void BindingMode::output_BindingMode(int num_result, char* end_strfile, char* tmp_end_strfile, char* dockinp, char* gainp, int minPoints)
{
// File and Output variables declarations
cfstr CF; /* complementarity function value */
resid *pRes = NULL;
cfstr* pCF = NULL;
char sufix[25];
char remark[MAX_REMARK];
char tmpremark[MAX_REMARK];
// 0. elect a Pose representative (Rep) of the current BindingMode
std::vector<Pose>::const_iterator Rep_lowCF = this->elect_Representative(false);
std::vector<Pose>::const_iterator Rep_lowOPTICS = this->elect_Representative(true);
// 1. build FA->opt_par[GB->num_genes]
for(int k = 0; k < this->Population->GB->num_genes; ++k) this->Population->FA->opt_par[k] = Rep_lowCF->chrom->genes[k].to_ic;
// for(int k = 0; k < this->Population->GB->num_genes; ++k) this->Population->FA->opt_par[k] = Rep_lowOPTICS->chrom->genes[k].to_ic;
// 2. get CF with ic2cf()
CF = ic2cf(this->Population->FA, this->Population->VC, this->Population->atoms, this->Population->residue, this->Population->cleftgrid, this->Population->GB->num_genes, this->Population->FA->opt_par);
// 3. print REMARKS for FA->optres (res_ptr && cf_ptr for each optimizable residue)
strcpy(remark,"REMARK optimized structure\n");
sprintf(tmpremark,"REMARK Fast OPTICS clustering algorithm used to output the lowest CF as Binding Mode representative\n");
// sprintf(tmpremark,"REMARK Fast OPTICS clustering algorithm used to output the lowest OPTICS ordering as Binding Mode representative\n");
strcat(remark,tmpremark);
sprintf(tmpremark,"REMARK CF=%8.5f\n",get_cf_evalue(&CF));
strcat(remark,tmpremark);
sprintf(tmpremark,"REMARK CF.app=%8.5f\n",get_apparent_cf_evalue(&CF));
strcat(remark,tmpremark);
for(int j = 0; j < this->Population->FA->num_optres; ++j)
{
pRes = &this->Population->residue[this->Population->FA->optres[j].rnum];
pCF = &this->Population->FA->optres[j].cf;
sprintf(tmpremark,"REMARK optimizable residue %s %c %d\n", pRes->name, pRes->chn, pRes->number);
strcat(remark,tmpremark);
sprintf(tmpremark ,"REMARK CF.com=%8.5f\n", pCF->com);
strcat(remark, tmpremark);
sprintf(tmpremark ,"REMARK CF.sas=%8.5f\n", pCF->sas);
strcat(remark, tmpremark);
sprintf(tmpremark ,"REMARK CF.wal=%8.5f\n", pCF->wal);
strcat(remark, tmpremark);
sprintf(tmpremark ,"REMARK CF.con=%8.5f\n", pCF->con);
strcat(remark, tmpremark);
sprintf(tmpremark, "REMARK Residue has an overall SAS of %.3f\n", pCF->totsas);
strcat(remark, tmpremark);
}
sprintf(tmpremark,"REMARK Binding Mode:%d Best CF in Binding Mode:%8.5f OPTICS Center (CF):%8.5f Binding Mode Total CF:%8.5f Binding Mode Frequency:%d\n",
num_result, Rep_lowCF->CF, Rep_lowOPTICS->CF, this->compute_energy(), this->get_BindingMode_size());
strcat(remark,tmpremark);
for(int j=0; j < this->Population->FA->npar; ++j)
{
sprintf(tmpremark, "REMARK [%8.3f]\n",this->Population->FA->opt_par[j]);
strcat(remark,tmpremark);
}
// 4. if(REF) prints RMSD to REF
if(this->Population->FA->refstructure == 1)
{
bool Hungarian = false;
sprintf(tmpremark,"REMARK %8.5f RMSD to ref. structure (no symmetry correction)\n",
calc_rmsd(this->Population->FA,this->Population->atoms,this->Population->residue,this->Population->cleftgrid,this->Population->FA->npar,this->Population->FA->opt_par, Hungarian));
strcat(remark,tmpremark);
Hungarian = true;
sprintf(tmpremark,"REMARK %8.5f RMSD to ref. structure (symmetry corrected)\n",
calc_rmsd(this->Population->FA,this->Population->atoms,this->Population->residue,this->Population->cleftgrid,this->Population->FA->npar,this->Population->FA->opt_par, Hungarian));
strcat(remark,tmpremark);
}
sprintf(tmpremark,"REMARK inputs: %s & %s\n",dockinp,gainp);
strcat(remark,tmpremark);
sprintf(sufix,"_%d_%d.pdb", minPoints, num_result);
strcpy(tmp_end_strfile,end_strfile);
strcat(tmp_end_strfile,sufix);
// 5. write_pdb(FA,atoms,residue,tmp_end_strfile,remark)
write_pdb(this->Population->FA,this->Population->atoms,this->Population->residue,tmp_end_strfile,remark);
