/*
- *
+ *
* This source code is part of
- *
+ *
* G R O M A C S
- *
+ *
* GROningen MAchine for Chemical Simulations
- *
+ *
* VERSION 3.2.0
* Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* If you want to redistribute modifications, please consider that
* scientific software is very special. Version control is crucial -
* bugs must be traceable. We will be happy to consider code for
* inclusion in the official distribution, but derived work must not
* be called official GROMACS. Details are found in the README & COPYING
* files - if they are missing, get the official version at www.gromacs.org.
- *
+ *
* To help us fund GROMACS development, we humbly ask that you cite
* the papers on the package - you can find them in the top README file.
- *
+ *
* For more info, check our website at http://www.gromacs.org
- *
+ *
* And Hey:
* Green Red Orange Magenta Azure Cyan Skyblue
*/
#include "gstat.h"
#include "gmx_fatal.h"
#include "index.h"
-
-t_dlist *mk_dlist(FILE *log,
- t_atoms *atoms, int *nlist,
- gmx_bool bPhi, gmx_bool bPsi, gmx_bool bChi, gmx_bool bHChi,
- int maxchi, int r0, gmx_residuetype_t rt)
+
+t_dlist *mk_dlist(FILE *log,
+ t_atoms *atoms, int *nlist,
+ gmx_bool bPhi, gmx_bool bPsi, gmx_bool bChi, gmx_bool bHChi,
+ int maxchi, int r0, gmx_residuetype_t rt)
{
- int ires,i,j,k,ii;
- t_dihatms atm,prev;
- int nl=0,nc[edMax];
- char *thisres;
- t_dlist *dl;
-
- snew(dl,atoms->nres+1);
- prev.C = prev.O = -1;
- for(i=0; (i<edMax); i++)
- nc[i]=0;
- ires = -1;
- i = 0;
- while (i<atoms->nr) {
- ires = atoms->atom[i].resind;
-
- /* Initiate all atom numbers to -1 */
- atm.minC=atm.H=atm.N=atm.C=atm.O=atm.minO=-1;
- for(j=0; (j<MAXCHI+3); j++)
- atm.Cn[j]=-1;
-
- /* Look for atoms in this residue */
- /* maybe should allow for chis to hydrogens? */
- while ((i<atoms->nr) && (atoms->atom[i].resind == ires)) {
- if ((strcmp(*(atoms->atomname[i]),"H") == 0) ||
- (strcmp(*(atoms->atomname[i]),"H1") == 0) )
- atm.H=i;
- else if (strcmp(*(atoms->atomname[i]),"N") == 0)
- atm.N=i;
- else if (strcmp(*(atoms->atomname[i]),"C") == 0)
- atm.C=i;
- else if ((strcmp(*(atoms->atomname[i]),"O") == 0) ||
- (strcmp(*(atoms->atomname[i]),"O1") == 0))
- atm.O=i;
- else if (strcmp(*(atoms->atomname[i]),"CA") == 0)
- atm.Cn[1]=i;
- else if (strcmp(*(atoms->atomname[i]),"CB") == 0)
- atm.Cn[2]=i;
- else if ((strcmp(*(atoms->atomname[i]),"CG") == 0) ||
- (strcmp(*(atoms->atomname[i]),"CG1") == 0) ||
- (strcmp(*(atoms->atomname[i]),"OG") == 0) ||
- (strcmp(*(atoms->atomname[i]),"OG1") == 0) ||
- (strcmp(*(atoms->atomname[i]),"SG") == 0))
