molSimplify 1.7.4__py3-none-any.whl

molSimplify/Informatics/partialcharges.py

@@ -0,0 +1,345 @@
+import numpy as np
+
+from molSimplify.Scripts.geometry import distance
+
+
+def fpriority(mol):
+    # setting up variables
+    fidx_list = []
+    sidx_list = []
+    satno_list = []
+    ref_list = []
+    fd_list = []
+    # fa_list = []
+    # idx_list = [0] * 6
+    exit_signal = True
+    # getting bond-order matrix
+    mol.convert2OBMol()
+    BOMatrix = mol.populateBOMatrix()
+
+    # preping for the loop
+    fidx_list.append(mol.findMetal())
+    for i in range(len(fidx_list)):
+        for fidx in fidx_list[i]:
+            for sidx in mol.getBondedAtoms(fidx):
+                sidx_list.append([sidx])
+
+    for i in range(len(fidx_list)):
+        for fidx in fidx_list[i]:
+            for j in range(len(sidx_list)):
+                for sidx in sidx_list[j]:
+                    BO = int(BOMatrix[fidx][sidx])
+                    if BO == 0:
+                        BO = 1
+                    satno_str = str(mol.getAtom(sidx).atno)
+                    satno_list.append(int(BO * satno_str))
+
+    for satno in set(satno_list):
+        satnocount = satno_list.count(satno)
+        if satnocount > 1:
+            s_sel_list = [i for i, atno in enumerate(satno_list) if atno is satno]
+            exit_signal = False
+
+    for i in range(len(fidx_list)):
+        for fidx in fidx_list[i]:
+            ref_list.append(fidx)
+
+    # starting the loop
+    tidx_list = []
+    tatno_list = []
+    for i in range(len(sidx_list)):
+        tidx_list.append([])
+        tatno_list.append([])
+
+    while not exit_signal:
+        fpriority_list = []
+        for i in s_sel_list:
+            t_list = []
+            for sidx in sidx_list[i]:
+                for tidx in mol.getBondedAtoms(sidx):
+                    if tidx not in ref_list:
+                        t_list.append(tidx)
+            tidx_list[i] = t_list
+        # print(sidx_list)
+        # print(tidx_list)
+        for i in s_sel_list:
+            for sidx in sidx_list[i]:
+                atno_list = tatno_list[i]
+                ls = []
+                for j in s_sel_list:
+                    for tidx in tidx_list[j]:
+                        BO = int(BOMatrix[sidx][tidx])
+                        tatno_str = str(mol.getAtom(tidx).atno)
+                        ls.append(BO * tatno_str)
+                sorted(ls, reverse=True)
+                for j in ls:
+                    atno_list.append(j)
+                a = ''.join(atno_list)
+            tatno_list[i] = [a]
+        sidx_list = []
+        for i in range(len(tidx_list)):
+            sidx_list.append(tidx_list[i])
+        for i in s_sel_list:
+            for sidx in sidx_list[i]:
+                ref_list.append(sidx)
+        test_list = []
+        for i in range(len(sidx_list)):
+            test_list.append([])
+        # get priorities
+        for i in range(len(satno_list)):
+            atno_list = []
+            atno_list.append(str(satno_list[i]))
+            if tatno_list[i] == []:
+                atno_list.append('')
+            else:
+                atno_list.append(tatno_list[i][0])
+            a = '.'.join(atno_list)
+            fpriority_list.append(float(a))
+        if tidx_list == test_list or len(set(fpriority_list)) == 6:
+            exit_signal = True
+    # get distance
+    fd_list = []
+    mcoord = mol.atoms[mol.findMetal()[0]].coords()
+    idx_list = np.argsort(np.array(fpriority_list))
+    fpriority_list = np.array(fpriority_list)[idx_list].tolist()
+    sidx_list = mol.getBondedAtoms(fidx_list[0][0])
+    for idx in idx_list:
+        scoord = mol.getAtom(sidx_list[idx]).coords()
+        r = distance(mcoord, scoord)
+        fd_list.append(r)
+
+    # idx = np.argsort(np.array(fpriority_list))[-1]
+    # sidx_list = mol.getBondedAtomsByCoordNo(fidx_list[0][0],6)
+    # refcoord = mol.getAtom(sidx_list[idx]).coords()
