def __init__(self, name='Lone Pair Merger', **kw):
kw['name'] = name
NetworkNode.__init__(*(self, ), **kw)
ip = self.inputPortsDescr
ip.append(datatype='MoleculeSet', name='mols')
ip.append(datatype='int',
required=False,
name='renumber',
defaultValue=1)
op = self.outputPortsDescr
op.append(datatype='MoleculeSet', name='mols')
op.append(datatype='int', name='num_lps')
code = """def doit(self,mols, renumber):
if mols:
lps_merger = LonepairMerger()
num_lps = 0
for mol in mols:
if not len(mol.allAtoms.bonds[0]):
mol.buildBondsByDistance()
lps = lps_merger.mergeLPS(mol.allAtoms, renumber=renumber)
num_lps += len(lps)
self.outputData(mols=mols, num_lps=num_lps)\n"""
self.setFunction(code)
def __init__(self, name='Ligand_Writer_AD4', **kw):
kw['name'] = name
NetworkNode.__init__(*(self, ), **kw)
fileTypes = [('pdbqt', '*.pdbqt'), ('all', '*')]
self.widgetDescr['output_filename'] = {
'class': 'NEEntryWithFileSaver',
'master': 'node',
'filetypes': fileTypes,
'title': 'save AD4 Ligand',
'width': 10,
'labelCfg': {
'text': 'file:'
},
}
ip = self.inputPortsDescr
ip.append(datatype='Molecule', name='mol')
ip.append(datatype='string', name='output_filename')
op = self.outputPortsDescr
op.append(datatype='Molecule', name='mol')
op.append(datatype='string', name='output_filename')
code = """def doit(self, mol, output_filename):
if mol:
writer = AD4LigandWriter()
writer.write(mol, output_filename)
self.outputData(mol=mol, output_filename=output_filename)\n"""
self.setFunction(code)
def __init__(self, name='Docking Parameter File Browser', **kw):
kw['name'] = name
NetworkNode.__init__(*(self, ), **kw)
#self.readOnly = 1
code = """def doit(self, filename):
if filename:
self.outputData(filename=filename)
"""
self.setFunction(code)
# show the entry widget by default
self.inNodeWidgetVisibleByDefault = True
fileTypes = [('dpf', '*')]
self.widgetDescr['filename'] = {
'class': 'NEEntryWithFileBrowser',
'master': 'node',
'filetypes': fileTypes,
'title': 'read file',
'width': 16,
'labelCfg': {
'text': 'dpf file:'
},
}
self.inputPortsDescr.append(datatype='string', name='filename')
self.outputPortsDescr.append(datatype='string', name='filename')
def __init__(self, name='AutogridResURL', **kw):
kw['name'] = name
NetworkNode.__init__(*(self, ), **kw)
kw['name'] = name
NetworkNode.__init__(*(self, ), **kw)
ip = self.inputPortsDescr
ip.append(datatype='string', name='url')
self.widgetDescr['url'] = {
'class': 'NEEntry',
'master': 'node',
'width': 40,
'labelCfg': {
'text': 'URL to Autogrid Results: '
}
}
op = self.outputPortsDescr
op.append(datatype='autogrid_results', name='autogrid_res_obj')
code = """def doit(self, url):
autogrid_res_obj=autogrid_results(url, "url")
self.outputData(autogrid_res_obj=autogrid_res_obj)
"""
self.setFunction(code)
def __init__(self, name='StructureBrowser', **kw):
kw['name'] = name
NetworkNode.__init__(*(self,), **kw)
kw['name'] = name
NetworkNode.__init__(*(self,), **kw)
ip = self.inputPortsDescr
ip.append(datatype='string', name='receptor_file')
filetypes = [('All supported files', '*.pdb *.pqr *.pdbqt')]
self.widgetDescr['receptor_file'] = {
'class':'NEEntryWithFileBrowser', 'master':'node', 'width':20,
'filetypes':filetypes,
'initialValue':'', 'labelCfg':{'text':'Structure file: '}
}
op = self.outputPortsDescr
op.append(datatype='receptor', name='receptor_obj')
code = """def doit(self, receptor_file):
import os
receptor_file = os.path.abspath(receptor_file)
if not(os.path.exists(receptor_file)):
print "ERROR: structure file " + receptor_file + " does not exist!"
