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py_molecule.C File Reference

#include "py_commands.h"
#include <ctype.h>
#include <stdlib.h>
#include "config.h"
#include "utilities.h"
#include "VMDApp.h"
#include "JString.h"
#include "Molecule.h"
#include "MoleculeList.h"

Go to the source code of this file.

Functions

PyObject * mol_num (PyObject *self, PyObject *args)
PyObject * mol_listall (PyObject *self, PyObject *args)
PyObject * mol_exists (PyObject *self, PyObject *args)
PyObject * mol_name (PyObject *self, PyObject *args)
PyObject * mol_numatoms (PyObject *self, PyObject *args)
PyObject * mol_new (PyObject *self, PyObject *args)
PyObject * mol_load (PyObject *self, PyObject *args, PyObject *keywds)
PyObject * mol_cancel (PyObject *self, PyObject *args)
PyObject * mol_delete (PyObject *self, PyObject *args)
PyObject * get_top (PyObject *self, PyObject *args)
PyObject * set_top (PyObject *self, PyObject *args)
PyObject * readorwrite (PyObject *self, PyObject *args, PyObject *keywds, int do_read)
PyObject * mol_read (PyObject *self, PyObject *args, PyObject *keywds)
PyObject * mol_write (PyObject *self, PyObject *args, PyObject *keywds)
PyObject * numframes (PyObject *self, PyObject *args)
PyObject * get_frame (PyObject *self, PyObject *args)
PyObject * set_frame (PyObject *self, PyObject *args)
PyObject * delframe (PyObject *self, PyObject *args, PyObject *keywds)
PyObject * dupframe (PyObject *self, PyObject *args)
PyObject * mol_ssrecalc (PyObject *self, PyObject *args)
PyObject * mol_rename (PyObject *self, PyObject *args)
PyObject * mol_add_volumetric (PyObject *self, PyObject *args, PyObject *keywds)
PyObject * get_filenames (PyObject *self, PyObject *args)
PyObject * get_filetypes (PyObject *self, PyObject *args)
PyObject * get_databases (PyObject *self, PyObject *args)
PyObject * get_accessions (PyObject *self, PyObject *args)
PyObject * get_remarks (PyObject *self, PyObject *args)
PyObject * get_periodic (PyObject *self, PyObject *args, PyObject *kwds)
PyObject * set_periodic (PyObject *self, PyObject *args, PyObject *kwds)
PyObject * get_visible (PyObject *self, PyObject *args, PyObject *kwds)
PyObject * set_visible (PyObject *self, PyObject *args, PyObject *kwds)
PyObject * get_physical_time (PyObject *self, PyObject *args, PyObject *kwds)
PyObject * set_physical_time (PyObject *self, PyObject *args, PyObject *kwds)
void initmolecule ()

Variables

char mol_num_doc []
char mol_listall_doc []
char mol_exists_doc []
char mol_name_doc []
char mol_numatoms_doc []
char mol_new_doc []
char mol_load_doc []
char mol_cancel_doc []
char mol_delete_doc []
char get_top_doc []
char set_top_doc []
char mol_read_doc []
char mol_write_doc []
char numframes_doc []
char get_frame_doc []
char set_frame_doc []
char delframe_doc []
char dupframe_doc []
char mol_ssrecalc_doc []
char mol_rename_doc []
char add_volumetric_doc []
char filenames_doc [] = "get_filenames(molid): return list of files loaded in the molecule"
char filetypes_doc [] = "get_filetypes(molid): returns list of corresponding file types."
char databases_doc [] = "get_databases(molid): returns list of databases of origin "
char accessions_doc [] = "get_accessions(molid): returns list of database accession codes"
char remarks_doc [] = "get_remarks(molid): returns list of per-file remarks/comments"
char get_periodic_doc []
char set_periodic_doc []
char get_visible_doc []
char set_visible_doc []
PyMethodDef MolMethods []

Function Documentation

PyObject* delframe (  PyObject *    self,
PyObject *    args,
PyObject *    keywds
)  [static]
 

Definition at line 411 of file py_molecule.C.

References get_vmdapp, VMDApp::molecule_deleteframes, VMDApp::molecule_valid_id, and NULL.

