sobolevnrm

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I hereby claim:

• I am sobolevnrm on github.
• I am sobolevnrm (https://keybase.io/sobolevnrm) on keybase.
• I have a public key ASDSulnHmWBMl1ElCpaE8N8q4jdIuCeT0a2LP6DvMgAh-wo

To claim this, I am signing this object:

sobolevnrm

# Convert all bases to ribo form (i.e., not deoxy)
s/ U / RU /g
s/ G / RG /g
s/ C / RC /g
s/ A / RA /g

# Convert U 'H5' to H5''
s/ 'H5' RU / H5'' RU /g
s/ 'HO2 RU / H2'' RU /g

sobolevnrm

ACE DUMM 0.00000 0 0 0.000
ACE DUMM 0.00000 0 0 1.000
ACE DUMM 0.00000 0 0 1.000
ACE H1 0.01000 0 0 1.000
ACE CH3 -0.14200 0 0 1.090
ACE H2 0.01000 0 0 1.090
ACE H3 0.01000 0 0 1.090
ACE C 0.61600 0 0 1.530
ACE O -0.50400 0 0 1.229
ALA DUMM 0.00000 0 0 0.000

sobolevnrm

! C-alpha parameters for residues.  4.8 Å radius chosen based on work by
! D. Sept and A. Elcock
ALA   CA    0.0000 0.000  0.000  4.8000
ARG   CA    1.0000 0.000  0.000  4.8000
ASN   CA    0.0000 0.000  0.000  4.8000
ASP   CA   -1.0000 0.000  0.000  4.8000
CYS   CA    0.0000 0.000  0.000  4.8000
GLN   CA    0.0000 0.000  0.000  4.8000
GLU   CA   -1.0000 0.000  0.000  4.8000
GLY   CA    0.0000 0.000  0.000  4.8000

sobolevnrm

CHARMM23
! all-atom charges and radii from amber94 parameter set
! note that polar hydrogens are given radius 1A here
! 
! Converted to UHBD format by A. Elcock
! Ribo and URA params added in from AMBER data by N. Baker
! 
resi  atom   chrg   epsi   sigm   radi end
!
TE    TE    1.00   0.000  0.000  0.000

sobolevnrm

""" Process RIS format following the standard at",
http://referencemanager.com/sites/rm/files/m/direct_export_ris.pdf """
import re

ALLOWED_TAGS = {"TY" : "Record start",
                "ER" : "Record end",
                "A2" : "Secondary author", 
                "A3" : "Tertiary Author",
                "A4" : "Subsidiary Author",
                "AB" : "Abstract", 

sobolevnrm

<orgPdbCompositeQuery version="1.0">
    <resultCount>45981</resultCount>
    <queryId>A646F4B6</queryId>
 <queryRefinement>
  <queryRefinementLevel>0</queryRefinementLevel>
  <orgPdbQuery>
    <version>head</version>
    <queryType>org.pdb.query.simple.NumberOfChainsQuery</queryType>
    <description>Number of Chains Search : Min Number of Chains=1 Max Number of Chains=1</description>
    <queryId>14430407</queryId>

sobolevnrm

# I have lots of classes with very similar constructors.  I'd like to avoid a huge if elseif ... statement
# This works when all classes are specified in the global scope but breaks across modules -- it also doesn't seem very safe
class Foo:
  def __init__(self):
    self.bar = "FOOBAR"
    
class_name = "Foo"
ctor = globals()[class_name]
obj = ctor()
print(obj.bar)

sobolevnrm

"""
Transform exported data from OmniFocus into RememberTheMilk Smart Add file.  Fields from
OmniFocus are expected to be:

Task ID,Type,Name,Status,Project,Context,Start Date,Due Date,Completion Date,Duration,Flagged,Notes
"""
import csv
import sys
from datetime import datetime

sobolevnrm

tell application "Things"
	set todo_output to "
"
	repeat with the_list in lists
		set list_name to name of the_list
		set list_todos to to dos of the_list
		repeat with the_todo in list_todos
			if status of the_todo is open then
				set todo_name to name of the_todo
				set todo_due to due date of the_todo