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py_topo.C File Reference

#include "py_commands.h"
#include "VMDApp.h"
#include "Molecule.h"
#include "MoleculeList.h"
#include "DrawMolecule.h"

Go to the source code of this file.

Functions

PyObject * topo_get_bond (PyObject *self, PyObject *args, PyObject *kwargs)

PyObject * topo_get_angle (PyObject *self, PyObject *args, PyObject *kwargs)

PyObject * topo_get_dihed (PyObject *self, PyObject *args, PyObject *kwargs)

PyObject * topo_get_impro (PyObject *self, PyObject *args, PyObject *kwargs)

PyObject * topo_add_bond (PyObject *self, PyObject *args, PyObject *kwargs)

PyObject * topo_add_angle (PyObject *self, PyObject *args, PyObject *kwargs)

PyObject * topo_add_dihed (PyObject *self, PyObject *args, PyObject *kwargs)

PyObject * topo_add_improp (PyObject *self, PyObject *args, PyObject *kwargs)

PyObject * topo_del_bond (PyObject *self, PyObject *args, PyObject *kwargs)

PyObject * topo_del_angle (PyObject *self, PyObject *args, PyObject *kwargs)

PyObject * topo_del_dihed (PyObject *self, PyObject *args, PyObject *kwargs)

PyObject * topo_del_improper (PyObject *self, PyObject *args, PyObject *kwargs)

PyObject * topo_del_all_bonds (PyObject *self, PyObject *args, PyObject *kwargs)

PyObject * topo_del_all_angles (PyObject *self, PyObject *args, PyObject *kwargs)

PyObject * topo_del_all_dihed (PyObject *self, PyObject *args, PyObject *kwargs)

PyObject * topo_del_all_impropers (PyObject *self, PyObject *args, PyObject *kwargs)

PyObject * topo_bondtypes (PyObject *self, PyObject *args, PyObject *kwargs)

PyObject * topo_angletypes (PyObject *self, PyObject *args, PyObject *kwargs)

PyObject * topo_dihetypes (PyObject *self, PyObject *args, PyObject *kwargs)

PyObject * topo_imptypes (PyObject *self, PyObject *args, PyObject *kwargs)

PyObject * inittopology (void)

Variables

const char bond_doc []

const char angle_doc []

const char dihed_doc []

const char impropers_doc []

const char addbond_doc []

const char addangle_doc []

const char adddihed_doc []

const char addimproper_doc []

const char delbond_doc []

const char delangle_doc []

const char deldihed_doc []

const char delimproper_doc []

const char del_all_bond_doc []

const char del_all_angle_doc []

const char del_all_dihed_doc []

const char del_all_improper_doc []

const char btypes_doc []

const char atypes_doc []

const char dtypes_doc []

const char itypes_doc []

PyMethodDef methods []

const char topo_moddoc []

Function Documentation

PyObject* inittopology ( void )

Definition at line 1228 of file py_topo.C.
References methods, and topo_moddoc.

PyObject* topo_add_angle ( PyObject * self,

PyObject * args,

PyObject * kwargs

) [static]

Definition at line 388 of file py_topo.C.
References BaseMolecule::add_angle, NameList< int >::add_name, BaseMolecule::ANGLES, BaseMolecule::angleTypeNames, BaseMolecule::ANGLETYPES, as_pyint, get_vmdapp, MoleculeList::mol_from_id, VMDApp::molecule_top, VMDApp::moleculeList, NULL, and BaseMolecule::set_dataset_flag.

PyObject* topo_add_bond ( PyObject * self,

PyObject * args,

PyObject * kwargs

) [static]

Definition at line 331 of file py_topo.C.
References BaseMolecule::add_bond_dupcheck, NameList< int >::add_name, BaseMolecule::BONDORDERS, BaseMolecule::BONDS, BaseMolecule::bondTypeNames, BaseMolecule::BONDTYPES, get_vmdapp, MoleculeList::mol_from_id, VMDApp::molecule_top, VMDApp::moleculeList, NULL, and BaseMolecule::set_dataset_flag.