PyObject* dupframe (  PyObject *    self,
PyObject *    args
)  [static]
 

Definition at line 443 of file py_molecule.C.

References get_vmdapp, VMDApp::molecule_dupframe, VMDApp::molecule_valid_id, and NULL.

PyObject* get_accessions (  PyObject *    self,
PyObject *    args
)  [static]
 

Definition at line 661 of file py_molecule.C.

References Molecule::get_accession, get_vmdapp, MoleculeList::mol_from_id, VMDApp::moleculeList, NULL, num, and Molecule::num_files.

PyObject* get_databases (  PyObject *    self,
PyObject *    args
)  [static]
 

Definition at line 643 of file py_molecule.C.

References Molecule::get_database, get_vmdapp, MoleculeList::mol_from_id, VMDApp::moleculeList, NULL, num, and Molecule::num_files.

PyObject* get_filenames (  PyObject *    self,
PyObject *    args
)  [static]
 

Definition at line 607 of file py_molecule.C.

References Molecule::get_file, get_vmdapp, MoleculeList::mol_from_id, VMDApp::moleculeList, NULL, num, and Molecule::num_files.

PyObject* get_filetypes (  PyObject *    self,
PyObject *    args
)  [static]
 

Definition at line 625 of file py_molecule.C.

References Molecule::get_type, get_vmdapp, MoleculeList::mol_from_id, VMDApp::moleculeList, NULL, num, and Molecule::num_files.

PyObject* get_frame (  PyObject *    self,
PyObject *    args
)  [static]
 

Definition at line 371 of file py_molecule.C.

References get_vmdapp, VMDApp::molecule_frame, VMDApp::molecule_valid_id, and NULL.

PyObject* get_periodic (  PyObject *    self,
PyObject *    args,
PyObject *    kwds
)  [static]
 

Definition at line 707 of file py_molecule.C.

References Timestep::a_length, Timestep::alpha, Timestep::b_length, Timestep::beta, Timestep::c_length, Timestep::gamma, get_vmdapp, NULL, and parse_timestep.

PyObject* get_physical_time (  PyObject *    self,
PyObject *    args,
PyObject *    kwds
)  [static]
 

Definition at line 796 of file py_molecule.C.

References get_vmdapp, NULL, parse_timestep, and Timestep::physical_time.

PyObject* get_remarks (  PyObject *    self,
PyObject *    args
)  [static]
 

Definition at line 679 of file py_molecule.C.

References Molecule::get_remarks, get_vmdapp, MoleculeList::mol_from_id, VMDApp::moleculeList, NULL, num, and Molecule::num_files.

PyObject* get_top (  PyObject *    self,
PyObject *    args
)  [static]
 

Definition at line 223 of file py_molecule.C.

References get_vmdapp, and NULL.

PyObject* get_visible (  PyObject *    self,
PyObject *    args,
PyObject *    kwds
)  [static]
 

Definition at line 763 of file py_molecule.C.

References get_vmdapp, VMDApp::molecule_is_displayed, VMDApp::molecule_top, VMDApp::molecule_valid_id, and NULL.

void initmolecule (    ) 
 

Definition at line 859 of file py_molecule.C.

References MolMethods.

PyObject* mol_add_volumetric (  PyObject *    self,
PyObject *    args,
PyObject *    keywds
)  [static]
 

Definition at line 519 of file py_molecule.C.

References data, get_vmdapp, VMDApp::molecule_add_volumetric, VMDApp::molecule_valid_id, NULL, and py_array_from_obj.

PyObject* mol_cancel (  PyObject *    self,
PyObject *    args
)  [static]
 

Definition at line 184 of file py_molecule.C.

References get_vmdapp, VMDApp::molecule_cancel_io, VMDApp::molecule_valid_id, and NULL.

PyObject* mol_delete (  PyObject *    self,
PyObject *    args
)  [static]
 

Definition at line 204 of file py_molecule.C.

References get_vmdapp, VMDApp::molecule_delete, VMDApp::molecule_valid_id, and NULL.

PyObject* mol_exists (  PyObject *    self,
PyObject *    args
)  [static]
 

Definition at line 62 of file py_molecule.C.

References get_vmdapp, VMDApp::molecule_valid_id, and NULL.