}
int main (int argc, char *argv[]) {
static char usage[] = {
"Calculate positions of pseudo-atoms in a model for a transmembrane channel and\n"
"write output to FILE or pore.pdb and pore.itp.\n\n"
" -h\t\t show help\n"
" -v\t\t be verbose (= -debuglevel 30 )\n"
" -debug <NUM>\t set debuglevel (0..100)\n"
" -spec <NUM>\t default species id\n"
" -showspec\t show hard coded species\n\n"
" -o FILE\t pdb coordinate file\n"
" -s FILE\t itp topology file\n"
"\n"
" -f <file>\t read pore description from file (see below)\n"
" -R <r>\t Outer radius of the model\n"
" -P <r> <l>\t Pore region: inner radius and length\n"
" -M <r> <l>\t Mouth region: largest inner radius and length\n"
" -b dmin dmax g_min g_max (repeatable)\n"
"\t\tform bonds with angle gamma when atoms are no further apart\n"
"\t\tthan dmax Ang and g_min <= gamma <= g_max, g from [0°..90°] )\n"
" -c\t\t only write connectivity to output, no bond length or kB, kA\n"
" -x\t\t neither connectivity nor bond length to output (isolated atoms)\n"
" -kB <c>\t Force constant of bonds, in kJ mol^-1 nm^-2\n"
" -kA <c>\t Force constant of angles, in kJ mol^-1 rad^-2\n"
" -cc\t\t Center ccordinates on cavitybox, not on unitcell\n"
"\n"
"Pore volume calculation (setting any of these switches on profile calculation):\n"
"In order to enable volume calculation, set -volume explicitly!\n"
"ATTENTION: all these LENGTHs are in NANO METRE not Angstrom !\n"
" -profile [<file>] calculate the profile in addition to the volume\n"
" -z1, -z2 <z> profile between z1 and z2\n"
" -Rmax <r> integrate out to Rmax (also use for the total volume\n"
" integration if -profile is set)\n"
" -npoints <N> number of points per dimension in the integrals\n"
" -T temp Temperature in Kelvin [300]\n"
" -wca If set, only use the repulsive part of the Lennard-Jones\n"
" potential (split after Weeks, Chandler & Andersen [1971])\n"
" -plot xfarbe output of the potential in z slices\n"
" -nzplot number of plot slices \n"
"\nDescription of the input file:\n"
"------------------------------\n"
"Instead of using -R (RADIUS), -M (MOUTH), and -P (PORE) one can describe the system\n"
"in a more flexible manner with a geometry in put file. It can contain up to "
"MAXDOMAINS domains (i.e. MOUTH and PORE lines). Allowed lines:\n"
"# comment (skipped)\n"
"# RADIUS is the global outer radius (in Angstrom) of the cylinder\n"
"RADIUS r_outer\n"
"# domain type and radius at the upper and lower end of the domain;\n"
"# r_lower of domain i and r_upper of domain i+1 are typically identical\n"
"MOUTH r_upper r_lower length [species]\n"
"PORE r_upper r_lower length [species]\n"
};
int i, n_atoms, n_bonds, n_angles, n_bc;
int error;
real vol;
FILE *fp;
/*
segmentation fault if arrays to large
--->>
now that I have learned to calloc I should rewrite this
on purely aesthetical grounds !
<<----
*/
struct pdb_ATOM model[TOTALSITES];
struct itp_bond bonds[MAXBONDS];
struct itp_angle angles[MAXANGLES];
struct geom geometry;
struct std_input in;
struct potpars potential = {
NULL,
TEMPERATURE,
NFREEDOM_SPC,
CSIX_OW_MTH, CTWELVE_OW_MTH, 0.0,
0, NULL, NULL,
N_GAUSSLEG
};
struct pprofile profile = {
"LJprofile.dat",
FALSE,
FALSE,
POT_PLOT_SLICES,
NULL,
NZPROF,
1.5,
-2,2,
NULL
};
/* argument processing */
/* *** no sanity checks *** */
n_atoms = 0; /* number of sites ('atoms') in the model */
n_bonds = 0; /* number of bonds */
n_angles = 0; /* number of angles between bonds */
n_bc = 0; /* number of constraint conditions for generating bonds */
if (argc < 2) {
printf("Running with default values.\n\nType %s -h for help.\n", argv[0]);
debuglevel = IMPORTANT;
};
/* initialize defaults */
in = default_input ();
potential.u1 = vljcyl; /* use the full Lennard-Jones potential in
the configurational volume calculations
by default */
profile.pp = &potential;
/* rudimentary opt-processing.. yarch */
for (i = 1; i < argc; i++)
