diff --git a/CHANGELOG b/CHANGELOG
new file mode 100644
index 00000000..2a8b363f
--- /dev/null
+++ b/CHANGELOG
@@ -0,0 +1,11 @@
+## [0.6] - 2022-12-05
+### Removed
+- Removed invalid docker code
+
+### Fixed
+- Moved doc files out of package
+- Cleaned up installation disorder
+
+### Added
+- `MANIFEST.in` for two files which are required by the package
+- Submodule `quick` for a quick download of the data as it appears on the site, which is what most folks want anyway
\ No newline at end of file
diff --git a/Dockerfile b/Dockerfile
deleted file mode 100755
index 27f716a6..00000000
--- a/Dockerfile
+++ /dev/null
@@ -1,9 +0,0 @@
-FROM conda/miniconda3
-ADD . /code
-RUN apt-get update -y
-RUN apt-get install -y build-essential python-dev python-pmw libglew-dev freeglut3-dev libpng-dev libfreetype6-dev libxml2-dev libmsgpack-dev python-pyqt5.qtopengl libglm-dev libnetcdf-dev
-RUN apt-get install -y git-all
-RUN chmod 775 /code/docker_install.sh
-RUN /code/docker_install.sh
-RUN conda init bash
-RUN cd /code; conda env create -f environment.yml 
diff --git a/MANIFEST.in b/MANIFEST.in
new file mode 100644
index 00000000..594fb4fd
--- /dev/null
+++ b/MANIFEST.in
@@ -0,0 +1,2 @@
+include fragalysis-api/fragalysis_api/xcglobalscripts/config.ini
+include fragalysis_api/xcimporter/non_ligs.json
\ No newline at end of file
diff --git a/README.md b/README.md
index fd91bf5c..b26850fd 100755
--- a/README.md
+++ b/README.md
@@ -4,50 +4,44 @@
 
 [![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/xchem/fragalysis-api.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/xchem/fragalysis-api/context:python)
 
-Documentation: https://xchem.github.io/fragalysis-api/
+Documentation: [https://xchem.github.io/fragalysis-api/](https://xchem.github.io/fragalysis-api/)
 
-This api aims to allow any user to upload pdb files from the pdb or that they have created themselves,
+This API aims to allow any user to upload pdb files from the pdb or that they have created themselves,
 and analyse the ligand binding using the fragalysis webpage (https://fragalysis.diamond.ac.uk).
+Namely:
+
+* Upload data, i.e. import into Fragalysis -> **xcimporter** functionality (_vide infra_)
+* Download data, i.e. export from Fragalysis -> **xcexporter** functionality (_vide infra_)
+
+The full list of Fragalysis API endpoints can be found at [fragalysis.diamond.ac.uk/api](https://fragalysis.diamond.ac.uk/api/).
 
 ## Installation
 
-Starting out by initialising an environment and activating it.
-Clone the repository and cd to the relevant directory.
-Install rdkit via conda, and the other dependencies via the setup.py file:
+In order to manipulate the data for upload (e.g. aligning crystal maps), 
+some additional dependencies are required,
+namely [xchem/gemmi_pandda](https://github.com/xchem/gemmi_pandda) and [xchem/pandda_gemmi](https://github.com/xchem/pandda_gemmi).
 
 ```bash
-conda create -n fragalysis_env anaconda -y
-conda activate fragalysis_env
-conda install -c conda-forge rdkit -y
-
-# Install our-bespoke version of gemmi # Required
-git clone https://github.com/xchem/gemmi_pandda.git
-cd gemmi_pandda/
-pip install -U --force-reinstall .
-cd ..
-
-# Also Required
-git clone https://github.com/xchem/pandda_gemmi.git
-cd pandda_gemmi/
-pip install -e .
-cd ..
-
-# Finally install the api
-git clone "https://github.com/xchem/fragalysis-api.git"
-cd fragalysis-api/
-pip install -e .
-cd ..
-```
+# Install our-bespoke version of gemmi # Required for upload
+# Do note this is a drop-in replacement for gemmi, so will interfere with other packages that use gemmi.
+pip install -U --force-reinstall git+https://github.com/xchem/gemmi_pandda.git
 
-You can check if it has installed using: `conda list`
+# Also Required for upload
+pip install -e git+https://github.com/xchem/pandda_gemmi.git
+```
+The API itself can be installed via pypi or from the Git repo:
+```bash
+pip install fragalysis-api
+# or (for a later version if available)
+pip install git+https://github.com/xchem/fragalysis-api.git
+```
 
 ### How to use API
 
-1. Set up environment
-2. Download PDB files and query the PDB for structures of the same protein bound to the same or different ligands
-3. Submit PDB files - you will be given a query ID
-4. Push your files into fragalysis and view them online :construction:
-5. Analyse the binding of ligands to your target protein!
