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tim |
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/********************************************************************** |
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Copyright (C) 2002 by Steffen Reith <streit@streit.cc> |
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Some portions Copyright (C) 2003-2005 by Geoffrey R. Hutchison |
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Some portions Copyright (C) 2004 by Chris Morley |
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This program is free software; you can redistribute it and/or modify |
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it under the terms of the GNU General Public License as published by |
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the Free Software Foundation version 2 of the License. |
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This program is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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***********************************************************************/ |
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#include "povrayformat.hpp" |
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using namespace std; |
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namespace OpenBabel |
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{ |
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/* ---- Make a prefix from title of molecule ---- */ |
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string MakePrefix(const char* title) |
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{ |
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int pos; /* Position in prefix */ |
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char *titleCpy = (char*) NULL; |
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char *str = (char*) NULL; |
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char *last = (char*) NULL; |
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/* ---- Copy molecule title to 'str' ---- */ |
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if ((titleCpy = strdup(title)) == (char *) NULL) |
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return string("NoMemory"); |
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/* --- Find last '/' and set 'str' to it if needed ----- */ |
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last = strrchr(titleCpy, '/'); |
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if (last != (char *) NULL) |
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str = (last + 1); |
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else |
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str = titleCpy; |
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/* ---- Check for nonempty string ---- */ |
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if (strlen(str) == 0) |
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return string("InValid"); |
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/* ---- Look for first . and replace with \0 ----- */ |
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pos = 0; |
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while((str[pos] != '\0') && (str[pos] != '.')) |
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{ |
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/* ---- Remove all tabs and spaces ---- */ |
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if ((str[pos] == ' ') || (str[pos] == '\t')) |
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str[pos] = '_'; |
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/* ---- Check next position ---- */ |
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pos++; |
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} |
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/* ---- If we have found a '.' cut the string there ---- */ |
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str[pos] = '\0'; |
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/* ---- Cast to C++ string-type the above operations are a mess with C++ strings ---- */ |
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string prefix(str); |
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/* ---- Free allocated memory ---- */ |
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free(titleCpy); |
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/* ---- Return the prefix ---- */ |
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return prefix; |
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} |
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void OutputHeader(ostream &ofs, OBMol &mol, string prefix) |
