Handle duplicates by only reading in first active site in PDB file#1
Handle duplicates by only reading in first active site in PDB file#1greyson9 wants to merge 5 commits intoucsf-bmi-203:masterfrom
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… are no duplicate sites in sequence
tlnagy
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tlnagy
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Hey Greyson, thanks for submitting a PR! We'll need to make some changes before I merge into in. I've commented on your code below. You can push more commits to this branch to fix things. I'll squash everything before we merge.
cheers,
-tamas
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| from .utils import Atom, Residue, ActiveSite | |||
| from hw2skeleton.utils import Atom, Residue, ActiveSite | |||
| return active_sites | ||
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| # modified to only read the first chain of a PDB |
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| # make a new residue if needed | ||
| if residue_number != r_num: | ||
| residue = Residue(residue_type, residue_number) | ||
| residue = Residue(residue_type, str(residue_number)) |
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This isn't needed any more because of my changes in 376deba
| @@ -0,0 +1,37 @@ | |||
| import sys | |||
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Not everyone wants to go the FASTA route so I don't think we should add this file to this PR.
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| def __init__(self, type): | ||
| self.type = type | ||
| def __init__(self, type_var): |
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Why make this change? Is there a conflict with the name?
| ("4629.pdb", ["ASP", "THR", "ARG", "SER", "LYS", "TYR", "SER", "ASN", "ASP"], [10, 14, 41, 118, 151, 157, 176, 177, 180]), | ||
| ("276.pdb", ["HIS", "HIS", "HIS", "HIS", "ASP"], ['55', '57', '201', '230', '301']), | ||
| ("4629.pdb", ["ASP", "THR", "ARG", "SER", "LYS", "TYR", "SER", "ASN", "ASP"], ['10', '14', '41', '118', '151', '157', '176', '177', '180']), | ||
| ]) |
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Residue number should be a integer, not a string. See my change in 376deba.
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Also, can you add a test for your code? For example, load a PDB with known duplicate active sites and make sure that it is read in correctly.
tlnagy
changed the title
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modified io.py to only read the first chain of each PDB so that there are no duplicate sites in sequence