+1. Download PDB files and query the PDB for structures of the same protein bound to the same or different ligands
+2. Submit PDB files - you will be given a query ID
+3. Push your files into fragalysis and view them online :construction:
+4. Analyse the binding of ligands to your target protein!
 
 Other functionalities that are available:
 
@@ -59,9 +53,40 @@ Other functionalities that are available:
 
 ## Usage in Python
 
+### Export from Fragalysis
+> TL;DR: This is a Python package for accurately interacting with the Fragalysis API, 
+> if you simply want to download everything of a target,
+> please see the [quick download notes](quick_download.md).
+
+Download relevant data off Fragalysis. 
+
+
+See also [extractor notes](extractor.md).
+
+```python
+import fragalysis_api
+import os
+import pandas as pd
+
+hit_data: pd.DataFrame = fragalysis_api.xcextracter(target_name='NUDT5A')
+```
+The columns in the dataframe are:
+
+* `id`
+* `prot_id`: unique integer id per crystal, e.g. `protein_code`:`NUDT5A-x0114_1` and `protein_code`:`NUDT5A-x0114_2` have different `prot_id` but same `cmpd_id`.
+* `protein_code`, a string form of the above (e.g. `NUDT5A-x0114_1`)
+* `cmpd_id`, an integer, unique per ligand, but not per crystal
+* `lig_id`, the chemical compounent name, generally `LIG`
+* `chain_id`, the chain id of the ligand
+* `smiles` and `sdf_info`, the SMILE-String and the SDF block of the ligand
+* `molecule_protein`, the bound PDB file address
+* `mw`, `logp`, `tpsa`, `ha`, `hacc`, `hdon`, `rots`, `rings`, `velec`: inferred chemical properties of the ligand
+
+### Import into Fragalysis
 To prepare input data-files using python you api can import the `xcimporer` or `import_single_file` functions and then provide the necessary values to the functions.
+ See also [importer notes](importer.md).
 
-e.g
+Example:
 
 ```python
 from fragalysis_api import xcimporter, import_single_file
@@ -209,8 +234,8 @@ A description of the arguments are as follows:
 
 ### Enforced rules :scroll:
 
-- The pdb file shall not be greater than 5mb.
-- The pdb filename shall not contain non English language ascii characters
+- The pdb file shall not be greater than 5MB.
+- The pdb filename shall only contain non ASCII characters (e.g. Unicode characters such as é or ü).
   and shall be between 4 and 20 characters in length.
 - Each pdb file for alignment shall contain the same number of chains.
 - All pdb files to be aligned must be in the same directory.
diff --git a/fragalysis_api/xcextracter/benzene.pdb b/data/benzene.pdb
similarity index 100%
rename from fragalysis_api/xcextracter/benzene.pdb
rename to data/benzene.pdb
diff --git a/docker_install.sh b/docker_install.sh
deleted file mode 100755
index 4dd69165..00000000
--- a/docker_install.sh
+++ /dev/null
@@ -1,7 +0,0 @@
-#!/bin/bash
-
-git clone https://github.com/schrodinger/pymol-open-source.git
-cd pymol-open-source
-prefix=$HOME/pymol-open-source-build
-# sudo apt-get install build-essential python-dev python-pmw libglew-dev freeglut3-dev libpng-dev libfreetype6-dev libxml2-dev libmsgpack-dev python-pyqt5.qtopengl libglm-dev libnetcdf-dev
-python setup.py build install --home=$prefix
diff --git a/fragalysis_api/xcextracter/README.md b/extractor.md
similarity index 100%
rename from fragalysis_api/xcextracter/README.md
rename to extractor.md
diff --git a/fragalysis_api/__init__.py b/fragalysis_api/__init__.py
index 935c9896..067de7f4 100755
--- a/fragalysis_api/__init__.py
+++ b/fragalysis_api/__init__.py
@@ -1,15 +1,28 @@
-from .xcglobalscripts.set_config import ConfigSetup
-
-from .xcimporter.validate import Validate, ValidatePDB
-from .xcimporter.conversion_pdb_mol import set_up, convert_small_AA_chains, copy_extra_files
-from .xcimporter.align import Align
-from .xcimporter.xc_utils import to_fragalysis_dir
-from .xcimporter.sites import Sites, contextualize_crystal_ligands
-from .xcimporter.xcimporter import xcimporter
-from .xcimporter.single_import import import_single_file
+from .xcglobalscripts.set_config import ConfigSetup  # this requires `config.ini` in the working directory
+
+# import into Fragalysis requires gemmi
+try:
+    from .xcimporter.validate import Validate, ValidatePDB
+    from .xcimporter.conversion_pdb_mol import set_up, convert_small_AA_chains, copy_extra_files
+    from .xcimporter.xc_utils import to_fragalysis_dir
+    from .xcimporter.sites import Sites, contextualize_crystal_ligands
+    from .xcimporter.xcimporter import xcimporter
+    from .xcimporter.single_import import import_single_file
+    from .xcimporter.align import Align
+except ImportError:
+    import warnings
+    warnings.warn("The xcimporter functionality is unavailable without Gemmi", category=ImportWarning)
+
+# extract from Fragalysis does not require gemmi
 from .xcextracter.getdata import GetTargetsData, GetMoleculesData, GetPdbData, GetMolgroupData
 from .xcextracter.frag_web_live import can_connect
 from .xcextracter.xcextracter import xcextracter
 
 from .xcanalyser.graphcreator import GraphRequest, xcgraphcreator
 from .xcanalyser.xcanalyser import xcanalyser
+
+# this is not part of canonical Fragalysis wrapper, but a quick way to get the data.