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{ |
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time_t akttime; /* Systemtime */ |
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char timestr[TIME_STR_SIZE + 1] = ""; /* Timestring */ |
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size_t time_res; /* Result of strftime */ |
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/* ---- Get the system-time ---- */ |
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akttime = time((time_t *) NULL); |
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time_res = strftime(timestr, |
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TIME_STR_SIZE, |
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"%a %b %d %H:%M:%S %Z %Y", |
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localtime((time_t *) &akttime) |
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); |
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/* ---- Write some header information ---- */ |
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ofs << "//Povray V3.1 code generated by Open Babel" << endl; |
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ofs << "//Author: Steffen Reith <streit@streit.cc>" << endl; |
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/* ---- Include timestamp in header ---- */ |
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ofs << "//Date: " << timestr << endl << endl; |
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/* ---- Include header statement for babel ---- */ |
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ofs << "//Include header for povray" << endl; |
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ofs << "#include \"babel31.inc\"" << endl << endl; |
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/* ---- You should do a spacefill model for molecules without bonds ---- */ |
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if (mol.NumBonds() == 0) |
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{ |
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/* ---- Check if a spacefill-model is selected ---- */ |
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ofs << "#if (BAS | CST)\"" << endl; |
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ofs << "#warning \"Molecule without bonds!\"" << endl; |
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ofs << "#warning \"You should do a spacefill-model\"" << endl; |
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ofs << "#end" << endl << endl; |
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} |
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/* ---- Set version ---- */ |
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ofs << "//Use PovRay3.1" << endl; |
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ofs << "#version 3.1;" << endl << endl; |
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/* ---- Print of name of molecule (#\b depends on size of babel.inc!) ---- */ |
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ofs << "//Print name of molecule while rendering" << endl; |
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ofs << "#render \"\\b\\b " << mol.GetTitle() << "\\n\\n\"" << endl << endl; |
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} |
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void CalcBoundingBox(OBMol &mol, |
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double &min_x, double &max_x, |
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double &min_y, double &max_y, |
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double &min_z, double &max_z |
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) |
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{ |
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/* ---- Init bounding-box variables ---- */ |
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min_x = (double) 0.0; |
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max_x = (double) 0.0; |
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min_y = (double) 0.0; |
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max_y = (double) 0.0; |
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min_z = (double) 0.0; |
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max_z = (double) 0.0; |
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/* ---- Check all atoms ---- */ |
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for(unsigned int i = 1; i <= mol.NumAtoms(); ++i) |
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{ |
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/* ---- Get a pointer to ith atom ---- */ |
