i have changes here?

cctk/molecule.py

@@ -1648,19 +1648,20 @@ def optimize(self, inplace=True, nprocs=1):
         else:
             return optimized
 
-    def csearch(self, nprocs=1, constraints=[], logfile=None, noncovalent=False):
+    def csearch(self, nprocs=1, constraints=[], logfile=None, noncovalent=False, use_tempdir=True):
         """
         Optimize molecule at the GFN2-xtb level of theory.
 
         Args:
             nprocs (int): number of processors to use
             constraints (list): atoms numbers to freeze
-            noncovalent (Bool): whether or not to use non-covalent settings
+            noncovalent (bool): whether or not to use non-covalent settings
             logfile (str): file to write ongoing ``crest`` output to
+            use_tempdir (bool): write intermediate files to hidden directory (as opposed to current directory)
 
         Returns
             ConformationalEnsemble
         """
         import cctk.optimize as opt
         assert isinstance(nprocs, int), "nprocs must be int!"
-        return opt.csearch(self, nprocs=nprocs, constraints=constraints, noncovalent=noncovalent, logfile=logfile)
+        return opt.csearch(molecule=self, nprocs=nprocs, constraints=constraints, noncovalent=noncovalent, logfile=logfile, use_tempdir=use_tempdir)

cctk/optimize.py

@@ -78,7 +78,7 @@ def run_xtb(molecule, nprocs=1, return_energy=False):
     else:
         return output_mol
 
-def csearch(molecule, constraints=None, rotamers=False, nprocs=1, noncovalent=False, logfile=None):
+def csearch(use_tempdir=True, **kwargs):
     """
     Run a conformational search on a molecule using ``crest``.
 
@@ -93,45 +93,54 @@ def csearch(molecule, constraints=None, rotamers=False, nprocs=1, noncovalent=Fa
     Returns:
         cctk.ConformationalEnsemble
     """
+    assert installed("crest"), "crest must be installed!"
+
+    ensemble = None
+    try:
+        if use_tempdir:
+            with tempfile.TemporaryDirectory() as tmpdir:
+                ensemble = _do_csearch(directory=tmpdir, **kwargs)
+        else:
+            ensemble = _do_csearch(directory=os.getcwd(), **kwargs)
+    except Exception as e:
+        raise ValueError(f"Error running xtb:\n{e}")
+
+    return ensemble
+
+def _do_csearch(molecule, nprocs, logfile, noncovalent, directory, constraints):
     assert isinstance(molecule, cctk.Molecule), "need a valid molecule!"
     assert isinstance(nprocs, int)
     assert isinstance(logfile, str)
 
-    assert installed("crest"), "crest must be installed!"
+    cctk.XYZFile.write_molecule_to_file(f"{directory}/xtb-in.xyz", molecule)
 
     nci = ""
     if noncovalent:
         nci = "-nci"
 
-    ensemble = None
-    try:
-        with tempfile.TemporaryDirectory() as tmpdir:
-            cctk.XYZFile.write_molecule_to_file(f"{tmpdir}/xtb-in.xyz", molecule)
+    if constraints is not None:
+        assert isinstance(constraints, list)
+        assert all(isinstance(n, int) for n in constraints)
+        command = f"crest xtb-in.xyz --constrain {','.join([str(c) for c in constraints])}"
+        result = sp.run(command, stdout=sp.PIPE, stderr=sp.PIPE, cwd=directory, shell=True)
+        result.check_returncode()
 
-            if constraints is not None:
-                assert isinstance(constraints, list)
-                assert all(isinstance(n, int) for n in constraints)
-                command = f"crest xtb-in.xyz --constrain {','.join([str(c) for c in constraints])}"
-                result = sp.run(command, stdout=sp.PIPE, stderr=sp.PIPE, cwd=tmpdir, shell=True)
-                result.check_returncode()
+    command = f"crest xtb-in.xyz --chrg {molecule.charge} --uhf {molecule.multiplicity - 1} -T {nprocs} {nci}"
 
-            command = f"crest xtb-in.xyz --chrg {molecule.charge} --uhf {molecule.multiplicity - 1} -T {nprocs} {nci}"
+    if logfile:
+        with open(logfile, "w") as f:
+            result = sp.run(command, stdout=f, stderr=f, cwd=directory, shell=True)
+    else:
+        result = sp.run(command, stdout=sp.PIPE, stderr=sp.PIPE, cwd=directory, shell=True)
 
-            if logfile:
-                with open(logfile, "w") as f:
-                    result = sp.run(command, stdout=f, stderr=f, cwd=tmpdir, shell=True)
-            else:
-                result = sp.run(command, stdout=sp.PIPE, stderr=sp.PIPE, cwd=tmpdir, shell=True)
+    result.check_returncode()
 
-            result.check_returncode()
+    if rotamers:
+        ensemble = cctk.XYZFile.read_ensemble(f"{directory}/crest_rotamers.xyz")
+    else:
+        ensemble = cctk.XYZFile.read_ensemble(f"{directory}/crest_conformers.xyz")
 
-            if rotamers:
-                ensemble = cctk.XYZFile.read_ensemble(f"{tmpdir}/crest_rotamers.xyz")
-            else:
-                ensemble = cctk.XYZFile.read_ensemble(f"{tmpdir}/crest_conformers.xyz")
+    return ensemble
 
-    except Exception as e:
-        raise ValueError(f"Error running xtb:\n{e}")
 
-    return ensemble