Mercurial > repos > bgruening > enumerate_charges
changeset 0:0f3e5c69251e draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
| author | bgruening |
|---|---|
| date | Tue, 10 Mar 2020 12:57:24 -0400 |
| parents | |
| children | 3d96dc99698f |
| files | dimorphite_dl.py enumerate_charges.xml rdkit_descriptors.py sdf_to_tab.py site_substructures.smarts test-data/CID_3037.sdf test-data/CID_3037.tab test-data/ligand.sdf test-data/ligand.tab test-data/mols.smi test-data/rdkit_descriptors_result1.csv test-data/rdkit_descriptors_result1.tab test-data/sucos_cluster.sdf |
| diffstat | 13 files changed, 3578 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dimorphite_dl.py Tue Mar 10 12:57:24 2020 -0400 @@ -0,0 +1,1084 @@ +# Copyright 2018 Jacob D. Durrant +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +""" +This script identifies and enumerates the possible protonation sites of SMILES +strings. +""" + +from __future__ import print_function +import copy +import os +import argparse +import sys + +try: + # Python2 + from StringIO import StringIO +except ImportError: + # Python3 + from io import StringIO + +# Always let the user know a help file is available. +print("\nFor help, use: python dimorphite_dl.py --help") + +# And always report citation information. +print("\nIf you use Dimorphite-DL in your research, please cite:") +print("Ropp PJ, Kaminsky JC, Yablonski S, Durrant JD (2019) Dimorphite-DL: An") +print("open-source program for enumerating the ionization states of drug-like small") +print("molecules. J Cheminform 11:14. doi:10.1186/s13321-019-0336-9.\n") + +try: + import rdkit + from rdkit import Chem + from rdkit.Chem import AllChem +except: + msg = "Dimorphite-DL requires RDKit. See https://www.rdkit.org/" + print(msg) + raise Exception(msg) + +def main(params=None): + """The main definition run when you call the script from the commandline. + + :param params: The parameters to use. Entirely optional. If absent, + defaults to None, in which case argments will be taken from + those given at the command line. + :param params: dict, optional + :return: Returns a list of the SMILES strings return_as_list parameter is + True. Otherwise, returns None. + """ + + parser = ArgParseFuncs.get_args() + args = vars(parser.parse_args()) + + # Add in any parameters in params. + if params is not None: + for k, v in params.items(): + args[k] = v + + # If being run from the command line, print out all parameters. + if __name__ == "__main__": + print("\nPARAMETERS:\n") + for k in sorted(args.keys()): + print(k.rjust(13) + ": " + str(args[k])) + print("") + + if args["test"]: + # Run tests. + TestFuncs.test() + else: + # Run protonation + if "output_file" in args and args["output_file"] is not None: + # An output file was specified, so write to that. + with open(args["output_file"], "w") as file: + for protonated_smi in Protonate(args): + file.write(protonated_smi + "\n") + elif "return_as_list" in args and args["return_as_list"] == True: + return list(Protonate(args)) + else: + # No output file specified. Just print it to the screen. + for protonated_smi in Protonate(args): + print(protonated_smi) + +class MyParser(argparse.ArgumentParser): + """Overwrite default parse so it displays help file on error. See + https://stackoverflow.com/questions/4042452/display-help-message-with-python-argparse-when-script-is-called-without-any-argu""" + + def error(self, message): + """Overwrites the default error message. + + :param message: The default error message. + """ + + self.print_help() + msg = "ERROR: %s\n\n" % message + print(msg) + raise Exception(msg) + + def print_help(self, file=None): + """Overwrite the default print_help function + + :param file: Output file, defaults to None + """ + + print("") + + if file is None: + file = sys.stdout + self._print_message(self.format_help(), file) + print(""" +examples: + python dimorphite_dl.py --smiles_file sample_molecules.smi + python dimorphite_dl.py --smiles "CCC(=O)O" --min_ph -3.0 --max_ph -2.0 + python dimorphite_dl.py --smiles "CCCN" --min_ph -3.0 --max_ph -2.0 --output_file output.smi + python dimorphite_dl.py --smiles_file sample_molecules.smi --pka_precision 2.0 --label_states + python dimorphite_dl.py --test""") + print("") + +class ArgParseFuncs: + """A namespace for storing functions that are useful for processing + command-line arguments. To keep things organized.""" + + @staticmethod + def get_args(): + """Gets the arguments from the command line. + + :return: A parser object. + """ + + parser = MyParser(description="Dimorphite 1.2: Creates models of " + + "appropriately protonated small moleucles. " + + "Apache 2.0 License. Copyright 2018 Jacob D. " + + "Durrant.") + parser.add_argument('--min_ph', metavar='MIN', type=float, default=6.4, + help='minimum pH to consider (default: 6.4)') + parser.add_argument('--max_ph', metavar='MAX', type=float, default=8.4, + help='maximum pH to consider (default: 8.4)') + parser.add_argument('--pka_precision', metavar='PRE', type=float, default=1.0, + help='pKa precision factor (number of standard devations, default: 1.0)') + parser.add_argument('--smiles', metavar='SMI', type=str, + help='SMILES string to protonate') + parser.add_argument('--smiles_file', metavar="FILE", type=str, + help='file that contains SMILES strings to protonate') + parser.add_argument('--output_file', metavar="FILE", type=str, + help='output file to write protonated SMILES (optional)') + parser.add_argument('--label_states', action="store_true", + help='label protonated SMILES with target state ' + \ + '(i.e., "DEPROTONATED", "PROTONATED", or "BOTH").') + parser.add_argument('--test', action="store_true", + help='run unit tests (for debugging)') + + return parser + + @staticmethod + def clean_args(args): + """Cleans and normalizes input parameters + + :param args: A dictionary containing the arguments. + :type args: dict + :raises Exception: No SMILES in params. + """ + + defaults = {'min_ph' : 6.4, + 'max_ph' : 8.4, + 'pka_precision' : 1.0, + 'label_states' : False, + 'test' : False} + + for key in defaults: + if key not in args: + args[key] = defaults[key] + + keys = list(args.keys()) + for key in keys: + if args[key] is None: + del args[key] + + if not "smiles" in args and not "smiles_file" in args: + msg = "Error: No SMILES in params. Use the -h parameter for help." + print(msg) + raise Exception(msg) + + # If the user provides a smiles string, turn it into a file-like StringIO + # object. + if "smiles" in args: + if isinstance(args["smiles"], str): + args["smiles_file"] = StringIO(args["smiles"]) + + args["smiles_and_data"] = LoadSMIFile(args["smiles_file"]) + + return args + +class UtilFuncs: + """A namespace to store functions for manipulating mol objects. To keep + things organized.""" + + @staticmethod + def neutralize_mol(mol): + """All molecules should be neuralized to the extent possible. The user + should not be allowed to specify the valence of the atoms in most cases. + + :param rdkit.Chem.rdchem.Mol mol: The rdkit Mol objet to be neutralized. + :return: The neutralized Mol object. + """ + + # Get the reaction data + rxn_data = [ + ['[Ov1-1:1]', '[Ov2+0:1]-[H]'], # To handle O- bonded to only one atom (add hydrogen). + ['[#7v4+1:1]-[H]', '[#7v3+0:1]'], # To handle N+ bonded to a hydrogen (remove hydrogen). + ['[Ov2-:1]', '[Ov2+0:1]'], # To handle