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OBAtom *atom = mol.GetAtom(i); |
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/* ---- Check for minimal/maximal x-position ---- */ |
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if (atom -> GetX() < min_x) |
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min_x = atom -> GetX(); |
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if (atom -> GetX() > max_x) |
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max_x = atom -> GetX(); |
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/* ---- Check for minimal/maximal y-position ---- */ |
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if (atom -> GetY() < min_y) |
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min_y = atom -> GetY(); |
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if (atom -> GetY() > max_y) |
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max_y = atom -> GetY(); |
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/* ---- Check for minimal/maximal z-position ---- */ |
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if (atom -> GetZ() < min_z) |
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min_z = atom -> GetZ(); |
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if (atom -> GetZ() > max_z) |
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max_z = atom -> GetZ(); |
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} |
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} |
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void OutputAtoms(ostream &ofs, OBMol &mol, string prefix) |
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{ |
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/* ---- Write all coordinates ---- */ |
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ofs << "//Coodinates of atoms 1 - " << mol.NumAtoms() << endl; |
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unsigned int i; |
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for(i = 1; i <= mol.NumAtoms(); ++i) |
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{ |
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/* ---- Get a pointer to ith atom ---- */ |
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OBAtom *atom = mol.GetAtom(i); |
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/* ---- Write position of atom i ---- */ |
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ofs << "#declare " << prefix << "_pos_" << i << " = <" |
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<< atom -> GetX() << "," |
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<< atom -> GetY() << "," |
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<< atom -> GetZ() |
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<< ">;" << endl; |
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} |
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/* ---- Write povray-description of all atoms ---- */ |
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ofs << endl << "//Povray-description of atoms 1 - " << mol.NumAtoms() << endl; |
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for(i = 1; i <= mol.NumAtoms(); ++i) |
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{ |
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/* ---- Get a pointer to ith atom ---- */ |
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OBAtom *atom = mol.GetAtom(i); |
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/* ---- Write full description of atom i ---- */ |
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ofs << "#declare " << prefix << "_atom" << i << " = "; |
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ofs << "object {" << endl |
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<< "\t Atom_" << etab.GetSymbol(atom->GetAtomicNum()) << endl |
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<< "\t translate " << prefix << "_pos_" << i << endl << "\t }" << endl; |
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} |
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/* ---- Add empty line ---- */ |
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ofs << endl; |
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} |
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void OutputBASBonds(ostream &ofs, OBMol &mol, string prefix) |
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{ |
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/* ---- Write povray-description of all bonds---- */ |
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for(unsigned int i = 0; i < mol.NumBonds(); ++i) |
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{ |
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double x1,y1,z1,x2,y2,z2; /* Start and stop coordinates of a bond */ |
