pyviblib.molecule

Module for handling molecules

Classes

Atom

describing atoms

Bond

describing bonds

Molecule

describing molecules

Cluster

describing clusters

Author:Maxim Fedorovsky

class pyviblib.molecule.Atom(index, coord, element)

Class for describing atoms.

An atom can be a part of a bond.

The following read-only properties are exposed:

index

one-based index of the atom

coord

coordinates of the atom (one-based ndarray)

element

element for the atom (pyviblib.util.pse.Element)

Initializer of the class.

Parameters:

• index – one-based index of the atom
• coord – coordinates of the atom (one-based ndarray)
• element – element for the atom (pyviblib.util.pse.Element)

class pyviblib.molecule.Bond(atom1, atom2, is_hydrogen=False)

Class for describing bonds.

A bond is made up of two atoms and can be a part of a molecule.

The following read-only properties are exposed:

atom1

first atom comprising the bond

atom2

second atom comprising the bond

is_hydrogen

whether it is a hydrogen bond

The following public methods are exposed:

length()

length of the bond

Initializer of the class.

Parameters:

• atom1 – first atom comprising the bond (Atom)
• atom2 – second atom comprising the bond (Atom)
• is_hydrogen – whether it is a hydrogen bond

length()

Calculate the bond length.

class pyviblib.molecule.Molecule(parser, **kw)

Class for describing molecules.

A molecule consists of atoms and bonds. The bonds can be automatically generated from the cartesian coordinates of the atoms.

The following read-only properties are exposed:

parser

parser object used to create the molecule

elements

elements for the atoms (one-based list of pyviblib.util.pse.Element)

masses

masses (a.m.u.) of the atoms (one-based ndarray)

atoms

atoms (null-based list of Atom)

Natoms

number of atoms (int)

bonds

bonds (null-based list of Bond)

bonds_matrix

matrix of the bonds (one-based ndarray). If a bond between atoms a and b exists, then bonds_matrix[a, b] = 1

nrot

number of rotational degrees of freedom (int)

The properties below are set if the normal modes are available (tr/rot stands for translations/rotations):

NFreq

number of frequencies (int, -1 unless set)

Lx

cartesian excursions (one-based ndarray) shape: (1 + NFreq, 1 + Natoms, 4)

Lx_norm

normalized cartesian excursions (one-based ndarray) shape: (1 + NFreq, 1 + Natoms, 4)

L_tr_rot

mass-weighted excursions for tr/rot (one-based ndarray) shape: (4 + nrot, 1 + Natoms, 4)

Lx_tr_rot

cartesian excursions for tr/rot one-based ndarray) shape: (4 + nrot, 1 + Natoms, 4)

Lx_tr_rot_norm

normalized cartesian excursions for tr/rot (one-based ndarray) shape: (4 + nrot, 1 + Natoms, 4)

hessian

hessian (one-based ndarray) shape: (1 + Natoms, 4, 1 + Natoms, 4)

orig_enantiomer

whether it is the original enantiomer

molecule_id

unique identifier of the molecule

The following readable and writable properties are exposed:

coords

cartesian coordinates (one-based ndarray) shape: (1 + Natoms, 4)

name

name of the molecule (string)

raman_roa_tensors

Raman/ROA tensors (set if the data available) (pyviblib.calc.spectra.RamanROATensors)

ir_vcd_tensors

IR/VCD tensors (set if the data available) (pyviblib.calc.spectra.IRVCDTensors)

E_Gibbs

Gibbs energy

the properties below are set if the normal modes are available:

freqs

wavenumbers of the vibrations in cm**(-1) (one-based ndarray)

L

mass-weighted excursions (one-based ndarray) shape: (1 + NFreq, 1 + Natoms, 4)

parts

list or tuple with parts of the molecule

sum_mono_only

whether to sum the mononuclear terms only

groups

groups with colors

The following public methods are exposed:

mass_center()

coordinates of the mass center

update_masses()

update the masses of atoms

distance()

distance between atoms

angle()

angle between atoms

dihedral()

dihedral angle between atoms

make_enantiomer()

make the virtual enantiomer

transform()

perform a geometrical transformation

set_new_molecule_id()

generate and set a new molecule_id

The following public static method is exported:

pack_pickle()

create a dictionary for a molecule to be pickled

Initializer of the class.

Positional arguments: parser – parser object

Keyword arguments are used if the parser object is not supplied.

angle(i1, i2, i3)

Angle in grad between atoms.

Positional arguments: :param i1: one-based index of the first atom :param i2: one-based index of the second atom :param i3: one-based index of the third atom

dihedral(i1, i2, i3, i4)

Dihedral angle in grad between atoms.

Parameters:

• i1 – one-based index of the first atom
• i2 – one-based index of the second atom
• i3 – one-based index of the third atom
• i4 – one-based index of the fourth atom

distance(i1, i2)

Distance between two atoms.

Parameters:

• i1 – one-based index of the first atom
• i2 – one-based index of the second atom

make_enantiomer()

Make the virtual enantiomer.

mass_center(atom_list=None)

Return the coordinates of the mass center.

Parameter:atom_list – list of atoms, if None use all atoms

static pack_pickle(mol)

Create a dictionary for a molecule to be pickled.

Parameter:mol (Molecule) – molecule

set_new_molecule_id()

Generate and set a new molecule_id.

transform(rotmat, cur_origin=None, new_origin=None, trans_grad=True)

Perform a geometrical transformation.

Parameters:

• rotmat (ndarray, shape: (4, 4)) – rotation matrix
• cur_origin (ndarray, shape: (4,)) – current origin
• new_origin (ndarray, shape: (4,)) – new origin
• tran_grad – whether to translate the gradients

The coordinates are assumed to be given in angstrom.

update_masses(data_pairs)

Modify the masses of atoms.

Parameter:data_pairs – information about the atoms (null-based ndarray) shape: (Natoms_to_modify, 2) atom numbers are one-based

class pyviblib.molecule.Cluster(cluster, parts, pairs_alignment=None, pairs_grads=None, sum_trans_only=False)

Class for describing clusters.

A cluster is considered to be a molecule which can be divided into several parts in a reasonable way. An example might be a dimer or a polypeptide.

The following read-only properties are exposed:

cluster

original molecule of the cluster

art_cluster

synthesized cluster created from the V-tensors

art_cluster2

synthesized cluster created from the transformed grads

Initializer of the class.

Parameters:

• cluster – cluster which should be synthesized from parts
• parts – list of the parts of the cluster (Molecule objects)
• pairs_alignment – list of the pairs to be used for the orientational alignment of the parts generated automatically unless provided
• pairs_grads – list of the pairs whose gradients are to be taken to synthesize the artificial cluster coincides with pairs_alignment unless provided
• sum_trans_only – whether only the translational contributions are to be taken into account for the intermolecular terms the option has effect for art_cluster