O- bonded to two atoms. Should not be Negative. + ['[#7v3+1:1]', '[#7v3+0:1]'], # To handle N+ bonded to three atoms. Should not be positive. + ['[#7v2-1:1]', '[#7+0:1]-[H]'], # To handle N- Bonded to two atoms. Add hydrogen. + # ['[N:1]=[N+0:2]=[N:3]-[H]', '[N:1]=[N+1:2]=[N+0:3]-[H]'], # To + # handle bad azide. Must be protonated. (Now handled elsewhere, before + # SMILES converted to Mol object.) + ['[H]-[N:1]-[N:2]#[N:3]', '[N:1]=[N+1:2]=[N:3]-[H]'] # To handle bad azide. R-N-N#N should be R-N=[N+]=N + ] + + # Add substructures and reactions (initially none) + for i, rxn_datum in enumerate(rxn_data): + rxn_data[i].append(Chem.MolFromSmarts(rxn_datum[0])) + rxn_data[i].append(None) + + # Add hydrogens (respects valence, so incomplete). + # Chem.calcImplicitValence(mol) + mol.UpdatePropertyCache(strict=False) + mol = Chem.AddHs(mol) + + while True: # Keep going until all these issues have been resolved. + current_rxn = None # The reaction to perform. + current_rxn_str = None + + for i, rxn_datum in enumerate(rxn_data): + reactant_smarts, product_smarts, substruct_match_mol, rxn_placeholder = rxn_datum + if mol.HasSubstructMatch(substruct_match_mol): + if rxn_placeholder is None: + current_rxn_str = reactant_smarts + '>>' + product_smarts + current_rxn = AllChem.ReactionFromSmarts(current_rxn_str) + rxn_data[i][3] = current_rxn # Update the placeholder. + else: + current_rxn = rxn_data[i][3] + break + + # Perform the reaction if necessary + if current_rxn is None: # No reaction left, so break out of while loop. + break + else: + mol = current_rxn.RunReactants((mol,))[0][0] + mol.UpdatePropertyCache(strict=False) # Update valences + + # The mols have been altered from the reactions described above, we need + # to resanitize them. Make sure aromatic rings are shown as such This + # catches all RDKit Errors. without the catchError and sanitizeOps the + # Chem.SanitizeMol can crash the program. + sanitize_string = Chem.SanitizeMol( + mol, + sanitizeOps=rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_ALL, + catchErrors = True + ) + + return mol if sanitize_string.name == "SANITIZE_NONE" else None + + @staticmethod + def convert_smiles_str_to_mol(smiles_str): + """Given a SMILES string, check that it is actually a string and not a + None. Then try to convert it to an RDKit Mol Object. + + :param string smiles_str: The SMILES string. + :return: A rdkit.Chem.rdchem.Mol object, or None if it is the wrong type or + if it fails to convert to a Mol Obj + """ + + # Check that there are no type errors, ie Nones or non-string + # A non-string type will cause RDKit to hard crash + if smiles_str is None or type(smiles_str) is not str: + return None + + # Try to fix azides here. They are just tricky to deal with. + smiles_str = smiles_str.replace("N=N=N", "N=[N+]=N") + smiles_str = smiles_str.replace("NN#N", "N=[N+]=N") + + # Now convert to a mol object. Note the trick that is necessary to + # capture RDKit error/warning messages. See + # https://stackoverflow.com/questions/24277488/in-python-how-to-capture-the-stdout-from-a-c-shared-library-to-a-variable + stderr_fileno = sys.stderr.fileno() + stderr_save = os.dup(stderr_fileno) + stderr_pipe = os.pipe() + os.dup2(stderr_pipe[1], stderr_fileno) + os.close(stderr_pipe[1]) + + mol = Chem.MolFromSmiles(smiles_str) + + os.close(stderr_fileno) + os.close(stderr_pipe[0]) + os.dup2(stderr_save, stderr_fileno) + os.close(stderr_save) + + # Check that there are None type errors Chem.MolFromSmiles has sanitize on + # which means if there is even a small error in the SMILES (kekulize, + # nitrogen charge...) then mol=None. ie. + # Chem.MolFromSmiles("C[N]=[N]=[N]") = None this is an example of an + # nitrogen charge error. It is cased in a try statement to be overly + # cautious. + + return None if mol is None else mol + + @staticmethod + def eprint(*args, **kwargs): + """Error messages should be printed to STDERR. See + https://stackoverflow.com/questions/5574702/how-to-print-to-stderr-in-python""" + + print(*args, file=sys.stderr, **kwargs) + +class LoadSMIFile(object): + """A generator class for loading in the SMILES strings from a file, one at + a time.""" + + def __init__(self, filename): + """Initializes this class. + + :param filename: The filename or file object (i.e., StringIO). + :type filename: str or StringIO + """ + + if type(filename) is str: + # It's a filename + self.f = open(filename, "r") + else: + # It's a file object (i.e., StringIO) + self.f = filename + + def __iter__(self): + """Returns this generator object. + + :return: This generator object. + :rtype: LoadSMIFile + """ + + return self + + def __next__(self): + """Ensure Python3 compatibility. + + :return: A dict, where the "smiles" key contains the canonical SMILES + string and the "data" key contains the remaining information + (e.g., the molecule name). + :rtype: dict + """ + + return self.next() + + def next(self): + """Get the data associated with the next line. + + :raises StopIteration: If there are no more lines left iin the file. + :return: A dict, where the "smiles" key contains the canonical SMILES + string and the "data" key contains the remaining information + (e.g., the molecule name). + :rtype: dict + """ + + line = self.f.readline() + + if line == "": + # EOF + self.f.close() + raise StopIteration() + return + + # Divide line into smi and data + splits = line.split() + if len(splits) != 0: + # Generate mol object + smiles_str = splits[0] + + # Convert from SMILES string to RDKIT Mol. This series of tests is + # to make sure the SMILES string is properly formed and to get it + # into a canonical form. Filter if failed. + mol = UtilFuncs.convert_smiles_str_to_mol(smiles_str) + if mol is None: + UtilFuncs.eprint("WARNING: Skipping poorly formed SMILES string: " + line) + return self.next() + + # Handle nuetralizing the molecules. Filter if failed. + mol = UtilFuncs.neutralize_mol(mol) + if mol is None: + UtilFuncs.eprint("WARNING: Skipping poorly formed SMILES string: " + line) + return self.next() + + # Remove the hydrogens. + try: + mol = Chem.RemoveHs(mol) + except: + UtilFuncs.eprint("WARNING: Skipping poorly formed SMILES string: " + line) + return self.next() + + if mol is None: + UtilFuncs.eprint("WARNING: Skipping poorly formed SMILES string: " + line) + return self.next() + + # Regenerate the smiles string (to standardize). + new_mol_string = Chem.MolToSmiles(mol, isomericSmiles=True) + + return { + "smiles": new_mol_string, + "data": splits[1:] + } + else: + # Blank line? Go to next one. + return self.next() + +class Protonate(object): + """A generator class for protonating SMILES strings, one at a time.""" + + def __init__(self, args): + """Initialize the generator. + + :param args: A dictionary containing the arguments. + :type args: dict + """ + + # Make the args an object variable variable. + self.args = args + + # A list to store the protonated SMILES strings associated with a + # single input model. + self.cur_prot_SMI = [] + + # Clean and normalize the args + self.args = ArgParseFuncs.clean_args(args) + + # Load the substructures that can be protonated. + self.subs = ProtSubstructFuncs.load_protonation_substructs_calc_state_for_ph( + self.args["min_ph"], self.args["max_ph"], self.args["pka_precision"] + ) + + def __iter__(self): + """Returns this generator object. + + :return: This