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########################################################################
#
# Vision Macro - Python source code - file generated by vision
# Thursday 01 June 2006 11:29:09
#
# The Scripps Research Institute (TSRI)
# Molecular Graphics Lab
# La Jolla, CA 92037, USA
#
# Copyright: Daniel Stoffler, Michel Sanner and TSRI
#
# revision: Guillaume Vareille
#
#########################################################################
#
# $Header: /opt/cvs/python/packages/share1.5/AutoDockTools/VisionInterface/PrepareAD3Ligand.py,v 1.1 2006/06/05 22:45:41 rhuey Exp $
#
# $Id: PrepareAD3Ligand.py,v 1.1 2006/06/05 22:45:41 rhuey Exp $
#
from NetworkEditor.macros import MacroNode
class PrepareAD3Ligand(MacroNode):
def __init__(self, constrkw={}, name='Prepare AD3 Ligand', **kw):
kw['name'] = name
apply( MacroNode.__init__, (self,), kw)
def beforeAddingToNetwork(self, net):
MacroNode.beforeAddingToNetwork(self, net)
## loading libraries ##
from AutoDockTools.VisionInterface.AdtNodes import adtlib
net.editor.addLibraryInstance(adtlib,"AutoDockTools.VisionInterface.AdtNodes", "adtlib")
from MolKit.VisionInterface.MolKitNodes import molkitlib
net.editor.addLibraryInstance(molkitlib,"MolKit.VisionInterface.MolKitNodes", "molkitlib")
def afterAddingToNetwork(self):
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
## loading libraries ##
from AutoDockTools.VisionInterface.AdtNodes import adtlib
from MolKit.VisionInterface.MolKitNodes import molkitlib
## building macro network ##
Prepare_AD3_Ligand_0 = self
from traceback import print_exc
## loading libraries ##
from AutoDockTools.VisionInterface.AdtNodes import adtlib
self.macroNetwork.getEditor().addLibraryInstance(adtlib,"AutoDockTools.VisionInterface.AdtNodes", "adtlib")
from MolKit.VisionInterface.MolKitNodes import molkitlib
self.macroNetwork.getEditor().addLibraryInstance(molkitlib,"MolKit.VisionInterface.MolKitNodes", "molkitlib")
try:
## saving node input Ports ##
input_Ports_1 = self.macroNetwork.ipNode
input_Ports_1.move(183, 27)
except:
print "WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
print_exc()
input_Ports_1=None
try:
## saving node output Ports ##
output_Ports_2 = self.macroNetwork.opNode
output_Ports_2.move(181, 338)
except:
print "WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
print_exc()
output_Ports_2=None
try:
## saving node Calculate Gasteiger Charges ##
from MolKit.VisionInterface.MolKitNodes import CalculateGasteigerCharges
Calculate_Gasteiger_Charges_3 = CalculateGasteigerCharges(constrkw = {}, name='Calculate Gasteiger Charges', library=molkitlib)
self.macroNetwork.addNode(Calculate_Gasteiger_Charges_3,200,131)
apply(Calculate_Gasteiger_Charges_3.inputPortByName['mols'].configure, (), {'color': '#c64e70', 'cast': True, 'shape': 'oval'})
apply(Calculate_Gasteiger_Charges_3.outputPortByName['mols'].configure, (), {'color': '#c64e70', 'shape': 'oval'})
apply(Calculate_Gasteiger_Charges_3.outputPortByName['charge_total'].configure, (), {'color': 'green', 'shape': 'circle'})
except:
print "WARNING: failed to restore CalculateGasteigerCharges named Calculate Gasteiger Charges in network self.macroNetwork"
print_exc()
Calculate_Gasteiger_Charges_3=None
try:
## saving node Add Hydrogens ##
from MolKit.VisionInterface.MolKitNodes import AddHydrogens
Add_Hydrogens_4 = AddHydrogens(constrkw = {}, name='Add Hydrogens', library=molkitlib)
self.macroNetwork.addNode(Add_Hydrogens_4,200,80)
apply(Add_Hydrogens_4.inputPortByName['molecules'].configure, (), {'color': '#c64e70', 'cast': True, 'shape': 'oval'})
apply(Add_Hydrogens_4.outputPortByName['molecules'].configure, (), {'color': '#c64e70', 'shape': 'oval'})
apply(Add_Hydrogens_4.outputPortByName['new_h_ct'].configure, (), {'color': 'yellow', 'shape': 'circle'})
except:
print "WARNING: failed to restore AddHydrogens named Add Hydrogens in network self.macroNetwork"
print_exc()
Add_Hydrogens_4=None
try:
## saving node Merge NonPolar Hydrogens ##
from AutoDockTools.VisionInterface.AdtNodes import MergeNonPolarHydrogens
Merge_NonPolar_Hydrogens_5 = MergeNonPolarHydrogens(constrkw = {}, name='Merge NonPolar Hydrogens', library=adtlib)
self.macroNetwork.addNode(Merge_NonPolar_Hydrogens_5,200,182)
apply(Merge_NonPolar_Hydrogens_5.inputPortByName['mols'].configure, (), {'color': '#c64e70', 'cast': True, 'shape': 'oval'})
apply(Merge_NonPolar_Hydrogens_5.inputPortByName['renumber'].configure, (), {'color': 'yellow', 'cast': True, 'shape': 'circle'})
apply(Merge_NonPolar_Hydrogens_5.outputPortByName['mols'].configure, (), {'color': '#c64e70', 'shape': 'oval'})
apply(Merge_NonPolar_Hydrogens_5.outputPortByName['num_nphs'].configure, (), {'color': 'yellow', 'shape': 'circle'})
except:
print "WARNING: failed to restore MergeNonPolarHydrogens named Merge NonPolar Hydrogens in network self.macroNetwork"
print_exc()
Merge_NonPolar_Hydrogens_5=None
try:
## saving node Manage Rotatable Bonds ##
from AutoDockTools.VisionInterface.AdtNodes import ManageRotatableBonds
Manage_Rotatable_Bonds_6 = ManageRotatableBonds(constrkw = {}, name='Manage Rotatable Bonds', library=adtlib)
self.macroNetwork.addNode(Manage_Rotatable_Bonds_6,200,235)
apply(Manage_Rotatable_Bonds_6.inputPortByName['mols'].configure, (), {'color': '#c64e70', 'cast': True, 'shape': 'oval'})
apply(Manage_Rotatable_Bonds_6.inputPortByName['root'].configure, (), {'color': 'white', 'cast': True, 'shape': 'oval'})
apply(Manage_Rotatable_Bonds_6.inputPortByName['allowed_bonds'].configure, (), {'color': 'white', 'cast': True, 'shape': 'oval'})
apply(Manage_Rotatable_Bonds_6.inputPortByName['check_for_fragments'].configure, (), {'color': 'yellow', 'cast': True, 'shape': 'circle'})
apply(Manage_Rotatable_Bonds_6.inputPortByName['bonds_to_inactivate'].configure, (), {'color': 'white', 'cast': True, 'shape': 'oval'})
apply(Manage_Rotatable_Bonds_6.inputPortByName['limit_torsions'].configure, (), {'color': 'white', 'cast': True, 'shape': 'oval'})
apply(Manage_Rotatable_Bonds_6.outputPortByName['mol'].configure, (), {'color': '#c64e70', 'shape': 'oval'})
except:
print "WARNING: failed to restore ManageRotatableBonds named Manage Rotatable Bonds in network self.macroNetwork"
print_exc()
Manage_Rotatable_Bonds_6=None
try:
## saving node AD4_typer ##
from AutoDockTools.VisionInterface.AdtNodes import Assign_AD4Types
AD4_typer_7 = Assign_AD4Types(constrkw = {}, name='AD4_typer', library=adtlib)
self.macroNetwork.addNode(AD4_typer_7,198,288)
apply(AD4_typer_7.inputPortByName['mols'].configure, (), {'color': '#c64e70', 'cast': True, 'shape': 'oval'})
apply(AD4_typer_7.inputPortByName['renameAtoms'].configure, (), {'color': 'yellow', 'cast': True, 'shape': 'circle'})
apply(AD4_typer_7.inputPortByName['set_aromatic_carbons'].configure, (), {'color': 'yellow', 'cast': True, 'shape': 'circle'})
apply(AD4_typer_7.inputPortByName['reassign'].configure, (), {'color': 'yellow', 'cast': True, 'shape': 'circle'})
apply(AD4_typer_7.outputPortByName['typed_mols'].configure, (), {'color': '#c64e70', 'shape': 'oval'})
except:
print "WARNING: failed to restore Assign_AD4Types named AD4_typer in network self.macroNetwork"
print_exc()
AD4_typer_7=None
self.macroNetwork.freeze()
## saving connections for network Prepare AD3 Ligand ##
input_Ports_1 = self.macroNetwork.ipNode
if input_Ports_1 is not None and Add_Hydrogens_4 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1, Add_Hydrogens_4, "new", "molecules", blocking=True)
except:
print "WARNING: failed to restore connection between input_Ports_1 and Add_Hydrogens_4 in network self.macroNetwork"
if Add_Hydrogens_4 is not None and Calculate_Gasteiger_Charges_3 is not None:
try:
self.macroNetwork.connectNodes(
Add_Hydrogens_4, Calculate_Gasteiger_Charges_3, "molecules", "mols", blocking=True)
except:
print "WARNING: failed to restore connection between Add_Hydrogens_4 and Calculate_Gasteiger_Charges_3 in network self.macroNetwork"
if Calculate_Gasteiger_Charges_3 is not None and Merge_NonPolar_Hydrogens_5 is not None:
try:
self.macroNetwork.connectNodes(
Calculate_Gasteiger_Charges_3, Merge_NonPolar_Hydrogens_5, "mols", "mols", blocking=True)
except:
print "WARNING: failed to restore connection between Calculate_Gasteiger_Charges_3 and Merge_NonPolar_Hydrogens_5 in network self.macroNetwork"
if Merge_NonPolar_Hydrogens_5 is not None and Manage_Rotatable_Bonds_6 is not None:
try:
self.macroNetwork.connectNodes(
Merge_NonPolar_Hydrogens_5, Manage_Rotatable_Bonds_6, "mols", "mols", blocking=True)
except:
print "WARNING: failed to restore connection between Merge_NonPolar_Hydrogens_5 and Manage_Rotatable_Bonds_6 in network self.macroNetwork"
if Manage_Rotatable_Bonds_6 is not None and AD4_typer_7 is not None:
try:
self.macroNetwork.connectNodes(
Manage_Rotatable_Bonds_6, AD4_typer_7, "mol", "mols", blocking=True)
except:
print "WARNING: failed to restore connection between Manage_Rotatable_Bonds_6 and AD4_typer_7 in network self.macroNetwork"
output_Ports_2 = self.macroNetwork.opNode
if AD4_typer_7 is not None and output_Ports_2 is not None:
try:
self.macroNetwork.connectNodes(
AD4_typer_7, output_Ports_2, "typed_mols", "new", blocking=True)
except:
print "WARNING: failed to restore connection between AD4_typer_7 and output_Ports_2 in network self.macroNetwork"
self.macroNetwork.unfreeze()
Prepare_AD3_Ligand_0.shrink()
## reset modifications ##
Prepare_AD3_Ligand_0.resetTags()
Prepare_AD3_Ligand_0.buildOriginalList()
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