/usr/include/mmdb/mmdb_selmngr.h is in libmmdb-dev 1.23.2.1-0ubuntu1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 | // =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
// functionality in protein crystallography applications.
//
// Copyright (C) Eugene Krissinel 2000-2008.
//
// This library is free software: you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License version 3, modified in accordance with the provisions
// of the license to address the requirements of UK law.
//
// You should have received a copy of the modified GNU Lesser
// General Public License along with this library. If not, copies
// may be downloaded from http://www.ccp4.ac.uk/ccp4license.php
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU Lesser General Public License for more details.
//
// =================================================================
//
// 08.07.08 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
// **** Module : mmdb_selmngr <interface>
// ~~~~~~~~~
// Project : MacroMolecular Data Base (MMDB)
// ~~~~~~~~~
// **** Classes : CMMDBSelManager ( MMDB atom selection manager )
// ~~~~~~~~~
//
// (C) E. Krissinel 2000-2008
//
// =================================================================
//
#ifndef __MMDB_SelMngr__
#define __MMDB_SelMngr__
#ifndef __MMDB_CoorMngr__
#include "mmdb_coormngr.h"
#endif
#ifndef __MMDB_Mask__
#include "mmdb_mask.h"
#endif
// ====================== CMMDBSelManager =========================
// Selection keys. These specify how the requested selection
// operation applies to the existing selection for the given mask:
// SKEY_NEW previous selection is wiped out
// SKEY_OR new selection is added to the already selected set;
// if no selection preexists, SKEY_NEW and SKEY_OR
// are equivalent. This key is the default one in
// all selection functions.
// SKEY_AND new selection is made on the already selected set;
// this corresponds to logical 'and' of former and
// current selections. If no selection preexists,
// no selection will be made.
// SKEY_XOR only those atoms will be left which are found
// in either former or newly selected sets, but not
// in both of them; this corresponds to logical
// 'exclusive or' of previous and current selections.
// If no selection preexists, it is equivalent to
// SKEY_OR.
#define SKEY_NEW 0
#define SKEY_OR 1
#define SKEY_AND 2
#define SKEY_XOR 3
#define SKEY_CLR 4
// Selection types
#define STYPE_INVALID (-1)
#define STYPE_UNDEFINED 0
#define STYPE_ATOM 1
#define STYPE_RESIDUE 2
#define STYPE_CHAIN 3
#define STYPE_MODEL 4
// Residue properties for SelectProperties()
#define SELPROP_Solvent 0
#define SELPROP_Aminoacid 1
#define SELPROP_Nucleotide 2
#define SELPROP_Sugar 3
#define SELPROP_ModRes 4
// comparison rules for SelectUDD function
#define UDSCR_LT 1
#define UDSCR_LE 2
#define UDSCR_EQ 3
#define UDSCR_NE 4
#define UDSCR_GE 5
#define UDSCR_GT 6
#define UDSCR_LTcase 7
#define UDSCR_LEcase 8
#define UDSCR_EQcase 9
#define UDSCR_NEcase 10
#define UDSCR_GEcase 11
#define UDSCR_GTcase 12
#define UDSCR_LTn 13
#define UDSCR_LEn 14
#define UDSCR_EQn 15
#define UDSCR_NEn 16
#define UDSCR_GEn 17
#define UDSCR_GTn 18
#define UDSCR_LTncase 19
#define UDSCR_LEncase 20
#define UDSCR_EQncase 21
#define UDSCR_NEncase 22
#define UDSCR_GEncase 23
#define UDSCR_GTncase 24
#define UDSCR_Substr 25
#define UDSCR_NoSubstr 26
#define UDSCR_Substr1 27
#define UDSCR_NoSubstr1 28
DefineClass(CMMDBSelManager)
DefineStreamFunctions(CMMDBSelManager)
class CMMDBSelManager : public CMMDBCoorManager {
public :
CMMDBSelManager ();
CMMDBSelManager ( RPCStream Object );
~CMMDBSelManager();
// ==================== Selecting atoms =======================
// NewSelection() creates a new selection mask and returns its
// handle. A handle is always a positive (non-zero) integer.
