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AtomSel Class Reference

This interacts with the AtomParser. More...

#include <AtomSel.h>

Inheritance diagram for AtomSel:

List of all members.

Public Types
enum	{ TS_LAST = -2, TS_NOW = -1 }
enum	{ NO_PARSE = -1, NO_EVAL = -2, PARSE_SUCCESS = 0 }
	return codes for the change() method. NO_PARSE if the string is not correct NO_EVAL if there was some problem finding the atoms in the selection otherwise PARSE_SUCCESS. NO_EVAL will still allow the atom selection to be used, although warning messages will be printed; whether this is the best semantics is questionable but since I don't know how to produce this kind of error we may as well let it slide. More...
Public Methods
int	molid () const
	molid of "my" molecule. More...
	AtomSel (VMDApp *vmdapp, SymbolTable *, int mymolid)
	~AtomSel ()
int	change (const char *newcmd, DrawMolecule *)
	provide new settings; does a 'find' at the end if a mol has been previously provided and returns the results for the given molecule, find atoms for the molecule. Stores the indices in 'on' for quick retrieval later. If newcmd is NULL, use existing atom selection text return one of the above enum's. More...
float *	coordinates (MoleculeList *) const
	get the current coordinates (or NULL if it doesn't exist/ no molecule) FIXME: This is just a wrapper around timestep() and should be eliminated. More...
Timestep *	timestep (MoleculeList *) const
	get the current timestep (or NULL if it doesn't exist/ no molecule). More...
Static Public Methods
int	get_frame_value (const char *s, int *val)
	given a string ("first", "last", "now", or a value) return the timestep value in *val returns -1 if there was a problem on error, if val > 0, the value of s wasn't understood if val < 0, the value was negative. More...
Public Attributes
char *	cmdStr
	string with the selection command. More...
int *	on
	per-atom 'selected' flags; 1=on, 0=off. More...
unsigned int *	on256
	per-256-atom first, last, selected count. More...
int	num_atoms
	number of atoms in mol. More...
int	num_atoms256
	number of atoms in mol. More...
int	selected
	number of selected atoms the molecule. More...
int	firstsel
	index of first selected atom. More...
int	lastsel
	index of final selected atom. More...
int	which_frame
int	do_update

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Detailed Description

This interacts with the AtomParser.

Definition at line 45 of file AtomSel.h.

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Member Enumeration Documentation

anonymous enum

Enumeration values: TS_LAST  TS_NOW  Definition at line 67 of file AtomSel.h.

anonymous enum

return codes for the change() method. NO_PARSE if the string is not correct NO_EVAL if there was some problem finding the atoms in the selection otherwise PARSE_SUCCESS. NO_EVAL will still allow the atom selection to be used, although warning messages will be printed; whether this is the best semantics is questionable but since I don't know how to produce this kind of error we may as well let it slide. Enumeration values: NO_PARSE  NO_EVAL  PARSE_SUCCESS  Definition at line 81 of file AtomSel.h.

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Constructor & Destructor Documentation

AtomSel::AtomSel (  VMDApp *    vmdapp, SymbolTable *   , int    mymolid )

Definition at line 2341 of file AtomSel.C. References cmdStr, do_update, firstsel, lastsel, NO_PARSE, NULL, num_atoms, num_atoms256, on, on256, selected, TS_NOW, and which_frame.

AtomSel::~AtomSel (    )

Definition at line 2361 of file AtomSel.C. References cmdStr, firstsel, lastsel, NO_PARSE, NULL, num_atoms, num_atoms256, on, on256, and selected.

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Member Function Documentation

int AtomSel::change (  const char *    newcmd, DrawMolecule *    )

