molSimplify 1.7.4__py3-none-any.whl

molSimplify/Ligands/uthiol.mol

@@ -0,0 +1,11 @@
+
+ OpenBabel11111617123D
+
+  3  2  0  0  0  0  0  0  0  0999 V2000
+   -2.3792    2.4761   -0.1357 S   0  5  0  0  0  0  0  0  0  0  0  0
+   -3.2982    2.0407    0.8369 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.4676    3.3012   -0.4742 H   0  0  0  0  0  0  0  0  0  0  0  0
+  2  1  1  0  0  0  0
+  3  1  1  0  0  0  0
+M  CHG  1   1   0
+M  END

molSimplify/Ligands/uthiolme2.mol

@@ -0,0 +1,23 @@
+
+ OpenBabel11111614373D
+
+  9  8  0  0  0  0  0  0  0  0999 V2000
+   -2.2902    2.9376    0.3036 S   0  5  0  0  0  0  0  0  0  0  0  0
+   -2.8952    1.6702    0.3801 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.9734    3.1884   -0.9006 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.7134    4.1613   -1.2622 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.0284    3.1420   -0.7285 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.6978    2.4525   -1.6269 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.5596    1.1674    1.2630 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.6279    1.0947   -0.4815 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.9585    1.7842    0.4170 H   0  0  0  0  0  0  0  0  0  0  0  0
+  2  1  1  0  0  0  0
+  2  7  1  0  0  0  0
+  2  8  1  0  0  0  0
+  2  9  1  0  0  0  0
+  3  1  1  0  0  0  0
+  3  4  1  0  0  0  0
+  3  5  1  0  0  0  0
+  3  6  1  0  0  0  0
+M  CHG  1   1   0
+M  END

molSimplify/Ligands/valine.mol

@@ -0,0 +1,42 @@
+
+ OpenBabel04201614323D
+
+ 19 18  0  0  1  0  0  0  0  0999 V2000
+    0.0950   -0.1810    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+    1.5470   -0.0260    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
+    1.9350    1.4340    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.0900    2.3370    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    2.1660   -0.7720   -1.2480 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.9770   -2.3080   -1.2170 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.6830   -0.5510   -1.5010 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.5710    0.6690    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.3770   -1.1520    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
+    1.9520   -0.4680    0.9280 H   0  0  0  0  0  0  0  0  0  0  0  0
+    1.6380   -0.3950   -2.1500 H   0  0  0  0  0  0  0  0  0  0  0  0
+    2.5290   -2.7820   -0.3840 H   0  0  0  0  0  0  0  0  0  0  0  0
+    0.9140   -2.5900   -1.1070 H   0  0  0  0  0  0  0  0  0  0  0  0
+    2.3230   -2.7830   -2.1550 H   0  0  0  0  0  0  0  0  0  0  0  0
+    4.3070   -0.8760   -0.6470 H   0  0  0  0  0  0  0  0  0  0  0  0
+    4.0430   -1.0940   -2.3960 H   0  0  0  0  0  0  0  0  0  0  0  0
+    3.9280    0.5110   -1.6960 H   0  0  0  0  0  0  0  0  0  0  0  0
+    3.3380    1.7080    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    3.8620    0.8210    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
+  2  3  1  0  0  0  0
+  2  1  1  0  0  0  0
+  2 10  1  1  0  0  0
+  4  3  2  0  0  0  0
+  5  6  1  0  0  0  0
+  5  2  1  0  0  0  0
+  6 13  1  0  0  0  0
+  6 12  1  0  0  0  0
+  7  5  1  0  0  0  0
+  7 15  1  0  0  0  0
+  8  1  1  0  0  0  0
+  9  1  1  0  0  0  0
+ 11  5  1  0  0  0  0
+ 14  6  1  0  0  0  0
+ 16  7  1  0  0  0  0
+ 17  7  1  0  0  0  0
+ 18  3  1  0  0  0  0
+ 19 18  1  0  0  0  0
+M  END

molSimplify/Ligands/water.mol

@@ -0,0 +1,10 @@
+
+ OpenBabel05081517533D
+
+  3  2  0  0  0  0  0  0  0  0999 V2000
+   -0.6304    3.4532    1.1538 O   0  0  0  0  0  0  0  0  0  0  0  0
+    0.3424    3.4532    1.3389 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.0533    3.4532    2.0492 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  1  3  1  0  0  0  0
+M  END