// Calling NewSelection() is the only way to create a new
// selection mask. Notice however that masks will be automatically
// copied from another MMDB (see Copy(..) in CMMDBManager) if
// coordinates are copied; if this is the case, the mask handles
// will be inherited from the source MMDB as well. The masks will
// also be automatically deleted (see Delete(..) in CMMDBManager())
// if coordinates are deleted.
int NewSelection ();
int GetSelType ( int selHnd ); // returns STYPE_XXXX
// DeleteSelection(..) deletes the specified selection mask
// and removes the corresponding selection attributes from
// all atoms, which were selected with this mask. If an atom
// was selected also with other mask(s), the other selection(s)
// will remain, provided that the corresponding masks are valid.
// After DeleteSelection() returns, the corresponding mask
// becomes invalid.
void DeleteSelection ( int selHnd );
// DeleteAllSelections() deletes all selection masks and
// unselects all atoms in the file. All mask handles become
// invalid.
void DeleteAllSelections();
// SelectAtoms(..) selects atoms in the serial number range
// of iSer1 to iSer2 by adding them to the set of atoms
// marked by the given mask. If iSer1=iSer2=0 then all atoms
// are selected. Each atom may be selected by a number of masks
// simultaneously.
void SelectAtoms ( int selHnd, int iSer1, int iSer2,
int selKey=SKEY_OR // selection key
);
// SelectAtoms(..) selects atoms with serial numbers given in
// vector asn[0..nsn-1].
void SelectAtoms ( int selHnd, ivector asn, int nsn,
int selKey=SKEY_OR // selection key
);
// UnselectAtoms(..) clears the specified mask for atoms in
// the serial number range of iSer1 to iSer2. If iSer1=iSer2=0
// then all atoms are cleared of the specified mask. If selHnd
// is set to 0, then the atoms are cleared of any mask.
void UnselectAtoms ( int selHnd, int iSer1, int iSer2 );
// SelectAtom(..) selects a single atom according to the value
// of selection key. If makeIndex is False, then the routine
// does not update the selection index. This saves time, but
// prevents GetSelIndex(..) from accessing all selected atoms.
// In order to update the index after all single-atom selections
// are done, use MakeSelIndex(selHnd) found next.
void SelectAtom ( int selHnd, PCAtom A, int selKey=SKEY_OR,
Boolean makeIndex=True );
// SelectResidue(..), SelectChain(..) and SelectModel(..)
// select a single residue, chain or model, or all their
// hierarchical descendants depending on the value of selType
// (i.e. atoms, residues (in chain and model) and chains
// (in model only). Ascending hierarchical objects should be
// selected explicitely, e.g. atom->GetResidue()->SelectResidue(..)
void SelectResidue ( int selHnd, PCResidue Res,
int selType, int selKey,
Boolean makeIndex );
void SelectChain ( int selHnd, PCChain Chain,
int selType, int selKey,
Boolean makeIndex );
void SelectModel ( int selHnd, PCModel model,
int selType, int selKey,
Boolean makeIndex );
// MakeSelIndex(.) calculates selection index for selection
// adressed by selHnd. All selection functions except the
// SelectAtom(..) above, update selection index automatically.
// This function is for use after a series of calls to
// SelectAtom(..) with makeIndex parameter set False. This
// combination of SelectAtom - MakeSelIndex considerably saves CPU
// at extensive selections.
// MakeSelIndex(.) returns the number of selected objects.
int MakeSelIndex ( int selHnd );
void MakeAllSelIndexes();
// Selecting by atom ID, space condition (a sphere) and some
// other bits.
void SelectAtoms (
int selHnd, // must be obtained from NewSelection()
int iModel, // model number; iModel=0 means
// 'any model'
cpstr Chains, // may be several chains "A,B,W"; "*"
// means 'any chain' (in selected
// model(s))
int ResNo1, // starting residue sequence number
cpstr Ins1, // starting residue insertion code; "*"
// means 'any code'
int ResNo2, // ending residue sequence number.
