diff --git a/README.md b/README.md index 27935ce0..b1dd239a 100644 --- a/README.md +++ b/README.md @@ -29,6 +29,16 @@ at [Scripps Research](https://www.scripps.edu/). ### Documentation In-depth documentation can be found on [ReadTheDocs](https://ringtail.readthedocs.io). + + +### Version 2.2.0: enhancements and bug fixes +- New method added to enable exporting receptor pdb with flexible residues given ligand (currently for API only) +- During results writing: check to ensure files provided with `file` option, and directories provided with `file_path` option +- Multiprocess removed from clustering methods, speeding up the process significantly +- Minor sqlite query updates for enhanced query speed, such as replacing `LIKE` with `=` where possible when matching text +- Initializing ringtail with full path to a database could result in issues exporting SDFs to specified folder, this has been fixed +- Clustering without filtering could result in error, this has been fixed + ### Version 2.1.2 bug fixes - Removing of union operand that made Ringtail incompatible with python=3.9 - Pymol now displays receptor if present in database diff --git a/docs/source/api.rst b/docs/source/api.rst index a41b2114..8a789826 100644 --- a/docs/source/api.rst +++ b/docs/source/api.rst @@ -241,6 +241,27 @@ It is also possible to write a database query and export the results of the quer query_string = "SELECT docking_score, leff, Pose_ID, LigName FROM Results" rtc.export_csv(requested_data = query_string, csv_name = "query_results.csv", table = False) +Exporting flexible residues (as PDB) of a receptor given a docked ligand +======================================================================== +When processing docking data for a receptor docked with flexible residues, it might be of interest to produce a PDB of the flexible residues for a given docked ``ligand``. This is currently possible using the following method (only through API). +The user needs to provide a meeko.Polymer object, and the ligand has to be part of a filtered bookmark ``bookmark_name``. Finally, a file output name must be provided, and the extension ``.pdb`` will be added if not provided. +The meeko.Polymer object available with meeko>=0.6.1. The polymer is a deserialized version of the receptor/polymer json which can be produced by the method ``mk_prepare_receptor.py`` with the flag ``--write_json`` (see the `meeko documentation `_ for more details on how to prepare the receptor). + +.. code-block:: python + + rtc.write_flexres_pdb(receptor_polymer = polymer, ligname = "best_ligand", filename = "flexres_receptor", bookmark_name = "eworst6") + + #results in creation of flexres_receptor.pdb + +A polymer can then be prepared using the following code snippet, given ``receptor.json``: + +.. code-block:: python + + with open("recptor.json") as f: + json_string = f.read() + polymer = meeko.Polymer.from_json(json_string) + + Creating a new database from a bookmark ======================================= A bookmark may also be exported as a separate SQLite dabase with the ``export_bookmark_db`` method. This will create a database of name ``_.db``. This is currently only possible if using SQLite. diff --git a/docs/source/changes.rst b/docs/source/changes.rst index 11298bcc..b49ba1f5 100644 --- a/docs/source/changes.rst +++ b/docs/source/changes.rst @@ -3,6 +3,21 @@ Changes in Ringtail ###################### + +Changes in 2.2.0: new API method for flex res receptor export and bug fixes +************************************************************************** +Enhancements +============ +* New method added to enable exporting receptor pdb with flexible residues given ligand (currently for API only) +* During results writing: check to ensure files provided with `file` option, and directories provided with `file_path` option +* Multiprocess removed from clustering methods, speeding up the process significantly +* Minor sqlite query updates for enhanced