provide new settings; does a 'find' at the end if a mol has been previously provided and returns the results for the given molecule, find atoms for the molecule. Stores the indices in 'on' for quick retrieval later. If newcmd is NULL, use existing atom selection text return one of the above enum's. Definition at line 2376 of file AtomSel.C. References analyze_selection_aligned_dispatch, cmdStr, VMDApp::cpucaps, ParseTree::evaluate, firstsel, lastsel, BaseMolecule::nAtoms, NO_EVAL, NO_PARSE, NULL, num_atoms, num_atoms256, on, on256, SymbolTable::parse, PARSE_SUCCESS, selected, stringdup, ParseTree::use_context, and which_frame. Referenced by access_tcl_atomsel, MoleculeList::add_rep, atomsel_new, VolMapCreate::calculate_minmax, DrawMolItem::change_sel, VolMapCreateCoulombPotentialMSM::compute_frame, VolMapCreateCoulombPotential::compute_frame, VolMapCreateDistance::compute_frame, VolMapCreateOccupancy::compute_frame, VolMapCreateInterp::compute_frame, VolMapCreateDensity::compute_frame, VolMapCreateMask::compute_frame, SaveTrajectoryFltkMenu::do_save, make_tcl_atomsel, measure_gofr, measure_rdf, py_atomselect, py_update, and AtomSelThr::update.

float * AtomSel::coordinates (  MoleculeList *    )  const

get the current coordinates (or NULL if it doesn't exist/ no molecule) FIXME: This is just a wrapper around timestep() and should be eliminated. Definition at line 2468 of file AtomSel.C. References NULL, Timestep::pos, and timestep. Referenced by assign_atoms, atomselect_move, atomselect_moveby, build_xyzr_from_sel, calc_density_bounds, VolMapCreate::calculate_minmax, center, center_of_mass, centerperresidue, VolMapCreateCoulombPotentialMSM::compute_frame, VolMapCreateCoulombPotential::compute_frame, VolMapCreateDistance::compute_frame, VolMapCreateOccupancy::compute_frame, VolMapCreateInterp::compute_frame, VolMapCreateDensity::compute_frame, VolMapCreateMask::compute_frame, contacts, fit, mdff_cc, mdff_sim, measure_clustsize, measure_dipole, measure_hbonds, measure_inertia, measure_rgyr, measure_rmsd_perresidue, measure_sasa_thread, minmax, VMDApp::molecule_from_selection_list, py_fit, py_hbonds, py_move, py_moveby, py_rmsd, py_rmsd_q, sasa, vmd_measure_center, vmd_measure_centerperresidue, vmd_measure_contacts, vmd_measure_fit, vmd_measure_hbonds, vmd_measure_minmax, vmd_measure_rmsd, vmd_measure_rmsd_qcp, vmd_measure_sasa, vmd_measure_surface, vmd_measure_volinterior, and vmd_volmap_ils.

int AtomSel::get_frame_value (  const char *    s, int *    val )  [static]

given a string ("first", "last", "now", or a value) return the timestep value in *val returns -1 if there was a problem on error, if val > 0, the value of s wasn't understood if val < 0, the value was negative. Definition at line 2502 of file AtomSel.C. References TS_LAST, and TS_NOW. Referenced by access_tcl_atomsel, make_tcl_atomsel, and molecule_tcl.

int AtomSel::molid (    )  const [inline]

molid of "my" molecule. Definition at line 58 of file AtomSel.h. Referenced by access_tcl_atomsel, assign_atoms, atomsel_repr, atomsel_set, atomselect_move, atomselect_moveby, AtomSelThr::AtomSelThr, build_xyzr_from_sel, calc_cc, calc_density_bounds, VolMapCreate::calculate_max_radius, VolMapCreate::calculate_minmax, center_of_mass, VolMapCreate::compute_all, VolMapCreateCoulombPotentialMSM::compute_frame, VolMapCreateCoulombPotential::compute_frame, VolMapCreateDistance::compute_frame, VolMapCreateOccupancy::compute_frame, VolMapCreateInterp::compute_frame, VolMapCreateDensity::compute_frame, VolMapCreateMask::compute_frame, contacts, fit, fpbc_join, fpbc_recenter, fpbc_unwrap, fpbc_wrap, get_molecule, get_weights_from_attribute, getmolid, mask, mdff_cc, mdff_sim, measure_avpos, measure_avpos_perresidue, measure_center_perresidue, measure_cluster, measure_dipole, measure_gofr, measure_inertia, measure_rdf, measure_rmsd_perresidue, measure_rmsdmat_qcp, measure_rmsdmat_qcp_ooc, measure_rmsf, measure_rmsf_perresidue, measure_sasa_thread, VMDApp::molecule_from_selection_list, py_hbonds, py_mol_write, py_move, py_moveby, py_rmsdmat_q, tcl_get_weights, text_cmd_animate, timestep, vmd_measure_cluster, vmd_measure_clustsize, vmd_measure_contacts, vmd_measure_hbonds, vmd_measure_inertia, vmd_measure_minmax, vmd_measure_pbc_neighbors, vmd_measure_rmsdmat_qcp, vmd_measure_sasa, vmd_measure_symmetry, vmd_measure_trans_overlap, vmd_measure_volinterior, vmd_volmap_ils, and vmd_volmap_new_fromtype.