+    # mcoord = mol.getAtom(fidx_list[0][0]).coords()
+    # idx0 = 0
+    # dist5 = 0
+    # idx5 = 0
+    # idx1_4 = []
+    # fprio1_4 = []
+    # sxyzs = []
+    # ssd_list = []
+    # for i, sidx in enumerate(sidx_list):
+    #     sxyz = mol.getAtom(sidx).coords()
+    #     dist = distance(refcoord,sxyz)
+    #     if dist == 0:
+    #         idx0 = i
+    #     elif dist > dist5:
+    #         dist5 = dist
+    #         idx5 = i
+    #     idx1_4.append(i)
+    #     fprio1_4.append(fpriority_list[i])
+    #     sxyzs.append(sxyz)
+    #     ssd_list.append(dist)
+    #     fd_list.append(distance(mcoord,sxyz))
+    # idx1_4.pop(idx0)
+    # idx1_4.pop(idx5)
+    # fprio1_4.pop(idx0)
+    # fprio1_4.pop(idx5)
+    # idx_list[0] = idx0
+    # idx_list[5] = idx5
+    # idx1 = idx1_4[np.argsort(np.array(fprio1_4))[3]]
+    # sxyz1 = sxyzs[idx1]
+    # idx2_ = idx1_4[np.argsort(np.array(fprio1_4))[2]]
+    # sxyz2_ = sxyzs[idx2_]
+    # idx3_ = idx1_4[np.argsort(np.array(fprio1_4))[1]]
+    # sxyz3_ = sxyzs[idx3_]
+    # idx4_ = idx1_4[np.argsort(np.array(fprio1_4))[0]]
+    # sxyz4_ = sxyzs[idx4_]
+    # fd1_4 = []
+    # fd1_4.append(distance(sxyz1, sxyz1))
+    # fd1_4.append(distance(sxyz1, sxyz2_))
+    # fd1_4.append(distance(sxyz1, sxyz3_))
+    # fd1_4.append(distance(sxyz1, sxyz4_))
+    # idx3 = idx1_4[np.argsort(np.array(fd1_4))[-1]] + idx1 - 4
+    # if idx3 == idx2_:
+    #     if fpriority_list[idx3_] > fpriority_list[idx4_]:
+    #         idx2 = idx3_
+    #         idx4 = idx4_
+    #     else:
+    #         idx2 = idx4_
+    #         idx4 = idx2_
+    # elif idx3 == idx4_:
+    #     if fpriority_list[idx2_] > fpriority_list[idx3_]:
+    #         idx2 = idx2_
+    #         idx4 = idx3_
+    #     else:
+    #         idx2 = idx3_
+    #         idx4 = idx2_
+    # else:
+    #     if fpriority_list[idx2_] > fpriority_list[idx4_]:
+    #         idx2 = idx2_
+    #         idx4 = idx4_
+    #     else:
+    #         idx2 = idx4_
+    #         idx4 = idx2_
+    # # get ax, eq, ax idxes
+    # idx_list[1] = idx1
+    # idx_list[2] = idx2
+    # idx_list[3] = idx3
+    # idx_list[4] = idx4
+    # fpriority_list = np.array(fpriority_list)[idx_list].tolist()
+    # fd_list = np.array(fd_list)[idx_list].tolist()
+
+    return fpriority_list, fd_list, idx_list
+
+
+def fsym(mol):
+    # getting idxs of interest
+    midx = mol.findMetal()[0]  # monometallic complexes
+    fidx_list = mol.getBondedAtoms(midx)  # list of idx of the first-coord sphere
+    fsym_list = []
+    for idx in fidx_list:
+        sym = mol.getAtom(idx).sym
+        fsym_list.append(sym)
+    return fsym_list
+
+
+def fvalency(mol):
+    # getting idxs of interest
+    midx = mol.findMetal()[0]  # monometallic complexes
+    fidx_list = mol.getBondedAtoms(midx)  # list of idx of the first-coord sphere
+    fvalency_list = []
+    for idx in fidx_list:
+        valency = len(mol.getBondedAtoms(idx)) - 1
+        fvalency_list.append(valency)
+    return fvalency_list
+
+
+def fcharge(mol, charge, bond=False):
+    # getting idxs of interest
+    midx = mol.findMetal()[0]  # monometallic complexes
+    fidx_list = mol.getBondedAtoms(midx)  # list of idx of the first-coord sphere
+    mol.calcCharges(charge, bond)
+    fcharge_list = []
+    for idx in fidx_list:
+        partialq = mol.partialcharges[idx]
+        fcharge_list.append(float(partialq))
+    return fcharge_list
+
+
+def scharge_ave(mol, charge, bond=False):
+    mol.calcCharges(charge)
+    # getting idxs of interest
+    midx = mol.findMetal()[0]  # monometallic complexes
+    fidx_list = mol.getBondedAtoms(midx)  # list of idx of the first-coord sphere
+    mol.calcCharges(charge, bond)
+    sidx_list = [mol.getBondedAtoms(fidx) for fidx in fidx_list]
+    scharge_ave_list = []
+    for i in range(len(sidx_list)):
+        partialq = 0
+        for j in range(len(sidx_list[i])):
+            idx = sidx_list[i][j]
+            if idx is not midx:
+                partialq += mol.partialcharges[idx]
