int +#define true 1 +#define false 0 + +real calc_ca_energy(atom_type **c_alpha, real **new_c_alpha, real **init_c_alpha, real **gradient, real alpha, real *ene, bool calc_gradient) +{ + int i, j; + real dx, dy, dz; + real dist, ddist, ddist2; + real new_e_pot; + real theta0, tdif, th, aa, bb, ab; + real ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; + real adiff[3], bdiff[3]; + real deriv, theta, dtheta, len1, len2, cos_theta, sin_theta; + real dx1, dy1, dz1; + real dx2, dy2, dz2; + real dx3, dy3, dz3; + real vx1, vy1, vz1; + real vx2, vy2, vz2; + real vx3, vy3, vz3; + + real r12x, r12y, r12z; + real r32x, r32y, r32z; + real d12, d32, d12inv, d32inv, c1, c2, diff; + real f1x, f1y, f1z; + real f2x, f2y, f2z; + real f3x, f3y, f3z; + + for (i=0; i<chain_length; i++) { + new_c_alpha[i][0]=c_alpha[i]->x+alpha*gradient[i][0]; + new_c_alpha[i][1]=c_alpha[i]->y+alpha*gradient[i][1]; + new_c_alpha[i][2]=c_alpha[i]->z+alpha*gradient[i][2]; + } + + new_e_pot = 0.0; + + ene[0]=ene[1]=ene[2]=ene[3]=0.0; + + for (i=0; i<chain_length; i++) { +#ifdef CALC_C_ALPHA_START + dx=new_c_alpha[i][0]-init_c_alpha[i][0]; + dy=new_c_alpha[i][1]-init_c_alpha[i][1]; + dz=new_c_alpha[i][2]-init_c_alpha[i][2]; + dist=sqrt(dx*dx+dy*dy+dz*dz); + ddist = -dist; + if (dist>_CA_START_DIST) { + ddist2=dist*dist; + new_e_pot+=CA_START_K*ddist2; + ene[1] += CA_START_K*ddist2; + if (calc_gradient) { + grad = ddist * (-2.0*CA_START_K)/dist; + gradient[i][0]-=grad*dx; + gradient[i][1]-=grad*dy; + gradient[i][2]-=grad*dz; + } + } + +#endif + + +#ifdef CALC_C_ALPHA + if (i>0) { + dx=new_c_alpha[i][0]-new_c_alpha[i-1][0]; + dy=new_c_alpha[i][1]-new_c_alpha[i-1][1]; + dz=new_c_alpha[i][2]-new_c_alpha[i-1][2]; + dist=sqrt(dx*dx+dy*dy+dz*dz); + if (c_alpha[i]->cispro) { + ddist=CA_DIST_CISPRO-dist; +// if (fabs(ddist)<CA_DIST_CISPRO_TOL) ddist=0.0; + } else { + ddist=CA_DIST-dist; +// if (fabs(ddist)<CA_DIST_TOL) ddist=0.0; + } + ddist2=ddist*ddist; + new_e_pot+=CA_K*ddist2; + ene[0] += CA_K*ddist2; + if (calc_gradient) { + grad = ddist * (-2.0*CA_K)/dist; + gradient[i][0]-=grad*dx; + gradient[i][1]-=grad*dy; + gradient[i][2]-=grad*dz; + gradient[i-1][0]+=grad*dx; + gradient[i-1][1]+=grad*dy; + gradient[i-1][2]+=grad*dz; + } + } +#endif + +#ifdef CALC_C_ALPHA_XVOL + for (j=0;j<i;j++) { + if (abs(i-j)>2) { + dx=new_c_alpha[i][0]-new_c_alpha[j][0]; + dy=new_c_alpha[i][1]-new_c_alpha[j][1]; + dz=new_c_alpha[i][2]-new_c_alpha[j][2]; + dist=sqrt(dx*dx+dy*dy+dz*dz); + ddist = dist-_CA_XVOL_DIST; + if (dist<_CA_XVOL_DIST) { + ddist2 = dist*dist; + new_e_pot+=CA_XVOL_K*ddist2; + ene[3] += CA_XVOL_K*ddist2; + if (calc_gradient) { + grad = ddist*(8.0*CA_XVOL_K)/dist; + gradient[i][0]-=grad*dx; + gradient[i][1]-=grad*dy; + gradient[i][2]-=grad*dz; + gradient[j][0]+=grad*dx; + gradient[j][1]+=grad*dy; + gradient[j][2]+=grad*dz; + } + } + } + } +#endif + +#ifdef CALC_C_ALPHA_ANGLES + + if (i>0 && i<chain_length-1) { + r12x=new_c_alpha[i-1][0]-new_c_alpha[i][0]; + r12y=new_c_alpha[i-1][1]-new_c_alpha[i][1]; + r12z=new_c_alpha[i-1][2]-new_c_alpha[i][2]; + r32x=new_c_alpha[i+1][0]-new_c_alpha[i][0]; + r32y=new_c_alpha[i+1][1]-new_c_alpha[i][1]; + r32z=new_c_alpha[i+1][2]-new_c_alpha[i][2]; + d12 = sqrt(r12x*r12x+r12y*r12y+r12z*r12z); + d32 = sqrt(r32x*r32x+r32y*r32y+r32z*r32z); + cos_theta = (r12x*r32x+r12y*r32y+r12z*r32z)/(d12*d32); + if (cos_theta>1.0) + cos_theta = 1.0; + else + if (cos_theta<-1.0) + cos_theta = -1.0; + sin_theta = sqrt(1.0-cos_theta*cos_theta); + theta = acos(cos_theta); + + if (RADDEG*theta<80.) + diff = theta-80.*DEGRAD; + else + if (RADDEG*theta>150.) + diff = theta-150.*DEGRAD; + else + diff = 0.0; + + new_e_pot += CA_ANGLE_K*diff*diff; + ene[2] += CA_ANGLE_K*diff*diff; + if (calc_gradient) { + d12inv = 1.0/d12; + d32inv = 1.0/d32; + diff *= (-2.0*CA_ANGLE_K)/sin_theta; + c1 = diff*d12inv; + c2 = diff*d32inv; + f1x = c1*(r12x*(d12inv*cos_theta)-r32x*d32inv); + f1y = c1*(r12y*(d12inv*cos_theta)-r32y*d32inv); + f1z = c1*(r12z*(d12inv*cos_theta)-r32z*d32inv); + f3x = c2*(r32x*(d32inv*cos_theta)-r12x*d12inv); + f3y = c2*(r32y*(d32inv*cos_theta)-r12y*d12inv); + f3z = c2*(r32z*(d32inv*cos_theta)-r12z*d12inv); + f2x = -f1x-f3x; + f2y = -f1y-f3y; + f2z = -f1z-f3z; + gradient[i-1][0]+=f1x; + gradient[i-1][1]+=f1y; + gradient[i-1][2]+=f1z; + gradient[i][0]+=f2x; + gradient[i][1]+=f2y; + gradient[i][2]+=f2z; + gradient[i+1][0]+=f3x; + gradient[i+1][1]+=f3y; + gradient[i+1][2]+=f3z; + } + } + +#endif + + } + +//printf("ene[3] = %f\n", ene[3]); + + return new_e_pot; +} + +/* + * Steepest gradient optimization using v=k*(r0-r)^2 + * k = CA_K, r0 = CA_DIST + */ +void ca_optimize(char *tname, char *iname) +{ + char buf[1000]; + int i, j, hx, my_iter; + real dx, dy, dz, dd, dist, dist2, dist3, ddist, ddist2; + real e_pot, new_e_pot, grad, alpha, e_pot1, e_pot2, e_pot3; + real adiff[3], bdiff[3]; + real ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; + real theta0, deg_th, maxgrad, sum; + real f0[3], f2[3]; + real x, y, z; + int numsteps, numsteps2, msteps; + int *sec; + real **new_c_alpha, **gradient, **init_c_alpha, last_alpha, tmp, last_good_alpha, d_alpha, last_e_pot; + atom_type *atom, **c_alpha; + res_type *res; + FILE *inp, *out; + int mnum, init, ok; + real alpha1, alpha2, alpha3, a0; + real ene1, ene2, ene3, e0; + real energies[4]; + real w1, w2, w3, eps; + real gnorm, last_gnorm; + int mode, fcnt; + + + if (_CA_TRAJECTORY) { + out = fopen(tname,"w"); + if (out) fclose(out); + } + + if (_VERBOSE) printf("Alpha carbons optimization...\n"); + + new_c_alpha = (real**)calloc(sizeof(real*)*(chain_length+1),1); + init_c_alpha = (real**)calloc(sizeof(real*)*(chain_length+1),1); + for (i=0;i<=chain_length;i++) { + new_c_alpha[i] = (real*)calloc(sizeof(real)*3,1); + init_c_alpha[i] = (real*)calloc(sizeof(real)*3,1); + } + gradient = (real**)calloc(sizeof(real*)*(chain_length+1),1); + for (i=0;i<=chain_length;i++) { + gradient[i] = (real*)calloc(sizeof(real)*3,1); + } + + c_alpha = (atom_type**)calloc(sizeof(atom_type*)*(chain_length+1),1); + + i = 0; + res = chain->residua; + while (res) { + atom = res->atoms; + while (atom) { + if (atom->name[0]=='C' && atom->name[1]=='A') { + if (i<chain_length) { + c_alpha[i] = atom; + i++; + break; + } else { + if (_VERBOSE) printf("WARNING: number of C-alpha atoms exceeds the chain length!\n"); + break; + } + } + atom = atom->next; + } + res = res->next; + } + + if (i<chain_length) chain_length = i; + + for (i=0; i<chain_length; i++) { + init_c_alpha[i][0] = c_alpha[i]->x; + init_c_alpha[i][1] = c_alpha[i]->y; + init_c_alpha[i][2] = c_alpha[i]->z; + } + + if (_CISPRO) { + for (i=1; i<chain_length; i++) { + dx = c_alpha[i]->x-c_alpha[i-1]->x; + dy = c_alpha[i]->y-c_alpha[i-1]->y; + dz = c_alpha[i]->z-c_alpha[i-1]->z; + dd = sqrt(dx*dx+dy*dy+dz*dz); + if ((setseq(c_alpha[i]->res->name)=='P') && (dd>CA_DIST_CISPRO-5*CA_DIST_CISPRO_TOL) && (dd<CA_DIST_CISPRO+5*CA_DIST_CISPRO_TOL)) { + if (_VERBOSE) printf("Probable cis-proline found at postion %d\n", c_alpha[i]->res->num); + c_alpha[i]->cispro = 1; + } + } + } + + if (_CA_RANDOM) { + if (_VERBOSE) printf("Generating random C-alpha coordinates...\n"); + c_alpha[0]->x = 0.0; + c_alpha[0]->y = 0.0; + c_alpha[0]->z = 0.0; + for (i=1;i<chain_length;i++) { + dx = 0.01*(100-rand()%200); + dy = 0.01*(100-rand()%200); + dz = 0.01*(100-rand()%200); + dd = 3.8/sqrt(dx*dx+dy*dy+dz*dz); + dx *= dd; + dy *= dd; + dz *= dd; + c_alpha[i]->x = c_alpha[i-1]->x+dx; + c_alpha[i]->y = c_alpha[i-1]->y+dy; + c_alpha[i]->z = c_alpha[i-1]->z+dz; + } + } + + if (iname) { + inp = fopen(iname,"r"); + if (inp) { + if (_VERBOSE) printf("Reading initial structure %s...