Timestep * AtomSel::timestep (  MoleculeList *    )  const

get the current timestep (or NULL if it doesn't exist/ no molecule). Definition at line 2476 of file AtomSel.C. References DrawMolecule::current, DrawMolecule::get_frame, DrawMolecule::get_last_frame, MoleculeList::mol_from_id, molid, NULL, TS_LAST, TS_NOW, and which_frame. Referenced by VolMapCreateCoulombPotentialMSM::compute_frame, coordinates, measure_gofr, measure_rdf, measure_surface, and VMDApp::molecule_from_selection_list.

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Member Data Documentation

char* AtomSel::cmdStr

string with the selection command. Definition at line 57 of file AtomSel.h. Referenced by access_tcl_atomsel, add_rep_to_browser, AtomSel, atomsel_repr, atomsel_str, change, VolMapCreateCoulombPotentialMSM::compute_init, VolMapCreateCoulombPotential::compute_init, VolMapCreateDistance::compute_init, VolMapCreateOccupancy::compute_init, VolMapCreateInterp::compute_init, VolMapCreateDensity::compute_init, VolMapCreateMask::compute_init, contacts, molinfo_get, VMDApp::molrep_get_selection, py_hbonds, py_move, py_moveby, GraphicsFltkMenu::update_rep, and ~AtomSel.

int AtomSel::do_update

Definition at line 69 of file AtomSel.h. Referenced by AtomSel, VMDApp::molrep_get_selupdate, VMDApp::molrep_set_selupdate, and GraphicsFltkMenu::update_rep.

int AtomSel::firstsel

index of first selected atom. Definition at line 64 of file AtomSel.h. Referenced by access_tcl_atomsel, Tool::assign_rep, AtomSel, atomsel_default_weights, atomsel_get, atomsel_set, atomselect_moveby, build_set_values, build_xyzr_from_coords, calc_density_bounds, QuickSurf::calc_surf, VolMapCreate::calculate_max_radius, center_convert_single_soa, center_convert_soa, center_of_mass, change, cluster_get_fitrmsd, cluster_get_rgyrd, VolMapCreateCoulombPotentialMSM::compute_frame, VolMapCreateCoulombPotential::compute_frame, VolMapCreateOccupancy::compute_frame, VolMapCreateInterp::compute_frame, VolMapCreateDensity::compute_frame, VolMapCreateMask::compute_frame, fpbc_exec_wrapatomic, fpbc_exec_wrapcompound, fpbc_recenter, fpbc_unwrap, fpbc_wrap, get_weights_from_attribute, getbonds, measure_avpos, measure_avpos_perresidue, measure_center, measure_center_perresidue, measure_clustsize, measure_dipole, measure_fit, measure_inertia, measure_move, measure_rgyr, measure_rmsd, measure_rmsd_perresidue, measure_rmsf, measure_sasa, measure_sasa_thread, measure_sumweights, measure_surface, VMDApp::molecule_from_selection_list, moveby, py_moveby, setbonds, Tool::target, tcl_get_weights, Tool::tug, vmd_gpu_selection_indexlist, vmd_measure_clustsize, and ~AtomSel.

int AtomSel::lastsel

index of final selected atom. Definition at line 65 of file AtomSel.h. Referenced by access_tcl_atomsel, Tool::assign_rep, AtomSel, atomsel_default_weights, atomsel_get, atomsel_set, atomselect_moveby, build_set_values, build_xyzr_from_coords, calc_density_bounds, QuickSurf::calc_surf, VolMapCreate::calculate_max_radius, center_of_mass, change, cluster_get_fitrmsd, cluster_get_rgyrd, VolMapCreateCoulombPotentialMSM::compute_frame, VolMapCreateCoulombPotential::compute_frame, VolMapCreateOccupancy::compute_frame, VolMapCreateInterp::compute_frame, VolMapCreateDensity::compute_frame, VolMapCreateMask::compute_frame, fpbc_exec_wrapatomic, fpbc_exec_wrapcompound, fpbc_recenter, fpbc_unwrap, fpbc_wrap, get_weights_from_attribute, getbonds, measure_avpos, measure_avpos_perresidue, measure_center, measure_center_perresidue, measure_clustsize, measure_dipole, measure_fit, measure_inertia, measure_move, measure_rgyr, measure_rmsf, measure_sasa, measure_sasa_thread, measure_sumweights, measure_surface, VMDApp::molecule_from_selection_list, moveby, py_moveby, setbonds, Tool::target, tcl_get_weights, Tool::tug, vmd_gpu_selection_indexlist, vmd_measure_clustsize, and ~AtomSel.

