Package schrodinger :: Package application :: Package desmond :: Module fep_mapping

Module fep_mapping

Classes

AtomMappingData
Class to store intermediary and final data structures for atom mapping

Functions

cleanup(topdir=None)
Cleanup function to be run atexit

map_core_hydrogen(source_ct, dest_ct, core_map, s_remaining_indices, d_remaining_indices)
Mapping hydrogen atoms connected to the core.

find_fragment_by_cond(bridge_atom, cond)

find_noncore_fragment(bridge_atom, core_atom_indices)
Finding non-core fragment from bridged

find_noncore_subfragment(bridge_atom, core_atom_indices, frag_atom_indices)
Finding non-core fragment from bridged

find_all_fragment_pairs(source_ct, dest_ct, attachment_points, core_atom_indices)

get_atom_mapping(data)
mapping atoms based on the result from RGA

get_fepio_atom_mapping(atom_mapping)
converting to atom mapping format required by mmfepio library.

fragment_size_cond(frag1, frag2, threshold=10)

heavy_atom_num_cond(frag1, frag2, threshold=7)

get_heavy_fragment(frag)

find_fragment_MCS(data, cond=<function heavy_atom_num_cond at 0x324ef500>, atomtype=11)
Finding MCS in fragment if the fragment pair satisfied specified conditions.

convert_rga_data(rga_data, input_file)
Converting RGA internal data to AtomMappingData object

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

get_atom_mapping_data(input_file, atomtype=11)

run_rga(input_file, atomtype=11)

unique_list(seq, idfun=None)
A fast function to remove duplicate element from sequence by preserving the order at the same time.

get_atom_marking(data, output_file)

get_bridge_atoms(data)

check_mapping(data, n1, n2)

reorder_st(st, index_map)

is_ring_open_or_closed(s_frag_indices, d_frag_indices, s2d_bridge_atom, d2s_bridge_atom)

write_fepsubst_to_file(data, filename, overwrite=True)

reorder_atoms(data, source_ct, dest_ct)

check1_subst_code(source_ct, dest_ct)
take input cts and check single ring-atom/attachment subst_code, return true if pass

random_shuffle(data, atomtype)
generate atommap with random shuffled atom order, return atommaps in original order

Variables

[hide private]

logger = log.get_output_logger(name= "fep_mapping")

schrod_tmp = '/home/buildbot/.schrodinger/tmp'

topdir = '/home/buildbot/.schrodinger/tmp/fep-mapping-tmpfH_1G0'

TEMP_DIR = '/home/buildbot/.schrodinger/tmp/fep-mapping-tmpfH_...

FRAGMENT_SIZE_THRESHOLD = 10

HEAVY_ATOM_NUM_THERESHOLD = 7

FEP_MAPPING_ORIGINAL_INDEX = 'i_fep_mapping_origial_index'

FEP_MAPPING_BRIDGE = 'i_fep_mapping_bridge'

DEFAULT_ATOM_TYPE = 11

__package__ = 'schrodinger.application.desmond'

Function Details

[hide private]

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.

find_noncore_fragment(bridge_atom, core_atom_indices)

Finding non-core fragment from bridged

Parameters:

bridge_atom (_StructureAtom) - atom bonded to the attachment core atom.
core_atoms (set of int) - a set of core atom indices. @return a list of atoms.

find_noncore_subfragment(bridge_atom, core_atom_indices, frag_atom_indices)

Finding non-core fragment from bridged

Parameters:

bridge_atom (_StructureAtom) - atom bonded to the attachment core atom.
core_atom_indices (set of int) - a set of core atom indices. @return a list of atoms.

get_atom_mapping(data)

mapping atoms based on the result from RGA

Parameters:

data (AtomMappingData) - intermediary and finals data structures from RGA

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

convert_rga_data(rga_data, input_file)

Converting RGA internal data to AtomMappingData object

Parameters:

rga_data (r_group_analysis.Data)
input_file (string) - input file

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), ...]

Variables Details

[hide private]

TEMP_DIR

Value:

'/home/buildbot/.schrodinger/tmp/fep-mapping-tmpfH_1G0/tmpLpk2PT'