#include <AtomSel.h>
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 (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 *) |
| 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 *) |
| 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... | |
| int | num_atoms |
| number of atoms in mol. More... | |
| int | selected |
| number of selected atoms the molecule. More... | |
| int | which_frame |
| int | do_update |
Definition at line 44 of file AtomSel.h.
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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.
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Definition at line 2150 of file AtomSel.C. References cmdStr, do_update, NO_PARSE, NULL, num_atoms, on, selected, TS_NOW, and which_frame. |
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Definition at line 2165 of file AtomSel.C. References cmdStr, NO_PARSE, NULL, num_atoms, on, and selected. |
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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 2206 of file AtomSel.C. References NULL, Timestep::pos, and timestep. Referenced by assign_atoms, atomselect_move, atomselect_moveby, VolMapCreate::calculate_minmax, center, center_of_mass, VolMapCreateCoulombPotential::compute_frame, VolMapCreateFastEnergy::compute_frame, VolMapCreateSlowEnergy::compute_frame, VolMapCreateDistance::compute_frame, VolMapCreateOccupancy::compute_frame, VolMapCreateInterp::compute_frame, VolMapCreateDensity::compute_frame, VolMapCreateMask::compute_frame, VolMapCreateFastEnergy::compute_init, contacts, measure_dipole, measure_inertia, measure_rgyr, minmax, py_align, py_fit, py_move, py_moveby, py_rmsd, sasa, vmd_measure_center, vmd_measure_contacts, vmd_measure_fit, vmd_measure_hbonds, vmd_measure_minmax, vmd_measure_rmsd, vmd_measure_sasa, and vmd_measure_surface. |
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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 2238 of file AtomSel.C. References TS_LAST, and TS_NOW. Referenced by access_tcl_atomsel, make_tcl_atomsel, and molecule_tcl. |
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get the current timestep (or NULL if it doesn't exist/ no molecule).
Definition at line 2213 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 coordinates, measure_gofr, and measure_surface. |
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string with the selection command.
Definition at line 55 of file AtomSel.h. Referenced by access_tcl_atomsel, add_rep_to_browser, AtomSel, atomsel_repr, atomsel_str, change, VolMapCreateCoulombPotential::compute_init, VolMapCreateFastEnergy::compute_init, VolMapCreateSlowEnergy::compute_init, VolMapCreateDistance::compute_init, VolMapCreateOccupancy::compute_init, VolMapCreateInterp::compute_init, VolMapCreateDensity::compute_init, VolMapCreateMask::compute_init, molinfo_get, VMDApp::molrep_get_selection, GraphicsFltkMenu::update_rep, VolMapCreateFastEnergy::write_map, and ~AtomSel. |
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Definition at line 63 of file AtomSel.h. Referenced by AtomSel, VMDApp::molrep_get_selupdate, VMDApp::molrep_set_selupdate, and GraphicsFltkMenu::update_rep. |
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number of selected atoms the molecule.
Definition at line 59 of file AtomSel.h. Referenced by access_tcl_atomsel, assign_atoms, AtomSel, atomsel_get, atomsel_set, change, VolMapCreateCoulombPotential::compute_frame, VolMapCreateFastEnergy::compute_frame, create, getbonds, Symmetry::guess, iter_len, measure_avpos, measure_dipole, measure_fit, measure_gofr, measure_move, measure_pbc_neighbors, measure_rmsd, measure_rmsf, measure_sasa, measure_sumweights, measure_trans_overlap, VMDApp::molrep_numselected, parse_two_selections_return_weight, parse_weight, py_rmsd, sel_from_py, setbonds, Symmetry::Symmetry, tcl_get_weights, vmd_measure_avpos, vmd_measure_center, vmd_measure_fit, vmd_measure_pbc_neighbors, vmd_measure_rgyr, vmd_measure_rmsd, vmd_measure_rmsf, vmd_measure_sumweights, vmd_measure_symmetry, vmd_volmap_new_fromtype, and ~AtomSel. |
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1.2.14 written by Dimitri van Heesch,
© 1997-2002