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Acedrg draw dative in report #18

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Acedrg draw dative in report #18

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8f9c8aa
Fix drawing of OEX.
stuartjamesmcnicholas Nov 28, 2024
c012eec
Remove print
stuartjamesmcnicholas Nov 28, 2024
e7d97ab
Fix bond orders of some pictures/smiles in reports.
stuartjamesmcnicholas Nov 28, 2024
e6234f9
OEX appears to draw OK now as well.
stuartjamesmcnicholas Nov 29, 2024
dcb1ef5
More flexibility with cif atom/bond tags.
stuartjamesmcnicholas Dec 11, 2024
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24 changes: 19 additions & 5 deletions wrappers/acedrgNew/script/acedrgNew.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@
import math
from core import CCP4Modules,CCP4Utils
from . import atomMatching, cifToMolBlock, mol2svg
from .setDativeBonds import set_dative_bonds
import platform
from rdkit.Chem.Draw import rdMolDraw2D
from rdkit import Chem
Expand Down Expand Up @@ -92,16 +93,13 @@ def processInputFiles(self):

if self.container.inputData.MOLORSMILES.__str__() == 'DICT' or try_mmCIF == True:
self.originalMolFilePath = os.path.normpath(os.path.join(self.getWorkDirectory(),'MOLIN.mol'))
print(self.originalMolFilePath)
try:
if self.container.inputData.DICTIN2.isSet():
molBlock = cifToMolBlock.cifFileToMolBlock(self.container.inputData.DICTIN2.__str__())
elif self.container.inputData.PDBMMCIFIN.isSet() and try_mmCIF:
molBlock = cifToMolBlock.cifFileToMolBlock(self.container.inputData.PDBMMCIFIN.__str__())
else:
pass # should not happen
print("molBlock:")
print(molBlock)
with open(self.originalMolFilePath,'w') as molinFile:
molinFile.write(molBlock)
except:
Expand All @@ -114,8 +112,14 @@ def processInputFiles(self):
try:
if self.container.inputData.MOL2IN.isSet():
mol = Chem.MolFromMol2File(self.originalMolFilePath)
if not mol:
mol = Chem.MolFromMol2File(self.originalMolFilePath, sanitize=False)
mol = set_dative_bonds(mol)
else:
mol = Chem.MolFromMolFile(self.originalMolFilePath)
if not mol:
mol = Chem.MolFromMolFile(self.originalMolFilePath, sanitize=False)
mol = set_dative_bonds(mol)
for iAtom in range(mol.GetNumAtoms()):
atom = mol.GetAtomWithIdx(iAtom)
atom.ClearProp('molAtomMapNumber')
Expand Down Expand Up @@ -307,16 +311,26 @@ def processOutputFiles(self):
# chirality information
referenceMol = None
referenceMolToDraw = None
doSanitize = True
if self.container.inputData.MOL2IN.isSet():
referenceMol = Chem.MolFromMol2File(self.originalMolFilePath)
referenceMolToDraw = Chem.MolFromMol2File(self.originalMolFilePath)
if not referenceMol:
referenceMol = Chem.RemoveHs(Chem.MolFromMol2File(self.originalMolFilePath, sanitize=False), sanitize=False)
referenceMolToDraw = Chem.RemoveHs(Chem.MolFromMol2File(self.originalMolFilePath, sanitize=False), sanitize=False)
doSanitize = False
else:
referenceMol = Chem.MolFromMolFile(self.originalMolFilePath)
referenceMolToDraw = Chem.MolFromMolFile(self.originalMolFilePath)
if not referenceMol:
referenceMol = Chem.RemoveHs(Chem.MolFromMolFile(self.originalMolFilePath, sanitize=False), sanitize=False)
referenceMolToDraw = Chem.RemoveHs(Chem.MolFromMolFile(self.originalMolFilePath, sanitize=False), sanitize=False)
doSanitize = False

try:
Chem.SanitizeMol(referenceMol)
Chem.Kekulize(referenceMol)
if doSanitize:
Chem.SanitizeMol(referenceMol)
Chem.Kekulize(referenceMol)
molToWrite = referenceMol
# Output a MOL file
molBlock = Chem.MolToMolBlock(molToWrite)
Expand Down
67 changes: 60 additions & 7 deletions wrappers/acedrgNew/script/cifToMolBlock.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,13 @@ def cifFileToMolBlock(input_file):

searches_SMILES = ["_pdbx_chem_comp_descriptor.type","_pdbx_chem_comp_descriptor.descriptor"]

bond_searches = ["_chem_comp_atom.comp_id",
"_chem_comp_bond.atom_id_1",
"_chem_comp_bond.atom_id_2",
"_chem_comp_bond.value_order"
"_chem_comp_bond.type"
]

searches = ["_chem_comp_atom.comp_id",
"_chem_comp_atom.atom_id",
"_chem_comp_atom.type_symbol",
Expand All @@ -27,6 +34,7 @@ def cifFileToMolBlock(input_file):
"_chem_comp_atom.model_Cartn_z" ]