PyObject* topo_add_dihed ( PyObject * self,

PyObject * args,

PyObject * kwargs

) [static]

Definition at line 437 of file py_topo.C.
References BaseMolecule::add_dihedral, NameList< int >::add_name, BaseMolecule::ANGLES, BaseMolecule::ANGLETYPES, as_pyint, BaseMolecule::dihedralTypeNames, get_vmdapp, MoleculeList::mol_from_id, VMDApp::molecule_top, VMDApp::moleculeList, NULL, and BaseMolecule::set_dataset_flag.

PyObject* topo_add_improp ( PyObject * self,

PyObject * args,

PyObject * kwargs

) [static]

Definition at line 487 of file py_topo.C.
References BaseMolecule::add_improper, NameList< int >::add_name, BaseMolecule::ANGLES, BaseMolecule::ANGLETYPES, as_pyint, get_vmdapp, BaseMolecule::improperTypeNames, MoleculeList::mol_from_id, VMDApp::molecule_top, VMDApp::moleculeList, NULL, and BaseMolecule::set_dataset_flag.

PyObject* topo_angletypes ( PyObject * self,

PyObject * args,

PyObject * kwargs

) [static]

Definition at line 1044 of file py_topo.C.
References BaseMolecule::angleTypeNames, as_pystring, get_vmdapp, MoleculeList::mol_from_id, VMDApp::molecule_top, VMDApp::moleculeList, NameList< int >::name, NULL, and NameList< int >::num.

PyObject* topo_bondtypes ( PyObject * self,

PyObject * args,

PyObject * kwargs

) [static]

Definition at line 994 of file py_topo.C.
References as_pystring, BaseMolecule::bondTypeNames, get_vmdapp, MoleculeList::mol_from_id, VMDApp::molecule_top, VMDApp::moleculeList, NameList< int >::name, NULL, and NameList< int >::num.

PyObject* topo_del_all_angles ( PyObject * self,

PyObject * args,

PyObject * kwargs

) [static]

Definition at line 885 of file py_topo.C.
References BaseMolecule::angles, BaseMolecule::angleTypes, as_pyint, ResizeArray< int >::clear, get_vmdapp, MoleculeList::mol_from_id, VMDApp::molecule_top, VMDApp::moleculeList, NULL, and BaseMolecule::num_angles.

PyObject* topo_del_all_bonds ( PyObject * self,

PyObject * args,

PyObject * kwargs

) [static]

Definition at line 850 of file py_topo.C.
References as_pyint, BaseMolecule::clear_bonds, BaseMolecule::count_bonds, get_vmdapp, MoleculeList::mol_from_id, VMDApp::molecule_top, VMDApp::moleculeList, and NULL.

PyObject* topo_del_all_dihed ( PyObject * self,

PyObject * args,

PyObject * kwargs

) [static]

Definition at line 921 of file py_topo.C.
References as_pyint, ResizeArray< int >::clear, BaseMolecule::dihedrals, BaseMolecule::dihedralTypes, get_vmdapp, MoleculeList::mol_from_id, VMDApp::molecule_top, VMDApp::moleculeList, NULL, and BaseMolecule::num_dihedrals.

PyObject* topo_del_all_impropers ( PyObject * self,

PyObject * args,

PyObject * kwargs

) [static]

Definition at line 957 of file py_topo.C.
References as_pyint, ResizeArray< int >::clear, get_vmdapp, BaseMolecule::impropers, BaseMolecule::improperTypes, MoleculeList::mol_from_id, VMDApp::molecule_top, VMDApp::moleculeList, NULL, and BaseMolecule::num_impropers.

PyObject* topo_del_angle ( PyObject * self,

PyObject * args,

PyObject * kwargs

) [static]

Definition at line 609 of file py_topo.C.
References BaseMolecule::ANGLES, BaseMolecule::angles, BaseMolecule::angleTypes, get_vmdapp, MoleculeList::mol_from_id, VMDApp::molecule_top, VMDApp::moleculeList, BaseMolecule::nAtoms, NULL, ResizeArray< int >::num, BaseMolecule::num_angles, ResizeArray< int >::pop, result, and BaseMolecule::set_dataset_flag.