- atm.Cn[3]=i;
- else if ((strcmp(*(atoms->atomname[i]),"CD") == 0) ||
- (strcmp(*(atoms->atomname[i]),"CD1") == 0) ||
- (strcmp(*(atoms->atomname[i]),"SD") == 0) ||
- (strcmp(*(atoms->atomname[i]),"OD1") == 0) ||
- (strcmp(*(atoms->atomname[i]),"ND1") == 0))
- atm.Cn[4]=i;
- /* by grs - split the Cn[4] into 2 bits to check allowing dih to H */
- else if (bHChi && ((strcmp(*(atoms->atomname[i]),"HG") == 0) ||
- (strcmp(*(atoms->atomname[i]),"HG1") == 0)) )
- atm.Cn[4]=i;
- else if ((strcmp(*(atoms->atomname[i]),"CE") == 0) ||
- (strcmp(*(atoms->atomname[i]),"CE1") == 0) ||
- (strcmp(*(atoms->atomname[i]),"OE1") == 0) ||
- (strcmp(*(atoms->atomname[i]),"NE") == 0))
- atm.Cn[5]=i;
- else if ((strcmp(*(atoms->atomname[i]),"CZ") == 0) ||
- (strcmp(*(atoms->atomname[i]),"NZ") == 0))
- atm.Cn[6]=i;
- /* HChi flag here too */
- else if (bHChi && (strcmp(*(atoms->atomname[i]),"NH1") == 0))
- atm.Cn[7]=i;
- i++;
- }
+ int ires, i, j, k, ii;
+ t_dihatms atm, prev;
+ int nl = 0, nc[edMax];
+ char *thisres;
+ t_dlist *dl;
- thisres = *(atoms->resinfo[ires].name);
-
- /* added by grs - special case for aromatics, whose chis above 2 are
- not real and produce rubbish output - so set back to -1 */
- if (strcmp(thisres,"PHE") == 0 ||
- strcmp(thisres,"TYR") == 0 ||
- strcmp(thisres,"PTR") == 0 ||
- strcmp(thisres,"TRP") == 0 ||
- strcmp(thisres,"HIS") == 0 ||
- strcmp(thisres,"HISA") == 0 ||
- strcmp(thisres,"HISB") == 0 ) {
- for (ii=5 ; ii<=7 ; ii++)
- atm.Cn[ii]=-1;
+ snew(dl, atoms->nres+1);
+ prev.C = prev.O = -1;
+ for (i = 0; (i < edMax); i++)
+ {
+ nc[i] = 0;
}
- /* end fixing aromatics */
+ ires = -1;
+ i = 0;
+ while (i < atoms->nr)
+ {
+ ires = atoms->atom[i].resind;
+
+ /* Initiate all atom numbers to -1 */
+ atm.minC = atm.H = atm.N = atm.C = atm.O = atm.minO = -1;
+ for (j = 0; (j < MAXCHI+3); j++)
+ {
+ atm.Cn[j] = -1;
+ }
+
+ /* Look for atoms in this residue */
+ /* maybe should allow for chis to hydrogens? */
+ while ((i < atoms->nr) && (atoms->atom[i].resind == ires))
+ {
+ if ((strcmp(*(atoms->atomname[i]), "H") == 0) ||
+ (strcmp(*(atoms->atomname[i]), "H1") == 0) )
+ {
+ atm.H = i;
+ }
+ else if (strcmp(*(atoms->atomname[i]), "N") == 0)
+ {
+ atm.N = i;
+ }
+ else if (strcmp(*(atoms->atomname[i]), "C") == 0)
+ {
+ atm.C = i;
+ }
+ else if ((strcmp(*(atoms->atomname[i]), "O") == 0) ||
+ (strcmp(*(atoms->atomname[i]), "O1") == 0))
+ {
+ atm.O = i;
+ }
+ else if (strcmp(*(atoms->atomname[i]), "CA") == 0)
+ {
+ atm.Cn[1] = i;
+ }
+ else if (strcmp(*(atoms->atomname[i]), "CB") == 0)
+ {
+ atm.Cn[2] = i;
+ }