cpstr Ins2, // ending residue insertion code; "*"
// means 'any code'. Combination of
// ResNo1=ResNo2=ANY_RES and
// Ins1=Ins2="*" means 'any residue'
// (in selected chain(s))
cpstr RNames, // may be several residue names
// "ALA,GLU,CIS"; "*" means 'any
// residue name'
cpstr ANames, // may be several names "CA,CB"; "*"
// means 'any atom' (in selected
// residue(s))
cpstr Elements, // may be several element types
// 'H,C,O,CU'; "*" means 'any element'
cpstr altLocs, // may be several alternative
// locations 'A,B'; "*" means
// 'any alternative location'
cpstr Segments, // may be several segment IDs
// like "S1,S2,A234"; "*" means
// 'any segment'
cpstr Charges, // may be several charges like
// "+1,-2, "; "*" means 'any charge'
realtype occ1, // lowest occupancy
realtype occ2, // highest occupancy; occ1=occ2<0.0
// means "any occupancy"
realtype x0, // reference x-point
realtype y0, // reference y-point
realtype z0, // reference z-point
realtype d0, // selection distance from the
// reference point; d0<=0.0
// means "any distance" and values
// of x0, y0 and z0 are ignored
int selKey=SKEY_OR // selection key
);
// Selecting by just atom ID, no other conditions
void SelectAtoms (
int selHnd, // must be obtained from NewSelection()
int iModel, // model number; iModel=0 means
// 'any model'
cpstr Chains, // may be several chains "A,B,W"; "*"
// means 'any chain' (in selected
// model(s))
int ResNo1, // starting residue sequence number
cpstr Ins1, // starting residue insertion code; "*"
// means 'any code'
int ResNo2, // ending residue sequence number.
cpstr Ins2, // ending residue insertion code; "*"
// means 'any code'. Combination of
// ResNo1=ResNo2=ANY_RES and
// Ins1=Ins2="*" means 'any residue
// number' (in selected chain(s))
cpstr RNames, // may be several residue names
// "ALA,GLU,CIS"; "*" means 'any
// residue name'
cpstr ANames, // may be several names "CA,CB"; "*"
// means 'any atom' (in selected
// residue(s))
cpstr Elements, // may be several element types
// "H,C,O,CU"; "*" means 'any element'
cpstr altLocs, // may be several alternative
// locations 'A,B'; "*" means
// 'any alternative location'
int selKey=SKEY_OR // selection key
);
// Selecting by integer User-Defined Data
void SelectUDD (
int selHnd, // must be obtained from NewSelection()
int selType, // selection type STYPE_XXXXX
int UDDhandle, // UDD handle
int selMin, // lower selection boundary
int selMax, // upper selection boundary
int selKey // selection key
);
void SelectUDD (
int selHnd, // must be obtained from NewSelection()
int selType, // selection type STYPE_XXXXX
int UDDhandle, // UDD handle
realtype selMin, // lower selection boundary
realtype selMax, // upper selection boundary
int selKey // selection key
);
void SelectUDD (
int selHnd, // must be obtained from NewSelection()
int selType, // selection type STYPE_XXXXX
int UDDhandle, // UDD handle
cpstr selStr, // selection string
int cmpRule, // comparison rule
int selKey // selection key
);
// Selecting a sphere
void SelectSphere (
int selHnd, // must be obtained from NewSelection()
int selType, // selection type STYPE_XXXXX
realtype x, // x-coordinate of the sphere's center
realtype y, // y-coordinate of the sphere's center
realtype z, // z-coordinate of the sphere's center
realtype r, // radius of the sphere
int selKey=SKEY_OR // selection key
);
// Selecting a cylinder
void SelectCylinder (
int selHnd, // must be obtained from NewSelection()
int selType, // selection type STYPE_XXXXX
realtype x1, // x-coordinate of the cylinder axis' 1st end
realtype y1, // y-coordinate of the cylinder axis' 1st end
realtype z1, // z-coordinate of the cylinder axis' 1st end
realtype x2, // x-coordinate of the cylinder axis' 2nd end
realtype y2, // y-coordinate of the cylinder axis' 2nd end
realtype z2, // z-coordinate of the cylinder axis' 2nd end
realtype r, // radius of the cylinder
int selKey=SKEY_OR // selection key
);
// Selecting all atoms on a given distance from a plane
void SelectSlab (
int selHnd, // must be obtained from NewSelection()
int selType, // selection type STYPE_XXXXX
realtype a, // a-parameter of the plane ax+by+cz=d
realtype b, // b-parameter of the plane ax+by+cz=d
realtype c, // c-parameter of the plane ax+by+cz=d
realtype d, // d-parameter of the plane ax+by+cz=d
realtype r, // distance to the plane
int selKey=SKEY_OR // selection key
);
// Selecting all atoms on a given distance from already selected