PyObject* mol_listall (  PyObject *    self,
PyObject *    args
)  [static]
 

Definition at line 46 of file py_molecule.C.

References get_vmdapp, VMDApp::molecule_id, NULL, num, and VMDApp::num_molecules.

PyObject* mol_load (  PyObject *    self,
PyObject *    args,
PyObject *    keywds
)  [static]
 

Definition at line 128 of file py_molecule.C.

References get_vmdapp, VMDApp::molecule_load, VMDApp::molecule_new, and NULL.

PyObject* mol_name (  PyObject *    self,
PyObject *    args
)  [static]
 

Definition at line 73 of file py_molecule.C.

References get_vmdapp, VMDApp::molecule_name, and NULL.

PyObject* mol_new (  PyObject *    self,
PyObject *    args
)  [static]
 

Definition at line 109 of file py_molecule.C.

References get_vmdapp, VMDApp::molecule_new, and NULL.

PyObject* mol_num (  PyObject *    self,
PyObject *    args
)  [static]
 

Definition at line 36 of file py_molecule.C.

References get_vmdapp, and NULL.

PyObject* mol_numatoms (  PyObject *    self,
PyObject *    args
)  [static]
 

Definition at line 92 of file py_molecule.C.

References get_vmdapp, VMDApp::molecule_numatoms, VMDApp::molecule_valid_id, and NULL.

PyObject* mol_read (  PyObject *    self,
PyObject *    args,
PyObject *    keywds
)  [static]
 

Definition at line 332 of file py_molecule.C.

References readorwrite.

PyObject* mol_rename (  PyObject *    self,
PyObject *    args
)  [static]
 

Definition at line 492 of file py_molecule.C.

References get_vmdapp, VMDApp::molecule_rename, VMDApp::molecule_valid_id, and NULL.

PyObject* mol_ssrecalc (  PyObject *    self,
PyObject *    args
)  [static]
 

Definition at line 467 of file py_molecule.C.

References get_vmdapp, VMDApp::molecule_ssrecalc, VMDApp::molecule_valid_id, and NULL.

PyObject* mol_write (  PyObject *    self,
PyObject *    args,
PyObject *    keywds
)  [static]
 

Definition at line 349 of file py_molecule.C.

References readorwrite.

PyObject* numframes (  PyObject *    self,
PyObject *    args
)  [static]
 

Definition at line 355 of file py_molecule.C.

References get_vmdapp, VMDApp::molecule_numframes, VMDApp::molecule_valid_id, and NULL.

Referenced by molinfo_set, and readorwrite.

PyObject* readorwrite (  PyObject *    self,
PyObject *    args,
PyObject *    keywds,
int    do_read
)  [static]
 

Definition at line 250 of file py_molecule.C.

References atomsel_AsAtomSel, FileSpec::first, get_vmdapp, FileSpec::last, VMDApp::molecule_load, VMDApp::molecule_savetrajectory, VMDApp::molecule_valid_id, AtomSel::molid, NULL, numframes, FileSpec::nvolsets, AtomSel::on, FileSpec::selection, FileSpec::setids, FileSpec::stride, and FileSpec::waitfor.

Referenced by mol_read, and mol_write.

PyObject* set_frame (  PyObject *    self,
PyObject *    args
)  [static]
 

Definition at line 389 of file py_molecule.C.

References DrawMolecule::change_ts, get_vmdapp, MoleculeList::mol_from_id, VMDApp::moleculeList, NULL, and DrawMolecule::override_current_frame.

PyObject* set_periodic (  PyObject *    self,
PyObject *    args,
PyObject *    kwds
)  [static]
 

Definition at line 731 of file py_molecule.C.

References Timestep::a_length, Timestep::alpha, Timestep::b_length, Timestep::beta, Timestep::c_length, Timestep::gamma, get_vmdapp, NULL, and parse_timestep.

PyObject* set_physical_time (  PyObject *    self,
PyObject *    args,
PyObject *    kwds
)  [static]
 

Definition at line 807 of file py_molecule.C.

References get_vmdapp, NULL, parse_timestep, and Timestep::physical_time.

PyObject* set_top (  PyObject *    self,
PyObject *    args
)  [static]
 

Definition at line 233 of file py_molecule.C.

