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).