+        charge_ave = partialq/len(sidx_list[i])
+        scharge_ave_list.append(float(charge_ave))
+
+    return scharge_ave_list
+
+# def fdistance(mol):
+#     # getting idxs of interest
+#     midx = mol.findMetal()[0] # monometallic complexes
+#     mcoord = mol.getAtom(midx).coords()
+#     fidx_list = mol.getBondedAtoms(midx) # list of idx of the first-coord sphere
+#     fdistance_list = []
+#     for idx in fidx_list:
+#         fcoord = mol.getAtom(idx).coords()
+#         d = distance(mcoord,fcoord)
+#         fdistance_list.append(float(d))
+
+#     return fdistance_list
+
+
+def all_prop(mol, charge, bond=False):
+    fprio_list, fd_list, idx_list = fpriority(mol)
+    # fsym_list = fsym(mol)
+    fva_list = fvalency(mol)
+    fq_list = fcharge(mol, charge, bond)
+    sq_ave_list = scharge_ave(mol, charge, bond)
+    # fd_list = fdistance(mol)
+    fd_list = np.array(fd_list)
+    idx_list = idx_list(fprio_list, fd_list)
+    # rearranging
+    fprio_list = [fprio_list[idx] for idx in idx_list]
+    fq_list = [fq_list[idx] for idx in idx_list]
+    sq_ave_list = [sq_ave_list[idx] for idx in idx_list]
+    fva_list = [fva_list[idx] for idx in idx_list]
+    fd_list = [fd_list[idx] for idx in idx_list]
+
+    prop_list = fprio_list + fq_list + sq_ave_list + fva_list + fd_list
+
+    return prop_list
+
+
+def f_prop(mol, charge, bond=False):
+    fprio_list, fd_list, idx_list = fpriority(mol)
+    # fsym_list = fsym(mol)
+    fva_list = fvalency(mol)
+    fq_list = fcharge(mol, charge, bond)
+    # sq_ave_list = scharge_ave(mol, charge, bond)
+    # fd_list = fdistance(mol)
+    idx_list = idx_list(fprio_list, fd_list)
+    # rearranging
+    fprio_list = [fprio_list[idx] for idx in idx_list]
+    fq_list = [fq_list[idx] for idx in idx_list]
+    fva_list = [fva_list[idx] for idx in idx_list]
+
+    prop_list = fprio_list + fq_list + fva_list
+
+    return prop_list
+
+
+def features(mol, charge, bond=False):
+    feature = []
+    feature_names = []
+    prop_list = all_prop(mol, charge, bond)
+    midx = mol.findMetal()[0]
+    manto = mol.getAtom(midx).atno
+    # a = np.array(prop_list)
+    # b = a.T[a[0].argsort()].T
+    # feature_list = b.tolist()
+    fatno_list = [int(str(i).split('.')[0]) for i in prop_list[:6]]
+    feature.append(manto)
+    for i in range(len(fatno_list)):
+        prop_list[i] = fatno_list[i]
+    feature += prop_list
+    # for i in range(len(feature_list)):
+    #     for j in range(len(feature_list[i])):
+    #         feature.append(feature_list[i][j])
+    feature_names = [
+        'mato', 'fatno_1', 'fatno_2', 'fatno_3', 'fatno_4', 'fatno_5', 'fatno_6',
+        'fq_1', 'fq_2', 'fq_3', 'fq_4', 'fq_5', 'fq_6',
+        'sqave_1', 'sqave_2', 'sqave_3', 'sqave_4', 'sqave_5', 'sqave_6',
+        'fval_1', 'fval_2', 'fval_3', 'fval_4', 'fval_5', 'fval_6',
+        'bl_1', 'bl_2', 'bl_3', 'bl_4', 'bl_5', 'bl_6']
+
+    return feature_names, feature
+    # return feature
+
+
+def ffeatures(mol, charge, bond=False):
+    feature = []
+    feature_names = []
+    prop_list = f_prop(mol, charge, bond)
+    midx = mol.findMetal()[0]
+    manto = mol.getAtom(midx).atno
+    fatno_list = [int(str(i).split('.')[0]) for i in prop_list[:6]]
+    feature.append(manto)
+    for i in range(len(fatno_list)):
+        prop_list[i] = fatno_list[i]
+    feature += prop_list
+    # a = np.array(prop_list)
+    # b = a.T[a[0].argsort()].T
+    # feature_list = b.tolist()
+    # feature_list[0] = [int(str(i).split('.')[0]) for i in feature_list[0]]
+    # feature.append(manto)
+    # for i in range(len(feature_list)):
+    #     for j in range(len(feature_list[i])):
+    #         feature.append(feature_list[i][j])
+    feature_names = [
+        'mato', 'fatno_1', 'fatno_2', 'fatno_3', 'fatno_4', 'fatno_5', 'fatno_6',
+        'fq_1', 'fq_2', 'fq_3', 'fq_4', 'fq_5', 'fq_6',
+        'fval_1', 'fval_2', 'fval_3', 'fval_4', 'fval_5', 'fval_6']
+
+    return feature_names, feature