return 'stop'
receptor_obj = receptor(receptor_file)
self.outputData(receptor_obj=receptor_obj)
"""
self.setFunction(code)
def __init__(self, name='AutogridResDirectoryBrowser', **kw):
kw['name'] = name
NetworkNode.__init__(*(self,), **kw)
kw['name'] = name
NetworkNode.__init__(*(self,), **kw)
ip = self.inputPortsDescr
ip.append(datatype='string', name='directory')
self.widgetDescr['directory'] = {
'class':'NEEntryWithDirectoryBrowser', 'master':'node', 'width':16,
'initialValue':'', 'labelCfg':{'text':'Autogrid result directory: '}
}
op = self.outputPortsDescr
op.append(datatype='autogrid_results', name='autogrid_result')
op = self.outputPortsDescr
op.append(datatype='string', name='zip_file_path')
code = """def doit(self, directory):
autogrid_result = autogrid_results(directory, "local")
self.outputData(autogrid_result=autogrid_result, zip_file_path=autogrid_result.path)
"""
self.setFunction(code)
def __init__(self, name='AD4_typer', **kw):
kw['name'] = name
NetworkNode.__init__(*(self, ), **kw)
ip = self.inputPortsDescr
ip.append(datatype='MoleculeSet', name='mols')
ip.append(datatype='int',
required=False,
name='set_aromatic_carbons',
defaultValue=1)
ip.append(datatype='int',
required=False,
name='reassign',
defaultValue=1)
ip.append(datatype='int',
required=False,
name='renameAtoms',
defaultValue=0)
op = self.outputPortsDescr
op.append(datatype='MoleculeSet', name='typed_mols')
code = """def doit(self,mols, set_aromatic_carbons=1, reassign=1, renameAtoms=0):
if mols:
at_typer = AutoDock4_AtomTyper(set_aromatic_carbons=1, renameAtoms=renameAtoms)
for mol in mols:
if not len(mol.allAtoms.bonds[0]):
mol.buildBondsByDistance()
at_typer.setAutoDockElements(mol, reassign=reassign)
self.outputData(typed_mols=mols)\n"""
self.setFunction(code)
def __init__(self, constrkw={}, name='ADTFileNames', **kw):
kw['constrkw'] = constrkw
kw['name'] = name
NetworkNode.__init__(*(self, ), **kw)
ip = self.inputPortsDescr
ip.append({'name': 'recpetor_obj', 'datatype': 'receptor'})
op = self.outputPortsDescr
op.append({'name': 'GPF_template', 'datatype': 'gpf_template'})
op.append({'name': 'DPF_template', 'datatype': 'dpf_template'})
op.append({'name': 'result_dir', 'datatype': 'string'})
code = """def doit(self, receptor_obj):
import os
from AutoDockTools.VisionInterface.Adt.receptor import receptor
from AutoDockTools.VisionInterface.Adt.dpf_template import dpf_template
from AutoDockTools.VisionInterface.Adt.gpf_template import gpf_template
receptor_id = receptor_obj.get_id()
receptor_dir = receptor_obj.get_workdir()
gpf_file = receptor_dir + os.sep + receptor_id + '.gpf'
dpf_file = receptor_dir + os.sep + receptor_id + '.dpf'
GPF_template = gpf_template(gpf_file)
DPF_template = dpf_template(dpf_file)
result_dir = os.path.abspath(receptor_dir + os.sep + '..' + os.sep + receptor_id)
if not(os.path.exists(gpf_file)):
print "ERROR: GPF template " + gpf_file + " does not exist!"
return 'stop'
elif not(os.path.exists(dpf_file)):
print "ERROR: DPF template " + dpf_file + " does not exist!"