atom_dict = {}
bond_dict = {}
found_molecule = False
found_SMILES = False

Expand Down Expand Up @@ -57,12 +65,13 @@ def cifFileToMolBlock(input_file):
print("Not successful Chem.MolFromSmiles(ss) for ss =", ss)
try:
mol = Chem.MolFromSmiles(ss, sanitize=False)
mol = set_dative_bonds(mol)
#mol = set_dative_bonds(mol)
print("Success with",ss)
except:
print("Not successful try Chem.MolFromSmiles(ss, sanitize=False) or set_dative_bonds(mol) for ss =", ss)
print("Not successful try Chem.MolFromSmiles(ss, sanitize=False) for ss =", ss)
continue
if not mol:
print("Not successful Chem.MolFromSmiles(ss, sanitize=False) or set_dative_bonds(mol) for ss =", ss)
print("Not successful Chem.MolFromSmiles(ss, sanitize=False) for ss =", ss)
continue
if mol:
try:
Expand All @@ -71,17 +80,17 @@ def cifFileToMolBlock(input_file):
molBlock = Chem.MolToMolBlock(mol, includeStereo=True, forceV3000=False)
return molBlock
except:
print("Not successful try set_dative_bonds(mol) for ", ss)
print("Not successful for ", ss)
continue
else: # invalid SMILES
print("Not successful set_dative_bonds(mol) for", ss)
print("Not successful for", ss)
continue

#If no SMILES string, we hope there is at least one molecule, either in PDB or acedrg chem_comp format.
try:
for block in doc:
if found_molecule:
break # We only tke the first molecule.
break # We only take the first molecule.
for search in searches:
i = 0
for thing in block.find_loop(search):
Expand All @@ -91,11 +100,19 @@ def cifFileToMolBlock(input_file):
atom_dict[i] = {}
atom_dict[i][search] = thing
i += 1
for search in bond_searches:
i = 0
for thing in block.find_loop(search):
if not i in bond_dict:
bond_dict[i] = {}
bond_dict[i][search] = thing
i += 1
except Exception as e:
print("Oops. %s" % e)
return ""

atom_list = list(atom_dict.values())
bond_list = list(bond_dict.values())

if len(atom_list) > 0:
s = gemmi.Structure()
Expand All @@ -109,7 +126,8 @@ def cifFileToMolBlock(input_file):
a = gemmi.Atom()
a.name = atom['_chem_comp_atom.atom_id']
a.element = gemmi.Element(atom['_chem_comp_atom.type_symbol'])
a.charge = int(float(atom['_chem_comp_atom.charge']))
if '_chem_comp_atom.charge' in atom:
a.charge = int(float(atom['_chem_comp_atom.charge']))
if '_chem_comp_atom.x' in atom:
pos = gemmi.Position(float(atom['_chem_comp_atom.x']),float(atom['_chem_comp_atom.y']),float(atom['_chem_comp_atom.z']))
elif '_chem_comp_atom.model_Cartn_x' in atom:
Expand All @@ -121,6 +139,41 @@ def cifFileToMolBlock(input_file):
s.add_model(m)
s.write_pdb(output_file)
mol = Chem.MolFromPDBFile(output_file)
for b in mol.GetBonds():
at1 = atom_list[b.GetBeginAtomIdx()]['_chem_comp_atom.atom_id']
at2 = atom_list[b.GetEndAtomIdx()]['_chem_comp_atom.atom_id']
for b2 in bond_list:
if '_chem_comp_bond.atom_id_1' in b2 and '_chem_comp_bond.atom_id_2' in b2:
if (b2['_chem_comp_bond.atom_id_1'] == at1 and b2['_chem_comp_bond.atom_id_2'] == at2) or (b2['_chem_comp_bond.atom_id_1'] == at2 and b2['_chem_comp_bond.atom_id_2'] == at1):
if "_chem_comp_bond.value_order" in b2:
orderString = "_chem_comp_bond.value_order"
elif "_chem_comp_bond.type" in b2:
orderString = "_chem_comp_bond.type"
else:
continue
if b2[orderString].upper()[0:4] == "AROM":
b.SetBondType(Chem.BondType.AROMATIC)
elif b2[orderString].upper()[0:4] == "SING":
b.SetBondType(Chem.BondType.SINGLE)
elif b2[orderString].upper()[0:4] == "DOUB":
b.SetBondType(Chem.BondType.DOUBLE)
elif b2[orderString].upper()[0:4] == "TRIP":
b.SetBondType(Chem.BondType.TRIPLE)
elif b2[orderString].upper()[0:4] == "QUAD":
b.SetBondType(Chem.BondType.QUADRUPLE)
elif b2[orderString].upper()[0:4] == "QUIN":
b.SetBondType(Chem.BondType.QUINTUPLE)
elif b2[orderString].upper()[0:3] == "HEX":
b.SetBondType(Chem.BondType.HEXTUPLE)
elif b2[orderString].upper() == "DATIVE":
b.SetBondType(Chem.BondType.DATIVE)
elif b2[orderString].upper() == "DATIVEL":
b.SetBondType(Chem.BondType.DATIVEL)
elif b2[orderString].upper() == "DATIVER":
b.SetBondType(Chem.BondType.DATIVER)
elif b2[orderString].upper() == "DATIVEONE":
b.SetBondType(Chem.BondType.DATIVEONE)
print("Match!",b.GetBondType(),b2[orderString])
AllChem.Compute2DCoords(mol)
mol.SetProp("_MolFileChiralFlag","1")
molBlock = Chem.MolToMolBlock(mol, includeStereo=True, forceV3000=False)
Expand Down