#include "gmx_ana.h"
#include "string2.h"
-int gmx_membed(int argc,char *argv[])
+int gmx_membed(int argc, char *argv[])
{
const char *desc[] = {
"[TT]g_membed[tt] embeds a membrane protein into an equilibrated lipid bilayer at the position",
"(see Wolf et al, J Comp Chem 31 (2010) 2169-2174), to re-equilibrate the membrane. Clearly",
"protein equilibration might require longer.[PAR]"
};
- t_filenm fnm[] = {
+ t_filenm fnm[] = {
{ efTPX, "-f", "into_mem", ffREAD },
{ efNDX, "-n", "index", ffOPTRD },
{ efTOP, "-p", "topol", ffOPTRW },
#define NFILE asize(fnm)
/* Command line options ! */
- real xy_fac = 0.5;
- real xy_max = 1.0;
- real z_fac = 1.0;
- real z_max = 1.0;
- int it_xy = 1000;
- int it_z = 0;
- real probe_rad = 0.22;
- int low_up_rm = 0;
- int maxwarn=0;
- int pieces=1;
- gmx_bool bALLOW_ASYMMETRY=FALSE;
- gmx_bool bStart=FALSE;
- int nstepout=100;
- gmx_bool bVerbose=FALSE;
- char *mdrun_path=NULL;
-
- t_pargs pa[] = {
+ real xy_fac = 0.5;
+ real xy_max = 1.0;
+ real z_fac = 1.0;
+ real z_max = 1.0;
+ int it_xy = 1000;
+ int it_z = 0;
+ real probe_rad = 0.22;
+ int low_up_rm = 0;
+ int maxwarn = 0;
+ int pieces = 1;
+ gmx_bool bALLOW_ASYMMETRY = FALSE;
+ gmx_bool bStart = FALSE;
+ int nstepout = 100;
+ gmx_bool bVerbose = FALSE;
+ char *mdrun_path = NULL;
+
+ t_pargs pa[] = {
{ "-xyinit", FALSE, etREAL, {&xy_fac},
- "Resize factor for the protein in the xy dimension before starting embedding" },
+ "Resize factor for the protein in the xy dimension before starting embedding" },
{ "-xyend", FALSE, etREAL, {&xy_max},
- "Final resize factor in the xy dimension" },
+ "Final resize factor in the xy dimension" },
{ "-zinit", FALSE, etREAL, {&z_fac},
- "Resize factor for the protein in the z dimension before starting embedding" },
+ "Resize factor for the protein in the z dimension before starting embedding" },
{ "-zend", FALSE, etREAL, {&z_max},
- "Final resize faction in the z dimension" },
+ "Final resize faction in the z dimension" },
{ "-nxy", FALSE, etINT, {&it_xy},
- "Number of iteration for the xy dimension" },
+ "Number of iteration for the xy dimension" },
{ "-nz", FALSE, etINT, {&it_z},
- "Number of iterations for the z dimension" },
+ "Number of iterations for the z dimension" },
{ "-rad", FALSE, etREAL, {&probe_rad},
- "Probe radius to check for overlap between the group to embed and the membrane"},
+ "Probe radius to check for overlap between the group to embed and the membrane"},
{ "-pieces", FALSE, etINT, {&pieces},
- "Perform piecewise resize. Select parts of the group to insert and resize these with respect to their own geometrical center." },
- { "-asymmetry",FALSE, etBOOL,{&bALLOW_ASYMMETRY},
- "Allow asymmetric insertion, i.e. the number of lipids removed from the upper and lower leaflet will not be checked." },
- { "-ndiff" , FALSE, etINT, {&low_up_rm},
- "Number of lipids that will additionally be removed from the lower (negative number) or upper (positive number) membrane leaflet." },
+ "Perform piecewise resize. Select parts of the group to insert and resize these with respect to their own geometrical center." },
+ { "-asymmetry", FALSE, etBOOL, {&bALLOW_ASYMMETRY},
+ "Allow asymmetric insertion, i.e. the number of lipids removed from the upper and lower leaflet will not be checked." },
+ { "-ndiff", FALSE, etINT, {&low_up_rm},
+ "Number of lipids that will additionally be removed from the lower (negative number) or upper (positive number) membrane leaflet." },