{
if (!strcmp(argv[i], "-debug")) {
debuglevel = atoi(argv[++i]);
} else if (!strcmp(argv[i], "-v")) {
debuglevel = VERBOSE;
} else if (!strcmp(argv[i], "-h")) {
print_usage(argv[0],usage);
exit(1);
} else if (!strcmp(argv[i], "-showspec")) {
print_species ();
exit(1);
} else if (!strcmp(argv[i], "-o")) {
in.coordfile = argv[++i];
} else if (!strcmp(argv[i], "-s")) {
in.topofile = argv[++i];
} else if (!strcmp(argv[i], "-f")) {
in.datafile = argv[++i];
} else if (!strcmp(argv[i], "-R")) {
in.r_outer = atof(argv[++i]);
} else if (!strcmp(argv[i], "-M")) {
in.r_mouth = atof(argv[++i]);
in.l_mouth = atof(argv[++i]);
} else if (!strcmp(argv[i], "-P")) {
in.r_pore = atof(argv[++i]);
in.l_pore = atof(argv[++i]);
} else if (!strcmp(argv[i], "-spec")) {
in.specid = atoi(argv[++i]);
} else if (!strcmp(argv[i], "-b")) {
if (n_bc > MAXBONDCONSTRAINTS) {
fatal_error (1,
"Error: too many bond constraints, maximum is %d.\n",
MAXBONDCONSTRAINTS);
}
in.bc[n_bc].serial = n_bc;
in.bc[n_bc].dmin = atof(argv[++i]);
in.bc[n_bc].dmax = atof(argv[++i]);
in.bc[n_bc].gamma_min = atof(argv[++i]);
in.bc[n_bc].gamma_max = atof(argv[++i]);
in.n_bc = ++n_bc;
} else if (!strcmp(argv[i], "-c")) {
in.connectonly = TRUE;
} else if (!strcmp(argv[i], "-x")) {
in.atomsonly = TRUE;
} else if (!strcmp(argv[i], "-cc")) {
in.shiftcbox = TRUE;
} else if (!strcmp(argv[i], "-kB")) {
in.k_bond = atof(argv[++i]);
} else if (!strcmp(argv[i], "-kA")) {
in.k_angle = atof(argv[++i]);
} else if (!strcmp(argv[i], "-volume")) {
profile.bSet = TRUE;
} else if (!strcmp(argv[i], "-z1")) {
profile.bSet = TRUE;
profile.z1 = atof(argv[++i]);
} else if (!strcmp(argv[i], "-z2")) {
profile.bSet = TRUE;
profile.z2 = atof(argv[++i]);
} else if (!strcmp(argv[i], "-Rmax")) {
profile.bSet = TRUE;
profile.Rmax = atof(argv[++i]);
} else if (!strcmp(argv[i], "-profile")) {
profile.bSet = TRUE;
if (i < argc-1 && argv[i+1][0] != '-')
strncpy(profile.fn,argv[++i],STRLEN);
} else if (!strcmp(argv[i], "-npoints")) {
potential.ngaussleg = atof(argv[++i]);
} else if (!strcmp(argv[i], "-T")) {
potential.Temp = atof(argv[++i]);
} else if (!strcmp(argv[i], "-wca")) {
potential.u1 = vRljcyl;
} else if (!strcmp(argv[i], "-plot")) {
profile.bPlot = TRUE;
} else if (!strcmp(argv[i], "-nzplot")) {
profile.bPlot = TRUE;
profile.nzplot = atoi(argv[++i]);
} else {
mesg(OFF,"Unknown option: %s",argv[i]);
};
};
mesg (ALL, "TOTALSITES %d\n", TOTALSITES);
mesg (ALL,
"MAXBONDS %d\nsizeof struct bond %d, sizeof bonds[] %d\n",
MAXBONDS, sizeof (struct itp_bond), sizeof (bonds));
mesg (ALL,
"MAXANGLES %d\nsizeof struct angle %d, sizeof angles[] %d\n",
MAXANGLES, sizeof (struct itp_angle), sizeof (angles));
error = input_geom (&in, &geometry);
setup_domain (&geometry);
unitcell (&geometry);
cavitybox (&geometry);
n_atoms = do_coordinates (model, &geometry);
if (!geometry.atomsonly) {
n_bonds = do_bonds (bonds, model, &geometry);
n_angles = do_angles (angles, bonds, &geometry);
} else {
n_bonds = n_angles = 0;
}
print_geom (&geometry);
mesg (WARN, "\nNumber of sites: %d", n_atoms);
if (!geometry.atomsonly) {
mesg (WARN,
"Number of bonds: %d within max cut-off %5.2f Ang (no double-counting)",
n_bonds, find_dmax (geometry.bc, geometry.nbc));
mesg (WARN, "Number of angles: %d (no double-counting)\n", n_angles);
}
center (model, &geometry);
error = write_topology (model, bonds, angles, &geometry);
error = write_pdb (model, bonds, &geometry);
/*
calculate pore volume, based on J. S. Rowlinson, J Chem Soc,
Faraday Trans. 2, 82 (1986), 1801, (which didnt really work), and
discussion with Andrew Horsefield. */
if (profile.bSet) {
vol = volume(&potential,model,geometry.domain[1],&profile);
/* pore profile (already calculated in volume ) */
fp=fopen(profile.fn,"w");
if (fp) {
for(i=0;i<NZPROF;i++) {
fprintf(fp,"%f %f\n",profile.r[i][0],profile.r[i][1]);
}
fclose(fp);
}
free(profile.r);
}
return error < 0 ? 1 : 0;
};
