pyef.geometry

Module Contents

Classes

Geometry

Visualize

Create PDB visualizations of electrostatic properties.
class Geometry(filexyz)
getGeomInfo()

Input: filepathtoxyz: string of xyz filename Output: dataframe with atomic symbols and coordinates

getGeomInfovDW()

Input: filepathtoxyz: string of xyz filename Output: dataframe with atomic symbols and coordinates

getCentroidDistance(ref_xyz)
getSubstrateFramePosition(idx_substrate)
getBondedAtoms(atomidx)

Input: filepathtoxyz: string of xyz filename atomidx: integer of atom index Output: list of integers of bonded atom indices

weak_Hbond_check(donors_weak, hydrogens, acceptors_weak, CH_bond_cutoff, HA_bond_cutoff, weak_angle_cutoff)
hbond_check(donors_strong, hydrogens, acceptors_strong, hconv_cutoff, hcoor_cutoff, strong_angle_cutoff)
createpdbfromcoords(charges, atoms, output_filename)

Input: xyz_coords: list of tuples of coordinates charges: list of charges atoms: list of atomic symbols output_filename: string of output filename

Output: .pdb file with partial charges

getCloseHcontacts(res_atoms)
countCloseContacts(res_atoms, factor)
class Visualize(filexyz='None')

Create PDB visualizations of electrostatic properties.

This class generates PDB files with electrostatic properties (ESP, E-field, energies) stored in the B-factor column for visualization in molecular viewers like PyMOL, VMD, or Chimera.

PDB File Naming Convention Quick Reference

ESP: esp_{charge_type}_{structure}_atom{idx}.pdb E-field: ef_{charge_type}_{structure}_bond{i}-{j}.pdb

ef_{charge_type}_{structure}_combined.pdb

Estab: estab_{charge_type}_{structure}_atomwise.pdb

estab_{charge_type}_{structure}_tensor_sub{N}_env{M}.pdb

Where: - {charge_type}: Hirshfeld_I, CHELPG, Becke, etc. - {structure}: Job directory name or XYZ filename - {idx}, {i}, {j}: Atom indices (0-based) - {N}, {M}: Multipole orders (1=monopole, 2=+dipole, 3=+quadrupole)

See makePDB() docstring for complete details and visualization examples.

makePDBpercentEfield()
makePDBcontributionEfield()
makePDBcontributionESP()
compareESP()
pdb_esp()
makePDB(output_filename, b_col, pdbName)

Generate PDB files with data in B-factor column for visualization.

Creates a PDB file from XYZ coordinates with custom values (e.g., charges, electric fields, energies) stored in the B-factor column for visualization in programs like PyMOL, VMD, or Chimera.

Parameters:

  • output_filename (str) – Path to input file containing atom data (typically charges or multipoles)

  • b_col (array-like) – Values to store in B-factor column (0-indexed, length = number of atoms) Examples: partial charges, E-field magnitudes, energy contributions

  • pdbName (str) – Output PDB filename

  • Conventions (Output PDB Naming) –

  • ------------------------------ –

  • names (PyEF automatically generates PDB files with descriptive) –

  • Potential) (**ESP (Electrostatic) –

  • Format (-) –

  • Example (-) –

  • B-factor (-) –

  • bond) (**Electric Field (per) –

  • Format –

  • Example –

  • B-factor –

  • (combined (**Electric Field) –

  • bonds) (all) –

  • Format –

  • Example –

  • B-factor –

  • (atomwise) (**Electrostatic Stabilization) –

  • Format –

  • Example –

  • B-factor –

  • formalism) (**Electrostatic Stabilization (tensor) –

  • Format –

  • Example –

  • B-factor –

Notes

  • All atom indices in filenames use 0-based indexing

  • Structure name is derived from the job directory or XYZ filename

  • Charge type indicates the partitioning scheme (Hirshfeld_I, CHELPG, etc.)

  • B-factor values can be positive or negative depending on the property

In PyMOL: ` load esp_Hirshfeld_I_complex_atom25.pdb spectrum b, blue_white_red, minimum=-10, maximum=10 `

In VMD: ` mol new esp_Hirshfeld_I_complex_atom25.pdb mol modcolor 0 0 Beta `

diff_pdbs(initial_pdb, change_pdb, new_pdb_name, new_to_old_map='None')