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double dist; /* Distance between (x1|y1|z1) and (x2|y2|z2) */ |
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double phi,theta; /* Angles between (x1|y1|z1) and (x2|y2|z2) */ |
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double dy; /* Distance between (x1|0|z1) and (x2|0|z2) */ |
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/* ---- Get a pointer to ith atom ---- */ |
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OBBond *bond = mol.GetBond(i); |
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/* ---- Assign start of bond i ---- */ |
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x1 = (bond -> GetBeginAtom()) -> GetX(); |
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y1 = (bond -> GetBeginAtom()) -> GetY(); |
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z1 = (bond -> GetBeginAtom()) -> GetZ(); |
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/* ---- Assign end of bond i ---- */ |
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x2 = (bond -> GetEndAtom()) -> GetX(); |
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y2 = (bond -> GetEndAtom()) -> GetY(); |
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z2 = (bond -> GetEndAtom()) -> GetZ(); |
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/* ---- Calculate length of bond and (x1|0|z1) - (x2|0|z2) ---- */ |
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dist = sqrt(SQUARE(x2-x1) + SQUARE(y2-y1) + SQUARE(z2-z1)); |
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dy = sqrt(SQUARE(x2-x1) + SQUARE(z2-z1)); |
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/* ---- Calculate Phi and Theta ---- */ |
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phi = (double) 0.0; |
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theta = (double) 0.0; |
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if (fabs(dist) >= EPSILON) |
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phi = acos((y2-y1)/dist); |
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if (fabs(dy) >= EPSILON) |
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theta = acos((x2-x1)/dy); |
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/* ---- Full description of bond i ---- */ |
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ofs << "#declare " << prefix << "_bond" << i |
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<< " = object {" << endl << "\t bond_" << bond -> GetBondOrder() << endl; |
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/* ---- Scale bond if needed ---- */ |
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if (fabs(dist) >= EPSILON) |
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{ |
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/* ---- Print povray scale-statement (x-Axis) ---- */ |
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ofs << "\t scale <" << dist << ",1.0000,1.0000>\n"; |
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} |
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/* ---- Rotate (Phi) bond if needed ---- */ |
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if (fabs(RAD2DEG(-phi) + (double) 90.0) >= EPSILON) |
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{ |
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/* ---- Rotate along z-axis ---- */ |
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ofs << "\t rotate <0.0000,0.0000," |
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<< RAD2DEG(-phi) + (double) 90.0 |
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<< ">" << endl; |
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} |
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/* ---- Check angle between (x1|0|z1) and (x2|0|z2) ---- */ |
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if (theta >= EPSILON) |
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{ |
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/* ---- Check direction ---- */ |
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if ((z2 - z1) >= (double) 0.0) |
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{ |
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/* ---- Rotate along y-Axis (negative) ---- */ |
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ofs << "\t rotate <0.0000," |
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<< RAD2DEG((double) -1.0 * theta) << ",0.0000>" |
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<< endl; |
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} |
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else |
