// Expand l-system into production string.
// object_string is read with the k counter and
// the next generation is built up in otemp
void L_system()
{
// Map rule names
typedef std::map<char, unsigned long> map_t;
map_t S;
// Each char gets a rule number
for(unsigned long i = rules.size(); i > 0; i--)
if(rules[i - 1].size())
S[(rules[i - 1][0])] = i - 1;
// For each recursion
unsigned long max = max_string - 10L;
bool incomplete = false;
for(unsigned long l = 0; l < lev; l++)
{
// Need markers ?
bool marker = (l == (lev - 1)) && (fraction != 0.0);
std::string otemp("");
unsigned long ss = 0;
// For each char in the string
for(unsigned long k = 0; k < object_string.size(); k++)
{
// Default rule which does nothing
unsigned long i = rules.size() - 1;
// i = rule number attached to current char
map_t::const_iterator find_rule = S.find(object_string[k]);
if(find_rule != S.end())
i = find_rule->second;
// s = size of current rule
unsigned long s = rules[i].size() - 2;
ss += s;
// Overflow
if(ss >= max)
{
l = lev;
incomplete = true;
break;
}
// Add mark char
if(marker && marks[i])
{
otemp += '@';
otemp += std::string(rules[i], 2, s);
otemp += '@';
}
else
{
// Copy
otemp += std::string(rules[i], 2, s);
}
}
// Copy the temp string to object_string and repeat cycle
object_string = otemp;
}
}
int NanoShaperInterface::compute_from_file(int surftype, float gspacing,
float probe_radius,
float skin_parm,
float blob_parm,
int n, int *ids, float *xyzr,
int *flgs) {
const char *nsbin = "NanoShaper";
// generate output file name and try to create
char *dirname = vmd_tempfile("");
int uid = vmd_getuid();
int rnd = vmd_random() % 999;
char *filebase = new char[strlen(dirname) + 100];
sprintf(filebase, "%svmdns.u%d.%d.", dirname, uid, rnd);
delete [] dirname;
char *pfilename = new char[strlen(filebase) + 100];
char *ofilename = new char[strlen(filebase) + 100];
sprintf(pfilename, "%sprm", filebase);
sprintf(ofilename, "%sxyzr", filebase);
FILE *pfile = fopen(pfilename, "wt");
if (!pfile) {
delete [] filebase;
delete [] pfilename;
delete [] ofilename;
msgErr << "Failed to create NanoShaper parameter input file" << sendmsg;
return 0; // failure
}
const char *surfstr = "ses";
const char *modestr = "normal";
switch(surftype) {
case NS_SURF_SES:
surfstr = "ses";
modestr = "normal";
break;
case NS_SURF_SKIN:
surfstr = "skin";
modestr = "normal";
break;
case NS_SURF_BLOBBY:
surfstr = "blobby";
modestr = "normal";
break;
case NS_SURF_POCKETS:
surfstr = "pockets";
modestr = "pockets";
break;
}
//
// Emit surface calculation configuration into NS input file
//
fprintf(pfile, "Operative_Mode = %s\n", modestr);
fprintf(pfile, "Pocket_Radius_Small = %.1f\n", 1.4);
fprintf(pfile, "Pocket_Radius_Big = %.1f\n", 3.0);
fprintf(pfile, "Surface = %s\n", surfstr);
if (gspacing < 0.05f)
gspacing = 0.05f;
fprintf(pfile, "Grid_scale = %.1f\n", 1.0f/gspacing);
fprintf(pfile, "XYZR_FileName = %s\n", ofilename);
fprintf(pfile, "Probe_Radius = %.1f\n", probe_radius);
fprintf(pfile, "Skin_Surface_Parameter = %.2f\n", skin_parm);
fprintf(pfile, "Blobbyness = %.1f\n", blob_parm);
// enable all to emulate MSMS
fprintf(pfile, "Compute_Vertex_Normals = true\n");
fprintf(pfile, "Save_Mesh_MSMS_Format = true\n");
fprintf(pfile, "Vertex_Atom_Info = true\n");
// various parameters copied from example input file
fprintf(pfile, "Grid_perfil = %.1f\n", 70.0);
fprintf(pfile, "Build_epsilon_maps = false\n");
fprintf(pfile, "Build_status_map = true\n");
fprintf(pfile, "Smooth_Mesh = true\n");
fprintf(pfile, "Triangulation = true\n");
// SD: optimized value for big structures
fprintf(pfile, "Max_Probes_Self_Intersections = 5000\n");
fprintf(pfile, "Self_Intersections_Grid_Coefficient = 5.0\n");
fprintf(pfile, "Accurate_Triangulation = true\n");
// Tell NS to store all files by appending to a base filename provided
// by the caller, so we don't end up with problems on multi-user systems
// or when multiple VMD sessions are running concurrently on the same
// machine. VMD chooses the base filename via OS temp file APIs.