generator object. + :rtype: Protonate + """ + + return self + + def __next__(self): + """Ensure Python3 compatibility. + + :return: A dict, where the "smiles" key contains the canonical SMILES + string and the "data" key contains the remaining information + (e.g., the molecule name). + :rtype: dict + """ + + return self.next() + + def next(self): + """Get the next protonated SMILES string. + + :raises StopIteration: If there are no more lines left iin the file. + :return: TODO A dict, where the "smiles" key contains the canonical SMILES + string and the "data" key contains the remaining information + (e.g., the molecule name). + :rtype: dict + """ + + # If there are any SMILES strings in self.cur_prot_SMI, just return + # the first one and update the list to include only the remaining. + if len(self.cur_prot_SMI) > 0: + first, self.cur_prot_SMI = self.cur_prot_SMI[0], self.cur_prot_SMI[1:] + return first + + # self.cur_prot_SMI is empty, so try to add more to it. + + # Get the next SMILES string from the input file. + try: + smile_and_datum = self.args["smiles_and_data"].next() + except StopIteration: + # There are no more input smiles strings... + raise StopIteration() + + smi = smile_and_datum["smiles"] + data = smile_and_datum["data"] # Everything on SMILES line but the + # SMILES string itself (e.g., the + # molecule name). + + # Collect the data associated with this smiles (e.g., the molecule + # name). + tag = " ".join(data) + + # sites is a list of (atom index, "PROTONATED|DEPROTONATED|BOTH"). + # Note that the second entry indicates what state the site SHOULD be + # in (not the one it IS in per the SMILES string). It's calculated + # based on the probablistic distributions obtained during training. + sites = ProtSubstructFuncs.get_prot_sites_and_target_states(smi, self.subs) + + new_smis = [smi] + for site in sites: + # Make a new smiles with the correct protonation state. Note that + # new_smis is a growing list. This is how multiple protonation + # sites are handled. + + # new_smis_to_perhaps_add = ProtSubstructFuncs.protonate_site(new_smis, site) + new_smis = ProtSubstructFuncs.protonate_site(new_smis, site) + # print(site, new_smis) # Good for debugging. + + # Only add new smiles if not already in the list. + # for s in new_smis_to_perhaps_add: + # if not s in new_smis: + # new_smis.append(s) + + # In some cases, the script might generate redundant molecules. + # Phosphonates, when the pH is between the two pKa values and the + # stdev value is big enough, for example, will generate two identical + # BOTH states. Let's remove this redundancy. + new_smis = list(set(new_smis)) + + # Deprotonating protonated aromatic nitrogen gives [nH-]. Change this + # to [n-]. This is a hack. + new_smis = [s.replace("[nH-]", "[n-]") for s in new_smis] + + # Sometimes Dimorphite-DL generates molecules that aren't actually + # possible. Simply convert these to mol objects to eliminate the bad + # ones (that are None). + new_smis = [s for s in new_smis if UtilFuncs.convert_smiles_str_to_mol(s) is not None] + + # If there are no smi left, return the input one at the very least. + # All generated forms have apparently been judged + # inappropriate/mal-formed. + if len(new_smis) == 0: + new_smis = [smi] + + # If the user wants to see the target states, add those + # to the ends of each line. + if self.args["label_states"]: + states = '\t'.join([x[1] for x in sites]) + new_lines = [x + "\t" + tag + "\t" + states for x in new_smis] + else: + new_lines = [x + "\t" + tag for x in new_smis] + + self.cur_prot_SMI = new_lines + + return self.next() + +class ProtSubstructFuncs: + """A namespace to store functions for loading the substructures that can + be protonated. To keep things organized.""" + + @staticmethod + def load_protonation_substructs_calc_state_for_ph(min_ph=6.4, max_ph=8.4, pka_std_range=1): + """A pre-calculated list of R-groups with protonation sites, with their + likely pKa bins. + + :param float min_ph: The lower bound on the pH range, defaults to 6.4. + :param float max_ph: The upper bound on the pH range, defaults to 8.4. + :param pka_std_range: Basically the precision (stdev from predicted pKa to + consider), defaults to 1. + :return: A dict of the protonation substructions for the specified pH + range. + """ + + subs = [] + pwd = os.path.dirname(os.path.realpath(__file__)) + + site_structures_file = "{}/{}".format(pwd, "site_substructures.smarts") + with open(site_structures_file, 'r') as substruct: + for line in substruct: + line = line.strip() + sub = {} + if line is not "": + splits = line.split() + sub["name"] = splits[0] + sub["smart"] = splits[1] + sub["mol"] = Chem.MolFromSmarts(sub["smart"]) + + # NEED TO DIVIDE THIS BY 3s + pka_ranges = [splits[i:i+3] for i in range(2, len(splits)-1, 3)] + + prot = [] + for pka_range in pka_ranges: + site = pka_range[0] + std = float(pka_range[2]) * pka_std_range + mean = float(pka_range[1]) + protonation_state = ProtSubstructFuncs.define_protonation_state( + mean, std, min_ph, max_ph + ) + + prot.append([site, protonation_state]) + + sub["prot_states_for_pH"] = prot + subs.append(sub) + return subs + + @staticmethod + def define_protonation_state(mean, std, min_ph, max_ph): + """Updates the substructure definitions to include the protonation state + based on the user-given pH range. The size of the pKa range is also based + on the number of standard deviations to be considered by the user param. + + :param float mean: The mean pKa. + :param float std: The precision (stdev). + :param float min_ph: The min pH of the range. + :param float max_ph: The max pH of the range. + :return: A string describing the protonation state. + """ + + min_pka = mean - std + max_pka = mean + std + + # This needs to be reassigned, and 'ERROR' should never make it past the + # next set of checks. + if min_pka <= max_ph and min_ph <= max_pka: + protonation_state = 'BOTH' + elif mean > max_ph: + protonation_state = 'PROTONATED' + else: + protonation_state = 'DEPROTONATED' + + return protonation_state + + @staticmethod + def get_prot_sites_and_target_states(smi, subs): + """For a single molecule, find all possible matches in the protonation + R-group list, subs. Items that are higher on the list will be matched + first, to the exclusion of later items. + + :param string smi: A SMILES string. + :param list subs: Substructure information. + :return: A list of protonation sites and their pKa bin. ('PROTONATED', + 'BOTH', or 'DEPROTONATED') + """ + + # Convert the Smiles string (smi) to an RDKit Mol Obj + mol = UtilFuncs.convert_smiles_str_to_mol(smi) + + # Check Conversion worked + if mol is None: + UtilFuncs.eprint("ERROR: ", smi) + return [] + + # Try to Add hydrogens. if failed return [] + try: + mol = Chem.AddHs(mol) + except: + UtilFuncs.eprint("ERROR: ", smi) + return [] + + # Check adding Hs worked + if mol is None: + UtilFuncs.eprint("ERROR: ", smi) + return [] + + ProtectUnprotectFuncs.unprotect_molecule(mol) + protonation_sites = [] + + for item in subs: + smart = item["mol"] + if mol.HasSubstructMatch(smart): + matches = ProtectUnprotectFuncs.get_unprotected_matches(mol, smart) + prot = item["prot_states_for_pH"] + for match in matches: + # We want to move the site from being relative to the + # substructure, to the index on the main molecule. + for site in prot: + proton = int(site[0]) + category = site[1] + new_site = (match[proton], category, item["name"]) + + if not new_site in protonation_sites: + # Because sites must be unique. + protonation_sites.append(new_site) + + ProtectUnprotectFuncs.protect_molecule(mol, match) + + return protonation_sites + + @staticmethod + def protonate_site(smis, site): + """Given a list of SMILES strings, we protonate the site. + + :param list smis: The list of SMILES strings. + :param tuple site: Information about the protonation site. + (idx, target_prot_state, prot_site_name) + :return: A list of the appropriately protonated SMILES. + """ + + # Decouple the atom index and its target protonation state from the site + # tuple + idx, target_prot_state, prot_site_name = site + + # Initialize the output list + output_smis = [] + + state_to_charge = {"DEPROTONATED": [-1], + "PROTONATED": [0], + "BOTH": [-1, 0]} + + charges = state_to_charge[target_prot_state] + + # Now make the actual smiles match the target protonation state. + output_smis = ProtSubstructFuncs.set_protonation_charge(smis, idx, charges, prot_site_name) + + return output_smis + + @staticmethod + def set_protonation_charge(smis, idx, charges, prot_site_name): + """Sets the atomic charge on a particular site for a set of SMILES. + + :param list smis: A list of the SMILES strings. + :param int idx: The index of the atom to consider. + :param list charges: A list of the charges (ints) to assign at + this site. + :param string prot_site_name: The name of the protonation site. + :return: A list of the processed SMILES strings. + """ + + # Sets up the output list and the Nitrogen charge + output = [] + + for charge in charges: + # The charge for Nitrogens is 1 higher than others (i.e., protonated + # state is positively charged). + nitro_charge = charge + 1 + + # But there are a few nitrogen moieties where the acidic group is the + # neutral one. Amides are a good example. I gave some thought re. how + # to best flag these. I decided that those nitrogen-containing + # moieties where the acidic group is neutral (rather than positively + # charged) will have "*" in the name. + if "*" in prot_site_name: + nitro_charge = nitro_charge - 1 # Undo what was done previously. + + for smi in smis: + + # Convert smilesstring (smi) into a RDKit Mol + mol = UtilFuncs.convert_smiles_str_to_mol(smi) + + # Check that the conversion worked, skip if it fails + if mol is None: + continue + + atom = mol.GetAtomWithIdx(idx) + + # Assign the protonation charge, with special care for Nitrogens + element = atom.GetAtomicNum() + if element == 7: + atom.SetFormalCharge(nitro_charge) + else: + atom.SetFormalCharge(charge) + + # Convert back to SMILE and add to output + out_smile = Chem.MolToSmiles(mol, isomericSmiles=True,canonical=True) + output.append(out_smile) + + return output + +class ProtectUnprotectFuncs: + """A namespace for storing functions that are useful for protecting and + unprotecting molecules. To keep things organized. We need to identify and + mark groups that have been matched with a substructure.""" + + @staticmethod + def unprotect_molecule(mol): + """Sets the protected property on all atoms to 0. This also creates the + property for new molecules. + + :param rdkit.Chem.rdchem.Mol mol: The rdkit Mol object. + :type mol: The rdkit Mol object with atoms unprotected. + """ + + for atom in mol.GetAtoms(): + atom.SetProp('_protected', '0') + + @staticmethod + def protect_molecule(mol, match): + """Given a 'match', a list of molecules idx's, we set the protected status + of each atom to 1. This will prevent any matches using that atom in the + future. + + :param rdkit.Chem.rdchem.Mol mol: The rdkit Mol object to protect. + :param list match: A list of molecule idx's. + """ + + for idx in match: + atom = mol.GetAtomWithIdx(idx) + atom.SetProp('_protected', '1') + + @staticmethod + def get_unprotected_matches(mol, substruct): + """Finds substructure matches with atoms that have not been protected. + Returns list of matches, each match a list of atom idxs. + + :param rdkit.Chem.rdchem.Mol mol: The Mol object to consider. + :param string substruct: The SMARTS string of the substructure ot match. + :return: A list of the matches. Each match is itself a list of atom idxs. + """ + + matches = mol.GetSubstructMatches(substruct) + unprotected_matches = [] + for match in matches: + if ProtectUnprotectFuncs.is_match_unprotected(mol, match): + unprotected_matches.append(match) + return unprotected_matches + + @staticmethod + def is_match_unprotected(mol, match): + """Checks a molecule to see if the substructure match contains any + protected atoms. + + :param rdkit.Chem.rdchem.Mol mol: The Mol object to check. + :param list match: The match to check. + :return: A boolean, whether the match is present or not. + """ + + for idx in match: + atom = mol.GetAtomWithIdx(idx) + protected = atom.GetProp("_protected") + if protected == "1": + return False + return True + +class TestFuncs: + """A namespace for storing functions that perform tests on the code. To + keep things organized.""" + + @staticmethod + def test(): + """Tests all the 38 groups.""" + + smis = [ + # [input smiles, pka, protonated, deprotonated, category] + ["C#CCO", "C#CCO", "C#CC[O-]", "Alcohol"], + ["C(=O)N", "NC=O", "[NH-]C=O", "Amide"], + ["CC(=O)NOC(C)=O", "CC(=O)NOC(C)=O", "CC(=O)[N-]OC(C)=O", "Amide_electronegative"], + ["COC(=N)N", "COC(N)=[NH2+]", "COC(=N)N", "AmidineGuanidine2"], + ["Brc1ccc(C2NCCS2)cc1", "Brc1ccc(C2[NH2+]CCS2)cc1", "Brc1ccc(C2NCCS2)cc1", "Amines_primary_secondary_tertiary"], + ["CC(=O)[n+]1ccc(N)cc1", "CC(=O)[n+]1ccc([NH3+])cc1", "CC(=O)[n+]1ccc(N)cc1", "Anilines_primary"], + ["CCNc1ccccc1", "CC[NH2+]c1ccccc1", "CCNc1ccccc1", "Anilines_secondary"], + ["Cc1ccccc1N(C)C", "Cc1ccccc1[NH+](C)C", "Cc1ccccc1N(C)C", "Anilines_tertiary"], + ["BrC1=CC2=C(C=C1)NC=C2", "Brc1ccc2[nH]ccc2c1", "Brc1ccc2[n-]ccc2c1", "Indole_pyrrole"], + ["O=c1cc[nH]cc1", "O=c1cc[nH]cc1", "O=c1cc[n-]cc1", "Aromatic_nitrogen_protonated"], + ["C-N=[N+]=[N@H]", "CN=[N+]=N", "CN=[N+]=[N-]", "Azide"], + ["BrC(C(O)=O)CBr", "O=C(O)C(Br)CBr", "O=C([O-])C(Br)CBr", "Carboxyl"], + ["NC(NN=O)=N", "NC(=[NH2+])NN=O", "N=C(N)NN=O", "AmidineGuanidine1"], + ["C(F)(F)(F)C(=O)NC(=O)C", "CC(=O)NC(=O)C(F)(F)F", "CC(=O)[N-]C(=O)C(F)(F)F", "Imide"], + ["O=C(C)NC(C)=O", "CC(=O)NC(C)=O", "CC(=O)[N-]C(C)=O", "Imide2"], + ["CC(C)(C)C(N(C)O)=O", "CN(O)C(=O)C(C)(C)C", "CN([O-])C(=O)C(C)(C)C", "N-hydroxyamide"], + ["C[N+](O)=O", "C[N+](=O)O", "C[N+](=O)[O-]", "Nitro"], + ["O=C1C=C(O)CC1", "O=C1C=C(O)CC1", "O=C1C=C([O-])CC1", "O=C-C=C-OH"], + ["C1CC1OO", "OOC1CC1", "[O-]OC1CC1", "Peroxide2"], + ["C(=O)OO", "O=COO", "O=CO[O-]", "Peroxide1"], + ["Brc1cc(O)cc(Br)c1", "Oc1cc(Br)cc(Br)c1", "[O-]c1cc(Br)cc(Br)c1", "Phenol"], + ["CC(=O)c1ccc(S)cc1", "CC(=O)c1ccc(S)cc1", "CC(=O)c1ccc([S-])cc1", "Phenyl_Thiol"], + ["C=CCOc1ccc(C(=O)O)cc1", "C=CCOc1ccc(C(=O)O)cc1", "C=CCOc1ccc(C(=O)[O-])cc1", "Phenyl_carboxyl"], + ["COP(=O)(O)OC", "COP(=O)(O)OC", "COP(=O)([O-])OC", "Phosphate_diester"], + ["CP(C)(=O)O", "CP(C)(=O)O", "CP(C)(=O)[O-]", "Phosphinic_acid"], + ["CC(C)OP(C)(=O)O", "CC(C)OP(C)(=O)O", "CC(C)OP(C)(=O)[O-]", "Phosphonate_ester"], + ["CC1(C)OC(=O)NC1=O", "CC1(C)OC(=O)NC1=O", "CC1(C)OC(=O)[N-]C1=O", "Ringed_imide1"], + ["O=C(N1)C=CC1=O", "O=C1C=CC(=O)N1", "O=C1C=CC(=O)[N-]1", "Ringed_imide2"], + ["O=S(OC)(O)=O", "COS(=O)(=O)O", "COS(=O)(=O)[O-]", "Sulfate"], + ["COc1ccc(S(=O)O)cc1", "COc1ccc(S(=O)O)cc1", "COc1ccc(S(=O)[O-])cc1", "Sulfinic_acid"], + ["CS(N)(=O)=O", "CS(N)(=O)=O", "CS([NH-])(=O)=O", "Sulfonamide"], + ["CC(=O)CSCCS(O)(=O)=O", "CC(=O)CSCCS(=O)(=O)O", "CC(=O)CSCCS(=O)(=O)[O-]", "Sulfonate"], + ["CC(=O)S", "CC(=O)S", "CC(=O)[S-]", "Thioic_acid"], + ["C(C)(C)(C)(S)", "CC(C)(C)S", "CC(C)(C)[S-]", "Thiol"], + ["Brc1cc[nH+]cc1", "Brc1cc[nH+]cc1", "Brc1ccncc1", "Aromatic_nitrogen_unprotonated"], + ["C=C(O)c1c(C)cc(C)cc1C", "C=C(O)c1c(C)cc(C)cc1C", "C=C([O-])c1c(C)cc(C)cc1C", "Vinyl_alcohol"], + ["CC(=O)ON", "CC(=O)O[NH3+]", "CC(=O)ON", "Primary_hydroxyl_amine"] + ] + + smis_phos = [ + ["O=P(O)(O)OCCCC", "CCCCOP(=O)(O)O", "CCCCOP(=O)([O-])O", "CCCCOP(=O)([O-])[O-]", "Phosphate"], + ["CC(P(O)(O)=O)C", "CC(C)P(=O)(O)O", "CC(C)P(=O)([O-])O", "CC(C)P(=O)([O-])[O-]", "Phosphonate"] + ] + + # Load the average pKa values. + average_pkas = {l.split()[0].replace("*", ""):float(l.split()[3]) for l in open("site_substructures.smarts") if l.split()[0] not in ["Phosphate", "Phosphonate"]} + average_pkas_phos = {l.split()[0].replace("*", ""):[float(l.split()[3]), float(l.split()[6])] for l in open("site_substructures.smarts") if l.split()[0] in ["Phosphate", "Phosphonate"]} + + print("Running Tests") + print("=============") + print("") + + print("Very Acidic (pH -10000000)") + print("--------------------------") + print("") + + args = { + "min_ph": -10000000, + "max_ph": -10000000, + "pka_precision": 0.5, + "smiles": "", + "label_states": True + } + + for smi, protonated, deprotonated, category in smis: + args["smiles"] = smi + TestFuncs.test_check(args, [protonated], ["PROTONATED"]) + + for smi, protonated, mix, deprotonated, category in smis_phos: + args["smiles"] = smi + TestFuncs.test_check(args, [protonated], ["PROTONATED"]) + + args["min_ph"] = 10000000 + args["max_ph"] = 10000000 + + print("") + print("Very Basic (pH 10000000)") + print("------------------------") + print("") + + for smi, protonated, deprotonated, category in smis: + args["smiles"] = smi + TestFuncs.test_check(args, [deprotonated], ["DEPROTONATED"]) + + for smi, protonated, mix, deprotonated, category in smis_phos: + args["smiles"] = smi + TestFuncs.test_check(args, [deprotonated], ["DEPROTONATED"]) + + print("") + print("pH is Category pKa") + print("------------------") + print("") + + for smi, protonated, deprotonated, category in smis: + avg_pka = average_pkas[category] + + args["smiles"] = smi + args["min_ph"] = avg_pka + args["max_ph"] = avg_pka + + TestFuncs.test_check(args, [protonated, deprotonated], ["BOTH"]) + + for smi, protonated, mix, deprotonated, category in smis_phos: + args["smiles"] = smi + + avg_pka = average_pkas_phos[category][0] + args["min_ph"] = avg_pka + args["max_ph"] = avg_pka + + TestFuncs.test_check(args, [mix, protonated], ["BOTH"]) + + avg_pka = average_pkas_phos[category][1] + args["min_ph"] = avg_pka + args["max_ph"] = avg_pka + + TestFuncs.test_check(args, [mix, deprotonated], ["DEPROTONATED", "DEPROTONATED"]) + + avg_pka = 0.5 * (average_pkas_phos[category][0] + average_pkas_phos[category][1]) + args["min_ph"] = avg_pka + args["max_ph"] = avg_pka + args["pka_precision"] = 5 # Should give all three + + TestFuncs.test_check(args, [mix, deprotonated, protonated], ["BOTH", "BOTH"]) + + @staticmethod + def test_check(args, expected_output, labels): + """Tests most ionizable groups. The ones that can only loose or gain a single proton. + + :param args: The arguments to pass to protonate() + :param expected_output: A list of the expected SMILES-strings output. + :param labels: The labels. A list containing combo of BOTH, PROTONATED, + DEPROTONATED. + :raises Exception: Wrong number of states produced. + :raises Exception: Unexpected output SMILES. + :raises Exception: Wrong labels. + """ + + output = list(Protonate(args)) + output = [o.split() for o in output] + + num_states = len(expected_output) + + if (len(output) != num_states): + msg = args["smiles"] + " should have " + str(num_states) + \ + " states at at pH " + str(args["min_ph"]) + ": " + str(output) + print(msg) + raise Exception(msg) + + if (len(set([l[0] for l in output]) - set(expected_output)) != 0): + msg = args["smiles"] + " is not " + " AND ".join(expected_output) + \ + " at pH " + str(args["min_ph"]) + " - " + str(args["max_ph"]) + \ + "; it is " + " AND ".join([l[0] for l in output]) + print(msg) + raise Exception(msg) + + if (len(set([l[1] for l in output]) - set(labels)) != 0): + msg = args["smiles"] + " not labeled as " + " AND ".join(labels) + \ + "; it is " + " AND ".join([l[1] for l in output]) + print(msg) + raise Exception(msg) + + ph_range = sorted(list(set([args["min_ph"], args["max_ph"]]))) + ph_range_str = "(" + " - ".join("{0:.2f}".format(n) for n in ph_range) + ")" + print("(CORRECT) " + ph_range_str.ljust(10) + " " + args["smiles"] + " => " + " AND ".join([l[0] for l in output])) + +def run(**kwargs): + """A helpful, importable function for those who want to call Dimorphite-DL + from another Python script rather than the command line. Note that this + function accepts keyword arguments that match the command-line parameters + exactly. If you want to pass and return a list of RDKit Mol objects, import + run_with_mol_list() instead. + + :param **kwargs: For a complete description, run dimorphite_dl.py from the + command line with the -h option. + :type kwargs: dict + """ + + # Run the main function with the specified arguments. + main(kwargs) + +def run_with_mol_list(mol_lst, **kwargs): + """A helpful, importable function for those who want to call Dimorphite-DL + from another Python script rather than the command line. Note that this + function is for passing Dimorphite-DL a list of RDKit Mol objects, together + with command-line parameters. If you want to use only the same parameters + that you would use from the command line, import run() instead. + + :param mol_lst: A list of rdkit.Chem.rdchem.Mol objects. + :type mol_lst: list + :raises Exception: If the **kwargs includes "smiles", "smiles_file", + "output_file", or "test" parameters. + :return: A list of properly protonated rdkit.Chem.rdchem.Mol objects. + :rtype: list + """ + + # Do a quick check to make sure the user input makes sense. + for bad_arg in ["smiles", "smiles_file", "output_file", "test"]: + if bad_arg in kwargs: + msg = "You're using Dimorphite-DL's run_with_mol_list(mol_lst, " + \ + "**kwargs) function, but you also passed the \"" + \ + bad_arg + "\" argument. Did you mean to use the " + \ + "run(**kwargs) function instead?" + print(msg) + raise Exception(msg) + + # Set the return_as_list flag so main() will return the protonated smiles + # as a list. + kwargs["return_as_list"] = True + + # Having reviewed the code, it will be very difficult to rewrite it so + # that a list of Mol objects can be used directly. Intead, convert this + # list of mols to smiles and pass that. Not efficient, but it will work. + protonated_smiles_and_props = [] + for m in mol_lst: + props = m.GetPropsAsDict() + kwargs["smiles"] = Chem.MolToSmiles(m, isomericSmiles=True) + protonated_smiles_and_props.extend( + [(s.split("\t")[0], props) for s in main(kwargs)] + ) + + # Now convert the list of protonated smiles strings back to RDKit Mol + # objects. Also, add back in the properties from the original mol objects. + mols = [] + for s, props in protonated_smiles_and_props: + m = Chem.MolFromSmiles(s) + if m: + for prop, val in props.items(): + if type(val) is int: + m.SetIntProp(prop, val) + elif type(val) is float: + m.SetDoubleProp(prop, val) + elif type(val) is bool: + m.SetBoolProp(prop, val) + else: + m.SetProp(prop, str(val)) + mols.append(m) + else: + UtilFuncs.eprint("WARNING: Could not process molecule with SMILES string " + s + " and properties " + str(props)) + + return mols + +if __name__ == "__main__": + main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/enumerate_charges.xml Tue Mar 10 12:57:24 2020 -0400 @@ -0,0 +1,98 @@ +<tool id="enumerate_charges" name="Enumerate changes" version="0.1"> + <description>calculated with Dimorphite DL and RDKit</description> + <requirements> + <requirement type="package" version="2019.09.2">rdkit</requirement> + </requirements> + <command detect_errors="exit_code"> +<![CDATA[ + python '$__tool_directory__/dimorphite_dl.py' + --smiles_file '$input' + --output_file '$output' + --min_ph $min_ph + --max_ph $max_ph +]]> + </command> + <inputs> + <param name="input" format="smi" type="data" label="Input molecule data" + help="In SMILES format"/> + <param name="min_ph" type="float" label="Minimum pH" value="6.4" min="0" max="14"/> + <param name="max_ph" type="float" label="Maximum pH" value="8.4" min="0" max="14"/> + </inputs> + <outputs> + <data format="smi" name="output" /> + </outputs> + <tests> + <test> + <param name="input" ftype='smi' value="mols.smi" /> + <param name="min_ph" value="6.4" /> + <param name="max_ph" value="8.4" /> + <output name="output" ftype='smi'> + <!-- there are problems comparing the output to the expected due to whitespace differences + so we just check that the number of lines is as expected --> + <assert_contents> + <has_n_lines n="7" /> + <has_text text="NC(CCCC[NH3+])C(=O)[O-]" /> + <has_text text="NCCCCC(N)C(=O)[O-]" /> + <has_text text="NCCCCC([NH3+])C(=O)[O-]" /> + </assert_contents> + </output> + </test> + <test> + <param name="input" ftype='smi' value="mols.smi" /> + <param name="min_ph" value="4.4" /> + <param name="max_ph" value="10.4" /> + <output name="output" ftype='smi'> + <assert_contents> + <has_n_lines n="14" /> + <has_text text="NC(CCCC[NH3+])C(=O)O" /> + <has_text text="NCCCCC([NH3+])C(=O)[O-]" /> + <has_text text="NC(CCCC[NH3+])C(=O)[O-]" /> + <has_text text="NCCCCC([NH3+])C(=O)O" /> + <has_text text="NC(CCCC[NH3+])C(=O)O" /> + <has_text text="NCCCCC(N)C(=O)O" /> + </assert_contents> + </output> + </test> + </tests> + <help> +<![CDATA[ + +.. class:: infomark + +**What this tool does** + +Dimorphite DL provides rules on how to enumerate the different charge forms of molecules using RDKit. +Source code can be found here: https://git.durrantlab.pitt.edu/jdurrant/dimorphite_dl + + +----- + +.. class:: infomark + +**Input** + +- `SMILES Format`_ + +.. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification + +----- + +.. class:: infomark + + **Output** + +SMILES format with the enumerated molecules. If an ID was provided in the input this is retained in the output. + + +]]> + </help> + <citations> + <citation type="doi">10.1186/s13321-019-0336-9</citation> + <citation type="bibtex"> + @article{rdkit, + author = {Greg Landrum and others}, + title = {RDKit: Open-source cheminformatics}, + url ={http://www.rdkit.org} + }</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rdkit_descriptors.py Tue Mar 10 12:57:24 2020 -0400 @@ -0,0 +1,76 @@ +#!/usr/bin/env python + +from rdkit.Chem import Descriptors +from rdkit import Chem +import sys, os, re +import argparse +import inspect + +def get_supplier( infile, format = 'smiles' ): + """ + Returns a generator over a SMILES or InChI file. Every element is of RDKit + molecule and has its original string as _Name property. + """ + with open(infile) as handle: + for line in handle: + line = line.strip() + if format == 'smiles': + mol = Chem.MolFromSmiles( line, sanitize=True ) + elif format == 'inchi': + mol = Chem.inchi.MolFromInchi( line, sanitize=True, removeHs=True, logLevel=None, treatWarningAsError=False ) + if mol is None: + yield False + else: + mol.SetProp( '_Name', line.split('\t')[0] ) + yield mol + +def get_rdkit_descriptor_functions(): + """ + Returns all descriptor functions under the Chem.Descriptors Module as tuple of (name, function) + """ + ret = [ (name, f) for name, f in inspect.getmembers( Descriptors ) if inspect.isfunction( f ) and not name.startswith( '_' ) ] + ret.sort() + return ret + + +def descriptors( mol, functions ): + """ + Calculates the descriptors of a given molecule. + """ + for name, function in functions: + yield (name, function( mol )) + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument('-i', '--infile', required=True, help='Path to the input file.') + parser.add_argument("--iformat", help="Specify the input file format.") + + parser.add_argument('-o', '--outfile', type=argparse.FileType('w+'), + default=sys.stdout, help="path to the result file, default it sdtout") + + parser.add_argument("--header", dest="header", action="store_true", + default=False, + help="Write header line.") + + args = parser.parse_args() + + if args.iformat == 'sdf': + supplier = Chem.SDMolSupplier( args.infile ) + elif args.iformat =='smi': + supplier = get_supplier( args.infile, format = 'smiles' ) + elif args.iformat == 'inchi': + supplier = get_supplier( args.infile, format = 'inchi' ) + + functions = get_rdkit_descriptor_functions() + + if args.header: + args.outfile.write( '%s\n' % '\t'.join( ['MoleculeID'] + [name for name, f in functions] ) ) + + for mol in supplier: + if not mol: + continue + descs = descriptors( mol, functions ) + molecule_id = mol.GetProp("_Name") + args.outfile.write( "%s\n" % '\t'.join( [molecule_id]+ [str(round(res, 6)) for name, res in descs] ) ) +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sdf_to_tab.py Tue Mar 10 12:57:24 2020 -0400 @@ -0,0 +1,46 @@ +#!/usr/bin/env python3 +import argparse +import pandas as pd +from rdkit import Chem + +def sdf_to_tab(vars): + mols = Chem.SDMolSupplier(vars.inp, sanitize=False) + df = pd.DataFrame() # for output + + for n in range(len(mols)): + if mols[n]: + d = mols[n].GetPropsAsDict() + # filter dict for desired props + if vars.props.strip() == '': # none specified, return all + d = {prop: val for (prop, val) in d.items() if not any(x in str(val) for x in ['\n', '\t'])} # remove items containing newlines or tabs + else: + d = {prop: val for (prop, val) in d.items() if prop in vars.props.replace(' ', '').split(',')} # remove items not requested via CLI + if vars.name: + d['Name'] = mols[n].GetProp('_Name') + if vars.smiles: + d['SMILES'] = Chem.MolToSmiles(mols[n], isomericSmiles=False) + d['Index'] = int(n) + + df = df.append(d, ignore_index=True) + else: + print("Molecule could not be read - skipped.") + + df = df.astype({'Index': int}).set_index('Index') + df.to_csv(vars.out, sep='\t', header=vars.header) + +def main(): + parser = argparse.ArgumentParser(description="Convert SDF to tabular") + parser.add_argument('--inp', '-i', help="The input file", required=True) + parser.add_argument('--out', '-o', help="The output file", required=True) + parser.add_argument('--props', '-p', help="Properties to filter (leave blank for all)", required=True) + parser.add_argument('--header', '-t', action='store_true', + help="Write