query speed, such as replacing `LIKE` with `=` where possible when matching text + +Bug fixes +========== +* Initializing ringtail with full path to a database could result in issues exporting SDFs to specified folder, this has been fixed +* Clustering without filtering could result in error, this has been fixed + Changes in 2.1.2: bug fixes **************************** * Removing of union operand that made Ringtail incompatible with python=3.9 diff --git a/ringtail/mpmanager.py b/ringtail/mpmanager.py index a966b111..59917999 100644 --- a/ringtail/mpmanager.py +++ b/ringtail/mpmanager.py @@ -12,7 +12,7 @@ from .mpreaderwriter import DockingFileReader from .mpreaderwriter import Writer from .logutils import LOGGER -from .exceptions import MultiprocessingError, RTCoreError +from .exceptions import MultiprocessingError, RTCoreError, OptionError import traceback from datetime import datetime @@ -157,22 +157,32 @@ def _process_data_sources(self): if self.file_sources.file != (None and [[]]): for file_list in self.file_sources.file: for file in file_list: - if ( - fnmatch.fnmatch(file, self.file_pattern) - and file != self.receptor_file - ): - self._add_to_queue(file) + if os.path.isfile(file): + if ( + fnmatch.fnmatch(file, self.file_pattern) + and file != self.receptor_file + ): + self._add_to_queue(file) + else: + raise OptionError( + f"The file {file} is not a a file (or does not exist), and will not be processed." + ) # add files from file path(s) if self.file_sources.file_path != (None and [[]]): for path_list in self.file_sources.file_path: for path in path_list: # scan for ligand dlgs - for files in self._scan_dir( - path, self.file_pattern, recursive=True - ): - for file in files: - self._add_to_queue(file) + if os.path.isdir(path): + for files in self._scan_dir( + path, self.file_pattern, recursive=True + ): + for file in files: + self._add_to_queue(file) + else: + raise OptionError( + f"The path {path} is not a directory (or does note exist), and will not be processed." + ) # add files from file list(s) if self.file_sources.file_list != (None and [[]]): diff --git a/ringtail/ringtailcore.py b/ringtail/ringtailcore.py index b2b43c05..24ef18ab 100644 --- a/ringtail/ringtailcore.py +++ b/ringtail/ringtailcore.py @@ -7,6 +7,7 @@ import matplotlib.pyplot as plt import json from meeko import RDKitMolCreate +from meeko.export_flexres import pdb_updated_flexres_from_rdkit from .storagemanager import StorageManager from .resultsmanager import ResultsManager from .receptormanager import ReceptorManager @@ -1475,6 +1476,69 @@ def filter( return ligands_passed + def write_flexres_pdb( + self, receptor_polymer, ligname: str, filename: str, bookmark_name: str = None + ): + """ + Writes a receptor pdb with flexible residues based on the ligand provided + + Args: + receptor_polymer (Polymer): version of receptor produced by meeko + ligname (str): ligand name for which the receptor flexible residue info should be collected + filename (str): name of the output pdb, extension is optional, will default to '.pdb' + bookmark_name (str, optional): will use last used bookmark if not specified, will not work in a db without any filtering performed + """ + # make flexres rdkit mols for ligand-receptor docking + if bookmark_name is not None: + self.set_storageman_attributes(bookmark_name=bookmark_name) + + with self.storageman: + self.storageman.create_temp_table_from_bookmark() + ligname, ligand_smile, atom_index_map, hydrogen_parents = ( + self.storageman.fetch_single_ligand_output_info(ligname) + ) + flexible_residues, flexres_atomnames = self.storageman.fetch_flexres_info() + if flexible_residues is None: + flexible_residues, flexres_atomnames = [], [] + elif flexible_residues != []: # converts string to list + flexible_residues = json.loads(flexible_residues) + flexres_atomnames = json.loads(flexres_atomnames) + + ligand_mol, flexres_mols, _ = self._create_rdkit_mol( + ligname, + ligand_smile, + atom_index_map, + hydrogen_parents, + flexible_residues, + flexres_atomnames, + ) + if filename: + # if providing filename, make sure it has .pdb extension + root, ext = os.path.splitext(filename) + if not ext: + ext = ".pdb" + path = root + ext + else: + # name if after the receptor + receptor_name, _ = self.storageman.fetch_receptor_objects()[0] + path = receptor_name + ".pdb" + + flexmoldict = {} + # string in list of strings + for index, flexres in enumerate(flexible_residues): + residue = flexres.split(":")[1] + chain = residue[0] + resnum = residue[1:] + # res id is chain:resnum + flexmoldict[f"{chain}:{resnum}"] = flexres_mols[index] + + pdb_str = pdb_updated_flexres_from_rdkit(receptor_polymer, flexmoldict) + # write pdb string to file + with open(path, "w") as file: + file.write(pdb_str) + + return ligand_mol, flexmoldict + def write_molecule_sdfs( self, sdf_path: str = None, @@ -1519,7 +1583,7 @@ def write_molecule_sdfs( # determine filename if all_in_one: # will write one SDF file for all molecules in bookmark (_None if no bookmark present) - db_file_name = os.path.splitext(self.db_file)[0] + db_file_name = os.path.splitext(os.path.basename(self.db_file))[0] sdf_file_name = ("{0}_{1}.sdf").format( db_file_name, str(self.storageman.bookmark_name) ) diff --git a/ringtail/storagemanager.py b/ringtail/storagemanager.py index 71ba9bc7..9b038710 100644 --- a/ringtail/storagemanager.py +++ b/ringtail/storagemanager.py @@ -28,8 +28,6 @@ ) from .exceptions import DatabaseQueryError, DatabaseViewCreationError, OptionError -import multiprocess - class StorageManager: @@ -39,7 +37,7 @@ class StorageManager: _db_schema_code_compatibility = { "1.0.0": ["1.0.0"], "1.1.0": ["1.1.0"], - "2.0.0": ["2.0.0", "2.1.0", "2.1.1", "2.1.2"], + "2.0.0": ["2.0.0", "2.1.0", "2.1.1", "2.1.2", "2.2.0"], } """Base class for a generic virtual screening database object. @@ -1958,7 +1956,7 @@ def fetch_single_ligand_output_info(self, ligname) -> str: try: cur = self.conn.cursor() cur.execute( - f"SELECT LigName, ligand_smile, atom_index_map, hydrogen_parents FROM Ligands WHERE LigName LIKE '{ligname}'" + f"SELECT LigName, ligand_smile, atom_index_map, hydrogen_parents FROM Ligands WHERE LigName = '{ligname}'" ) info = cur.fetchone() cur.close() @@ -2540,6 +2538,8 @@ def _generate_result_filtering_query(self, filters_dict): # process filter values to lists and dicts that are easily incorporated in sql queries processed_filters = self._process_filters_for_query(filters_dict) + # check if clustering + clustering = bool(self.mfpt_cluster or self.interaction_cluster) # raise error if no filters are present and no clusterings if not processed_filters and not clustering: @@ -2547,8 +2547,6 @@ def _generate_result_filtering_query(self, filters_dict): "Ringtail query strings are empty, please check filter options." ) - # check if clustering - clustering = bool(self.mfpt_cluster or self.interaction_cluster) # if clustering without filtering if clustering: # allows for clustering without filtering @@ -2695,23 +2693,11 @@ def _clusterFps(fps, cutoff): cutoff distance (float) """ - # first generate the distance matrix: dists = [] nfps = len(fps) - inputs = [] - - def gen(fps): - for i in range(1, len(fps)): - yield (i, fps) - - def mp_wrapper(input_tpl): - i, fps = input_tpl - return DataStructs.BulkTanimotoSimilarity(fps[i], fps[:i]) - - with multiprocess.Pool() as p: - inputs = gen(fps) - for sims in p.imap(mp_wrapper, inputs): - dists.extend([1 - x for x in sims]) + for i in range(1, nfps): + sims = DataStructs.BulkTanimotoSimilarity(fps[i], fps[:i]) + dists.extend([1 - x for x in sims]) # now cluster the data: cs = Butina.ClusterData(dists, nfps, cutoff, isDistData=True) diff --git a/setup.py b/setup.py index 0aa1b391..c73163a9 100644 --- a/setup.py +++ b/setup.py @@ -22,7 +22,7 @@ def find_files(directory): setup( name="ringtail", - version="2.1.2", + version="2.2.0", author="Forli