DimerFrag

class optking.dimerfrag.DimerFrag(A_idx, A_atoms, B_idx, B_atoms, A_weights=None, B_weights=None, A_lbl='A', B_lbl='B', frozen=None)

Bases: object

Set of (up to 6) coordinates between two distinct fragments. The fragments ‘A’ and ‘B’ have up to 3 reference atoms each (dA[3] and dB[3]). The reference atoms are defined in one of two ways: 1. If interfrag_mode == FIXED, then fixed, linear combinations of atoms

in A and B are used.

2. (NOT YET IMPLEMENTED) If interfrag_mode == PRINCIPAL_AXES, then the references points are

   1. the center of mass

   2. a point a unit distance along the principal axis corresponding to the largest moment.

   3. a point a unit distance along the principal axis corresponding to the 2nd largest moment.

# For simplicity, we sort the atoms in the reference point structure according to the assumed connectivity of the coordinates. ref_geom[0] = dA[2]; ref_geom[1] = dA[1]; ref_geom[2] = dA[0]; ref_geom[3] = dB[0]; ref_geom[4] = dB[1]; ref_geom[5] = dB[2]; # The six coordinates, if present, formed from the d{A-B}{0-2} sets are assumed to be the following in this canonical order: pos sym type atom-definition present, if ——————————————————————————— 0 RAB distance dA[0]-dB[0] always 1 theta_A angle dA[1]-dA[0]-dB[0] A has > 1 atom 2 theta_B angle dA[0]-dB[0]-dB[1] B has > 1 atom 3 tau dihedral dA[1]-dA[0]-dB[0]-dB[1] A and B have > 1 atom 4 phi_A dihedral dA[2]-dA[1]-dA[0]-dB[0] A has > 2 atoms and is not linear 5 phi_B dihedral dA[0]-dB[0]-dB[1]-dB[2] B has > 2 atoms and is not linear # :param A_idx: index of fragment in molecule list :type A_idx: int :param A_atoms: index of atoms used to define each reference point on A :type A_atoms: list of (up to 3) lists of ints :param B_idx: index of fragment in molecule list :type B_idx: int :param B_atoms: index of atoms used to define each reference point on B :type B_atoms: list of (up to 3) lists of ints :param A_weights (optional): weights of atoms used to define each reference point of A :type A_weights (optional): list of (up to 3) lists of floats :param B_weights (optional): weights of atoms used to define each reference point of B :type B_weights (optional): list of (up to 3) lists of floats :param A_lbl: name for fragment A :type A_lbl: string :param B_lbl: name for fragment B :type B_lbl: string :param The arguments are potentially confusing: :param so we’ll do a lot of checking.:

Attributes Summary

A_idx
B_idx
frozen_list
n_arefs
n_brefs
num_intcos
pseudo_frag

Methods Summary

Bmat(A_geom, B_geom, Bmat_in[, A_xyz_off, ...])	This function adds interfragment rows into an existing B matrix.
a_ref_geom()
active_labels()
b_ref_geom()
d_on(i)
dq_discontinuity_correction(dq)
freeze([coords_to_freeze])
fromUserDict(userDict)
from_dict(D)
get_ref_geom()
label2index(label_in)
orient_fragment(Ageom_in, Bgeom_in, q_target_in)	orient_fragment() moves the geometry of fragment B so that the
print_intcos()
q()
q_array()
q_show()
q_show_array()
set_ref_geom(ArefGeom, BrefGeom)
test_B(Axyz, Bxyz[, printInfo])
to_dict()
update_reference_geometry(Ageom, Bgeom)
validate_intcos(Ageom_in, Bgeom_in)

Attributes Documentation

A_idx

B_idx

frozen_list

n_arefs

n_brefs

num_intcos

pseudo_frag

Methods Documentation

Bmat(A_geom, B_geom, Bmat_in, A_xyz_off=None, B_xyz_off=None)

This function adds interfragment rows into an existing B matrix.

B is (internals, Cartesians). Often, 6 x 3*(Natoms).

Parameters

• A_geom (numpy array) – geometry of fragment A, array is (A atoms,3)

• B_geom (numpy array that is (B atoms,3)) – geometry of fragment B, array is (B atoms,3)

• Bmat_int (numpy array) – provided B matrix

• intco_off (int) – index of first row of Bmatrix to start writing the interfragment rows.

• A_off (int) – Column of B matrix at which the cartesian coordinates of atoms in fragment A begin. Needed since columns may span full molecular system.

• B_off (int) – Column of B matrix at which the cartesian coordinates of atoms in fragment B begin.

• given (If A_off and B_off are not) –

• returned. (then the minimal (dimer-only) B-matrix is) –

a_ref_geom()

active_labels()

b_ref_geom()

d_on(i)

dq_discontinuity_correction(dq)

freeze(coords_to_freeze=None)

classmethod fromUserDict(userDict)

classmethod from_dict(D)

get_ref_geom()

label2index(label_in)

orient_fragment(Ageom_in, Bgeom_in, q_target_in, printCoords=False, unit_length='bohr', unit_angle='rad')

orient_fragment() moves the geometry of fragment B so that the

interfragment coordinates have the given values

Parameters

• Ageom_in (array) – Cartesian geometry of fragment A

• Bgeom_in (array) – Cartesian geometry of fragment B

• q_target (array float[6]) – Target values of 6 interfragment coordinates after moving fragment B

• printCoords (boolean) – whether to print the starting and final values of the q’s

• unit_length (string ; default 'bohr') – indicate unit of length, q[0]

• unit_angle (string ; default 'rad') – indicate unit of angles, q[1-5]

• ------------ –

Returns

new Cartesian geometry for B

Return type

array

print_intcos()

q()

q_array()

q_show()

q_show_array()

set_ref_geom(ArefGeom, BrefGeom)

test_B(Axyz, Bxyz, printInfo=False)

to_dict()

update_reference_geometry(Ageom, Bgeom)

validate_intcos(Ageom_in, Bgeom_in)