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{ |
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/* ---- Rotate along y-Axis (positive) ---- */ |
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ofs << "\t rotate <0.0000," |
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<< RAD2DEG(theta) << ",0.0000>" |
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<< endl; |
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} |
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} |
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/* ---- Translate bond to start ---- */ |
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ofs << "\t translate " << prefix << "_pos_" << bond -> GetBeginAtomIdx() |
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<< endl << "\t }" << endl; |
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} |
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} |
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void OutputCSTBonds(ostream &ofs, OBMol &mol, string prefix) |
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{ |
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/* ---- Write povray-description of all bonds---- */ |
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for(unsigned int i = 0; i < mol.NumBonds(); ++i) |
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{ |
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double x1,y1,z1,x2,y2,z2; /* Start and stop coordinates of a bond */ |
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double dist; /* Distance between (x1|y1|z1) and (x2|y2|z2) */ |
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double phi,theta; /* Angles between (x1|y1|z1) and (x2|y2|z2) */ |
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double dy; /* Distance between (x1|0|z1) and (x2|0|z2) */ |
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/* ---- Get a pointer to ith atom ---- */ |
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OBBond *bond = mol.GetBond(i); |
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/* ---- Assign start of bond i ---- */ |
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x1 = (bond -> GetBeginAtom()) -> GetX(); |
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y1 = (bond -> GetBeginAtom()) -> GetY(); |
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z1 = (bond -> GetBeginAtom()) -> GetZ(); |
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/* ---- Assign end of bond i ---- */ |
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x2 = (bond -> GetEndAtom()) -> GetX(); |
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y2 = (bond -> GetEndAtom()) -> GetY(); |
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z2 = (bond -> GetEndAtom()) -> GetZ(); |
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/* ---- Calculate length of bond and (x1|0|z1) - (x2|0|z2) ---- */ |
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dist = sqrt(SQUARE(x2-x1) + SQUARE(y2-y1) + SQUARE(z2-z1)); |
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dy = sqrt(SQUARE(x2-x1) + SQUARE(z2-z1)); |
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/* ---- Calculate Phi and Theta ---- */ |
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phi = (double) 0.0; |
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theta = (double) 0.0; |
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if (fabs(dist) >= EPSILON) |
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phi = acos((y2-y1)/dist); |
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if (fabs(dy) >= EPSILON) |
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theta = acos((x2-x1)/dy); |
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/* ---- Begin of description of bond i (for a capped sticks model) ---- */ |
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ofs << "#declare " << prefix << "_bond" << i << " = object {" << endl; |
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ofs << "\t union {" << endl; |
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/* ---- Begin of Start-Half of Bond (i) ---- */ |
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ofs << "\t object {" << endl << "\t bond_" << bond -> GetBondOrder() << "\n"; |
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/* ---- Add a pigment - statement for start-atom of bond ---- */ |
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ofs << "\t pigment{color Color_" |
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<< bond -> GetBeginAtom() -> GetType() |
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<< "}" << endl; |
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/* ---- Scale bond if needed ---- */ |
