#include "py_commands.h"#include "VMDApp.h"#include "Molecule.h"#include "MoleculeList.h"#include "DrawMolecule.h"Go to the source code of this file.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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"
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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"
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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"
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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"
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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."
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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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."
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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"
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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."
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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"
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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.
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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.