1150 lines
46 KiB
Python
1150 lines
46 KiB
Python
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import math
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import re
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import pymol
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cmd = __import__("sys").modules["pymol.cmd"]
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from . import setting
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from . import parsing
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import threading
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from .cmd import DEFAULT_ERROR, DEFAULT_SUCCESS, _raising, \
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is_list, is_string, is_error
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QuietException = parsing.QuietException
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_prefix = "_tmp_editor"
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tmp_wild = _prefix + "*"
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tmp_editor = _prefix + "0"
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tmp_connect = _prefix + "_con"
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tmp_domain = _prefix + "_dom"
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tmp1 = _prefix + "1"
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tmp2 = _prefix + "2"
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tmp3 = _prefix + "3"
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tmp4 = _prefix + "4"
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# routines to assist in molecular editing
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class undocontext:
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def __init__(self, cmd, sele):
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# not implemented in open-source
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pass
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def __enter__(self):
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# not implemented in open-source
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pass
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def __exit__(self, exc_type, exc_value, traceback):
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# not implemented in open-source
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pass
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def attach_fragment(selection,fragment,hydrogen,anchor,*,_self=cmd):
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'''
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ARGUMENTS
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selection = str: Name of a single-atom selection. If no such named
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selection exists, then create a new object with name `fragment`.
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fragment = str: fragment name to load from fragment library
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hydrogen = int: atom ID in fragment to fuse
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anchor = int: (unused)
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'''
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remove_hydrogens = _self.get_setting_boolean("auto_remove_hydrogens")
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if selection not in _self.get_names("selections"):
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if fragment in _self.get_names("objects"):
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raise pymol.CmdException("an object with that name already exists")
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_self.fragment(fragment)
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if remove_hydrogens:
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_self.remove(f"(hydro and {fragment})")
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else:
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fragment_label = _self.get_unused_name(_prefix + "_attach_fragment")
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_self.fragment(fragment, fragment_label, origin=0)
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try:
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_self.fuse(f"{fragment_label} and id {hydrogen}", f"({selection})", 1)
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if remove_hydrogens:
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_self.remove("(hydro and pkmol)")
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elif _self.count_atoms('hydro and (neighbor pk2)'):
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_self.h_fill()
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finally:
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_self.delete(fragment_label)
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def combine_fragment(selection,fragment,hydrogen,anchor,_self=cmd):
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with undocontext(_self, selection):
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_self.fragment(fragment,tmp_editor)
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try:
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if _self.get_setting_boolean("auto_remove_hydrogens"):
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_self.remove("(hydro and ?%s)" % tmp_editor)
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_self.fuse("?%s" % tmp_editor, "(%s)" % selection, 3)
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finally:
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_self.delete(tmp_editor)
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def attach_amino_acid(selection,amino_acid,center=0,animate=-1,object="",hydro=-1,ss=-1,_self=cmd):
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'''
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ARGUMENTS
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selection = str: named selection of single N or C atom
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amino_acid = str: fragment name to load from fragment library
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center = bool: center on new terminus (pk1)
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animate = int: animate centering
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object = str: name of new object (if selection is none)
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hydro = int (-1/0/1): keep hydrogens
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ss = int: Secondary structure 1=alpha helix, 2=antiparallel beta, 3=parallel beta, 4=flat
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'''
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r = DEFAULT_SUCCESS
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ss = int(ss)
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center = int(center)
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if hydro<0:
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hydro = not int(_self.get_setting_boolean("auto_remove_hydrogens"))
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if (selection not in _self.get_names('all')
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if selection == 'pk1' # legacy, calling functions should pass '?pk1'
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else _self.count_atoms(selection) == 0):
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if object == "":
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object = amino_acid
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# create new object
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if amino_acid in _self.get_names("objects"):
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print("Error: an object with than name already exists")
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raise QuietException
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r = _self.fragment(amino_acid,object)
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if not hydro:
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_self.remove("(hydro and %s)"%object)
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if _self.count_atoms("((%s) and name C)"%object):
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_self.edit("((%s) and name C)"%object)
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elif _self.count_atoms("((%s) and name N)"%object):
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_self.edit("((%s) and name N)"%object)
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elif _self.select(tmp_connect,"(%s) & elem N,C"%selection) != 1:
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print("Error: invalid connection point: must be one atom, name N or C.")
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_self.delete(tmp_wild)
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raise QuietException
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elif amino_acid in ["nhh","nme"] and _self.select(tmp_connect,"(%s) & elem C"%selection) != 1:
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print("Error: invalid connection point: must be C for residue '%s'"%(amino_acid))
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_self.delete(tmp_wild)
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raise QuietException
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elif amino_acid in ["ace"] and _self.select(tmp_connect,"(%s) & elem N"%selection) != 1:
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print("Error: invalid connection point: must be N for residue '%s'"%(amino_acid))
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_self.delete(tmp_wild)
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raise QuietException