+from .quick import QuickDownloader
+
+
+
diff --git a/fragalysis_api/quick.py b/fragalysis_api/quick.py
new file mode 100644
index 00000000..ef507614
--- /dev/null
+++ b/fragalysis_api/quick.py
@@ -0,0 +1,185 @@
+"""
+A quick download functionality for the impatient.
+"""
+
+import warnings
+from typing import Optional, Tuple, List, Dict, Any
+
+import io
+import os
+import pandas as pd
+import requests
+import zipfile
+from rdkit.Chem import PandasTools
+
+
+class QuickDownloader:
+    """
+    This is simply a polished interface to the `api/download_structures` endpoint,
+    which is the same as the download button on the Fragalysis website.
+    Namely, it lacks the extended functionality of the `xcexporter` module.
+    Instantiating it with the target name will download the zip file of these and can be interactive with via different
+    methods.
+
+    :cvar: fragalysis_api_url: The URL of the Fragalysis API.
+    :cvar: api_data: The default options for the API endpoint. Can be also overridden in the constructor.
+    :ivar: target_name: The name of the target as on the main Fragalysis page, e.g. 'Mpro', case sensitive
+    :ivar: zf: The zip file object. see https://docs.python.org/3/library/zipfile.html
+
+    The contents of the ``zipfile.ZipFile`` object stored in the attribute ``.zf`` can be written to disk
+    with ``.write_all()``.
+
+    The contents of a file within the zipfile can be accessed by subscripting the ``QuickDownloader`` instance,
+    with a string that is contained in the filename, e.g. ``quick['metadata']``, will return the metadata.csv file
+    content without having to waste time with filepaths.
+
+    .. code-block:: python
+        from fragalysis_api import QuickDownloader
+        import pandas as pd
+        from typing import List
+        print(f'Default settings are: {QuickDownloader.api_data}')
+
+        # Check if the target name is right
+        target_names: List[str] = QuickDownloader.retrieve_target_names()
+        target_name='Mpro'
+        assert target_name in target_names, f'Target named "{target_name}" not found in the list of targets'
+
+        # Download the data
+        quick = QuickDownloader(target_name=target_name)
+        quick.write_all(directory='downloads')
+        hits: pd.DataFrame = quick.to_pandas(star_dummy=True)
+
+        # Not all files have the reference pdb block, so if it does not the template is returned:
+        reference_pdbblock: str = quick.reference_pdbblock
+
+    The class method ``QuickDownloader.retrieve_target_data`` will download all the metadata for the targets.
+    while ``QuickDownloader.retrieve_target_names`` will return their names.
+    """
+    fragalysis_api_url = 'fragalysis.diamond.ac.uk/api/download_structures/'
+    api_data = {
+        'proteins': '',
+        'event_info': False,
+        'sigmaa_info': False,
+        'diff_info': False,
+        'trans_matrix_info': False,
+        'NAN': False,
+        'mtz_info': False,
+        'cif_info': False,
+        'NAN2': False,
+        'map_info': False,
+        'single_sdf_file': True,
+        'sdf_info': False,
+        'pdb_info': False,
+        'bound_info': True,
+        'metadata_info': True,
+        'smiles_info': True,
+        'static_link': False,
+        'file_url': ''}
+
+    def __init__(self, target_name: str, **options):
+        """
+        Given a target download the zip file and store it in ``self.zf``.
+
+        :param target_name: The name of the target as on the main Fragalysis page, e.g. 'Mpro', case sensitive
+        :param options: Any of the options for the endpoint, e.g. ``event_info=True``, cf. ``cls.api_data``
+        """
+        self.target_name = target_name
+        self.api_data = {options.get(k, v) for k, v in self.api_data.items()}
+        url_response: requests.Response = requests.post(f'https://{self.fragalysis_api_url}',
+                                                        json={'target_name': self.target_name, **self.api_data})
+        url_response.raise_for_status()
+        self.file_url: str = url_response.json()['file_url']
+        response: requests.Response = requests.get(f"https://{self.fragalysis_api_url}?file_url={self.file_url}",
+                                                   allow_redirects=True)
+        response.raise_for_status()
+        self.zf = zipfile.ZipFile(io.BytesIO(response.content), "r")
+
+    def __getitem__(self, item: str) -> str:
+        """
+        Subscript via filename, e.g. ``quick['metadata']`` will return the metadata.csv file content.