\n", iname); + i = 0; + while (!feof(inp)) { + if (fgets(buf,1000,inp)==buf && buf[13]=='C' && buf[14]=='A') { + if (i<chain_length) { + if (sscanf(&buf[30],"%lf%lf%lf",&x,&y,&z)==3) { + c_alpha[i]->x = x; + c_alpha[i]->y = y; + c_alpha[i]->z = z; + i++; + } + } else { + if (_VERBOSE) printf("WARNING: number of ini-file C-alpha atoms exceeds the chain length!\n"); + break; + } + } + } + fclose(inp); + } else + if (_VERBOSE) printf("WARNING: can't read initial corrdinates %s\n", iname); + } + + mnum = 1; + mode = 0; + init = 0; + numsteps=numsteps2=0; + last_alpha = 0.0; + + + if (_VERBOSE) printf("Optimizing alpha carbons...\n"); + + eps = 0.5; + + fcnt=0; + + last_gnorm = 1000.; + + do { + last_e_pot = e_pot; + + if (_CA_TRAJECTORY) { + out = fopen(tname,"a"); + if (out) { + fprintf(out,"MODEL %d\n",mnum++); + for (i=0; i<chain_length; i++) { + fprintf(out, "ATOM %5d %-3s %3s %c%4d %8.3f%8.3f%8.3f\n", + i+1, "CA ", c_alpha[i]->res->name, ' ', c_alpha[i]->res->num, + c_alpha[i]->x, c_alpha[i]->y, c_alpha[i]->z); + + } + fprintf(out,"ENDMDL\n"); + fclose(out); + } + } + +// calculate gradients + + e_pot=e_pot1=e_pot2=e_pot3=0.; + + for (i=0; i<chain_length; i++) + gradient[i][0]=gradient[i][1]=gradient[i][2]=0.; + + e_pot = calc_ca_energy(c_alpha, new_c_alpha, init_c_alpha, gradient, 0.0, energies, true); + + if (_VERBOSE && !init) { + printf("Initial energy: bond=%.5lf angle=%.5f restraints=%.5f xvol=%.5f total=%.5f\n", energies[0], energies[2], energies[1], energies[3], e_pot); + } + + if (!init) init=1; + +// LINE SEARCH + + alpha1 = -1.0; + alpha2 = 0.0; + alpha3 = 1.0; + + ene1 = calc_ca_energy(c_alpha, new_c_alpha, init_c_alpha, gradient, alpha1, energies, false); + ene2 = calc_ca_energy(c_alpha, new_c_alpha, init_c_alpha, gradient, alpha2, energies, false); + ene3 = calc_ca_energy(c_alpha, new_c_alpha, init_c_alpha, gradient, alpha3, energies, false); + + msteps = 0; + while (ene2>MIN(ene1,ene3) && msteps<_CA_ITER) { + msteps++; + alpha1 *= 2.0; + alpha3 *= 2.0; + ene1 = calc_ca_energy(c_alpha, new_c_alpha, init_c_alpha, gradient, alpha1, energies, false); + ene3 = calc_ca_energy(c_alpha, new_c_alpha, init_c_alpha, gradient, alpha3, energies, false); + } + + msteps = 0; + do { + if (alpha3-alpha2>alpha2-alpha1) { + a0 = 0.5*(alpha2+alpha3); + e0 = calc_ca_energy(c_alpha, new_c_alpha, init_c_alpha, gradient, a0, energies, false); + e0 = calc_ca_energy(c_alpha, new_c_alpha, init_c_alpha, gradient, a0-1e-5, energies, false); + e0 = calc_ca_energy(c_alpha, new_c_alpha, init_c_alpha, gradient, a0+1e-5, energies, false); + e0 = calc_ca_energy(c_alpha, new_c_alpha, init_c_alpha, gradient, a0, energies, false); + if (e0<ene2) { + alpha1 = alpha2; + alpha2 = a0; + ene1 = ene2; + ene2 = e0; + } else { + alpha3 = a0; + ene3 = e0; + } + } else { + a0 = 0.5*(alpha1+alpha2); + e0 = calc_ca_energy(c_alpha, new_c_alpha, init_c_alpha, gradient, a0, energies, false); + e0 = calc_ca_energy(c_alpha, new_c_alpha, init_c_alpha, gradient, a0-1e-5, energies, false); + e0 = calc_ca_energy(c_alpha, new_c_alpha, init_c_alpha, gradient, a0+1e-5, energies, false); + e0 = calc_ca_energy(c_alpha, new_c_alpha, init_c_alpha, gradient, a0, energies, false); + if (e0<ene2) { + alpha3 = alpha2; + alpha2 = a0; + ene3 = ene2; + ene2 = e0; + } else { + alpha1 = a0; + ene1 = e0; + } + } + msteps++; + } while (alpha3-alpha1>1e-6 && msteps<20); + + last_alpha = alpha2; + e_pot = ene2; + + for (i=0; i<chain_length; i++) { + c_alpha[i]->x=c_alpha[i]->x+(last_alpha+last_alpha*(rnd()-0.5)*eps)*gradient[i][0]; + c_alpha[i]->y=c_alpha[i]->y+(last_alpha+last_alpha*(rnd()-0.5)*eps)*gradient[i][1]; + c_alpha[i]->z=c_alpha[i]->z+(last_alpha+last_alpha*(rnd()-0.5)*eps)*gradient[i][2]; + } + + e_pot = calc_ca_energy(c_alpha, new_c_alpha, init_c_alpha, gradient, 0.0, energies, false); + + eps *= 0.75; + if (eps<1e-3) eps=0.0; + + numsteps++; + + gnorm = 0.0; + + for (i=0; i<chain_length; i++) { + gnorm += gradient[i][0]*gradient[i][0] + gradient[i][1]*gradient[i][1] + gradient[i][2]*gradient[i][2]; + } + + gnorm = sqrt(gnorm/(double)chain_length); + + if (last_gnorm-gnorm<1e-3) fcnt++; + + last_gnorm = gnorm; + + } while ( (fcnt<3) && (gnorm>0.01) && (numsteps<_CA_ITER)); + + + if (_VERBOSE) { + for (i=0; i<chain_length; i++) { + +#ifdef CALC_C_ALPHA + if (i>0) { + dx=c_alpha[i]->x-c_alpha[i-1]->x; + dy=c_alpha[i]->y-c_alpha[i-1]->y; + dz=c_alpha[i]->z-c_alpha[i-1]->z; + dist=sqrt(dx*dx+dy*dy+dz*dz); + if (c_alpha[i]->cispro) { + ddist=CA_DIST_CISPRO-dist; + if (fabs(ddist)<CA_DIST_CISPRO_TOL) ddist=0.0; + } else { + ddist=CA_DIST-dist; + if (fabs(ddist)<CA_DIST_TOL) ddist=0.0; + } + ddist2=ddist*ddist; + if (fabs(ddist)>=CA_DIST_TOL) printf("WARNING: distance %d = %.3lf A\n", i, dist); + } +#endif + } + + for (i=0; i<chain_length; i++) { +#ifdef CALC_C_ALPHA_ANGLES + if (i>0 && i<chain_length-1) { + aa=ab=bb=0.0; + adiff[0]=c_alpha[i-1]->x-c_alpha[i]->x; + bdiff[0]=c_alpha[i+1]->x-c_alpha[i]->x; + aa+=adiff[0]*adiff[0]; + ab+=adiff[0]*bdiff[0]; + bb+=bdiff[0]*bdiff[0]; + adiff[1]=c_alpha[i-1]->y-c_alpha[i]->y; + bdiff[1]=c_alpha[i+1]->y-c_alpha[i]->y; + aa+=adiff[1]*adiff[1]; + ab+=adiff[1]*bdiff[1]; + bb+=bdiff[1]*bdiff[1]; + adiff[2]=c_alpha[i-1]->z-c_alpha[i]->z; + bdiff[2]=c_alpha[i+1]->z-c_alpha[i]->z; + aa+=adiff[2]*adiff[2]; + ab+=adiff[2]*bdiff[2]; + bb+=bdiff[2]*bdiff[2]; + + th=ab/sqrt(aa*bb); + if (th<-1.0) th=-1.0; + if (th>1.0) th=1.0; + th=acos(th); + deg_th=RADDEG*th; + if (deg_th>150.) theta0=DEGRAD*150.; else + if (deg_th<75.) theta0=DEGRAD*75.; else + theta0=th; + if (fabs(deg_th-RADDEG*theta0)>1.0) printf("WARNING: angle %d = %.3lf degrees\n", i, deg_th); + } +#endif + } + } + + if (_VERBOSE) printf("Optimization done after %d step(s).\nFinal energy: bond=%.5lf angle=%.5f restraints=%.5f xvol=%.5f total=%.5f\n", numsteps, energies[0], energies[2], energies[1], energies[3], e_pot); + + if (_CA_TRAJECTORY) { + out = fopen(tname,"a"); + if (out) { + fprintf(out,"END\n"); + } + } + + for (i=0;i<chain_length+1;i++) { + free(init_c_alpha[i]); + free(new_c_alpha[i]); + free(gradient[i]); + } + free(new_c_alpha); + free(gradient); + free(c_alpha); + free(init_c_alpha); +} + +void center_chain(mol_type *mol) +{ + real cx, cy, cz; + int natom; + res_type *res; + atom_type *atom; + + cx = cy = cz = 0.0; + natom = 0; + + res = mol->residua; + while (res) { + atom = res->atoms; + while (atom) { + cx += atom->x; + cy += atom->y; + cz += atom->z; + natom++; + atom=atom->next; + } + res = res->next; + } + + cx /= (real)natom; + cy /= (real)natom; + cz /= (real)natom; + + if (_VERBOSE) printf("Molecule center: %8.3f %8.3f %8.3f -> 0.000 0.000 0.000\n", cx, cy, cz); + + res = mol->residua; + while (res) { + atom = res->atoms; + while (atom) { + atom->x -= cx; + atom->y -= cy; + atom->z -= cz; + natom++; + atom=atom->next; + } + res = res->next; + } + +} + +void write_pdb(char *name, mol_type *mol) +{ + FILE *out; + res_type *res; + atom_type *atom; + int anum; + + out = fopen(name,"w"); + if (!out) { + if (_VERBOSE) printf("Can't open output file!\n"); + return; + } + fprintf(out,"REMARK 999 REBUILT BY PULCHRA V.%.2f\n", PULCHRA_VERSION); + anum=1; + res = mol->residua; + while (res) { + if (res->protein) { + if (!_BB_REARRANGE) { + atom = res->atoms; + while (atom) { + if (!(atom->name[0]=='D' && atom->name[1]=='U') && + !(atom->name[0]=='S' && atom->name[1]=='C') && + !(atom->name[0]=='C' && atom->name[1]=='M') && + !(atom->name[0]=='H' && !_REBUILD_H)) + fprintf(out, "ATOM %5d %-3s %3s %c%4d %8.3f%8.3f%8.3f\n", + anum++, atom->name, res->name, ' ', res->num, + atom->x, atom->y, atom->z); + atom=atom->next; + } + } else { + atom = res->atoms; + while (atom) { + if (!(atom->name[0]=='D' && atom->name[1]=='U') && + !(atom->name[0]=='S' && atom->name[1]=='C') && + !(atom->name[0]=='C' && atom->name[1]==' ') && + !(atom->name[0]=='O' && atom->name[1]==' ') && + !