Lab", author_email="forli@scripps.edu", url="https://github.com/forlilab/Ringtail", diff --git a/test/.DS_Store b/test/.DS_Store index 69c01bf9..148205a3 100644 Binary files a/test/.DS_Store and b/test/.DS_Store differ diff --git a/test/test_data/.DS_Store b/test/test_data/.DS_Store index 128a303a..c2efb6f8 100644 Binary files a/test/test_data/.DS_Store and b/test/test_data/.DS_Store differ diff --git a/test/test_data/flexres/ligand.pdbqt b/test/test_data/flexres/ligand.pdbqt new file mode 100644 index 00000000..eef1fc26 --- /dev/null +++ b/test/test_data/flexres/ligand.pdbqt @@ -0,0 +1,414 @@ +MODEL 1 +REMARK VINA RESULT: -2.577 0.000 0.000 +REMARK INTER + INTRA: -3.527 +REMARK INTER: -2.879 +REMARK INTRA: -0.649 +REMARK UNBOUND: -0.649 +REMARK SMILES CNC(=O)Oc1ccccc1 +REMARK SMILES IDX 3 1 4 2 2 3 1 4 5 6 6 7 7 8 8 9 9 10 11 11 10 12 +REMARK H PARENT 2 5 +ROOT +ATOM 1 C UNL 1 -0.053 0.290 -4.432 1.00 0.00 0.412 C +ATOM 2 O UNL 1 -0.268 0.495 -5.618 1.00 0.00 -0.224 OA +ATOM 3 N UNL 1 1.047 -0.361 -3.945 1.00 0.00 -0.324 N +ATOM 4 C UNL 1 2.132 -0.764 -4.797 1.00 0.00 0.146 C +ATOM 5 H UNL 1 1.165 -0.348 -2.942 1.00 0.00 0.166 HD +ENDROOT +BRANCH 1 6 +ATOM 6 O UNL 1 -0.854 0.678 -3.370 1.00 0.00 -0.410 OA +BRANCH 6 7 +ATOM 7 C UNL 1 -2.190 0.272 -3.462 1.00 0.00 0.132 A +ATOM 8 C UNL 1 -3.200 1.203 -3.702 1.00 0.00 0.047 A +ATOM 9 C UNL 1 -4.514 0.759 -3.846 1.00 0.00 0.004 A +ATOM 10 C UNL 1 -4.805 -0.604 -3.765 1.00 0.00 0.000 A +ATOM 11 C UNL 1 -2.465 -1.092 -3.399 1.00 0.00 0.047 A +ATOM 12 C UNL 1 -3.781 -1.529 -3.544 1.00 0.00 0.004 A +ENDBRANCH 6 7 +ENDBRANCH 1 6 +TORSDOF 2 +BEGIN_RES HIS A 2 +REMARK INDEX MAP 3 1 15 2 18 3 19 4 20 5 21 6 22 7 23 8 +ROOT +ATOM 1 CA HIS A 2 3.690 0.569 0.155 1.00 0.00 0.177 C +ENDROOT +BRANCH 1 2 +ATOM 2 CB HIS A 2 3.958 0.658 1.602 1.00 0.00 0.090 C +BRANCH 2 3 +ATOM 3 CG HIS A 2 4.658 -0.448 2.271 1.00 0.00 0.037 A +ATOM 4 ND1 HIS A 2 4.180 -1.734 2.355 1.00 0.00 -0.347 N +ATOM 5 CD2 HIS A 2 5.895 -0.507 2.881 1.00 0.00 0.134 A +ATOM 6 HD1 HIS A 2 3.119 -1.872 2.022 1.00 0.00 0.167 HD +ATOM 7 CE1 HIS A 2 5.066 -2.502 2.973 1.00 0.00 0.196 A +ATOM 8 NE2 HIS A 2 6.153 -1.743 3.312 1.00 0.00 -0.245 NA +ENDBRANCH 2 3 +ENDBRANCH 1 2 +END_RES HIS A 2 +ENDMDL +MODEL 2 +REMARK VINA RESULT: -2.567 0.785 1.457 +REMARK INTER + INTRA: -3.516 +REMARK INTER: -2.871 +REMARK INTRA: -0.645 +REMARK UNBOUND: -0.649 +REMARK SMILES CNC(=O)Oc1ccccc1 +REMARK SMILES IDX 3 1 4 2 2 3 1 4 5 6 6 7 7 8 8 9 9 10 11 11 10 12 +REMARK H PARENT 2 5 +ROOT +ATOM 1 C UNL 1 -0.228 0.175 -4.424 1.00 0.00 0.412 C +ATOM 2 O UNL 1 -0.428 0.306 -5.623 1.00 0.00 -0.224 OA +ATOM 3 N UNL 1 0.923 -0.328 -3.880 1.00 0.00 -0.324 N +ATOM 4 C UNL 1 2.071 -0.640 -4.686 1.00 0.00 0.146 C +ATOM 5 H UNL 1 1.008 -0.260 -2.876 1.00 0.00 0.166 HD +ENDROOT +BRANCH 1 6 +ATOM 6 O UNL 1 -1.099 0.514 -3.400 1.00 0.00 -0.410 OA +BRANCH 6 7 +ATOM 7 C UNL 1 -2.385 -0.022 -3.522 1.00 0.00 0.132 A +ATOM 8 C UNL 1 -2.607 -1.387 -3.337 1.00 0.00 0.047 A +ATOM 9 C UNL 1 -3.909 -1.881 -3.409 1.00 0.00 0.004 A +ATOM 10 C UNL 1 -4.975 -1.011 -3.648 1.00 0.00 0.000 A +ATOM 11 C UNL 1 -3.444 0.857 -3.743 1.00 0.00 0.047 A +ATOM 12 C UNL 1 -4.743 0.356 -3.812 1.00 0.00 0.004 A +ENDBRANCH 6 7 +ENDBRANCH 1 6 +TORSDOF 2 +BEGIN_RES HIS A 2 +REMARK INDEX MAP 3 1 15 2 18 3 19 4 20 5 21 6 22 7 23 8 +ROOT +ATOM 1 CA HIS A 2 3.690 0.569 0.155 1.00 0.00 0.177 C +ENDROOT +BRANCH 1 2 +ATOM 2 CB HIS A 2 3.958 0.658 1.602 1.00 0.00 0.090 C +BRANCH 2 3 +ATOM 3 CG HIS A 2 4.773 -0.383 2.245 1.00 0.00 0.037 A +ATOM 4 ND1 HIS A 2 5.920 -0.917 1.708 1.00 0.00 -0.347 N +ATOM 5 CD2 HIS A 2 4.655 -1.002 3.473 1.00 0.00 0.134 A +ATOM 6 HD1 HIS A 2 6.126 -0.631 0.645 1.00 0.00 0.167 HD +ATOM 7 CE1 HIS A 2 6.445 -1.792 2.552 1.00 0.00 0.196 A +ATOM 8 NE2 HIS A 2 5.659 -1.859 3.671 1.00 0.00 -0.245 NA +ENDBRANCH 2 3 +ENDBRANCH 1 2 +END_RES HIS A 2 +ENDMDL +MODEL 3 +REMARK VINA RESULT: -2.558 6.765 7.540 +REMARK INTER + INTRA: -3.506 +REMARK INTER: -2.902 +REMARK INTRA: -0.604 +REMARK UNBOUND: -0.649 +REMARK SMILES CNC(=O)Oc1ccccc1 +REMARK SMILES IDX 3 1 4 2 2 3 1 4 5 6 6 7 7 8 8 9 9 10 11 11 10 12 +REMARK H PARENT 2 5 +ROOT +ATOM 1 C UNL 1 0.987 -1.646 4.199 1.00 0.00 0.412 C +ATOM 2 O UNL 1 1.659 -2.024 5.148 1.00 0.00 -0.224 OA +ATOM 3 N UNL 1 -0.158 -0.904 4.307 1.00 0.00 -0.324 N +ATOM 4 C UNL 1 -0.613 -0.387 5.567 1.00 0.00 0.146 C +ATOM 5 H UNL 1 -0.543 -0.551 3.442 1.00 0.00 0.166 HD +ENDROOT +BRANCH 1 6 +ATOM 6 O UNL 1 1.249 -1.878 2.858 1.00 0.00 -0.410 OA +BRANCH 6 7 +ATOM 7 C UNL 1 1.272 -3.227 2.488 1.00 0.00 0.132 A +ATOM 8 C UNL 1 0.151 -4.035 2.676 1.00 0.00 0.047 A +ATOM 9 C UNL 1 0.186 -5.360 2.244 1.00 0.00 0.004 A +ATOM 10 C UNL 1 1.330 -5.861 1.619 1.00 0.00 0.000 A +ATOM 11 C UNL 1 2.412 -3.711 1.848 1.00 0.00 0.047 A +ATOM 12 C UNL 1 2.440 -5.037 1.419 1.00 0.00 0.004 A +ENDBRANCH 6 7 +ENDBRANCH 1 6 +TORSDOF 2 +BEGIN_RES HIS A 2 +REMARK INDEX MAP 3 1 15 2 18 3 19 4 20 5 21 6 22 7 23 8 +ROOT +ATOM 1 CA HIS A 2 3.690 0.569 0.155 1.00 0.00 0.177 C +ENDROOT +BRANCH 1 2 +ATOM 2 CB HIS A 2 3.958 0.658 1.602 1.00 0.00 0.090 C +BRANCH 2 3 +ATOM 3 CG HIS A 2 4.575 -0.486 2.288 1.00 0.00 0.037 A +ATOM 4 ND1 HIS A 2 4.248 -0.901 3.558 1.00 0.00 -0.347 N +ATOM 5 CD2 HIS A 2 5.513 -1.405 1.864 1.00 0.00 0.134 A +ATOM 6 HD1 HIS A 2 3.583 -0.205 4.130 1.00 0.00 0.167 HD +ATOM 7 CE1 HIS A 2 4.943 -1.985 3.867 1.00 0.00 0.196 A +ATOM 8 NE2 HIS A 2 5.747 -2.316 2.810 1.00 0.00 -0.245 NA +ENDBRANCH 2 3 +ENDBRANCH 1 2 +END_RES HIS A 2 +ENDMDL +MODEL 4 +REMARK VINA RESULT: -2.517 2.547 3.522 +REMARK INTER + INTRA: -3.459 +REMARK INTER: -2.898 +REMARK INTRA: -0.561 +REMARK UNBOUND: -0.649 +REMARK SMILES CNC(=O)Oc1ccccc1 +REMARK SMILES IDX 3 1 4 2 2 3 1 4 5 6 6 7 7 8 8 9 9 10 11 11 10 12 +REMARK H PARENT 2 5 +ROOT +ATOM 1 C UNL 1 -3.509 -0.437 -3.504 1.00 0.00 0.412 C +ATOM 2 O UNL 1 -2.624 -1.111 -2.997 1.00 0.00 -0.224 OA +ATOM 3 N UNL 1 -3.564 0.930 -3.461 1.00 0.00 -0.324 N +ATOM 4 C UNL 1 -2.498 1.716 -2.908 1.00 0.00 0.146 C +ATOM 5 H UNL 1 -4.277 1.365 -4.030 1.00 0.00 0.166 HD +ENDROOT +BRANCH 1 6 +ATOM 6 O UNL 1 -4.599 -0.910 -4.218 1.00 0.00 -0.410 OA +BRANCH 6 7 +ATOM 7 C UNL 1 -5.782 -1.020 -3.479 1.00 0.00 0.132 A +ATOM 8 C UNL 1 -6.842 -0.141 -3.699 1.00 0.00 0.047 A +ATOM 9 C UNL 1 -8.029 -0.313 -2.988 1.00 0.00 0.004 A +ATOM 10 C UNL 1 -8.152 -1.366 -2.078 1.00 0.00 0.000 A +ATOM 11 C UNL 1 -5.900 -2.085 -2.588 1.00 0.00 0.047 A +ATOM 12 C UNL 1 -7.090 -2.252 -1.880 1.00 0.00 0.004 A +ENDBRANCH 6 7 +ENDBRANCH 1 6 +TORSDOF 2 +BEGIN_RES HIS A 2 +REMARK INDEX MAP 3 1 15 2 18 3 19 4 20 5 21 6 22 7 23 8 +ROOT +ATOM 1 CA HIS A 2 3.690 0.569 0.155 1.00 0.00 0.177 C +ENDROOT +BRANCH 1 2 +ATOM 2 CB HIS A 2 3.958 0.658 1.602 1.00 0.00 0.090 C +BRANCH 2 3 +ATOM 3 CG HIS A 2 4.722 -0.414 2.257 1.00 0.00 0.037 A +ATOM 4 ND1 HIS A 2 5.544 -0.231 3.343 1.00 0.00 -0.347 N +ATOM 5 CD2 HIS A 2 4.769 -1.773 2.022 1.00 0.00 0.134 A +ATOM 6 HD1 HIS A 2 5.741 0.836 3.619 1.00 0.00 0.167 HD +ATOM 7 CE1 HIS A 2 6.045 -1.396 3.726 1.00 0.00 0.196 A +ATOM 8 NE2 HIS A 2 5.568 -2.379 2.902 1.00 0.00 -0.245 NA +ENDBRANCH 2 3 +ENDBRANCH 1 2 +END_RES HIS A 2 +ENDMDL +MODEL 5 +REMARK VINA RESULT: -2.347 6.813 7.142 +REMARK INTER + INTRA: -3.270 +REMARK INTER: -2.701 +REMARK INTRA: -0.570 +REMARK UNBOUND: -0.649 +REMARK SMILES CNC(=O)Oc1ccccc1 +REMARK SMILES IDX 3 1 4 2 2 3 1 4 5 6 6 7 7 8 8 9 9 10 11 11 10 12 +REMARK H PARENT 2 5 +ROOT +ATOM 1 C UNL 1 3.286 -4.622 1.229 1.00 0.00 0.412 C +ATOM 2 O UNL 1 3.191 -5.406 0.296 1.00 0.00 -0.224 OA +ATOM 3 N UNL 1 4.127 -4.785 2.296 1.00 0.00 -0.324 N +ATOM 4 C UNL 1 5.083 -5.855 2.354 1.00 0.00 0.146 C +ATOM 5 H UNL 1 4.200 -4.001 2.929 1.00 0.00 0.166 HD +ENDROOT +BRANCH 1 6 +ATOM 6 O UNL 1 2.587 -3.434 1.383 1.00 0.00 -0.410 OA +BRANCH 6 7 +ATOM 7 C UNL 1 1.575 -3.469 2.348 1.00 0.00 0.132 A +ATOM 8 C UNL 1 1.490 -2.476 3.323 1.00 0.00 0.047 A +ATOM 9 C UNL 1 0.435 -2.506 4.235 1.00 0.00 0.004 A +ATOM 10 C UNL 1 -0.527 -3.515 