topology

Python operations available from the topology module, used to query and set topological relations (bonds, angles, etc.) between atoms in a molecule. For large-scale regeneration of angles and dihedrals given a bonded topology, use topotools via evaltcl, as shown below in an example script.

import topology
from VMD import evaltcl
#Load molecule here... (not shown)

#Delete existing angles and dihedrals
topology.delallangles()
topology.delalldihedrals()
topology.delallimpropers()
evaltcl("package require topotools; topo guessangles")
evaltcl("topo guessdihedrals; topo guessimpropers")

• bonds(molid=top, type=0): Returns all unique bonds within the structure of the specified molid. Each bond will be its own 2-element list within the list. Optionally, the bond type and order can be returned by modifying the type parameter. 0=bond indexes only, 1 adds bond type information, 2 adds bond order, and 3 adds both.

• angles(molid=top, type=0): Returns all unique angles within the structure of the specified molid. Each angle will be its own 3-element list within the list. Optionally, the angle type can be returned by modifying the type parameter. 0=angle indexes only, 1 adds angle type information.

• dihedrals(molid=top, type=0): Returns all unique dihedrals within the structure of the specified molid. Each dihedral will be its own 4-element list within the list. Optionally, the dihedral type can be returned by modifying the type parameter. 0=dihedral indexes only, 1 adds dihedral type information.

• impropers(molid=top, type=0): Returns all unique impropers within the structure of the specified molid. Each improper will be its own 4-element list within the list. Optionally, the improper type can be returned by modifying the type parameter. 0=improper indexes only, 1 adds improper type information.

• impropers(molid=top, type=0): Returns all unique impropers within the structure of the specified molid. Each improper will be its own 4-element list within the list. Optionally, the improper type can be returned by modifying the type parameter. 0=improper indexes only, 1 adds improper type information.

• addbond(i, j, molid=top, order=1.0, type=None): Adds one bond between the atoms at index i and j of the molecule given by molid, with bondorder order and bondtype type. Bonds cannot be added twice, and will be ignored if present. Returns 0 on success, -1 on failure.

• addangle(i, j, k, molid=top, type=None): Adds one angle between the atoms at index i, j and k of the molecule given by molid, with angletype type. Duplicates are not checked!!! Will return the index of the added angle.

• adddihedral(i, j, k, l, molid=top, type=None): Adds one dihedral between the atoms at index i, j, k, and l of the molecule given by molid, with dihedraltype type. Duplicates are not checked!!! Will return the index of the added dihedral.

• addimproper(i, j, k, l, molid=top, type=None): Adds one improper between the atoms at index i, j, k, and l of the molecule given by molid, with type type. No duplicate checks are made. Will return the index of the added improper.

• delbond(i, j, molid=top): Deletes bond between atoms i and j, if present. Method returns the number of bonds deleted (0 or 1).

• delangle(i, j, k, molid=top): Deletes angle between atoms i, j, and k, if present. Method returns the number of angles deleted (0 or 1).

• deldihedral(i, j, k, l, molid=top): Deletes dihedral between atoms i, j, k, and l, if present. Method returns the number of dihedrals deleted (0 or 1).

• delimproper(i, j, k, l, molid=top): Deletes improper between atoms i, j, k, and l, if present. Method returns the number of impropers deleted (0 or 1).

• delallbonds(molid=top): Deletes all bonds associated with a molid, returning the number of bonds deleted.

• delallangles(molid=top): Deletes all angles associated with a molid, returning the number of angles deleted.

• delalldihedrals(molid=top): Deletes all dihedrals associated with a molid, returning the number of dihedrals deleted.

• delallimpropers(molid=top): Deletes all impropers associated with a molid, returning the number of impropers deleted.