(atom->name[0]=='C' && atom->name[1]=='M') && + !(atom->name[0]=='H' && !_REBUILD_H)) + fprintf(out, "ATOM %5d %-3s %3s %c%4d %8.3f%8.3f%8.3f\n", + anum++, atom->name, res->name, ' ', res->num, + atom->x, atom->y, atom->z); + atom=atom->next; + } + atom = res->atoms; + while (atom) { + if (((atom->name[0]=='C' && atom->name[1]==' ') || + (atom->name[0]=='O' && atom->name[1]==' ')) && + !(atom->name[0]=='H' && !_REBUILD_H)) + fprintf(out, "ATOM %5d %-3s %3s %c%4d %8.3f%8.3f%8.3f\n", + anum++, atom->name, res->name, ' ', res->num, + atom->x, atom->y, atom->z); + atom=atom->next; + } + } + } + res = res->next; + } + fprintf(out,"TER\nEND\n"); + fclose(out); +} + + +void write_pdb_sg(char *name, mol_type *mol) +{ + FILE *out; + res_type *res; + atom_type *atom; + int anum; + + out = fopen(name,"w"); + if (!out) { + if (_VERBOSE) printf("Can't open output file!\n"); + return; + } + fprintf(out,"REMARK 999 REBUILT BY PULCHRA V.%.2f\n", PULCHRA_VERSION); + anum=1; + res = mol->residua; + while (res) { + if (res->protein) { + atom = res->atoms; + while (atom) { + if ((atom->name[0]=='C' && atom->name[1]=='A')) + fprintf(out, "ATOM %5d %-3s %3s %c%4d %8.3f%8.3f%8.3f\n", + anum++, atom->name, res->name, ' ', res->num, + atom->x, atom->y, atom->z); + atom=atom->next; + } + fprintf(out, "ATOM %5d %-3s %3s %c%4d %8.3f%8.3f%8.3f\n", + anum++, "CM ", res->name, ' ', res->num, + res->cmx, res->cmy, res->cmz); + } + res = res->next; + } + fprintf(out,"TER\nEND\n"); + fclose(out); +} + +real calc_distance(real x1, real y1, real z1, + real x2, real y2, real z2) +{ + real dx,dy,dz; + real dist2; + + dx = (x1) - (x2); + dy = (y1) - (y2); + dz = (z1) - (z2); + if (dx || dy || dz ) { + dist2 = dx*dx+dy*dy+dz*dz; + return (sqrt(dist2)); + } else + return 0.0; +} + +real calc_r14(real x1, real y1, real z1, + real x2, real y2, real z2, + real x3, real y3, real z3, + real x4, real y4, real z4) +{ + real r, dx, dy, dz; + real vx1, vy1, vz1, vx2, vy2, vz2, vx3, vy3, vz3; + real hand; + + dx = x4-x1; + dy = y4-y1; + dz = z4-z1; + + r = sqrt(dx*dx+dy*dy+dz*dz); + + vx1=x2-x1; + vy1=y2-y1; + vz1=z2-z1; + vx2=x3-x2; + vy2=y3-y2; + vz2=z3-z2; + vx3=x4-x3; + vy3=y4-y3; + vz3=z4-z3; + + hand = (vy1*vz2-vy2*vz1)*vx3+ + (vz1*vx2-vz2*vx1)*vy3+ + (vx1*vy2-vx2*vy1)*vz3; + + if (hand<0) r=-r; + + return r; +} + +real superimpose2(real **coords1, real **coords2, int npoints, real **tpoints, int ntpoints) +{ + real mat_s[3][3], mat_a[3][3], mat_b[3][3], mat_g[3][3]; + real mat_u[3][3], tmp_mat[3][3]; + real val, d, alpha, beta, gamma, x, y, z; + real cx1, cy1, cz1, cx2, cy2, cz2, tmpx, tmpy, tmpz; + int i, j, k, n; + + cx1=cy1=cz1=cx2=cy2=cz2=0.; + + for (i=0; i<npoints; i++) { + cx1+=coords1[i][0]; + cy1+=coords1[i][1]; + cz1+=coords1[i][2]; + cx2+=coords2[i][0]; + cy2+=coords2[i][1]; + cz2+=coords2[i][2]; + } + + cx1/=(real)npoints; + cy1/=(real)npoints; + cz1/=(real)npoints; + + cx2/=(real)npoints; + cy2/=(real)npoints; + cz2/=(real)npoints; + + for (i=0; i<npoints; i++) { + coords1[i][0]-=cx1; + coords1[i][1]-=cy1; + coords1[i][2]-=cz1; + coords2[i][0]-=cx2; + coords2[i][1]-=cy2; + coords2[i][2]-=cz2; + } + + for (i=0; i<ntpoints; i++) { + tpoints[i][0]-=cx2; + tpoints[i][1]-=cy2; + tpoints[i][2]-=cz2; + } + + for (i=0; i<3; i++) + for (j=0; j<3; j++) { + if (i==j) + mat_s[i][j]=mat_a[i][j]=mat_b[i][j]=mat_g[i][j]=1.0; + else + mat_s[i][j]=mat_a[i][j]=mat_b[i][j]=mat_g[i][j]=0.0; + mat_u[i][j]=0.; + } + + for (n=0; n<npoints; n++) { + mat_u[0][0]+=coords1[n][0]*coords2[n][0]; + mat_u[0][1]+=coords1[n][0]*coords2[n][1]; + mat_u[0][2]+=coords1[n][0]*coords2[n][2]; + mat_u[1][0]+=coords1[n][1]*coords2[n][0]; + mat_u[1][1]+=coords1[n][1]*coords2[n][1]; + mat_u[1][2]+=coords1[n][1]*coords2[n][2]; + mat_u[2][0]+=coords1[n][2]*coords2[n][0]; + mat_u[2][1]+=coords1[n][2]*coords2[n][1]; + mat_u[2][2]+=coords1[n][2]*coords2[n][2]; + } + + for (i=0; i<3; i++) + for (j=0; j<3; j++) + tmp_mat[i][j]=0.; + + do { + d=mat_u[2][1]-mat_u[1][2]; + if (d==0) alpha=0; else alpha=atan(d/(mat_u[1][1]+mat_u[2][2])); + if (cos(alpha)*(mat_u[1][1]+mat_u[2][2])+sin(alpha)*(mat_u[2][1]-mat_u[1][2])<0.0) alpha+=M_PI; + mat_a[1][1]=mat_a[2][2]=cos(alpha); + mat_a[2][1]=sin(alpha); + mat_a[1][2]=-mat_a[2][1]; + for (i=0; i<3; i++) + for (j=0; j<3; j++) + for (k=0; k<3; k++) + tmp_mat[i][j]+=mat_u[i][k]*mat_a[j][k]; + for (i=0; i<3; i++) + for (j=0; j<3; j++) { + mat_u[i][j]=tmp_mat[i][j]; + tmp_mat[i][j]=0.; + } + for (i=0; i<3; i++) + for (j=0; j<3; j++) + for (k=0; k<3; k++) + tmp_mat[i][j]+=mat_a[i][k]*mat_s[k][j]; + for (i=0; i<3; i++) + for (j=0; j<3; j++) { + mat_s[i][j]=tmp_mat[i][j]; + tmp_mat[i][j]=0.; + } + d=mat_u[0][2]-mat_u[2][0]; + if (d==0) beta=0; else beta=atan(d/(mat_u[0][0]+mat_u[2][2])); + if (cos(beta)*(mat_u[0][0]+mat_u[2][2])+sin(beta)*(mat_u[0][2]-mat_u[2][0])<0.0) beta+=M_PI; + mat_b[0][0]=mat_b[2][2]=cos(beta); + mat_b[0][2]=sin(beta); + mat_b[2][0]=-mat_b[0][2]; + for (i=0; i<3; i++) + for (j=0; j<3; j++) + for (k=0; k<3; k++) + tmp_mat[i][j]+=mat_u[i][k]*mat_b[j][k]; + for (i=0; i<3; i++) + for (j=0; j<3; j++) { + mat_u[i][j]=tmp_mat[i][j]; + tmp_mat[i][j]=0.; + } + for (i=0; i<3; i++) + for (j=0; j<3; j++) + for (k=0; k<3; k++) + tmp_mat[i][j]+=mat_b[i][k]*mat_s[k][j]; + for (i=0; i<3; i++) + for (j=0; j<3; j++) { + mat_s[i][j]=tmp_mat[i][j]; + tmp_mat[i][j]=0.; + } + d=mat_u[1][0]-mat_u[0][1]; + if (d==0) gamma=0; else gamma=atan(d/(mat_u[0][0]+mat_u[1][1])); + if (cos(gamma)*(mat_u[0][0]+mat_u[1][1])+sin(gamma)*(mat_u[1][0]-mat_u[0][1])<0.0) + gamma+=M_PI; + mat_g[0][0]=mat_g[1][1]=cos(gamma); + mat_g[1][0]=sin(gamma); + mat_g[0][1]=-mat_g[1][0]; + for (i=0; i<3; i++) + for (j=0; j<3; j++) + for (k=0; k<3; k++) + tmp_mat[i][j]+=mat_u[i][k]*mat_g[j][k]; + for (i=0; i<3; i++) + for (j=0; j<3; j++) { + mat_u[i][j]=tmp_mat[i][j]; + tmp_mat[i][j]=0.; + } + for (i=0; i<3; i++) + for (j=0; j<3; j++) + for (k=0; k<3; k++) + tmp_mat[i][j]+=mat_g[i][k]*mat_s[k][j]; + for (i=0; i<3; i++) + for (j=0; j<3; j++) { + mat_s[i][j]=tmp_mat[i][j]; + tmp_mat[i][j]=0.; + } + val=fabs(alpha)+fabs(beta)+fabs(gamma); + } while (val>0.001); + + val=0.; + for (i=0; i<npoints; i++) { + x=coords2[i][0]; + y=coords2[i][1]; + z=coords2[i][2]; + tmpx=x*mat_s[0][0]+y*mat_s[0][1]+z*mat_s[0][2]; + tmpy=x*mat_s[1][0]+y*mat_s[1][1]+z*mat_s[1][2]; + tmpz=x*mat_s[2][0]+y*mat_s[2][1]+z*mat_s[2][2]; + x=coords1[i][0]-tmpx; + y=coords1[i][1]-tmpy; + z=coords1[i][2]-tmpz; + val+=x*x+y*y+z*z; + } + + for (i=0; i<ntpoints; i++) { + x=tpoints[i][0]; + y=tpoints[i][1]; + z=tpoints[i][2]; + tpoints[i][0]=x*mat_s[0][0]+y*mat_s[0][1]+z*mat_s[0][2]; + tpoints[i][1]=x*mat_s[1][0]+y*mat_s[1][1]+z*mat_s[1][2]; + tpoints[i][2]=x*mat_s[2][0]+y*mat_s[2][1]+z*mat_s[2][2]; + } + + for (i=0; i<npoints; i++) { + coords1[i][0]+=cx1; + coords1[i][1]+=cy1; + coords1[i][2]+=cz1; + coords2[i][0]+=cx2; + coords2[i][1]+=cy2; + coords2[i][2]+=cz2; + } + + for (i=0; i<ntpoints; i++) { + tpoints[i][0]+=cx1; + tpoints[i][1]+=cy1; + tpoints[i][2]+=cz1; + } + + return sqrt(val/(real)npoints); +} + + +atom_type *find_atom(res_type *res, char *aname) +{ + atom_type *atom; + + atom = res->atoms; + while (atom) { + if (atom->name[0]==aname[0] && atom->name[1]==aname[1] && atom->name[2]==aname[2]) { + return atom; + break; + } + atom = atom->next; + } + + return NULL; +} + + +void add_replace(res_type *res, char *aname, real x, real y, real z, int flags) +{ + atom_type *atom, *newatom; + + atom = res->atoms; + while (atom) { + if (atom->name[0]==aname[0] && atom->name[1]==aname[1] && atom->name[2]==aname[2]) { + atom->x = x; atom->y = y; atom->z = z; + atom->flag |= flags; + break; + } + atom = atom->next; + } + + if (!atom) { + newatom = (atom_type*)calloc(sizeof(atom_type),1); + newatom->x = x; + newatom->y = y; + newatom->z = z; + newatom->flag |= flags; + newatom->res = res; + newatom->name = (char*)calloc(4,1); + strcpy(newatom->name,aname); + + atom = res->atoms; + while (atom) { + if (atom->name[0]=='C' && atom->name[1]=='A') + break; + atom = atom->next; + } + if (aname[0]=='N' && aname[1]==' ') { + newatom->next = res->atoms; + res->atoms = newatom; + } else { + while (atom->next) atom=atom->next; + atom->next = newatom; + } + } +} + + +int **RBINS; +real **X_COORDS, **C_ALPHA; + +#ifdef COMPILE_BB + +void rebuild_backbone(void) +{ + + res_type *res, *prevres; + atom_type *atom; + real **cacoords, **tmpcoords, **tmpstat; + real x1, y1, z1; + real x2, y2, z2; + real x3, y3, z3; + real x4, y4, z4; + real r13_1, r13_2, r14; + real besthit, hit; + int bestpos; + int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; + int b13_1, b13_2, b14; + real rmsd, total, maxrms; + FILE *debug, *out; + + if (_VERBOSE) printf("Rebuilding backbone...