AtomRep.C

00001 /***************************************************************************
00002 *cr 
00003 *cr (C) Copyright 1995-2019 The Board of Trustees of the 
00004 *cr University of Illinois 
00005 *cr All Rights Reserved 
00006 *cr 
00007 ***************************************************************************/
00008 
00009 /***************************************************************************
00010 * RCS INFORMATION:
00011 *
00012 * $RCSfile: AtomRep.C,v $
00013 * $Author: johns $ $Locker: $ $State: Exp $
00014 * $Revision: 1.134 $ $Date: 2019年01月17日 21:20:58 $
00015 *
00016 ***************************************************************************
00017 * DESCRIPTION:
00018 * 
00019 * Parse and maintain the data for how a molecule should be represented.
00020 *
00021 ***************************************************************************/
00022 
00023 #include <string.h>
00024 #include <stdlib.h>
00025 #include "AtomRep.h"
00026 #include "Inform.h"
00027 #include "utilities.h"
00028 #include "config.h"
00029 
00030 /*********************** NOTES on ADDING NEW REPRESENTATIONS ************
00031 So, you wanna add a new representation ... here's what you have to do:
00032 1. Choose a a name for the rep, and decide how many parameters it needs.
00033 This object has support for up to MAX_ATOMREP_DATA parameters.
00034 2. Choose the order in which these will be specified in the text command.
00035 3. Add a new identifier in the main RepMethod enumeration for this new
00036 rep. The order is important; where you put the new item is where it
00037 will appear in lists of the different representations.
00038 4. Add a new element to the AtomRepInfo structure array (below). This element
00039 defines the name of the new rep, and gives info about all the parameters
00040 needed for that rep. You must put the item into the array in the same
00041 position where the new enum value was inserted into RepMethod.
00042 5. Once this structure is properly defined, the GUI and text interface will
00043 properly process and display the info for the new rep. At this point,
00044 you must add the code to display the new rep in DrawMolItem.
00045 6. Sit back and enjoy ...
00046 
00047 FORMAT for AtomRepInfo STRUCTURE:
00048 ---------------------------------
00049 Easiest thing to do is to copy an item with the same number of parameters,
00050 and change the necessary values. The items in each structure are:
00051 a. Integer enum code for the rep (same as was put in RepMethod enum)
00052 b. Name of rep (should be a single small word; this is the name
00053 used in the GUI list, and what the user calls the rep when typing
00054 in a command to change to this rep)
00055 c. Number of parameters required.
00056 d. An array of Structures which define how each parameter is used
00057 for the representation. The format for these items are:
00058 1. Index of the parameter in the AtomRep internal data
00059 storage array. This should be used when retrieving the
00060 data; call 'get_data' with this index value to retrieve
00061 the value for this parameter. Each parameter for the
00062 representation should have a different index, and they
00063 should be in the range 0 ... MAX_ATOMREP_DATA-1.
00064 There is an enumeration giving names for these indices,
00065 which is used right now primarily for historical reasons.
00066 Older parts of VMD used explicit calls to routines to get
00067 values for things such as the line thickness and sphere
00068 resolution, and these routines are still present. But
00069 since new reps may not necessarily have characteristics
00070 which map to these items, this should not be used in the
00071 future.