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if (fabs((double) 2.0 * dist) >= EPSILON) |
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{ |
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/* ---- Print povray scale-statement (x-Axis) ---- */ |
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ofs << "\t scale <" << (double) 0.5 * dist << ",1.0000,1.0000>" << endl; |
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} |
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/* ---- Rotate (Phi) bond if needed ---- */ |
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if (fabs(RAD2DEG(-phi) + (double) 90.0) >= EPSILON) |
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|
{ |
| 361 |
|
|
|
| 362 |
|
|
/* ---- Rotate along z-axis ---- */ |
| 363 |
|
|
ofs << "\t rotate <0.0000,0.0000," |
| 364 |
|
|
<< RAD2DEG(-phi) + (double) 90.0 |
| 365 |
|
|
<< ">" << endl; |
| 366 |
|
|
|
| 367 |
|
|
} |
| 368 |
|
|
|
| 369 |
|
|
/* ---- Check angle between (x1|0|z1) and (x2|0|z2) ---- */ |
| 370 |
|
|
if (theta >= EPSILON) |
| 371 |
|
|
{ |
| 372 |
|
|
|
| 373 |
|
|
/* ---- Check direction ---- */ |
| 374 |
|
|
if ((z2 - z1) >= (double) 0.0) |
| 375 |
|
|
{ |
| 376 |
|
|
|
| 377 |
|
|
/* ---- Rotate along y-Axis (negative) ---- */ |
| 378 |
|
|
ofs << "\t rotate <0.0000," |
| 379 |
|
|
<< RAD2DEG((double) -1.0 *theta) << ",0.0000>" |
| 380 |
|
|
<< endl; |
| 381 |
|
|
|
| 382 |
|
|
} |
| 383 |
|
|
else |
| 384 |
|
|
{ |
| 385 |
|
|
|
| 386 |
|
|
/* ---- Rotate along y-Axis (positive) ---- */ |
| 387 |
|
|
ofs << "\t rotate <0.0000," << RAD2DEG(theta) << ",0.0000>" << endl; |
| 388 |
|
|
|
| 389 |
|
|
} |
| 390 |
|
|
|
| 391 |
|
|
} |
| 392 |
|
|
|
| 393 |
|
|
/* ---- Translate bond to start ---- */ |
| 394 |
|
|
|
| 395 |
|
|
ofs << "\t translate " << prefix << "_pos_" << bond -> GetBeginAtomIdx() << endl; |
| 396 |
|
|
|
| 397 |
|
|
/* ---- End of description of Start-Bond ---- */ |
| 398 |
|
|
ofs << "\t }" << endl; |
| 399 |
|
|
|
| 400 |
|
|
/* ---- Begin of End-Half of Bond i ---- */ |
| 401 |
|
|
ofs << "\t object {" << endl << "\t bond_" << bond -> GetBondOrder() << endl; |
| 402 |
|
|
|
| 403 |
|
|
/* ---- Add a pigment - statement for end-atom of bond i ---- */ |
| 404 |
|
|
ofs << "\t pigment{color Color_" |
| 405 |
|
|
<< bond -> GetEndAtom() -> GetType() |
| 406 |
|
|
<< "}" << endl; |
| 407 |
|
|
|
| 408 |
|
|
/* ---- Scale bond if needed ---- */ |
| 409 |
|
|
if (fabs((double) 2.0 * dist) >= EPSILON) |
| 410 |
|
|
{ |
| 411 |
|
|
|
| 412 |
|
|
/* ---- Print povray scale-statement (x-Axis) ---- */ |
| 413 |
|
|
ofs << "\t scale <" << (double) 0.5 * dist << ",1.0000,1.0000>" << endl; |
| 414 |
|
|
|
| 415 |
|
|
} |
| 416 |
|
|
|
| 417 |
|
|
/* ---- Rotate (Phi) bond if needed ---- */ |
| 418 |
|
|
if (fabs(RAD2DEG(-phi) + (double) 270.0) >= EPSILON) |
| 419 |
|
|
{ |
| 420 |
|
|
|
| 421 |
|
|
/* ---- Rotate along z-axis (oposite to start half) ---- */ |
| 422 |
|
|
ofs << "\t rotate <0.0000,0.0000," |
| 423 |
|
|
<< (RAD2DEG(-phi) + (double) 90.0) + (double) 180.0 |
| 424 |
|
|
<< ">" << endl; |
| 425 |
|
|
|
| 426 |
|
|
} |
| 427 |
|
|
|
| 428 |
|
|
/* ---- Check angle between (x1|0|z1) and (x2|0|z2) ---- */ |
| 429 |
|
|
if (fabs(theta) >= EPSILON) |
| 430 |
|
|
{ |
| 431 |
|
|
|
| 432 |
|
|
/* ---- Check direction ---- */ |
| 433 |
|
|
if ((z2 - z1) >= (double) 0.0) |
| 434 |
|
|
{ |
| 435 |
|
|
|
| 436 |
|
|
/* ---- Rotate along y-Axis (negative) (oposite orientation) ---- */ |
| 437 |
|
|
ofs << "\t rotate <0.0000," |
| 438 |
|
|
<< RAD2DEG((double) -1.0 * theta) |
| 439 |
|
|
<< ",0.0000>" |
| 440 |
|
|
<< endl; |
| 441 |
|
|
|
| 442 |
|
|
} |
| 443 |
|
|
else |
| 444 |
|
|
{ |
| 445 |
|
|
|
| 446 |
|
|
/* ---- Rotate along y-Axis (positive) (oposite orientation) ---- */ |
| 447 |
|
|
ofs << "\t rotate <0.0000," << RAD2DEG(theta) << ",0.0000>" << endl; |
| 448 |
|
|
|
| 449 |
|
|
} |
| 450 |
|
|
|
| 451 |
|
|
} |
| 452 |
|
|
|
| 453 |
|
|
/* ---- Translate bond to end ---- */ |
| 454 |
|
|
ofs << "\t translate " << prefix << "_pos_" << bond -> GetEndAtomIdx() << endl; |
| 455 |
|
|
|
| 456 |
|
|
/* ---- End of description of End-Bond ---- */ |
| 457 |
|
|
ofs << "\t }" << endl; |
| 458 |
|
|
|
| 459 |
|
|
/* ---- End of description of bond i ---- */ |
| 460 |
|
|
ofs << "\t }" << endl << "\t }" << endl << endl; |
| 461 |
|
|
|
| 462 |
|
|
} |
| 463 |
|
|
|
| 464 |
|
|
} |
| 465 |
|
|
|
| 466 |
|
|
void OutputUnions(ostream &ofs, OBMol &mol, string prefix) |
| 467 |
|
|
{ |
| 468 |
|
|
/* ---- Build union of all atoms ---- */ |
| 469 |
|
|
ofs << endl << "//All atoms of molecule " << prefix << endl; |
| 470 |
|
|
ofs << "#ifdef (TRANS)" << endl; |
| 471 |
|
|
ofs << "#declare " << prefix << "_atoms = merge {" << endl; |