void SelectNeighbours (
int selHnd, // must be obtained from NewSelection()
int selType, // selection type STYPE_XXXXX
PPCAtom sA, // array of already selected atoms
int alen, // length of A
realtype d1, // minimal distance to already selected atoms
realtype d2, // maximal distance to already selected atoms
int selKey=SKEY_OR // selection key
);
int GetSelLength ( int selHnd );
// Getting an array of atoms selected for a certain mask
void GetSelIndex (
int selHnd, // selection mask
PPCAtom & SelAtom, // continuous index of selected
// atoms; application must not
// dispose either index or atoms
int & nSelAtoms // length of index
// [0..nSelectedAtoms-1]
);
// Getting an array of residues selected for a certain mask
void GetSelIndex (
int selHnd, // selection mask
PPCResidue & SelResidues, // continuous index of selected
// residues; application must
// not dispose either index or
// residues
int & nSelResidues // length of index
// [0..nSelResidues-1]
);
// Getting an array of chains selected for a certain mask
void GetSelIndex (
int selHnd, // selection mask
PPCChain & SelChains, // continuous index of selected
// chains; application must not
// dispose either index or chains
int & nSelChains // length of index
// [0..nSelChains-1]
);
// Getting an array of models selected for a certain mask
void GetSelIndex (
int selHnd, // selection mask
PPCModel & SelModels, // continuous index of selected
// models; application must not
// dispose either index or models
int & nSelModels // length of index
// [0..nSelModels-1]
);
void GetAtomStatistics ( int selHnd, RSAtomStat AS );
// =============== General selection functions ================
// Selecting by atom ID, space condition (a sphere) and some
// other bits.
void Select (
int selHnd, // must be obtained from NewSelection()
int selType, // selection type STYPE_XXXXX
int iModel, // model number; iModel=0 means
// 'any model'
cpstr Chains, // may be several chains "A,B,W"; "*"
// means 'any chain' (in selected
// model(s))
int ResNo1, // starting residue sequence number
cpstr Ins1, // starting residue insertion code; "*"
// means 'any code'
int ResNo2, // ending residue sequence number.
cpstr Ins2, // ending residue insertion code; "*"
// means 'any code'. Combination of
// ResNo1=ResNo2=ANY_RES and
// Ins1=Ins2="*" means 'any residue'
// (in selected chain(s))
cpstr RNames, // may be several residue names
// "ALA,GLU,CIS"; "*" means
// 'any residue name'
cpstr ANames, // may be several names "CA,CB"; "*"
// means 'any atom' (in selected
// residue(s))
cpstr Elements, // may be several element types
// 'H,C,O,CU'; "*" means 'any element'
cpstr altLocs, // may be several alternative
// locations 'A,B'; "*" means
// 'any alternative location'
cpstr Segments, // may be several segment IDs like
// "S1,S2,A234"; "*" means
// 'any segment'
cpstr Charges, // may be several charges like
// "+1,-2, "; "*" means 'any charge'
realtype occ1, // lowest occupancy
realtype occ2, // highest occupancy; occ1=occ2<0.0
// means "any occupancy"
realtype x0, // reference x-point
realtype y0, // reference y-point
realtype z0, // reference z-point
realtype d0, // selection distance from the
// reference point; d0<=0.0
// means "any distance" and values
// of x0, y0 and z0 are ignored
int selKey=SKEY_OR // selection key
);
// Selecting by just atom ID, no other conditions
void Select (
int selHnd, // must be obtained from NewSelection()
int selType, // selection type STYPE_XXXXX
int iModel, // model number; iModel=0 means
// 'any model'
cpstr Chains, // may be several chains "A,B,W"; "*"
// means 'any chain' (in selected
// model(s))
int ResNo1, // starting residue sequence number
cpstr Ins1, // starting residue insertion code; "*"
// means 'any code'
int ResNo2, // ending residue sequence number.
cpstr Ins2, // ending residue insertion code; "*"
// means 'any code'. Combination of
// ResNo1=ResNo2=ANY_RES and
// Ins1=Ins2="*" means 'any residue
// number' (in selected chain(s))
cpstr RNames, // may be several residue names
// "ALA,GLU,CIS"; "*" means
// 'any residue name'
cpstr ANames, // may be several names "CA,CB"; "*"
// means 'any atom' (in selected
// residue(s))
cpstr Elements, // may be several element types
// "H,C,O,CU"; "*" means 'any element'
cpstr altLocs, // may be several alternative
// locations 'A,B'; "*" means
// 'any alternative location'
int selKey=SKEY_OR // selection key
);
// Selecting by coordinate ID.