int AtomSel::num_atoms

number of atoms in mol. Definition at line 61 of file AtomSel.h. Referenced by access_tcl_atomsel, assign_atoms, AtomSel, atomsel_default_weights, atomsel_get, atomsel_set, atomselection_subscript, AtomSelThr::AtomSelThr, calc_density_bounds, QuickSurf::calc_surf, VolMapCreate::calculate_minmax, change, cluster_get_rmsd, VolMapCreateDistance::compute_frame, VolMapCreate::compute_init, contacts, fit, get_weights_from_attribute, get_weights_from_tcl_list, gpu_ooc_bench, iter_next, mdff_cc, measure_avpos, measure_clustsize, measure_dipole, measure_fit, measure_gofr, measure_hbonds, measure_inertia, measure_move, measure_pbc_neighbors, measure_rdf, measure_rmsd, measure_rmsd_perresidue, measure_rmsd_qcp, measure_rmsdmat_qcp, measure_rmsf, measure_rmsf_perresidue, measure_sasa, measure_sasa_thread, measure_sumweights, measure_surface, measure_trans_overlap, minmax, py_hbonds, qcp_soa_gpu_ooc, reset_origin, PickModeMoveRep::rotate, tcl_get_weights, PickModeMoveRep::translate, AtomSelThr::update, vmd_measure_cluster, vmd_measure_clustsize, vmd_measure_contacts, vmd_measure_hbonds, vmd_measure_minmax, vmd_measure_symmetry, vmd_volmap_ils, vmd_volmap_new_fromtype, and ~AtomSel.

int AtomSel::num_atoms256

number of atoms in mol. Definition at line 62 of file AtomSel.h. Referenced by AtomSel, change, and ~AtomSel.

int* AtomSel::on

per-atom 'selected' flags; 1=on, 0=off. Definition at line 59 of file AtomSel.h. Referenced by access_tcl_atomsel, assign_atoms, Tool::assign_rep, DrawMolItem::atom_displayed, AtomSel, atomsel_default_weights, atomsel_get, atomsel_set, atomselect_moveby, atomselection_subscript, AtomSelThr::AtomSelThr, build_set_values, build_xyzr_from_coords, calc_density_bounds, QuickSurf::calc_surf, VolMapCreate::calculate_max_radius, VolMapCreate::calculate_minmax, center_convert_single_soa, center_convert_soa, center_of_mass, change, cluster_get_fitrmsd, cluster_get_rgyrd, compoundmapper, VolMapCreateCoulombPotentialMSM::compute_frame, VolMapCreateCoulombPotential::compute_frame, VolMapCreateDistance::compute_frame, VolMapCreateOccupancy::compute_frame, VolMapCreateInterp::compute_frame, VolMapCreateDensity::compute_frame, VolMapCreateMask::compute_frame, contacts, SaveTrajectoryFltkMenu::do_save, fpbc_exec_wrapatomic, fpbc_exec_wrapcompound, fpbc_recenter, fpbc_unwrap, fpbc_wrap, get_weights_from_attribute, getbonds, iter_next, measure_avpos, measure_avpos_perresidue, measure_center, measure_center_perresidue, measure_clustsize, measure_dipole, measure_fit, measure_gofr, measure_hbonds, measure_inertia, measure_move, measure_pbc_neighbors, measure_rdf, measure_rgyr, measure_rmsd, measure_rmsd_perresidue, measure_rmsf, measure_sasa, measure_sasa_thread, measure_sumweights, measure_surface, minmax, VMDApp::molecule_from_selection_list, moveby, py_atomselect, py_mol_write, py_moveby, py_write, PickModeMoveRep::rotate, setbonds, Tool::target, tcl_get_weights, text_cmd_animate, PickModeMoveRep::translate, Tool::tug, AtomSelThr::update, vmd_gpu_selection_indexlist, vmd_measure_clustsize, vmd_measure_contacts, vmd_measure_minmax, vmd_measure_symmetry, vmd_volmap_ils, and ~AtomSel.

unsigned int* AtomSel::on256

per-256-atom first, last, selected count. Definition at line 60 of file AtomSel.h. Referenced by AtomSel, change, and ~AtomSel.

int AtomSel::selected

number of selected atoms the molecule. Definition at line 63 of file AtomSel.h. Referenced by access_tcl_atomsel, assign_atoms, AtomSel, atomsel_get, atomsel_set, AtomSelThr::AtomSelThr, build_xyzr_from_coords, QuickSurf::calc_surf, center_convert_single_soa, center_convert_soa, centerperresidue, change, cluster_get_fitrmsd, compoundmapper, VolMapCreateCoulombPotentialMSM::compute_frame, VolMapCreateCoulombPotential::compute_frame, contacts, fit, fpbc_exec_recenter, fpbc_exec_wrapatomic, fpbc_exec_wrapcompound, fpbc_join, fpbc_recenter, fpbc_unwrap, fpbc_wrap, getbonds, Symmetry::guess, Symmetry::impose, iter_len, mask, mdff_cc, mdff_sim, measure_avpos, measure_clustsize, measure_dipole, measure_fit, measure_gofr, measure_move, measure_pbc_neighbors, measure_rdf, measure_rmsd, measure_rmsd_perresidue, measure_rmsd_qcp, measure_rmsdmat_qcp, measure_rmsdmat_qcp_ooc, measure_rmsdmat_qcp_thread, measure_rmsf, measure_rmsf_perresidue, measure_sasa, measure_sasa_thread, measure_sumweights, measure_surface, measure_trans_overlap, VMDApp::molecule_from_selection_list, VMDApp::molrep_numselected, parse_two_selections_return_weight, parse_weight, py_hbonds, py_move, py_moveby, py_rmsd, py_rmsd_q, py_rmsdmat_q, py_rmsdperresidue, py_rmsf, py_rmsfperresidue, qcp_soa_gpu, rotate, Symmetry::score_axis, Symmetry::score_inversion, Symmetry::score_plane, Symmetry::score_rotary_reflection, setbonds, Symmetry::Symmetry, tcl_get_weights, AtomSelThr::update, vmd_cuda_calc_density, vmd_cuda_compare_sel_refmap, vmd_gpu_selection_indexlist, vmd_measure_avpos, vmd_measure_center, vmd_measure_centerperresidue, vmd_measure_clustsize, vmd_measure_fit, vmd_measure_pbc_neighbors, vmd_measure_rgyr, vmd_measure_rmsd, vmd_measure_rmsd_qcp, vmd_measure_rmsdmat_qcp, vmd_measure_rmsdmat_qcp_ooc, vmd_measure_rmsdperresidue, vmd_measure_rmsf, vmd_measure_rmsfperresidue, vmd_measure_sumweights, vmd_measure_symmetry, vmd_measure_volinterior, vmd_volmap_ils, vmd_volmap_new_fromtype, ~AtomSel, and Symmetry::~Symmetry.

int AtomSel::which_frame

Definition at line 68 of file AtomSel.h. Referenced by access_tcl_atomsel, AtomSel, atomsel_get, atomsel_new, atomsel_repr, atomsel_set, AtomSelThr::AtomSelThr, VolMapCreate::calculate_minmax, change, VolMapCreate::compute_all, VolMapCreateCoulombPotentialMSM::compute_frame, VolMapCreateCoulombPotential::compute_frame, VolMapCreateDistance::compute_frame, VolMapCreateOccupancy::compute_frame, VolMapCreateInterp::compute_frame, VolMapCreateDensity::compute_frame, VolMapCreateMask::compute_frame, get_weights_from_attribute, getframe, mdff_cc, measure_gofr, measure_rdf, py_atomselect, py_write, setframe, tcl_get_weights, timestep, AtomSelThr::update, vmd_measure_cluster, and vmd_measure_clustsize.

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The documentation for this class was generated from the following files:

• AtomSel.h
• AtomSel.C

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