| 472 |
|
|
ofs << "#else" << endl; |
| 473 |
|
|
ofs << "#declare " << prefix << "_atoms = union {" << endl; |
| 474 |
|
|
ofs << "#end //(End of TRANS)" << endl; |
| 475 |
|
|
|
| 476 |
|
|
/* ---- Write definition of all atoms ---- */ |
| 477 |
|
|
for(unsigned int i = 1; i <= mol.NumAtoms(); ++i) |
| 478 |
|
|
{ |
| 479 |
|
|
|
| 480 |
|
|
/* ---- Write definition of atom i ---- */ |
| 481 |
|
|
ofs << "\t object{" << prefix << "_atom" << i << "}" << endl; |
| 482 |
|
|
|
| 483 |
|
|
} |
| 484 |
|
|
ofs << "\t }" << endl << endl; |
| 485 |
|
|
|
| 486 |
|
|
/* ---- Check for number of bonds ---- */ |
| 487 |
|
|
if(mol.NumBonds() > 0) |
| 488 |
|
|
{ |
| 489 |
|
|
|
| 490 |
|
|
/* ---- Do a BAS or CST model ? ---- */ |
| 491 |
|
|
ofs << "//Bonds only needed for ball and sticks or capped sticks models" << endl; |
| 492 |
|
|
ofs << "#if (BAS | CST)" << endl; |
| 493 |
|
|
ofs << "#declare " << prefix <<"_bonds = union {" << endl; |
| 494 |
|
|
|
| 495 |
|
|
/* ---- Description of all bonds ---- */ |
| 496 |
|
|
for(unsigned int i = 0; i < mol.NumBonds(); ++i) |
| 497 |
|
|
{ |
| 498 |
|
|
|
| 499 |
|
|
/* ---- Write Definition of Bond i ---- */ |
| 500 |
|
|
ofs << "\t object{" << prefix << "_bond" << i << "}" << endl; |
| 501 |
|
|
|
| 502 |
|
|
} |
| 503 |
|
|
|
| 504 |
|
|
/* ---- End of povray-conditional for ball and sticks ---- */ |
| 505 |
|
|
ofs << "\t }" << endl << "#end" << endl << endl; |
| 506 |
|
|
|
| 507 |
|
|
} |
| 508 |
|
|
|
| 509 |
|
|
} |
| 510 |
|
|
|
| 511 |
|
|
void OutputMoleculeBonds(ostream &ofs, |
| 512 |
|
|
string prefix, |
| 513 |
|
|
double min_x, double max_x, |
| 514 |
|
|
double min_y, double max_y, |
| 515 |
|
|
double min_z, double max_z |
| 516 |
|
|
) |
| 517 |
|
|
{ |
| 518 |
|
|
/* ---- Write a comment ---- */ |
| 519 |
|
|
ofs << endl << "//Definition of molecule " << prefix << endl; |
| 520 |
|
|
|
| 521 |
|
|
/* ---- Check for space-fill model ---- */ |
| 522 |
|
|
ofs << "#if (SPF)" << endl; |
| 523 |
|
|
ofs << "#declare " << prefix << " = object{" |
| 524 |
|
|
<< endl << "\t " << prefix << "_atoms" << endl; |
| 525 |
|
|
|
| 526 |
|
|
/* ---- Here we do BAS oder CST models ---- */ |
| 527 |
|
|
ofs << "#else" << endl; |
| 528 |
|
|
ofs << "#declare " << prefix << " = union {" << endl; |
| 529 |
|
|
|
| 530 |
|
|
/* ---- Add all Atoms ---- */ |
| 531 |
|
|
ofs << "\t object{" << prefix << "_atoms}" << endl; |
| 532 |
|
|
|
| 533 |
|
|
/* ---- Add difference between bonds and atoms ---- */ |
| 534 |
|
|
ofs << "#if (BAS | CST)//(Not really needed at moment!)" << endl; |
| 535 |
|
|
|
| 536 |
|
|
/* ---- Use disjunct objects for transparent pics? ---- */ |
| 537 |
|
|
ofs << "#if (TRANS)" << endl; |
| 538 |
|
|
ofs << "\t difference {" << endl; |
| 539 |
|
|
ofs << "\t object{" << prefix << "_bonds}" << endl |
| 540 |
|
|
<< "\t object{" << prefix << "_atoms}" << endl |
| 541 |
|
|
<< "\t }" << endl; |
| 542 |
|
|
|
| 543 |
|
|
/* ---- Do a solid model ? ---- */ |
| 544 |
|
|
ofs << "#else" << endl; |
| 545 |
|
|
ofs << "\t object{" << prefix << "_bonds}" << endl; |
| 546 |
|
|
ofs << "#end //(End of TRANS)" << endl; |
| 547 |
|
|
ofs << "#end //(End of (BAS|CST))" << endl; |
| 548 |
|
|
|
| 549 |
|
|
/* ---- End of CST or BAS model ---- */ |
| 550 |
|
|
ofs << "#end //(End of SPF)" << endl; |
| 551 |
|
|
|
| 552 |
|
|
/* ---- Add comment (bounding box) ---- */ |
| 553 |
|
|
ofs << "//\t bounded_by {" << endl |
| 554 |
|
|
<< "//\t box {" << endl |
| 555 |
|
|
<< "//\t <" |
| 556 |
|
|
<< min_x - MAXRADIUS << "," |
| 557 |
|
|
<< min_y - MAXRADIUS << "," |
| 558 |
|
|
<< min_z - MAXRADIUS << ">" << endl; |
| 559 |
|
|
|
| 560 |
|
|
ofs << "//\t <" |
| 561 |
|
|
<< max_x + MAXRADIUS << "," |
| 562 |
|
|
<< max_y + MAXRADIUS << "," |
| 563 |
|
|
<< max_z + MAXRADIUS << ">" << endl; |
| 564 |
|
|
|
| 565 |
|
|
ofs << "\t }" << endl << endl; |
| 566 |
|
|
|
| 567 |
|
|
} |
| 568 |
|
|
|
| 569 |
|
|
void OutputMoleculeNoBonds(ostream &ofs, string prefix) |
| 570 |
|
|
{ |
| 571 |
|
|
/* ---- Print description of molecule without bonds ---- */ |
| 572 |
|
|
ofs << endl << "//Definition of Molecule " << prefix << " (no bonds)" << endl; |
| 573 |
|
|
ofs << "#declare " << prefix << " = object {" << prefix << "_atoms}" << endl << endl; |
| 574 |
|
|
|
| 575 |
|
|
} |
| 576 |
|
|
|
| 577 |
|
|
void OutputCenterComment(ostream &ofs, |
| 578 |
|
|
string prefix, |
| 579 |
|
|
double min_x, double max_x, |
| 580 |
|
|
double min_y, double max_y, |
| 581 |
|
|
double min_z, double max_z |
| 582 |
|
|
) |
| 583 |
|
|
{ |
| 584 |
|
|
/* ---- Print center comment (Warn: Vector is multiplied by -1.0)---- */ |
| 585 |
|
|
ofs << "//Center of molecule " << prefix << " (bounding box)" << endl; |