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else:
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if ss<0:
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ss = _self.get_setting_int("secondary_structure")
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if ss:
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if ss==1: # helix
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phi=-57.0
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psi=-47.0
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elif ss==2: # antipara-beta
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phi=-139.0
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psi=135.0
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elif ss==3: # para-beta
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phi=-119.0
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psi=113.0
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else:
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phi=180.0
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psi=180.0
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_self.fragment(amino_acid,tmp_editor, origin=0)
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if _self.count_atoms("elem N",domain=tmp_connect):
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tmp = [ None ]
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_self.iterate(tmp_connect,"tmp[0]=resv", space={ 'tmp' : tmp })
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tmp[0] = str(tmp[0]-1) # counting down
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_self.alter(tmp_editor,"resi=tmp[0]",space={ 'tmp' : tmp})
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_self.set_geometry(tmp_connect, 3, 3) # make nitrogen planar
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_self.fuse("(%s and name C)"%(tmp_editor),tmp_connect,2)
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_self.select(tmp_domain, "byresi (pk1 | pk2)")
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if not hydro:
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_self.remove("(pkmol and hydro)")
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if ((_self.select(tmp1,"?pk1",domain=tmp_domain)==1) and
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(_self.select(tmp2,"?pk2",domain=tmp_domain)==1)):
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if ((_self.select(tmp3,"(name CA,CH3 & nbr. ?pk1)",domain=tmp_domain)==1) and
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(_self.select(tmp4,"(name CA,CH3 & nbr. ?pk2)",domain=tmp_domain)==1)):
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_self.set_dihedral(tmp4,tmp2,tmp1,tmp3,180.0)
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if hydro:
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_self.h_fix(tmp2) # fix hydrogen position
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if ss:
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if amino_acid[0:3]!='pro':
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if ((_self.select(tmp4,
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"(!(resn PRO) & name C & nbr. (name CA & nbr. "+tmp2+"))",
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domain=tmp_domain)==1) and
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(_self.select(tmp3,
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"(!(resn PRO) & name CA & nbr. "+tmp2+")",
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domain=tmp_domain)==1)):
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_self.set_dihedral( # PHI
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tmp4, # C
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tmp3, # CA
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tmp2, # N
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tmp1, # C
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phi)
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if ((_self.select(tmp4,"(name N & nbr. (name CA & nbr. "+tmp1+"))",
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domain=tmp_domain)==1) and
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(_self.select(tmp3,"(name CA & nbr. "+tmp1+")",domain=tmp_domain)==1)):
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_self.set_dihedral( # PSI (n-1)
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tmp2, # N
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tmp1, # C
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tmp3, # CA
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tmp4, # N
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psi)
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sele = ("(name N & (byres nbr. %s) &! (byres %s))"% (tmp_connect,tmp_connect))
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if _self.select(tmp1,sele,domain=tmp_domain):
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_self.edit(tmp1)
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if center:
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_self.center(tmp1,animate=animate)
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elif _self.count_atoms("elem C",domain=tmp_connect): # forward
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tmp = [ None ]
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_self.iterate(tmp_connect,"tmp[0]=resv", space={ 'tmp' : tmp })
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tmp[0] = str(tmp[0]+1) # counting up
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_self.alter(tmp_editor,"resi=tmp[0]",space={ 'tmp' : tmp})
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_self.set_geometry(tmp_editor + " & name N", 3, 3) # make nitrogen planar
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_self.fuse("(%s and name N)"%tmp_editor,tmp_connect,2)
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_self.select(tmp_domain, "byresi (pk1 | pk2)")
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if not hydro:
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_self.remove("(pkmol and hydro)")
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if (( _self.select(tmp1,"?pk1",domain=tmp_domain)==1) and
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( _self.select(tmp2,"?pk2",domain=tmp_domain)==1)):
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if ((_self.select(tmp3,"(name CA,CH3 & nbr. ?pk1)",domain=tmp_domain)==1) and
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(_self.select(tmp4,"(name CA,CH3 & nbr. ?pk2)",domain=tmp_domain)==1)):
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_self.set_dihedral(tmp4,tmp2,tmp1,tmp3,180.0)
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if hydro:
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_self.h_fix("pk1") # fix hydrogen position
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if ss:
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if hydro and amino_acid[0:3]=='nhh': # fix amide hydrogens
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if ((_self.select(tmp3,"(name H1 & nbr. "+tmp1+")",domain=tmp_domain)==1) and
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(_self.select(tmp4,"(name O & nbr. "+tmp2+")",domain=tmp_domain)==1)):
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_self.set_dihedral(
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tmp4, # O
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tmp2, # C
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tmp1, # N
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tmp3, # H1
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180)
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if amino_acid[0:3]!='pro':
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if ((_self.select(tmp3,"(name CA & nbr. "+tmp1+")",domain=tmp_domain)==1) and
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(_self.select(tmp4,"(name C & nbr. (name CA & nbr. "+tmp1+"))",domain=tmp_domain)==1)):
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_self.set_dihedral( # PHI
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tmp2, # C
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tmp1, # N
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tmp3, # CA
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tmp4, # C
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phi)
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if ((_self.select(tmp3,"(name CA & nbr. "+tmp2+")",domain=tmp_domain)==1) and
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(_self.select(tmp4,"(name N & nbr. (name CA & nbr. "+tmp2+"))",domain=tmp_domain)==1)):
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_self.set_dihedral( # PSI (n-1)
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tmp4, # N
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tmp3, # CA
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tmp2, # C
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tmp1, # N
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psi)
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sele = ("(name C & (byres nbr. %s) & !(byres %s))"% (tmp_connect,tmp_connect))
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if _self.select(tmp1,sele,domain=tmp_domain):
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_self.edit(tmp1)
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if center:
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_self.center(tmp1,animate=animate)
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else:
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_self.unpick()
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elif _self.count_atoms("((%s) and elem H)"%selection):
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print("Error: please pick a nitrogen or carbonyl carbon to grow from.")
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_self.delete(tmp_wild)