molSimplify/Informatics/protein/activesite.py

@@ -0,0 +1,53 @@
+from molSimplify.Classes.monomer3D import monomer3D
+from molSimplify.Classes.mol3D import mol3D
+import pickle
+
+# filename.txt = txt file with a list of PDB codes
+# chosen_confs = folder with pickle files of protein3D objects
+# the string "metal" should be replaced with the periodic table symbol of the desired metal
+# pdbs = folder of pdb files; can be replaced with a urllib query
+# activesites = folder of metal active sites
+
+with open("filename.txt", 'r') as fin:
+    text = fin.readlines()
+for pdbid in text:
+    with open('chosen_confs/' + pdbid + '.pkl', 'rb') as fin:
+        p = pickle.load(fin)
+    for metal in p.findAtom("metal", False):
+        pdb = 'pdbs/' + pdbid
+        with open(pdb+'.pdb', 'r') as fin:
+            pdbfile = fin.readlines()
+        activesite = mol3D()
+        ids = []  # atom IDs
+        metal_aa3ds = p.getBoundMols(metal, True)
+        if metal_aa3ds is None:
+            continue
+        metal_all = p.getBoundMols(metal)
+        metal_aas = []
+        for aa3d in metal_aa3ds:
+            metal_aas.append(aa3d.three_lc)
+        coords = []
+        with open('activesites/' + pdbid + "_" + str(metal) + '.pdb', "a") as fout:
+            fout.write("HEADER " + pdbid + "_" + str(metal) + "\n")
+            ids.append(metal)
+            activesite.addAtom(p.atoms[metal], metal)
+            fout.write(p.atoms[metal].line)
+            coords.append(p.atoms[metal].coords())
+            for m in metal_all:
+                if type(m) == monomer3D:
+                    for (a_id, a) in m.atoms:
+                        if a.coords() not in coords:
+                            ids.append(a_id)
+                            activesite.addAtom(a, a_id)
+                            fout.write(a.line)
+                            coords.append(a.coords())
+                else:
+                    for a in m.atoms:
+                        if a.coords() not in coords:
+                            ids.append(p.getIndex(a))
+                            activesite.addAtom(a, p.getIndex(a))
+                            fout.write(a.line)
+                            coords.append(a.coords())
+            for lines in range(0, len(pdbfile)):
+                if "CONECT" in pdbfile[lines] and int(pdbfile[lines][6:11]) in ids:
+                    fout.write(pdbfile[lines])