| 586 |
|
|
ofs << "#declare " << prefix << "_center = <" |
| 587 |
|
|
<< (double) -1.0 * (min_x + max_x) / (double) 2.0 << "," |
| 588 |
|
|
<< (double) -1.0 * (min_y + max_y) / (double) 2.0 << "," |
| 589 |
|
|
<< (double) -1.0 * (min_z + max_z) / (double) 2.0 << ">" << endl << endl; |
| 590 |
|
|
} |
| 591 |
|
|
|
| 592 |
|
|
//////////////////////////////////////////////////////////////// |
| 593 |
|
|
|
| 594 |
|
|
bool PovrayFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv) |
| 595 |
|
|
{ |
| 596 |
|
|
OBMol* pmol = dynamic_cast<OBMol*>(pOb); |
| 597 |
|
|
if(pmol==NULL) |
| 598 |
|
|
return false; |
| 599 |
|
|
|
| 600 |
|
|
//Define some references so we can use the old parameter names |
| 601 |
|
|
ostream &ofs = *pConv->GetOutStream(); |
| 602 |
|
|
OBMol &mol = *pmol; |
| 603 |
|
|
const char* title = pmol->GetTitle(); |
| 604 |
|
|
|
| 605 |
|
|
static long num = 0; |
| 606 |
|
|
double min_x, max_x, min_y, max_y, min_z, max_z; /* Edges of bounding box */ |
| 607 |
|
|
string prefix; |
| 608 |
|
|
|
| 609 |
|
|
/* ---- We use the molecule-title as our prefix ---- */ |
| 610 |
|
|
if(title != (const char*) NULL) |
| 611 |
|
|
prefix = MakePrefix(title); |
| 612 |
|
|
else if (mol.GetTitle() != (const char *) NULL) |
| 613 |
|
|
prefix = MakePrefix(mol.GetTitle()); |
| 614 |
|
|
else |
| 615 |
|
|
prefix = MakePrefix("Unknown"); |
| 616 |
|
|
|
| 617 |
|
|
/* ---- Check if we have already written a molecule to this file ---- */ |
| 618 |
|
|
if (num == 0) |
| 619 |
|
|
{ |
| 620 |
|
|
|
| 621 |
|
|
/* ---- Print the header ---- */ |
| 622 |
|
|
OutputHeader(ofs, mol, prefix); |
| 623 |
|
|
|
| 624 |
|
|
} |
| 625 |
|
|
else |
| 626 |
|
|
{ |
| 627 |
|
|
|
| 628 |
|
|
/* ---- Convert the unique molecule-number to a string and set the prefix ---- */ |
| 629 |
|
|
#if defined(HAVE_SSTREAM) |
| 630 |
|
|
ostringstream numStr; |
| 631 |
|
|
numStr << num << ends; |
| 632 |
|
|
prefix += numStr.str().c_str(); |
| 633 |
|
|
#else |
| 634 |
|
|
|
| 635 |
|
|
ostrstream numStr; |
| 636 |
|
|
numStr << num << ends; |
| 637 |
|
|
prefix += numStr.str(); |
| 638 |
|
|
#endif |
| 639 |
|
|
|
| 640 |
|
|
} |
| 641 |
|
|
|
| 642 |
|
|
/* ---- Print positions and descriptions of all atoms ---- */ |
| 643 |
|
|
OutputAtoms(ofs, mol, prefix); |
| 644 |
|
|
|
| 645 |
|
|
/* ---- Check #bonds ---- */ |
| 646 |
|
|
if (mol.NumBonds() > 0) |
| 647 |
|
|
{ |
| 648 |
|
|
|
| 649 |
|
|
/* ---- Write an comment ---- */ |
| 650 |
|
|
ofs << "//Povray-description of bonds 1 - " << mol.NumBonds() << endl; |
| 651 |
|
|
|
| 652 |
|
|
/* ---- Do a ball and sticks model? ---- */ |
| 653 |
|
|
ofs << "#if (BAS)" << endl; |
| 654 |
|
|
|
| 655 |
|
|
/* ---- Print bonds using "ball and sticks style" ---- */ |
| 656 |
|
|
OutputBASBonds(ofs, mol, prefix); |
| 657 |
|
|
|
| 658 |
|
|
/* ---- End of povray-conditional for ball and sticks ---- */ |
| 659 |
|
|
ofs << "#end //(BAS-Bonds)" << endl << endl; |
| 660 |
|
|
|
| 661 |
|
|
/* ---- Do a capped-sticks model? ---- */ |
| 662 |
|
|
ofs << "#if (CST)" << endl; |
| 663 |
|
|
|
| 664 |
|
|
/* ---- Print bonds using "capped sticks style" ---- */ |
| 665 |
|
|
OutputCSTBonds(ofs, mol, prefix); |
| 666 |
|
|
|
| 667 |
|
|
/* ---- End of povray-conditional for capped sticks ---- */ |
| 668 |
|
|
ofs << "#end // (CST-Bonds)" << endl << endl; |
| 669 |
|
|
|
| 670 |
|
|
} |
| 671 |
|
|
|
| 672 |
|
|
/* ---- Print out unions of atoms and bonds ---- */ |
| 673 |
|
|
OutputUnions(ofs, mol, prefix); |
| 674 |
|
|
|
| 675 |
|
|
/* ---- Calculate bounding-box ---- */ |
| 676 |
|
|
CalcBoundingBox(mol, min_x, max_x, min_y, max_y, min_z, max_z); |
| 677 |
|
|
|
| 678 |
|
|
/* ---- Check #bonds ---- */ |
| 679 |
|
|
if (mol.NumBonds() > 0) |
| 680 |
|
|
{ |
| 681 |
|
|
|
| 682 |
|
|
/* ---- Print out description of molecule ---- */ |
| 683 |
|
|
OutputMoleculeBonds(ofs, |
| 684 |
|
|
prefix, |
| 685 |
|
|
min_x, max_x, |
| 686 |
|
|
min_y, max_y, |
| 687 |
|
|
min_z, max_z); |
| 688 |
|
|
|
| 689 |
|
|
} |
| 690 |
|
|
else |
| 691 |
|
|
{ |
| 692 |
|
|
|
| 693 |
|
|
/* ---- Now we can define the molecule without bonds ---- */ |
| 694 |
|
|
OutputMoleculeNoBonds(ofs, prefix); |
| 695 |
|
|
|
| 696 |
|
|
} |
| 697 |
|
|
|
| 698 |
|
|
/* ---- Insert declaration for centering the molecule ---- */ |
| 699 |
|
|
OutputCenterComment(ofs, |
| 700 |
|
|
prefix, |
| 701 |
|
|
min_x, max_x, |
| 702 |
|
|
min_y, max_y, |
| 703 |
|
|
min_z, max_z); |
| 704 |
|
|
|
| 705 |
|
|
/* ---- Increment the static molecule output-counter ---- */ |
| 706 |
|
|
num++; |
| 707 |
|
|
|
| 708 |
|
|
/* ---- Everything is ok! ---- */ |
| 709 |
|
|
return(true); |
| 710 |
|
|
} |
| 711 |
|
|
|
| 712 |
|
|
} //namespace OpenBabel |