molSimplify/Ligands/x.mol

@@ -0,0 +1,6 @@
+
+ OpenBabel05071516093D
+
+  1  0  0  0  0  0  0  0  0  0999 V2000
+   -0.1892    0.7358    0.0000 H  0  0  0  0  0 15  0  0  0  0  0  0
+M  END

molSimplify/Scripts/addtodb.py

@@ -0,0 +1,308 @@
+# @file addtodb.py
+#  Adds new molecules to database
+#
+#  Written by Tim Ioannidis for HJK Group
+#  Modified by JP Janet and Aditya Nandy
+#  Dpt of Chemical Engineering, MIT
+
+from molSimplify.Scripts.io import (copy_to_custom_path, readdict,
+                                    lig_load, core_load, bind_load)
+from molSimplify.Classes.globalvars import globalvars
+import os
+import sys
+import re
+import unicodedata
+try:
+    from openbabel import openbabel  # version 3 style import
+except ImportError:
+    import openbabel  # fallback to version 2
+import shutil
+import pathlib
+
+
+def initialize_custom_database(globs):
+    print('To add to database, you need to set a custom path. Please enter a writeable file path:')
+    # Strip double quotes from the string
+    raw_input = input('path=').replace('"', '')
+    # Resolve the path to get the absolute path and convert back to string
+    new_path = str(pathlib.Path(raw_input).resolve())
+    globs.add_custom_path(new_path)
+    globs.custom_path = new_path
+    copy_to_custom_path()
+
+
+# Add molecule to ligand database
+#  @param smimol SMILES string or molecule file to be added
+#  @param sminame Name of ligand for key in dictionary
+#  @param smident Denticity of ligand
+#  @param smicat Ligand connecting atoms
+#  @param smigrps Ligand groups
+#  @param smictg Ligand category
+#  @param ffopt Flag for ligand FF optimization
+#  @return Error messages
+def addtoldb(smimol, sminame, smident, smicat, smigrps, smictg, ffopt, smichg=None):
+    emsg = False
+    globs = globalvars()
+    if not globs.custom_path or not os.path.exists(str(globs.custom_path)):
+        initialize_custom_database(globs)
+
+    lipath = globs.custom_path + "/Ligands/ligands.dict"
+    licores = readdict(lipath)
+    ligands_folder = globs.custom_path + "/Ligands/"
+    print("ligands_folder is : " + str(ligands_folder))
+    # check if ligand exists
+    if sminame in list(licores.keys()):
+        emsg = 'Ligand '+sminame+' already existing in ligands database.'
+        emsg += ' To replace, delete the existing entry first.'
+        return emsg
+    else:
+        # get connection atoms
+        ccats = [_f for _f in re.split(' |,|\t', smicat) if _f]
+        # get groups
+        groups = [_f for _f in re.split(' |,|\t', smigrps) if _f]
+        grp = 'build '+' '.join(groups)
+        grp += ' '+smictg
+        if smicat == '':
+            cats = list(range(0, int(smident)))
+        else:
+            cats = [int(a)-1 for a in ccats]
+        cs = [str(a) for a in cats]
+        # allows for pi-bonded ligands to be added
+        if smident == 1 and len(cs) > 1:
+            cs.append('pi')
+        css = ' '.join(cs)
+        # convert to unicode
+        smimol = unicodedata.normalize(
+            'NFKD', smimol)
+        sminame = unicodedata.normalize(
+            'NFKD', sminame)
+        if '~' in smimol:
+            smimol = smimol.replace('~', os.expanduser('~'))
+        # convert ligand from smiles/file
+        lig, emsg = lig_load(smimol, licores)
+        if emsg:
+            return emsg
+        lig.convert2mol3D()  # convert to mol3D
+
+        shortname = sminame
+        print("smimol is "+str(smimol))
+        print("sminame is "+str(sminame))
+        # sanitize ff options:
+        if ffopt not in ["A", "B", "BA", "N"]:
+            print('warning: incompatible ffopt choice. Options are ' +
+                  str(["A", "B", "BA", "N"]))
+            sys.exit(1)
+
+        if smichg is not None:
+            lig.charge = smichg
+        # new entry for dictionary
+        if '.mol' in smimol:
+            ext = '.' + smimol.split('.')[-1]
+            shutil.copy2(smimol, ligands_folder + sminame+ ext)
+            snew = str(sminame)+':'+str(sminame)+ext + ','+str(shortname)+','+str(css)+','+str(grp)+','+str(ffopt)+','+str(lig.charge)