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raise QuietException
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else:
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print("Error: unable to attach fragment.")
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_self.delete(tmp_wild)
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raise QuietException
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_self.delete(tmp_wild)
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return r
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_aa_codes = {
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'A' : 'ala',
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'B' : 'ace',
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'C' : 'cys',
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'D' : 'asp',
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'E' : 'glu',
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'F' : 'phe',
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'G' : 'gly',
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'H' : 'his',
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'I' : 'ile',
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'K' : 'lys',
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'L' : 'leu',
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'M' : 'met',
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'N' : 'asn',
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'P' : 'pro',
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'Q' : 'gln',
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'R' : 'arg',
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'S' : 'ser',
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'T' : 'thr',
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'V' : 'val',
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'W' : 'trp',
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'Y' : 'tyr',
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'Z' : 'nme',
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}
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_fab_codes = {
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'peptide' : _aa_codes,
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}
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_pure_number = re.compile("[0-9]+")
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def _fab(input,name,mode,resi,chain,segi,state,dir,hydro,ss,quiet,_self=cmd):
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r = DEFAULT_ERROR
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code = _fab_codes.get(mode,None)
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quiet = int(quiet)
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resi = int(resi)
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state = int(state)
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dir = int(dir)
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hydro = int(hydro)
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if hydro < 0:
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hydro = not _self.get_setting_boolean("auto_remove_hydrogens")
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seq_len = 0
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if (mode == 'peptide') and is_string(input):
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# '123/ ADC B/234/ AFCD' to [ '123/','A','D','C','B/234/','F','C','D' ]
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frags = input.split()
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input = []
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for frag in frags:
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if '/' in frag:
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input.append(frag)
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else:
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seq_len = seq_len + len(frag)
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input.extend(list(frag))
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input.append("/") # breaks chain
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if name is None:
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name = _self.get_unused_name("obj")
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elif name in _self.get_names():
|
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_self.delete(name)
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if mode in [ 'peptide' ]: # polymers
|
||
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if (seq_len>99) and not quiet:
|
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print(" Generating a %d residue peptide from sequence..."%seq_len)
|
||
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input.reverse()
|
||
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sequence = input
|
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if code is not None:
|
||
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while len(sequence):
|
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while len(sequence) and '/' in sequence[-1]:
|
||
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part = sequence.pop().split('/')
|
||
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if len(part)>1:
|
||
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if len(part[-2]):
|
||
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resi = int(part[-2])
|
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if len(part)>2:
|
||
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chain = part[-3]
|
||
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if len(part)>3:
|
||
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segi = part[-4]
|
||
|
|
if len(sequence) and not _self.count_atoms("?pk1"): # new polymer segment
|
||
|
|
tmp_obj = _self.get_unused_name()
|
||
|
|
first = sequence.pop()
|
||
|
|
_self.fragment(code[first], tmp_obj)
|
||
|
|
if not hydro:
|
||
|
|
_self.remove(tmp_obj + ' and hydro')
|
||
|
|
_self.alter(tmp_obj,'resi="""%s""";chain="""%s""";segi="""%s"""'%(resi,chain,segi))
|
||
|
|
_self.create(name,tmp_obj+" or ?"+name,1,1,zoom=0)
|
||
|
|
tmp_sel = _self.get_unused_name()
|
||
|
|
if mode == 'peptide':
|
||
|
|
if dir>0:
|
||
|
|
_self.select(tmp_sel,"name C and "+tmp_obj)
|
||
|
|
resi = resi + 1
|
||
|
|
else:
|
||
|
|
_self.select(tmp_sel,"name N and "+tmp_obj)
|
||
|
|
resi = resi - 1
|
||
|
|
_self.edit(name+" in "+tmp_sel) # set the editor's pk1 selection
|
||
|
|
_self.delete(tmp_sel+" "+tmp_obj)
|
||
|
|
if mode == 'peptide':
|
||
|
|
while len(sequence):
|
||
|
|
if '/' in sequence[-1]:
|
||
|
|
_self.unpick() # break chain at this point
|
||
|
|
break
|
||
|
|
if not _self.count_atoms("?pk1"):
|
||
|
|
break
|
||
|
|
else:
|
||
|
|
attach_amino_acid("pk1",code[sequence.pop()],animate=0,ss=ss,hydro=hydro,_self=_self)
|
||
|
|
if dir>0:
|
||
|
|
resi = resi + 1
|
||
|
|
else:
|
||
|
|
resi = resi - 1
|
||
|
|
if not len(sequence):
|
||
|
|
r = DEFAULT_SUCCESS
|
||
|
|
|
||
|
|
if _self.get_setting_int('auto_zoom'):
|
||
|
|
_self.zoom(name)
|
||
|
|
|
||
|
|
return r
|
||
|
|
|
||
|
|
_threeNA_to_OneNA = { "atp" : "A", "ctp" : "C", "gtp" : "G", "ttp" : "T", "utp" : "U"}
|
||
|
|
_oneNA_to_threeNA = { "A" : "atp", "C" : "ctp", "G" : "gtp", "T" : "ttp", "U" : "utp"}
|
||
|
|
|
||
|
|
_base_pair = { "DNA" : {"atp" : "ttp", "ctp" : "gtp", "gtp" : "ctp", "ttp" : "atp" },
|
||
|
|
"RNA" : {"atp" : "utp", "ctp" : "gtp", "gtp" : "ctp", "utp" : "atp" }}
|
||
|
|
|
||
|
|
_oneNA_base_pair = {"DA" : "DT", "DC" : "DG", "DG" : "DC", "DT" : "DA", "A" : "U",
|
||
|
|
"C" : "G", "G" : "C", "U" : "A"}
|
||
|
|
|
||
|
|
def iterate_to_list(selection: str, expression: str, *, _self=cmd):
|
||
|
|
outlist = []
|
||
|
|
_self.iterate(selection,f"outlist.append(({expression}))", space={"outlist":outlist})
|
||
|
|
return outlist
|
||
|
|
|
||
|
|
def rename_three_to_one(nuc_acid, sele, nuc_type, *, _self=cmd):
|
||
|
|
"""
|
||
|
|
Renames nucleobase from 3-letter to 1-letter representation
|
||
|
|
|
||
|
|
:param nuc_acid: (str) 3-letter nucleic acid representation
|
||
|
|
:param sele: (str) selection of nucleic acid to rename
|
||
|
|
:param nuc_type: (str) "DNA" or "RNA"
|
||
|
|
"""
|
||
|
|
new_name = _threeNA_to_OneNA[nuc_acid]
|
||
|
|
if nuc_type == "DNA":
|
||
|
|
new_name = "D" + new_name
|
||
|
|
_self.alter(sele, f"resn='{new_name}'")
|
||
|
|
|
||
|
|
def fit_sugars(mobile, target, *, _self=cmd):
|
||
|
|
"""
|
||
|
|
Fits appending base pairs to form appropriate hydrogen bond
|
||
|
|
|
||
|
|
:param mobile: (str) selection for the sense (main) strand
|
||
|
|
:param target: (str) selection for the antisense (opposing) strand
|
||
|
|
"""
|
||
|
|
try:
|
||
|
|
_self.pair_fit(f"{mobile} & name C1'",
|
||
|
|
f"{target} & name C1'",
|
||
|
|
f"{mobile} & name C2'",
|
||
|
|
f"{target} & name C2'",
|
||
|
|
f"{mobile} & name C3'",
|
||
|
|
f"{target} & name C3'",
|
||
|
|
f"{mobile} & name C4'",
|
||
|
|
f"{target} & name C4'",
|
||
|
|
f"{mobile} & name O4'",
|
||
|
|
f"{target} & name O4'", quiet=1)
|
||
|
|
except:
|
||
|
|
_self.delete(tmp_wild)
|
||
|
|
raise pymol.CmdException("Something went wrong when fitting the new residue.")
|
||
|
|
|
||
|
|
def fit_DS_fragment(mobile_A, target_A, mobile_B, target_B, *, _self=cmd):
|
||
|
|
"""
|
||
|
|
Fits dummy fragment to the detected structure using atoms
|
||
|
|
on both stands for a more accurate alignment.
|
||
|
|
|
||
|
|
:param mobile_A: (str) selection for the base being created and attached
|
||
|
|
:param target_A: (str) selection for the base selected to build on
|
||
|
|
:param mobile_B: (str) selection for the opposing base being created
|
||
|
|
:param target_B: (str) selection for the detected opposing base
|
||
|
|
"""
|
||
