/pmpdelaney

Primary LanguagePython

Data for Delaney logS in PMP format

The PMP format for Delaney logS set contains following information:

  • Smiles and Exp. logS for 1128 molecules
  • HF/6-31G* optimized structure
  • HF/6-31G* based RESP charge
  • Molecular ELectrostatic Solvation Energy and Atomic ELectrostatic Solvation Energy (MIBPB, RESP charge, mbondi radius)
  • Dipole and Quadrapole based on GDMA analysis (H radius at default 0.325)
  • Molecular Area/Volume (0.2 grid size, 1.4 probe radius)
  • Atomic Area

The exact features containing now:

Molecule Level

  • SMILES (s) : origin smiles from origin data
  • ExpLogS (f) : origin Experimental LogS value
  • MolVolume (f) : Molecular Volume
  • MolArea (f) : Molecular Surface Area
  • ElecSolvEng (f) : Electrostatic Solvation Energy based on MIBPB5
  • Dipole (f) : Molecular Dipole from GDMA result
  • Quadrupole (f) : Molecular Quadrupole from GDMA result
  • Area_* (f) : Surface Area of given element in molecule

Atom Level

  • AtomArea (10f) : Atomic surface area
  • AtomSolEng (10f) : Atomic Solvation Energy
  • Dipole (10f) : Atomic dipole
  • Quadrupole (10f) : Atomic quadrupole
  • resp (10f) : RESP atomic charge
  • mbondi (10f) : MBONDI atomic radiis
  • AT_gaff (6s) : Atom type based on GAFF definition
  • AT_sybyl (6s) : Atom type based on SYBYL definition

Usage

import PMPformat as PMP

Read file as molecule

  • Open PMP molecule file
pmpf = PMP.PMPFormator(pmpfile="Data/Delaney_1.pmp")
  • Get the molecule.

You can replace "MolFromSmiles" to this function to load molecule.

mol = pmpf.GetMol()

Get molecular or atomic features

  • Get All Properties/Features on the Molecular Level
mol_prop = mol.GetPropsAsDict()
print mol_prop
  • Get a certain feature by name.

Recommend use the ExpLogS/MoleArea/Volume/ElecSolvEng/Dipole and so on.
I don't recommend to use element based area, such as Area_F, Area_S et al. But you can also try.

mol_prop['MolArea']

An alternative method is to use GetProp, GetIntProp or GetDoubleProp methods to obtain properties when you exactly know the data type for the proporty.

mol_area = mol.GetDoubleProp('MolArea')
  • Get Property/Feature on the Atom Level

The atom type AT_gaff, AT_sybyl somehow can be represented by NGF and it's string based data. If you want to use it, you can use int value to represent it.

atom0 = mol.GetAtomWithIdx(0)
atom_prop = atom0.GetPropsAsDict()
print atom_prop

atom_prop['AtomArea']

## or using exactly method

features = [
    atom0.GetProps('AT_gaff'), atom0.GetDoubleProps('AtomArea')
]