+ else if ((strcmp(*(atoms->atomname[i]), "CG") == 0) ||
+ (strcmp(*(atoms->atomname[i]), "CG1") == 0) ||
+ (strcmp(*(atoms->atomname[i]), "OG") == 0) ||
+ (strcmp(*(atoms->atomname[i]), "OG1") == 0) ||
+ (strcmp(*(atoms->atomname[i]), "SG") == 0))
+ {
+ atm.Cn[3] = i;
+ }
+ else if ((strcmp(*(atoms->atomname[i]), "CD") == 0) ||
+ (strcmp(*(atoms->atomname[i]), "CD1") == 0) ||
+ (strcmp(*(atoms->atomname[i]), "SD") == 0) ||
+ (strcmp(*(atoms->atomname[i]), "OD1") == 0) ||
+ (strcmp(*(atoms->atomname[i]), "ND1") == 0))
+ {
+ atm.Cn[4] = i;
+ }
+ /* by grs - split the Cn[4] into 2 bits to check allowing dih to H */
+ else if (bHChi && ((strcmp(*(atoms->atomname[i]), "HG") == 0) ||
+ (strcmp(*(atoms->atomname[i]), "HG1") == 0)) )
+ {
+ atm.Cn[4] = i;
+ }
+ else if ((strcmp(*(atoms->atomname[i]), "CE") == 0) ||
+ (strcmp(*(atoms->atomname[i]), "CE1") == 0) ||
+ (strcmp(*(atoms->atomname[i]), "OE1") == 0) ||
+ (strcmp(*(atoms->atomname[i]), "NE") == 0))
+ {
+ atm.Cn[5] = i;
+ }
+ else if ((strcmp(*(atoms->atomname[i]), "CZ") == 0) ||
+ (strcmp(*(atoms->atomname[i]), "NZ") == 0))
+ {
+ atm.Cn[6] = i;
+ }
+ /* HChi flag here too */
+ else if (bHChi && (strcmp(*(atoms->atomname[i]), "NH1") == 0))
+ {
+ atm.Cn[7] = i;
+ }
+ i++;
+ }
+
+ thisres = *(atoms->resinfo[ires].name);
+
+ /* added by grs - special case for aromatics, whose chis above 2 are
+ not real and produce rubbish output - so set back to -1 */
+ if (strcmp(thisres, "PHE") == 0 ||
+ strcmp(thisres, "TYR") == 0 ||
+ strcmp(thisres, "PTR") == 0 ||
+ strcmp(thisres, "TRP") == 0 ||
+ strcmp(thisres, "HIS") == 0 ||
+ strcmp(thisres, "HISA") == 0 ||
+ strcmp(thisres, "HISB") == 0)
+ {
+ for (ii = 5; ii <= 7; ii++)
+ {
+ atm.Cn[ii] = -1;
+ }
+ }
+ /* end fixing aromatics */
+
+ /* Special case for Pro, has no H */
+ if (strcmp(thisres, "PRO") == 0)
+ {
+ atm.H = atm.Cn[4];
+ }
+ /* Carbon from previous residue */
+ if (prev.C != -1)
+ {
+ atm.minC = prev.C;
+ }
+ if (prev.O != -1)
+ {
+ atm.minO = prev.O;
+ }
+ prev = atm;
- /* Special case for Pro, has no H */
- if (strcmp(thisres,"PRO") == 0)
- atm.H=atm.Cn[4];
- /* Carbon from previous residue */
- if (prev.C != -1)
- atm.minC = prev.C;
- if (prev.O != -1)
- atm.minO = prev.O;
- prev = atm;
-
- /* Check how many dihedrals we have */
- if ((atm.N != -1) && (atm.Cn[1] != -1) && (atm.C != -1) &&
- (atm.O != -1) && ((atm.H != -1) || (atm.minC != -1))) {
- dl[nl].resnr = ires+1;
- dl[nl].atm = atm;
- dl[nl].atm.Cn[0] = atm.N;
- if ((atm.Cn[3] != -1) && (atm.Cn[2] != -1) && (atm.Cn[1] != -1)) {
- nc[0]++;
- if (atm.Cn[4] != -1) {