\n"); + + RBINS = (int**)calloc(sizeof(int*)*(chain_length+1),1); + for (i=0;i<chain_length+1;i++) + RBINS[i] = (int*)calloc(sizeof(int)*3,1); + + X_COORDS = (real**)calloc(sizeof(real*)*(chain_length+10),1); + for (i=0;i<chain_length+10;i++) + X_COORDS[i] = (real*)calloc(sizeof(real)*3,1); + + i = 5; + + res = chain->residua; + while (res) { + atom = res->atoms; + while (atom) { + if (atom->name[0]=='C' && atom->name[1]=='A') { + X_COORDS[i][0] = atom->x; + X_COORDS[i][1] = atom->y; + X_COORDS[i][2] = atom->z; + i++; + } + atom = atom->next; + } + res = res->next; + } + + cacoords = (real**)calloc(sizeof(real*)*(8),1); + tmpcoords = (real**)calloc(sizeof(real*)*(8),1); + tmpstat = (real**)calloc(sizeof(real*)*(8),1); + for (i=0;i<8;i++) { + cacoords[i] = (real*)calloc(sizeof(real)*3,1);; + tmpcoords[i] = (real*)calloc(sizeof(real)*3,1);; + tmpstat[i] = (real*)calloc(sizeof(real)*3,1);; + } + + C_ALPHA = &X_COORDS[5]; + + // rebuild ends... + + for (i=0,j=0;i<5;i++,j++) + for (k=0;k<3;k++) + tmpcoords[j][k] = C_ALPHA[i][k]; + for (i=2,j=0;i<5;i++,j++) + for (k=0;k<3;k++) + cacoords[j][k] = C_ALPHA[i][k]; + for (i=0,j=0;i<3;i++,j++) + for (k=0;k<3;k++) + tmpstat[j][k] = C_ALPHA[i][k]; + + superimpose2(tmpstat,cacoords,3,tmpcoords,5); + + for (i=-2,j=0;i<0;i++,j++) + for (k=0;k<3;k++) + C_ALPHA[i][k] = tmpcoords[j][k]; + + for (i=chain_length-5,j=0;i<chain_length;i++,j++) + for (k=0;k<3;k++) + tmpcoords[j][k] = C_ALPHA[i][k]; + for (i=chain_length-5,j=0;i<chain_length-2;i++,j++) + for (k=0;k<3;k++) + cacoords[j][k] = C_ALPHA[i][k]; + for (i=chain_length-3,j=0;i<chain_length;i++,j++) + for (k=0;k<3;k++) + tmpstat[j][k] = C_ALPHA[i][k]; + + superimpose2(tmpstat,cacoords,3,tmpcoords,5); + + for (i=chain_length-3,j=0;i<chain_length;i++,j++) + for (k=0;k<3;k++) + C_ALPHA[i+3][k] = tmpcoords[j+3][k]; + + + prevres = NULL; + res = chain->residua; + + + total = maxrms = 0.0; + + for (i=0;i<chain_length+1;i++) { + x1 = C_ALPHA[i-2][0]; + y1 = C_ALPHA[i-2][1]; + z1 = C_ALPHA[i-2][2]; + + x2 = C_ALPHA[i-1][0]; + y2 = C_ALPHA[i-1][1]; + z2 = C_ALPHA[i-1][2]; + + x3 = C_ALPHA[i][0]; + y3 = C_ALPHA[i][1]; + z3 = C_ALPHA[i][2]; + + x4 = C_ALPHA[i+1][0]; + y4 = C_ALPHA[i+1][1]; + z4 = C_ALPHA[i+1][2]; + + r13_1 = calc_distance(x1, y1, z1, x3, y3, z3); + r13_2 = calc_distance(x2, y2, z2, x4, y4, z4); + r14 = calc_r14(x1, y1, z1, x2, y2, z2, x3, y3, z3, x4, y4, z4); + + bin13_1 = (int)((r13_1-4.6)/0.3); + bin13_2 = (int)((r13_2-4.6)/0.3); + bin14 = (int)((r14+11.)/0.3); + + if (bin13_1<0) bin13_1=0; + if (bin13_2<0) bin13_2=0; + if (bin14<0) bin14=0; + if (bin13_1>9) bin13_1=9; + if (bin13_2>9) bin13_2=9; + if (bin14>73) bin14=73; + + RBINS[i][0] = bin13_1; + RBINS[i][1] = bin13_2; + RBINS[i][2] = bin14; + + cacoords[0][0] = x1; + cacoords[0][1] = y1; + cacoords[0][2] = z1; + + cacoords[1][0] = x2; + cacoords[1][1] = y2; + cacoords[1][2] = z2; + + cacoords[2][0] = x3; + cacoords[2][1] = y3; + cacoords[2][2] = z3; + + cacoords[3][0] = x4; + cacoords[3][1] = y4; + cacoords[3][2] = z4; + + pro = 0; + + if (prevres && !strncmp(prevres->name,"PRO",3)) { + j=0; + besthit=1000.; + bestpos=0; + do { + hit = abs(nco_stat_pro[j].bins[0]-bin13_1)+abs(nco_stat_pro[j].bins[1]-bin13_2)+0.2*abs(nco_stat_pro[j].bins[2]-bin14); + if (hit<besthit) { + besthit=hit; + bestpos=j; + } + j++; + } while (nco_stat_pro[j].bins[0]>=0 && hit>1e-3); + for (j=0;j<4;j++) { + for (k=0;k<3;k++) { + tmpstat[j][k] = nco_stat_pro[bestpos].data[j][k]; + } + } + for (j=0;j<8;j++) { + for (k=0;k<3;k++) { + tmpcoords[j][k] = nco_stat_pro[bestpos].data[j][k]; + } + } + } else { + j=0; + besthit=1000.; + bestpos=0; + do { + hit = abs(nco_stat[j].bins[0]-bin13_1)+abs(nco_stat[j].bins[1]-bin13_2)+0.2*abs(nco_stat[j].bins[2]-bin14); + if (hit<besthit) { + besthit=hit; + bestpos=j; + } + j++; + } while (nco_stat[j].bins[0]>=0 && hit>1e-3); + for (j=0;j<4;j++) { + for (k=0;k<3;k++) { + tmpstat[j][k] = nco_stat[bestpos].data[j][k]; + } + } + for (j=0;j<8;j++) { + for (k=0;k<3;k++) { + tmpcoords[j][k] = nco_stat[bestpos].data[j][k]; + } + } + } + + rmsd=superimpose2(cacoords, tmpstat, 4, tmpcoords, 8); + + total += rmsd; + if (rmsd>maxrms) maxrms=rmsd; + +// add-or-replace + + if (prevres) { + add_replace(prevres, "C ", tmpcoords[4][0], tmpcoords[4][1], tmpcoords[4][2], FLAG_BACKBONE); + add_replace(prevres, "O ", tmpcoords[5][0], tmpcoords[5][1], tmpcoords[5][2], FLAG_BACKBONE); + } + + if (res) { + add_replace(res, "N ", tmpcoords[6][0], tmpcoords[6][1], tmpcoords[6][2], FLAG_BACKBONE); + } + + prevres = res; + if (res) + res = res->next; + } + + if (_VERBOSE) printf("Backbone rebuilding deviation: average = %.3f, max = %.3f\n", total/(real)chain_length, maxrms); +} + +#endif + + +#ifdef COMPILE_ROT + +typedef struct _rot_struct { + int r13_1, r13_2, r14; + int nc; + real ***coords; + struct _rot_struct *next; +} rot_struct; + +rot_struct *rotamers[20]; + +/* this is obsolete in a standalone version of PULCHRA */ +void read_rotamers(void) +{ + FILE *inp; + char buf[1000]; + char dum[100]; + int aa, i, j, k, l, n; + rot_struct *new_rot, *last_rot; + real x, y, z; + + if (_VERBOSE) printf("Reading rotamer library...\n"); + + inp = fopen("NEWROT","r"); + last_rot=NULL; + while (!feof(inp)) { + if (fgets(buf,1000,inp)==buf) { + if (buf[0]=='A') { + sscanf(buf,"%s %d", dum, &aa); + if (last_rot) last_rot->next = NULL; + last_rot = NULL; + if (fgets(buf,1000,inp)!=buf) break; + } +// printf("aa: %d\n", aa); + if (aa==20) break; + sscanf(buf,"%d %d %d %s %d", &i, &j, &k, dum, &l); + new_rot = (rot_struct*)calloc(sizeof(rot_struct),1); +// printf("%d %d %d nc: %d\n", i, j, k, l); + new_rot->r13_1 = i; + new_rot->r13_2 = j; + new_rot->r14 = k; + new_rot->nc = l; + new_rot->next = NULL; + new_rot->coords = (real***)calloc(sizeof(real**)*l,1); + for (i=0;i<l;i++) { + new_rot->coords[i]=(real**)calloc(sizeof(real*)*(nheavy[aa]+1),1); + for (j=0;j<(nheavy[aa]+1);j++) { + new_rot->coords[i][j]=(real*)calloc(sizeof(real)*3,1); + } + } + for (i=0;i<l;i++) { + fgets(buf,1000,inp); + for (j=0;j<(nheavy[aa]+1);j++) { + fgets(buf,1000,inp); + sscanf(buf,"%lf%lf%lf",&x, &y, &z); + new_rot->coords[i][j][0]=x; + new_rot->coords[i][j][1]=y; + new_rot->coords[i][j][2]=z; + } + if (last_rot) { + last_rot->next = new_rot; + } else { + rotamers[aa] = new_rot; + } + last_rot = new_rot; + } + } + } + fclose(inp); +} + + +void cross(real *v1, real *v2, real *v3) +{ + v3[0] = v1[1]*v2[2]-v1[2]*v2[1]; + v3[1] = v1[2]*v2[0]-v1[0]*v2[2]; + v3[2] = v1[0]*v2[1]-v1[1]*v2[0]; +} + +void norm(real *v) +{ + real d; + + d = sqrt(v[0]*v[0]+v[1]*v[1]+v[2]*v[2]); + v[0] /= d; + v[1] /= d; + v[2] /= d; +} + + +int check_xvol(res_type *res) +{ + res_type *res2; + atom_type *atom1, *atom2; + real dx, dy, dz, dd; + + res2 = chain->residua; + + while (res2) { + atom2 = res2->atoms; + if (res!