Relocated get_xyz_string and get_xyz_matrix

From Species to Parser
to avoid circular import (plus, it makes sense)

arc/parser.py

@@ -6,6 +6,7 @@
 import numpy as np
 import os
 
+from rmgpy.molecule.element import getElement
 from arkane.statmech import Log
 
 from arc.exceptions import InputError
@@ -72,6 +73,82 @@ def parse_e0(path):
     return e0
 
 
+def get_xyz_string(xyz, mol=None, number=None, symbol=None):
+    """
+    Convert list of lists xyz form:
+    [[0.6616514836, 0.4027481525, -0.4847382281],
+    [-0.6039793084, 0.6637270105, 0.0671637135],
+    [-1.4226865648, -0.4973210697, -0.2238712255],
+    [-0.4993010635, 0.6531020442, 1.0853092315],
+    [-2.2115796924, -0.4529256762, 0.4144516252],
+    [-1.8113671395, -0.3268900681, -1.1468957003]]
+    into a geometry form read by ESS:
+    C    0.6616514836    0.4027481525   -0.4847382281
+    N   -0.6039793084    0.6637270105    0.0671637135
+    H   -1.4226865648   -0.4973210697   -0.2238712255
+    H   -0.4993010635    0.6531020442    1.0853092315
+    H   -2.2115796924   -0.4529256762    0.4144516252
+    H   -1.8113671395   -0.3268900681   -1.1468957003
+    The atom symbol is derived from either an RMG Molecule object (`mol`) or atom numbers ('number`)
+    or explicitly given (`symbol`).
+    `number` and `symbol` are lists (optional parameters)
+    `xyz` is an array of arrays, as shown in the example above.
+    This function isn't defined as a method of ARCSpecies since it is also used when parsing opt geometry in Scheduler
+    """
+    result = ''
+    if symbol is not None:
+        elements = symbol
+    elif number is not None:
+        elements = []
+        for num in number:
+            elements.append(getElement(int(num)).symbol)
+    elif mol is not None:
+        elements = []
+        for atom in mol.atoms:
+            elements.append(atom.element.symbol)
+    else:
+        raise ValueError("Must have either an RMG:Molecule object input as `mol`, or atomic numbers \ symbols.")
+    for i, coord in enumerate(xyz):
+        result += elements[i] + ' ' * (4 - len(elements[i]))
+        for c in coord:
+            result += '{0:14.8f}'.format(c)
+        result += '\n'
+    return result
+
+
+def get_xyz_matrix(xyz):
+    """
+    Convert a string xyz form:
+    C    0.6616514836    0.4027481525   -0.4847382281
+    N   -0.6039793084    0.6637270105    0.0671637135
+    H   -1.4226865648   -0.4973210697   -0.2238712255
+    H   -0.4993010635    0.6531020442    1.0853092315
+    H   -2.2115796924   -0.4529256762    0.4144516252
+    H   -1.8113671395   -0.3268900681   -1.1468957003
+    into a list of lists xyz form:
+    [[0.6616514836, 0.4027481525, -0.4847382281],
+    [-0.6039793084, 0.6637270105, 0.0671637135],
+    [-1.4226865648, -0.4973210697, -0.2238712255],
+    [-0.4993010635, 0.6531020442, 1.0853092315],
+    [-2.2115796924, -0.4529256762, 0.4144516252],
+    [-1.8113671395, -0.3268900681, -1.1468957003]]
+
+    Returns xyz as well as atoms, x, y, z seperately
+    """
+    x, y, z, atoms = [], [], [], []
+    for line in xyz.split('\n'):
+        if line:
+            atom, xx, yy, zz = line.split()
+            x.append(float(xx))
+            y.append(float(yy))
+            z.append(float(zz))
+            atoms.append(atom)
+    xyz = []
+    for i, _ in enumerate(x):
+        xyz.append([x[i], y[i], z[i]])
+    return xyz, atoms, x, y, z
+
+
 def parse_xyz_from_file(path):
     """
     Parse xyz coordinated from:

arc/plotter.py

@@ -25,7 +25,8 @@
 from rmgpy.quantity import ScalarQuantity
 from rmgpy.species import Species
 
-from arc.species import ARCSpecies, mol_from_xyz, get_xyz_matrix, rdkit_conf_from_mol
+from arc.species import ARCSpecies, mol_from_xyz, rdkit_conf_from_mol
+from arc.parser import get_xyz_matrix
 from arc.exceptions import InputError
 
