schrodinger.application.desmond.fep_mapping module¶
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schrodinger.application.desmond.fep_mapping.
cleanup
(topdir=None)¶ Cleanup function to be run atexit
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class
schrodinger.application.desmond.fep_mapping.
AtomMappingData
(source_ct, dest_ct)¶ Bases:
object
Class to store intermediary and final data structures for atom mapping
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addAttachmentPoint
(attachment_point)¶ Adding attachment point. :type attachment_point: two-element tuple. :param attachment_point:
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getAttachmentPoints
()¶
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getBridgeAtoms
()¶
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getAnchorAtoms
()¶
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extendCoreAtoms
(core_atoms)¶ Adding core atoms.
Note that, adding new core atoms can resulting smaller attached fragments
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getCoreAtoms
()¶
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schrodinger.application.desmond.fep_mapping.
map_core_hydrogen
(source_ct, dest_ct, core_map, s_remaining_indices, d_remaining_indices)¶ Mapping hydrogen atoms connected to the core. The number of hydrogen atoms connected to the corresponding atoms should be equal except the core atoms which have attachment.
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schrodinger.application.desmond.fep_mapping.
find_fragment_by_cond
(bridge_atom, cond)¶
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schrodinger.application.desmond.fep_mapping.
find_noncore_fragment
(bridge_atom, core_atom_indices)¶ Finding non-core fragment from bridged :type bridge_atom: _StructureAtom :param bridge_atom: atom bonded to the attachment core atom. :type core_atoms: set of int :param core_atoms: a set of core atom indices. :return a list of atoms.
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schrodinger.application.desmond.fep_mapping.
find_noncore_subfragment
(bridge_atom, core_atom_indices, frag_atom_indices)¶ Finding non-core fragment from bridged :type bridge_atom: _StructureAtom :param bridge_atom: atom bonded to the attachment core atom. :type core_atom_indices: set of int :param core_atom_indices: a set of core atom indices. :return a list of atoms.
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schrodinger.application.desmond.fep_mapping.
find_all_fragment_pairs
(source_ct, dest_ct, attachment_points, core_atom_indices)¶
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schrodinger.application.desmond.fep_mapping.
get_atom_mapping
(data)¶ mapping atoms based on the result from RGA :type data: AtomMappingData :param data: intermediary and finals data structures from RGA
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schrodinger.application.desmond.fep_mapping.
get_fepio_atom_mapping
(atom_mapping)¶ converting to atom mapping format required by mmfepio library. Below is an example: 1 1 2 2 3 -1 4 -1 5 3 -6 4 -7 5
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schrodinger.application.desmond.fep_mapping.
fragment_size_cond
(frag1, frag2, threshold=10)¶
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schrodinger.application.desmond.fep_mapping.
heavy_atom_num_cond
(frag1, frag2, threshold=7)¶
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schrodinger.application.desmond.fep_mapping.
get_heavy_fragment
(frag)¶
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schrodinger.application.desmond.fep_mapping.
find_fragment_MCS
(data, cond=<function heavy_atom_num_cond>, atomtype=11)¶ Finding MCS in fragment if the fragment pair satisfied specified conditions. @FIXME: need to convert it to a recursive algorithm
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schrodinger.application.desmond.fep_mapping.
convert_rga_data
(rga_data, input_file)¶ Converting RGA internal data to AtomMappingData object :type rga_data: r_group_analysis.Data :param rga_data: :type input_file: string :param input_file: input file
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schrodinger.application.desmond.fep_mapping.
convert_data
(source_ct, dest_ct, source_core_atoms, dest_core_atoms, source_attachments, dest_attachments)¶ source_ct: dest_ct: source_core_atoms: list of source core atoms dest_core_atoms: list of dest core atoms source_attachments: list of source attachment points dest_attachments: list of dest attachment points
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schrodinger.application.desmond.fep_mapping.
get_atom_mapping_data
(input_file, atomtype=11)¶
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schrodinger.application.desmond.fep_mapping.
run_rga
(input_file, atomtype=11)¶
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schrodinger.application.desmond.fep_mapping.
unique_list
(seq, idfun=None)¶ A fast function to remove duplicate element from sequence by preserving the order at the same time.
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schrodinger.application.desmond.fep_mapping.
get_atom_marking
(data, output_file)¶
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schrodinger.application.desmond.fep_mapping.
get_bridge_atoms
(data)¶
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schrodinger.application.desmond.fep_mapping.
check_mapping
(data, n1, n2)¶
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schrodinger.application.desmond.fep_mapping.
reorder_st
(st, index_map)¶ Parameters: - ct (Structure) – Structure object
- index_map (list of tuple) – index mapping between old and new index [(new_index, old_index), …]
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schrodinger.application.desmond.fep_mapping.
is_ring_open_or_closed
(s_frag_indices, d_frag_indices, s2d_bridge_atom, d2s_bridge_atom)¶
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schrodinger.application.desmond.fep_mapping.
write_fepsubst_to_file
(data, filename, overwrite=True)¶
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schrodinger.application.desmond.fep_mapping.
reorder_atoms
(data, source_ct, dest_ct)¶
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schrodinger.application.desmond.fep_mapping.
check1_subst_code
(source_ct, dest_ct)¶ take input cts and check single ring-atom/attachment subst_code, return true if pass
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schrodinger.application.desmond.fep_mapping.
random_shuffle
(data, atomtype)¶ generate atommap with random shuffled atom order, return atommaps in original order
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schrodinger.application.desmond.fep_mapping.
get_subst_from_mapping
(mol0, mol1)¶ Given two CTs:
ct0
andct1
, withi_fep_mapping
atom properties properly set for all atoms ofct1
, sets thei_fep_subst
atom properties for both CTs.