00072 2. Default value
00073 ***************************************************************************/
00074 
00075 // default res of cartoon cylinders
00076 #define DEF_CART_RES 12.0 
00077 
00078 // default res of bond cylinders
00079 #define DEF_BOND_RES 12.0
00080 
00081 // default res of spheres
00082 #define DEF_SPH_RES 12.0 
00083 
00084 // default res of licorice reps
00085 #define DEF_LIC_RES 12.0 
00086 
00087 // default thickness of lines
00088 #define DEF_LINE_RES 1.0 
00089 
00090 // default point size
00091 #define DEF_POINT_SIZE 1.0 
00092 
00093 //const AtomRepDataInfo UNUSED = {0, 0.0};
00094 #define UNUSED {0, 0.0}
00095 
00096 // define structures which indicate what data is needed by each rep
00097 const AtomRepParamStruct AtomRepInfo[AtomRep::TOTAL] = {
00098 //
00099 // Bond-oriented reps
00100 //
00101 
00102 // Lines
00103 { "Lines", 2, {
00104 { AtomRep::LINETHICKNESS, DEF_LINE_RES },
00105 { AtomRep::ISOLINETHICKNESS, 0.0f },
00106 UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED,
00107 UNUSED, UNUSED, UNUSED }
00108 },
00109 
00110 // Bonds
00111 { "Bonds", 2, {
00112 { AtomRep::BONDRAD, 0.3f },
00113 { AtomRep::BONDRES, DEF_BOND_RES },
00114 UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED,
00115 UNUSED, UNUSED, UNUSED }
00116 },
00117 
00118 // DynamicBonds
00119 { "DynamicBonds", 3, {
00120 { AtomRep::SPHERERAD, 3.0f }, // distance
00121 { AtomRep::BONDRAD, 0.3f },
00122 { AtomRep::BONDRES, DEF_BOND_RES },
00123 UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED,
00124 UNUSED, UNUSED, UNUSED }
00125 },
00126 
00127 // HBonds
00128 { "HBonds", 3, {
00129 { AtomRep::BONDRAD, 3.0f}, // distance
00130 { AtomRep::SPHERERAD, 20.0f}, // angle
00131 { AtomRep::LINETHICKNESS, 1.0f}, 
00132 UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED,
00133 UNUSED, UNUSED, UNUSED }
00134 },
00135 
00136 
00137 //
00138 // Atom-oriented reps
00139 //
00140 
00141 // Points
00142 { "Points", 1, { 
00143 { AtomRep::LINETHICKNESS, DEF_POINT_SIZE}, // size
00144 UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, 
00145 UNUSED, UNUSED, UNUSED, UNUSED }
00146 },
00147 
00148 // VDW
00149 { "VDW", 2, {
00150 { AtomRep::SPHERERAD, 1.0f},
00151 { AtomRep::SPHERERES, DEF_SPH_RES },
00152 UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED,
00153 UNUSED, UNUSED, UNUSED }
00154 },
00155 
00156 // CPK
00157 { "CPK", 5, {
00158 { AtomRep::SPHERERAD, 1.0f},
00159 { AtomRep::BONDRAD, 0.3f},
00160 { AtomRep::SPHERERES, DEF_SPH_RES},
00161 { AtomRep::BONDRES, DEF_BOND_RES},
00162 { AtomRep::ISOLINETHICKNESS, 0.0f },
00163 UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED }
00164 },
00165 
00166 // Licorice
00167 { "Licorice", 4, {
00168 { AtomRep::BONDRAD, 0.3f },
00169 { AtomRep::SPHERERES, DEF_LIC_RES},
00170 { AtomRep::BONDRES, DEF_LIC_RES},
00171 { AtomRep::ISOLINETHICKNESS, 0.0f }, // if nonzero, cutoff distance
00172 UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED,
00173 UNUSED, UNUSED, UNUSED }
00174 },
00175 
00176 
00177 #ifdef VMDPOLYHEDRA
00178 // Polyhedra
00179 { "Polyhedra", 1, {
00180 { AtomRep::SPHERERAD, 3.0f }, // distance
00181 UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, 
00182 UNUSED, UNUSED, UNUSED, UNUSED }
00183 },
00184 #endif
00185 
00186 //
00187 // Secondary structure reps
00188 //
00189 
00190 // C-alpha trace
00191 { "Trace", 2, {
00192 { AtomRep::BONDRAD, 0.3f},
00193 { AtomRep::BONDRES, DEF_BOND_RES},
00194 UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED,
00195 UNUSED, UNUSED, UNUSED }
00196 },
00197 
00198 // Tube
00199 { "Tube", 2, {