|
|
try:
|
||
|
|
_self.pair_fit(f"{mobile_A} & name C1'",
|
||
|
|
f"{target_A} & name C1'",
|
||
|
|
f"{mobile_A} & name C2'",
|
||
|
|
f"{target_A} & name C2'",
|
||
|
|
f"{mobile_A} & name C5'",
|
||
|
|
f"{target_A} & name C5'",
|
||
|
|
f"{mobile_A} & name O4'",
|
||
|
|
f"{target_A} & name O4'",
|
||
|
|
f"{mobile_A} & name O3'",
|
||
|
|
f"{target_A} & name O3'",
|
||
|
|
f"{mobile_A} & name P",
|
||
|
|
f"{target_A} & name P",
|
||
|
|
f"{mobile_B} & name O3'",
|
||
|
|
f"{target_B} & name O3'",
|
||
|
|
f"{mobile_B} & name C1'",
|
||
|
|
f"{target_B} & name C1'",
|
||
|
|
f"{mobile_B} & name C2'",
|
||
|
|
f"{target_B} & name C2'",
|
||
|
|
f"{mobile_B} & name C5'",
|
||
|
|
f"{target_B} & name C5'",
|
||
|
|
f"{mobile_B} & name P",
|
||
|
|
f"{target_B} & name P",
|
||
|
|
f"{mobile_B} & name O4'",
|
||
|
|
f"{target_B} & name O4'", quiet=1)
|
||
|
|
except:
|
||
|
|
_self.delete(tmp_wild)
|
||
|
|
raise pymol.CmdException("Something went wrong when fitting the new residue.")
|
||
|
|
|
||
|
|
def add2pO(domain, nuc_acid, resv, *, _self=cmd):
|
||
|
|
if nuc_acid == "utp": #utp comes with O2'
|
||
|
|
return
|
||
|
|
c_2p = _prefix + "_c2p"
|
||
|
|
_self.select(c_2p, "%s & resi \\%i & name %s" % (domain, resv, "C2'"))
|
||
|
|
_self.unpick()
|
||
|
|
_self.edit(c_2p)
|
||
|
|
_self.attach("O", 4, 4)
|
||
|
|
_self.unpick()
|
||
|
|
_self.alter("(byres %s) & resi \\%i & name O01" % (domain, resv), "name=\"O2'\"")
|
||
|
|
|
||
|
|
def move_atom_in_res(atom, dummy_res, new_res, twist, rise, *, _self=cmd):
|
||
|
|
prev_coords = _self.get_coords(f"{dummy_res} & name {atom}", state=1)
|
||
|
|
curr_coords = _self.get_coords(f"{new_res} & name {atom}", state=1)
|
||
|
|
|
||
|
|
if curr_coords is None or prev_coords is None:
|
||
|
|
return
|
||
|
|
curr_coord = curr_coords[0]
|
||
|
|
prev_coord = prev_coords[0]
|
||
|
|
|
||
|
|
r = math.sqrt(prev_coord[0] ** 2 +
|
||
|
|
prev_coord[1] ** 2)
|
||
|
|
old_phi = math.degrees(math.atan2(prev_coord[1],prev_coord[0]))
|
||
|
|
phi = old_phi - twist
|
||
|
|
phi = math.radians(phi)
|
||
|
|
new_pos = [r * math.cos(phi),
|
||
|
|
r * math.sin(phi),
|
||
|
|
prev_coord[2] - rise]
|
||
|
|
|
||
|
|
trans = list(new_pos - curr_coord)
|
||
|
|
_self.translate(trans, f"{new_res} & name {atom}", camera=0)
|
||
|
|
|
||
|
|
def move_new_res(frag_string, full_frag, old, old_oppo, double_stranded_bool=False, form="B", chain="A", antisense=False, *, _self=cmd):
|
||
|
|
"""
|
||
|
|
Attaches new residue (or pair) onto current nucleotide chain
|
||
|
|
|
||
|
|
:param frag_string: (str) Name of appending nucleic acid or pair
|
||
|
|
:param full_frag: (str) Selection of the created fragment
|
||
|
|
:param old: (str) Selection of previous residue
|
||
|
|
:param old_oppo: (str) Selection of previous opposing residue
|
||
|
|
:param double_stranded_bool: (bool) Flag represing if double helix was detected
|
||
|
|
:param antisense (bool) Flag for antisense
|
||
|
|
:param form: (str) DNA form ('A'/'B')
|
||
|
|
"""
|
||
|
|
if form == 'B':
|
||
|
|
twist = -36.0
|
||
|
|
rise = -3.375
|
||
|
|
elif form == 'A':
|
||
|
|
twist = -32.7
|
||
|
|
rise = -2.548
|
||
|
|
else:
|
||
|
|
raise ValueError("Form not recognized")
|
||
|
|
|
||
|
|
rise = rise if antisense else -rise
|
||
|
|
twist = twist if antisense else -twist
|
||
|
|
|
||
|
|
dummy_fragment = _prefix + "_dummyfrag"
|
||
|
|
dummy_res_A = _prefix + "_dummyresA"
|
||
|
|
dummy_res_B = _prefix + "_dummyresB"
|
||
|
|
new_fragment = _prefix + "_newfrag"
|
||
|
|
new_res_A = _prefix + "_newresA"
|
||
|
|
new_res_B = _prefix + "_newresB"
|
||
|
|
|
||
|
|
_self.select(new_fragment, f"{full_frag}")
|
||
|
|
_self.select(new_res_A,f"{full_frag} and chain A")
|
||
|
|
_self.select(new_res_B,f"{full_frag} and chain B")
|
||
|
|
|
||
|
|
_self.fragment(frag_string, dummy_fragment, origin=0)
|
||
|
|
_self.select(dummy_res_A, f"{dummy_fragment} and chain A")
|
||
|
|
_self.select(dummy_res_B, f"{dummy_fragment} and chain B")
|
||
|
|
|
||
|
|
if old_oppo == "none":
|
||
|
|
# This is the case where a single residue is being added
|
||
|
|
_self.select(dummy_res_A, f"{dummy_fragment}")
|
||
|
|
_self.select(new_res_A, f"{full_frag}")
|
||
|
|
|
||
|
|
atoms_A = iterate_to_list(dummy_res_A, "name")
|
||
|
|
atoms_B = iterate_to_list(dummy_res_B, "name")
|
||
|
|
|
||
|
|
#A new base is created by copying the coordinates of the previous
|
||
|
|
#base and doing a cylindrical rotation (phi degrees) and a translation
|
||
|
|
#down the z-axis by the rise amount
|
||
|
|
for atom in atoms_A:
|
||
|
|
move_atom_in_res(atom, dummy_res_A, new_res_A, twist, rise)
|
||
|
|
for atom in atoms_B:
|
||
|
|
move_atom_in_res(atom, dummy_res_B, new_res_B, twist, rise)
|
||
|
|
if double_stranded_bool == True:
|
||
|
|
fit_DS_fragment(dummy_res_A, old, dummy_res_B, old_oppo)
|
||
|
|
orient_flag = check_dummy_oriention(old,dummy_res_A)
|
||
|
|
if orient_flag == 0:
|
||
|
|
fit_sugars(dummy_res_A,old)
|
||
|
|
elif double_stranded_bool == False:
|
||
|
|
fit_sugars(dummy_res_A, old)
|
||
|
|
else:
|
||
|
|
raise pymol.CmdException("Double stranded bool was not provided to move_new_res")
|
||
|
|
|
||
|
|
dummy_fragment_transform = _self.get_object_matrix(dummy_fragment)
|
||
|
|
_self.transform_object(full_frag, dummy_fragment_transform)
|
||
|
|
_self.delete(dummy_fragment)
|
||
|
|
|
||
|
|
def check_dummy_oriention(old, dummy_res_A, *, _self=cmd):
|
||
|
|
dummy_orient = _prefix + "_dummy_orient"
|
||
|
|
orient_flag = 0
|
||
|
|
orient_flag = _self.select(dummy_orient, f"({old} & name O4') within 1.0 of ({dummy_res_A} & name O4')")
|
||
|
|
|
||
|
|
return orient_flag
|
||
|
|
|
||
|
|
class NascentNucAcidInfo:
|
||
|
|
def __init__(self, fragment_name, nuc_acid, nuc_type, form, dbl_helix):
|
||
|
|
self.fragment_name = fragment_name
|
||
|
|
self.nuc_acid = nuc_acid
|
||
|
|
self.nuc_type = nuc_type
|
||
|
|
self.form = form
|
||
|
|
self.dbl_helix = dbl_helix
|
||
|
|
|
||
|
|
def attach_O5_phosphate(_self=cmd):
|
||
|
|
if "pk1" not in _self.get_names("selections"):
|
||
|
|
raise pymol.CmdException("Selection must be pk1 to attach O5' phosphate")
|
||
|
|
|
||
|
|
print("This building selection has an unphosphorylated O5' end.")
|
||
|
|
attach_fragment("pk1","phosphite",4,0)
|
||
|
|
# Initailize selection strings
|
||
|
|
P_center = _prefix + "_P_center"
|
||
|
|
H_extra = _prefix + "_H_extra"
|
||
|
|
O_one = _prefix + "_O_one"
|
||
|
|
O_two = _prefix + "_O_two"
|
||
|
|
O_three = _prefix + "_O_three"
|
||
|
|
|
||
|
|
# Selection
|
||
|
|
_self.select(P_center,"n. P01")
|
||
|
|
_self.select(H_extra, f"h. and bound_to {P_center} or n. H02")
|
||
|
|
_self.select(O_one, f"n. O01 and bound_to {P_center}")
|
||
|
|
_self.select(O_two, f"n. O02 and bound_to {P_center}")
|
||
|
|
_self.select(O_three, f"n. O03 and bound_to {P_center}")
|
||
|
|
|
||
|
|
# Removing unnecessary atoms
|
||
|
|
_self.remove(H_extra)
|
||
|
|
_self.remove(O_one)
|
||
|
|
|
||
|
|
# Fix bonding
|
||
|
|
_self.unbond(P_center,O_three)
|
||
|
|
_self.bond(P_center,O_three,1)
|
||
|
|
_self.unbond(P_center,O_two)
|
||
|
|
_self.bond(P_center,O_two,2)
|
||
|
|
|
||
|
|
# Rename P correctly
|
||
|
|
_self.alter(P_center,"name = 'P'")
|
||
|
|
|
||
|
|
# Set Pk1 correctly
|
||
|
|
_self.select("pk1",P_center)
|
||
|
|
|
||
|
|
def check_DNA_base_pair(sele_oppo_atom, selection, *, _self=cmd):
|
||
|
|
base_pair_dist = _prefix + "_base_pair_dist"
|
||
|
|
base_pair_bool = 0
|
||
|
|
tmp_last_resn = iterate_to_list(selection,"resn")
|
||
|
|
tmp_last_resn_oppo = iterate_to_list(sele_oppo_atom,"resn")
|
||
|
|
|
||
|
|
if len(tmp_last_resn_oppo) != 0:
|
||
|
|
last_resn = str(tmp_last_resn[0])
|
||
|
|
last_resn_oppo = str(tmp_last_resn_oppo[0])
|
||
|
|
|
||
|
|
if (_oneNA_base_pair[last_resn] == last_resn_oppo and
|
||
|
|
_self.select(base_pair_dist, f"(byres {sele_oppo_atom}) within 3.5 of (byres {selection})") != 0):
|
||
|
|
base_pair_bool = 1
|
||
|
|
else:
|
||
|
|
base_pair_bool = 0
|
||
|
|
else:
|
||
|
|
print("check_DNA_base_pair has no opposing residue to check")
|
||
|
|
return base_pair_bool
|
||
|
|
|
||
|
|
def get_chains_oppo (chain, tmp_connect, *, _self=cmd):
|
||
|
|
models = iterate_to_list(tmp_connect,"model")
|
||
|
|
|
||
|
|
close_chains = []
|
||
|
|
close_chains = _self.get_chains(f"({models[0]}) within 15.0 of {tmp_connect}")
|
||
|
|
close_chains = [c for c in close_chains if c != chain]
|
||
|
|
|
||
|
|
return close_chains
|
||
|
|
|
||
|
|
def get_new_chain (chain, tmp_connect, *, _self=cmd):
|
||
|
|
models = iterate_to_list(tmp_connect,"model")
|
||
|
|
model_chains = _self.get_chains(models[0])
|
||
|
|
search_chain_flag = 0
|
||
|
|
|
||
|
|
if len(model_chains) != 0:
|
||
|
|
last_chain = f"{model_chains[-1]}"
|
||
|
|
last_chain_front = last_chain[:-1]
|
||
|
|
last_chain_back = last_chain[-1]
|
||
|
|
if last_chain_back != 'Z' and last_chain_back != 'z':
|
||
|
|
new_chain_back = chr(ord(last_chain_back)+1)
|
||
|
|
elif last_chain_back == 'Z':
|
||
|
|
new_chain_back = "ZA"
|
||
|
|
print("Z chain was detected. New chain will append A")
|
||
|
|
else:
|
||
|
|
new_chain_back = "za"
|
||
|
|
print("z chain was detected. New chain will append a")
|
||
|
|
else:
|
||
|
|
new_chain_back = "A"
|
||
|
|
|
||
|
|
chain_oppo = last_chain_front + new_chain_back
|
||
|
|
return chain_oppo
|
||
|
|
|
||
|
|
def check_valid_attachment(nascent, atom_selection_name, selection, resv, *, _self=cmd):
|
||
|
|
atom_selection_name_partner = "O3'" if atom_selection_name == "P" else "P"
|
||
|
|
atom_sele = _prefix + "atom_sele"
|
||
|
|
_self.select(atom_sele, f"{selection}")
|
||
|
|
bound = _prefix + "atom_sele_bound"
|
||
|
|
if _self.count_atoms(f"(bound_to {atom_sele}) & name {atom_selection_name_partner}") != 0:
|
||
|
|
_self.delete(tmp_wild)
|
||
|
|
raise pymol.CmdException(f"{atom_selection_name} already bonded!")
|
||
|
|
|
||
|
|
def bond_single_stranded(tmp_editor, object, chain, resv, last_resi_sele, atom_selection_name, atom_name_oppo, *, _self=cmd):
|
||
|
|
"""
|
||
|
|
Forms a bond between the last atoms on selected structure and the newly created fragment
|
||
|
|
:param tmp_editor: (str) Object representing the newly created fragment
|
||
|
|
:param object: (str) object/model name of the selected structure
|
||
|
|
:param chain: (str) Chain ID
|
||
|
|
:param resv: (int)
|
||
|
|
:param last_resi_sele: (str) The selection string of the selected residue
|
||
|
|
:param atom_selection_name: (str) Name of the atom selected
|
||
|
|
:param atom_name_oppo: (str) Name of the corresponding opposing atom
|
||
|
|
"""
|
||
|
|
object_fuse = _prefix + f"_{chain}_fuse"
|
||
|
|
object_connect = _prefix + f"_{chain}_con"
|
||
|
|
|
||
|
|
print("The program did not detect a double stranded structure, so the opposing residue will not be attached.")
|
||
|
|
|
||
|
|
# Select and fuse
|
||
|
|
_self.select(object_fuse, f"{last_resi_sele} & name {atom_selection_name}")
|
||
|
|
_self.fuse(f"{tmp_editor} & chain {chain} & name {atom_name_oppo}", object_fuse, mode=3)
|
||
|
|
_self.select(object_connect, f"{last_resi_sele} & name {atom_selection_name} & chain {chain}")
|
||
|
|
|
||
|
|
# Target is on the new fragment
|
||
|
|
object_bond_target = _prefix + f"_{chain}_con_target"
|
||
|
|
if (_self.select(object_bond_target, f"{object} & resi \\{resv} & name {atom_name_oppo} & chain {chain}") == 1):
|
||
|
|
bond_dist = _prefix + "_bond_dist"
|
||
|
|
if (_self.select(bond_dist, f"{object_connect} within 3.0 of {object_bond_target}") != 0):
|
||
|
|
_self.bond(object_connect, object_bond_target)
|
||
|
|
else:
|
||
|
|
print("Identified bond targets were too far apart, so this will not be bound")
|
||
|
|
else:
|
||
|
|
print("More than one bond target was identified, so this will not be bound")
|
||
|
|
|
||
|
|
def bond_double_stranded(tmp_editor, object, chain, chain_oppo, resv, resv_oppo, last_resi_sele, prev_oppo_res, atom_selection_name,
|
||
|
|
atom_name_oppo, *, _self=cmd):
|
||
|
|
"""
|
||
|
|
Forms a bond between the last atoms on selected structure and the newly created fragment
|
||
|
|
:param tmp_editor: (str) Object representing the newly created fragment
|
||
|
|
:param object: (str) object/model name of the selected structure
|
||
|
|
:param chain: (str) Chain ID
|
||
|
|
:param chain_oppo: (str) Opposing chain ID
|
||
|
|
:param resv: (int)
|
||
|
|
:param resv_oppo: (int)
|
||
|
|
:param last_resi_sele: (str) The selection string of the selected residue
|
||
|
|
:param prev_oppo_res: (str) The selection string of the previous opposing residue
|
||
|
|
:param atom_selection_name: (str) Name of the atom selected
|
||
|
|
:param atom_name_oppo: (str) Name of the corresponding opposing atom
|
||
|
|
"""
|
||
|
|
object_fuse = _prefix + f"_{chain}_fuse"
|
||
|
|
object_oppo_fuse = _prefix + f"_oppo_{chain_oppo}_fuse"
|
||
|
|
object_connect = _prefix + f"_{chain}_con"
|
||
|
|
object_oppo_connect = _prefix + f"_oppo_{chain_oppo}_con"
|
||
|
|
|
||
|
|
# Target is on the new fragment
|
||
|
|
object_bond_target = _prefix + f"_{chain}_con_target"
|
||
|
|
object_oppo_bond_target = _prefix + f"_oppo_{chain_oppo}_con_target"
|
||
|
|
|
||
|
|
# Select and fuse
|
||
|
|
_self.select(object_fuse, f"{last_resi_sele} & name {atom_selection_name}")
|
||
|
|
_self.select(object_oppo_fuse, f"{prev_oppo_res} & name {atom_name_oppo}")
|
||
|
|
_self.fuse(f"{tmp_editor} & chain {chain} & name {atom_name_oppo}", object_fuse, mode=3)
|
||
|
|
|
||
|
|
if ((_self.select(object_bond_target, f"{object} & resi \\{resv} & name {atom_name_oppo} & chain {chain}") == 1) and
|
||
|
|
(_self.select(object_connect, f"{last_resi_sele} & name {atom_selection_name} & chain {chain}") == 1)):
|
||
|
|
bond_dist = _prefix + "_bond_dist"
|
||
|
|
if (_self.select(bond_dist, f"{object_connect} within 3.0 of {object_bond_target}") != 0):
|
||
|
|
_self.bond(object_connect, object_bond_target)
|
||
|
|
else:
|
||
|
|
print("Identified bond targets were too far apart, so this will not be bound")
|
||
|
|
else:
|
||
|
|
print("More than one bond target was found on selected chain, so this will not be bound.")
|
||
|
|
|
||
|
|
if ((_self.select(object_oppo_bond_target, f"{object} & resi \\{resv_oppo} & name {atom_selection_name} & chain {chain_oppo}") == 1) and
|
||
|
|
(_self.select(object_oppo_connect, f"{prev_oppo_res} & name {atom_name_oppo} & chain {chain_oppo}") == 1)):
|
||
|
|
bond_dist = _prefix + "_bond_dist"
|
||
|
|
if (_self.select(bond_dist, f"{object_oppo_connect} within 3.0 of {object_oppo_bond_target}") != 0):
|
||
|
|
_self.bond(object_oppo_connect, object_oppo_bond_target)
|
||
|
|
else:
|
||
|
|
print("Identified bond targets were too far apart, so this will not be bound")
|
||
|
|
else:
|
||
|
|
print("More than one bond target was found on opposing chain, so this will not be bound.")
|
||
|
|
|
||
|
|
def attach_nuc_acid(selection, nuc_acid, nuc_type, object= "", form ="B",
|
||
|
|
dbl_helix=True, *, _self=cmd):
|
||
|
|
"""
|
||
|
|
Creates new nuc acid attached to existing PDB structure
|
||
|
|
:param selection: (str) selection of picked nascent chain (or nothing)
|
||
|
|
:param nuc_acid: (str) appending nucleic acid
|
||
|
|
:param nuc_type: (str) sugar type of nucleic acid
|
||
|
|
:param object: (str) name of appending nucleobase
|
||
|
|
:param form: (str) DNA structure form: A, B, or Z
|
||
|
|
:param dbl_helix: (bool) flag for double-strandedness
|
||
|
|
"""
|
||
|
|
original_sele = _prefix + "_original_sele"
|
||
|
|
_self.select(original_sele,selection)
|
||
|
|
|
||
|
|
if nuc_type == "RNA" and form != 'A':
|
||
|
|
form = 'A'
|
||
|
|
dbl_helix = False
|
||
|
|
|
||
|
|
nascent = NascentNucAcidInfo(nuc_acid + form, nuc_acid, nuc_type, form, dbl_helix)
|
||
|
|
nuc_acid_partner_temp = _base_pair[nuc_type][nuc_acid].lower()
|
||
|
|
nascent_partner = NascentNucAcidInfo(nuc_acid_partner_temp + form, nuc_acid_partner_temp,
|
||
|
|
nuc_type, form, dbl_helix)
|
||
|
|
|
||
|
|
if _self.cmd.count_atoms(selection) == 0:
|
||
|
|
if object == "":
|
||
|
|
object = nuc_acid
|
||
|
|
|
||
|
|
if dbl_helix:
|
||
|
|
frag_string = nascent.nuc_acid + "_"+ _base_pair["DNA"][nascent.nuc_acid] + nascent.form
|
||
|
|
_self.fragment(frag_string,object)
|
||
|
|
elif not dbl_helix:
|
||
|
|
_self.fragment(nascent.fragment_name, object, origin=0)
|
||
|
|
_self.alter(object, f"segi='A';chain='A';resv=1")
|
||
|
|
rename_three_to_one(nascent.nuc_acid, object, nascent.nuc_type)
|
||
|
|
|
||
|
|
if nascent.nuc_type == "RNA":
|
||
|
|
add2pO(object, nascent.nuc_acid, 1)
|
||
|
|
|
||
|
|
if _self.count_atoms(f"{object} & segi A & name P"):
|
||
|
|
_self.edit(f"{object} & segi A & name P")
|
||
|
|
elif _self.count_atoms(f"{object} & segi A & name O3'"):
|
||
|
|
_self.edit(f"{object} & segi A & name O3'")
|
||
|
|
_self.edit(f"{object} & segi A & name O3'")
|
||
|
|
_self.select("pk1", f"{object} & name O3' & chain A")
|
||
|
|
elif _self.select(tmp_connect, f'{selection}') == 1:
|
||
|
|
chain, name, object = iterate_to_list(selection,"chain,name,model")[0]
|
||
|
|
|
||
|
|
if name == "O5'":
|
||
|
|
attach_O5_phosphate()
|
||
|
|
name = "P"
|
||
|
|
# FIXME Don't use `selection` as the name, or ensure that it's
|
||
|
|
# indeed just a name and not a selection expression.
|
||
|
|
_self.select(selection,f"name P & bound_to {original_sele}")
|
||
|
|
_self.delete("_pkdihe")
|
||
|
|
_self.select(tmp_connect,f"{selection}")
|
||
|
|
|
||
|
|
if name == "P" or name == "O3'":
|
||
|
|
extend_nuc_acid(nascent, nascent_partner, selection, object, name, chain, _self=_self)
|
||
|
|
|
||
|
|
_self.select("pk1","_tmp_editor_new_selection")
|
||
|
|
else:
|
||
|
|
_self.delete(tmp_wild)
|
||
|
|
raise pymol.CmdException("invalid connection point: must be one atom, name O3' or P")
|
||
|
|
|
||
|
|
_self.show("cartoon", f"byobject {selection}")
|
||
|
|
_self.delete(tmp_wild)
|
||
|
|
|
||
|
|
def extend_nuc_acid(nascent, nascent_partner, selection,
|
||
|
|
object, atom_selection_name, chain = 'A', *, _self=cmd):
|
||
|
|
"""
|
||
|
|
Creates new nuc acid (or pair) or attaches to PDB chain
|
||
|
|
:param nascent: (NascentNucAcidInfo) appending nucleic acid
|
||
|
|
:param nascent_partner: (NascentNucAcidInfo) partner of appending nucleic acid
|
||
|
|
:param selection: (str) selection string of selected residue
|
||
|
|
:param object: (str) object of selected residue
|
||
|
|
:param atom_selection_name: (str) O3' or P
|
||
|
|
:param chain: (str) chain ID
|
||
|
|
|
||
|
|
FIXME Eliminate `tmp_connect` pre-condition (or at least document it
|
||
|
|
properly). Looks like `tmp_connect` must be the same as `selection`?
|
||
|
|
"""
|
||
|
|
# Making a temporary selection
|
||
|
|
original_sele = _prefix + "_original_sele"
|
||
|
|
_self.select(original_sele,selection)
|
||
|
|
|
||
|
|
# Alter the segi to match the chain selection
|
||
|
|
chain_sele = "_chain_sele"
|
||
|
|
_self.select(chain_sele, f"chain {chain}")
|
||
|
|
_self.alter(chain_sele,f"segi = '{chain}'")
|
||
|
|
_self.delete(chain_sele)
|
||
|
|
|
||
|
|
if not nascent.dbl_helix:
|
||
|
|
frag_string = nascent.fragment_name
|
||
|
|
_self.fragment(frag_string, tmp_editor, origin=0)
|
||
|
|
rename_three_to_one(nascent.nuc_acid, tmp_editor, nascent.nuc_type)
|
||
|
|
elif nascent.dbl_helix:
|
||
|
|
frag_string = nascent.nuc_acid + "_"+ _base_pair["DNA"][nascent.nuc_acid] + nascent.form
|
||
|
|
_self.fragment(frag_string, tmp_editor, origin=0)
|
||
|
|
else:
|
||
|
|
raise pymol.CmdException("No helix state selected")
|
||
|
|
|
||
|
|
if _self.count_atoms(f"name {atom_selection_name}", domain=tmp_connect):
|
||
|
|
tmp_resv = iterate_to_list(tmp_connect,"resv")
|
||
|
|
|
||
|
|
# Assign last res before adjustment is made
|
||
|
|
last_resv = int(tmp_resv[0])
|
||
|
|
|
||
|
|
if atom_selection_name == "O3'":
|
||
|
|
tmp_resv[0] = str(tmp_resv[0] + 1)
|
||
|
|
elif atom_selection_name == "P":
|
||
|
|
tmp_resv[0] = str(tmp_resv[0] - 1)
|
||
|
|
else:
|
||
|
|
raise pymol.CmdException("Something went wrong with resv loop in extend_nuc")
|
||
|
|
|
||
|
|
# Resv and resi assignment and testing
|
||
|
|
resv = int(tmp_resv[0])
|
||
|
|
resi = resv
|
||
|
|
|
||
|
|
check_valid_attachment(nascent, atom_selection_name, selection, resv)
|
||
|
|
|
||
|
|
reverse = False if atom_selection_name == "O3'" else True
|
||
|
|
|
||
|
|
last_resi_sele = _prefix + "_last_resi"
|
||
|
|
_self.select(last_resi_sele, f"(byobject {selection}) & chain {chain} & resi \\{last_resv}")
|
||
|
|
|
||
|
|
if not nascent.dbl_helix:
|
||
|
|
_self.alter(tmp_editor, f"chain='{chain}';segi='{chain}';resi=tmp_resv[0]",
|
||
|
|
space={'tmp_resv': tmp_resv})
|
||
|
|
# Set parameters so that move_new_res can be used
|
||
|
|
prev_oppo_res = "none"
|
||
|
|
double_stranded_bool = False
|
||
|
|
|
||
|
|
# Move and fuse
|
||
|
|
move_new_res(frag_string, tmp_editor, last_resi_sele, prev_oppo_res, double_stranded_bool, nascent.form, antisense=reverse)
|
||
|
|
_self.fuse(f"{tmp_editor} & name P", tmp_connect, mode=3)
|
||
|
|
|
||
|
|
_self.select(tmp_domain, "byresi (pk1 | pk2)")
|
||
|
|
|
||
|
|
if atom_selection_name == "O3'":
|
||
|
|
_self.bond(f"{tmp_domain} & resi \\{last_resv} & name O3'",
|
||
|
|
f"{tmp_domain} & resi \\{resv} & name P")
|
||
|
|
elif atom_selection_name == "P":
|
||
|
|
_self.bond(f"{tmp_domain} & resi \\{resv} & name O3'",
|
||
|
|
f"{tmp_domain} & resi \\{last_resv} & name P")
|
||
|
|
|
||
|
|
elif nascent.dbl_helix:
|
||
|
|
#Initialize strings for selection
|
||
|
|
prev_oppo_res = _prefix + "_prev_oppo_res"
|
||
|
|
end_oppo_atom = _prefix + "_end_oppo_atom"
|
||
|
|
|
||
|
|
#Initialize a double stranded bool for the detection of existing double strand
|
||
|
|
double_stranded_bool = False
|
||
|
|
base_pair_result = 0
|
||
|
|
|
||
|
|
# Get oppo information
|
||
|
|
atom_name_oppo = "O3'" if atom_selection_name == "P" else "P"
|
||
|
|
|
||
|
|
# Get opposing chains and iterate looking for basepairs
|
||
|
|
chains_oppo = get_chains_oppo(chain, tmp_connect)
|
||
|
|
for tmp_chain_oppo in chains_oppo:
|
||
|
|
# Create selection strings
|
||
|
|
last_oppo_atom = _prefix + "_last_oppo_atom"
|
||
|
|
first_oppo_atom = _prefix + "_first_oppo_atom"
|
||
|
|
same_oppo_res = _prefix + "_same_oppo_atom"
|
||
|
|
|
||
|
|
_self.select(last_oppo_atom, f"last (({object} and chain {tmp_chain_oppo} and (not {tmp_editor})) and polymer.nuc)")
|
||
|
|
_self.select(first_oppo_atom, f"first (({object} and chain {tmp_chain_oppo} and (not {tmp_editor})) and polymer.nuc)")
|
||
|
|
base_pair_last = check_DNA_base_pair(last_oppo_atom, original_sele)
|
||
|
|
base_pair_first = check_DNA_base_pair(first_oppo_atom, original_sele)
|
||
|
|
|
||
|
|
same_base_flag = _self.select(same_oppo_res, f"({object} and (byres {last_oppo_atom}) and (byres {first_oppo_atom}))")
|
||
|
|
|
||
|
|
if ((base_pair_first == 1 or base_pair_last == 1) and base_pair_result == 1 and same_base_flag == 0):
|
||
|
|
print("Multiple residues meet base pairing requirements. Building as if no opposing strand detected.")
|
||
|
|
base_pair_result = 0
|
||
|
|
break
|
||
|
|
elif (base_pair_first == 1 and base_pair_last ==1):
|
||
|
|
chain_oppo = tmp_chain_oppo
|
||
|
|
base_pair_result = 1
|
||
|
|
|
||
|
|
check_DNA_base_pair(first_oppo_atom, original_sele)
|
||
|
|
atoms_first = iterate_to_list(_prefix + "_base_pair_dist","name")
|
||
|
|
check_DNA_base_pair(last_oppo_atom, original_sele)
|
||
|
|
atoms_last = iterate_to_list(_prefix + "_base_pair_dist", "name")
|
||
|
|
|
||
|
|
if (len(atoms_first) > len(atoms_last)):
|
||
|
|
_self.select(end_oppo_atom,first_oppo_atom)
|
||
|
|
else:
|
||
|
|
_self.select(end_oppo_atom,last_oppo_atom)
|
||
|
|
|
||
|
|
elif (base_pair_last == 1):
|
||
|
|
base_pair_result = 1
|
||
|
|
chain_oppo = tmp_chain_oppo
|
||
|
|
_self.select(end_oppo_atom,last_oppo_atom)
|
||
|
|
elif (base_pair_first == 1):
|
||
|
|
base_pair_result = 1
|
||
|
|
chain_oppo = tmp_chain_oppo
|
||
|
|
_self.select(end_oppo_atom,first_oppo_atom)
|
||
|
|
else:
|
||
|
|
print("No based pair was found on chain ", tmp_chain_oppo)
|
||
|
|
|
||
|
|
if (base_pair_result == 1):
|
||
|
|
double_stranded_bool = True
|
||
|
|
# Confirm base pair result and set _base_pair_dist
|
||
|
|
check_DNA_base_pair(end_oppo_atom, original_sele)
|
||
|
|
|
||
|
|
tmp_last_resv_oppo = iterate_to_list(end_oppo_atom,"resv")
|
||
|
|
if len(tmp_last_resv_oppo) == 1:
|
||
|
|
last_resv_oppo = tmp_last_resv_oppo[0]
|
||
|
|
else:
|
||
|
|
# This is arbitrary and may be changed. Using neg selected resv for now.
|
||
|
|
last_resv_oppo = -last_resv
|
||
|
|
|
||
|
|
_self.select(prev_oppo_res, "byres (_tmp_editor_base_pair_dist)")
|
||
|
|
elif (base_pair_result == 0):
|
||
|
|
last_resv_oppo = -last_resv
|
||
|
|
chain_oppo = get_new_chain(chain, tmp_connect)
|
||
|
|
else:
|
||
|
|
raise pymol.CmdException("Base pairing result is not returning 0 or 1")
|
||
|
|
|
||
|
|
# Alter the opposing segi to match chain
|
||
|
|
chain_oppo_sele = "_chain_oppo_sele"
|
||
|
|
_self.select(chain_oppo_sele, f"chain {chain_oppo}")
|
||
|
|
_self.alter(chain_oppo_sele,f"segi = '{chain_oppo}'")
|
||
|
|
_self.delete(chain_oppo_sele)
|
||
|
|
|
||
|
|
# Get oppo resv value based on selection
|
||
|
|
if atom_selection_name == "O3'":
|
||
|
|
resv_oppo = last_resv_oppo - 1
|
||
|
|
elif atom_selection_name == "P":
|
||
|
|
resv_oppo = last_resv_oppo + 1
|
||
|
|
|
||
|
|
# If picking O3', check O5' phosphate based on info found in this loop
|
||
|
|
if (atom_selection_name == "O3'" and double_stranded_bool == True):
|
||
|
|
tmp_phosphate_check = _prefix + "_phosphate_check"
|
||
|
|
|
||
|
|
if(_self.select(tmp_phosphate_check, f"{prev_oppo_res} and name P ") == 0):
|
||
|
|
_self.select("pk1", f"{prev_oppo_res} and name O5'")
|
||
|
|
_self.select("pk2", f"{prev_oppo_res} and name O5'") # This is so attach frag has a pk2
|
||
|
|
|
||
|
|
attach_O5_phosphate()
|
||
|
|
|
||
|
|
_self.unpick()
|
||
|
|
_self.select("pk1",original_sele)
|
||
|
|
_self.select(tmp_connect,f"{selection}")
|
||
|
|
_self.select(prev_oppo_res, f"byres ({prev_oppo_res})")
|
||
|
|
|
||
|
|
if (_self.select(tmp_phosphate_check, f"{prev_oppo_res} and name P")==1):
|
||
|
|
print("Phosphate has been successfully added")
|
||
|
|
|
||
|
|
# Move the fragment
|
||
|
|
move_new_res(frag_string, tmp_editor, last_resi_sele, prev_oppo_res, double_stranded_bool, nascent.form, antisense=reverse)
|
||
|
|
|
||
|
|
# Alter residues created
|
||
|
|
_self.alter("_tmp_editor_newresA",f"chain='{chain}';segi='{chain}';resv={resv}")
|
||
|
|
_self.alter("_tmp_editor_newresB",f"chain='{chain_oppo}';segi='{chain_oppo}';resv={resv_oppo}")
|
||
|
|
|
||
|
|
# Connect the created residues
|
||
|
|
if double_stranded_bool == True:
|
||
|
|
bond_double_stranded(tmp_editor, object, chain, chain_oppo, resv, resv_oppo, last_resi_sele, prev_oppo_res,
|
||
|
|
atom_selection_name, atom_name_oppo)
|
||
|
|
elif double_stranded_bool == False:
|
||
|
|
bond_single_stranded(tmp_editor, object, chain, resv, last_resi_sele, atom_selection_name, atom_name_oppo)
|
||
|
|
else:
|
||
|
|
raise pymol.CmdException("double_stranded_bool is not returning True or False")
|
||
|
|
|
||
|
|
if nascent.nuc_type == "RNA":
|
||
|
|
add2pO(tmp_domain, nascent.nuc_acid, resv)
|
||
|
|
|
||
|
|
new_term = _prefix + "_new_selection"
|
||
|
|
_self.select(new_term, f"{object} & chain {chain} & resi \\{resv} & name {atom_selection_name}")
|
||
|
|
#_self.edit(new_term)
|
||
|
|
|
||
|
|
def fab(input,name=None,mode='peptide',resi=1,chain='',segi='',state=-1,
|
||
|
|
dir=1,hydro=-1,ss=0,async_=0,quiet=1,_self=cmd, **kwargs):
|
||
|
|
'''
|
||
|
|
DESCRIPTION
|
||
|
|
|
||
|
|
Build a peptide
|
||
|
|
|
||
|
|
ARGUMENTS
|
||
|
|
|
||
|
|
input = str: sequence in one-letter code
|
||
|
|
|
||
|
|
name = str: name of object to create {default: }
|
||
|
|
|
||
|
|
ss = int: Secondary structure 1=alpha helix, 2=antiparallel beta, 3=parallel beta, 4=flat
|
||
|
|
|
||
|
|
EXAMPLE
|
||
|
|
|
||
|
|
fab ACDEFGH
|
||
|
|
fab ACDEFGH, helix, ss=1
|
||
|
|
'''
|
||
|
|
async_ = int(kwargs.pop('async', async_))
|
||
|
|
|
||
|
|
if kwargs:
|
||
|
|
raise pymol.CmdException('unknown argument: ' + ', '.join(kwargs))
|
||
|
|
|
||
|
|
if async_ < 1:
|
||
|
|
r = _fab(input,name,mode,resi,chain,segi,
|
||
|
|
state,dir,hydro,ss,quiet,_self)
|
||
|
|
else:
|
||
|
|
fab_thread = threading.Thread(target=_fab, args=(input,name,mode,
|
||
|
|
resi,chain,
|
||
|
|
segi,state,dir,
|
||
|
|
hydro,ss,quiet,_self))
|
||
|
|
fab_thread.setDaemon(1)
|
||
|
|
fab_thread.start()
|
||
|
|
r = DEFAULT_SUCCESS
|
||
|
|
return r
|
||
|
|
|
||
|
|
def fnab(input, name=None, mode="DNA", form="B", dbl_helix=1, *, _self=cmd):
|
||
|
|
"""
|
||
|
|
DESCRIPTION
|
||
|
|
|
||
|
|
Builds a nucleotide acid from sequence
|
||
|
|
|
||
|
|
Fragments provided by:
|
||
|
|
Lu, Xiang-Jun, Olson, Wilma K. 3DNA: a software package for the analysis,
|
||
|
|
rebuilding and visualization of three-dimensional nucleic acid structures,
|
||
|
|
Nucleic Acids Research, 32, W667-W675 (2004).
|
||
|
|
|
||
|
|
USAGE
|
||
|
|
|
||
|
|
fnab input [, name [, type [, form [, dbl_helix ]]]]
|
||
|
|
|
||
|
|
ARGUMENTS
|
||
|
|
|
||
|
|
input = str: Sequence as an array of one letter codes
|
||
|
|
|
||
|
|
name = str: Name of the object to create {default: obj}
|
||
|
|
|
||
|
|
mode = str: "DNA" or "RNA"
|
||
|
|
|
||
|
|
form = str: "A" or "B"
|
||
|
|
|
||
|
|
dbl_helix = bool (0/1): flag for using double helix in DNA
|
||
|
|
|
||
|
|
EXAMPLE
|
||
|
|
|
||
|
|
fnab ATGCGATAC
|
||
|
|
fnab ATGCGATAC, name=myDNA, mode=DNA, form=B, dbl_helix=1
|
||
|
|
fnab AAUUUUCCG, mode=RNA
|
||
|
|
"""
|
||
|
|
_self.unpick()
|
||
|
|
|
||
|
|
if name is None:
|
||
|
|
name = _self.get_unused_name(prefix="obj")
|
||
|
|
elif name in _self.get_names('all'):
|
||
|
|
name = _self.get_unused_name(prefix=name)
|
||
|
|
|
||
|
|
dbl_helix = int(dbl_helix) > 0
|
||
|
|
|
||
|
|
mode = mode.upper()
|
||
|
|
if mode not in ('DNA', 'RNA'):
|
||
|
|
raise pymol.CmdException("\"mode\" must be \"DNA\" or \"RNA\" only.")
|
||
|
|
if mode == "RNA" and dbl_helix != 0:
|
||
|
|
print ("Double helix RNA building is not currently supported.")
|
||
|
|
dbl_helix = 0
|
||
|
|
|
||
|
|
#first pass for error checking
|
||
|
|
for oneNA in input:
|
||
|
|
oneNA = oneNA.upper()
|
||
|
|
threeNA = _oneNA_to_threeNA.get(oneNA)
|
||
|
|
if threeNA is None:
|
||
|
|
raise pymol.CmdException("\"%s\" not of %s type..." % (oneNA, mode))
|
||
|
|
|
||
|
|
if threeNA not in _base_pair[mode]:
|
||
|
|
raise pymol.CmdException("\"%s\" not of %s type..." % (oneNA, mode))
|
||
|
|
|
||
|
|
for oneNA in input:
|
||
|
|
oneNA = oneNA.upper()
|
||
|
|
threeNA = _oneNA_to_threeNA[oneNA]
|
||
|
|
attach_nuc_acid(selection="?pk1", nuc_acid=threeNA, nuc_type=mode,
|
||
|
|
object=name, form=form, dbl_helix=dbl_helix)
|
||
|
|
_self.unpick()
|
||
|
|
return DEFAULT_SUCCESS
|
||
|
|
|
||
|
|
def build_peptide(sequence,_self=cmd): # legacy
|
||
|
|
for aa in sequence:
|
||
|
|
attach_amino_acid("pk1",_aa_codes[aa])
|