=res2) { + while (atom2) { + atom1 = res->atoms; + while (atom1) { + if (atom1->flag & FLAG_SIDECHAIN) { + dx = atom1->x-atom2->x; + dy = atom1->y-atom2->y; + dz = atom1->z-atom2->z; + dd = dx*dx+dy*dy+dz*dz; + if (dd<(1.7*1.7)) { + return 1; + } + } + atom1=atom1->next; + } + atom2=atom2->next; + } + } + res2=res2->next; + } + + return 0; +} + + +real ***SORTED_ROTAMERS; + +void rebuild_sidechains(void) +{ + FILE *out; + res_type *res, *prevres, *testres; + atom_type *atom, *atom1, *atom2; + real **cacoords, **tmpcoords, **tmpstat; + real x1, y1, z1; + real x2, y2, z2; + real x3, y3, z3; + real x4, y4, z4; + real x5, y5, z5; + real r14, r13_1, r13_2; + real dx, dy, dz, dd; + real hit, besthit; + int exvol, bestpos; + int i, j, k, l, m, bin13_1, bin13_2, bin14; + real rmsd, total; + real v1[3], v2a[3], v2b[3], v2[3], v3[3]; + int nsc, nca; + real cax, cay, caz; + real **lsys, **vv, **sc; + char scn[12][4]; + rot_struct *rot; + int ok, last_a, last_b, last_c, last_d, jpos; + int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; + int crot, bestrot, minexvol, totexvol, rtried, pos, cpos; + real cmx, cmy, cmz, ddx, ddy, ddz, ddd, bestdd; + real sort_rot[100][2]; + + if (_VERBOSE) printf("Rebuilding side chains...\n"); + + lsys = (real**)calloc(sizeof(real*)*3,1); + vv = (real**)calloc(sizeof(real*)*3,1); + sc = (real**)calloc(sizeof(real*)*12,1); + for (i=0;i<12;i++) + sc[i] = (real*)calloc(sizeof(real)*3,1); + for (i=0;i<3;i++) { + lsys[i] = (real*)calloc(sizeof(real)*3,1); + vv[i] = (real*)calloc(sizeof(real)*3,1); + } + + SORTED_ROTAMERS = (real***)calloc(sizeof(real**)*(chain_length+1),1); + for (i=0;i<chain_length+1;i++) { + SORTED_ROTAMERS[i] = (real**)calloc(sizeof(real*)*10,1); + for (j=0;j<10;j++) { + SORTED_ROTAMERS[i][j] = (real*)calloc(sizeof(real)*2,1); + } + } + + prevres = NULL; + res = chain->residua; + totexvol = 0; + + for (i=0;i<chain_length;i++) { + if (!strncmp(res->name,"GLY",3) || !res->protein) { + if (res->next) res = res->next; + continue; + } + + x1 = C_ALPHA[i-2][0]; + y1 = C_ALPHA[i-2][1]; + z1 = C_ALPHA[i-2][2]; + x2 = C_ALPHA[i-1][0]; + y2 = C_ALPHA[i-1][1]; + z2 = C_ALPHA[i-1][2]; + x3 = C_ALPHA[i][0]; + y3 = C_ALPHA[i][1]; + z3 = C_ALPHA[i][2]; + x4 = C_ALPHA[i+1][0]; + y4 = C_ALPHA[i+1][1]; + z4 = C_ALPHA[i+1][2]; + + bin13_1 = RBINS[i][0]; + bin13_2 = RBINS[i][1]; + bin14 = RBINS[i][2]; + + v1[0] = x4-x2; + v1[1] = y4-y2; + v1[2] = z4-z2; + + v2a[0] = x4-x3; + v2a[1] = y4-y3; + v2a[2] = z4-z3; + + v2b[0] = x3-x2; + v2b[1] = y3-y2; + v2b[2] = z3-z2; + + cross(v2a, v2b, v2); + cross(v1, v2, v3); + + norm(v1); + norm(v2); + norm(v3); + +// gather 10 closest rotamer conformations... + + for (j=0;j<10;j++) + SORTED_ROTAMERS[i][j][0] = 500.; + + j = 0; + besthit = 1000.; + bestpos = 0; + do { + if (rot_stat_idx[j][0]==res->type) { + hit = abs(rot_stat_idx[j][1]-bin13_1)+abs(rot_stat_idx[j][2]-bin13_2)+0.2*abs(rot_stat_idx[j][3]-bin14); + if (hit<SORTED_ROTAMERS[i][9][0]) { + k = 9; + while (k>=0 && hit<SORTED_ROTAMERS[i][k][0]) { + k--; + } + k++; + // k = hit + for (l=9;l>k;l--) { + SORTED_ROTAMERS[i][l][0]=SORTED_ROTAMERS[i][l-1][0]; + SORTED_ROTAMERS[i][l][1]=SORTED_ROTAMERS[i][l-1][1]; + } + SORTED_ROTAMERS[i][k][0]=hit; + SORTED_ROTAMERS[i][k][1]=j; + } + } + j++; + } while (rot_stat_idx[j][0]>=0); + + + besthit = SORTED_ROTAMERS[i][0][0]; + bestpos = SORTED_ROTAMERS[i][0][1]; + + +// new rebuild... + + pos = rot_stat_idx[bestpos][5]; + nsc = nheavy[res->type]+1; + + if (_PDB_SG) { // more than one rotamer - check SC + bestdd = 100.; crot = 0; + for (l=0;l<2;l++) { // check two closest conformations + cpos = SORTED_ROTAMERS[i][l][1]; + for (m=0;m<rot_stat_idx[cpos][4];m++) { + for (j=0;j<3;j++) { + vv[0][j] = v1[j]; vv[1][j] = v2[j]; vv[2][j] = v3[j]; + for (k=0;k<3;k++) { + if (j==k) lsys[j][k]=1.; else lsys[j][k]=0.; + } + } + pos = rot_stat_idx[cpos][5]+nsc*m; + for (j=0;j<nsc;j++) { + for (k=0;k<3;k++) { + sc[j][k] = rot_stat_coords[pos+j][k]; + } + } + superimpose2(vv,lsys,3,sc,nsc); + for (j=0;j<nsc;j++) { + sc[j][0] += x3; + sc[j][1] += y3; + sc[j][2] += z3; + } + cmx = 0.; cmy = 0.; cmz = 0.; + for (j=0;j<nsc;j++) { + cmx += sc[j][0]; + cmy += sc[j][1]; + cmz += sc[j][2]; + } + cmx /= (real) nsc; + cmy /= (real) nsc; + cmz /= (real) nsc; + ddx = res->cmx-cmx; + ddy = res->cmy-cmy; + ddz = res->cmz-cmz; + ddx *= ddx; + ddy *= ddy; + ddz *= ddz; + ddd = ddx+ddy+ddz; + if (ddd<bestdd) { + bestdd = ddd; + crot = pos; // closest rotamer position + } + } + } + pos = crot; + } // PDB_SG + + for (j=0;j<3;j++) { + vv[0][j] = v1[j]; vv[1][j] = v2[j]; vv[2][j] = v3[j]; + for (k=0;k<3;k++) { + if (j==k) lsys[j][k]=1.; else lsys[j][k]=0.; + } + } + + for (j=0;j<nsc;j++) { + for (k=0;k<3;k++) { + sc[j][k] = rot_stat_coords[pos+j][k]; + } + } + + superimpose2(vv,lsys,3,sc,nsc); + + for (j=0;j<nsc;j++) { + sc[j][0] += x3; + sc[j][1] += y3; + sc[j][2] += z3; + } + + for (j=1;j<nsc;j++) { + add_replace(res, heavy_atoms[10*res->type+j-1], sc[j][0], sc[j][1], sc[j][2], FLAG_SIDECHAIN); + } + + if (res->next) res = res->next; + + } // i++, next res + + for (i=0;i<12;i++) + free(sc[i]); + for (i=0;i<3;i++) { + free(lsys[i]); + free(vv[i]); + } + free(sc); + free(lsys); + free(vv); +} + + +typedef struct _atom_list { + atom_type *atom; + struct _atom_list *next; +} atom_list; + +int get_conflicts(res_type *res, atom_list ****grid, int xgrid, int ygrid, int zgrid) +{ + atom_list *llist; + atom_type *atom, *atom2; + int i, j, k, x, y, z; + int ii, jj, kk, con, iter, maxcon, merged; + real dx, dy, dz, dd; + + con = 0; + atom = res->atoms; + while (atom) { + i = atom->gx; + j = atom->gy; + k = atom->gz; + for (ii=i-2;ii<=i+2;ii++) + for (jj=j-2;jj<=j+2;jj++) + for (kk=k-2;kk<=k+2;kk++) { + if (ii>=0 && ii<xgrid && jj>=0 && jj<ygrid && kk>=0 && kk<zgrid) { + llist = grid[ii][jj][kk]; + while (llist) { + atom2 = llist->atom; + if (atom && atom2 && res && atom2->res) { + merged=0; + if (res==atom2->res) { // self-xvol + if (atom->flag & FLAG_SIDECHAIN && atom2->flag & FLAG_SIDECHAIN) merged=1; + if (atom->flag & FLAG_BACKBONE && atom2->flag & FLAG_BACKBONE) merged=1; + if (atom->name[0]=='C' && atom->name[1]=='A' && atom2->name[0]=='C' && atom2->name[1]=='B') merged=1; + if (atom->name[0]=='C' && atom->name[1]=='B' && atom2->name[0]=='C' && atom2->name[1]=='A') merged=1; + if (res->name[0]=='P') { + if (atom->name[0]=='C' && atom->name[1]=='D' && atom2->name[0]=='N' && atom2->name[1]==' ') merged=1; + if (atom->name[0]=='N' && atom->name[1]==' ' && atom2->name[0]=='C' && atom2->name[1]=='D') merged=1; + } + + if (!merged) { +// printf("merged: %s[%d] %s-%s %d %d\n", res->name,res->num,atom->name,atom2->name,atom->flag,atom2->flag); + } + } else + if (res->next==atom2->res || res==atom2->res->next) { + if (atom->name[0]=='C' && atom->name[1]==' ' && atom2->name[0]=='N' && atom2->name[1]==' ') merged=1; + if (atom->name[0]=='N' && atom->name[1]==' ' && atom2->name[0]=='C' && atom2->name[1]==' ') merged=1; + } + if (atom->flag & FLAG_BACKBONE && atom2->flag & FLAG_BACKBONE) merged=1; // for now + if (atom->flag & FLAG_SCM || atom2->flag & FLAG_SCM) merged=1; // for now + if (!merged) { + dx = atom->x-atom2->x; + dx*=dx; + dy = atom->y-atom2->y; + dy*=dy; + dz = atom->z-atom2->z; + dz*=dz; + dd = dx+dy+dz; + if (dd<_SG_XVOL_DIST*_SG_XVOL_DIST) { + con++; + } + } + } + llist = llist->next; + } + } + } + atom = atom->next; + } + + return con; +} + +int display_conflicts(res_type *res, atom_list ****grid, int xgrid, int ygrid, int zgrid) +{ + atom_list *llist; + atom_type *atom, *atom2; + int i, j, k, x, y, z; + int ii, jj, kk, con, iter, maxcon, merged; + real dx, dy, dz, dd; + + con = 0; + atom = res->atoms; + while (atom) { + i = atom->gx; + j = atom->gy; + k = atom->gz; + for (ii=i-2;ii<=i+2;ii++) + for (jj=j-2;jj<=j+2;jj++) + for (kk=k-2;kk<=k+2;kk++) { + if (ii>=0 && ii<xgrid && jj>=0 && jj<ygrid && kk>=0 && kk<zgrid) { + llist = grid[ii][jj][kk]; + while (llist) { + atom2 = llist->atom; + if (atom && atom2 && res && atom2->res) { + merged=0; + if (res==atom2->res) { // self-xvol + if (atom->flag & FLAG_SIDECHAIN && atom2->flag & FLAG_SIDECHAIN) merged=1; + if (atom->flag & FLAG_BACKBONE && atom2->flag & FLAG_BACKBONE) merged=1; + if (atom->name[0]=='C' && atom->name[1]=='A' && atom2->name[0]=='C' && atom2->name[1]=='B') merged=1; + if (atom->name[0]=='C' && atom->name[1]=='B' && atom2->name[0]=='C' && atom2->name[1]=='A') merged=1; + if (res->name[0]=='P') { + if (atom->name[0]=='C' && atom->name[1]=='D' && atom2->name[0]=='N' && atom2->name[1]==' ') merged=1; + if (atom->name[0]=='N' && atom->name[1]==' ' && atom2->name[0]=='C' && atom2->name[1]=='D') merged=1; + } + if (!merged) { +// printf("merged: %s[%d] %s-%s %d %d\n", res->name,res->num,atom->name,atom2->name,atom->flag,atom2->flag); + } + } else + if (res->next==atom2->res || res==atom2->res->next) { + if (atom->name[0]=='C' && atom->name[1]==' ' && atom2->name[0]=='N' && atom2->name[1]==' ') merged=1; + if (atom->name[0]=='N' && atom->name[1]==' ' && atom2->name[0]=='C' && atom2->name[1]==' ') merged=1; + } + if (atom->flag & FLAG_BACKBONE && atom2->flag & FLAG_BACKBONE) merged=1; // for now + if (atom->flag & FLAG_SCM || atom2->flag & FLAG_SCM) merged=1; // for now + if (!merged) { + dx = atom->x-atom2->x; + dx*=dx; + dy = atom->y-atom2->y; + dy*=dy; + dz = atom->z-atom2->z; + dz*=dz; + dd = dx+dy+dz; + if (dd<1.6*1.6) { + printf("STERIC CONFLICT: %s[%d]%s-%s[%d]%s\n", atom->res->name,atom->res->num,atom->name,atom2->res->name,atom2->res->num,atom2->name); + con++; + } + } + } + llist = llist->next; + } + } + } + atom = atom->next; + } + + return con; +} + + +void allocate_grid(atom_list *****grid_, int *xgrid_, int *ygrid_, int *zgrid_) +{ + static int xgrid, ygrid, zgrid; + static atom_list ****grid = NULL; + atom_list *llist, *alist; + real min[3], max[3]; + res_type *res, *worst; + atom_type *atom, *atom2; + int i, j, x, y, z; + + if (!grid && chain->residua && chain->residua->atoms) { + res = chain->residua; + min[0]=max[0]=res->atoms->x; + min[1]=max[1]=res->atoms->y; + min[2]=max[2]=res->atoms->z; + while (res) { + atom = res->atoms; + while (atom) { + if (atom->x<min[0]) min[0]=atom->x; + if (atom->y<min[1]) min[1]=atom->y; + if (atom->z<min[2]) min[2]=atom->z; + if (atom->x>max[0]) max[0]=atom->x; + if (atom->y>max[1]) max[1]=atom->y; + if (atom->z>max[2]) max[2]=atom->z; + atom = atom->next; + } + res = res->next; + } + + xgrid = (max[0]-min[0])/GRID_RES; + ygrid = (max[1]-min[1])/GRID_RES; + zgrid = (max[2]-min[2])/GRID_RES; + + if (_VERBOSE) printf("Allocating grid (%d %d %d)...\n", xgrid, ygrid, zgrid); + + grid = (atom_list****)calloc(sizeof(atom_list***)*(xgrid+1),1); + for (i=0;i<xgrid+1;i++) { + grid[i] = (atom_list***)calloc(sizeof(atom_list**)*(ygrid+1),1); + for (j=0;j<ygrid+1;j++) { + grid[i][j] = (atom_list**)calloc(sizeof(atom_list*)*(zgrid+1),1); + } + } + + res = chain->residua; + while (res) { + atom = res->atoms; + while (atom) { + x = xgrid*(atom->x-min[0])/(max[0]-min[0]); + y = ygrid*(atom->y-min[1])/(max[1]-min[1]); + z = zgrid*(atom->z-min[2])/(max[2]-min[2]); + alist = (atom_list*)calloc(sizeof(atom_list),1); + alist->atom = atom; + atom->gx = x; + atom->gy = y; + atom->gz = z; + if (grid[x][y][z]!=NULL) { + llist = grid[x][y][z]; + while (llist->next) llist=llist->next; + llist->next = alist; + } else { + grid[x][y][z]=alist; + } + atom = atom->next; + } + res = res->next; + } + } else { + if (_VERBOSE) printf("Grid already allocated (%d %d %d)\n", xgrid, ygrid, zgrid); + } + + *grid_ = grid; + *xgrid_ = xgrid; + *ygrid_ = ygrid; + *zgrid_ = zgrid; +} + +void optimize_exvol(void) +{ + real min[3], max[3]; + res_type *res, *worst; + atom_type *atom, *atom2; + int xgrid, ygrid, zgrid; + atom_list ****grid, *llist, *alist; + int i, j, k, l, m, x, y, z; + int ii, jj, kk, con, iter, maxcon, totcon; + int cpos, bestpos, pos, con0; + real v1[3], v2a[3], v2b[3], v2[3], v3[3]; + int nsc, nca; + real cax, cay, caz; + real **lsys, **vv, **sc; + real x1, y1, z1; + real x2, y2, z2; + real x3, y3, z3; + real x4, y4, z4; + + min[0]=1e5; + min[1]=1e5; + min[2]=1e5; + max[0]=-1e5; + max[1]=-1e5; + max[2]=-1e5; + + lsys = (real**)calloc(sizeof(real*)*3,1); + vv = (real**)calloc(sizeof(real*)*3,1); + sc = (real**)calloc(sizeof(real*)*12,1); + for (i=0;i<12;i++) + sc[i] = (real*)calloc(sizeof(real)*3,1); + for (i=0;i<3;i++) { + lsys[i] = (real*)calloc(sizeof(real)*3,1); + vv[i] = (real*)calloc(sizeof(real)*3,1); + } + + allocate_grid(&grid, &xgrid, &ygrid, &zgrid); + + if (_VERBOSE) printf("Finding excluded volume conflicts...\n"); + + iter = 0; + + do { +//printf("ITER: %d\n", iter); + + maxcon = 0; + totcon=0; + + res = chain->residua; + while (res) { + if (res->protein) { + con = get_conflicts(res, grid, xgrid, ygrid, zgrid); + if (con>0) { + totcon+=con; + if (con>maxcon) { + maxcon = con; + worst = res; + } + } + } + res = res->next; + } + + if (_VERBOSE && iter==0) { + printf("Total number of conflicts: %d\n", totcon); + } + + if (totcon==0) break; + + if (_VERBOSE && iter==0) { + printf("Maximum number of conflicts: %s[%d] : %d\n", worst->name, worst->num, maxcon); + } + + totcon=0; + + if (maxcon>0) { + +// try to fix... + + res = chain->residua; + for (i=0;i<chain_length;i++) { + if (!strncmp(res->name,"GLY",3) || !res->protein) { + if (res->next) res = res->next; + continue; + } + + nsc = nheavy[res->type]+1; + + x1 = C_ALPHA[i-2][0]; + y1 = C_ALPHA[i-2][1]; + z1 = C_ALPHA[i-2][2]; + x2 = C_ALPHA[i-1][0]; + y2 = C_ALPHA[i-1][1]; + z2 = C_ALPHA[i-1][2]; + x3 = C_ALPHA[i][0]; + y3 = C_ALPHA[i][1]; + z3 = C_ALPHA[i][2]; + x4 = C_ALPHA[i+1][0]; + y4 = C_ALPHA[i+1][1]; + z4 = C_ALPHA[i+1][2]; + + v1[0] = x4-x2; + v1[1] = y4-y2; + v1[2] = z4-z2; + + v2a[0] = x4-x3; + v2a[1] = y4-y3; + v2a[2] = z4-z3; + + v2b[0] = x3-x2; + v2b[1] = y3-y2; + v2b[2] = z3-z2; + + cross(v2a, v2b, v2); + cross(v1, v2, v3); + + norm(v1); + norm(v2); + norm(v3); + + con = get_conflicts(res, grid, xgrid, ygrid, zgrid); + + if (con>0) { + + bestpos=0; + con0 = 100; + for (l=0;l<10;l++) { // check two closest conformations + cpos = SORTED_ROTAMERS[i][l][1]; + for (m=0;m<rot_stat_idx[cpos][4];m++) { + for (j=0;j<3;j++) { + vv[0][j] = v1[j]; vv[1][j] = v2[j]; vv[2][j] = v3[j]; + for (k=0;k<3;k++) { + if (j==k) lsys[j][k]=1.; else lsys[j][k]=0.; + } + } + pos = rot_stat_idx[cpos][5]+nsc*m; + for (j=0;j<nsc;j++) { + for (k=0;k<3;k++) { + sc[j][k] = rot_stat_coords[pos+j][k]; + } + } + superimpose2(vv,lsys,3,sc,nsc); + for (j=0;j<nsc;j++) { + sc[j][0] += x3; + sc[j][1] += y3; + sc[j][2] += z3; + } + for (j=1;j<nsc;j++) { + add_replace(res, heavy_atoms[10*res->type+j-1], sc[j][0], sc[j][1], sc[j][2], FLAG_SIDECHAIN); + } + con = get_conflicts(res, grid, xgrid, ygrid, zgrid); +//printf("test: %d\n", con); + + if (con<con0) { + con0 = con; + bestpos = pos; + } + if (con==0) break; + } + if (con==0) break; + } + + totcon += con0; + + for (j=0;j<3;j++) { + vv[0][j] = v1[j]; vv[1][j] = v2[j]; vv[2][j] = v3[j]; + for (k=0;k<3;k++) { + if (j==k) lsys[j][k]=1.; else lsys[j][k]=0.; + } + } + pos = bestpos; + for (j=0;j<nsc;j++) { + for (k=0;k<3;k++) { + sc[j][k] = rot_stat_coords[pos+j][k]; + } + } + superimpose2(vv,lsys,3,sc,nsc); + for (j=0;j<nsc;j++) { + sc[j][0] += x3; + sc[j][1] += y3; + sc[j][2] += z3; + } + for (j=1;j<nsc;j++) { + add_replace(res, heavy_atoms[10*res->type+j-1], sc[j][0], sc[j][1], sc[j][2], FLAG_SIDECHAIN); + } + } + + + + res=res->next; + + } // i + } + + iter++; + + } while (iter<_XVOL_ITER); + + + if (_VERBOSE) { + if (totcon>0) + printf("WARNING: %d steric conflict(s) are still there.