return 'stop'
pdbqt_loc = receptor_obj.get_ext_loc('pdbqt')
pqr_loc = receptor_obj.get_ext_loc('pqr')
pdb_loc = receptor_obj.get_ext_loc('pdb')
if pdbqt_loc == None and pqr_loc == None and pdb_loc == None:
print "ERROR: No valid structure file found, none of the following exist"
print " " + pdbqt_loc + ", " + pqr_loc + ", " + pdb_loc
return 'stop'
print "-------------------------------------------------------"
print " INPUTS THAT WILL BE USED FOR VIRTUAL SCREENING "
print "GPF Template: " + GPF_template.fullpath
print "DPF Template: " + DPF_template.fullpath
print "Results will be downloaded to: " + result_dir
print "-------------------------------------------------------"
pass
self.outputData(GPF_template=GPF_template, DPF_template=DPF_template, result_dir=result_dir)
"""
self.configure(function=code)
def __init__(self, constrkw={}, name='Docking', **kw):
kw['constrkw'] = constrkw
kw['name'] = name
NetworkNode.__init__(*(self, ), **kw)
code = """def doit(self, docking_logs, rmsTool):
from AutoDockTools.Docking import Docking
d = Docking()
for f in docking_logs:
d.readDlg(f)
d.clusterer.rmsTool = rmsTool
self.outputData(docking = d)
## to ouput data on port docking use
## self.outputData(docking=data)
"""
self.configure(function=code)
self.inputPortsDescr.append({
'name': 'docking_logs',
'cast': True,
'datatype': 'list',
'balloon':
'list of docking log files to be read into as a single Docking',
'height': 12,
'width': 12,
'shape': 'oval',
'color': 'cyan'
})
self.inputPortsDescr.append({
'name': 'rmsTool',
'cast': True,
'datatype': 'None',
'balloon': 'rmsTool to be used for clustering',
'height': 8,
'width': 12,
'shape': 'diamond',
'color': 'white'
})
self.outputPortsDescr.append({
'name': 'docking',
'datatype': 'None',
'balloon': 'docking instance',
'height': 8,
'width': 12,
'shape': 'diamond',
'color': 'white'
})
def __init__(self, name='RemoveWaters', **kw):
kw['name'] = name
NetworkNode.__init__(*(self, ), **kw)
ip = self.inputPortsDescr
ip.append(datatype='MoleculeSet', name='molecules')
ip.append(datatype='str',
required=False,
name='residue_type_str',
defaultValue='HOH')
op = self.outputPortsDescr
op.append(datatype='MoleculeSet',
name='molecules_with_no_water_residues')
op.append(datatype='int', name='num_water_res')
code = """def doit(self, molecules, residue_type_str):
if molecules:
from MolKit.molecule import BondSet
lenHOHs = 0
for mol in molecules:
hohs = mol.allAtoms.get(lambda x: x.parent.type==residue_type_str)
if hohs:
#remove(hohs)
lenHOHs = len(hohs)
for h in hohs:
for b in h.bonds:
c = b.atom1
if c==h:
c = b.atom2
c.bonds.remove(b)
h.bonds = BondSet()
res = h.parent
h.parent.remove(h)
if len(h.parent.children)==0:
res = h.parent
chain = res.parent
#print 'removing residue: ', res.name
chain.remove(res)
if len(chain.children)==0:
mol = chain.parent
print 'removing chain', chain.id
mol.remove(chain)
del chain
del res
del h
#fix allAtoms short cut
mol.allAtoms = mol.chains.residues.atoms
self.outputData(molecules_with_no_water_residues=molecules, num_water_res=lenHOHs)"""
self.setFunction(code)
def __init__(self, name='UrlLigandDB', **kw):
kw['name'] = name
NetworkNode.__init__(*(self, ), **kw)
kw['name'] = name
NetworkNode.__init__(*(self, ), **kw)
ip = self.inputPortsDescr
ip.append(datatype='string', name='url')
# ip.append(datatype='string', name='local_dir')
self.widgetDescr['url'] = {
'class': 'NEEntry',
'master': 'node',
'width': 40,
'labelCfg': {
'text': 'URL to ligands: '
}
}
# self.widgetDescr['local_dir'] = {
# 'class':'NEEntryWithDirectoryBrowser', 'master':'node', 'width':30,
# 'labelCfg':{'text':'Local directory to save ligands: '}
# }
op = self.outputPortsDescr
op.append(datatype='LigandDB', name='ligDB')
# code = """def doit(self, url, local_dir):
code = """def doit(self, url):
# ligDB = LigandDB(url_compressed_file=url)
ligDB = LigandDB(url_lib=url)
bname = os.path.basename(url)
# if bname.endwith('.tar.gz'):
# print "TEST tar.gz"
# elif bname.endswith('.zip'):
# print "TEST ZIP"
if not(url.startswith('http://kryptonite.nbcr.net/app')):
print "ERROR: the URL must be a directory on kryptonite.nbcr.net"
sys.exit()
self.outputData(ligDB=ligDB)
"""
self.setFunction(code)
def __init__(self, name='MakeDPFCopies', **kw):
kw['name'] = name
NetworkNode.__init__(*(self, ), **kw)
kw['name'] = name
NetworkNode.__init__(*(self, ), **kw)
ip = self.inputPortsDescr
ip.append(datatype='dpf_template', name='dpf_file')
ip.append(datatype='string', name='struct_dir')
op = self.outputPortsDescr
op.append(datatype='list', name='dpf_list')
code = """def doit(self, dpf_file, struct_dir):
import os
import shutil
from AutoDockTools.VisionInterface.Adt.dpf_template import dpf_template
file_path = dpf_file.fullpath
if not(os.path.exists(file_path)):
print "ERROR: DPF template file " + file_path + " does not exist!"
return 'stop'
name_list = set()
dpf_list = []
d = os.path.abspath(struct_dir)
for i in os.listdir(struct_dir):
if i.endswith(".pdbqt") or i.endswith(".pdb") or i.endswith(".pqr"):
name_list.add(i.split('.')[0])
for i in name_list:
dst = os.path.join(d, i + '.dpf')
dpf_list.append(dst)
if not(os.path.exists(dst)):
shutil.copyfile(file_path, dst)
self.outputData(dpf_list=dpf_list)
"""
self.setFunction(code)
def __init__(self, name='Manage Aromatic Carbons', **kw):
kw['name'] = name
NetworkNode.__init__(*(self, ), **kw)
self.widgetDescr['cutoff'] = {
'class': 'NEDial',
'size': 50,
'oneTurn': 5.0,
'min': 1.0,
'lockMin': 1,
'type': 'float',
'initialValue': 7.5,
'labelGridCfg': {
'sticky': 'w'
},
'labelCfg': {
'text': 'cutoff'
},
}
ip = self.inputPortsDescr
ip.append(datatype='MoleculeSet', name='mols')
ip.append(datatype='float',
required=False,
name='cutoff',
defaultValue=7.5)
op = self.outputPortsDescr
op.append(datatype='MoleculeSet', name='mols')
op.append(datatype='int', name='num_aromaticCs')
code = """def doit(self, mols, cutoff):
if mols:
aromC_manager = AromaticCarbonManager(cutoff=cutoff)
num_aromCs = 0
for mol in mols:
if not len(mol.allAtoms.bonds[0]):
mol.buildBondsByDistance()
aromCs = aromC_manager.setAromaticCarbons(mol, cutoff=cutoff)
num_aromCs+=len(aromCs)
self.outputData(mols=mols, num_aromaticCs=num_aromCs)\n"""
self.setFunction(code)
def __init__(self, name='AD4_SolvationParameterizer', **kw):
kw['name'] = name
NetworkNode.__init__(*(self, ), **kw)
ip = self.inputPortsDescr
ip.append(datatype='MoleculeSet', name='mols')
op = self.outputPortsDescr
op.append(datatype='MoleculeSet', name='typed_mols')
op.append(datatype='list', name='AtSolPar')
code = """def doit(self,mols):
if mols:
SP = SolvationParameterizer()
for mol in mols:
unknown_atoms = SP.addParameters(mol.chains.residues.atoms)
#?keep information about unknown_atoms?
if unknown_atoms is not None: mol.unknown_atoms = len(unknown_atoms)
self.outputData(typed_mols=mols, AtSolPar=mols.allAtoms.AtSolPar)\n"""
self.setFunction(code)
def __init__(self, name='Manage Rotatable Bonds', **kw):
kw['name'] = name
NetworkNode.__init__(*(self, ), **kw)
ip = self.inputPortsDescr
ip.append(datatype='MoleculeSet', name='mols', defaultValue='auto')
ip.append(datatype='string', required=False, name='root')
ip.append(datatype='string',
required=False,
name='allowed_bonds',
defaultValue='backbone')
ip.append(datatype='int',
required=False,
name='check_for_fragments',
defaultValue=0)
ip.append(datatype='string',
required=False,
name='bonds_to_inactivate',
defaultValue='')
ip.append(datatype='string',
required=False,
name='limit_torsions',
defaultValue='')
op = self.outputPortsDescr
op.append(datatype='MoleculeSet', name='mols')
code = """def doit(self, mols, root, allowed_bonds, check_for_fragments,
bonds_to_inactivate, limit_torsions):
if mols:
#mol = mols[0]
for mol in mols:
if not len(mol.allAtoms.bonds[0]):
mol.buildBondsByDistance()
print "root=", root
mol.RBM = RotatableBondManager(mol, allowed_bonds, root,
check_for_fragments=check_for_fragments,
bonds_to_inactivate=bonds_to_inactivate)
if limit_torsions:
mol.RBM.limit_torsions(limit_torsions)
self.outputData(mols=mols)\n"""
self.setFunction(code)
def __init__(self, name='DPFTemplateBrowser', **kw):
kw['name'] = name
NetworkNode.__init__(*(self, ), **kw)
kw['name'] = name
NetworkNode.__init__(*(self, ), **kw)
ip = self.inputPortsDescr
ip.append(datatype='string', name='dpf_template_file')
filetypes = [('All supported files', '*.dpf')]
self.widgetDescr['dpf_template_file'] = {
'class': 'NEEntryWithFileBrowser',
'master': 'node',
'width': 20,
'filetypes': filetypes,
'initialValue': '',
'labelCfg': {
'text': 'DPF template file: '
}
}
op = self.outputPortsDescr
op.append(datatype='dpf_template', name='dpf_template')
code = """def doit(self, dpf_template_file):
import os
from AutoDockTools.VisionInterface.Adt.dpf_template import dpf_template
dpf_template_file = os.path.abspath(dpf_template_file)
if not(os.path.exists(dpf_template_file)):
print "ERROR: DPF template file " + dpf_template_file + " does not exist!"
return 'stop'
dpf_template = dpf_template(dpf_template_file)
self.outputData(dpf_template=dpf_template)
"""
self.setFunction(code)
def __init__(self, name='Prepare Autodock3 Dpf', **kw):
kw['name'] = name
NetworkNode.__init__(*(self, ), **kw)
ip = self.inputPortsDescr
ip.append(datatype='string', name='ligand_filename')
ip.append(datatype='string', name='receptor_filename')
ip.append(datatype='string',
required=False,
name='dpf_filename',
defaultValue='')
ip.append(datatype='dict',
required=False,
name='parameters',
defaultValue={})
ip.append(datatype='string',
required=False,
name='outputfilename',
defaultValue='')
op = self.outputPortsDescr
op.append(datatype='string', name='ad3_parameter_file')
code = """def doit(self, ligand_filename, receptor_filename, dpf_filename, parameters, outputfilename):
if ligand_filename and receptor_filename:
from AutoDockTools.DockingParameters import DockingParameterFileMaker
dpfm = DockingParameterFileMaker()
dpfm.set_ligand(ligand_filename)
dpfm.set_receptor(receptor_filename)
if dpf_filename:
dpfm.read_reference(dpf_filename)
if len(parameters):
dpfm.set_docking_parameters(parameters)
if not outputfilename:
outputfilename = dpfm.ligand.name+'_'+dpfm.receptor_stem + ".dpf"
dpfm.write_dpf(outputfilename)
self.outputData(ad3_parameter_file=outputfilename)\n"""
self.setFunction(code)
def __init__(self, name='Prepare Autogrid4 Gpf', **kw):
kw['name'] = name
NetworkNode.__init__(*(self, ), **kw)
ip = self.inputPortsDescr
ip.append(datatype='string', name='ligand_filename')
ip.append(datatype='string', name='receptor_filename')
ip.append(datatype='string',
required=False,
name='gpf_filename',
defaultValue='')
ip.append(datatype='dict',
required=False,
name='parameters',
defaultValue={})
ip.append(datatype='string',
required=False,
name='outputfilename',
defaultValue='')
op = self.outputPortsDescr
op.append(datatype='string', name='ag4_parameter_file')
code = """def doit(self, ligand_filename, receptor_filename, gpf_filename, parameters, outputfilename):
if ligand_filename and receptor_filename:
from AutoDockTools.GridParameters import GridParameter4FileMaker
gpfm = GridParameter4FileMaker()
gpfm.set_ligand(ligand_filename)
gpfm.set_receptor(receptor_filename)
if gpf_filename:
gpfm.read_reference(gpf_filename)
if len(parameters):
gpfm.set_grid_parameters(parameters)
if not outputfilename:
outputfilename = gpfm.ligand.name+'_'+gpfm.receptor_stem + ".gpf"
gpfm.write_gpf(outputfilename)
self.outputData(ag4_parameter_file=outputfilename)\n"""
self.setFunction(code)
def __init__(self, constrkw = {}, name='ADTFileNames', **kw):
kw['constrkw'] = constrkw
kw['name'] = name
NetworkNode.__init__(*(self,), **kw)
ip = self.inputPortsDescr
ip.append({'name': 'recpetor_obj', 'datatype': 'receptor'})
op = self.outputPortsDescr
op.append({'name': 'GPF_template', 'datatype': 'gpf_template'})
op.append({'name': 'DPF_template', 'datatype': 'dpf_template'})
op.append({'name': 'result_dir', 'datatype': 'string'})
code = """def doit(self, receptor_obj):
import os
from AutoDockTools.VisionInterface.Adt.receptor import receptor
from AutoDockTools.VisionInterface.Adt.dpf_template import dpf_template
from AutoDockTools.VisionInterface.Adt.gpf_template import gpf_template
receptor_id = receptor_obj.get_id()
receptor_dir = receptor_obj.get_workdir()
GPF_template = gpf_template(receptor_dir + os.sep + receptor_id + '.gpf')
DPF_template = dpf_template(receptor_dir + os.sep + receptor_id + '.dpf')
result_dir = os.path.abspath(receptor_dir + os.sep + '..' + os.sep + receptor_id)
print "-------------------------------------------------------"
print " INPUTS THAT WILL BE USED FOR VIRTUAL SCREENING "
print "GPF Template: " + GPF_template.fullpath
print "DPF Template: " + DPF_template.fullpath
print "Results will be downloaded to: " + result_dir
print "-------------------------------------------------------"
pass
self.outputData(GPF_template=GPF_template, DPF_template=DPF_template, result_dir=result_dir)
"""
self.configure(function=code)
def __init__(self, name='Ligand_Writer', **kw):
kw['name'] = name
NetworkNode.__init__(*(self, ), **kw)
fileTypes = [('pdbq', '*.pdbq'), ('all', '*')]
self.widgetDescr['output_filename'] = {
'class': 'NEEntryWithFileSaver',
'master': 'node',
'filetypes': fileTypes,
'title': 'save AD3 Ligand',
'width': 10,
'labelCfg': {
'text': 'file:'
},
}
ip = self.inputPortsDescr
ip.append(datatype='Molecule', name='mol')
ip.append(datatype='string', name='output_filename')
op = self.outputPortsDescr
op.append(datatype='Molecule', name='mol')
code = """def doit(self, mol, output_filename):
if mol:
#mol = mols[0]
#check for bonds with 'possibleTors/activeTOrs keys'
#check for root
#check for TORSDOF
#check for charges
writer = LigandWriter()
writer.write(mol, output_filename)
self.outputData(mol=mol)\n"""
self.setFunction(code)
def __init__(self, name='MakeDPFCopies', **kw):
kw['name'] = name
NetworkNode.__init__(*(self, ), **kw)
kw['name'] = name
NetworkNode.__init__(*(self, ), **kw)
ip = self.inputPortsDescr
ip.append(datatype='gpf_template', name='gpf_file', required=False)
ip.append(datatype='dpf_template', name='dpf_file', required=False)
ip.append(datatype='string', name='struct_dir', required=True)
op = self.outputPortsDescr
op.append(datatype='list', name='gpf_list')
op.append(datatype='list', name='dpf_list')
op.append(datatype='string', name='struct_dir')
code = """def doit(self, gpf_file, dpf_file, struct_dir):
import os
import shutil
from AutoDockTools.VisionInterface.Adt.dpf_template import dpf_template
from AutoDockTools.VisionInterface.Adt.gpf_template import gpf_template
if dpf_file == None and gpf_file == None:
print "ERROR: DPF and GPF input missing"
return 'stop'
if dpf_file != None:
dpf_file_path = dpf_file.fullpath
if not(os.path.exists(dpf_file_path)):
print "ERROR: DPF template file " + dpf_file_path + " does not exist!"
return 'stop'
if gpf_file != None:
gpf_file_path = gpf_file.fullpath
if not(os.path.exists(gpf_file_path)):
print "ERROR: GPF template file " + gpf_file_path + " does not exist!"
return 'stop'
name_list = set()
d = os.path.abspath(struct_dir)
for i in os.listdir(struct_dir):
if i.endswith(".pdbqt") or i.endswith(".pdb") or i.endswith(".pqr"):
name_list.add(i.split('.')[0])
dpf_list = []
gpf_list = []
if dpf_file != None:
for i in name_list:
d_dst = os.path.join(d, i + '.dpf')
dpf_list.append(d_dst)
if not(os.path.exists(d_dst)):
shutil.copyfile(dpf_file_path, d_dst)
if gpf_file != None:
for i in name_list:
g_dst = os.path.join(d, i + '.gpf')
gpf_list.append(g_dst)
if not(os.path.exists(g_dst)):
shutil.copyfile(gpf_file_path, g_dst)
self.outputData(dpf_list=dpf_list, gpf_list=gpf_list, struct_dir=struct_dir)
"""
self.setFunction(code)
def __init__(self, constrkw={}, name='GetStructuresFromDir', **kw):
kw['constrkw'] = constrkw
kw['name'] = name
NetworkNode.__init__(*(self, ), **kw)
ip = self.inputPortsDescr
ip.append({'name': 'directory', 'datatype': 'string'})
self.widgetDescr['directory'] = {
'class': 'NEEntryWithDirectoryBrowser',
'master': 'node',
'width': 20,
'initialValue': '',
'labelCfg': {
'text': 'Structure Directory: '
}
}
op = self.outputPortsDescr
op.append({'name': 'structure_list_obj', 'datatype': 'list'})
# op = self.outputPortsDescr
# op.append({'name': 'structure_list', 'datatype': 'list'})
code = """def doit(self, directory):
import glob, os
from AutoDockTools.VisionInterface.Adt.receptor import receptor
directory = os.path.abspath(directory)
if directory == None:
return 'stop'
if directory is not None:
cwd = os.getcwd()
os.chdir(directory)
try:
filenames_pdbqt = glob.glob('*.pdbqt')
filenames_pqr = glob.glob('*.pqr')
filenames_pdb = glob.glob('*.pdb')
structure_list = filenames_pdbqt
for f in filenames_pqr:
sid = f.rstrip('.pqr')
s = sid + '.pdbqt'
found = False
for i in structure_list:
if i == s:
found = True
break
if found == False:
structure_list.append(f)
for f in filenames_pdb:
sid = f.rstrip('.pdb')
found = False
for i in structure_list:
if i == sid + '.pdb' or i == sid + '.pdbqt':
found = True
break
if found == False:
structure_list.append(f)
structure_list = [os.path.join(directory, x) for x in filenames_pdbqt]
structure_list_obj = [receptor(x) for x in structure_list]
finally:
if directory is not None:
os.chdir(cwd)
print "--------------------------------------------------------------"
print "The following structures are found in the structure directory:"
count = 0
for i in structure_list:
count = count + 1
print str(count) + '. ' + i
print "--------------------------------------------------------------"
pass
# self.outputData(structure_list_obj=structure_list_obj, structure_list=structure_list)
self.outputData(structure_list_obj=structure_list_obj)
"""
self.configure(function=code)
def __init__(self, name='PublicServerLigandDB', **kw):
import urllib.request, urllib.parse, urllib.error
kw['name'] = name
NetworkNode.__init__(*(self, ), **kw)
kw['name'] = name
NetworkNode.__init__(*(self, ), **kw)
ip = self.inputPortsDescr
ip.append(
datatype='string',
name='server_lib',
required=True,
)
fqdn = "kryptonite.nbcr.net"
url = "http://" + fqdn + "/pub_ligand_libs.txt"
publibdir = os.path.join(getResourceFolderWithVersion(), 'ws')
if not (os.path.exists(publibdir)):
os.mkdir(publibdir)
publiblocal = os.path.join(publibdir, 'publibs.txt')
lock = publiblocal + '.lock'
if os.path.exists(lock) and time.time() - os.path.getmtime(lock) > 15:
os.remove(lock)
try:
if not (os.path.exists(lock)):
open(lock, 'w').close()
publibweb = urllib.request.urlopen(url)
outfile = open(publiblocal, 'w')
outfile.write(publibweb.read())
outfile.close()
os.remove(lock)
except:
print("[INFO]: Getting list of public server libs from cache")
pass
try:
f = open(publiblocal, 'r')
self.choices = f.read().split()
f.close()
except:
self.choices = []
print(
"[ERROR]: Unable to public server libs from the web and from cache"
)
self.widgetDescr['server_lib'] = {
'class': 'NEComboBox',
'master': 'node',
'choices': self.choices,
'fixedChoices': True,
'entryfield_entry_width': 18,
'labelGridCfg': {
'sticky': 'w'
},
'widgetGridCfg': {
'sticky': 'w'
},
'labelCfg': {
'text': 'Server Libraries:'
}
}
op = self.outputPortsDescr
op.append(datatype='LigandDB', name='ligDB')
code = """def doit(self, server_lib):
ligDB = LigandDB(server_lib=server_lib)
self.outputData(ligDB=ligDB)
"""
self.setFunction(code)
def __init__(self, constrkw={}, name='ReadDockingParameterFile', **kw):
kw['constrkw'] = constrkw
kw['name'] = name
NetworkNode.__init__(*(self, ), **kw)
fileTypes = [('dpf', '*')]
self.widgetDescr['filename'] = {
'class': 'NEEntryWithFileBrowser',
'master': 'node',
'filetypes': fileTypes,
'title': 'read file',
'width': 16,
'labelCfg': {
'text': 'file:'
},
}
code = """def doit(self, template_dpf_filename):
if template_dpf_filename:
from AutoDockTools.DockingParameters import DockingParameters
gpo = DockingParameters()
gpo.read(template_dpf_filename)
self.outputData(gpo=gpo)
"""
self.configure(function=code)
self.inputPortsDescr.append({
'name': 'template_dpf_filename',
'cast': True,
'datatype': 'string',
'balloon': 'template grid parameter filename',
'required': False,
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
self.outputPortsDescr.append({
'name': 'gpo',
'datatype': 'None',
'balloon':
'gpo, grid parameter object, instance of AutoDockTools.DockingParameters',
'height': 8,
'width': 12,