References get_vmdapp, VMDApp::molecule_make_top, VMDApp::molecule_valid_id, and NULL.

PyObject* set_visible (  PyObject *    self,
PyObject *    args,
PyObject *    kwds
)  [static]
 

Definition at line 777 of file py_molecule.C.

References get_vmdapp, VMDApp::molecule_display, VMDApp::molecule_top, VMDApp::molecule_valid_id, and NULL.

Variable Documentation

char accessions_doc[] = "get_accessions(molid): returns list of database accession codes" [static]
 

Definition at line 605 of file py_molecule.C.

char add_volumetric_doc[] [static]
 

Initial value:

 
  "add_volumetric(molid, name, origin, xaxis, yaxis, zaxis,\n"
  "               xsize, ysize, zsize, data)\n"
  "  Add a new volumetric data set to a molecule.  origin, xaxis, yaxis,\n"
  "  and zaxis are 3-vectors represented as lists.  xsize, ysize, zsize\n"
  "  give the size of the volumetric grid data.  data must be a list of\n"
  "  floats of size xsize * ysize * zsize.  origin represents the point\n"
  "  at the lower left rear corner of the grid."

Definition at line 511 of file py_molecule.C.

char databases_doc[] = "get_databases(molid): returns list of databases of origin " [static]
 

Definition at line 604 of file py_molecule.C.

char delframe_doc[] [static]
 

Initial value:

  "delframe(molid, beg=0, end=-1, skip=0)\n"
  "Delete frames in the range [beg, end] inclusive, keeping every\n"
  "  'skip' frame between beg and end."

Definition at line 407 of file py_molecule.C.

char dupframe_doc[] [static]
 

Initial value:

  "dupframe(molid, frame) -> Duplicate given frame.\n"
  "If frame is -1, duplicate the current frame; this also creates\n"
  "a new frame with coordinates all zero if there are no frames in\n"
  "the molecule."

Definition at line 438 of file py_molecule.C.

char filenames_doc[] = "get_filenames(molid): return list of files loaded in the molecule" [static]
 

Definition at line 602 of file py_molecule.C.

char filetypes_doc[] = "get_filetypes(molid): returns list of corresponding file types." [static]
 

Definition at line 603 of file py_molecule.C.

char get_frame_doc[] [static]
 

Initial value:

  "get_frame(molid) -> current frame of molecule with id 'molid'."

Definition at line 369 of file py_molecule.C.

char get_periodic_doc[] [static]
 

Initial value:

 
  "get_periodic(molid=-1, frame=-1)\n"
  "return dict with keys 'a', 'b', 'c', 'alpha', 'beta', and 'gamma'\n"
  "representing the periodic cell layout for a particular frame.\n"
  "a, b, and c are the lengths of the unit cell along the first, second\n"
  "and third unit cell vectors, respectively.  alpha, beta, and gamma\n"
  "give the angle between sides B and C, A and C, and A and B,\n"
  "respectively."

Definition at line 699 of file py_molecule.C.

char get_top_doc[] [static]
 

Initial value:

  "get_top(molid) -> molid\n"
  "Return molid of top molecule."

Definition at line 220 of file py_molecule.C.

char get_visible_doc[] [static]
 

Initial value:

  "get_visible(molid=-1) -> boolean\n"
  "  Get visibility state for selected molecule, default top molecule\n"

Definition at line 756 of file py_molecule.C.

char mol_cancel_doc[] [static]
 

Initial value:

  "cancel(molid) -> None\n"
  "Cancel background loading of files for given molid."

Definition at line 181 of file py_molecule.C.

char mol_delete_doc[] [static]
 

Initial value:

  "delete(molid) -> None\n"
  "Delete molecule with given molid."

Definition at line 201 of file py_molecule.C.

char mol_exists_doc[] [static]
 

Initial value:

 
  "exists(molid) -> boolean\n"
  "Return True if molid is valid."

Definition at line 59 of file py_molecule.C.

char mol_listall_doc[] [static]
 

Initial value:

  "listall() -> list\n"
  "Returns list of all valid molid's."