+        elif '.xyz' in smimol:
+            shutil.copy2(smimol, ligands_folder + sminame+'.xyz')
+            snew = str(sminame)+':'+str(sminame)+'.xyz,'+str(shortname)+','+str(css)+','+str(grp)+','+str(ffopt)+','+str(lig.charge)
+        elif lig.OBMol:
+            # write smiles file in Ligands directory
+            obConversion = openbabel.OBConversion()
+            obConversion.SetOutFormat("smi")
+            obConversion.Read(lig.OBMol)
+            obConversion.WriteFile(lig.OBMol, ligands_folder + sminame+'.smi')
+            # lig.OBMol.write('smi',ligands_folder + sminame+'.smi')
+            snew = str(sminame)+':'+str(sminame)+'.smi,'+str(shortname)+','+str(css)+','+str(grp)+','+str(ffopt)+','+str(lig.charge)
+        else:
+            # write xyz file in Ligands directory
+            lig.writexyz(ligands_folder+sminame+'.xyz')  # write xyz file
+            snew = str(sminame)+':'+str(sminame)+'.xyz,'+str(shortname)+','+str(css)+','+str(grp)+','+str(ffopt)+','+str(lig.charge)
+        # update dictionary
+
+        with open(lipath, 'r') as f:
+            ss = f.read().splitlines()
+        ss.append(snew)
+        ssort = sorted(ss[1:])
+        with open(lipath, 'w') as f:
+            f.write(ss[0]+'\n')
+            for s in ssort:
+                f.write(s+'\n')
+    return emsg
+
+
+# Add molecule to cores database
+#  @param smimol SMILES string or molecule file to be added
+#  @param sminame Name of core for key in dictionary
+#  @param smicat Core connecting atoms
+#  @return Error messages
+def addtocdb(smimol, sminame, smicat):
+    emsg = False
+    globs = globalvars()
+    if not globs.custom_path or not os.path.exists(str(globs.custom_path)):
+        initialize_custom_database(globs)
+    cpath = globs.custom_path + "/Cores/cores.dict"
+    mcores = readdict(cpath)
+    cores_folder = globs.custom_path + "/Cores/"
+    # check if core exists
+    if sminame in list(mcores.keys()):
+        emsg = 'Core '+sminame+' already existing in core database.'
+        return emsg
+    else:
+        # get connection atoms
+        ccats = [_f for _f in re.split(' |,|\t', smicat) if _f]
+        cats = [int(a)-1 for a in ccats]
+        if len(cats) == 0:
+            cats = [0]
+        cs = [str(a) for a in cats]
+        css = ' '.join(cs)
+        # convert to unicode
+        smimol = unicodedata.normalize(
+            'NFKD', smimol)
+        if '~' in smimol:
+            smimol = smimol.replace('~', os.expanduser('~'))
+        # convert ligand from smiles/file
+        core, emsg = core_load(smimol, mcores)
+        if emsg:
+            return emsg
+        core.convert2mol3D()  # convert to mol3D
+        # write xyz file in Cores directory
+        # new entry for dictionary
+        if '.mol' in smimol:
+            shutil.copy2(smimol, cores_folder+sminame+'.mol')
+            snew = sminame+':'+sminame+'.mol,'+css+','+'1'
+        elif '.xyz' in smimol:
+            shutil.copy2(smimol, cores_folder + sminame+'.xyz')
+            snew = sminame+':'+sminame+'.xyz,'+css+','+'1'
+        else:
+            core.writexyz(cores_folder + sminame+'.xyz')  # write xyz file
+            # new entry for dictionary
+            snew = sminame+':'+sminame+'.xyz,'+css+','+'1'
+        # update dictionary
+        with open(cpath, 'r') as f:
+            ss = f.read().splitlines()
+        ss.append(snew)
+        ssort = sorted(ss[1:])
+        with open(cpath, 'w') as f:
+            f.write(ss[0]+'\n')
+            for s in ssort:
+                f.write(s+'\n')
+    return emsg
+
+
+# Add molecule to binding species database
+#  @param smimol SMILES string or molecule file to be added
+#  @param sminame Name of binding species for key in dictionary
+#  @return Error messages
+def addtobdb(smimol, sminame):
+    globs = globalvars()
+    if not globs.custom_path or not os.path.exists(str(globs.custom_path)):
+        initialize_custom_database(globs)
+    bpath = globs.custom_path + "/Bind/bind.dict"
+    bindcores = readdict(bpath)
+    bind_folder = globs.custom_path + "/Bind/"