- nc[1]++;
- if (atm.Cn[5] != -1) {
- nc[2]++;
- if (atm.Cn[6] != -1) {
- nc[3]++;
- if (atm.Cn[7] != -1) {
- nc[4]++;
- if (atm.Cn[8] != -1) {
- nc[5]++;
- }
- }
- }
- }
- }
- }
- if ((atm.minC != -1) && (atm.minO != -1))
- nc[6]++;
- dl[nl].index=gmx_residuetype_get_index(rt,thisres);
-
- sprintf(dl[nl].name,"%s%d",thisres,ires+r0);
- nl++;
+ /* Check how many dihedrals we have */
+ if ((atm.N != -1) && (atm.Cn[1] != -1) && (atm.C != -1) &&
+ (atm.O != -1) && ((atm.H != -1) || (atm.minC != -1)))
+ {
+ dl[nl].resnr = ires+1;
+ dl[nl].atm = atm;
+ dl[nl].atm.Cn[0] = atm.N;
+ if ((atm.Cn[3] != -1) && (atm.Cn[2] != -1) && (atm.Cn[1] != -1))
+ {
+ nc[0]++;
+ if (atm.Cn[4] != -1)
+ {
+ nc[1]++;
+ if (atm.Cn[5] != -1)
+ {
+ nc[2]++;
+ if (atm.Cn[6] != -1)
+ {
+ nc[3]++;
+ if (atm.Cn[7] != -1)
+ {
+ nc[4]++;
+ if (atm.Cn[8] != -1)
+ {
+ nc[5]++;
+ }
+ }
+ }
+ }
+ }
+ }
+ if ((atm.minC != -1) && (atm.minO != -1))
+ {
+ nc[6]++;
+ }
+ dl[nl].index = gmx_residuetype_get_index(rt, thisres);
+
+ sprintf(dl[nl].name, "%s%d", thisres, ires+r0);
+ nl++;
+ }
+ else if (debug)
+ {
+ fprintf(debug, "Could not find N atom but could find other atoms"
+ " in residue %s%d\n", thisres, ires+r0);
+ }
+ }
+ fprintf(stderr, "\n");
+ fprintf(log, "\n");
+ fprintf(log, "There are %d residues with dihedrals\n", nl);
+ j = 0;
+ if (bPhi)
+ {
+ j += nl;
+ }
+ if (bPsi)
+ {
+ j += nl;
+ }
+ if (bChi)
+ {
+ for (i = 0; (i < maxchi); i++)
+ {
+ j += nc[i];
+ }
+ }
+ fprintf(log, "There are %d dihedrals\n", j);
+ fprintf(log, "Dihedral: ");
+ if (bPhi)
+ {
+ fprintf(log, " Phi ");
+ }
+ if (bPsi)
+ {
+ fprintf(log, " Psi ");
}
- else if (debug)
- fprintf(debug,"Could not find N atom but could find other atoms"
- " in residue %s%d\n",thisres,ires+r0);
- }
- fprintf(stderr,"\n");
- fprintf(log,"\n");
- fprintf(log,"There are %d residues with dihedrals\n",nl);
- j=0;
- if (bPhi) j+=nl;
- if (bPsi) j+=nl;
- if (bChi)
- for(i=0; (i<maxchi); i++)
- j+=nc[i];
- fprintf(log,"There are %d dihedrals\n",j);
- fprintf(log,"Dihedral: ");
- if (bPhi)
- fprintf(log," Phi ");
- if (bPsi)
- fprintf(log," Psi ");
- if (bChi)
- for(i=0; (i<maxchi); i++)
- fprintf(log,"Chi%d ",i+1);
- fprintf(log,"\nNumber: ");
- if (bPhi)
- fprintf(log,"%4d ",nl);
- if (bPsi)
- fprintf(log,"%4d ",nl);
- if (bChi)
- for(i=0; (i<maxchi); i++)
- fprintf(log,"%4d ",nc[i]);
- fprintf(log,"\n");
-
- *nlist=nl;
+ if (bChi)
+ {
+ for (i = 0; (i < maxchi); i++)
+ {
+ fprintf(log, "Chi%d ", i+1);
+ }
+ }
+ fprintf(log, "\nNumber: ");
+ if (bPhi)
+ {
+ fprintf(log, "%4d ", nl);
+ }