4.157 1.00 0.00 0.000 A +ATOM 11 C UNL 1 0.610 -4.469 2.249 1.00 0.00 0.047 A +ATOM 12 C UNL 1 -0.442 -4.493 3.164 1.00 0.00 0.004 A +ENDBRANCH 6 7 +ENDBRANCH 1 6 +TORSDOF 2 +BEGIN_RES HIS A 2 +REMARK INDEX MAP 3 1 15 2 18 3 19 4 20 5 21 6 22 7 23 8 +ROOT +ATOM 1 CA HIS A 2 3.690 0.569 0.155 1.00 0.00 0.177 C +ENDROOT +BRANCH 1 2 +ATOM 2 CB HIS A 2 3.958 0.658 1.602 1.00 0.00 0.090 C +BRANCH 2 3 +ATOM 3 CG HIS A 2 4.691 -0.431 2.264 1.00 0.00 0.037 A +ATOM 4 ND1 HIS A 2 4.651 -0.689 3.613 1.00 0.00 -0.347 N +ATOM 5 CD2 HIS A 2 5.491 -1.432 1.752 1.00 0.00 0.134 A +ATOM 6 HD1 HIS A 2 4.146 0.095 4.234 1.00 0.00 0.167 HD +ATOM 7 CE1 HIS A 2 5.376 -1.763 3.886 1.00 0.00 0.196 A +ATOM 8 NE2 HIS A 2 5.914 -2.245 2.723 1.00 0.00 -0.245 NA +ENDBRANCH 2 3 +ENDBRANCH 1 2 +END_RES HIS A 2 +ENDMDL +MODEL 6 +REMARK VINA RESULT: -2.337 1.813 2.073 +REMARK INTER + INTRA: -3.259 +REMARK INTER: -2.642 +REMARK INTRA: -0.617 +REMARK UNBOUND: -0.649 +REMARK SMILES CNC(=O)Oc1ccccc1 +REMARK SMILES IDX 3 1 4 2 2 3 1 4 5 6 6 7 7 8 8 9 9 10 11 11 10 12 +REMARK H PARENT 2 5 +ROOT +ATOM 1 C UNL 1 -1.135 1.351 -3.609 1.00 0.00 0.412 C +ATOM 2 O UNL 1 -0.856 1.079 -4.768 1.00 0.00 -0.224 OA +ATOM 3 N UNL 1 -0.482 2.286 -2.854 1.00 0.00 -0.324 N +ATOM 4 C UNL 1 0.534 3.137 -3.408 1.00 0.00 0.146 C +ATOM 5 H UNL 1 -0.896 2.504 -1.958 1.00 0.00 0.166 HD +ENDROOT +BRANCH 1 6 +ATOM 6 O UNL 1 -2.151 0.789 -2.852 1.00 0.00 -0.410 OA +BRANCH 6 7 +ATOM 7 C UNL 1 -3.442 1.009 -3.346 1.00 0.00 0.132 A +ATOM 8 C UNL 1 -3.917 2.305 -3.540 1.00 0.00 0.047 A +ATOM 9 C UNL 1 -5.186 2.490 -4.088 1.00 0.00 0.004 A +ATOM 10 C UNL 1 -5.959 1.384 -4.450 1.00 0.00 0.000 A +ATOM 11 C UNL 1 -4.197 -0.101 -3.721 1.00 0.00 0.047 A +ATOM 12 C UNL 1 -5.464 0.091 -4.269 1.00 0.00 0.004 A +ENDBRANCH 6 7 +ENDBRANCH 1 6 +TORSDOF 2 +BEGIN_RES HIS A 2 +REMARK INDEX MAP 3 1 15 2 18 3 19 4 20 5 21 6 22 7 23 8 +ROOT +ATOM 1 CA HIS A 2 3.690 0.569 0.155 1.00 0.00 0.177 C +ENDROOT +BRANCH 1 2 +ATOM 2 CB HIS A 2 3.958 0.658 1.602 1.00 0.00 0.090 C +BRANCH 2 3 +ATOM 3 CG HIS A 2 4.868 -0.314 2.223 1.00 0.00 0.037 A +ATOM 4 ND1 HIS A 2 5.906 -0.936 1.571 1.00 0.00 -0.347 N +ATOM 5 CD2 HIS A 2 4.960 -0.776 3.521 1.00 0.00 0.134 A +ATOM 6 HD1 HIS A 2 5.929 -0.788 0.461 1.00 0.00 0.167 HD +ATOM 7 CE1 HIS A 2 6.566 -1.713 2.417 1.00 0.00 0.196 A +ATOM 8 NE2 HIS A 2 5.982 -1.624 3.652 1.00 0.00 -0.245 NA +ENDBRANCH 2 3 +ENDBRANCH 1 2 +END_RES HIS A 2 +ENDMDL +MODEL 7 +REMARK VINA RESULT: -2.217 5.076 5.744 +REMARK INTER + INTRA: -3.124 +REMARK INTER: -2.495 +REMARK INTRA: -0.629 +REMARK UNBOUND: -0.649 +REMARK SMILES CNC(=O)Oc1ccccc1 +REMARK SMILES IDX 3 1 4 2 2 3 1 4 5 6 6 7 7 8 8 9 9 10 11 11 10 12 +REMARK H PARENT 2 5 +ROOT +ATOM 1 C UNL 1 -5.216 -3.871 0.653 1.00 0.00 0.412 C +ATOM 2 O UNL 1 -5.316 -3.066 1.569 1.00 0.00 -0.224 OA +ATOM 3 N UNL 1 -4.060 -4.520 0.314 1.00 0.00 -0.324 N +ATOM 4 C UNL 1 -2.864 -4.401 1.100 1.00 0.00 0.146 C +ATOM 5 H UNL 1 -4.146 -5.252 -0.376 1.00 0.00 0.166 HD +ENDROOT +BRANCH 1 6 +ATOM 6 O UNL 1 -6.231 -4.285 -0.195 1.00 0.00 -0.410 OA +BRANCH 6 7 +ATOM 7 C UNL 1 -6.909 -3.251 -0.849 1.00 0.00 0.132 A +ATOM 8 C UNL 1 -8.127 -2.779 -0.360 1.00 0.00 0.047 A +ATOM 9 C UNL 1 -8.749 -1.708 -1.002 1.00 0.00 0.004 A +ATOM 10 C UNL 1 -8.146 -1.112 -2.111 1.00 0.00 0.000 A +ATOM 11 C UNL 1 -6.289 -2.651 -1.944 1.00 0.00 0.047 A +ATOM 12 C UNL 1 -6.917 -1.581 -2.580 1.00 0.00 0.004 A +ENDBRANCH 6 7 +ENDBRANCH 1 6 +TORSDOF 2 +BEGIN_RES HIS A 2 +REMARK INDEX MAP 3 1 15 2 18 3 19 4 20 5 21 6 22 7 23 8 +ROOT +ATOM 1 CA HIS A 2 3.690 0.569 0.155 1.00 0.00 0.177 C +ENDROOT +BRANCH 1 2 +ATOM 2 CB HIS A 2 3.958 0.658 1.602 1.00 0.00 0.090 C +BRANCH 2 3 +ATOM 3 CG HIS A 2 4.617 -0.468 2.279 1.00 0.00 0.037 A +ATOM 4 ND1 HIS A 2 3.954 -1.494 2.909 1.00 0.00 -0.347 N +ATOM 5 CD2 HIS A 2 5.951 -0.802 2.402 1.00 0.00 0.134 A +ATOM 6 HD1 HIS A 2 2.850 -1.345 3.029 1.00 0.00 0.167 HD +ATOM 7 CE1 HIS A 2 4.828 -2.374 3.374 1.00 0.00 0.196 A +ATOM 