#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <float.h>
#include "Inform.h"
#include "utilities.h"
#include "AtomSel.h"
#include "VMDApp.h"
#include "MoleculeList.h"
#include "VolumetricData.h"
#include "VolMapCreate.h"
#include "PluginMgr.h"
#include "MolFilePlugin.h"
#include "CUDAMDFF.h"
#include "MDFF.h"
#include "TclMDFF.h"
#include <math.h>
#include <tcl.h>
#include "TclCommands.h"
#include "Measure.h"
#include "Voltool.h"
#include <iostream>
#include <string>
#include <sstream>
Go to the source code of this file.
Functions | |
void | moveby (AtomSel *sel, float *vect, MoleculeList *mlist, float *framepos) |
void | move (AtomSel *sel, Matrix4 mat, MoleculeList *mlist, float *framepos) |
double | density_calc_cc (VolumetricData *volmapA, VolumetricData *volmapB, double thresholddensity) |
double | calc_cc (AtomSel *sel, VolumetricData *volmapA, float resolution, MoleculeList *mlist, float *framepos) |
void | do_rotate (int stride, float *com, AtomSel *sel, int amt, float *axis, MoleculeList *mlist, float *framepos) |
void | do_density_rotate (int stride, int amt, float *axis, VolumetricData *synthvol) |
void | rotate (int stride, int max_rot, float *com, float *returncc, float *bestpos, AtomSel *sel, MoleculeList *mlist, VolumetricData *volmapA, float resolution, float *origin, float *framepos) |
void | density_rotate (int stride, int max_rot, float *com, float *returncc, int *bestrot, VolumetricData *volmapA, VolumetricData *synthvol, float resolution, double *origin, double *dx, double *dy, double *dz) |
void | reset_density (int stride, int *bestrot, VolumetricData *synthvol, float *synthcom, float *framepos, float *com, AtomSel *sel, MoleculeList *mlist) |
void | reset_origin (float *origin, float *newpos, AtomSel *sel) |
int | density_com (VMDApp *app, int argc, Tcl_Obj *const objv[], Tcl_Interp *interp) |
int | density_move (VMDApp *app, int argc, Tcl_Obj *const objv[], Tcl_Interp *interp) |
int | density_moveto (VMDApp *app, int argc, Tcl_Obj *const objv[], Tcl_Interp *interp) |
int | fit (VMDApp *app, int argc, Tcl_Obj *const objv[], Tcl_Interp *interp) |
int | mask (VMDApp *app, int argc, Tcl_Obj *const objv[], Tcl_Interp *interp) |
int | density_trim (VMDApp *app, int argc, Tcl_Obj *const objv[], Tcl_Interp *interp) |
int | density_crop (VMDApp *app, int argc, Tcl_Obj *const objv[], Tcl_Interp *interp) |
int | density_clamp (VMDApp *app, int argc, Tcl_Obj *const objv[], Tcl_Interp *interp) |
int | density_smult (VMDApp *app, int argc, Tcl_Obj *const objv[], Tcl_Interp *interp) |
int | density_smooth (VMDApp *app, int argc, Tcl_Obj *const objv[], Tcl_Interp *interp) |
int | density_sadd (VMDApp *app, int argc, Tcl_Obj *const objv[], Tcl_Interp *interp) |
int | density_range (VMDApp *app, int argc, Tcl_Obj *const objv[], Tcl_Interp *interp) |
int | density_downsample (VMDApp *app, int argc, Tcl_Obj *const objv[], Tcl_Interp *interp) |
int | density_supersample (VMDApp *app, int argc, Tcl_Obj *const objv[], Tcl_Interp *interp) |
int | density_sigma (VMDApp *app, int argc, Tcl_Obj *const objv[], Tcl_Interp *interp) |
int | density_mdff_potential (VMDApp *app, int argc, Tcl_Obj *const objv[], Tcl_Interp *interp) |
int | density_histogram (VMDApp *app, int argc, Tcl_Obj *const objv[], Tcl_Interp *interp) |
int | density_info (VMDApp *app, int argc, Tcl_Obj *const objv[], Tcl_Interp *interp) |
int | density_binmask (VMDApp *app, int argc, Tcl_Obj *const objv[], Tcl_Interp *interp) |
int | density_add (VMDApp *app, int argc, Tcl_Obj *const objv[], Tcl_Interp *interp) |
int | density_subtract (VMDApp *app, int argc, Tcl_Obj *const objv[], Tcl_Interp *interp) |
int | density_multiply (VMDApp *app, int argc, Tcl_Obj *const objv[], Tcl_Interp *interp) |
int | density_average (VMDApp *app, int argc, Tcl_Obj *const objv[], Tcl_Interp *interp) |
int | density_correlate (VMDApp *app, int argc, Tcl_Obj *const objv[], Tcl_Interp *interp) |
int | density_save (VMDApp *app, int argc, Tcl_Obj *const objv[], Tcl_Interp *interp) |
int | obj_voltool (ClientData cd, Tcl_Interp *interp, int argc, Tcl_Obj *const objv[]) |
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Definition at line 73 of file TclVoltool.C. References QuickSurf::calc_density_map, cc, cc_threaded, MoleculeList::mol_from_id, AtomSel::molid, NULL, BaseMolecule::radius, vmd_cuda_compare_sel_refmap, volmap, and volmapA. Referenced by gaussdensity_cc, and rotate. |
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Definition at line 2667 of file TclVoltool.C. References add, VMDApp::guess_filetype, init_new_volume, init_new_volume_molecule, BaseMolecule::modify_volume_data, MoleculeList::mol_from_id, VMDApp::molecule_load, VMDApp::molecule_new, VMDApp::moleculeList, newvol, FileSpec::WAIT_BACK, FileSpec::waitfor, and write_file. Referenced by obj_voltool. |
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Definition at line 3196 of file TclVoltool.C. References average, VMDApp::guess_filetype, init_new_volume, init_new_volume_molecule, BaseMolecule::modify_volume_data, MoleculeList::mol_from_id, VMDApp::molecule_load, VMDApp::molecule_new, VMDApp::moleculeList, newvol, FileSpec::WAIT_BACK, FileSpec::waitfor, and write_file. Referenced by obj_voltool. |
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Definition at line 2555 of file TclVoltool.C. References VolumetricData::binmask, DrawMolecule::force_recalc, VMDApp::guess_filetype, BaseMolecule::modify_volume_data, MoleculeList::mol_from_id, DrawMolItem::MOL_REGEN, VMDApp::molecule_load, VMDApp::molecule_new, VMDApp::moleculeList, threshold, FileSpec::WAIT_BACK, FileSpec::waitfor, and write_file. Referenced by obj_voltool. |
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Definition at line 66 of file TclVoltool.C. References cc, cc_threaded, and volmapA. Referenced by density_rotate. |
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Definition at line 1284 of file TclVoltool.C. References VolumetricData::clamp, DrawMolecule::force_recalc, VMDApp::guess_filetype, BaseMolecule::modify_volume_data, MoleculeList::mol_from_id, DrawMolItem::MOL_REGEN, VMDApp::molecule_load, VMDApp::molecule_new, VMDApp::moleculeList, FileSpec::WAIT_BACK, FileSpec::waitfor, and write_file. Referenced by obj_voltool. |
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Definition at line 320 of file TclVoltool.C. References VMDApp::guess_filetype, BaseMolecule::modify_volume_data, MoleculeList::mol_from_id, VMDApp::molecule_load, VMDApp::molecule_new, VMDApp::moleculeList, NULL, vol_com, volmapA, FileSpec::WAIT_BACK, and FileSpec::waitfor. Referenced by obj_voltool. |
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Definition at line 3372 of file TclVoltool.C. References cc_threaded, VMDApp::guess_filetype, BaseMolecule::modify_volume_data, MoleculeList::mol_from_id, VMDApp::molecule_load, VMDApp::molecule_new, VMDApp::moleculeList, FileSpec::WAIT_BACK, and FileSpec::waitfor. Referenced by obj_voltool. |
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Definition at line 1163 of file TclVoltool.C. References VolumetricData::crop, DrawMolecule::force_recalc, VMDApp::guess_filetype, BaseMolecule::modify_volume_data, MoleculeList::mol_from_id, DrawMolItem::MOL_REGEN, VMDApp::molecule_load, VMDApp::molecule_new, VMDApp::moleculeList, FileSpec::WAIT_BACK, FileSpec::waitfor, and write_file. Referenced by obj_voltool. |
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Definition at line 1851 of file TclVoltool.C. References VolumetricData::downsample, DrawMolecule::force_recalc, VMDApp::guess_filetype, BaseMolecule::modify_volume_data, MoleculeList::mol_from_id, DrawMolItem::MOL_REGEN, VMDApp::molecule_load, VMDApp::molecule_new, VMDApp::moleculeList, FileSpec::WAIT_BACK, FileSpec::waitfor, and write_file. Referenced by obj_voltool. |
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Definition at line 2254 of file TclVoltool.C. References VMDApp::guess_filetype, histogram, BaseMolecule::modify_volume_data, MoleculeList::mol_from_id, VMDApp::molecule_load, VMDApp::molecule_new, VMDApp::moleculeList, FileSpec::WAIT_BACK, and FileSpec::waitfor. Referenced by obj_voltool. |
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Definition at line 2145 of file TclVoltool.C. References DrawMolecule::force_recalc, VMDApp::guess_filetype, VolumetricData::mdff_potential, BaseMolecule::modify_volume_data, MoleculeList::mol_from_id, DrawMolItem::MOL_REGEN, VMDApp::molecule_load, VMDApp::molecule_new, VMDApp::moleculeList, threshold, FileSpec::WAIT_BACK, FileSpec::waitfor, and write_file. Referenced by obj_voltool. |
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Definition at line 407 of file TclVoltool.C. References DrawMolecule::force_recalc, VMDApp::guess_filetype, mat, BaseMolecule::modify_volume_data, MoleculeList::mol_from_id, DrawMolItem::MOL_REGEN, VMDApp::molecule_load, VMDApp::molecule_new, VMDApp::moleculeList, tcl_get_matrix, vol_move, FileSpec::WAIT_BACK, FileSpec::waitfor, and write_file. Referenced by obj_voltool. |
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Definition at line 517 of file TclVoltool.C. References DrawMolecule::force_recalc, VMDApp::guess_filetype, BaseMolecule::modify_volume_data, MoleculeList::mol_from_id, DrawMolItem::MOL_REGEN, VMDApp::molecule_load, VMDApp::molecule_new, VMDApp::moleculeList, vol_com, vol_moveto, FileSpec::WAIT_BACK, FileSpec::waitfor, and write_file. Referenced by obj_voltool. |
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Definition at line 3020 of file TclVoltool.C. References VMDApp::guess_filetype, init_new_volume, init_new_volume_molecule, BaseMolecule::modify_volume_data, MoleculeList::mol_from_id, VMDApp::molecule_load, VMDApp::molecule_new, VMDApp::moleculeList, multiply, newvol, FileSpec::WAIT_BACK, FileSpec::waitfor, and write_file. Referenced by obj_voltool. |
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Definition at line 1729 of file TclVoltool.C. References DrawMolecule::force_recalc, VMDApp::guess_filetype, BaseMolecule::modify_volume_data, MoleculeList::mol_from_id, DrawMolItem::MOL_REGEN, VMDApp::molecule_load, VMDApp::molecule_new, VMDApp::moleculeList, VolumetricData::rescale_voxel_value_range, FileSpec::WAIT_BACK, FileSpec::waitfor, and write_file. Referenced by obj_voltool. |
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Definition at line 202 of file TclVoltool.C. References cc, density_calc_cc, do_density_rotate, num, VolumetricData::origin, vol_com, vol_moveto, volmapA, VolumetricData::xaxis, VolumetricData::yaxis, z, and VolumetricData::zaxis. |
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Definition at line 1621 of file TclVoltool.C. References DrawMolecule::force_recalc, VMDApp::guess_filetype, BaseMolecule::modify_volume_data, MoleculeList::mol_from_id, DrawMolItem::MOL_REGEN, VMDApp::molecule_load, VMDApp::molecule_new, VMDApp::moleculeList, VolumetricData::scalar_add, FileSpec::WAIT_BACK, FileSpec::waitfor, and write_file. Referenced by obj_voltool. |
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Definition at line 3530 of file TclVoltool.C. References VMDApp::guess_filetype, BaseMolecule::modify_volume_data, MoleculeList::mol_from_id, VMDApp::molecule_load, VMDApp::molecule_new, VMDApp::moleculeList, FileSpec::WAIT_BACK, FileSpec::waitfor, and write_file. Referenced by obj_voltool. |
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Definition at line 2047 of file TclVoltool.C. References DrawMolecule::force_recalc, VMDApp::guess_filetype, BaseMolecule::modify_volume_data, MoleculeList::mol_from_id, DrawMolItem::MOL_REGEN, VMDApp::molecule_load, VMDApp::molecule_new, VMDApp::moleculeList, VolumetricData::sigma_scale, FileSpec::WAIT_BACK, FileSpec::waitfor, and write_file. Referenced by obj_voltool. |
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Definition at line 1513 of file TclVoltool.C. References DrawMolecule::force_recalc, VolumetricData::gaussian_blur, VMDApp::guess_filetype, BaseMolecule::modify_volume_data, MoleculeList::mol_from_id, DrawMolItem::MOL_REGEN, VMDApp::molecule_load, VMDApp::molecule_new, VMDApp::moleculeList, FileSpec::WAIT_BACK, FileSpec::waitfor, and write_file. Referenced by obj_voltool. |
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Definition at line 1405 of file TclVoltool.C. References DrawMolecule::force_recalc, VMDApp::guess_filetype, BaseMolecule::modify_volume_data, MoleculeList::mol_from_id, DrawMolItem::MOL_REGEN, VMDApp::molecule_load, VMDApp::molecule_new, VMDApp::moleculeList, VolumetricData::scale_by, FileSpec::WAIT_BACK, FileSpec::waitfor, and write_file. Referenced by obj_voltool. |
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Definition at line 2843 of file TclVoltool.C. References VMDApp::guess_filetype, init_new_volume, init_new_volume_molecule, BaseMolecule::modify_volume_data, MoleculeList::mol_from_id, VMDApp::molecule_load, VMDApp::molecule_new, VMDApp::moleculeList, newvol, subtract, FileSpec::WAIT_BACK, FileSpec::waitfor, and write_file. Referenced by obj_voltool. |
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Definition at line 1949 of file TclVoltool.C. References DrawMolecule::force_recalc, VMDApp::guess_filetype, BaseMolecule::modify_volume_data, MoleculeList::mol_from_id, DrawMolItem::MOL_REGEN, VMDApp::molecule_load, VMDApp::molecule_new, VMDApp::moleculeList, VolumetricData::supersample, FileSpec::WAIT_BACK, FileSpec::waitfor, and write_file. Referenced by obj_voltool. |
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Definition at line 1042 of file TclVoltool.C. References DrawMolecule::force_recalc, VMDApp::guess_filetype, BaseMolecule::modify_volume_data, MoleculeList::mol_from_id, DrawMolItem::MOL_REGEN, VMDApp::molecule_load, VMDApp::molecule_new, VMDApp::moleculeList, VolumetricData::pad, FileSpec::WAIT_BACK, FileSpec::waitfor, and write_file. Referenced by obj_voltool. |
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Definition at line 138 of file TclVoltool.C. References DEGTORAD, Matrix4::mat, mat, Matrix4::rotate_axis, and vol_move. Referenced by density_rotate, and reset_density. |
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Definition at line 131 of file TclVoltool.C. References DEGTORAD, mat, move, and Matrix4::rotate_axis. Referenced by reset_density, and rotate. |
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Definition at line 61 of file TclVoltool.C. References mat, and measure_move. Referenced by do_rotate. |
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Definition at line 52 of file TclVoltool.C. References AtomSel::firstsel, AtomSel::lastsel, AtomSel::on, and vec_add. Referenced by fit, reset_density, and rotate. |
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Definition at line 3626 of file TclVoltool.C. References density_add, density_average, density_binmask, density_clamp, density_com, density_correlate, density_crop, density_downsample, density_histogram, density_info, density_mdff_potential, density_move, density_moveto, density_multiply, density_range, density_sadd, density_save, density_sigma, density_smooth, density_smult, density_subtract, density_supersample, density_trim, fit, mask, mdff_cc, mdff_sim, and strupncmp. |
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Definition at line 281 of file TclVoltool.C. References do_density_rotate, do_rotate, moveby, vec_scale, vol_com, and vol_moveto. |
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Definition at line 314 of file TclVoltool.C. References AtomSel::num_atoms. Referenced by fit. |
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Definition at line 151 of file TclVoltool.C. References calc_cc, cc, do_rotate, moveby, AtomSel::selected, vec_scale, volmapA, and z. Referenced by fit, and colvarmodule::quaternion::rotate. |