From e23a2ac69c4e88bad1312c6a6d6d366f9ec9a7c6 Mon Sep 17 00:00:00 2001 From: haezurath Date: Wed, 17 Mar 2021 21:27:48 -0400 Subject: [PATCH 1/2] Fold.py changes --- fold.py | 24 ++++++++++++++---------- 1 file changed, 14 insertions(+), 10 deletions(-) diff --git a/fold.py b/fold.py index 50b2e22..c524574 100755 --- a/fold.py +++ b/fold.py @@ -7,15 +7,20 @@ import sys import argparse -parser = argparse.ArgumentParser(description='Fold some proteins.') -parser.add_argument('--scratch', action='store_true') -parser.add_argument('--temp', type=int, default=300) -parser.add_argument('--steps', type=int, default=100000, help="2500000000 should fold the protein") -parser.add_argument('--writes', type=int, default=1000, help="default is 1000") -parser.add_argument('--out', type=str, default="/tmp/output.pdb") -parser.add_argument('--pdb', type=str, default="proteins/villin/1vii.pdb") -parser.add_argument('--fasta', type=str, default=None) -args = parser.parse_args(sys.argv[1:]) +class Fold: + + def __init__(self): + self.parser = argparse.ArgumentParser(description='Fold some proteins.') + self.parser.add_argument('--scratch', action='store_true') + self.parser.add_argument('--temp', type=int, default=300) + self.parser.add_argument('--steps', type=int, default=100000, help="2500000000 should fold the protein") + self.parser.add_argument('--writes', type=int, default=1000, help="default is 1000") + self.parser.add_argument('--out', type=str, default="/tmp/output.pdb") + self.parser.add_argument('--pdb', type=str, default="proteins/villin/1vii.pdb") + self.parser.add_argument('--fasta', type=str, default=None) + +a = Fold() +args = a.parser.parse_args(sys.argv[1:]) try: platform = Platform.getPlatformByName("CUDA") @@ -59,4 +64,3 @@ simulation.reporters.append(PDBReporter(args.out, steps_write)) simulation.reporters.append(StateDataReporter(stdout, steps_write, step=True, potentialEnergy=True, temperature=True)) simulation.step(steps) - From de19376e01c6ef8ff5b88703b8d06f71d02a310a Mon Sep 17 00:00:00 2001 From: haezurath Date: Wed, 17 Mar 2021 23:16:53 -0400 Subject: [PATCH 2/2] corona.py changes --- corona.py | 61 ++++++++++++++++--------------------------------------- 1 file changed, 17 insertions(+), 44 deletions(-) diff --git a/corona.py b/corona.py index 9110aab..ab08c11 100644 --- a/corona.py +++ b/corona.py @@ -43,47 +43,20 @@ # 16 = 2'-O-methyltransferase (2'-O-MT) # https://en.wikipedia.org/wiki/MRNA_(nucleoside-2%27-O-)-methyltransferase -# in front "the untranslated leader sequence that ends with the Transcription Regulation Sequence" -corona['untranslated_region'] = cc[0:265] - -corona['orf1a'] = translate(cc[266-1:13483], True) - -# cc[266-1+4398*3:13468] = 'TTT_TTA_AAC' aka 'X_XXY_YYZ' -# https://en.wikipedia.org/wiki/Ribosomal_frameshift -# Programmed −1 Ribosomal Frameshifting -# TODO: add this to the translate function with automatic detection -corona['orf1b'] = translate(cc[13468-1:21555], False).strip("*") # chop off the stop, note this doesn't have a start - -# exploit vector, this attaches to ACE2. also called "surface glycoprotein" -# https://www.ncbi.nlm.nih.gov/Structure/pdb/6VYB -- open state -# https://www.ncbi.nlm.nih.gov/Structure/pdb/6VXX -- closed state -# 1273 amino acids -# S1 = 14-685 -# S2 = 686-1273 -# S2' = 816-1273 -# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750777/ -corona['spike_glycoprotein'] = translate(cc[21563-1:25384], True) - -# Forms homotetrameric potassium sensitive ion channels (viroporin) and may modulate virus release. -corona['orf3a'] = translate(cc[25393-1:26220], True) - -# these two things stick out, used in assembly aka they package the virus -corona['envelope_protein'] = translate(cc[26245-1:26472], True) # also known as small membrane -corona['membrane_glycoprotein'] = translate(cc[26523-1:27191], True) - -corona['orf6'] = translate(cc[27202-1:27387], True) - -corona['orf7a'] = translate(cc[27394-1:27759], True) -corona['orf7b'] = translate(cc[27756-1:27887], True) # is this one real? - -corona['orf8'] = translate(cc[27894-1:28259], True) - -# https://en.wikipedia.org/wiki/Capsid -# Packages the positive strand viral genome RNA into a helical ribonucleocapsid -# Includes the "internal" protein (from Coronavirus Pathogenesis) -# https://www.sciencedirect.com/topics/veterinary-science-and-veterinary-medicine/human-coronavirus-oc43 -corona['nucleocapsid_phosphoprotein'] = translate(cc[28274-1:29533], True) - -# might be called the internal protein (Coronavirus Pathogenesis) -corona['orf10'] = translate(cc[29558-1:29674], True) - +class RNA: + + def __init__(self): + + self.corona['untranslated_region'] = cc[0:265] + self.corona['orf1a'] = translate(cc[266-1:13483], True) + self.corona['orf1b'] = translate(cc[13468-1:21555], False).strip("*") # chop off the stop, note this doesn't have a start + self.corona['spike_glycoprotein'] = translate(cc[21563-1:25384], True) + self.corona['orf3a'] = translate(cc[25393-1:26220], True) + self.corona['envelope_protein'] = translate(cc[26245-1:26472], True) # also known as small membrane + self.corona['membrane_glycoprotein'] = translate(cc[26523-1:27191], True) + self.corona['orf6'] = translate(cc[27202-1:27387], True) + self.corona['orf7a'] = translate(cc[27394-1:27759], True) + self.corona['orf7b'] = translate(cc[27756-1:27887], True) # is this one real? + self.corona['orf8'] = translate(cc[27894-1:28259], True) + self.corona['nucleocapsid_phosphoprotein'] = translate(cc[28274-1:29533], True) + self.corona['orf10'] = translate(cc[29558-1:29674], True)