Miscellaneous utilities.
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| def | cross_link_db_filter_parser |
| | example '"{ID_Score}" > 28 AND "{Sample}" == "%10_1%" OR ":Sample}" == "%10_2%" OR ":Sample}" == "%10_3%" OR ":Sample}" == "%8_1%" OR ":Sample}" == "%8_2%"' More...
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| def | get_closest_residue_position |
| | this function works with plain hierarchies, as read from the pdb, no multi-scale hierarchies More...
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| def | get_position_terminal_residue |
| | this function get the xyz position of the C or N terminal residue of a hierarchy, given the resolution. More...
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| def | get_prot_name_from_particle |
| | this function returns the component name provided a particle and a list of names More...
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| def | get_random_cross_link_dataset |
| | returns a random cross-link dataset into a string were every line is a residue pair, together with UniqueIdentifier and XL score More...
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| def | get_residue_gaps_in_hierarchy |
| | returns the residue index gaps and contiguous segments as tuples given the hierarchy, the first residue and the last residue indexes. More...
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| def | get_residue_indexes |
| | This "overloaded" function retrieves the residue indexes for each particle which is an instance of Fragment,Residue or Atom. More...
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| def | list_chunks_iterator |
| | Yield successive length-sized chunks from a list. More...
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| def | parse_dssp |
| | read dssp file, get SSEs. More...
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| def | scatter_and_gather |
| | Synchronize data over a parallel run. More...
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| def | scatter_and_gather_dict_append |
| | Synchronize data over a parallel run. More...
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| def | select |
| | this function uses representation=SimplifiedModel it returns the corresponding selected particles representation_type="Beads", "Res:X", "Densities", "Representation", "Molecule" More...
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| def | sse_selections_to_chimera_colors |
| | get chimera command to check if you've correctly made the dssp dictionary colors each helix and beta sheet More...
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| def | sublist_iterator |
| | this iterator yields all sublists of length >= lmin and <= lmax More...
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| def | translate_hierarchy |
| | this will apply a translation to a hierarchy along the input vector More...
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| |
| def IMP.pmi.tools.cross_link_db_filter_parser |
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inputstring | ) |
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example '"{ID_Score}" > 28 AND "{Sample}" == "%10_1%" OR ":Sample}" == "%10_2%" OR ":Sample}" == "%10_3%" OR ":Sample}" == "%8_1%" OR ":Sample}" == "%8_2%"'
Definition at line 422 of file tools.py.
| def IMP.pmi.tools.get_closest_residue_position |
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hier, |
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resindex, |
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terminus = 'N' |
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) |
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this function works with plain hierarchies, as read from the pdb, no multi-scale hierarchies
Definition at line 490 of file tools.py.
| def IMP.pmi.tools.get_position_terminal_residue |
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hier, |
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terminus = 'C', |
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resolution = 1 |
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) |
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this function get the xyz position of the C or N terminal residue of a hierarchy, given the resolution.
the argument of terminus can be either N or C
Definition at line 521 of file tools.py.
| def IMP.pmi.tools.get_prot_name_from_particle |
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p, |
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list_of_names |
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) |
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this function returns the component name provided a particle and a list of names
Definition at line 900 of file tools.py.
| def IMP.pmi.tools.get_random_cross_link_dataset |
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representation, |
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resolution = 1.0, |
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number_of_cross_links = 10, |
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ambiguity_probability = 0.1, |
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confidence_score_range = [0, |
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avoid_same_particles = False |
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) |
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returns a random cross-link dataset into a string were every line is a residue pair, together with UniqueIdentifier and XL score
Definition at line 312 of file tools.py.
| def IMP.pmi.tools.get_residue_gaps_in_hierarchy |
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hierarchy, |
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start, |
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end |
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) |
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returns the residue index gaps and contiguous segments as tuples given the hierarchy, the first residue and the last residue indexes.
The list is organized as [[1,100,"cont"],[101,120,"gap"],[121,200,"cont"]]
Definition at line 552 of file tools.py.
| def IMP.pmi.tools.get_residue_indexes |
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hier | ) |
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This "overloaded" function retrieves the residue indexes for each particle which is an instance of Fragment,Residue or Atom.
Definition at line 920 of file tools.py.
| def IMP.pmi.tools.list_chunks_iterator |
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list, |
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length |
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) |
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Yield successive length-sized chunks from a list.
Definition at line 1035 of file tools.py.
| def IMP.pmi.tools.parse_dssp |
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dssp_fn, |
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limit_to_chains = '' |
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) |
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read dssp file, get SSEs.
values are all PDB residue numbering. returns dict of sel tuples helix : [ [ ['A',5,7] ] , [['B',15,17]] , ...] two helices A:5-7,B:15-17 beta : [ [ ['A',1,3] , ['A',100,102] ] , ...] one sheet: A:1-3 & A:100-102 loop : same format as helix, it's the contiguous loops
Definition at line 1258 of file tools.py.
| def IMP.pmi.tools.scatter_and_gather |
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data | ) |
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Synchronize data over a parallel run.
Definition at line 961 of file tools.py.
| def IMP.pmi.tools.scatter_and_gather_dict_append |
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data | ) |
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Synchronize data over a parallel run.
Definition at line 988 of file tools.py.
| def IMP.pmi.tools.select |
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representation, |
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resolution = None, |
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hierarchies = None, |
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selection_arguments = None, |
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name = None, |
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name_is_ambiguous = False, |
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first_residue = None, |
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last_residue = None, |
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residue = None, |
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representation_type = None |
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) |
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this function uses representation=SimplifiedModel it returns the corresponding selected particles representation_type="Beads", "Res:X", "Densities", "Representation", "Molecule"
Definition at line 624 of file tools.py.
| def IMP.pmi.tools.sse_selections_to_chimera_colors |
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dssp_dict, |
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chimera_model_num = 0 |
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) |
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get chimera command to check if you've correctly made the dssp dictionary colors each helix and beta sheet
Definition at line 1345 of file tools.py.
| def IMP.pmi.tools.sublist_iterator |
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l, |
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lmin = None, |
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lmax = None |
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this iterator yields all sublists of length >= lmin and <= lmax
Definition at line 1015 of file tools.py.
| def IMP.pmi.tools.translate_hierarchy |
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hierarchy, |
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translation_vector |
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this will apply a translation to a hierarchy along the input vector
Definition at line 1058 of file tools.py.
