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// $Id: mmdb_selmngr.h $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
// functionality in protein crystallography applications.
//
// Copyright (C) Eugene Krissinel 2000-2013.
//
// 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.
//
// =================================================================
//
// 15.09.13 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
// **** Module : mmdb_selmngr <interface>
// ~~~~~~~~~
// Project : MacroMolecular Data Base (MMDB)
// ~~~~~~~~~
// **** Classes : mmdb::Manager ( MMDB atom selection manager )
// ~~~~~~~~~
//
// (C) E. Krissinel 2000-2013
//
// =================================================================
//
#ifndef __MMDB_SelMngr__
#define __MMDB_SelMngr__
#include "mmdb_coormngr.h"
#include "mmdb_mask.h"
namespace mmdb {
// ======================= SelManager ==========================
// 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.
enum SELECTION_KEY {
SKEY_NEW = 0,
SKEY_OR = 1,
SKEY_AND = 2,
SKEY_XOR = 3,
SKEY_CLR = 4,
SKEY_XAND = 100 // used internally
};
// Selection types
enum SELECTION_TYPE {
STYPE_INVALID = -1,
STYPE_UNDEFINED = 0,
STYPE_ATOM = 1,
STYPE_RESIDUE = 2,
STYPE_CHAIN = 3,
STYPE_MODEL = 4
};
// Residue properties for SelectProperties()
enum SELECTION_PROPERTY {
SELPROP_Solvent = 0,
SELPROP_Aminoacid = 1,
SELPROP_Nucleotide = 2,
SELPROP_Sugar = 3,
SELPROP_ModRes = 4
};
// comparison rules for SelectUDD function
enum UDD_CMP_RULE {
UDSCR_LT = 1,
UDSCR_LE = 2,
UDSCR_EQ = 3,
UDSCR_NE = 4,
UDSCR_GE = 5,
UDSCR_GT = 6,
UDSCR_LTcase = 7,
UDSCR_LEcase = 8,
UDSCR_EQcase = 9,
UDSCR_NEcase = 10,
UDSCR_GEcase = 11,
UDSCR_GTcase = 12,
UDSCR_LTn = 13,
UDSCR_LEn = 14,
UDSCR_EQn = 15,
UDSCR_NEn = 16,
UDSCR_GEn = 17,
UDSCR_GTn = 18,
UDSCR_LTncase = 19,
UDSCR_LEncase = 20,
UDSCR_EQncase = 21,
UDSCR_NEncase = 22,
UDSCR_GEncase = 23,
UDSCR_GTncase = 24,
UDSCR_Substr = 25,
UDSCR_NoSubstr = 26,
UDSCR_Substr1 = 27,
UDSCR_NoSubstr1 = 28
};
DefineClass(SelManager);
DefineStreamFunctions(SelManager);
class SelManager : public CoorManager {
public :
SelManager ();
SelManager ( io::RPStream Object );
~SelManager();
// ==================== 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,
SELECTION_KEY 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,
SELECTION_KEY 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, PAtom A,
SELECTION_KEY selKey=SKEY_OR,
bool makeIndex=true );
// SelectResidue(..), SelectChain(..) and SelectModel(..)
