if __name__ == '__main__':
# tf.config.list_physical_devices('GPU')
# exit()
print("loading molecules")
# name1 = "1K74_l_b"
# name2 = "1K74_r_b"
# name1 = "1KTZ_l_b"
# name2 = "1KTZ_r_b"
name1 = "1MAH_l_b"
name2 = "1MAH_r_b"
mol1 = Protein()
mol1.fromFile("structures/" + name1 + ".pdb")
mol2 = Protein()
mol2.fromFile("structures/" + name2 + ".pdb")
mol1.prepare()
mol2.prepare()
Chem.makeHydrogenDeplete(mol1)
Chem.makeHydrogenDeplete(mol2)
Biomol.FilePDBMolecularGraphWriter("compute/" + name1 + ".pdb").write(mol1)
Biomol.FilePDBMolecularGraphWriter("compute/" + name2 + ".pdb").write(mol2)
# ProteinTools.writePDB("compute/" + name1 + ".pdb", mol1)
# ProteinTools.writePDB("compute/" + name2 + ".pdb", mol2)
print("computing molecule surface")
os.system("~/EDTSurf/EDTSurf -i " + "compute/" + name1 + ".pdb" +
" -h 2 -s 3")
for e in shape:
e.setRadius(e.getRadius() * scaleFactor)
shapeFunc.setMaxOrder(6)
shapeFunc.setShape(shape)
return shape, shapeFunc
def getShapeWithIncreasedRadius(mol, increase=0.5):
shape = Shape.GaussianShape()
shapeFunc = Shape.GaussianShapeFunction()
Shape.generateGaussianShape(mol, shape, inc_h=True)
for e in shape:
e.setRadius(e.getRadius() + increase)
shapeFunc.setMaxOrder(6)
shapeFunc.setShape(shape)
return shape, shapeFunc
path = '../Data/benchmark5.5/structures/'
p = Protein()
p.fromFile('{}1A2K_l_b.pdb'.format(path))
# remove ligands and other crystalization artifacts
p.removeLigands()
sanitized = sanitize_mol(p, makeHydrogenComplete=True)
Pharm.prepareForPharmacophoreGeneration(p)
Chem.generateHydrogen3DCoordinates(p, True)
for i in range(10):
scale = 1 + i / 10
shape, shapeFunc = getShape(p, scaleFactor=scale)
print(scale, shapeFunc.surfaceArea)