+ if (bPsi)
+ {
+ fprintf(log, "%4d ", nl);
+ }
+ if (bChi)
+ {
+ for (i = 0; (i < maxchi); i++)
+ {
+ fprintf(log, "%4d ", nc[i]);
+ }
+ }
+ fprintf(log, "\n");
- return dl;
+ *nlist = nl;
+
+ return dl;
}
-gmx_bool has_dihedral(int Dih,t_dlist *dl)
+gmx_bool has_dihedral(int Dih, t_dlist *dl)
{
- gmx_bool b = FALSE;
- int ddd;
-
- switch (Dih) {
- case edPhi:
- b = ((dl->atm.H!=-1) && (dl->atm.N!=-1) && (dl->atm.Cn[1]!=-1) && (dl->atm.C!=-1));
- break;
- case edPsi:
- b = ((dl->atm.N!=-1) && (dl->atm.Cn[1]!=-1) && (dl->atm.C!=-1) && (dl->atm.O!=-1));
- break;
- case edOmega:
- b = ((dl->atm.minO!=-1) && (dl->atm.minC!=-1) && (dl->atm.N!=-1) && (dl->atm.Cn[1]!=-1));
- break;
- case edChi1:
- case edChi2:
- case edChi3:
- case edChi4:
- case edChi5:
- case edChi6:
- ddd = Dih - edChi1;
- b = ((dl->atm.Cn[ddd]!=-1) && (dl->atm.Cn[ddd+1]!=-1)&&
- (dl->atm.Cn[ddd+2]!=-1) && (dl->atm.Cn[ddd+3]!=-1));
- break;
- default:
- pr_dlist(stdout,1,dl,1,0,TRUE,TRUE,TRUE,TRUE,MAXCHI);
- gmx_fatal(FARGS,"Non existant dihedral %d in file %s, line %d",
- Dih,__FILE__,__LINE__);
- }
- return b;
+ gmx_bool b = FALSE;
+ int ddd;
+
+ switch (Dih)
+ {
+ case edPhi:
+ b = ((dl->atm.H != -1) && (dl->atm.N != -1) && (dl->atm.Cn[1] != -1) && (dl->atm.C != -1));
+ break;
+ case edPsi:
+ b = ((dl->atm.N != -1) && (dl->atm.Cn[1] != -1) && (dl->atm.C != -1) && (dl->atm.O != -1));
+ break;
+ case edOmega:
+ b = ((dl->atm.minO != -1) && (dl->atm.minC != -1) && (dl->atm.N != -1) && (dl->atm.Cn[1] != -1));
+ break;
+ case edChi1:
+ case edChi2:
+ case edChi3:
+ case edChi4:
+ case edChi5:
+ case edChi6:
+ ddd = Dih - edChi1;
+ b = ((dl->atm.Cn[ddd] != -1) && (dl->atm.Cn[ddd+1] != -1) &&
+ (dl->atm.Cn[ddd+2] != -1) && (dl->atm.Cn[ddd+3] != -1));
+ break;
+ default:
+ pr_dlist(stdout, 1, dl, 1, 0, TRUE, TRUE, TRUE, TRUE, MAXCHI);
+ gmx_fatal(FARGS, "Non existant dihedral %d in file %s, line %d",
+ Dih, __FILE__, __LINE__);
+ }
+ return b;
}
-static void pr_one_ro(FILE *fp,t_dlist *dl,int nDih,real dt)
+static void pr_one_ro(FILE *fp, t_dlist *dl, int nDih, real dt)
{
- int k ;
- for(k=0;k<NROT;k++)
- fprintf(fp," %6.2f",dl->rot_occ[nDih][k]);
- fprintf(fp,"\n");
+ int k;
+ for (k = 0; k < NROT; k++)
+ {
+ fprintf(fp, " %6.2f", dl->rot_occ[nDih][k]);
+ }
+ fprintf(fp, "\n");
}
-static void pr_ntr_s2(FILE *fp,t_dlist *dl,int nDih,real dt)
+static void pr_ntr_s2(FILE *fp, t_dlist *dl, int nDih, real dt)
{
- fprintf(fp," %6.2f %6.2f\n",(dt == 0) ? 0 : dl->ntr[nDih]/dt,dl->S2[nDih]);
+ fprintf(fp, " %6.2f %6.2f\n", (dt == 0) ? 0 : dl->ntr[nDih]/dt, dl->S2[nDih]);