'shape': 'diamond',
'color': 'white'
})
self.widgetDescr['template_dpf_filename'] = {
'initialValue': '',
'labelGridCfg': {
'column': 0,
'row': 0
},
'master': 'node',
'widgetGridCfg': {
'labelSide': 'left',
'column': 1,
'row': 0
},
'labelCfg': {
'text': ''
},
'class': 'NEEntryWithFileBrowser'
}
def __init__(self, name='filterLigands', **kw):
kw['name'] = name
NetworkNode.__init__(*(self, ), **kw)
# create filter object
lfilter = self.lfilter = FilterLigands()
lfilter.setFilter('default')
ip = self.inputPortsDescr
ip.append(datatype='LigandDB', name='ligands')
ip.append(datatype='string', name='filterMode')
self.widgetDescr['filterMode'] = {
'class':
'NEComboBox',
'master':
'node',
'choices': [
'None', 'default', 'Lipinski-like', 'Drug-like',
'Drug-like frag', 'Custom'
],
'fixedChoices':
True,
'initialValue':
'default',
'entryfield_entry_width':
8,
'labelGridCfg': {
'sticky': 'w'
},
'widgetGridCfg': {
'sticky': 'w'
},
'labelCfg': {
'text': 'filter type:'
}
}
labels = [
'Min num. of h-bond donors:', 'Max num. of h-bond donors:',
'Min num. of h-bond acceptors', 'Max num. of h-bond acceptors',
'Min molecular weight', 'Max molecular weight',
'Min num. of heavy atoms', 'Max num. of heavy atoms',
'Min num. of rotatable bonds', 'Max num. of rotatable bonds'
]
for i, param in enumerate([
'hbd_min', 'hbd_max', 'hba_min', 'hba_max', 'mw_min', 'mw_max',
'nat_min', 'nat_max', 'torsdof_min', 'torsdof_max'
]):
ip.append(datatype='int', name=param)
value = getattr(lfilter, self.attr[i])
self.widgetDescr[param] = {
'class': 'NEThumbWheel',
'master': 'ParamPanel',
'width': 75,
'height': 12,
'oneTurn': 10,
'type': 'int',
'wheelPad': 0,
'initialValue': value,
'min': 0,
'labelCfg': {
'text': labels[i]
}
}
op = self.outputPortsDescr
op.append(datatype='LigandDB', name='ligands')
op.append(datatype='int', name='num_accepted')
op.append(datatype='int', name='num_rejected')
code = """def doit(self, ligands, filterMode='default', hbd_min=None, hbd_max=None, hba_min=None, hba_max=None, mw_min=None, mw_max=None, nat_min=None, nat_max=None, torsdof_min=None, torsdof_max=None):
lfilter = self.lfilter
if filterMode != "Custom":
lfilter.setFilter(filterMode)
else:
kwargs = {"HbDMin": hbd_min,
"HbDMax": hbd_max,
"HbAMin": hba_min,
"HbAMax": hba_max,
"MWMin": mw_min,
"MWMax": mw_max,
"NatMin": nat_min,
"NatMax": nat_max,
"TORSDOFMin": torsdof_min,
"TORSDOFMax": torsdof_max}
lfilter.setFilterRanges('Custom', **kwargs)
if self.inputPorts[1].hasNewValidData(): # new mode -> update widgets
self.setParamPanelWidget(lfilter)
print "Running Filter node with parameters:"
print "min number of hydrogen bond donors: " + str(lfilter.HbDMin)
print "max number of hydrogen bond donors: " + str(lfilter.HbDMax)
print "min number of hydrogen bond acceptors: " + str(lfilter.HbAMin)
print "max number of hydrogen bond acceptors: " + str(lfilter.HbAMax)
print "min molecular weight: " + str(lfilter.MWMin)
print "max molecular weight: " + str(lfilter.MWMax)
print "min number of heavy atoms: " + str(lfilter.NatMin)
print "max number of heavy atoms: " + str(lfilter.NatMax)
print "min number of rotatable bonds: " + str(lfilter.TORSDOFMin)
print "max number of rotatable bonds: " + str(lfilter.TORSDOFMax)
# accepted, rejected = lfilter.filterTable(ligands.propertyTable)
accepted, rejected = lfilter.filterTable(ligands.propertyTable, ligands.accepted)
ligands.SetAcceptedLigands(accepted.filenames)
if len(accepted.filenames) > 2500:
print "ERROR: Sorry, we cannot send your virtual screening job to the server because the number of accepted ligands from the filter is greater than the maximum number of ligands (2500) the server can support"
return 'stop'
self.outputData(ligands=ligands, num_accepted = len(accepted.filenames), num_rejected=len(rejected))
"""
self.setFunction(code)