+
+        :param item: Part of the filename whose contents will be returned
+        :return: The contents of the file whose name contains ``item``
+        """
+        for fileinfo in self.zf.infolist():
+            if item in fileinfo.filename:
+                return self.zf.read(fileinfo.filename).decode('utf8')
+        else:
+            raise KeyError(f'No file with {item} in the name found.')
+
+    def __iter__(self) -> Tuple[str, str]:
+        for fileinfo in self.zf.infolist():
+            yield fileinfo.filename, self.zf.read(fileinfo.filename).decode('utf8')
+
+    def __len__(self):
+        """
+        :return: The number of molecules-protein PDBs in the zip file.
+        """
+        return sum(['aligned/' in info.filename for info in self.zf.infolist()])
+
+    def write_all(self, directory: Optional[str] = None):
+        """
+        Writes all the files within the zip file to disk in ``directory``.
+        """
+        if directory is None:
+            directory = self.target_name
+        if not os.path.exists(directory):
+            os.makedirs(directory)
+        for fileinfo in self.zf.infolist():
+            if os.path.split(fileinfo.filename)[0] != '':
+                os.makedirs(os.path.join(directory, os.path.split(fileinfo.filename)[0]), exist_ok=True)
+            with open(os.path.join(directory, fileinfo.filename), 'w') as f:
+                f.write(self.zf.read(fileinfo.filename).decode('utf8'))
+
+    def to_pandas(self, star_dummy=True) -> pd.DataFrame:
+        """
+        Combine the metadata (``self['metadata]``) with sdf block (``self['combined.sdf']``),
+        into a single pandas DataFrame.
+        Peculiarly, Fragalysis stores dummy atoms as `Xe` instead of `*` in older SMILES, which is the standard.
+        """
+        # make a combined table
+        # Fragalysis does not give attributes in the sdf entries. This is instead stored in metadata.csv.
+        sdf_block = self['combined.sdf']
+        df = PandasTools.LoadSDF(io.StringIO(sdf_block)).set_index('ID')
+        try:
+            metadata_block = self['metadata.csv'].replace('Xe', '*') if star_dummy else self['metadata.csv']
+            df = pd.concat([df,
+                            pd.read_csv(io.StringIO(metadata_block), index_col=0).set_index('crystal_name')
+                            ], axis=1)
+        except KeyError:
+            warnings.warn('No metadata.csv found (legacy data). Returning only the sdf file.')
+        return df
+
+    @property
+    def reference_pdbblock(self) -> str:
+        """
+        Not all files have the reference pdb block, so if it does not the template is returned.
+
+        :return: The reference PDB for the target.
+        """
+        try:
+            return self['reference']
+        except KeyError:
+            first_response: requests.Response = requests.get(f'https://{self.fragalysis_api_url}/api/targets/')
+            first_response.raise_for_status()
+            template_url = first_response.json()['results'][0]['template_protein']
+            # /media/pdbs/ path:
+            second_response: requests.Response = requests.get(f'https://{self.fragalysis_api_url}/{template_url}')
+            second_response.raise_for_status()
+            return second_response.text
+
+    @classmethod
+    def retrieve_target_data(cls) -> List[Dict[str, Any]]:
+        """
+        :return: A list of all the target metadata available on the Fragalysis API.
+        """
+        response: requests.Response = requests.get(f'https://{cls.fragalysis_api_url}/api/targets/')
+        response.raise_for_status()
+        return response.json()['results']
+
+    @classmethod
+    def retrieve_target_names(cls) -> List[str]:
+        """
+        :return: A list of all the target names available on the Fragalysis API.
