First version of pLDDT and LUR module #11
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iandaaci
reviewed
Oct 11, 2022
| if chopping: | ||
| for segment in chopping.segments: | ||
| segment_plddt += plddt_string[(segment.start - 1) : segment.end] | ||
| domain_length = len(segment_plddt) |
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domain_length needs to be a running total of the segments, then take the average after the loop, e.g.
domain_length = 0
for segment in chopping.segments:
segment_plddt += plddt_string[(segment.start - 1) : segment.end]
domain_length += len(segment_plddt)
average_plddt = ...
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Fixed in 'move domain_length out of loop to solve average'
iandaaci
reviewed
Oct 11, 2022
| for segment in chopping.segments: | ||
| segment_plddt += plddt_string[(segment.start - 1) : segment.end] | ||
| domain_length = len(segment_plddt) | ||
| average_plddt = round((sum(segment_plddt) / domain_length) * 100, 2) |
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not sure about the logic of this average calculation - is segment_plddt an int or a list of int? (sum usually takes an iterable)
sillitoe
reviewed
Oct 11, 2022
| mmcif_dict = MMCIF2Dict.MMCIF2Dict(cif_path) | ||
| chain_plddt = mmcif_dict["_ma_qa_metric_global.metric_value"][0] | ||
| plddt_string = mmcif_dict["_ma_qa_metric_local.metric_value"] | ||
| segment_plddt = "" |
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should this be initialised as an array (of float) that gets append to in the following loop?
segment_plddt = []
in pLDDTSummary
Fix LUR and pLDDT summary given a chopping segment. Change LUR threshold from 90 to 70 (residual from testing). Return LUR_perc,LUR_total and segment_length
to check against. Adjusted values in test to reflect change.
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First version of pLDDT and LUR module.
Input: CIF File
Output: Summary with Average pLDDT (by chain or domain depending on input) and percentage of residues in Long Unordered Regions (LUR, by chain or domain depending on input).
Add additional models, constant (for min_LUR_length) and writer.
Requires biopython for MMCIF reader.