// Examples:
//
// 1. /mdl/chn/s1.i1-s2.i2/at[el]:aloc
// 2. /mdl/chn/*(res).ic /at[el]:aloc
// 3. chn/*(res).ic /at[el]:aloc
// 4. s1.i1-s2.i2/at[el]:aloc
// 5. s1.i1 /at[el]:aloc
// 6. /mdl
// 7. chn
// 8. s1.i1-s2.i2
// 9. (res)
// 10. at[el]:aloc
// 11. chn//[el]
//
// mdl - the model's serial number or 0 or '*' for any model
// (default).
// chn - the chain ID or list of chains 'A,B,C' or '*' for
// any chain (default).
// s1,s2 - the starting and ending residue sequence numbers
// or '*' for any sequence number (default).
// i1,i2 - the residues insertion codes or '*' for any
// insertion code. If the sequence number other than
// '*' is specified, then insertion code defaults to ""
// (no insertion code), otherwise the default is '*'.
// at - atom name or list of atom names 'CA,N1,O' or '*'
// for any atom name (default)
// el - chemical element name or list of chemical element
// names 'C,N,O' or '*' for any chemical element name
// (default)
// aloc - the alternative location indicator or '*' for any
// alternate location. If the atom name and chemical
// element name is specified (both may be '*'), then
// the alternative location indicator defaults to ""
// (no alternate location), otherwise the default is
// '*'.
//
// All spaces are ignored.
//
// Returns -1 if numerical format of model is wrong, -2 if
// numerical format for sequence number is wrong, and 0
// otherwise.
int Select (
int selHnd, // must be obtained from NewSelection()
int selType, // selection type STYPE_XXXXX
cpstr CID, // coordinate ID
int selKey // selection key
);
// Propagating the selection up and down coordinate hierarchy
void Select (
int selHnd1, // must be obtained from NewSelection()
int selType, // selection type STYPE_XXXXX
int selHnd2, // must be obtained from NewSelection()
// and have been used for selection
int selKey=SKEY_OR // selection key
);
void SelectProperty (
int selHnd, // must be obtained from NewSelection()
int propKey, // property key SELPROP_XXXXXXX
int selType, // selection type STYPE_XXXXX
int selKey // selection key
);
// In SelectDomain, domainRange is of the following format:
// "*", "(all)" - take all file
// "-" - take chain without chain ID
// "a:Ni-Mj,b:Kp-Lq,..." - take chain a residue number N
// insertion code i to residue numberM
// insertion code j plus chain b
// residue number K insertion code p to
// residue number L insertion code q
// and so on.
// "a:,b:..." - take whole chains a and b and so on
// "a:,b:Kp-Lq,..." - any combination of the above.
int SelectDomain ( int selHnd , cpstr domainRange,
int selType, int selKey, int modelNo=1 );
void DeleteSelObjects ( int selHnd );
protected :
// --- SELECTION DATA NOT FOR PUBLIC ACCESS
int nSelections; // number of selections
PPCMask Mask; // vector of selections
ivector SelType; // vector of selection types
ivector nSelItems; // numbers of selected items
PPCMask * Selection; // vector of selected items
// --------------- Stream I/O -----------------------------
void write ( RCFile f );
void read ( RCFile f );
void InitMMDBSelManager();
void SelectAtom ( PCAtom atom, int maskNo,
int selKey, int & nsel );
void SelectObject ( int selType, PCAtom atom, int maskNo,
int selKey, int & nsel );
void SelectObject ( PCMask object, int maskNo,
int selKey, int & nsel );
void MakeSelIndex ( int selHnd, int selType,
int nsel );
void ResetManager();
PCMask GetSelMask ( int selHnd );
};
#endif
|