schrodinger.application.desmond.fep_mapping module¶
- schrodinger.application.desmond.fep_mapping.cleanup(topdir=None)[source]¶
Cleanup function to be run atexit
- class schrodinger.application.desmond.fep_mapping.AtomMappingData(source_ct, dest_ct)[source]¶
Bases:
object
Class to store intermediary and final data structures for atom mapping
- addAttachmentPoint(attachment_point)[source]¶
Adding attachment point. :type attachment_point: two-element tuple. :param attachment_point:
- schrodinger.application.desmond.fep_mapping.map_core_hydrogen(source_ct, dest_ct, core_map, s_remaining_indices, d_remaining_indices)[source]¶
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.
- schrodinger.application.desmond.fep_mapping.find_noncore_fragment(bridge_atom, core_atom_indices)[source]¶
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.
- schrodinger.application.desmond.fep_mapping.find_noncore_subfragment(bridge_atom, core_atom_indices, frag_atom_indices)[source]¶
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.
- schrodinger.application.desmond.fep_mapping.find_all_fragment_pairs(source_ct, dest_ct, attachment_points, core_atom_indices)[source]¶
- schrodinger.application.desmond.fep_mapping.get_atom_mapping(data)[source]¶
mapping atoms based on the result from RGA :type data: AtomMappingData :param data: intermediary and finals data structures from RGA
- schrodinger.application.desmond.fep_mapping.get_fepio_atom_mapping(atom_mapping)[source]¶
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
- schrodinger.application.desmond.fep_mapping.find_fragment_MCS(data, cond=<function heavy_atom_num_cond>, atomtype=11)[source]¶
Finding MCS in fragment if the fragment pair satisfied specified conditions. @FIXME: need to convert it to a recursive algorithm
- schrodinger.application.desmond.fep_mapping.convert_rga_data(rga_data, input_file)[source]¶
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
- schrodinger.application.desmond.fep_mapping.convert_data(source_ct, dest_ct, source_core_atoms, dest_core_atoms, source_attachments, dest_attachments)[source]¶
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
- schrodinger.application.desmond.fep_mapping.unique_list(seq, idfun=None)[source]¶
A fast function to remove duplicate element from sequence by preserving the order at the same time.
- schrodinger.application.desmond.fep_mapping.reorder_st(st, index_map)[source]¶
- Parameters
ct (Structure) – Structure object
index_map (list of tuple) – index mapping between old and new index [(new_index, old_index), …]
- schrodinger.application.desmond.fep_mapping.is_ring_open_or_closed(s_frag_indices, d_frag_indices, s2d_bridge_atom, d2s_bridge_atom)[source]¶
- schrodinger.application.desmond.fep_mapping.write_fepsubst_to_file(data, filename, overwrite=True)[source]¶
- schrodinger.application.desmond.fep_mapping.check1_subst_code(source_ct, dest_ct)[source]¶
take input cts and check single ring-atom/attachment subst_code, return true if pass