molSimplify/Informatics/protein/pymol_add_hs.py

@@ -0,0 +1,33 @@
+# add hydrogens to pdb file
+
+import os
+from pymol import cmd
+from molSimplify.Classes.protein3D import protein3D
+from molSimplify.Classes.mol3D import mol3D
+
+d1 = "Fe-2His_xyz_turned_pdb/"  # directory of pdb files
+d2 = 'h_added/'  # directory to add pdb files with hydrogens
+
+for filename in os.listdir(d1):
+    if filename[:-4]+"_h.pdb" not in os.listdir(d2):
+        p = protein3D()
+        p.readfrompdb(d1+filename)
+        m = p.findMetal()
+        print(m)
+        fe = p.atoms[m[0]]  # index of metal, not necessarily Fe
+        hoh_indices = []
+        for a in p.bonds[fe]:
+            if type(p.getMolecule(p.getIndex(a))) == mol3D and p.getMolecule(p.getIndex(a)).name == "HOH":
+                hoh_indices.append(str(p.getIndex(a)))
+        cmd.load(d1+filename)
+        sele = ""
+        for i in hoh_indices:
+            sele += "(idx " + i + ") or "
+        sele = sele[:-4]
+        if sele != "":
+            cmd.select(sele)
+            cmd.alter("sele", "formal_charge=1", quiet=1, space=None)
+        cmd.h_add("("+filename[:-4]+")")
+        cmd.save(d2+filename)
+        cmd.delete("all")
+        print(filename)

molSimplify/Informatics/rac155_geo.py

@@ -0,0 +1,48 @@
+"""
+This is the list of features in the RAC-155 set
+J. Phys. Chem. A ,2017, 121, 46, 8939-8954
+"""
+rac155_list = [
+    'misc-dent-ax', 'misc-dent-eq', 'ox', 'alpha',
+    'f-chi-0-ax', 'f-chi-1-ax', 'f-chi-2-ax', 'f-chi-3-ax',
+    'f-Z-0-ax', 'f-Z-1-ax', 'f-Z-2-ax', 'f-Z-3-ax',
+    'f-I-0-ax', 'f-I-1-ax', 'f-I-2-ax', 'f-I-3-ax',
+    'f-T-0-ax', 'f-T-1-ax', 'f-T-2-ax', 'f-T-3-ax',
+    'f-S-0-ax', 'f-S-1-ax', 'f-S-2-ax', 'f-S-3-ax',
+    'f-chi-0-eq', 'f-chi-1-eq', 'f-chi-2-eq', 'f-chi-3-eq',
+    'f-Z-0-eq', 'f-Z-1-eq', 'f-Z-2-eq', 'f-Z-3-eq',
+    'f-I-0-eq', 'f-I-1-eq', 'f-I-2-eq', 'f-I-3-eq',
+    'f-T-0-eq', 'f-T-1-eq', 'f-T-2-eq', 'f-T-3-eq',
+    'f-S-0-eq', 'f-S-1-eq', 'f-S-2-eq', 'f-S-3-eq',
+    'lc-chi-0-ax', 'lc-chi-1-ax', 'lc-chi-2-ax', 'lc-chi-3-ax',
+    'lc-Z-0-ax', 'lc-Z-1-ax', 'lc-Z-2-ax', 'lc-Z-3-ax',
+                 'lc-I-1-ax', 'lc-I-2-ax', 'lc-I-3-ax',
+    'lc-T-0-ax', 'lc-T-1-ax', 'lc-T-2-ax', 'lc-T-3-ax',
+    'lc-S-0-ax', 'lc-S-1-ax', 'lc-S-2-ax', 'lc-S-3-ax',
+    'lc-chi-0-eq', 'lc-chi-1-eq', 'lc-chi-2-eq', 'lc-chi-3-eq',
+    'lc-Z-0-eq', 'lc-Z-1-eq', 'lc-Z-2-eq', 'lc-Z-3-eq',
+                 'lc-I-1-eq', 'lc-I-2-eq', 'lc-I-3-eq',
+    'lc-T-0-eq', 'lc-T-1-eq', 'lc-T-2-eq', 'lc-T-3-eq',
+    'lc-S-0-eq', 'lc-S-1-eq', 'lc-S-2-eq', 'lc-S-3-eq',
+    'mc-chi-0-all', 'mc-chi-1-all', 'mc-chi-2-all', 'mc-chi-3-all',
+    'mc-Z-0-all', 'mc-Z-1-all', 'mc-Z-2-all', 'mc-Z-3-all',
+                                'mc-I-2-all', 'mc-I-3-all',
+                  'mc-T-1-all', 'mc-T-2-all', 'mc-T-3-all',
+    'mc-S-0-all', 'mc-S-1-all', 'mc-S-2-all', 'mc-S-3-all',
+    'f-chi-0-all', 'f-chi-1-all', 'f-chi-2-all', 'f-chi-3-all',
+    'f-Z-0-all', 'f-Z-1-all', 'f-Z-2-all', 'f-Z-3-all',
+    'f-I-0-all', 'f-I-1-all', 'f-I-2-all', 'f-I-3-all',
+    'f-T-0-all', 'f-T-1-all', 'f-T-2-all', 'f-T-3-all',
+    'f-S-0-all', 'f-S-1-all', 'f-S-2-all', 'f-S-3-all',
+                 'D_lc-chi-1-ax', 'D_lc-chi-2-ax', 'D_lc-chi-3-ax',
+                 'D_lc-Z-1-ax', 'D_lc-Z-2-ax', 'D_lc-Z-3-ax',
+                 'D_lc-T-1-ax', 'D_lc-T-2-ax', 'D_lc-T-3-ax',
+                 'D_lc-S-1-ax', 'D_lc-S-2-ax', 'D_lc-S-3-ax',
+                 'D_lc-chi-1-eq', 'D_lc-chi-2-eq', 'D_lc-chi-3-eq',
+                 'D_lc-Z-1-eq', 'D_lc-Z-2-eq', 'D_lc-Z-3-eq',
+                 'D_lc-T-1-eq', 'D_lc-T-2-eq', 'D_lc-T-3-eq',
+                 'D_lc-S-1-eq', 'D_lc-S-2-eq', 'D_lc-S-3-eq',
+                 'D_mc-chi-1-all', 'D_mc-chi-2-all', 'D_mc-chi-3-all',
+                 'D_mc-Z-1-all', 'D_mc-Z-2-all', 'D_mc-Z-3-all',
+                 'D_mc-T-1-all', 'D_mc-T-2-all', 'D_mc-T-3-all',
+                 'D_mc-S-1-all', 'D_mc-S-2-all', 'D_mc-S-3-all']