\n", totcon); + else + printf("All steric conflicts removed.\n"); + } + + for (i=0;i<12;i++) + free(sc[i]); + for (i=0;i<3;i++) { + free(lsys[i]); + free(vv[i]); + } + free(sc); + free(lsys); + free(vv); + + +} + + +void vcross(real ax,real ay,real az,real bx,real by,real bz,real *cx,real *cy,real *cz) +{ + *cx = ay * bz - by * az; + *cy = az * bx - bz * ax; + *cz = ax * by - bx * ay; +} + +real vdot(real ax,real ay,real az,real bx,real by,real bz) +{ + return ax*bx+ay*by+az*bz; +} + +real calc_torsion(atom_type *a1, atom_type *a2, atom_type *a3, atom_type *a4) +{ + real v12x, v12y, v12z; + real v43x, v43y, v43z; + real zx, zy, zz; + real px, py, pz; + real xx, xy, xz; + real yx, yy, yz; + real u, v, angle; + + v12x = a1->x-a2->x; + v12y = a1->y-a2->y; + v12z = a1->z-a2->z; + + v43x = a4->x-a3->x; + v43y = a4->y-a3->y; + v43z = a4->z-a3->z; + + zx = a2->x-a3->x; + zy = a2->y-a3->y; + zz = a2->z-a3->z; + + vcross(zx,zy,zz,v12x,v12y,v12z,&px,&py,&pz); + vcross(zx,zy,zz,v43x,v43y,v43z,&xx,&xy,&xz); + vcross(zx,zy,zz,xx,xy,xz,&yx,&yy,&yz); + + u = vdot(xx,xy,xz,xx,xy,xz); + v = vdot(yx,yy,yz,yx,yy,yz); + + angle = 360.; + + if (u<0. || v<0.) return angle; + + u = vdot(px,py,pz,xx,xy,xz) / sqrt(u); + v = vdot(px,py,pz,yx,yy,yz) / sqrt(v); + + if (u != 0.0 || v != 0.0) angle = atan2(v, u) * RADDEG; + + + return angle; + +} + + +// Ca-N-C-Cb angle should be close to 34 deg + +void chirality_check(void) +{ + int i; + atom_type *a_ca, *a_n, *a_c, *a_cb; + atom_type *atom; + res_type *res; + real angle; + real nx, ny, nz; + real px, py, pz; + real qx, qy, qz; + real rx, ry, rz; + real xx, xy, xz; + real yx, yy, yz; + real dd, costheta, sintheta; + + if (_VERBOSE) printf("Checking chirality...\n"); + res = chain->residua; + while (res) { + a_ca = a_n = a_c = a_cb = NULL; + a_ca = find_atom(res,"CA "); + a_n = find_atom(res,"N "); + a_c = find_atom(res,"C "); + a_cb = find_atom(res,"CB "); + if (a_ca && a_n && a_c && a_cb) { + angle = calc_torsion(a_ca, a_n, a_c, a_cb); + if (angle<0.) { + if (_VERBOSE) printf("WARNING: D-aa detected at %s %3d : %5.2f", res->name, res->num, angle); + xx = a_ca->x-a_n->x; + xy = a_ca->y-a_n->y; + xz = a_ca->z-a_n->z; + yx = a_c->x-a_ca->x; + yy = a_c->y-a_ca->y; + yz = a_c->z-a_ca->z; + vcross(xx,xy,xz,yx,yy,yz,&nx,&ny,&nz); + dd = sqrt(nx*nx+ny*ny+nz*nz); + nx /= dd; + ny /= dd; + nz /= dd; + // nx, ny, nz = reflection plane normal + rx = xx-yx; + ry = xy-yy; + rz = xz-yz; + dd = sqrt(rx*rx+ry*ry+rz*rz); + rx /= dd; + ry /= dd; + rz /= dd; + costheta = -1.; + sintheta = 0.; + atom = res->atoms; + while (atom) { + if (atom->flag & FLAG_SIDECHAIN) { + px = atom->x-a_ca->x; + py = atom->y-a_ca->y; + pz = atom->z-a_ca->z; + qx = qy = qz = 0.; + qx += (costheta + (1 - costheta) * rx * rx) * px; + qx += ((1 - costheta) * rx * ry - rz * sintheta) * py; + qx += ((1 - costheta) * rx * rz + ry * sintheta) * pz; + qy += ((1 - costheta) * rx * ry + rz * sintheta) * px; + qy += (costheta + (1 - costheta) * ry * ry) * py; + qy += ((1 - costheta) * ry * rz - rx * sintheta) * pz; + qz += ((1 - costheta) * rx * rz - ry * sintheta) * px; + qz += ((1 - costheta) * ry * rz + rx * sintheta) * py; + qz += (costheta + (1 - costheta) * rz * rz) * pz; + qx += a_ca->x; + qy += a_ca->y; + qz += a_ca->z; + atom->x = qx; + atom->y = qy; + atom->z = qz; + } + atom = atom->next; + } + angle = calc_torsion(a_ca, a_n, a_c, a_cb); + if (_VERBOSE) printf(", fixed : %5.2f\n", angle); + } + } + res = res->next; + } +} + + +#endif + +real hb_energy(res_type *res, atom_list ****grid, int xgrid, int ygrid, int zgrid) +{ + atom_type *atom, *c_atom1, *o_atom1, *n_atom1, *c_atom2, *o_atom2, *n_atom2, *tmp_atom; + atom_type h_atom; + int i, j, k, ii, jj, kk; + atom_list *llist, *alist; + real dx, dy, dz, dist, min_dist1, min_dist2; + real hx1, hy1, hz1, dd; + real dno, dnc, dho, dhc; + real ene, Q; + + ene = 1e3; + + if (!res || !res->prev) return ene; + + Q = -27888.0; // DSSP h-bond energy constant + + c_atom1 = o_atom1 = n_atom1 = NULL; + + atom = res->prev->atoms; + while (atom) { + if (atom->name[0]=='C' && atom->name[1]==' ') c_atom1 = atom; + if (atom->name[0]=='O' && atom->name[1]==' ') o_atom1 = atom; + atom = atom->next; + } + + atom = res->atoms; + while (atom) { + if (atom->name[0]=='N' && atom->name[1]==' ') { n_atom1 = atom; break; } + atom = atom->next; + } + +// first bond + + min_dist2 = 1e10; + o_atom2 = c_atom2 = NULL; + if (n_atom1) { + i = n_atom1->gx; + j = n_atom1->gy; + k = n_atom1->gz; + for (ii=i-1;ii<=i+1;ii++) { + for (jj=j-1;jj<=j+1;jj++) { + for (kk=k-1;kk<=k+1;kk++) { + if (ii>=0 && ii<xgrid && jj>=0 && jj<ygrid && kk>=0 && kk<=zgrid) { + llist = grid[ii][jj][kk]; + while (llist) { + if (llist->atom->name[0]=='O' && llist->atom->name[1]==' ' && abs(llist->atom->res->locnum-n_atom1->res->locnum)>2) { + tmp_atom = llist->atom; + dx = n_atom1->x-tmp_atom->x; + dy = n_atom1->y-tmp_atom->y; + dz = n_atom1->z-tmp_atom->z; + dist = dx*dx+dy*dy+dz*dz; + if (dist<min_dist2 && dist<25.0) { + o_atom2=tmp_atom; + min_dist2 = dist; + } + } + llist = llist->next; + } + } + } + } + } + } + + if (o_atom2) { + atom = o_atom2->res->atoms; + while (atom) { + if (atom->name[0]=='C' && atom->name[1]==' ') { c_atom2 = atom; break; } + atom = atom->next; + } + if (c_atom2) { + hx1 = o_atom1->x-c_atom1->x; + hy1 = o_atom1->y-c_atom1->y; + hz1 = o_atom1->z-c_atom1->z; + dd = -1.081f/sqrt(hx1*hx1+hy1*hy1+hz1*hz1); + hx1 *= dd; + hy1 *= dd; + hz1 *= dd; + + hx1 += n_atom1->x; + hy1 += n_atom1->y; + hz1 += n_atom1->z; + + add_replace(n_atom1->res, "H ", hx1, hy1, hz1, FLAG_BACKBONE); + + // dno + dx = n_atom1->x-o_atom2->x; + dy = n_atom1->y-o_atom2->y; + dz = n_atom1->z-o_atom2->z; + dno = sqrt(dx*dx+dy*dy+dz*dz); + + // dnc + dx = n_atom1->x-c_atom2->x; + dy = n_atom1->y-c_atom2->y; + dz = n_atom1->z-c_atom2->z; + dnc = sqrt(dx*dx+dy*dy+dz*dz); + + // dho + dx = hx1-o_atom2->x; + dy = hy1-o_atom2->y; + dz = hz1-o_atom2->z; + dho = sqrt(dx*dx+dy*dy+dz*dz); + + // dhc + dx = hx1-c_atom2->x; + dy = hy1-c_atom2->y; + dz = hz1-c_atom2->z; + dhc = sqrt(dx*dx+dy*dy+dz*dz); + + if (dho<0.01F || dhc<0.01F || dnc<0.01F || dno<0.01F) { + ene = -10.0; + } else { + ene = 0.001*(Q/dho - Q/dhc + Q/dnc - Q/dno); + } + } + } + +/****** +// second bond + + min_dist2 = 1e10; + n_atom2 = NULL; + if (n_atom1) { + i = o_atom1->gx; + j = o_atom1->gy; + k = o_atom1->gz; + for (ii=i-1;ii<=i+1;ii++) { + for (jj=j-1;jj<=j+1;jj++) { + for (kk=k-1;kk<=k+1;kk++) { + if (ii>=0 && ii<xgrid && jj>=0 && jj<ygrid && kk>=0 && kk<=zgrid) { + llist = grid[ii][jj][kk]; + while (llist) { + if (llist->atom->name[0]=='N' && llist->atom->name[1]==' ' && (abs(llist->atom->res->locnum-n_atom1->res->locnum)>2)) { + tmp_atom = llist->atom; + if (tmp_atom->res!