00200 { AtomRep::BONDRAD, 0.3f },
00201 { AtomRep::BONDRES, DEF_BOND_RES},
00202 UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED,
00203 UNUSED, UNUSED, UNUSED }
00204 },
00205 
00206 // Ribbons
00207 { "Ribbons", 3, {
00208 { AtomRep::BONDRAD, 0.3f},
00209 { AtomRep::BONDRES, DEF_BOND_RES},
00210 { AtomRep::LINETHICKNESS, 2.0f},
00211 UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED,
00212 UNUSED, UNUSED, UNUSED }
00213 },
00214 
00215 // NewRibbons
00216 { "NewRibbons", 4, {
00217 { AtomRep::BONDRAD, 0.3f },
00218 { AtomRep::BONDRES, 12.0f },
00219 { AtomRep::LINETHICKNESS, 3.0f},
00220 { AtomRep::SPHERERAD, 0}, // spline basis
00221 UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED,
00222 UNUSED, UNUSED, UNUSED }
00223 },
00224 
00225 // Structure
00226 { "Cartoon", 3, {
00227 { AtomRep::BONDRAD, 2.1f},
00228 { AtomRep::BONDRES, 24.0f },
00229 { AtomRep::LINETHICKNESS, 5.0f},
00230 UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED,
00231 UNUSED, UNUSED, UNUSED }
00232 },
00233 
00234 // NewCartoon
00235 { "NewCartoon", 4, {
00236 { AtomRep::BONDRAD, 0.3f },
00237 { AtomRep::BONDRES, 12.0f },
00238 { AtomRep::LINETHICKNESS, 4.5f},
00239 { AtomRep::SPHERERAD, 0}, // spline basis
00240 UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED,
00241 UNUSED, UNUSED, UNUSED }
00242 },
00243 
00244 #ifdef VMDWITHCARBS
00245 // PaperChain
00246 { "PaperChain", 2, {
00247 { AtomRep::LINETHICKNESS, 1.0f }, // bipyramid_height : height of the pyramids drawn to represent rings
00248 { AtomRep::ISOSTEPSIZE, 10 }, // maxringsize : maximum number of atoms in a small ring
00249 UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, 
00250 UNUSED, UNUSED, UNUSED, UNUSED, UNUSED }
00251 },
00252 
00253 // Twister
00254 { "Twister", 7, {
00255 { AtomRep::LINETHICKNESS, 1 }, // start_end_centroid : 0 - start ribbons at the edge of the ring, 1 - start ribbons at the ring centroids
00256 { AtomRep::BONDRES, 0 }, // hide_shared_links: 0 - show all linkage paths, 1 - hide linkage paths which share edges with other paths
00257 { AtomRep::SPHERERAD, 10 }, // rib_steps : number of steps to use when drawing ribbons
00258 { AtomRep::BONDRAD, 0.3f }, // rib_width : width of the ribbon
00259 { AtomRep::SPHERERES, 0.05f }, // rib_height : height of the ribbon
00260 { AtomRep::ISOSTEPSIZE, 10 }, // maxringsize : maximum number of atoms in a small ring
00261 { AtomRep::ISOLINETHICKNESS, 5 }, // maxpathlength : maximum number of atoms in a path joining two small rings
00262 UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED }
00263 },
00264 #endif
00265 
00266 
00267 //
00268 // Surface, Isosurface, and Solvent reps
00269 //
00270 
00271 #ifdef VMDQUICKSURF
00272 // QuickSurf
00273 { "QuickSurf", 4, {
00274 { AtomRep::SPHERERAD, 1.0f }, // sphere radius multiplier
00275 { AtomRep::BONDRAD, 0.5f }, // density isovalue for surface
00276 { AtomRep::GRIDSPACING, 1.0f}, // lattice grid spacing 
00277 { AtomRep::BONDRES, 0 }, // quality
00278 UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED,
00279 UNUSED, UNUSED, UNUSED }
00280 },
00281 #endif
00282 
00283 #ifdef VMDMSMS
00284 // MSMS surface
00285 { "MSMS", 4, {
00286 { AtomRep::SPHERERAD, 1.5f }, // probe radius
00287 { AtomRep::SPHERERES, 1.5f }, // density
00288 { AtomRep::LINETHICKNESS, 0}, // all atoms
00289 { AtomRep::BONDRES, 0}, // wireframe
00290 UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED,
00291 UNUSED, UNUSED, UNUSED }
00292 },
00293 #endif
00294 
00295 #ifdef VMDNANOSHAPER
00296 // NanoShaper surface
00297 { "NanoShaper", 6, {