molSimplify/Ligands/(1_methylbenzimidazol_2_yl)pyridine.xyz

@@ -0,0 +1,45 @@
+43
+
+C          1.18815       -2.01640        0.00000
+C          0.34469       -0.85240        0.00000
+C          0.87040        0.48444        0.00000
+C          2.26603        0.64663        0.00000
+N          2.90291       -0.52925        0.00000
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+H          0.71907       -2.98104        0.00000
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+C          3.25361        1.91008        0.00000
+N          4.55241        1.75897        0.00000
+C          5.23429        2.97750       -0.00000
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+N          2.99646        3.28141        0.00000
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+C          1.72767        3.97538        0.00000
+H          0.87834        3.28315        0.00000
+H          1.65340        4.61351       -0.90516
+H          1.65341        4.61351        0.90516
+C          2.84853       -5.15900       -0.00000
+H          1.85267       -4.70826       -0.00000
+H          2.93476       -5.79657        0.90477
+H          2.93476       -5.79657       -0.90478
+C          5.84699       -5.70966       -0.00000
+C          7.25039       -5.76446       -0.00000
+C          8.01509       -4.57517        0.00000
+C          7.38480       -3.31222        0.00000
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+C          5.93698        5.67325       -0.00000
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+H          7.96497       -2.39981        0.00000
+H          5.25894       -6.61902       -0.00000
+H          7.74503       -6.72796        0.00000

molSimplify/Ligands/1-4-dimethyl-1-2-3-triazole.xyz

@@ -0,0 +1,15 @@
+13
+5
+C         -1.23999        0.01104        0.00434
+C         -0.40524       -1.08460        0.00661
+N          0.89647       -0.65552        0.00580
+N          0.89554        0.67092        0.00325
+N         -0.38501        1.07078        0.00255
+C         -0.71909        2.46919        0.00051
+C         -0.72809       -2.52346        0.00966
+H          0.19584        3.06717        0.00146
+H         -1.30562        2.68518        0.89687
+H         -1.30263        2.68329       -0.89823
+H         -1.81003       -2.68853        0.01089
+H         -0.30856       -3.00602        0.89772
+H         -0.31000       -3.00950       -0.87718

molSimplify/Ligands/12crown4.mol

@@ -0,0 +1,62 @@
+
+ OpenBabel03301717123D
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+ 28  3  1  0  0  0  0
+M  CHG  1   1   0
+M  END

molSimplify/Ligands/Antipyrine.mol

@@ -0,0 +1,58 @@
+
+ OpenBabel03301714373D
+
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+M  END