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acedrg --metalPDB= option visible and used only if input CIF dictionary is provided (not in case of other input formats) #127

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acedrg --metalPDB= option visible and used only if input CIF dictionary is provided (not in case of other input formats) #127

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acedrg --metalPDB= option visible and used only if input dictionary i…
MartinMalyMM Feb 27, 2026
a22f510
delete duplicate lines
MartinMalyMM Feb 27, 2026
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4 changes: 2 additions & 2 deletions pipelines/LidiaAcedrgNew/script/lidiaAcedrgNew.py
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Original file line number Diff line number Diff line change
Expand Up @@ -91,6 +91,8 @@ def doAcedrg(self, inputType, inputObject):
acedrgPlugin.container.inputData.SMILESIN = inputObject
elif inputType == 'DICT':
acedrgPlugin.container.inputData.DICTIN2 = inputObject
if self.container.controlParameters.TOGGLE_METAL:
acedrgPlugin.container.inputData.METAL_STRUCTURE = self.container.inputData.METAL_STRUCTURE
try:
acedrgPlugin.container.inputData.TLC.set(self.container.inputData.TLC)
acedrgPlugin.container.controlParameters.NOPROT.set(self.container.controlParameters.NOPROT)
Expand All @@ -99,8 +101,6 @@ def doAcedrg(self, inputType, inputObject):
acedrgPlugin.container.inputData.NRANDOM.set(self.container.inputData.NRANDOM)
else:
acedrgPlugin.container.inputData.NRANDOM.set(0)
if self.container.controlParameters.TOGGLE_METAL:
acedrgPlugin.container.inputData.METAL_STRUCTURE = self.container.inputData.METAL_STRUCTURE
except:
exc_type, exc_value,exc_tb = sys.exc_info()[:3]
sys.stdout.write(str(exc_type)+'\n')
Expand Down
11 changes: 6 additions & 5 deletions pipelines/LidiaAcedrgNew/script/lidiaAcedrgNew_gui.py
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Expand Up @@ -33,6 +33,7 @@ def drawContents(self):
self.createLine(['subtitle','Start point'])
self.openSubFrame( frame=[True])
self.createLine ( [ 'label','Start with molecular structure from ','stretch','widget','MOLSMILESORSKETCH' ] )
self.connectDataChanged('MOLSMILESORSKETCH', self.ToggleShowContainsMetal)

self.createLine ( [ 'advice', 'Will launch Lidia to sketch molecule. Click Apply <b>and</b> Close in Lidia when sketch is ready.' ], toggle=['MOLSMILESORSKETCH','open',['SKETCH']])
self.createLine ( [ 'advice', 'Optionally can provide a starting monomer for the Lidia sketch:' ], toggle=['MOLSMILESORSKETCH','open',['SKETCH']])
Expand All @@ -44,10 +45,10 @@ def drawContents(self):
self.createLine ( [ 'label', 'SMILES file', 'widget', 'SMILESFILEIN' ] , toggle=['MOLSMILESORSKETCH','open',['SMILESFILE']])
self.createLine ( [ 'widget', 'DICTIN2' ] , toggle=['MOLSMILESORSKETCH','open',['DICT']])
self.connectDataChanged('DICTIN2', self.updateTLC)
self.createLine ( [ 'widget', 'TOGGLE_METAL', 'label' , 'This monomer contains a metal atom.' ] )
self.createLine ( [ 'widget', 'TOGGLE_METAL', 'label' , 'This monomer contains a metal atom.' ], toggle=['MOLSMILESORSKETCH','open',['DICT']])
self.connectDataChanged('controlParameters.TOGGLE_METAL', self.ToggleShowContainsMetal)
self.createLine ( [ 'label', indent + 'Provide a relevant structure model in complex with this monomer to get ideal bond angles in the output:'] , toggleFunction=[self.ToggleShowContainsMetal, ['controlParameters.TOGGLE_METAL']])
self.createLine ( [ 'label', indent, 'widget', 'METAL_STRUCTURE'] , toggleFunction=[self.ToggleShowContainsMetal, ['controlParameters.TOGGLE_METAL']])
self.createLine ( [ 'label', indent + 'Provide a relevant structure model in complex with this monomer to get ideal bond angles in the output:'] , toggleFunction=[self.ToggleShowContainsMetal, ['inputData.MOLSMILESORSKETCH', 'controlParameters.TOGGLE_METAL']])
self.createLine ( [ 'label', indent, 'widget', 'METAL_STRUCTURE'] , toggleFunction=[self.ToggleShowContainsMetal, ['inputData.MOLSMILESORSKETCH', 'controlParameters.TOGGLE_METAL']])
self.closeSubFrame()