=c_atom2->res) { + dx = o_atom1->x-tmp_atom->x; + dy = o_atom1->y-tmp_atom->y; + dz = o_atom1->z-tmp_atom->z; + dist = dx*dx+dy*dy+dz*dz; + if (dist<min_dist2 && dist<25.0) { + n_atom2=tmp_atom; + min_dist2 = dist; + } + } + } + llist = llist->next; + } + } + } + } + } + } + + if (n_atom2) { + c_atom2 = o_atom2 = NULL; + atom = n_atom2->res->atoms; + while (atom) { + if (atom->name[0]=='C' && atom->name[1]==' ') { c_atom2 = atom; } + if (atom->name[0]=='O' && atom->name[1]==' ') { c_atom2 = atom; } + atom = atom->next; + } + + if (c_atom2) { + hx1 = o_atom1->x-c_atom1->x; + hy1 = o_atom1->y-c_atom1->y; + hz1 = o_atom1->z-c_atom1->z; + dd = -1.081f/sqrt(hx1*hx1+hy1*hy1+hz1*hz1); + hx1 *= dd; + hy1 *= dd; + hz1 *= dd; + + hx1 += n_atom1->x; + hy1 += n_atom1->y; + hz1 += n_atom1->z; + + } +*******/ + + + return ene; +} + +// rotates a point around a vector +void rot_point_vector(real *x, real *y, real *z, real u, real v, real w, real angle) +{ + real ux, uy, uz, vx, vy, vz, wx, wy, wz, sa, ca; + + sa = sinf(10.0*M_PI*angle/180.0); + ca = cosf(10.0*M_PI*angle/180.0); + + ux = u**x; + uy = u**y; + uz = u**z; + vx = v**x; + vy = v**y; + vz = v**z; + wx = w**x; + wy = w**y; + wz = w**z; + + *x = u*(ux+vy+wz)+(*x*(v*v+w*w)-u*(vy+wz))*ca+(-wy+vz)*sa; + *y = v*(ux+vy+wz)+(*y*(u*u+w*w)-v*(ux+wz))*ca+( wx-uz)*sa; + *z = w*(ux+vy+wz)+(*z*(u*u+v*v)-w*(ux+vy))*ca+(-vx+uy)*sa; +} + + +// rotates a peptide plate + +void rot_peptide(res_type *res, real angle) +{ + atom_type *atom, *c_atom, *o_atom, *n_atom, *ca_atom1, *ca_atom2; + real u, v, w, x, y, z, dd; + + if (!res || !res->prev) return; + + c_atom = o_atom = n_atom = ca_atom1 = ca_atom2 = NULL; + + atom = res->prev->atoms; + while (atom) { + if (atom->name[0]=='C' && atom->name[1]=='A') ca_atom1 = atom; + if (atom->name[0]=='C' && atom->name[1]==' ') c_atom = atom; + if (atom->name[0]=='O' && atom->name[1]==' ') o_atom = atom; + atom = atom->next; + } + + atom = res->atoms; + while (atom) { + if (atom->name[0]=='C' && atom->name[1]=='A') ca_atom2 = atom; + if (atom->name[0]=='N' && atom->name[1]==' ') n_atom = atom; + atom = atom->next; + } + + if (c_atom && o_atom && n_atom && ca_atom1 && ca_atom2) { + u = ca_atom2->x-ca_atom1->x; + v = ca_atom2->y-ca_atom1->y; + w = ca_atom2->z-ca_atom1->z; + dd = 1.0f/sqrt(u*u+v*v+w*w); + u*=dd; v*=dd; w*=dd; // normalize ca-ca vector + x = n_atom->x-ca_atom1->x; + y = n_atom->y-ca_atom1->y; + z = n_atom->z-ca_atom1->z; + rot_point_vector(&x, &y, &z, u, v, w, angle); + n_atom->x = x+ca_atom1->x; + n_atom->y = y+ca_atom1->y; + n_atom->z = z+ca_atom1->z; + x = c_atom->x-ca_atom1->x; + y = c_atom->y-ca_atom1->y; + z = c_atom->z-ca_atom1->z; + rot_point_vector(&x, &y, &z, u, v, w, angle); + c_atom->x = x+ca_atom1->x; + c_atom->y = y+ca_atom1->y; + c_atom->z = z+ca_atom1->z; + x = o_atom->x-ca_atom1->x; + y = o_atom->y-ca_atom1->y; + z = o_atom->z-ca_atom1->z; + rot_point_vector(&x, &y, &z, u, v, w, angle); + o_atom->x = x+ca_atom1->x; + o_atom->y = y+ca_atom1->y; + o_atom->z = z+ca_atom1->z; + } + +} + +void optimize_backbone(mol_type *chain) +{ + int xgrid, ygrid, zgrid; + atom_list ****grid; + atom_type *atom; + res_type *res; + real ene, min_ene, tot1, tot2; + int i, k, best; + FILE *out; + + if (_VERBOSE) printf("Optimizing backbone...\n"); + + allocate_grid(&grid, &xgrid, &ygrid, &zgrid); + + tot1 = tot2 = 0.0; + + res = chain->residua; + while (res) { + ene = hb_energy(res, grid, xgrid, ygrid, zgrid); + if (ene<-0.5) tot1 += ene; + res = res->next; + } + + res = chain->residua; + while (res) { + if (res->type!=7) { + ene = hb_energy(res, grid, xgrid, ygrid, zgrid); + if (ene<1.0) { // try to optimize + min_ene = ene; + rot_peptide(res, -1.1); + best = 0; + for (i=-10;i<10;i++) { + rot_peptide(res, 0.1); + ene = hb_energy(res, grid, xgrid, ygrid, zgrid); + if (ene<min_ene) { + best = i; + min_ene = ene; + } + } + rot_peptide(res,-0.9); + ene = hb_energy(res, grid, xgrid, ygrid, zgrid); + if (min_ene<ene) { + rot_peptide(res,0.1*best); + ene = hb_energy(res, grid, xgrid, ygrid, zgrid); + } + } + } + res = res->next; + } + + res = chain->residua; + while (res) { + ene = hb_energy(res, grid, xgrid, ygrid, zgrid); + if (ene<-0.5) tot2 += ene; + res = res->next; + } + + if (_VERBOSE) printf("Backbone HB energy: before %g, after: %g, difference: %g\n", tot1, tot2, tot2-tot1); + +} + +int main(int argc, char **argv) +{ + int i, j, next; + char buf[100]; + char *name=NULL, *ini_name=NULL; + char *ptr, out_name[1000]; + real f; + mol_type *mol; + struct timeb time0, time1; + + for (i=1; i<argc; i++) { + if (argv[i][0]=='-') { + next=0; + for (j=1; j<(int)strlen(argv[i]); j++) { + switch(argv[i][j]) { + case 'v': _VERBOSE=1; break; + case 'c': _CA_OPTIMIZE=0; break; + case 'e': _BB_REARRANGE=1; break; + case 'r': _CA_RANDOM=1; break; + case 'z': _CHIRAL=0; break; + case 't': _CA_TRAJECTORY=1; break; + case 'n': _CENTER_CHAIN=1; break; + case 'b': _REBUILD_BB=0; break; + case 's': _REBUILD_SC=0; break; + case 'i': ini_name = argv[++i]; next=1; break; + case 'g': _PDB_SG=1; break; + case 'x': _TIME_SEED=1; break; + case 'o': _XVOLUME=0; break; + case 'h': _REBUILD_H=0; break; + case 'q': _BB_OPTIMIZE=1; break; + case 'p': _CISPRO=1; break; + case 'u': + if (sscanf(argv[++i],"%lf",&f)==1) { + _CA_START_DIST = f; + } + next=1; + break; + default: { + printf("Unknown option: %c\n", argv[i][j]); + return -1; + } + } + if (next) break; + } + } else { + if (!name) name=argv[i]; + } + } + + if (!name) { + printf("PULCHRA Protein Chain Restoration Algorithm version %4.2f\n", PULCHRA_VERSION); + printf("Usage: %s [options] <pdb_file>\n", argv[0]); + printf("The program default input is a PDB file.\n"); + printf("Output file <pdb_file.rebuild.pdb> will be created as a result.\n"); + printf("Valid options are:\n\n"); + printf(" -v : verbose output (default: off)\n"); + printf(" -n : center chain (default: off)\n"); + printf(" -x : time-seed random number generator (default: off)\n"); + printf(" -g : use PDBSG as an input format (CA=C-alpha, SC or CM=side chain c.m.)\n\n"); + printf(" -c : skip C-alpha positions optimization (default: on)\n"); + printf(" -p : detect cis-prolins (default: off)\n"); + printf(" -r : start from a random chain (default: off)\n"); + printf(" -i pdbfile : read the initial C-alpha coordinates from a PDB file\n"); + printf(" -t : save chain optimization trajectory to file <pdb_file.pdb.trajectory>\n"); + printf(" -u value : maximum shift from the restraint coordinates (default: 0.5A)\n\n"); + printf(" -e : rearrange backbone atoms (C, O are output after side chain) (default: off)\n"); + +#ifdef COMPILE_BB + printf(" -b : skip backbone reconstruction (default: on)\n"); + printf(" -q : optimize backbone hydrogen bonds pattern (default: off)\n"); + printf(" -h : outputs hydrogen atoms (default: off)\n"); +#endif + +#ifdef COMPILE_ROT + printf(" -s : skip side chains reconstruction (default: on)\n"); + printf(" -o : don't attempt to fix excluded volume conflicts (default: on)\n"); + printf(" -z : don't check amino acid chirality (default: on)\n"); +#endif + printf("\n"); + return -1; + } + + for (i=0; i<255; i++) /* prepare hash table*/ + AA_NUMS[i] = 20; /* dummy aa code */ + for (i=0; i<20; i++) + AA_NUMS[(int)SHORT_AA_NAMES[i]] = i; + + setbuf(stdout,0); + + if (_TIME_SEED) srand(time(NULL)); else srand(1234); + + if (_VERBOSE) printf("PULCHRA Protein Chain Restoration Algorithm version %4.2f\n", PULCHRA_VERSION); + + ftime(&time0); + + chain = new_mol(); + + if (read_pdb_file(name,chain,"chain")==FILE_NOT_FOUND) { + if (_VERBOSE) printf("Can't read the input file!\n"); + return -1; + } + + if (_VERBOSE) printf("%d residua read.\n", chain->nres); + + chain_length = chain->nres; + + if (_CA_OPTIMIZE) { + snprintf(out_name,1000,"%s.tra",name); + ca_optimize(out_name, ini_name); + } + +#ifdef COMPILE_BB + if (_REBUILD_BB) { + rebuild_backbone(); + if (_BB_OPTIMIZE) { + optimize_backbone(chain); + } + } +#endif + +#ifdef COMPILE_ROT + if (_REBUILD_BB && _REBUILD_SC) { + rebuild_sidechains(); + if (_XVOLUME) + optimize_exvol(); + if (_CHIRAL) + chirality_check(); + } +#endif + + if (_CENTER_CHAIN) { + center_chain(chain); + } + + + if (_BB_REARRANGE) { + if (_VERBOSE) printf("Rearranging backbone atoms...\n"); + } + + ptr = strstr(name,".pdb"); + if (ptr) ptr[0]=0; + + snprintf(out_name,1000,"%s.rebuilt.pdb",name); + + if (_VERBOSE) printf("Writing output file %s...\n", out_name); + write_pdb(out_name, chain); + + ftime(&time1); + + if (_VERBOSE) printf("Done. Reconstruction finished in %.3f s.\n", (real)0.001*(1000.*(time1.time-time0.time)+(time1.millitm-time0.millitm))); + + return 0; +} +