}
-void pr_dlist(FILE *fp,int nl,t_dlist dl[],real dt, int printtype,
-gmx_bool bPhi, gmx_bool bPsi,gmx_bool bChi,gmx_bool bOmega, int maxchi)
+void pr_dlist(FILE *fp, int nl, t_dlist dl[], real dt, int printtype,
+ gmx_bool bPhi, gmx_bool bPsi, gmx_bool bChi, gmx_bool bOmega, int maxchi)
{
- int i, Xi;
+ int i, Xi;
- void (*pr_props)(FILE *, t_dlist *, int, real);
-
- /* Analysis of dihedral transitions etc */
+ void (*pr_props)(FILE *, t_dlist *, int, real);
- if (printtype == edPrintST){
- pr_props=pr_ntr_s2 ;
- fprintf(stderr,"Now printing out transitions and OPs...\n");
- }else{
- pr_props=pr_one_ro ;
- fprintf(stderr,"Now printing out rotamer occupancies...\n");
- fprintf(fp,"\nXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX\n\n");
- }
+ /* Analysis of dihedral transitions etc */
- /* change atom numbers from 0 based to 1 based */
- for(i=0; (i<nl); i++) {
- fprintf(fp,"Residue %s\n",dl[i].name);
- if (printtype == edPrintST){
- fprintf(fp," Angle [ AI, AJ, AK, AL] #tr/ns S^2D \n"
- "--------------------------------------------\n");
- } else {
- fprintf(fp," Angle [ AI, AJ, AK, AL] rotamers 0 g(-) t g(+)\n"
- "--------------------------------------------\n");
- }
- if (bPhi) {
- fprintf(fp," Phi [%5d,%5d,%5d,%5d]",
- (dl[i].atm.H == -1) ? 1+dl[i].atm.minC : 1+dl[i].atm.H,
- 1+dl[i].atm.N, 1+dl[i].atm.Cn[1], 1+dl[i].atm.C);
- pr_props(fp,&dl[i],edPhi,dt);
+ if (printtype == edPrintST)
+ {
+ pr_props = pr_ntr_s2;
+ fprintf(stderr, "Now printing out transitions and OPs...\n");
}
- if (bPsi) {
- fprintf(fp," Psi [%5d,%5d,%5d,%5d]",1+dl[i].atm.N, 1+dl[i].atm.Cn[1],
- 1+dl[i].atm.C, 1+dl[i].atm.O);
- pr_props(fp,&dl[i],edPsi,dt);
+ else
+ {
+ pr_props = pr_one_ro;
+ fprintf(stderr, "Now printing out rotamer occupancies...\n");
+ fprintf(fp, "\nXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX\n\n");
}
- if (bOmega && has_dihedral(edOmega,&(dl[i]))) {
- fprintf(fp," Omega [%5d,%5d,%5d,%5d]",1+dl[i].atm.minO, 1+dl[i].atm.minC,
- 1+dl[i].atm.N, 1+dl[i].atm.Cn[1]);
- pr_props(fp,&dl[i],edOmega,dt);
+
+ /* change atom numbers from 0 based to 1 based */
+ for (i = 0; (i < nl); i++)
+ {
+ fprintf(fp, "Residue %s\n", dl[i].name);
+ if (printtype == edPrintST)
+ {
+ fprintf(fp, " Angle [ AI, AJ, AK, AL] #tr/ns S^2D \n"
+ "--------------------------------------------\n");
+ }
+ else
+ {
+ fprintf(fp, " Angle [ AI, AJ, AK, AL] rotamers 0 g(-) t g(+)\n"
+ "--------------------------------------------\n");
+ }
+ if (bPhi)
+ {
+ fprintf(fp, " Phi [%5d,%5d,%5d,%5d]",
+ (dl[i].atm.H == -1) ? 1+dl[i].atm.minC : 1+dl[i].atm.H,