self.createLine(['subtitle', 'Output monomer'])
Expand Down Expand Up @@ -106,12 +107,12 @@ def updateTLC(self):
pass

def ToggleShowContainsMetal(self, fromUpdateTLC=False):
if self.container.inputData.MOLSMILESORSKETCH != 'DICT':
return False
if self.container.controlParameters.TOGGLE_METAL and not fromUpdateTLC:
return True
if not self.container.controlParameters.TOGGLE_METAL and not fromUpdateTLC:
return False
if self.container.inputData.MOLSMILESORSKETCH != 'DICT':
return False
if not self.container.inputData.DICTIN2.isSet():
return False
if not os.path.isfile(str(self.container.inputData.DICTIN2.fullPath)):
Expand Down
46 changes: 14 additions & 32 deletions test/i2run/test_acedrg.py
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Original file line number Diff line number Diff line change
Expand Up @@ -91,40 +91,22 @@ def test_from_smiles_atom_name_matching():
check_output(job, "LIG")


def test_from_cif_rcsb_metal_OEX():
with download(rcsb_ligand_cif("AF3")) as cifOEX, download(rcsb_mmcif("4ub6")) as cif4ub6:
args = ["LidiaAcedrgNew"]
args += ["--MOLSMILESORSKETCH", "DICT"]
args += ["--TLC", "OEX"]
args += ["--DICTIN2", cifOEX]
args += ["--TOGGLE_METAL", "True"]
args += ["--METAL_STRUCTURE", cif4ub6]
with i2run(args) as job:
check_output(job, "OEX")


def check_output(job: Path, code: str):
doc = gemmi.cif.read(str(job / f"{code}.cif"))
if len(code) <= 3:
gemmi.read_pdb(str(job / f"{code}.pdb"))
doc = gemmi.cif.read(str(job / f"{code}.cif"))
comp = gemmi.make_chemcomp_from_block(doc[-1])
for atom in comp.atoms:
assert " " not in atom.id


# These tests crashes as acedrg or metalCoord crash themselves, not an i2 problem.

# @fixture(name="cif4ub6", scope="module")
# def cif4ub6_fixture():
# with download(rcsb_mmcif("4ub6")) as path:
# yield path

# def test_from_cif_rcsb_metal_OEX(cif4ub6):
# with download(rcsb_ligand_cif("OEX")) as cifOEX:
# args = ["LidiaAcedrgNew"]
# args += ["--MOLSMILESORSKETCH", "DICT"]
# args += ["--TLC", "OEX"]
# args += ["--DICTIN2", cifOEX]
# args += ["--TOGGLE_METAL", "True"]
# args += ["--METAL_STRUCTURE", cif4ub6]
# with i2run(args) as job:
# check_output(job, "OEX")

# def test_from_sdf_rcsb_metal_OEX(cif4ub6):
# with download(rcsb_ligand_sdf("OEX")) as sdfOEX:
# args = ["LidiaAcedrgNew"]
# args += ["--MOLSMILESORSKETCH", "MOL"]
# args += ["--TLC", "OEX"]
# args += ["--MOLIN", sdfOEX]
# args += ["--TOGGLE_METAL", "True"]
# args += ["--METAL_STRUCTURE", cif4ub6]
# with i2run(args) as job:
# check_output(job, "OEX")
assert " " not in atom.id
4 changes: 2 additions & 2 deletions wrappers/acedrgNew/script/acedrgNew.py
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Original file line number Diff line number Diff line change
Expand Up @@ -144,14 +144,14 @@ def makeCommandAndScript(self):
if self.container.inputData.DICTIN2.isSet():
self.appendCommandLine('-c')
self.appendCommandLine(str(self.container.inputData.DICTIN2))
if self.container.inputData.METAL_STRUCTURE.isSet():
self.appendCommandLine('--metalPDB=' + str(self.container.inputData.METAL_STRUCTURE))
elif self.container.inputData.MOLIN.isSet():
self.appendCommandLine('-m')
self.appendCommandLine(str(self.container.inputData.MOLIN))
elif self.container.inputData.MOL2IN.isSet():
self.appendCommandLine('-g')
self.appendCommandLine(str(self.container.inputData.MOL2IN))
if self.container.inputData.METAL_STRUCTURE.isSet():
self.appendCommandLine('--metalPDB=' + str(self.container.inputData.METAL_STRUCTURE))
if self.container.controlParameters.NOPROT:
self.appendCommandLine('--noProt')
if self.container.inputData.DICTIN2.isSet() or self.container.inputData.MOLIN.isSet() or self.container.inputData.MOL2IN.isSet():
Expand Down