PyObject* topo_del_bond ( PyObject * self,

PyObject * args,

PyObject * kwargs

) [static]

Definition at line 533 of file py_topo.C.
References BaseMolecule::atom, BaseMolecule::BONDORDERS, BaseMolecule::BONDS, MolAtom::bonds, MolAtom::bondTo, BaseMolecule::BONDTYPES, NameList< int * >::data, NameList< float * >::data, BaseMolecule::extraflt, BaseMolecule::extraint, get_vmdapp, MAXATOMBONDS, MoleculeList::mol_from_id, VMDApp::molecule_top, VMDApp::moleculeList, BaseMolecule::nAtoms, NULL, result, and BaseMolecule::set_dataset_flag.

PyObject* topo_del_dihed ( PyObject * self,

PyObject * args,

PyObject * kwargs

) [static]

Definition at line 688 of file py_topo.C.
References BaseMolecule::ANGLES, BaseMolecule::dihedrals, BaseMolecule::dihedralTypes, get_vmdapp, MoleculeList::mol_from_id, VMDApp::molecule_top, VMDApp::moleculeList, BaseMolecule::nAtoms, NULL, ResizeArray< int >::num, BaseMolecule::num_dihedrals, ResizeArray< int >::pop, result, and BaseMolecule::set_dataset_flag.

PyObject* topo_del_improper ( PyObject * self,

PyObject * args,

PyObject * kwargs

) [static]

Definition at line 771 of file py_topo.C.
References BaseMolecule::ANGLES, get_vmdapp, BaseMolecule::impropers, BaseMolecule::improperTypes, MoleculeList::mol_from_id, VMDApp::molecule_top, VMDApp::moleculeList, BaseMolecule::nAtoms, NULL, ResizeArray< int >::num, BaseMolecule::num_impropers, ResizeArray< int >::pop, result, and BaseMolecule::set_dataset_flag.

PyObject* topo_dihetypes ( PyObject * self,

PyObject * args,

PyObject * kwargs

) [static]

Definition at line 1094 of file py_topo.C.
References as_pystring, BaseMolecule::dihedralTypeNames, get_vmdapp, MoleculeList::mol_from_id, VMDApp::molecule_top, VMDApp::moleculeList, NameList< int >::name, NULL, and NameList< int >::num.

PyObject* topo_get_angle ( PyObject * self,

PyObject * args,

PyObject * kwargs

) [static]

Definition at line 145 of file py_topo.C.
References BaseMolecule::angles, BaseMolecule::angleTypeNames, BaseMolecule::get_angletype, get_vmdapp, MoleculeList::mol_from_id, VMDApp::molecule_top, VMDApp::moleculeList, NameList< int >::name, NULL, and BaseMolecule::num_angles.

PyObject* topo_get_bond ( PyObject * self,

PyObject * args,

PyObject * kwargs

) [static]

Definition at line 40 of file py_topo.C.
References as_int, BaseMolecule::atom, MolAtom::bonds, MolAtom::bondTo, BaseMolecule::bondTypeNames, get_vmdapp, BaseMolecule::getbondorder, BaseMolecule::getbondtype, is_pyint, MoleculeList::mol_from_id, VMDApp::molecule_top, VMDApp::moleculeList, NameList< int >::name, BaseMolecule::nAtoms, and NULL.

PyObject* topo_get_dihed ( PyObject * self,

PyObject * args,

PyObject * kwargs

) [static]

Definition at line 207 of file py_topo.C.
References BaseMolecule::dihedrals, BaseMolecule::dihedralTypeNames, BaseMolecule::get_dihedraltype, get_vmdapp, MoleculeList::mol_from_id, VMDApp::molecule_top, VMDApp::moleculeList, NameList< int >::name, NULL, and BaseMolecule::num_dihedrals.

PyObject* topo_get_impro ( PyObject * self,

PyObject * args,

PyObject * kwargs

) [static]

Definition at line 271 of file py_topo.C.
References BaseMolecule::get_impropertype, get_vmdapp, BaseMolecule::impropers, BaseMolecule::improperTypeNames, MoleculeList::mol_from_id, VMDApp::molecule_top, VMDApp::moleculeList, NameList< int >::name, NULL, and BaseMolecule::num_impropers.

PyObject* topo_imptypes ( PyObject * self,

PyObject * args,

PyObject * kwargs

) [static]

Definition at line 1144 of file py_topo.C.
References as_pystring, get_vmdapp, BaseMolecule::improperTypeNames, MoleculeList::mol_from_id, VMDApp::molecule_top, VMDApp::moleculeList, NameList< int >::name, NULL, and NameList< int >::num.

Variable Documentation

const char addangle_doc[] [static]

Initial value:
"Add an angle between three atoms with given indices. No checking for\n" "duplicate angles is performed\n\n" "Args:\n" " i (int): Index of first atom\n" " j (int): Index of second atom\n" " k (int): Index of third atom\n" " molid (int): Molecule ID to add angle to. Defaults to top molecule.\n" " type (str): Angle type. Can be from output of `topology.getangletypes()`,\n" " or can define a new angle type. Defaults to None\n" "Returns:\n" " (int) Index of new angle in system"

Definition at line 376 of file py_topo.C.

const char addbond_doc[] [static]

Initial value:
"Add a bond between two atoms with given indices. If bond is already present,\n" "nothing will be done.\n\n" "Args:\n" " i (int): Index of first atom\n" " j (int): Index of second atom\n" " molid (int): Molecule ID to add bond to. Defaults to top molecule.\n" " order (float): Bond order. Defaults to 1.0\n" " type (str): Bond type. Can be from output of `topology.bondtypes()`,\n" " or can define a new bond type. Defaults to None"

Definition at line 321 of file py_topo.C.

const char adddihed_doc[] [static]

Initial value:
"Add a dihedral between four atoms with the given indices. No checking for\n" "duplicate dihedrals is performed.\n\n" "Args:\n" " i (int): Index of first atom\n" " j (int): Index of second atom\n" " k (int): Index of third atom\n" " l (int): Index of fourth atom\n" " molid (int): Molecule ID to add dihedral in. Defaults to top molecule.\n" " type (str): Angle type. Can be from output of `topology.getangletypes()`,\n" " or can define a new angle type. Defaults to None\n" "Returns:\n" " (int) New number of dihedrals defined in system"

Definition at line 424 of file py_topo.C.

const char addimproper_doc[] [static]

Initial value:
"Add an improper dihedral between four atoms with the given indices. No\n" "checking for duplicate impropers is performed.\n\n" "Args:\n" " i (int): Index of first atom\n" " j (int): Index of second atom\n" " k (int): Index of third atom\n" " l (int): Index of fourth atom\n" " molid (int): Molecule ID to add dihedral in. Defaults to top molecule.\n" " type (str): Angle type. Can be from output of `topology.getangletypes()`,\n" " or can define a new angle type. Defaults to None\n" "Returns:\n" " (int) New number of improper dihedrals defined in system"

Definition at line 474 of file py_topo.C.

const char angle_doc[] [static]

Initial value:
"Get all unique angles within a specified molecule. Optionally, can get angle\n" "type as well\n\n" "Args:\n" " molid (int): Molecule ID to query. Defaults to top molecule\n" " type (bool): Whether to include angle type information in the result\n" " Defaults to False.\n" "Returns:\n" " (list of lists) Information about each angle in the system. Each angle \n" " will be a list with the indices of the three atoms comprising the\n" " angle, followed by angle type (as a string) if requested."

Definition at line 134 of file py_topo.C.

const char atypes_doc[] [static]

Initial value:
"Get all angle types defined in the molecule. If molecule does not have angle\n" "types, will return an empty list.\n\n" "Args:\n" " molid (int): Molecule ID to query. Defaults to top molecule\n" "Returns:\n" " (list of str): Angle types in molecule"

Definition at line 1037 of file py_topo.C.

const char bond_doc[] [static]

Initial value:
"Get all unique bonds within a specified molecule. Optionally, can get bond\n" "type and order by modifying the type parameter\n\n" "Args:\n" " molid (int): Molecule ID to query. Defaults to top molecule\n" " type (bool): Whether to include bond type information in the result\n" " Defaults to False.\n" " orders (bool): Whether to include bond order information in the result\n" " Defaults to False.\n" "Returns:\n" " (list of lists) Information about each bond in the system. Each bond\n" " will be a list with the indices of the two atoms in the\n" " bond, followed by bond type (as a string) and order (as a float) if\n" " requested"

Definition at line 27 of file py_topo.C.

const char btypes_doc[] [static]

Initial value:
"Get all bond types defined in the molecule. If molecule does not have\n" "bond types, will return an empty list.\n\n" "Args:\n" " molid (int): Molecule ID to query. Defaults to top molecule\n" "Returns:\n" " (list of str): Bond types in molecule"

Definition at line 987 of file py_topo.C.

const char del_all_angle_doc[] [static]

Initial value:
"Delete all angles in a given molecule\n\n" "Args:\n" " molid (int): Molecule ID to delete angles in. Defaults to top molecule.\n" "Returns:\n" " (int) Number of angles deleted"

Definition at line 879 of file py_topo.C.

const char del_all_bond_doc[] [static]

Initial value:
"Delete all bonds in a given molecule\n\n" "Args:\n" " molid (int): Molecule ID to delete bonds in. Defaults to top molecule.\n" "Returns:\n" " (int) Number of bonds deleted"

Definition at line 844 of file py_topo.C.

const char del_all_dihed_doc[] [static]

Initial value:
"Delete all dihedrals in a given molecule\n\n" "Args:\n" " molid (int): Molecule ID to delete in. Defaults to top molecule\n" "Returns:\n" " (int) Number of dihedrals deleted"

Definition at line 915 of file py_topo.C.

const char del_all_improper_doc[] [static]

Initial value:
"Delete all improper dihedrals in a given molecule\n\n" "Args:\n" " molid (int): Molecule ID to delete in. Defaults to top molecule\n" "Returns:\n" " (int) Number of impropers deleted"

Definition at line 951 of file py_topo.C.

const char delangle_doc[] [static]

Initial value:
"Delete an angle between atoms with the given indices. If the angle does not\n" "exist, does nothing.\n\n" "Args:\n" " i (int): Index of first atom\n" " j (int): Index of second atom\n" " k (int): Index of third atom\n" " molid (int): Molecule ID to delete from. Defaults to top molecule.\n" "Returns:\n" " (bool) True if angle exists and was deleted"

Definition at line 599 of file py_topo.C.

const char delbond_doc[] [static]

Initial value:
"Delete a bond between atoms with the given indices. If the bond does not\n" "exist, does nothing.\n\n" "Args:\n" " i (int): Index of first atom\n" " j (int): Index of second atom\n" " molid (int): Molecule ID to delete bond from. Defaults to top molecule.\n" "Returns:\n" " (bool) True if bond exists and was deleted"

Definition at line 524 of file py_topo.C.

const char deldihed_doc[] [static]

Initial value:
"Delete a dihedral angle between atoms with the given indices. If the\n" "dihedral does not exist, does nothing.\n\n" "Args:\n" " i (int): Index of first atom\n" " j (int): Index of second atom\n" " k (int): Index of third atom\n" " l (int): Index of fourth atom\n" " molid (int): Molecule ID to delete from. Defaults to top molecule.\n" "Returns:\n" " (bool) True if dihedral exists and was deleted"

Definition at line 677 of file py_topo.C.

const char delimproper_doc[] [static]

Initial value:
"Delete an improper dihedral angle between atoms with the given indices. If\n" "the improper does not exist, does nothing.\n\n" "Args:\n" " i (int): Index of first atom\n" " j (int): Index of second atom\n" " k (int): Index of third atom\n" " l (int): Index of fourth atom\n" " molid (int): Molecule ID to delete from. Defaults to top molecule.\n" "Returns:\n" " (bool) True if improper dihedral exists and was deleted"

Definition at line 760 of file py_topo.C.

const char dihed_doc[] [static]

Initial value:
"Get all unique dihedrals within a specified molecule. Optionally, can get\n" "dihedral type as well\n\n" "Args:\n" " molid (int): Molecule ID to query. Defaults to top molecule\n" " type (bool): Whether to include dihedral type information in the result\n" " Defaults to False.\n" "Returns:\n" " (list of lists) Information about each dihedral in the system. Each\n" " dihedral will be a list with the indices of the four atoms\n" " comprising the dihedral, followed by dihedral type (as a string) if\n" " requested."

Definition at line 195 of file py_topo.C.

const char dtypes_doc[] [static]

Initial value:
"Get all dihedral types defined in the molecule. If the molecule does not\n" "have dihedral types, will return an empty list.\n\n" "Args:\n" " molid (int): Molecule ID to query. Defaults to top molecule\n" "Returns:\n" " (list of str): Dihedral types in molecule"

Definition at line 1087 of file py_topo.C.

const char impropers_doc[] [static]

Initial value:
"Get all unique impropers within a specified molecule. Optionally, can get\n" "improper type as well\n\n" "Args:\n" " molid (int): Molecule ID to query. Defaults to top molecule\n" " type (bool): Whether to include improper type information in the result\n" " Defaults to False.\n" "Returns:\n" " (list of lists) Information about each improper in the system. Each\n" " improper will be a list with the indices of the four atoms\n" " comprising the improper, followed by improper type (as a string) if\n" " requested."

Definition at line 259 of file py_topo.C.

const char itypes_doc[] [static]

Initial value:
"Get all improper dihedral types defined in the molecule. If the molecule\n" "not have improper types, will return an empty list.\n\n" "Args:\n" " molid (int): Molecule ID to query. Defaults to top molecule\n" "Returns:\n" " (list of str): Improper dihedral types in molecule"

Definition at line 1137 of file py_topo.C.

PyMethodDef methods[] [static]

Initial value:
{ {"bonds", (PyCFunction)topo_get_bond, METH_VARARGS | METH_KEYWORDS, bond_doc}, {"angles", (PyCFunction)topo_get_angle, METH_VARARGS | METH_KEYWORDS, angle_doc}, {"dihedrals", (PyCFunction)topo_get_dihed, METH_VARARGS | METH_KEYWORDS, dihed_doc}, {"impropers", (PyCFunction)topo_get_impro, METH_VARARGS | METH_KEYWORDS, impropers_doc}, {"addbond", (PyCFunction)topo_add_bond, METH_VARARGS | METH_KEYWORDS, addbond_doc}, {"addangle", (PyCFunction)topo_add_angle, METH_VARARGS | METH_KEYWORDS, addangle_doc}, {"adddihedral", (PyCFunction)topo_add_dihed, METH_VARARGS | METH_KEYWORDS, adddihed_doc}, {"addimproper", (PyCFunction)topo_add_improp, METH_VARARGS | METH_KEYWORDS, addimproper_doc}, {"delbond", (PyCFunction)topo_del_bond, METH_VARARGS | METH_KEYWORDS, delbond_doc}, {"delangle", (PyCFunction)topo_del_angle, METH_VARARGS | METH_KEYWORDS, delangle_doc}, {"deldihedral", (PyCFunction)topo_del_dihed, METH_VARARGS | METH_KEYWORDS, deldihed_doc}, {"delimproper", (PyCFunction)topo_del_improper, METH_VARARGS | METH_KEYWORDS, delimproper_doc}, {"delallbonds", (PyCFunction)topo_del_all_bonds, METH_VARARGS | METH_KEYWORDS, del_all_bond_doc}, {"delallangles", (PyCFunction)topo_del_all_angles, METH_VARARGS | METH_KEYWORDS, del_all_angle_doc}, {"delalldihedrals", (PyCFunction)topo_del_all_dihed, METH_VARARGS | METH_KEYWORDS, del_all_dihed_doc}, {"delallimpropers", (PyCFunction)topo_del_all_impropers, METH_VARARGS | METH_KEYWORDS, del_all_improper_doc}, {"bondtypes", (PyCFunction)topo_bondtypes, METH_VARARGS | METH_KEYWORDS, btypes_doc}, {"angletypes", (PyCFunction)topo_angletypes, METH_VARARGS | METH_KEYWORDS, atypes_doc}, {"dihedraltypes", (PyCFunction)topo_dihetypes, METH_VARARGS | METH_KEYWORDS, dtypes_doc}, {"impropertypes", (PyCFunction)topo_imptypes, METH_VARARGS | METH_KEYWORDS, itypes_doc}, {NULL, NULL} }