+        """
+        return [target['title'] for target in cls.retrieve_target_data()]
diff --git a/fragalysis_api/xcglobalscripts/set_config.py b/fragalysis_api/xcglobalscripts/set_config.py
index d1154f27..9f35d73b 100755
--- a/fragalysis_api/xcglobalscripts/set_config.py
+++ b/fragalysis_api/xcglobalscripts/set_config.py
@@ -4,6 +4,7 @@
 
 def ConfigSetup():
     # use config parser to get settings from config.ini
+    # todo Do not read package files this way, use importlib/pkg_resources
     settings_file = os.path.join(os.path.dirname(__file__), "config.ini")
     settings = configparser.ConfigParser()
     settings._interpolation = configparser.ExtendedInterpolation()
diff --git a/fragalysis_api/xcimporter/README.md b/importer.md
similarity index 100%
rename from fragalysis_api/xcimporter/README.md
rename to importer.md
diff --git a/fragalysis_api/xcextracter/example_notebooks/Pulling mol sdf and 'api' pdb.ipynb b/notebooks/Pulling-mol-sdf-pdb.ipynb
similarity index 100%
rename from fragalysis_api/xcextracter/example_notebooks/Pulling mol sdf and 'api' pdb.ipynb
rename to notebooks/Pulling-mol-sdf-pdb.ipynb
diff --git a/Tutorials.ipynb b/notebooks/Tutorials.ipynb
similarity index 62%
rename from Tutorials.ipynb
rename to notebooks/Tutorials.ipynb
index c4500327..841ee814 100644
--- a/Tutorials.ipynb
+++ b/notebooks/Tutorials.ipynb
@@ -16,6 +16,7 @@
    "source": [
     "import fragalysis_api\n",
     "import os\n",
+    "import pandas as pd\n",
     "from importlib import reload"
    ]
   },
@@ -261,7 +262,7 @@
    "source": [
     "# A way to see which targets are in the database?\n",
     "\n",
-    "graphs = fragalysis_api.xcextracter(target_name='NUDT5A')\n",
+    "graphs: pd.DataFrame = fragalysis_api.xcextracter(target_name='NUDT5A')\n",
     "display(graphs.head())\n",
     "\n",
     "# load molecule protein for wonka input (is this the correct input?)"
@@ -300,21 +301,21 @@
      "evalue": "cannot release un-acquired lock",
      "output_type": "error",
      "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mKeyboardInterrupt\u001b[0m                         Traceback (most recent call last)",
-      "\u001b[0;32m~/anaconda3/envs/fragalysis_env/lib/python3.7/site-packages/pymol/importing.py\u001b[0m in \u001b[0;36mload\u001b[0;34m(filename, object, state, format, finish, discrete, quiet, multiplex, zoom, partial, mimic, object_props, atom_props, _self)\u001b[0m\n\u001b[1;32m    718\u001b[0m         \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 719\u001b[0;31m             \u001b[0m_self\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlock\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0m_self\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    720\u001b[0m             \u001b[0mplugin\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m''\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0;32m~/anaconda3/envs/fragalysis_env/lib/python3.7/site-packages/pymol/locking.py\u001b[0m in \u001b[0;36mlock\u001b[0;34m(_self)\u001b[0m\n\u001b[1;32m     75\u001b[0m             \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;31m# we're not getting lucky, so block for real\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 76\u001b[0;31m                 \u001b[0m_self\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlock_api\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0macquire\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     77\u001b[0m                 \u001b[0;32mbreak\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0;31mKeyboardInterrupt\u001b[0m: ",
+      "\u001B[0;31m---------------------------------------------------------------------------\u001B[0m",
+      "\u001B[0;31mKeyboardInterrupt\u001B[0m                         Traceback (most recent call last)",
+      "\u001B[0;32m~/anaconda3/envs/fragalysis_env/lib/python3.7/site-packages/pymol/importing.py\u001B[0m in \u001B[0;36mload\u001B[0;34m(filename, object, state, format, finish, discrete, quiet, multiplex, zoom, partial, mimic, object_props, atom_props, _self)\u001B[0m\n\u001B[1;32m    718\u001B[0m         \u001B[0;32mtry\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0;32m--> 719\u001B[0;31m             \u001B[0m_self\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mlock\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0m_self\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m    720\u001B[0m             \u001B[0mplugin\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0;34m''\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n",
+      "\u001B[0;32m~/anaconda3/envs/fragalysis_env/lib/python3.7/site-packages/pymol/locking.py\u001B[0m in \u001B[0;36mlock\u001B[0;34m(_self)\u001B[0m\n\u001B[1;32m     75\u001B[0m             \u001B[0;32melse\u001B[0m\u001B[0;34m:\u001B[0m \u001B[0;31m# we're not getting lucky, so block for real\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0;32m---> 76\u001B[0;31m                 \u001B[0m_self\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mlock_api\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0macquire\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0;36m1\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m     77\u001B[0m                 \u001B[0;32mbreak\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n",
+      "\u001B[0;31mKeyboardInterrupt\u001B[0m: ",
       "\nDuring handling of the above exception, another exception occurred:\n",
-      "\u001b[0;31mRuntimeError\u001b[0m                              Traceback (most recent call last)",
-      "\u001b[0;32m<ipython-input-4-39c806e84d9c>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      3\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      4\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 5\u001b[0;31m \u001b[0mfragalysis_api\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mxcimporter\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0min_dir\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0min_dir\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mout_dir\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mout_dir\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtarget\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m'ATAD2'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalidate\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m)\u001b[0m  \u001b[0;31m# Needs to delete tmp files\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      6\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      7\u001b[0m \u001b[0;31m# Change this dir into xcextractor format?