8 NE2 HIS A 2 6.093 -1.952 3.064 1.00 0.00 -0.245 NA +ENDBRANCH 2 3 +ENDBRANCH 1 2 +END_RES HIS A 2 +ENDMDL +MODEL 8 +REMARK VINA RESULT: -2.210 1.670 2.227 +REMARK INTER + INTRA: -3.117 +REMARK INTER: -2.506 +REMARK INTRA: -0.611 +REMARK UNBOUND: -0.649 +REMARK SMILES CNC(=O)Oc1ccccc1 +REMARK SMILES IDX 3 1 4 2 2 3 1 4 5 6 6 7 7 8 8 9 9 10 11 11 10 12 +REMARK H PARENT 2 5 +ROOT +ATOM 1 C UNL 1 -0.025 -1.257 -5.137 1.00 0.00 0.412 C +ATOM 2 O UNL 1 -0.071 -0.755 -6.251 1.00 0.00 -0.224 OA +ATOM 3 N UNL 1 0.044 -2.602 -4.896 1.00 0.00 -0.324 N +ATOM 4 C UNL 1 0.195 -3.558 -5.957 1.00 0.00 0.146 C +ATOM 5 H UNL 1 0.207 -2.875 -3.937 1.00 0.00 0.166 HD +ENDROOT +BRANCH 1 6 +ATOM 6 O UNL 1 -0.021 -0.581 -3.927 1.00 0.00 -0.410 OA +BRANCH 6 7 +ATOM 7 C UNL 1 -1.142 0.225 -3.701 1.00 0.00 0.132 A +ATOM 8 C UNL 1 -2.422 -0.327 -3.685 1.00 0.00 0.047 A +ATOM 9 C UNL 1 -3.514 0.493 -3.399 1.00 0.00 0.004 A +ATOM 10 C UNL 1 -3.316 1.846 -3.118 1.00 0.00 0.000 A +ATOM 11 C UNL 1 -0.931 1.570 -3.403 1.00 0.00 0.047 A +ATOM 12 C UNL 1 -2.027 2.384 -3.117 1.00 0.00 0.004 A +ENDBRANCH 6 7 +ENDBRANCH 1 6 +TORSDOF 2 +BEGIN_RES HIS A 2 +REMARK INDEX MAP 3 1 15 2 18 3 19 4 20 5 21 6 22 7 23 8 +ROOT +ATOM 1 CA HIS A 2 3.690 0.569 0.155 1.00 0.00 0.177 C +ENDROOT +BRANCH 1 2 +ATOM 2 CB HIS A 2 3.958 0.658 1.602 1.00 0.00 0.090 C +BRANCH 2 3 +ATOM 3 CG HIS A 2 4.708 -0.422 2.260 1.00 0.00 0.037 A +ATOM 4 ND1 HIS A 2 5.075 -0.419 3.585 1.00 0.00 -0.347 N +ATOM 5 CD2 HIS A 2 5.149 -1.642 1.789 1.00 0.00 0.134 A +ATOM 6 HD1 HIS A 2 4.914 0.550 4.122 1.00 0.00 0.167 HD +ATOM 7 CE1 HIS A 2 5.692 -1.553 3.881 1.00 0.00 0.196 A +ATOM 8 NE2 HIS A 2 5.748 -2.336 2.759 1.00 0.00 -0.245 NA +ENDBRANCH 2 3 +ENDBRANCH 1 2 +END_RES HIS A 2 +ENDMDL +MODEL 9 +REMARK VINA RESULT: -2.092 6.834 7.358 +REMARK INTER + INTRA: -2.986 +REMARK INTER: -2.424 +REMARK INTRA: -0.562 +REMARK UNBOUND: -0.649 +REMARK SMILES CNC(=O)Oc1ccccc1 +REMARK SMILES IDX 3 1 4 2 2 3 1 4 5 6 6 7 7 8 8 9 9 10 11 11 10 12 +REMARK H PARENT 2 5 +ROOT +ATOM 1 C UNL 1 6.500 -3.026 -1.655 1.00 0.00 0.412 C +ATOM 2 O UNL 1 7.556 -3.492 -2.057 1.00 0.00 -0.224 OA +ATOM 3 N UNL 1 5.542 -2.470 -2.459 1.00 0.00 -0.324 N +ATOM 4 C UNL 1 5.644 -2.496 -3.891 1.00 0.00 0.146 C +ATOM 5 H UNL 1 4.665 -2.241 -2.014 1.00 0.00 0.166 HD +ENDROOT +BRANCH 1 6 +ATOM 6 O UNL 1 6.066 -2.980 -0.339 1.00 0.00 -0.410 OA +BRANCH 6 7 +ATOM 7 C UNL 1 5.052 -3.890 -0.023 1.00 0.00 0.132 A +ATOM 8 C UNL 1 5.152 -5.227 -0.407 1.00 0.00 0.047 A +ATOM 9 C UNL 1 4.152 -6.121 -0.026 1.00 0.00 0.004 A +ATOM 10 C UNL 1 3.074 -5.678 0.743 1.00 0.00 0.000 A +ATOM 11 C UNL 1 3.990 -3.441 0.761 1.00 0.00 0.047 A +ATOM 12 C UNL 1 2.995 -4.341 1.139 1.00 0.00 0.004 A +ENDBRANCH 6 7 +ENDBRANCH 1 6 +TORSDOF 2 +BEGIN_RES HIS A 2 +REMARK INDEX MAP 3 1 15 2 18 3 19 4 20 5 21 6 22 7 23 8 +ROOT +ATOM 1 CA HIS A 2 3.690 0.569 0.155 1.00 0.00 0.177 C +ENDROOT +BRANCH 1 2 +ATOM 2 CB HIS A 2 3.958 0.658 1.602 1.00 0.00 0.090 C +BRANCH 2 3 +ATOM 3 CG HIS A 2 4.948 -0.246 2.205 1.00 0.00 0.037 A +ATOM 4 ND1 HIS A 2 6.178 -0.528 1.659 1.00 0.00 -0.347 N +ATOM 5 CD2 HIS A 2 4.939 -0.942 3.397 1.00 0.00 0.134 A +ATOM 6 HD1 HIS A 2 6.334 -0.153 0.616 1.00 0.00 0.167 HD +ATOM 7 CE1 HIS A 2 6.851 -1.334 2.466 1.00 0.00 0.196 A +ATOM 8 NE2 HIS A 2 6.084 -1.606 3.567 1.00 0.00 -0.245 NA +ENDBRANCH 2 3 +ENDBRANCH 1 2 +END_RES HIS A 2 +ENDMDL diff --git a/test/test_data/flexres/receptor.json b/test/test_data/flexres/receptor.json new file mode 100644 index 00000000..c8c9d16c --- /dev/null +++ b/test/test_data/flexres/receptor.json @@ -0,0 +1 @@ +{"residue_chem_templates": {"residue_templates": {"NME": {"mol": "{\"rdkitjson\":{\"version\":11},\"defaults\":{\"atom\":{\"z\":6,\"impHs\":0,\"chg\":0,\"nRad\":0,\"isotope\":0,\"stereo\":\"unspecified\"},\"bond\":{\"bo\":1,\"stereo\":\"unspecified\"}},\"molecules\":[{\"atoms\":[{},{\"z\":1},{\"z\":1},{\"z\":1},{\"z\":7,\"impHs\":1},{\"z\":1}],\"bonds\":[{\"atoms\":[0,1]},{\"atoms\":[0,2]},{\"atoms\":[0,3]},{\"atoms\":[0,4]},{\"atoms\":[4,5]}],\"extensions\":[{\"name\":\"rdkitRepresentation\",\"formatVersion\":2,\"toolkitVersion\":\"2024.03.4\",\"cipRanks\":[2,0,0,0,3,1]}]}]}", "link_labels": {"4": "N-term"}, "atom_names": ["CH3", "HH31", "HH32", "HH33", "N", "H"]}, "ACE": {"mol": 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b/test/test_data/flexres/receptor.pdbqt new file mode 100644 index 00000000..c80851b6 --- /dev/null +++ b/test/test_data/flexres/receptor.pdbqt @@ -0,0 +1,37 @@ +ATOM 1 C ALA A 1 4.995 1.645 -1.690 1.00 0.00 0.243 C +ATOM 2 O ALA A 1 5.294 0.515 -2.156 1.00 0.00 -0.272 OA +ATOM 3 CA ALA A 1 5.518 2.870 -2.403 1.00 0.00 0.168 C +ATOM 4 N ALA A 1 6.061 2.529 -3.691 1.00 0.00 -0.344 N +ATOM 5 CB ALA A 1 4.421 3.891 -2.559 1.00 0.00 0.041 C +ATOM 6 H ALA A 1 6.729 2.585 -4.473 1.00 0.00 0.164 HD +ATOM 7 C HIS A 2 2.368 0.239 -0.349 1.00 0.00 0.242 C +ATOM 8 O HIS A 2 1.827 0.959 -1.278 1.00 0.00 -0.272 OA +ATOM 9 N HIS A 2 4.201 1.774 -0.543 1.00 0.00 -0.343 N +ATOM 10 H HIS A 2 3.971 2.711 -0.182 1.00 0.00 0.164 HD +ATOM 11 C HIS A 3 -0.832 -0.126 -0.071 1.00 0.00 0.242 C +ATOM 12 O HIS A 3 -0.560 1.096 0.147 1.00 0.00 -0.272 OA +ATOM 13 CA HIS A 3 0.243 -1.075 -0.553 1.00 0.00 0.177 C +ATOM 14 N HIS A 3 1.527 -0.823 0.040 1.00 0.00 -0.343 N +ATOM 15 CB HIS A 3 -0.214 -2.454 -0.694 1.00 0.00 0.093 C +ATOM 16 CG HIS A 3 0.654 -3.363 -1.491 1.00 0.00 0.061 A +ATOM 17 ND1 HIS A 3 1.819 -2.985 -2.046 1.00 0.00 -0.242 NA +ATOM 18 CD2 HIS A 3 0.457 -4.684 -1.802 1.00 0.00 0.107 A +ATOM 19 CE1 HIS A 3 2.360 -4.051 -2.700 1.00 0.00 0.196 A +ATOM 20 NE2 HIS A 3 1.515 -5.068 -2.538 1.00 0.00 -0.350 N +ATOM 21 HE2 HIS A 3 1.651 -6.016 -2.918 1.00 0.00 0.167 HD +ATOM 22 H HIS A 3 1.850 -1.452 0.789 1.00 0.00 0.164 HD +ATOM 23 C TYR A 4 -3.373 0.217 2.071 1.00 0.00 0.065 C +ATOM 24 O TYR A 4 -4.293 0.998 2.728 1.00 0.00 -0.538 OA +ATOM 25 CA TYR A 4 -3.237 0.354 0.596 1.00 0.00 0.135 C +ATOM 26 N TYR A 4 -2.156 -0.543 0.154 1.00 0.00 -0.341 N +ATOM 27 OXT TYR A 4 -2.656 -0.595 2.677 1.00 0.00 -0.537 OA +ATOM 28 CB TYR A 4 -4.460 -0.123 -0.108 1.00 0.00 0.067 C +ATOM 29 CG TYR A 4 -5.699 0.602 0.156 1.00 0.00 -0.044 A +ATOM 30 CD1 TYR A 4 -6.089 1.698 -0.613 1.00 0.00 0.007 A +ATOM 31 CD2 TYR A 4 -6.492 0.168 1.200 1.00 0.00 0.007 A +ATOM 32 CE1 TYR A 4 -7.276 2.306 -0.282 1.00 0.00 0.047 A +ATOM 33 CE2 TYR A 4 -7.679 0.783 1.528 1.00 0.00 0.047 A +ATOM 34 CZ TYR A 4 -8.060 1.866 0.764 1.00 0.00 0.117 A +ATOM 35 OH TYR A 4 -9.262 2.477 1.103 1.00 0.00 -0.498 OA +ATOM 36 HH TYR A 4 -9.644 3.279 0.612 1.00 0.00 0.299 HD +ATOM 37 H TYR A 4 -2.383 -1.536 0.000 1.00 0.00 0.167 HD diff --git a/test/test_units.py b/test/test_units.py index f2639407..0521afa2 100644 --- a/test/test_units.py +++ b/test/test_units.py @@ -411,6 +411,42 @@ def test_logfile_write(self): assert line_content == "'11128', -7.25\n" + def test_write_flexres_pdb(self): + import meeko + + flexres_path = "test_data/flexres/" + export_file = "exported_flex_rec.pdb" + receptor_file = flexres_path + "receptor.pdbqt" + rtc = RingtailCore(db_file="flexres.db", docking_mode="vina") + rtc.add_results_from_files( + file=flexres_path + "ligand.pdbqt", + receptor_file=receptor_file, + recursive=True, + ) + rtc.filter(eworst=-1, bookmark_name="flexres") + polymer_file = flexres_path + "receptor.json" + with open(polymer_file) as f: + json_string = f.read() + polymer = meeko.Polymer.from_json(json_string) + rtc.write_flexres_pdb(polymer, "ligand", export_file, "flexres") + + assert os.path.exists(export_file) + + with open(export_file) as f: + file_contents = f.read() + + assert ( + "ATOM 11 C HIS A 2 2.368 0.239 -0.349 C" + in file_contents + ) + assert ( + "ATOM 44 HD2 HIS A 3 -0.400 -5.308 -1.507 H" + in file_contents + ) + + os.system(("rm " + export_file)) + os.system("rm flexres.db output_log.txt") + def test_plot(self): rtcore = RingtailCore(db_file="output.db") rtcore.filter(eworst=-7)