fprintf(pfile, "Root_FileName = %s\n", filebase);
// SD: optimized value for big structures
fprintf(pfile, "Max_skin_patches_per_auxiliary_grid_2d_cell = 2000\n");
fclose(pfile);
FILE *ofile = fopen(ofilename, "wt");
if (!ofile) {
delete [] ofilename;
msgErr << "Failed to create NanoShaper atom xyzr input file" << sendmsg;
return 0; // failure
}
char *facetfilename = new char[strlen(filebase) + 100];
char *vertfilename = new char[strlen(filebase) + 100];
char *errfilename = new char[strlen(filebase) + 100];
char *expfilename = new char[strlen(filebase) + 100];
char *expindfilename = new char[strlen(filebase) + 100];
char *areafilename = new char[strlen(filebase) + 100];
sprintf(facetfilename, "%striangulatedSurf.face", filebase);
sprintf(vertfilename, "%striangulatedSurf.vert", filebase);
sprintf(errfilename, "%sstderror.txt", filebase);
sprintf(expfilename, "%sexposed.xyz", filebase);
sprintf(expindfilename, "%sexposedIndices.txt", filebase);
sprintf(areafilename, "%striangleAreas.txt", filebase);
// temporary files we want to make sure to clean up
VMDTempFile ptemp(pfilename);
VMDTempFile otemp(ofilename);
VMDTempFile ftemp(facetfilename);
VMDTempFile vtemp(vertfilename);
VMDTempFile errtemp(errfilename);
VMDTempFile exptemp(expfilename);
VMDTempFile expindtemp(expindfilename);
VMDTempFile areatemp(areafilename);
//
// write atom coordinates and radii to the file we send to NanoShaper
//
for (int i=0; i<n; i++) {
fprintf(ofile, "%f %f %f %f\n",
xyzr[4L*i], xyzr[4L*i+1], xyzr[4L*i+2], xyzr[4L*i+3]);
}
fclose(ofile);
//
// call NanoShaper to calculate the surface for the given atoms
//
char *nscmd = new char[2*strlen(ofilename) + strlen(nsbin) + 100];
sprintf(nscmd, "\"%s\" %s", nsbin, pfilename);
vmd_system(nscmd);
delete [] nscmd;
delete [] pfilename;
//
// read NanoShaper output files
//
if (surftype == NS_SURF_POCKETS) {
// XXX pockets feature not complete yet
msgErr << "NanoShaper pockets mode currently unimplemented" << sendmsg;
return 0;
} else {
// Read output files for one of the normal surface modes
// read facets
FILE *facetfile = fopen(facetfilename, "r");
if (!facetfile) {
msgErr << "Cannot read NanoShaper facet file: " << facetfilename << sendmsg;
return 0; // failed
}
NanoShaperFace face;
char trash[256];
fgets(trash, sizeof(trash), facetfile); // eat text comments and counts
fgets(trash, sizeof(trash), facetfile);
fgets(trash, sizeof(trash), facetfile);
while (fscanf(facetfile, "%d %d %d %d %d",
face.vertex+0, face.vertex+1, face.vertex+2, &face.surface_type,
&face.anaface) == 5) {
face.component = 0; // XXX Unused by VMD, so why store?
face.vertex[0]--;
face.vertex[1]--;
face.vertex[2]--;
faces.append(face);
}
fclose(facetfile);
msgInfo << "NanoShaper face count: " << faces.num() << sendmsg;
// read verts
FILE *vertfile = fopen(vertfilename, "r");
if (!vertfile) {
msgErr << "Cannot read NanoShaper vertex file: " << vertfilename << sendmsg;
return 0; // failed
}
NanoShaperCoord norm, coord;
int atomid; // 1-based atom index
int l0fa; // number of of the level 0 SES face
int l; // SES face level? (1/2/3)
fgets(trash, sizeof(trash), vertfile);
fgets(trash, sizeof(trash), vertfile);
fgets(trash, sizeof(trash), vertfile);
while (fscanf(vertfile, "%f %f %f %f %f %f %d %d %d",
coord.x+0, coord.x+1, coord.x+2,
norm.x+0, norm.x+1, norm.x+2,
&l0fa, &atomid, &l) == 9) {
norms.append(norm);
coords.append(coord);
atomids.append(atomid-1);
}
fclose(vertfile);
msgInfo << "NanoShaper vert count: " << norms.num() << sendmsg;
if (ids) {
for (int i=0; i<atomids.num(); i++) {
atomids[i] = ids[atomids[i]];
}
}
}
return 1; // success
}
