schrodinger.application.desmond.packages.viparr1.viparr.viparr module¶
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class
schrodinger.application.desmond.packages.viparr1.viparr.viparr.
Struct
¶ Bases:
object
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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class
schrodinger.application.desmond.packages.viparr1.viparr.viparr.
Atom
¶ Bases:
object
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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schrodinger.application.desmond.packages.viparr1.viparr.viparr.
templates_convert
(templates)¶ Convert templates structure to internal data structure.
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schrodinger.application.desmond.packages.viparr1.viparr.viparr.
compress_residue_list
(residue_list)¶ Compress FF representation if possible
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schrodinger.application.desmond.packages.viparr1.viparr.viparr.
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.
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schrodinger.application.desmond.packages.viparr1.viparr.viparr.
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.
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schrodinger.application.desmond.packages.viparr1.viparr.viparr.
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.
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schrodinger.application.desmond.packages.viparr1.viparr.viparr.
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.
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schrodinger.application.desmond.packages.viparr1.viparr.viparr.
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.
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schrodinger.application.desmond.packages.viparr1.viparr.viparr.
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.
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schrodinger.application.desmond.packages.viparr1.viparr.viparr.
merge
(list0, list1)¶ Merge list1 into list0, as long as there are no entries in common.
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schrodinger.application.desmond.packages.viparr1.viparr.viparr.
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.
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schrodinger.application.desmond.packages.viparr1.viparr.viparr.
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.
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schrodinger.application.desmond.packages.viparr1.viparr.viparr.
construct_lists
(iffld, atoms, neighbors, rules, templates, residue_list, pseudo_residue_list)¶ Return lists that describe the structure.
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schrodinger.application.desmond.packages.viparr1.viparr.viparr.
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.
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schrodinger.application.desmond.packages.viparr1.viparr.viparr.
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.]
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schrodinger.application.desmond.packages.viparr1.viparr.viparr.
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
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schrodinger.application.desmond.packages.viparr1.viparr.viparr.
main
(vargs=[])¶