// select a single residue, chain or model, or all their
// hierarchical descendants depending on the value of sType
// (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, PResidue Res,
SELECTION_TYPE sType,
SELECTION_KEY sKey,
bool makeIndex );
void SelectChain ( int selHnd, PChain chain,
SELECTION_TYPE sType,
SELECTION_KEY sKey,
bool makeIndex );
void SelectModel ( int selHnd, PModel mdl,
SELECTION_TYPE sType,
SELECTION_KEY sKey,
bool 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
SELECTION_KEY 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'
SELECTION_KEY selKey=SKEY_OR // selection key
);
// Selecting by integer User-Defined Data
void SelectUDD (
int selHnd, // must be obtained from NewSelection()
SELECTION_TYPE sType, // selection type STYPE_XXXXX
int UDDhandle, // UDD handle
int selMin, // lower selection boundary
int selMax, // upper selection boundary
SELECTION_KEY sKey // selection key
);
void SelectUDD (
int selHnd, // must be obtained from NewSelection()
SELECTION_TYPE sType, // selection type STYPE_XXXXX
int UDDhandle, // UDD handle
realtype selMin, // lower selection boundary
realtype selMax, // upper selection boundary
SELECTION_KEY sKey // selection key
);
void SelectUDD (
int selHnd, // must be obtained from NewSelection()
SELECTION_TYPE sType, // selection type STYPE_XXXXX
int UDDhandle, // UDD handle
cpstr selStr, // selection string
int cmpRule, // comparison rule
SELECTION_KEY sKey // selection key
);
// Selecting a sphere
void SelectSphere (
int selHnd, // must be obtained from NewSelection()
SELECTION_TYPE sType, // 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
SELECTION_KEY sKey=SKEY_OR // selection key
);
// Selecting a cylinder
void SelectCylinder (
int selHnd, // must be obtained from NewSelection()
SELECTION_TYPE sType, // 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
SELECTION_KEY sKey=SKEY_OR // selection key
);
// Selecting all atoms on a given distance from a plane
void SelectSlab (
int selHnd, // must be obtained from NewSelection()
SELECTION_TYPE sType, // 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
SELECTION_KEY sKey=SKEY_OR // selection key
);
// Selecting all atoms on a given distance from already selected
void SelectNeighbours (
int selHnd, // must be obtained from NewSelection()
SELECTION_TYPE sType, // selection type STYPE_XXXXX
PPAtom 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
SELECTION_KEY sKey=SKEY_OR // selection key
);
int GetSelLength ( int selHnd );
// Getting an array of atoms selected for a certain mask
void GetSelIndex (
int selHnd, // selection mask
PPAtom & 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
PPResidue & 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
PPChain & 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
PPModel & 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, RAtomStat 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()
SELECTION_TYPE sType, // 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
SELECTION_KEY sKey=SKEY_OR // selection key
);
// Selecting by just atom ID, no other conditions
void Select (
int selHnd, // must be obtained from NewSelection()
SELECTION_TYPE sType, // 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'
SELECTION_KEY sKey=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()
SELECTION_TYPE sType, // selection type STYPE_XXXXX
cpstr CID, // coordinate ID
SELECTION_KEY sKey // selection key
);
// Propagating the selection up and down coordinate hierarchy
void Select (
int selHnd1, // must be obtained from NewSelection()
SELECTION_TYPE sType, // selection type STYPE_XXXXX
int selHnd2, // must be obtained from NewSelection()
// and have been used for selection
SELECTION_KEY sKey=SKEY_OR // selection key
);
void SelectProperty (
int selHnd, // must be obtained from NewSelection()
SELECTION_PROPERTY propKey, // property key SELPROP_XXXXXXX
SELECTION_TYPE sType, // selection type STYPE_XXXXX
SELECTION_KEY sKey // 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,
SELECTION_TYPE sType,
SELECTION_KEY sKey,
int modelNo=1 );
void DeleteSelObjects ( int selHnd );
protected :
// --- SELECTION DATA NOT FOR PUBLIC ACCESS
int nSelections; // number of selections
PPMask mask; // vector of selections
SELECTION_TYPE *selType; // vector of selection types
ivector nSelItems; // numbers of selected items
PPMask * selection; // vector of selected items
// --------------- Stream I/O -----------------------------
void write ( io::RFile f );
void read ( io::RFile f );
void InitSelManager();
void SelectAtom ( PAtom atm, int maskNo,
SELECTION_KEY sKey, int & nsel );
void SelectObject ( SELECTION_TYPE sType, PAtom atm,
int maskNo, SELECTION_KEY sKey,
int & nsel );
void SelectObject ( PMask object, int maskNo,
SELECTION_KEY sKey, int & nsel );
void MakeSelIndex ( int selHnd, SELECTION_TYPE sType,
int nsel );
void ResetManager();
PMask GetSelMask ( int selHnd );
};
} // namespace mmdb
#endif
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