def __init__(self, mol=None, parent=None):
#Also init the super class
super(MolEditWidget, self).__init__(parent)
#This sets the window to delete itself when its closed, so it doesn't keep querying the model
self.setAttribute(QtCore.Qt.WA_DeleteOnClose)
#Properties
self._prevmol = None #For undo
self.coordlist = None #SVG coords of the current mols atoms
#Standard atom types
self.symboltoint = symboltoint
self.bondtypes = Chem.rdchem.BondType.names #A dictionary with all available rdkit bondtypes
#Default actions
self._action = "Add"
self._bondtype = self.bondtypes["SINGLE"]
self._atomtype = 6
#Points to calculate the SVG to coord scaling
self.points = [Point2D(0, 0), Point2D(1, 1)]
#Bind signals to slots
self.finishedDrawing.connect(
self.update_coordlist
) #When drawing finished, update coordlist of SVG atoms.
#Init with a mol if passed at construction
#if mol != None:
self.mol = mol
def SVG_to_coord(self, x_svg, y_svg):
if self.drawer != None:
scale0 = self.drawer.GetDrawCoords(self.points[0])
scale1 = self.drawer.GetDrawCoords(self.points[1])
ax = scale1.x - scale0.x
bx = scale0.x
ay = scale1.y - scale0.y
by = scale0.y
return Point2D((x_svg - bx) / ax, (y_svg - by) / ay)
else:
return Point2D(0., 0.)
def computeNewCoords(self, ignoreExisting=False):
"""Computes new coordinates for the molecule taking into account all
existing positions (feeding these to the rdkit coordinate generation as
prev_coords).
"""
# This code is buggy when you are not using the CoordGen coordinate
# generation system, so we enable it here
rdDepictor.SetPreferCoordGen(True)
prev_coords = {}
if self._mol.GetNumConformers() == 0:
self.logger.debug("No Conformers found, computing all 2D coords")
elif ignoreExisting:
self.logger.debug("Ignoring existing conformers, computing all "
"2D coords")
else:
assert self._mol.GetNumConformers() == 1
self.logger.debug("1 Conformer found, computing 2D coords not in "
"found conformer")
conf = self._mol.GetConformer(0)
for a in self._mol.GetAtoms():
pos3d = conf.GetAtomPosition(a.GetIdx())
if (pos3d.x, pos3d.y) == (0, 0):
continue
prev_coords[a.GetIdx()] = Point2D(pos3d.x, pos3d.y)
rdDepictor.Compute2DCoords(self._mol, coordMap=prev_coords)
def read(self):
#found randomly online: https://binfalse.de/software/parseable-biodata/amino-acids/
table = r'''Alanine Ala A C3H7NO2 O=C(O)C(N)C nonpolar neutral 1.8 nonessential 6.01 2.35 9.87
Arginine Arg R C6H14N4O2 O=C(O)C(N)CCC/[NH+]=C(\[NH2])[NH2] polar positive −4.5 essential 10.76 1.82 8.99
Asparagine Asn N C4H8N2O3 O=C(N)CC(N)C(=O)O polar neutral −3.5 nonessential 5.41 2.14 8.72
Asparticacid Asp D C4H7NO4 O=C(O)CC(N)C(=O)[O-] polar negative −3.5 nonessential 2.85 1.99 9.90
Cysteine Cys C C3H7NO2S C(C(C(=O)O)N)S nonpolar neutral 2.5 nonessential 5.05 1.92 10.70
Glutamicacid Glu E C5H9NO4 C(CC(=O)[O-])C(C(=O)O)N polar negative −3.5 nonessential 3.15 2.10 9.47
Glutamine Gln Q C5H10N2O3 O=C(N)CCC(N)C(=O)O polar neutral −3.5 nonessential 5.65 2.17 9.13
Glycine Gly G C2H5NO2 C(C(=O)O)N nonpolar neutral −0.4 nonessential 6.06 2.35 9.78
Histidine His H C6H9N3O2 O=C(C(CC1=CNC=N1)N)O polar neutral(90%)−3.2 essential 7.60 1.80 9.33
Isoleucine Ile I C6H13NO2 CC[C@H](C)C(C(=O)O)N nonpolar neutral 4.5 essential 6.05 2.32 9.76
Leucine Leu L C6H13NO2 CC(C)CC(C(=O)O)N nonpolar neutral 3.8 essential 6.01 2.33 9.74
Lysine Lys K C6H14N2O2 C(CC[NH3+])CC(C(=O)O)N polar positive −3.9 essential 9.60 2.16 9.06
Methionine Met M C5H11NO2S CSCCC(C(=O)O)N nonpolar neutral 1.9 essential 5.74 2.13 9.28
Phenylalanine Phe F C9H11NO2 c1ccc(cc1)CC(C(=O)O)N nonpolar neutral 2.8 essential 5.49 2.20 9.31
Proline Pro P C5H9NO2 C1CC(NC1)C(=O)O nonpolar neutral −1.6 nonessential 6.30 1.95 10.64
Serine Ser S C3H7NO3 C(C(C(=O)O)N)O polar neutral −0.8 nonessential 5.68 2.19 9.21
Threonine Thr T C4H9NO3 C[C@H](C(C(=O)O)N)O polar neutral −0.7 essential 2.09 2.09 9.10
Tryptophan Trp W C11H12N2O2 c1ccc2c(c1)c(c[nH]2)CC(C(=O)O)N nonpolar neutral −0.9 essential 5.89 2.46 9.41
Tyrosine Tyr Y C9H11NO3 NC(Cc1ccc(O)cc1)C(O)=O polar neutral −1.3 nonessential 5.64 2.20 9.21
Valine Val V C5H11NO2 CC(C)C(C(=O)O)N nonpolar neutral 4.2 essential 6.00 2.39 9.74'''
aminoacids = {} # single letter to mol.
for aa in table.split('\n'):
a = aa.split()
mol = Chem.MolFromSmiles(a[4])
AllChem.Compute2DCoords(mol)
mol.SetProp('_Name', a[0])
if a[0] == 'Proline':
self.fix_carboxy(mol)
else:
self.fix_backbone(mol)
aminoacids[a[2]] = mol
ref = Chem.MolFromSmiles('NCC(=O)O')
AllChem.Compute2DCoords(ref,
coordMap={
0: Point2D(0, 0),
1: Point2D(0, 1.34),
})
for name1, mol in aminoacids.items():
AllChem.GenerateDepictionMatching2DStructure(mol, ref)
return aminoacids