add rotational initialization

build/lib/cctk/__init__.py

@@ -0,0 +1,18 @@
+from .file import File
+from .lines import LazyLineObject
+from .array import OneIndexedArray
+from .molecule import Molecule
+from .ensemble import Ensemble, ConformationalEnsemble
+from .group import Group
+from .vibrational_mode import VibrationalMode
+
+from .gaussian_file import GaussianJobType, GaussianFile
+from .orca_file import OrcaFile, OrcaJobType
+from .xyz_file import XYZFile
+from .mol2_file import MOL2File
+from .mae_file import MAEFile
+from .pdb_file import PDBFile
+
+from .si_file import SIFile
+
+from .point_charge import PointCharge

build/lib/cctk/array.py

@@ -0,0 +1,135 @@
+import numpy as np
+import copy
+
+class OneIndexedArray(np.ndarray):
+    """
+    Wrapper for ``np.ndarray`` that's indexed from one, not zero, to store atomic numbers and geometries.
+    This only works on 1D or 2D arrays. Additionally, only the first index of a 2D array will be 1-indexed.
+
+    Note that ``enumerate(one_indexed_array)`` will throw ``IndexError`` -- instead, use ``enumerate(one_indexed_array, start=1)``.
+    """
+
+    def __new__(cls, obj, **kwargs):
+        new = np.array(obj, **kwargs).view(cls)
+        return new
+
+    def __getitem__(self, index):
+        index = copy.deepcopy(index)
+        if isinstance(index, slice):
+            if index.start is None:
+                start = 0
+            else:
+                start = index.start - 1
+            if index.stop is None:
+                stop = -1
+            else:
+                stop = index.stop - 1
+            new_index = slice(start, stop, index.step)
+            return super().__getitem__(new_index)
+        elif isinstance(index, int):
+            if index > 0:
+                return super().__getitem__(index-1)
+            elif index == 0:
+                raise IndexError("this is a 1-indexed array: no element 0!")
+            elif index < 0:
+                return super().__getitem__(index)
+        elif (isinstance(index, tuple)) and (len(index) == 2):
+            if index[0] is None:
+                return super().__getitem__((index[0], index[1]))
+            elif index[0] > 0:
+                return super().__getitem__((index[0]-1, index[1]))
+            elif index[0] == 0:
+                raise IndexError("this is a 1-indexed array: no element 0!")
+            elif index[0] < 0:
+                return super().__getitem__((index[0], index[1]))
+        elif (isinstance(index, tuple)) and (len(index) == 1):
+            return self.__getitem__(index[0])
+        elif isinstance(index, np.ndarray):
+            if index.dtype == bool:
+                return super().__getitem__(index)
+            elif index.ndim == 1:
+                index[index >= 1] += -1
+                return super().__getitem__(index)
+            else:
+                index[0][index >= 1] += -1
+                return super().__getitem__(index)
+        elif isinstance(index, list):
+            if isinstance(index[0], bool):
+                return super().__getitem__(index)
+            elif isinstance(index[0], list):
+                if isinstance(index[0][0], bool):
+                    return super().__getitem__(index)
+                for i, v in enumerate(index[0]):
+                    if v >= 1:
+                        index[i] += -1
+                return super().__getitem__(index)
+            else:
+                for i, v in enumerate(index):
+                    if v >= 1:
+                        index[i] += -1
+                return super().__getitem__(index)
+        else:
+            return super().__getitem__(index)
+
+    def __setitem__(self, index, value):
+        index = copy.deepcopy(index)
+        if isinstance(index, int):
+            if index > 0:
+                if self.ndim == 1:
+                    super().__setitem__(index-1, value)
+                elif self.ndim == 2:
+                    super().__setitem__(index, value)
+                else:
+                    raise TypeError("this datatype is only defined for 1D and 2D ndarrays")
+            elif index == 0:
+                raise IndexError("this is a 1-indexed array: no element 0!")
+            elif index < 0:
+                super().__setitem__(index, value)
+        elif (isinstance(index, tuple)) and (len(index) == 2):
+            if index[0] is None:
+                super().__setitem__((index[0], index[1]), value)
+            elif index[0] > 0:
+                super().__setitem__((index[0]-1, index[1]), value)
+            elif index[0] == 0:
+                raise IndexError("this is a 1-indexed array: no element 0!")
+            elif index[0] < 0:
+                super().__setitem__((index[0], index[1]), value)
+        elif (isinstance(index, tuple)) and (len(index) == 1):
+            return self.__setitem__(index[0], value)
+        elif isinstance(index, np.ndarray):
+            if index.dtype == bool:
+                super().__setitem__(index, value)
+            elif index.ndim == 1:
+                index[index >= 1] += -1
+                super().__setitem__(index, value)
+            else:
+                index[0][index >= 1] += -1
+                super().__setitem__(index, value)
+        elif isinstance(index, list):
+            if isinstance(index[0], bool):
+                super().__setitem__(index, value)
+            elif isinstance(index[0], list):
+                if isinstance(index[0][0], bool):
+                    super().__setitem__(index, value)
+                for i, v in enumerate(index[0]):
+                    if v >= 1:
+                        index[i] += -1
+                super().__setitem__(index, value)
+            else:
+                for i, v in enumerate(index):
+                    if v >= 1:
+                        index[i] += -1
+                super().__setitem__(index, value)
+        else:
+            super().__setitem__(index, value)
+#            raise IndexError(f"invalid index {index} for OneIndexedArray")
+
+    def __iter__(self):
+        for idx in range(1,len(self)+1):
+            yield self.__getitem__(idx)
+
+    def __hash__(self):
+        return hash(self.data.tobytes())
+
+    def __str__(self):
+        return self.view(np.ndarray).__str__()

build/lib/cctk/data/covalent_radii.csv

@@ -0,0 +1,97 @@
+Number,Symbol,Radius,StdDev,NumAnalyzed 
+1,H,0.31,5,129
+2,He,0.28
+3,Li,1.28,7,5789
+4,Be,0.96,3,310
+5,B,0.84,3,1770
+6,C,0.76,1,10,000
+7,N,0.71,1,2200
+8,O,0.66,2,10,000
+9,F,0.57,3,10,000
+10,Ne,0.58
+11,Na,1.66,9,1629
+12,Mg,1.41,7,3234
+13,Al,1.21,4,3206
+14,Si,1.11,2,10,000
+15,P,1.07,3,10,000
+16,S,1.05,3,10,000
+17,Cl,1.02,4,1987
+18,Ar,1.06,10,9
+19,K,2.03,12,435
+20,Ca,1.76,10,2647
+21,Sc,1.70,7,32
+22,Ti,1.60,8,231
+23,V,1.53,8,389
+24,Cr,1.39,5,916
+25,Mn,1.61,8,929
+26,Fe,1.52,6,1540
+27,Co,1.50,7,780
+28,Ni,1.24,4,1030
+29,Cu,1.32,4,1149
+30,Zn,1.22,4,443
+31,Ga,1.22,3,1330
+32,Ge,1.20,4,1013
+33,As,1.19,4,2015
+34,Se,1.20,4,1717
+35,Br,1.20,3,2140
+36,Kr,1.16,4,5
+37,Rb,2.20,9,23
+38,Sr,1.95,10,1500
+39,Y,1.90,7,30
+40,Zr,1.75,7,93
+41,Nb,1.64,6,18
+42,Mo,1.54,5,97
+43,Tc,1.47,7,96
+44,Ru,1.46,7,1032
+45,Rh,1.42,7,458
+46,Pd,1.39,6,1892
+47,Ag,1.45,5,1728
+48,Cd,1.44,9,19
+49,In,1.42,5,546
+50,Sn,1.39,4,2999
+51,Sb,1.39,5,609
+52,Te,1.38,4,692
+53,I,1.39,3,451
+54,Xe,1.40,9,2
+55,Cs,2.44,11,24
+56,Ba,2.15,11,3076
+57,La,2.07,8,190
+58,Ce,2.04,9,47
+59,Pr,2.03,7,58
+60,Nd,2.01,6,96
+61,Pm,1.99
+62,Sm,1.98,8,53
+63,Eu,1.98,6,167
+64,Gd,1.96,6,178
+65,Tb,1.94,5,55
+66,Dy,1.92,7,59
+67,Ho,1.92,7,48
+68,Er,1.89,6,66
+69,Tm,1.90,10,15
+70,Yb,1.87,8,122
+71,Lu,1.87,8,61
+72,Hf,1.75,10,53
+73,Ta,1.70,8,88
+74,W,1.62,7,219
+75,Re,1.51,7,476
+76,Os,1.44,4,99
+77,Ir,1.41,6,131
+78,Pt,1.36,5,1768
+79,Au,1.36,6,114
+80,Hg,1.32,5,137
+81,Tl,1.45,7,291
+82,Pb,1.46,5,112
+83,Bi,1.48,4,51
+84,Po,1.40,4,4
+85,At,1.50
+86,Rn,1.50
+87,Fr,2.60
+88,Ra,2.21,2,3
+89,Ac,2.15,1
+90,Th,2.06,6,11
+91,Pa,2.00,1
+92,U,1.96,7,57
+93,Np,1.90,1,22
+94,Pu,1.87,1,9
+95,Am,1.80,6,11
+96,Cm,1.69,3,16