Definition at line 1186 of file py_topo.C.
Referenced by inittopology.

const char topo_moddoc[] [static]

Initial value:
"Methods for querying or modifying the topology of a molecule, which consists " "of all defined bonds, angles, dihedrals, and impropers, for applicable " "topology file formats."

Definition at line 1211 of file py_topo.C.
Referenced by inittopology.

Generated on Fri Apr 19 02:45:58 2024 for VMD (current) by

Functions
PyObject *	topo_get_bond (PyObject self, PyObject args, PyObject *kwargs)
PyObject *	topo_get_angle (PyObject self, PyObject args, PyObject *kwargs)
PyObject *	topo_get_dihed (PyObject self, PyObject args, PyObject *kwargs)
PyObject *	topo_get_impro (PyObject self, PyObject args, PyObject *kwargs)
PyObject *	topo_add_bond (PyObject self, PyObject args, PyObject *kwargs)
PyObject *	topo_add_angle (PyObject self, PyObject args, PyObject *kwargs)
PyObject *	topo_add_dihed (PyObject self, PyObject args, PyObject *kwargs)
PyObject *	topo_add_improp (PyObject self, PyObject args, PyObject *kwargs)
PyObject *	topo_del_bond (PyObject self, PyObject args, PyObject *kwargs)
PyObject *	topo_del_angle (PyObject self, PyObject args, PyObject *kwargs)
PyObject *	topo_del_dihed (PyObject self, PyObject args, PyObject *kwargs)
PyObject *	topo_del_improper (PyObject self, PyObject args, PyObject *kwargs)
PyObject *	topo_del_all_bonds (PyObject self, PyObject args, PyObject *kwargs)
PyObject *	topo_del_all_angles (PyObject self, PyObject args, PyObject *kwargs)
PyObject *	topo_del_all_dihed (PyObject self, PyObject args, PyObject *kwargs)
PyObject *	topo_del_all_impropers (PyObject self, PyObject args, PyObject *kwargs)
PyObject *	topo_bondtypes (PyObject self, PyObject args, PyObject *kwargs)
PyObject *	topo_angletypes (PyObject self, PyObject args, PyObject *kwargs)
PyObject *	topo_dihetypes (PyObject self, PyObject args, PyObject *kwargs)
PyObject *	topo_imptypes (PyObject self, PyObject args, PyObject *kwargs)
PyObject *	inittopology (void)
Variables
const char	bond_doc []
const char	angle_doc []
const char	dihed_doc []
const char	impropers_doc []
const char	addbond_doc []
const char	addangle_doc []
const char	adddihed_doc []
const char	addimproper_doc []
const char	delbond_doc []
const char	delangle_doc []
const char	deldihed_doc []
const char	delimproper_doc []
const char	del_all_bond_doc []
const char	del_all_angle_doc []
const char	del_all_dihed_doc []
const char	del_all_improper_doc []
const char	btypes_doc []
const char	atypes_doc []
const char	dtypes_doc []
const char	itypes_doc []
PyMethodDef	methods []
const char	topo_moddoc []