def __init__(self):
ok, nd1_plugin_path = find_plugin_dir("NanoDynamics-1")
if (not ok):
env.history.redmsg("Error: can't find " + nd1_plugin_path)
nd1_plugin_path = "."
fileName = os.path.join(nd1_plugin_path, "sim-params.txt")
self._parameterValues = {}
try:
print "sim parameters used by NE1 read from: [%s]" % fileName
parametersFile = open(fileName)
for line in parametersFile:
s = line.split()
if (len(s) > 0 and s[0] == "ne1"):
if (len(s) > 1):
key = s[1]
if (len(s) > 2):
value = " ".join(s[2:])
else:
value = True
self._parameterValues[key] = value
except IOError:
msg = "Error reading [%s]" % fileName
print_compact_traceback(msg + ": ")
env.history.redmsg(msg)
self._parameterValues = {}
def find_plugin_dir(self):
ok, path = find_plugin_dir(self.plugin_name)
if ok:
assert os.path.isdir(path)
return path
else:
errortext = path
self.fatal( errortext)
return None
pass
def __init__(self):
global _thePyrexSimulator
assert (_thePyrexSimulator is None)
_thePyrexSimulator = self
import sim # this import must not be done at toplevel
self.sim = sim.theSimulator()
ok, nd1_plugin_path = find_plugin_dir("NanoDynamics-1")
if (not ok):
env.history.redmsg("Error: can't find " + nd1_plugin_path)
nd1_plugin_path = "."
self.system_parameters_file = os.path.join(nd1_plugin_path, "sim-params.txt")
def __init__(self):
global _thePyrexSimulator
assert _thePyrexSimulator is None
_thePyrexSimulator = self
import sim # this import must not be done at toplevel
self.sim = sim.theSimulator()
ok, nd1_plugin_path = find_plugin_dir("NanoDynamics-1")
if not ok:
env.history.redmsg("Error: can't find " + nd1_plugin_path)
nd1_plugin_path = "."
self.system_parameters_file = os.path.join(nd1_plugin_path, "sim-params.txt")
self.amber_bonded_parameters_file = os.path.join(nd1_plugin_path, "ffamber03bon.itp")
self.amber_nonbonded_parameters_file = os.path.join(nd1_plugin_path, "ffamber03nb.itp")
self.amber_charges_file = os.path.join(nd1_plugin_path, "ffamber03charge.itp")
from dna.model.Dna_Constants import getDuplexBasesPerTurn
##from dna.updater.dna_updater_prefs import pref_dna_updater_convert_to_PAM3plus5
from simulation.sim_commandruns import adjustSinglet
from model.elements import PeriodicTable
from model.Line import Line
from model.chem import Atom_prekill_prep
Element_Ae3 = PeriodicTable.getElement('Ae3')
from dna.model.Dna_Constants import basesDict, dnaDict
from dna.model.dna_model_constants import LADDER_END0
basepath_ok, basepath = find_plugin_dir("DNA")
if not basepath_ok:
env.history.message(orangemsg("The cad/plugins/DNA directory is missing."))
RIGHT_HANDED = -1
LEFT_HANDED = 1
from geometry.VQT import V, Q, norm, cross
from geometry.VQT import vlen
from Numeric import dot
from utilities.debug import print_compact_stack
from model.bonds import bond_at_singlets
from dna.generators.Z_Dna_Generator import Z_Dna_Generator
@author: Mark Sims
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LICENSE file for details.
History:
Mark 2007-10-18:
- Created. Major rewrite of DnaGenHelper.py.
"""
import foundation.env as env
from platform_dependent.PlatformDependent import find_plugin_dir
from utilities.Log import orangemsg
from dna.model.Dna_Constants import dnaDict
basepath_ok, basepath = find_plugin_dir("DNA")
if not basepath_ok:
env.history.message(orangemsg("The cad/plugins/DNA directory is missing."))
RIGHT_HANDED = -1
from dna.generators.Dna_Generator import Dna_Generator
class A_Dna_Generator(Dna_Generator):
"""
Provides an atomistic model of the A form of DNA.
The geometry for A-DNA is very twisty and funky. We need to to research
the A form since it's not a simple helix (like B) or an alternating helix
(like Z).