\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0;32m~/Documents/01_Projects/fragalysis-api/fragalysis_api/xcimporter/xcimporter.py\u001b[0m in \u001b[0;36mxcimporter\u001b[0;34m(in_dir, out_dir, target, validate)\u001b[0m\n\u001b[1;32m     61\u001b[0m     \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"Aligning protein structures\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     62\u001b[0m     \u001b[0mstructure\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mAlign\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0min_dir\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mpdb_ref\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m\"\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 63\u001b[0;31m     \u001b[0mstructure\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0malign\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpath\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mjoin\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mout_dir\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"tmp\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     64\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     65\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0;32m~/Documents/01_Projects/fragalysis-api/fragalysis_api/xcimporter/align.py\u001b[0m in \u001b[0;36malign\u001b[0;34m(self, out_dir)\u001b[0m\n\u001b[1;32m    130\u001b[0m         \u001b[0mthe\u001b[0m \u001b[0mpdb\u001b[0m \u001b[0mfiles\u001b[0m \u001b[0mof\u001b[0m \u001b[0mthe\u001b[0m \u001b[0mstructure\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    131\u001b[0m         \"\"\"\n\u001b[0;32m--> 132\u001b[0;31m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_save_align\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mout_dir\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
-      "\u001b[0;32m~/Documents/01_Projects/fragalysis-api/fragalysis_api/xcimporter/align.py\u001b[0m in \u001b[0;36m_save_align\u001b[0;34m(self, path_save)\u001b[0m\n\u001b[1;32m    112\u001b[0m         \u001b[0mpymol\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpymol_argv\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m'pymol'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'-qc'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    113\u001b[0m         \u001b[0mpymol\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfinish_launching\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 114\u001b[0;31m         \u001b[0mpymol_cmd\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_load_objs\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    115\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    116\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpath\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mexists\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mpath_save\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m  \u001b[0;31m# Creating output directory if it doesn't already exist\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0;32m~/Documents/01_Projects/fragalysis-api/fragalysis_api/xcimporter/align.py\u001b[0m in \u001b[0;36m_load_objs\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m     36\u001b[0m         \u001b[0;31m# Looping through each pdb file in the directory and loading them into the cmd\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     37\u001b[0m         \u001b[0;32mfor\u001b[0m \u001b[0mnum\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfile\u001b[0m \u001b[0;32min\u001b[0m \u001b[0menumerate\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_get_files\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 38\u001b[0;31m             \u001b[0mpymol\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcmd\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mload\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfile\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpath\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msplitext\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpath\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbasename\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfile\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     39\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     40\u001b[0m         \u001b[0;31m# deal with files that have no conect records\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0;32m~/anaconda3/envs/fragalysis_env/lib/python3.7/site-packages/pymol/importing.py\u001b[0m in \u001b[0;36mload\u001b[0;34m(filename, object, state, format, finish, discrete, quiet, multiplex, zoom, partial, mimic, object_props, atom_props, _self)\u001b[0m\n\u001b[1;32m    818\u001b[0m             \u001b[0;32mreturn\u001b[0m \u001b[0mfunc\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m**\u001b[0m\u001b[0mkw\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    819\u001b[0m         \u001b[0;32mfinally\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 820\u001b[0;31m             \u001b[0m_self\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0munlock\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mr\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0m_self\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    821\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0m_self\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_raising\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mr\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0m_self\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;32mraise\u001b[0m \u001b[0mpymol\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mCmdException\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    822\u001b[0m         \u001b[0;32mreturn\u001b[0m \u001b[0mr\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0;32m~/anaconda3/envs/fragalysis_env/lib/python3.7/site-packages/pymol/locking.py\u001b[0m in \u001b[0;36munlock\u001b[0;34m(result, _self)\u001b[0m\n\u001b[1;32m    112\u001b[0m     \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    113\u001b[0m     \u001b[0;31m#         print \"lock: released by 0x%x (not glut), waiting queue\"%thread.get_ident()\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 114\u001b[0;31m         \u001b[0m_self\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlock_api\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrelease\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    115\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0m_cmd\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwait_queue\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0m_self\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_COb\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;31m# commands waiting to be executed?\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    116\u001b[0m             \u001b[0me\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mthreading\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mEvent\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;31m# abdicate control for a 100 usec for quick tasks\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0;31mRuntimeError\u001b[0m: cannot release un-acquired lock"
