schrodinger.application.matsci.zmutils module¶

Contains classes for working with Z-Matrices

schrodinger.application.matsci.zmutils.rotation_matrix(axis, angle)¶

Get rotation matrix based on the Euler-Rodrigues formula.

Parameters

axis (list) – Axis, defined by 3 floats, will be normalized
angle (float) – Angle (deg) to rotate around the axis

Return type

numpy.array

Returns

Rotation matrix (3 x 3)

class schrodinger.application.matsci.zmutils.ZAtom(index, element, values, constraints, neighbor_indexes, neighbor_elements)¶

Bases: object

A single atom in a Z-matrix

COORD_LETTERS = ['r', 'a', 'd']¶

__init__(index, element, values, constraints, neighbor_indexes, neighbor_elements)¶

Initialize ZAtom object

Parameters

index (int) – Atom index with the structure
element (str) – Atom element
values (list) – Atom values (bond distance, angle, torsion)
constraints (set) – Atom constraints
neighbor_indexes (list) – Atom neighboring indices
neighbor_elements (list) – Atom neighboring elements

classmethod fromJagin(jagin, index)¶

Create a ZAtom object from jaguar input.

Parameters

jagin (schrodinger.application.jaguar.input.JaguarInput) – The JaguarInput object the Z-matrix is for
index (int) – The atom index (1-based) that this ZAtom is for

Return type

ZAtom

Returns

New ZAtom object

constrainCoord(coord)¶

Constrain the given coord so it can’t be optimized

Parameters: coord (int) – 0 (bond), 1 (angle) or 2 (dihedral)

freeCoord(coord)¶

Allow the given coord to be optimized

Parameters: coord (int) – 0 (bond), 1 (angle) or 2 (dihedral)

constrainAll()¶: Constrain all the coords so they can’t be optimized

freeAll()¶: Allow all the coords to be optimized

bumpIndexes(bump)¶

Modify all the indexes (both for self and any referenced atoms) by a constant number. Used when this z-matrix is being added to another, and now atom 1 is actually atom 20…

Parameters: bump (int) – The amount to modify each index

getSymbolicLine()¶

Get the line that defines the atoms for the bond, angle and dihedral and also the coordinate names. i.e. C11 H1 r11 C2 a11 C7 d11

Return type: str
Returns: The string defining the z-matrix coordinates for this atom. Includes the trailing return character

getVariableLines()¶

Get a series of lines that defines each coordinate, i.e.:

r11 = 1.452
a11 = 102.4
d11 = 180

Return type: str
Returns: The string defining the z-matrix coordinate values for this atom. Includes the trailing return character at the end of the block.

getAtomName(element, index)¶

Get the name of an atom with the given element and index

Parameters

element (str) – The atomic symbol of the atom
index (int) – The index of the atom

Return type

str

Returns

The name of the atom, such as “C12”

getCoordName(coord)¶

Get the name of a coordinate for this atom, such as r11 or d7

Parameters: coord (int) – 0 (bond), 1 (angle) or 2 (dihedral)
Return type: str
Returns: The name of the coordinate, such as “r12”

addCoord(index, element, value)¶

Add an internal coordinate for this atom referenced to a target atom. Note that coordinates must be added in the order bond, angle, dihedral.

Parameters

index (int) – The atom index of the target atom (such as the atom the bond extends to)
element (str) – The element of the target atom
value (float) – The value of this coordinate

changeCoord(coord, value, index=None, element=None)¶

Change the definition of an existing internal coordinate. If index and element are passed in the target atom for the coordinate will be changed.

Parameters

coord (int) – 0 (bond), 1 (angle) or 2 (dihedral)
value (float) – The value of this coordinate
index (int) – The atom index of the target atom (such as the atom the bond extends to), 1-based. Both index and element must be supplied for them to be used.
element (str) – The element of the target atom. Both index and element must be supplied for them to be used.

class schrodinger.application.matsci.zmutils.ZMatrix(struct=None)¶

Bases: object

Contains the z-matrix for a structure

__init__(struct=None)¶

Create a ZMatrix instance

Parameters: struct (schrodinger.structure.Structure or None) – The structure this zmatrix is for

setBasisVectors(struct)¶

Set origin and basis vectors. These can be used to recover original Cartesian coordinates from Z-matrix.

Parameters: structure.Structure – Input structure

getStructure()¶

Create and return structure based on the zmatrix.