00298 { AtomRep::LINETHICKNESS, 0}, // surface type
00299 { AtomRep::BONDRES, 0}, // wireframe
00300 { AtomRep::GRIDSPACING, 0.5f}, // lattice grid spacing 
00301 { AtomRep::SPHERERAD, 1.40f }, // probe radius
00302 { AtomRep::SPHERERES, 0.45f }, // skin parm
00303 { AtomRep::BONDRAD, 0.5f }, // blob parm
00304 UNUSED, UNUSED, UNUSED, UNUSED, UNUSED,
00305 UNUSED, UNUSED, UNUSED }
00306 },
00307 #endif
00308 
00309 #ifdef VMDSURF
00310 // Surf
00311 { "Surf", 2, {
00312 { AtomRep::SPHERERAD, 1.4f }, // probe radius
00313 { AtomRep::BONDRES, 0}, // wireframe
00314 UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED,
00315 UNUSED, UNUSED, UNUSED }
00316 },
00317 #endif
00318 
00319 // Slice of volumetric data
00320 { "VolumeSlice", 4, {
00321 { AtomRep::SPHERERAD, 0.5f }, // slice
00322 { AtomRep::SPHERERES, 0 }, // VolID
00323 { AtomRep::LINETHICKNESS, 0 }, // slice axis
00324 { AtomRep::BONDRES, 2 }, // quality
00325 UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED,
00326 UNUSED, UNUSED, UNUSED }
00327 },
00328 
00329 // Isosurface of volumetric data
00330 { "Isosurface", 6, {
00331 { AtomRep::SPHERERAD, 0.5f }, // isoval
00332 { AtomRep::SPHERERES, 0}, // VolID
00333 { AtomRep::LINETHICKNESS, 2}, // draw box and isosurface by default
00334 { AtomRep::BONDRES, 2}, // use points method by default
00335 { AtomRep::ISOSTEPSIZE, 1}, // use step size of one by default
00336 { AtomRep::ISOLINETHICKNESS, 1}, // lines are thickness one by default
00337 UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED,
00338 UNUSED, UNUSED, UNUSED }
00339 },
00340 
00341 // Volumetric gradient field lines
00342 { "FieldLines", 8, {
00343 { AtomRep::SPHERERES, 0}, // VolID
00344 { AtomRep::SPHERERAD, 1.8f}, // seed value
00345 { AtomRep::BONDRAD, 10.0f}, // minimum line length
00346 { AtomRep::BONDRES, 50.0f}, // maximum line length
00347 { AtomRep::LINETHICKNESS, 1}, // line thickness
00348 { AtomRep::FIELDLINESTYLE, 0}, // field lines drawn as lines
00349 { AtomRep::FIELDLINESEEDUSEGRID, 0}, // field line seed type
00350 { AtomRep::FIELDLINEDELTA, 0.25}, // field lines integrator stepsize
00351 UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED}
00352 },
00353 
00354 // Molecular orbital
00355 { "Orbital", 10, {
00356 { AtomRep::SPHERERAD, 0.05f}, // isoval
00357 { AtomRep::SPHERERES, 0}, // Orbital ID
00358 { AtomRep::LINETHICKNESS, 0}, // draw only isosurface by default
00359 { AtomRep::BONDRES, 0}, // use solid method by default
00360 { AtomRep::GRIDSPACING, 0.075f}, // default orbital grid spacing
00361 { AtomRep::ISOLINETHICKNESS, 1}, // lines are thickness one by default
00362 { AtomRep::WAVEFNCTYPE, 0}, // default wavefunction type 
00363 { AtomRep::WAVEFNCSPIN, 0}, // default wavefunction spin
00364 { AtomRep::WAVEFNCEXCITATION, 0}, // default wavefunction excitation
00365 { AtomRep::ISOSTEPSIZE, 1}, // use step size of one by default
00366 UNUSED, UNUSED, UNUSED, UNUSED, UNUSED }
00367 },
00368 
00369 // Beads 
00370 { "Beads", 2, {
00371 { AtomRep::SPHERERAD, 1.0f},
00372 { AtomRep::SPHERERES, DEF_SPH_RES },
00373 UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED,
00374 UNUSED, UNUSED, UNUSED }
00375 },
00376 
00377 // Dotted
00378 { "Dotted", 2, {
00379 { AtomRep::SPHERERAD, 1.0f},
00380 { AtomRep::SPHERERES, DEF_SPH_RES},
00381 UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED,
00382 UNUSED, UNUSED, UNUSED }
00383 },
00384 
00385 // Dot surface
00386 { "Solvent", 3, {
00387 { AtomRep::SPHERERAD, 0 }, // probe
00388 // the max value is set in the constructor for AtomRep, so don't
00389 // change things around too much!