Definition at line 43 of file py_molecule.C.

char mol_load_doc[] [static]
 

Initial value:

 
  "load(structure, sfname, coor, cfname) -> molid\n"
  "Load new molecule with structure file type 'structure', \n"
  "  structure file name 'sfname', coordinate file type 'coor', and\n"
  "  coordinate file name 'cfname'.  'coor' and 'cfname' are optional."

Definition at line 122 of file py_molecule.C.

char mol_name_doc[] [static]
 

Initial value:

 
  "name(molid) -> string\n"
  "Returns name of given molecule"

Definition at line 70 of file py_molecule.C.

char mol_new_doc[] [static]
 

Initial value:

 
  "new(name) -> int\n"
  "Creates new molecule with given name and returns molid."

Definition at line 106 of file py_molecule.C.

char mol_num_doc[] [static]
 

Initial value:

 
  "num() -> int\n"
  "RAeturns the number of loaded molecules."

Definition at line 33 of file py_molecule.C.

char mol_numatoms_doc[] [static]
 

Initial value:

 
  "numatoms (molid) -> int\n"
  "Returns number of atoms in given molecule"

Definition at line 88 of file py_molecule.C.

char mol_read_doc[] [static]
 

Initial value:

  "read(molid, filetype, filename, beg=0, end=-1, skip=1, waitfor=1)\n"
  "Read data from file 'filename' of type 'filetype' into molecule with\n"
  "id 'molid'.  molid=-1 creates new molecule.  Return number of frames\n"
  "read (remaining frames will be loaded in the background.\n"
  "  First frame = beg; default 0\n"
  "  Last frame = end; default all frames\n"
  "  Frame stride = skip; default load all frames\n"
  "  Frames to load before returning = waitfor; default 1\n"

Definition at line 323 of file py_molecule.C.

char mol_rename_doc[] [static]
 

Initial value:

  "rename(molid, newname) -> rename molecule to 'newname'."

Definition at line 490 of file py_molecule.C.

char mol_ssrecalc_doc[] [static]
 

Initial value:

  "ssrecalc(molid) -> recalculate secondary structure for molecule.\n"
  "raises RuntimeError if structure could not be calculated, usually\n"
  "due to the Stride program not being available."

Definition at line 463 of file py_molecule.C.

char mol_write_doc[] [static]
 

Initial value:

  "write(molid, filetype, filename, beg=0, end=-1, skip=1, waitfor=-1,\n"
  "      selection=None)\n"
  "Write data into file 'filename' of type 'filetype' from molecule with\n"
  "id 'molid'.  Return number of frames written (remaining frames will be\n"
  "written in the background.\n"
  "  First frame = beg; default 0\n"
  "  Last frame = end; default all frames\n"
  "  Frame stride = skip; default load all frames\n"
  "  Frames to load before returning = waitfor; default 1\n"
  "  Specify selection of atoms to write with 'selection' keyword; pass\n"
  "    tuple of atom indexes as argument."

Definition at line 336 of file py_molecule.C.

PyMethodDef MolMethods[] [static]
 

Definition at line 822 of file py_molecule.C.

Referenced by initmolecule.

char numframes_doc[] [static]
 

Initial value:

  "numframes(molid) -> number of frames in molecule with id 'molid'."

Definition at line 353 of file py_molecule.C.

char remarks_doc[] = "get_remarks(molid): returns list of per-file remarks/comments" [static]
 

Definition at line 606 of file py_molecule.C.

char set_frame_doc[] [static]
 

Initial value:

  "set_frame(molid, frame)\n"
  "Change frame of molecule with id 'molid' to 'frame'."

Definition at line 385 of file py_molecule.C.

char set_periodic_doc[] [static]
 

Initial value:

  "set_periodic(molid=-1, frame=-1, a, b, c, alpha, beta, gamma)\n"
  "Set the periodic cell layout for a particular frame.\n"
  "All keywords except molid are optional.  See get_periodic for\n"
  "descriptions of the keywords."

Definition at line 726 of file py_molecule.C.

char set_top_doc[] [static]
 

Initial value:

  "set_top(molid) -> None\n"
  "Make the molecule top."

Definition at line 230 of file py_molecule.C.

char set_visible_doc[] [static]
 

Initial value:

  "set_visible(molid=-1, state)\n"
  "  Turn selected molecule on or off, default top molecule\n"

Definition at line 759 of file py_molecule.C.

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