Return type: schrodinger.structure.Structure
Returns: Newly created structure

fromStructure(struct)¶

Given the input structure, generate a ZMatrix with the same atom neighbors lists as self.

Parameters: struct (structure.Structure) – The structure this zmatrix is for
Return type: ZMatrix
Returns: Newly created ZMatrix

copy()¶

Copy Z-matrix.

Return type: ZMAtrix
Returns: Copied Z-matrix

difference(other_zmat)¶

Compute difference Z-matrix between other zmatrix and self zmatrix (in this order).

Parameters: other_zmat (ZMatrix) – Other Z-Matrix
Return type: ZMatrix
Returns: Difference Z-matrix

interpolate(other_zmat, disps, indices=None)¶

Interpolate between two Z-matrices. Initial Z-matrix is self, other zmatrix is final point.

Parameters

other_zmat (ZMatrix) – Final point of zmatrix
disps (list) – List of displacement coefficients
indices (list[int] or None) – List of atom indices to move, if None, will move all atoms

Return type

list[ZMatrix]

Returns

List of interpolated Z-matrices

bumpIndexes(bump)¶

Bump all atom indexes for this z-matrix

Parameters: bump (int) – The amount to modify each index

constrainAll()¶: Constrain all internal coordinates

freeAtom(index)¶

Free all the internal coordinates for a single atom

Parameters: index (int) – The atom index (1-based) of the atom to free

freeAtomBond(index)¶

Free all the bond internal coordinate for a single atom

Parameters: index (int) – The atom index (1-based) of the atom to free

freeAtomAngle(index)¶

Free all the angle internal coordinate for a single atom

Parameters: index (int) – The atom index (1-based) of the atom to free

freeAtomDihedral(index)¶

Free all the angle internal coordinate for a single atom

Parameters: index (int) – The atom index (1-based) of the atom to free

findNonlinearAngle(struct, atom_a, atom_b, do_not_use, index_less_than, linear)¶

Find an angle between atom_a, atom_b and some other atom that is smaller than linear

Parameters

struct (schrodinger.structure.Structure) – The struct to use
atom_a (int) – The 1-indexed index of atom A for the A-B-C angle
atom_b (int) – The 1-indexed index of atom B for the A-B-C angle
do_not_use (set) – An set of atom indexes that should not be used for the C atom for the A-B-C angle
index_less_than (int) – Only look for indexes less than this number
linear (float) – The threshold where any angle greater than this is considered linear

Return type

int, float or None, None

Returns

The index of an atom that forms an angle with atom_a and atom_b that is less than linear degrees, and the angle it forms. None, None is returned if none of the indexes in choose_from gave a non-linear angle.

merge(child_zmat, struct, glue_index)¶

Combine the atom lists from this (parent) z-matrix and another (child) z-matrix. This involves not just combining the lists, but also defining the following new internal coordinates:

child_atom_1: bond, angle, dihedral child_atom_2: angle, dihedral child_atom_3: dihedral

All new internal coordinates will reference an atom from the parent structure. These six new internal coordinates fully specify the parent-child orientation.

Parameters

child_zmat (ZMatrix) – The child z-matrix to merge with this one
struct (schrodinger.structure.Structure) – The structure that results from merging these two z-matrices. This is needed to compute the new bonds, angles and dihedrals.
glue_index (int) – The index of the atom in the parent structure that should be bonded to the first atom of the child structure. This index should be 1-based (i.e. structure.atom indexed, not list indexed)

schrodinger.application.matsci.zmutils.add_zmatrix_lines(lines, zmat)¶

Add the lines defining a z-matrix to the character string using the format required by Jaguar input files.

Parameters

lines (str) – The string to add the z-matrix to
zmat (schrodinger.application.matsci.zmutils.ZMatrix) – The ZMatrix that defines the lines to be added

Return type

str

Returns

The original lines with the z-matrix lines appended. The initial ‘&zmat’ and the closing ‘&’ are appended by this function

schrodinger.application.matsci.zmutils.replace_coords_with_zmat(path, zmat)¶

Replace the coordinate section in a jaguar input file with the z-matrix. Replaces the current:

&zmat … &

section with

&zmat … & &zvar … &

Parameters: path (str) – The path to the input file

@zmat: ZMatrix :param: The ZMatrix object to use to replace the coordinates