+    # check if binding species exists
+    if sminame in list(bindcores.keys()):
+        emsg = 'Molecule '+sminame+' already existing in binding species database.'
+        return emsg
+    else:
+        # convert to unicode
+        smimol = unicodedata.normalize(
+            'NFKD', smimol)
+        sminame = unicodedata.normalize(
+            'NFKD', sminame)
+        if '~' in smimol:
+            smimol = smimol.replace('~', os.expanduser('~'))
+        # convert ligand from smiles/file
+        bind, bsmi, emsg = bind_load(smimol, bindcores)
+        if emsg:
+            return emsg
+        bind.convert2mol3D()  # convert to mol3D
+        # new entry for dictionary
+        # create shortname
+        if len(sminame) > 5:
+            shortname = sminame[0:3]+sminame[-2:]
+        else:
+            shortname = sminame
+        if '.mol' in smimol:
+            shutil.copy2(smimol, bind_folder+sminame+'.mol')
+            snew = sminame+':'+sminame+'.mol,'+shortname+','
+        elif '.xyz' in smimol:
+            shutil.copy2(smimol, bind_folder + sminame+'.xyz')
+            snew = sminame+':'+sminame+'.xyz,'+shortname+','
+        elif bind.OBmol:
+            # write smiles file in Bind species directory
+            bind.OBmol.write('smi', bind_folder + sminame+'.smi')
+            snew = sminame+':'+sminame+'.smi,'+shortname+','
+        else:
+            # write xyz file in Bind species directory
+            bind.writexyz(bind_folder + sminame+'.xyz')  # write xyz file
+            snew = sminame+':'+sminame+'.xyz,'+shortname+','
+        # update dictionary
+        with open(bpath, 'r') as f:
+            ss = f.read().splitlines()
+        ss.append(snew)
+        ssort = sorted(ss[1:])
+        with open(bpath, 'w') as f:
+            f.write(ss[0]+'\n')
+            for s in ssort:
+                f.write(s+'\n')
+    return emsg
+
+
+# Remove molecule from database
+#  @param sminame Name of molecule for key in dictionary
+#  @param ropt Flag for molecule type (0 for core, 1 for ligand, 2 for binding species)
+#  @return Error messages
+def removefromDB(sminame, ropt):
+    emsg = False
+    globs = globalvars()
+    if not globs.custom_path or not os.path.exists(str(globs.custom_path)):
+        initialize_custom_database(globs)
+    li_path = globs.custom_path + "/Ligands/ligands.dict"
+    li_folder = globs.custom_path + "/Ligands/"
+    core_path = globs.custom_path + "/Cores/cores.dict"
+    core_folder = globs.custom_path + "/Cores/"
+    bind_path = globs.custom_path + "/Bind/bind.dict"
+    bind_folder = globs.custom_path + "/Bind/"
+
+    # convert to unicode
+    sminame = unicodedata.normalize('NFKD', sminame)
+
+    if ropt == 1:
+        # update dictionary
+        with open(li_path, 'r') as f:
+            ss = f.read().splitlines()
+        ssort = sorted(ss[1:])
+        with open(li_path, 'w') as f:
+            f.write(ss[0]+'\n')
+            for s in ssort:
+                sss = s.split(':')
+                if sminame != sss[0]:
+                    f.write(s+'\n')
+                else:
+                    os.remove(li_folder + sss[1].split(',')[0])
+    elif ropt == 0:
+        # update dictionary
+        with open(core_path, 'r') as f:
+            ss = f.read().splitlines()
+        ssort = sorted(ss[1:])
+        with open(core_path, 'w') as f:
+            f.write(ss[0]+'\n')
+            for s in ssort:
+                sss = s.split(':')
+                if sminame != sss[0]:
+                    f.write(s+'\n')
+                else:
+                    os.remove(core_folder+sss[1].split(',')[0])
+    elif ropt == 2:
+        # update dictionary
+        with open(bind_path, 'r') as f:
+            ss = f.read().splitlines()
+        ssort = sorted(ss[1:])
+        with open(bind_path, 'w') as f:
+            f.write(ss[0]+'\n')
+            for s in ssort:
+                sss = s.split(':')
+                if sminame != sss[0]:
+                    f.write(s+'\n')
+                else:
+                    os.remove(bind_folder+sss[1].split(',')[0])
+    return emsg