+      "\u001B[0;31mRuntimeError\u001B[0m                              Traceback (most recent call last)",
+      "\u001B[0;32m<ipython-input-4-39c806e84d9c>\u001B[0m in \u001B[0;36m<module>\u001B[0;34m\u001B[0m\n\u001B[1;32m      3\u001B[0m \u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m      4\u001B[0m \u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0;32m----> 5\u001B[0;31m \u001B[0mfragalysis_api\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mxcimporter\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0min_dir\u001B[0m\u001B[0;34m=\u001B[0m\u001B[0min_dir\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0mout_dir\u001B[0m\u001B[0;34m=\u001B[0m\u001B[0mout_dir\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0mtarget\u001B[0m\u001B[0;34m=\u001B[0m\u001B[0;34m'ATAD2'\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0mvalidate\u001B[0m\u001B[0;34m=\u001B[0m\u001B[0;32mTrue\u001B[0m\u001B[0;34m)\u001B[0m  \u001B[0;31m# Needs to delete tmp files\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m      6\u001B[0m \u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m      7\u001B[0m \u001B[0;31m# Change this dir into xcextractor format?\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n",
+      "\u001B[0;32m~/Documents/01_Projects/fragalysis-api/fragalysis_api/xcimporter/xcimporter.py\u001B[0m in \u001B[0;36mxcimporter\u001B[0;34m(in_dir, out_dir, target, validate)\u001B[0m\n\u001B[1;32m     61\u001B[0m     \u001B[0mprint\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0;34m\"Aligning protein structures\"\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m     62\u001B[0m     \u001B[0mstructure\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0mAlign\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0min_dir\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0mpdb_ref\u001B[0m\u001B[0;34m=\u001B[0m\u001B[0;34m\"\"\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0;32m---> 63\u001B[0;31m     \u001B[0mstructure\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0malign\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mos\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mpath\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mjoin\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mout_dir\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0;34m\"tmp\"\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m     64\u001B[0m \u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m     65\u001B[0m \u001B[0;34m\u001B[0m\u001B[0m\n",
+      "\u001B[0;32m~/Documents/01_Projects/fragalysis-api/fragalysis_api/xcimporter/align.py\u001B[0m in \u001B[0;36malign\u001B[0;34m(self, out_dir)\u001B[0m\n\u001B[1;32m    130\u001B[0m         \u001B[0mthe\u001B[0m \u001B[0mpdb\u001B[0m \u001B[0mfiles\u001B[0m \u001B[0mof\u001B[0m \u001B[0mthe\u001B[0m \u001B[0mstructure\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m    131\u001B[0m         \"\"\"\n\u001B[0;32m--> 132\u001B[0;31m         \u001B[0mself\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0m_save_align\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mout_dir\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m",
+      "\u001B[0;32m~/Documents/01_Projects/fragalysis-api/fragalysis_api/xcimporter/align.py\u001B[0m in \u001B[0;36m_save_align\u001B[0;34m(self, path_save)\u001B[0m\n\u001B[1;32m    112\u001B[0m         \u001B[0mpymol\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mpymol_argv\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0;34m[\u001B[0m\u001B[0;34m'pymol'\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0;34m'-qc'\u001B[0m\u001B[0;34m]\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m    113\u001B[0m         \u001B[0mpymol\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mfinish_launching\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0;32m--> 114\u001B[0;31m         \u001B[0mpymol_cmd\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0mself\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0m_load_objs\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m    115\u001B[0m \u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m    116\u001B[0m         \u001B[0;32mif\u001B[0m \u001B[0;32mnot\u001B[0m \u001B[0mos\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mpath\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mexists\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mpath_save\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m:\u001B[0m  \u001B[0;31m# Creating output directory if it doesn't already exist\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n",
+      "\u001B[0;32m~/Documents/01_Projects/fragalysis-api/fragalysis_api/xcimporter/align.py\u001B[0m in \u001B[0;36m_load_objs\u001B[0;34m(self)\u001B[0m\n\u001B[1;32m     36\u001B[0m         \u001B[0;31m# Looping through each pdb file in the directory and loading them into the cmd\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m     37\u001B[0m         \u001B[0;32mfor\u001B[0m \u001B[0mnum\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0mfile\u001B[0m \u001B[0;32min\u001B[0m \u001B[0menumerate\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mself\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0m_get_files\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0;32m---> 38\u001B[0;31m             \u001B[0mpymol\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mcmd\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mload\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mfile\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0mos\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mpath\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0msplitext\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mos\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mpath\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mbasename\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mfile\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m[\u001B[0m\u001B[0;36m0\u001B[0m\u001B[0;34m]\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m     39\u001B[0m \u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m     40\u001B[0m         \u001B[0;31m# deal with files that have no conect records\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n",