 

arc/scheduler.py

@@ -25,11 +25,12 @@
 import arc.rmgdb as rmgdb
 from arc import plotter
 from arc import parser
+from arc.parser import get_xyz_string
 from arc.species import determine_rotor_symmetry
 from arc.job.job import Job
 from arc.exceptions import SpeciesError, SchedulerError
 from arc.job.ssh import SSH_Client
-from arc.species import ARCSpecies, TSGuess, get_xyz_string
+from arc.species import ARCSpecies, TSGuess
 from arc.ts.atst import autotst
 from arc.settings import rotor_scan_resolution, inconsistency_ab, inconsistency_az, maximum_barrier
 

arc/species.py

@@ -1184,82 +1184,6 @@ def find_internal_rotors(mol):
     return rotors
 
 
-def get_xyz_string(xyz, mol=None, number=None, symbol=None):
-    """
-    Convert list of lists xyz form:
-    [[0.6616514836, 0.4027481525, -0.4847382281],
-    [-0.6039793084, 0.6637270105, 0.0671637135],
-    [-1.4226865648, -0.4973210697, -0.2238712255],
-    [-0.4993010635, 0.6531020442, 1.0853092315],
-    [-2.2115796924, -0.4529256762, 0.4144516252],
-    [-1.8113671395, -0.3268900681, -1.1468957003]]
-    into a geometry form read by ESS:
-    C    0.6616514836    0.4027481525   -0.4847382281
-    N   -0.6039793084    0.6637270105    0.0671637135
-    H   -1.4226865648   -0.4973210697   -0.2238712255
-    H   -0.4993010635    0.6531020442    1.0853092315
-    H   -2.2115796924   -0.4529256762    0.4144516252
-    H   -1.8113671395   -0.3268900681   -1.1468957003
-    The atom symbol is derived from either an RMG Molecule object (`mol`) or atom numbers ('number`)
-    or explicitly given (`symbol`).
-    `number` and `symbol` are lists (optional parameters)
-    `xyz` is an array of arrays, as shown in the example above.
-    This function isn't defined as a method of ARCSpecies since it is also used when parsing opt geometry in Scheduler
-    """
-    result = ''
-    if symbol is not None:
-        elements = symbol
-    elif number is not None:
-        elements = []
-        for num in number:
-            elements.append(getElement(int(num)).symbol)
-    elif mol is not None:
-        elements = []
-        for atom in mol.atoms:
-            elements.append(atom.element.symbol)
-    else:
-        raise ValueError("Must have either an RMG:Molecule object input as `mol`, or atomic numbers \ symbols.")
-    for i, coord in enumerate(xyz):
-        result += elements[i] + ' ' * (4 - len(elements[i]))
-        for c in coord:
-            result += '{0:14.8f}'.format(c)
-        result += '\n'
-    return result
-
-
-def get_xyz_matrix(xyz):
-    """
-    Convert a string xyz form:
-    C    0.6616514836    0.4027481525   -0.4847382281
-    N   -0.6039793084    0.6637270105    0.0671637135
-    H   -1.4226865648   -0.4973210697   -0.2238712255
-    H   -0.4993010635    0.6531020442    1.0853092315
-    H   -2.2115796924   -0.4529256762    0.4144516252
-    H   -1.8113671395   -0.3268900681   -1.1468957003
-    into a list of lists xyz form:
-    [[0.6616514836, 0.4027481525, -0.4847382281],
-    [-0.6039793084, 0.6637270105, 0.0671637135],
-    [-1.4226865648, -0.4973210697, -0.2238712255],
-    [-0.4993010635, 0.6531020442, 1.0853092315],
-    [-2.2115796924, -0.4529256762, 0.4144516252],
-    [-1.8113671395, -0.3268900681, -1.1468957003]]
-
-    Returns xyz as well as atoms, x, y, z seperately
-    """
-    x, y, z, atoms = [], [], [], []
-    for line in xyz.split('\n'):
-        if line:
-            atom, xx, yy, zz = line.split()
-            x.append(float(xx))
-            y.append(float(yy))
-            z.append(float(zz))
-            atoms.append(atom)
-    xyz = []
-    for i, _ in enumerate(x):
-        xyz.append([x[i], y[i], z[i]])
-    return xyz, atoms, x, y, z
-
-
 def determine_occ(label, xyz, charge):
     """
     Determines the number of occupied orbitals for an MRCI calculation

arc/speciesTest.py

@@ -13,8 +13,9 @@
 from rmgpy.species import Species
 from rmgpy.reaction import Reaction
 
-from arc.species import ARCSpecies, TSGuess, get_xyz_string, get_xyz_matrix, mol_from_xyz, check_xyz,\
+from arc.species import ARCSpecies, TSGuess, mol_from_xyz, check_xyz,\
     determine_rotor_type, determine_rotor_symmetry
+from arc.parser import get_xyz_string, get_xyz_matrix
 from arc.settings import arc_path
 
 ################################################################################

arc/ts/run_autotst.py

@@ -19,7 +19,7 @@
 
 from autotst.reaction import AutoTST_Reaction
 
-from arc.species import get_xyz_string
+from arc.parser import get_xyz_string
 from arc.exceptions import TSError
 from arc.settings import arc_path