00390 { AtomRep::SPHERERES, 7.0f}, // detail
00391 { AtomRep::LINETHICKNESS, 1.0f }, // method
00392 UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED,
00393 UNUSED, UNUSED, UNUSED }
00394 #ifdef VMDLATTICECUBES
00395 },
00396 
00397 // LatticeCubes
00398 { "LatticeCubes", 1, {
00399 { AtomRep::SPHERERAD, 1.0f},
00400 UNUSED, 
00401 UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED, UNUSED,
00402 UNUSED, UNUSED, UNUSED }
00403 }
00404 #else
00405 }
00406 #endif
00407 
00408 };
00409 
00410 
00412 // constructor; parse string and see if OK
00413 AtomRep::AtomRep(void) {
00414 int i, j;
00415 
00416 // initialize variables
00417 repMethod = DEFAULT_ATOMREP;
00418 repData = repDataStorage[repMethod];
00419 strcpy(cmdStr, AtomRepInfo[repMethod].name);
00420 for(j=0; j < TOTAL; j++) {
00421 memset(repDataStorage[j], 0, MAX_ATOMREP_DATA*sizeof(float));
00422 for(i=0; i < AtomRepInfo[j].numdata ; i++)
00423 repDataStorage[j][AtomRepInfo[j].repdata[i].index] =
00424 AtomRepInfo[j].repdata[i].defValue;
00425 }
00426 
00427 }
00428 
00429 AtomRep::~AtomRep(void) { }
00430 
00432 // parse the given command, and store results. Return success.
00433 int AtomRep::parse_cmd(const char *newcmd) {
00434 int argc, i, j;
00435 char *argv[256], *cmdStrTok = NULL;
00436 
00437 // make sure the new command is not too long
00438 if(newcmd && strlen(newcmd) > MAX_ATOMREP_CMD) {
00439 msgErr << "Atom representation string is too long (over ";
00440 msgErr << MAX_ATOMREP_CMD << " characters)." << sendmsg;
00441 return FALSE;
00442 }
00443 
00444 // XXX Hack to make the "Off" rep work: alias to "Lines"
00445 if (!strupncmp(newcmd, "off", 3)) newcmd = "Lines";
00446 
00447 // tokenize the command
00448 if(!newcmd || !(cmdStrTok = str_tokenize(newcmd, &argc, argv))) {
00449 // no command; keep current settings
00450 return TRUE;
00451 }
00452 
00453 // see if the command matches a representation we know about
00454 for(i=0; i < AtomRep::TOTAL; i++) {
00455 const AtomRepParamStruct *ari = &(AtomRepInfo[i]);
00456 
00457 if(!strupncmp(argv[0], ari->name, CMDLEN)) {
00458 // the name matches; make sure we do not have too many arguments
00459 if((argc - 1) > ari->numdata) {
00460 msgErr << "Incorrect atom representation command '" << newcmd << "':";
00461 msgErr << "\n '" << ari->name << "' only takes " << ari->numdata;
00462 msgErr << " arguments maximum." << sendmsg;
00463 
00464 delete [] cmdStrTok;
00465 return FALSE;
00466 }
00467 
00468 // indicate that we've changed to a new rep method
00469 repMethod = i;
00470 repData = repDataStorage[i];
00471 
00472 // copy out the data from the command and store it
00473 for(j=1; j < argc; j++) {
00474 // if a '-' is given, do not change that parameter
00475 if(!(argv[j][0] == '-' && argv[j][1] == '0円'))
00476 repData[ari->repdata[j-1].index] = (float) atof(argv[j]);
00477 }
00478 
00479 // found a match; break from for loop
00480 break;
00481 }
00482 }
00483 
00484 // if i is at the end of the list, we did not find a match
00485 if(i == AtomRep::TOTAL) {
00486 msgErr << "Unknown atom representation command '" << newcmd << "'.";
00487 msgErr << sendmsg;
00488 
00489 delete [] cmdStrTok;
00490 return FALSE;
00491 }
00492 
00493 // if we are here, everything went OK
00494 strcpy(cmdStr, newcmd);
00495 
00496 delete [] cmdStrTok;
00497 return TRUE;
00498 }
00499 
00500 
00502 
00503 // copy contents of another atomrep
00504 AtomRep &AtomRep::operator=(const AtomRep &ar) {
00505 strcpy(cmdStr, ar.cmdStr);
00506 repMethod = ar.repMethod;
00507 repData = repDataStorage[repMethod];
00508 for(int j=0; j < TOTAL; j++)
00509 for(int i=0; i < MAX_ATOMREP_DATA; i++)
00510 repDataStorage[j][i] = ar.repDataStorage[j][i];
00511 
00512 return *this;
00513 }
00514