{ "-maxwarn", FALSE, etINT, {&maxwarn},
- "Maximum number of warning allowed" },
+ "Maximum number of warning allowed" },
{ "-start", FALSE, etBOOL, {&bStart},
- "Call mdrun with membed options" },
+ "Call mdrun with membed options" },
{ "-stepout", FALSE, etINT, {&nstepout},
- "HIDDENFrequency of writing the remaining runtime" },
- { "-v", FALSE, etBOOL,{&bVerbose},
- "Be loud and noisy" },
+ "HIDDENFrequency of writing the remaining runtime" },
+ { "-v", FALSE, etBOOL, {&bVerbose},
+ "Be loud and noisy" },
{ "-mdrun_path", FALSE, etSTR, {&mdrun_path},
- "Path to the mdrun executable compiled with this g_membed version" }
+ "Path to the mdrun executable compiled with this g_membed version" }
};
- FILE *data_out;
+ FILE *data_out;
output_env_t oenv;
- char buf[256],buf2[64];
- gmx_bool bSucces;
+ char buf[256], buf2[64];
+ gmx_bool bSucces;
- parse_common_args(&argc,argv,0, NFILE,fnm,asize(pa),pa,
- asize(desc),desc,0,NULL, &oenv);
+ parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
+ asize(desc), desc, 0, NULL, &oenv);
- data_out = ffopen(opt2fn("-dat",NFILE,fnm),"w");
+ data_out = ffopen(opt2fn("-dat", NFILE, fnm), "w");
- fprintf(data_out,"nxy = %d\nnz = %d\nxyinit = %f\nxyend = %f\nzinit = %f\nzend = %f\n"
- "rad = %f\npieces = %d\nasymmetry = %s\nndiff = %d\nmaxwarn = %d\n",
- it_xy,it_z,xy_fac,xy_max,z_fac,z_max,probe_rad,pieces,
- bALLOW_ASYMMETRY ? "yes" : "no",low_up_rm,maxwarn);
+ fprintf(data_out, "nxy = %d\nnz = %d\nxyinit = %f\nxyend = %f\nzinit = %f\nzend = %f\n"
+ "rad = %f\npieces = %d\nasymmetry = %s\nndiff = %d\nmaxwarn = %d\n",
+ it_xy, it_z, xy_fac, xy_max, z_fac, z_max, probe_rad, pieces,
+ bALLOW_ASYMMETRY ? "yes" : "no", low_up_rm, maxwarn);
fclose(data_out);
- sprintf(buf,"%s -s %s -membed %s -o %s -c %s -e %s -nt 1 -cpt -1",
- (mdrun_path==NULL) ? "mdrun" : mdrun_path,
- opt2fn("-f",NFILE,fnm),opt2fn("-dat",NFILE,fnm),opt2fn("-o",NFILE,fnm),
- opt2fn("-c",NFILE,fnm),opt2fn("-e",NFILE,fnm));
+ sprintf(buf, "%s -s %s -membed %s -o %s -c %s -e %s -nt 1 -cpt -1",
+ (mdrun_path == NULL) ? "mdrun" : mdrun_path,
+ opt2fn("-f", NFILE, fnm), opt2fn("-dat", NFILE, fnm), opt2fn("-o", NFILE, fnm),
+ opt2fn("-c", NFILE, fnm), opt2fn("-e", NFILE, fnm));
- if (opt2bSet("-n",NFILE,fnm))
+ if (opt2bSet("-n", NFILE, fnm))
{
- sprintf(buf2," -mn %s",opt2fn("-n",NFILE,fnm));
- strcat(buf,buf2);
+ sprintf(buf2, " -mn %s", opt2fn("-n", NFILE, fnm));
+ strcat(buf, buf2);
}
- if (opt2bSet("-x",NFILE,fnm))
+ if (opt2bSet("-x", NFILE, fnm))
{
- sprintf(buf2," -x %s",opt2fn("-x",NFILE,fnm));
- strcat(buf,buf2);
+ sprintf(buf2, " -x %s", opt2fn("-x", NFILE, fnm));
+ strcat(buf, buf2);
}
- if (opt2bSet("-p",NFILE,fnm))
+ if (opt2bSet("-p", NFILE, fnm))
{
- sprintf(buf2," -mp %s",opt2fn("-p",NFILE,fnm));
- strcat(buf,buf2);
+ sprintf(buf2, " -mp %s", opt2fn("-p", NFILE, fnm));
+ strcat(buf, buf2);
}
if (bVerbose)
{
- sprintf(buf2," -v -stepout %d",nstepout);
- strcat(buf,buf2);
+ sprintf(buf2, " -v -stepout %d", nstepout);
+ strcat(buf, buf2);
}
if (bStart)
{
- printf("Start run with:\n%s\n",buf);
+ printf("Start run with:\n%s\n", buf);
bSucces = system(buf);
}
else
{
- printf("You can membed your protein now by:\n%s\n",buf);
+ printf("You can membed your protein now by:\n%s\n", buf);
}
- fprintf(stderr,"Please cite:\nWolf et al, J Comp Chem 31 (2010) 2169-2174.\n");
+ fprintf(stderr, "Please cite:\nWolf et al, J Comp Chem 31 (2010) 2169-2174.\n");
return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff