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SymFile.py
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SymFile.py
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import sys
from xyzMath import Vec
class VirtXYZ(object):
"""
>>> v1 = VirtXYZ( "test1", Vec(1,0,0), Vec(0,1,0), Vec(0,0,0) )
>>> v2 = VirtXYZ( "test2", Vec(-1,0,0), Vec(0,1,0), Vec(0,0,0) )
>>> print v1.symline()
xyz test1 +1.000000,+0.000000,+0.000000 +0.000000,+1.000000,+0.000000 +0.000000,+0.000000,+0.000000
>>> print v2.symline()
xyz test2 -1.000000,+0.000000,+0.000000 +0.000000,+1.000000,+0.000000 +0.000000,+0.000000,+0.000000
"""
def __init__(self, name, x, y, cen):
super(VirtXYZ, self).__init__()
self.name = name
self.x = x
self.y = y
self.cen = cen
def symline(self):
s = "xyz %s %+f,%+f,%+f %+f,%+f,%+f %+f,%+f,%+f" % (
self.name.ljust(20), self.x.x, self.x.y, self.x.z, self.y.x, self.y.y, self.y.z,
self.cen.x, self.cen.y, self.cen.z)
return s.rstrip()
class ConnectVirtual(object):
"""
>>> v1 = VirtXYZ( "test1", Vec(1,0,0), Vec(0,1,0), Vec(0,0,0) )
>>> v2 = VirtXYZ( "test2", Vec(-1,0,0), Vec(0,1,0), Vec(0,0,0) )
>>> print ConnectVirtual( "test_jump", v1, v2 ).symline()
connect_virtual test_jump test1 test2
"""
def __init__(self, name, virt1, virt2=None, chain=None):
super(ConnectVirtual, self).__init__()
self.name = name
self.virt1 = virt1
self.virt2 = virt2
self.chain = chain
def symline(self):
if self.chain:
s = "connect_virtual %s %s %s" % (self.name.rjust(20), self.virt1.name.ljust(20),
"SUBUNIT", chain)
else:
assert self.virt2
s = "connect_virtual %s %s %s" % (self.name.rjust(20), self.virt1.name.ljust(20),
self.virt2.name.ljust(20))
return s.rstrip()
if __name__ == '__main__':
import doctest
r = doctest.testmod()
print(r)
# some not-finished work making a symdef parsers
# from pyparsing import Dict,Group,Literal,Regex,Word,ZeroOrMore,OneOrMore,alphas,delimitedList,nums,LineStart,LineEnd,Optional,Keyword,NotAny,StringEnd
# def printf(*args):
# for i,a in enumerate(args): print i,a
# paren = Literal("(")|Literal(")")
# tag = Regex(r'[a-zA-Z0-9_]+')
# num = Word(nums).setParseAction( lambda s,l,t: int(t[0]) )
# real = Regex(r'-?\d+(\.\d*)?([eE]\d+)?')
# vec = real+","+real+","+real
# sname = Keyword("symmetry_name" )+tag
# anchor = Keyword("anchor_residue")+tag
# efirst = (real+"*"+tag)
# erest = ("+"+real+"*"+paren+tag+":"+tag+paren)
# eline = (Keyword("E")+"=" +efirst+OneOrMore(erest))
# vcoord = (Keyword('xyz') + tag + vec + vec + vec)
# vcoords = Keyword("virtual_coordinates_start") + OneOrMore(vcoord) + Keyword("virtual_coordinates_stop")
# subunit = Keyword("SUBUNIT") + Optional(Regex("[a-zA-Z0-9_]")) + Optional(tag|num)
# connect = Keyword("connect_virtual")+tag+tag+(NotAny("SUBUNIT")+tag|subunit)
# doftype = Keyword("x")|Keyword("y")|Keyword("z")|Keyword("angle_x")|Keyword("angle_y")|Keyword("angle_z")
# dof = (doftype+Optional(paren+real+paren))
# dofs = Keyword("set_dof")+tag+OneOrMore(dof )
# jgroup = Keyword("set_jump_group")+tag+OneOrMore(tag)
# symline = (sname|eline|anchor|vcoords|connect|dofs |jgroup)+LineEnd()
# symfile = ZeroOrMore(symline)+StringEnd()
# real .setParseAction( lambda s,l,t: float(t[0]) )
# sname .setParseAction(tuple)
# anchor .setParseAction(tuple)
# efirst .setParseAction(lambda s,l,t: (t[0],t[2]))
# erest .setParseAction(lambda s,l,t: ( t[1],t[4],t[6]))
# eline .setParseAction(lambda s,l,t: ('E',tuple(t[2:])))
# vcoord .setParseAction(lambda s,l,t: tuple(t[1:]))
# vcoords.setParseAction(lambda s,l,t: ('xyz',tuple(t[1:-1])))
# subunit.setParseAction(lambda s,l,t: ("subunit",t[1:]))
# connect.setParseAction(lambda s,l,t: ("connect",tuple([x for x in t[1:] if not x=='\n'])))
# dof .setParseAction(lambda s,l,t: ('dof',(t[0],t[2]) if len(t)>2 else (t[0],)))
# dofs .setParseAction(lambda s,l,t: ('dofs',tuple(t[1:])))
# jgroup .setParseAction(lambda s,l,t: ('jump_group',t[1:]))
# symline.setParseAction(lambda s,l,t: tuple([x for x in t if not x=='\n']))
# print dof .parseString("x(20.4244497891662)")
# print dof .parseString("angle_x")
# print dofs .parseString("set_dof JUMP0_0_to_com x(20.4244497891662)")
# #print dofs .parseString("set_dof JUMP0_0_to_subunit angle_x angle_y angle_z")
# #print dofs .parseString("set_dof JUMP0_0 x(3.81281197834553) angle_x")
# # print connect.parseString("connect_virtual JUMP0_0_to_com VRT0_0 VRT0_0_base")
# # print connect.parseString("connect_virtual JUMP0_0_to_subunit TEST SUBUNIT")
# # print connect.parseString("connect_virtual JUMP1_0_to_subunit VRT1_0_base SUBUNIT A")
# # print connect.parseString("connect_virtual JUMP1_0_to_subunit VRT1_0_base SUBUNIT A 8")
# sys.exit()
# s = "\n".join(open("/data/pdb/D3/1WAAA_D3.symm").readlines())
# for p in symline.searchString(s):
# print p
# testData = """
# +-------+------+------+------+------+------+------+------+------+
# | | A1 | B1 | C1 | D1 | A2 | B2 | C2 | D2 |
# +=======+======+======+======+======+======+======+======+======+
# | min | 7 | 43 | 7 | 15 | 82 | 98 | 1 | 37 |
# | max | 11 | 52 | 10 | 17 | 85 | 112 | 4 | 39 |
# | ave | 9 | 47 | 8 | 16 | 84 | 106 | 3 | 38 |
# | sdev | 1 | 3 | 1 | 1 | 1 | 3 | 1 | 1 |
# +-------+------+------+------+------+------+------+------+------+
# """
# underline = Word("-=")
# number = Word(nums).setParseAction( lambda s,l,t:(l,[int(t[0])]) )
# vert = Literal("|").suess()
# rowDelim = ("+" + ZeroOrMore( underline + "+" ) ).suess()
# columnHeader = Group(vert + vert + delimitedList(Word(alphas + nums), "|") + vert)
# heading = rowDelim + columnHeader.setResultsName("columns") + rowDelim
# rowData = Group( vert + Word(alphas) + vert + delimitedList(number,"|") + vert )
# trailing = rowDelim
# datatable = heading + Dict( ZeroOrMore(rowData) ) + trailing
# for i in datatable.parseString(testData): print i