+ 1+dl[i].atm.N, 1+dl[i].atm.Cn[1], 1+dl[i].atm.C);
+ pr_props(fp, &dl[i], edPhi, dt);
+ }
+ if (bPsi)
+ {
+ fprintf(fp, " Psi [%5d,%5d,%5d,%5d]", 1+dl[i].atm.N, 1+dl[i].atm.Cn[1],
+ 1+dl[i].atm.C, 1+dl[i].atm.O);
+ pr_props(fp, &dl[i], edPsi, dt);
+ }
+ if (bOmega && has_dihedral(edOmega, &(dl[i])))
+ {
+ fprintf(fp, " Omega [%5d,%5d,%5d,%5d]", 1+dl[i].atm.minO, 1+dl[i].atm.minC,
+ 1+dl[i].atm.N, 1+dl[i].atm.Cn[1]);
+ pr_props(fp, &dl[i], edOmega, dt);
+ }
+ for (Xi = 0; Xi < MAXCHI; Xi++)
+ {
+ if (bChi && (Xi < maxchi) && (dl[i].atm.Cn[Xi+3] != -1) )
+ {
+ fprintf(fp, " Chi%d[%5d,%5d,%5d,%5d]", Xi+1, 1+dl[i].atm.Cn[Xi],
+ 1+dl[i].atm.Cn[Xi+1], 1+dl[i].atm.Cn[Xi+2],
+ 1+dl[i].atm.Cn[Xi+3]);
+ pr_props(fp, &dl[i], Xi+edChi1, dt); /* Xi+2 was wrong here */
+ }
+ }
+ fprintf(fp, "\n");
}
- for(Xi=0; Xi<MAXCHI; Xi++)
- if (bChi && (Xi < maxchi) && (dl[i].atm.Cn[Xi+3] != -1) ) {
- fprintf(fp," Chi%d[%5d,%5d,%5d,%5d]",Xi+1, 1+dl[i].atm.Cn[Xi],
- 1+dl[i].atm.Cn[Xi+1], 1+dl[i].atm.Cn[Xi+2],
- 1+dl[i].atm.Cn[Xi+3]);
- pr_props(fp,&dl[i],Xi+edChi1,dt); /* Xi+2 was wrong here */
- }
- fprintf(fp,"\n");
- }
}
-int pr_trans(FILE *fp,int nl,t_dlist dl[],real dt,int Xi)
+int pr_trans(FILE *fp, int nl, t_dlist dl[], real dt, int Xi)
{
- /* never called at the moment */
+ /* never called at the moment */
- int i,nn,nz;
-
- nz=0;
- fprintf(fp,"\\begin{table}[h]\n");
- fprintf(fp,"\\caption{Number of dihedral transitions per nanosecond}\n");
- fprintf(fp,"\\begin{tabular}{|l|l|}\n");
- fprintf(fp,"\\hline\n");
- fprintf(fp,"Residue\t&$\\chi_%d$\t\\\\\n",Xi+1);
- for(i=0; (i<nl); i++) {
- nn=dl[i].ntr[Xi]/dt;
-
- if (nn == 0) {
- fprintf(fp,"%s\t&\\HL{%d}\t\\\\\n",dl[i].name,nn);
- nz++;
+ int i, nn, nz;
+
+ nz = 0;
+ fprintf(fp, "\\begin{table}[h]\n");
+ fprintf(fp, "\\caption{Number of dihedral transitions per nanosecond}\n");
+ fprintf(fp, "\\begin{tabular}{|l|l|}\n");
+ fprintf(fp, "\\hline\n");
+ fprintf(fp, "Residue\t&$\\chi_%d$\t\\\\\n", Xi+1);
+ for (i = 0; (i < nl); i++)
+ {
+ nn = dl[i].ntr[Xi]/dt;
+
+ if (nn == 0)
+ {
+ fprintf(fp, "%s\t&\\HL{%d}\t\\\\\n", dl[i].name, nn);
+ nz++;
+ }
+ else if (nn > 0)
+ {
+ fprintf(fp, "%s\t&\\%d\t\\\\\n", dl[i].name, nn);
+ }
}
- else if (nn > 0)
- fprintf(fp,"%s\t&\\%d\t\\\\\n",dl[i].name,nn);
- }
- fprintf(fp,"\\hline\n");
- fprintf(fp,"\\end{tabular}\n");
- fprintf(fp,"\\end{table}\n\n");
+ fprintf(fp, "\\hline\n");
+ fprintf(fp, "\\end{tabular}\n");
+ fprintf(fp, "\\end{table}\n\n");
- return nz;
+ return nz;
}
-
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff