Module viparr

Classes

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Struct

Atom

Functions

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templates_convert(templates)
Convert templates structure to internal data structure.

compress_residue_list(residue_list)
Compress FF representation if possible

get_atom_list(atoms, neighbors, templates, residue_list)
Return a list of atoms in the ct structure.

get_neighbor_list(atom_list)
Return list of neighbor lists; one neighbor list for each atom, in order.

get_bond_list(neighbor_list)
Return list of all bonds (i,j) such that i<j.

get_angle_list(neighbor_list)
Return list of all angles (i,j,k) such that i<k.

get_proper_list(neighbor_list, bond_list)
Return list of all propers (i,j,k,l) such that i<l.

get_bonded_term_list(fieldname, templates, residue_list, sorted)
Return a list of bonded items.

merge(list0, list1)
Merge list1 into list0, as long as there are no entries in common.

get_pseudo_terms(iffld, pseudo_residue_list, nres, nstart)
Return drude and virtual particle list (numbering starting at nstart) and list of 'bonds' between drudes, virtual sites and particles.

update_pseudo_residue_list(iffld, pseudo_residue_list, atoms, templates, residue_list)
pseudo_list is a list of all residues in ct block, and each residue is a list of pseudo particles.

construct_lists(iffld, atoms, neighbors, rules, templates, residue_list, pseudo_residue_list)
Return lists that describe the structure.

merge_blocks(first, second)
Merge second block into first; print warning message if element in second block is already in the first block.

merge_blocks2(first, second)
Merge first block into second; print warning message if element in first block will override element in second block.

add_water_constraints(ff_handle)
Add an ffio_constraints block to the ff_handle for a water ct by reading the ffio_c1 values from the angles and bonds, and append '_constrained' to the functional forms of the angles and bonds.

main(vargs=[])

Variables

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__package__ = 'schrodinger.application.desmond.packages.viparr...

Function Details

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get_atom_list(atoms, neighbors, templates, residue_list)

Return a list of atoms in the ct structure. Each atom has the following fields: pdbname, pdbres, resnum, atomic number, charge, atomtypes. Also check that all residue and atom names are in the templates data structure.

get_neighbor_list(atom_list)

Return list of neighbor lists; one neighbor list for each atom, in order. Each neighborlist is guaranteed to be sorted. Entries are 1-based.

get_bond_list(neighbor_list)

Return list of all bonds (i,j) such that i<j. List will be sorted meaningfully. Entries are 1-based.

get_angle_list(neighbor_list)

Return list of all angles (i,j,k) such that i<k. List will be sorted meaningfully. Entries are 1-based.

get_proper_list(neighbor_list, bond_list)

Return list of all propers (i,j,k,l) such that i<l. List will be sorted meaningfully. Entries are 1-based.

get_bonded_term_list(fieldname, templates, residue_list, sorted)

Return a list of bonded items. Each bonded item is a list, namely: [i,j] when fieldname = 'bonds' or 'exclusions'. if sorted, i<j [i,j,k] when fieldname = 'angles'. if sorted, i<k [i,j,k,l] when fieldname = 'propers' or 'impropers'. if sorted, i<l The returned list will be sorted in a meaningful way.

get_pseudo_terms(iffld, pseudo_residue_list, nres, nstart)

Return drude and virtual particle list (numbering starting at nstart) and list of 'bonds' between drudes, virtual sites and particles. The pseudo_list can be appended to the atom list.

merge_blocks(first, second)

Merge second block into first; print warning message if element in second block is already in the first block. Assumes blocks themselves hold unique entries. First block is the merged one.

merge_blocks2(first, second)

Merge first block into second; print warning message if element in first block will override element in second block. Assumes blocks themselves hold unique entries. Second block is the merged one. [NOT THE SAME BEHAVIOR AS ABOVE.]

add_water_constraints(ff_handle)

Add an ffio_constraints block to the ff_handle for a water ct by reading the ffio_c1 values from the angles and bonds, and append '_constrained' to the functional forms of the angles and bonds.

Parameters:

ff_handle (destro.Destro) - the handle of the ffio_block

Variables Details

[hide private]

package

Value:

'schrodinger.application.desmond.packages.viparr1.viparr'