+      "\u001B[0;32m~/anaconda3/envs/fragalysis_env/lib/python3.7/site-packages/pymol/importing.py\u001B[0m in \u001B[0;36mload\u001B[0;34m(filename, object, state, format, finish, discrete, quiet, multiplex, zoom, partial, mimic, object_props, atom_props, _self)\u001B[0m\n\u001B[1;32m    818\u001B[0m             \u001B[0;32mreturn\u001B[0m \u001B[0mfunc\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0;34m**\u001B[0m\u001B[0mkw\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m    819\u001B[0m         \u001B[0;32mfinally\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0;32m--> 820\u001B[0;31m             \u001B[0m_self\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0munlock\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mr\u001B[0m\u001B[0;34m,\u001B[0m\u001B[0m_self\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m    821\u001B[0m         \u001B[0;32mif\u001B[0m \u001B[0m_self\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0m_raising\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mr\u001B[0m\u001B[0;34m,\u001B[0m\u001B[0m_self\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m:\u001B[0m \u001B[0;32mraise\u001B[0m \u001B[0mpymol\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mCmdException\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m    822\u001B[0m         \u001B[0;32mreturn\u001B[0m \u001B[0mr\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n",
+      "\u001B[0;32m~/anaconda3/envs/fragalysis_env/lib/python3.7/site-packages/pymol/locking.py\u001B[0m in \u001B[0;36munlock\u001B[0;34m(result, _self)\u001B[0m\n\u001B[1;32m    112\u001B[0m     \u001B[0;32melse\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m    113\u001B[0m     \u001B[0;31m#         print \"lock: released by 0x%x (not glut), waiting queue\"%thread.get_ident()\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0;32m--> 114\u001B[0;31m         \u001B[0m_self\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mlock_api\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mrelease\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m    115\u001B[0m         \u001B[0;32mif\u001B[0m \u001B[0m_cmd\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mwait_queue\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0m_self\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0m_COb\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m:\u001B[0m \u001B[0;31m# commands waiting to be executed?\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m    116\u001B[0m             \u001B[0me\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0mthreading\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mEvent\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0;34m)\u001B[0m \u001B[0;31m# abdicate control for a 100 usec for quick tasks\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n",
+      "\u001B[0;31mRuntimeError\u001B[0m: cannot release un-acquired lock"
      ]
     }
    ],
diff --git a/quick_download.md b/quick_download.md
new file mode 100644
index 00000000..45476c58
--- /dev/null
+++ b/quick_download.md
@@ -0,0 +1,31 @@
+## Quick download
+
+This is not part of the regular package, which allows more precise control, but simply a wrapper to
+the `api/download_structures` endpoint (which is used by the download modal) to download all the data
+for a given target.
+
+This endpoint differs from the links in the `api/targets` endpoint response. Namely,
+for say NUDT7A, the JSON response to https://fragalysis.diamond.ac.uk/api/targets/?title=NUDT7A
+will feature `zip_archive` that will point to `https://fragalysis.diamond.ac.uk/media/targets/👾👾👾.zip`
+and a `template_protein`, which is (possibly) the reference structure for molecular replacement and 
+not necessary for alignment. NUDT7 is an older target and actually lacks a reference structure in the download.
+
+```python
+from fragalysis_api import QuickDownloader
+import pandas as pd
+from typing import List
+print(f'Default settings are: {QuickDownloader.api_data}')
+
+# Check if the target name is right
+target_names: List[str] = QuickDownloader.retrieve_target_names()
+target_name='Mpro'
+assert target_name in target_names, f'Target named "{target_name}" not found in the list of targets'
+
+# Download the data
+quick = QuickDownloader(target_name=target_name)
+quick.write_all(directory='downloads')
+hits: pd.DataFrame = quick.to_pandas(star_dummy=True)
+
+# Not all files have the reference pdb block, so if it does not the template is returned:
+reference_pdbblock: str = quick.reference_pdbblock
+```
diff --git a/setup.py b/setup.py
index 932a787c..d4a3db08 100755
--- a/setup.py
+++ b/setup.py
@@ -1,13 +1,16 @@
-import setuptools
+import setuptools, os
 
-with open("README.md", "r") as fh:
-    long_description = fh.read()
+if os.path.exists("README.md"):
+    with open("README.md", "r") as fh:
+        long_description = fh.read()
+else:
+    long_description = ""
 
 
 setuptools.setup(
     name='fragalysis_api',
-    version='0.0.5.1',
-    author='Fragment 5 + Tyler',
+    version='0.6',
+    author='XChem',
     author_email="",
     description="A package to load PDBs into fragalysis format.",
     long_description=long_description,  # README_1.md file as description
@@ -20,6 +23,7 @@
                       'pypdb',
                       'matplotlib',
                       'scipy',
+                      'rdkit',
                       'fragalysis'],  # Install requirements extracted from requirements.txt
     include_package_data=True,  # Allow to include other files than .py in package
     package_data={
@@ -27,10 +31,13 @@
              'fragalysis_api/xcglobalscripts/config.ini']
     },  # Define which additional files should be included in package
     classifiers=[
-        'Development Status :: 4 - Beta',
+        'Development Status :: 5 - Production/Stable',  # https://pypi.org/classifiers/
         "Programming Language :: Python :: 3.7",
         "License :: OSI Approved :: MIT License",
         "Operating System :: OS Independent",
+        'Intended Audience :: Science/Research',
+        'Topic :: Scientific/Engineering :: Bio-Informatics',
+        'Topic :: Scientific/Engineering :: Chemistry',
     ],
     python_requires='>=3.6',
 )