property name as the first row.") + parser.add_argument('--smiles', '-s', action='store_true', + help="Include SMILES in output.") + parser.add_argument('--name', '-n', action='store_true', + help="Include molecule name in output.") + sdf_to_tab(parser.parse_args()) + + +if __name__ == "__main__": + main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/site_substructures.smarts Tue Mar 10 12:57:24 2020 -0400 @@ -0,0 +1,39 @@ +*Azide [N+0:1]=[N+:2]=[N+0:3]-[H] 2 4.65 0.07071067811865513 +Nitro [C,c,N,n,O,o:1]-[NX3:2](=[O:3])-[O:4]-[H] 3 -1000.0 0 +AmidineGuanidine1 [N:1]-[C:2](-[N:3])=[NX2:4]-[H:5] 3 12.025333333333334 1.5941046150769165 +AmidineGuanidine2 [C:1](-[N:2])=[NX2+0:3] 2 10.035538461538462 2.1312826469414716 +Sulfate [SX4:1](=[O:2])(=[O:3])([O:4]-[C,c,N,n:5])-[OX2:6]-[H] 5 -2.36 1.3048043093561141 +Sulfonate [SX4:1](=[O:2])(=[O:3])(-[C,c,N,n:4])-[OX2:5]-[H] 4 -1.8184615384615386 1.4086213481855594 +Sulfinic_acid [SX3:1](=[O:2])-[O:3]-[H] 2 1.7933333333333332 0.4372070447739835 +Phenyl_carboxyl [c,n,o:1]-[C:2](=[O:3])-[O:4]-[H] 3 3.463441968255319 1.2518054407928614 +Carboxyl [C:1](=[O:2])-[O:3]-[H] 2 3.456652971502591 1.2871420886834017 +Thioic_acid [C,c,N,n:1](=[O,S:2])-[SX2,OX2:3]-[H] 2 0.678267 1.497048763660801 +Phenyl_Thiol [c,n:1]-[SX2:2]-[H] 1 4.978235294117647 2.6137000480499806 +Thiol [C,N:1]-[SX2:2]-[H] 1 9.12448275862069 1.3317968158171463 +Phosphate [PX4:1](=[O:2])(-[OX2:3]-[H])(-[O+0:4])-[OX2:5]-[H] 2 2.4182608695652172 1.1091177991945305 5 6.5055 0.9512787792174668 +Phosphonate [PX4:1](=[O:2])(-[OX2:3]-[H])(-[C,c,N,n:4])-[OX2:5]-[H] 2 1.8835714285714287 0.5925999820080644 5 7.247254901960784 0.8511476450801531 +Phenol [c,n,o:1]-[O:2]-[H] 1 7.065359866910526 3.277356122295936 +Peroxide1 [O:1]([$(C=O),$(C[Cl]),$(CF),$(C[Br]),$(CC#N):2])-[O:3]-[H] 2 8.738888888888889 0.7562592839596507 +Peroxide2 [C:1]-[O:2]-[O:3]-[H] 2 11.978235294117647 0.8697645895163075 +O=C-C=C-OH [O:1]=[C;R:2]-[C;R:3]=[C;R:4]-[O:5]-[H] 4 3.554 0.803339458581667 +Vinyl_alcohol [C:1]=[C:2]-[O:3]-[H] 2 8.871850714285713 1.660200255394124 +Alcohol [C:1]-[O:2]-[H] 1 14.780384615384616 2.546464970533435 +N-hydroxyamide [C:1](=[O:2])-[N:3]-[O:4]-[H] 3 9.301904761904762 1.2181897185891002 +*Ringed_imide1 [O,S:1]=[C;R:2]([$([#8]),$([#7]),$([#16]),$([#6][Cl]),$([#6]F),$([#6][Br]):3])-[N;R:4]([C;R:5]=[O,S:6])-[H] 3 6.4525 0.5555627777308341 +*Ringed_imide2 [O,S:1]=[C;R:2]-[N;R:3]([C;R:4]=[O,S:5])-[H] 2 8.681666666666667 1.8657779975741713 +*Imide [F,Cl,Br,S,s,P,p:1][#6:2][CX3:3](=[O,S:4])-[NX3+0:5]([CX3:6]=[O,S:7])-[H] 4 2.466666666666667 1.4843629385474877 +*Imide2 [O,S:1]=[CX3:2]-[NX3+0:3]([CX3:4]=[O,S:5])-[H] 2 10.23 1.1198214143335534 +*Amide_electronegative [C:1](=[O:2])-[N:3](-[Br,Cl,I,F,S,O,N,P:4])-[H] 2 3.4896 2.688124315081677 +*Amide [C:1](=[O:2])-[N:3]-[H] 2 12.00611111111111 4.512491341218857 +*Sulfonamide [SX4:1](=[O:2])(=[O:3])-[NX3+0:4]-[H] 3 7.9160326086956525 1.9842121316708763 +Anilines_primary [c:1]-[NX3+0:2]([H:3])[H:4] 1 3.899298673194805 2.068768503987161 +Anilines_secondary [c:1]-[NX3+0:2]([H:3])[!H:4] 1 4.335408163265306 2.1768842022330843 +Anilines_tertiary [c:1]-[NX3+0:2]([!H:3])[!H:4] 1 4.16690685045614 2.005865735782679 +Aromatic_nitrogen_unprotonated [n+0&H0:1] 0 4.3535441240733945 2.0714072661859584 +Amines_primary_secondary_tertiary [C:1]-[NX3+0:2] 1 8.159107682388349 2.5183597445318147 +Phosphinic_acid [PX4:1](=[O:2])(-[C,c,N,n,F,Cl,Br,I:3])(-[C,c,N,n,F,Cl,Br,I:4])-[OX2:5]-[H] 4 2.9745 0.6867886750744557 +Phosphate_diester [PX4:1](=[O:2])(-[OX2:3]-[C,c,N,n,F,Cl,Br,I:4])(-[O+0:5]-[C,c,N,n,F,Cl,Br,I:4])-[OX2:6]-[H] 6 2.7280434782608696 2.5437448856908316 +Phosphonate_ester [PX4:1](=[O:2])(-[OX2:3]-[C,c,N,n,F,Cl,Br,I:4])(-[C,c,N,n,F,Cl,Br,I:5])-[OX2:6]-[H] 5 2.0868 0.4503028610465036 +Primary_hydroxyl_amine [C,c:1]-[O:2]-[NH2:3] 2 4.035714285714286 0.8463816543155368 +*Indole_pyrrole [c;R:1]1[c;R:2][c;R:3][c;R:4][n;R:5]1[H] 4 14.52875 4.06702491591416 +*Aromatic_nitrogen_protonated [n:1]-[H] 0 7.17 2.94602395490212
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CID_3037.sdf Tue Mar 10 12:57:24 2020 -0400 @@ -0,0 +1,220 @@ +3037 + -OEChem-08231108593D + + 27 28 0 0 0 0 0 0 0999 V2000 + -4.8550 1.3401 0.2120 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + 4.8529 -1.3406 0.2121 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + -0.1809 -2.1668 -0.3789 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.1788 2.1664 -0.3787 O 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0011 -0.0002 1.4744 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2222 -0.2738 0.6597 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2377 0.2772 0.6480 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2586 -1.3462 -0.2316 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2565 1.3457 -0.2314 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.3343 0.5568 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3322 -0.5574 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4069 -1.5879 -0.9855 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4048 1.5875 -0.9852 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.4827 0.3152 0.0433 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.4807 -0.3156 0.0435 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.5190 -0.7571 -0.8481 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.5170 0.7568 -0.8478 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.1548 0.8649 2.1342 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.1601 -0.8435 2.1593 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.3089 1.3938 1.4913 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3053 -1.3909 1.4943 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4415 -2.4213 -1.6818 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4469 2.4191 -1.6835 H 0 0 0 0 0 0 0 0 0 0 0 0 + -4.4070 -0.9574 -1.4422 H 0 0 0 0 0 0 0 0 0 0 0 0 + 4.4050 0.9570 -1.4418 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.2961 -2.2262 0.4641 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.3872 2.8487 -1.0397 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 14 1 0 0 0 0 + 2 15 1 0 0 0 0 + 3 8 1 0 0 0 0 + 3 26 1 0 0 0 0 + 4 9 1 0 0 0 0 + 4 27 1 0 0 0 0 + 5 6 1 0 0 0 0 + 5 7 1 0 0 0 0 + 5 18 1 0 0 0 0 + 5 19 1 0 0 0 0 + 6 8 2 0 0 0 0 + 6 10 1 0 0 0 0 + 7 9 2 0 0 0 0 + 7 11 1 0 0 0 0 + 8 12 1 0 0 0 0 + 9 13 1 0 0 0 0 + 10 14 2 0 0 0 0 + 10 20 1 0 0 0 0 + 11 15 2 0 0 0 0 + 11 21 1 0 0 0 0 + 12 16 2 0 0 0 0 + 12 22 1 0 0 0 0 + 13 17 2 0 0 0 0 + 13 23 1 0 0 0 0 + 14 16 1 0 0 0 0 + 15 17 1 0 0 0 0 + 16 24 1 0 0 0 0 + 17 25 1 0 0 0 0 +M END +> <PUBCHEM_COMPOUND_CID> +3037 + +> <PUBCHEM_CONFORMER_RMSD> +0.6 + +> <PUBCHEM_CONFORMER_DIVERSEORDER> +8 +10 +12 +1 +7 +5 +11 +3 +6 +9 +4 +2 + +> <PUBCHEM_MMFF94_PARTIAL_CHARGES> +25 +1 -0.18 +10 -0.15 +11 -0.15 +12 -0.15 +13 -0.15 +14 0.18 +15 0.18 +16 -0.15 +17 -0.15 +2 -0.18 +20 0.15 +21 0.15 +22 0.15 +23 0.15 +24 0.15 +25 0.15 +26 0.45 +27 0.45 +3 -0.53 +4 -0.53 +5 0.29 +6 -0.14 +7 -0.14 +8 0.08 +9 0.08 + +> <PUBCHEM_EFFECTIVE_ROTOR_COUNT> +2 + +> <PUBCHEM_PHARMACOPHORE_FEATURES> +4 +1 3 donor +1 4 donor +6 6 8 10 12 14 16 rings +6 7 9 11 13 15 17 rings + +> <PUBCHEM_HEAVY_ATOM_COUNT> +17 + +> <PUBCHEM_ATOM_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_ATOM_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_ISOTOPIC_ATOM_COUNT> +0 + +> <PUBCHEM_COMPONENT_COUNT> +1 + +> <PUBCHEM_CACTVS_TAUTO_COUNT> +5 + +> <PUBCHEM_CONFORMER_ID> +00000BDD00000008 + +> <PUBCHEM_MMFF94_ENERGY> +44.6858 + +> <PUBCHEM_FEATURE_SELFOVERLAP> +20.297 + +> <PUBCHEM_SHAPE_FINGERPRINT> +10062212 137 18261117369936506423 +104564 63 17986963035811110412 +11458722 120 18339359768245870841 +11471102 22 5472872458301843344 +11578080 2 18190204380446433792 +116883 192 18265608969609498196 +12236239 1 18410856576819659107 +12592029 89 18338223951597366363 +13549 16 18410575084668353682 +13693222 15 6555421915516066822 +13764800 53 14189033175566991199 +14115302 16 18186237320680093898 +14341114 328 10087642619424135543 +14787075 74 9511159855286719151 +14993402 34 18410855451538227223 +15099037 51 18340768233908588503 +15207287 21 15719111361650760302 +15375358 24 15647053767618106914 +15775835 57 18272650117329930317 +16945 1 17906452130063974618 +17834072 14 15936410035134206066 +18186145 218 17132117918276567720 +19422 9 18271525295227750719 +20279233 1 15719389529571237654 +20645476 183 18339080393619327415 +23402539 116 18186809105365620101 +23402655 69 18342736308283284156 +23559900 14 17603590712323212176 +25 1 17561083592297532664 +26918003 58 6266902359448424189 +296302 2 15213020427345972082 +3082319 5 18338798905472319583 +34934 24 18341891845236497020 +633830 44 17703790310130762689 +74978 22 18266740181857992718 +7832392 63 18340206284835898173 +81228 2 15720767252053392762 +9981440 41 17403743242177431832 + +> <PUBCHEM_SHAPE_MULTIPOLES> +341.85 +8.38 +1.9 +1.1 +0.02 +0 +-1.15 +1.94 +-0.01 +0 +-0.39 +-4.15 +0.01 +0 + +> <PUBCHEM_SHAPE_SELFOVERLAP> +722.787 + +> <PUBCHEM_SHAPE_VOLUME> +193 + +> <PUBCHEM_COORDINATE_TYPE> +2 +5 +255 + +$$$$ +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CID_3037.tab Tue Mar 10 12:57:24 2020 -0400 @@ -0,0 +1,2 @@ +Index Name PUBCHEM_ATOM_DEF_STEREO_COUNT PUBCHEM_ATOM_UDEF_STEREO_COUNT PUBCHEM_BOND_DEF_STEREO_COUNT PUBCHEM_BOND_UDEF_STEREO_COUNT PUBCHEM_CACTVS_TAUTO_COUNT PUBCHEM_COMPONENT_COUNT PUBCHEM_COMPOUND_CID PUBCHEM_CONFORMER_ID PUBCHEM_CONFORMER_RMSD PUBCHEM_EFFECTIVE_ROTOR_COUNT PUBCHEM_FEATURE_SELFOVERLAP PUBCHEM_HEAVY_ATOM_COUNT PUBCHEM_ISOTOPIC_ATOM_COUNT PUBCHEM_MMFF94_ENERGY PUBCHEM_SHAPE_SELFOVERLAP PUBCHEM_SHAPE_VOLUME +0 3037 0.0 0.0 0.0 0.0 5.0 1.0 3037.0 00000BDD00000008 0.6 2.0 20.297 17.0 0.0 44.6858 722.787 193.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligand.sdf Tue Mar 10 12:57:24 2020 -0400 @@ -0,0 +1,612 @@ +pose1 + OpenBabel09021916093D + + 16 16 0 0 0 0 0 0 0 0999 V2000 + 30.7270 -43.7450 76.1540 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.2320 -43.8770 76.1820 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.9030 -44.5770 75.1900 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.2880 -44.7130 75.1870 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.9550 -45.4820 74.0800 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.0120 -44.1090 76.2270 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.3700 -43.3850 77.2450 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.1200 -42.7180 78.3740 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.9820 -43.2890 77.1920 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.4390 -44.2310 76.2340 N 0 0 0 0 0 0 0 0 0 0 0 0 + 36.8300 -44.9440 76.7890 H 0 0 0 0 0 0 0 0 0 0 0 0 + 37.2890 -43.4500 75.5420 C 0 0 0 0 0 0 0 0 0 0 0 0 + 37.0090 -42.3660 75.0480 O 0 0 0 0 0 0 0 0 0 0 0 0 + 38.6760 -43.9990 75.3480 C 0 0 0 0 0 0 0 0 0 0 0 0 + 38.7980 -44.7930 74.1950 O 0 0 0 0 0 0 0 0 0 0 0 0 + 38.6010 -46.1780 74.4680 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 9 2 0 0 0 0 + 3 2 1 0 0 0 0 + 4 3 2 0 0 0 0 + 4 6 1 0 0 0 0 + 5 4 1 0 0 0 0 + 6 10 1 0 0 0 0 + 6 7 2 0 0 0 0 + 7 8 1 0 0 0 0 + 9 7 1 0 0 0 0 + 10 11 1 0 0 0 0 + 12 10 1 0 0 0 0 + 13 12 2 0 0 0 0 + 14 12 1 0 0 0 0 + 15 16 1 0 0 0 0 + 15 14 1 0 0 0 0 +M END +> <MODEL> +1 + +> <REMARK> + VINA RESULT: -4.9 0.000 0.000 + Name = + 7 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_5 + 2 A between atoms: C_2 and C_12 + 3 A between atoms: C_2 and O_15 + 4 A between atoms: C_3 and O_15 + 5 A between atoms: C_4 and C_7 + 6 A between atoms: C_8 and N_13 + 7 A between atoms: C_9 and C_11 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> <TORSDO> +F 3 + +> <SCORE> +-4.9 + +> <RMSD_LB> +0.000 + +> <RMSD_UB> +0.000 + +$$$$ +pose2 + OpenBabel09021916093D + + 16 16 0 0 0 0 0 0 0 0999 V2000 + 30.7330 -43.6060 76.3350 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.2340 -43.7750 76.2880 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.0410 -43.2270 77.2740 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.4260 -43.3690 77.2600 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.2450 -42.7520 78.3610 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.0040 -44.0990 76.2100 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.2200 -44.6770 75.1980 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.8090 -45.4740 74.0590 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.8400 -44.4960 75.2690 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.4270 -44.2630 76.1860 N 0 0 0 0 0 0 0 0 0 0 0 0 + 36.8070 -45.0000 76.7160 H 0 0 0 0 0 0 0 0 0 0 0 0 + 37.2860 -43.4900 75.4970 C 0 0 0 0 0 0 0 0 0 0 0 0 + 37.0290 -42.3860 75.0350 O 0 0 0 0 0 0 0 0 0 0 0 0 + 38.6520 -44.0730 75.2620 C 0 0 0 0 0 0 0 0 0 0 0 0 + 38.7120 -44.8940 74.1230 O 0 0 0 0 0 0 0 0 0 0 0 0 + 38.5590 -46.2750 74.4420 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 0 0 0 + 2 3 2 0 0 0 0 + 4 3 1 0 0 0 0 + 4 5 1 0 0 0 0 + 6 4 2 0 0 0 0 + 7 9 2 0 0 0 0 + 7 6 1 0 0 0 0 + 8 7 1 0 0 0 0 + 9 2 1 0 0 0 0 + 10 6 1 0 0 0 0 + 10 11 1 0 0 0 0 + 12 10 1 0 0 0 0 + 13 12 2 0 0 0 0 + 14 12 1 0 0 0 0 + 15 16 1 0 0 0 0 + 15 14 1 0 0 0 0 +M END +> <MODEL> +2 + +> <REMARK> + VINA RESULT: -4.9 0.118 2.246 + Name = + 7 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_5 + 2 A between atoms: C_2 and C_12 + 3 A between atoms: C_2 and O_15 + 4 A between atoms: C_3 and O_15 + 5 A between atoms: C_4 and C_7 + 6 A between atoms: C_8 and N_13 + 7 A between atoms: C_9 and C_11 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> <TORSDO> +F 3 + +> <SCORE> +-4.9 + +> <RMSD_LB> +0.118 + +> <RMSD_UB> +2.246 + +$$$$ +pose3 + OpenBabel09021916093D + + 16 16 0 0 0 0 0 0 0 0999 V2000 + 38.0110 -46.2540 74.8060 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.6410 -45.6700 75.0590 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.3810 -44.9390 76.2080 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.1300 -44.3850 76.4670 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.9150 -43.6000 77.7320 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.1140 -44.5800 75.5190 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.3400 -45.3070 74.3390 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.2700 -45.5280 73.2950 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.6120 -45.8370 74.1410 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.8230 -44.0090 75.7650 N 0 0 0 0 0 0 0 0 0 0 0 0 + 32.7200 -43.0420 75.6150 H 0 0 0 0 0 0 0 0 0 0 0 0 + 31.7400 -44.6890 76.1850 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.7580 -45.8050 76.6870 O 0 0 0 0 0 0 0 0 0 0 0 0 + 30.4150 -44.0110 75.9720 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.3610 -43.2680 74.7800 O 0 0 0 0 0 0 0 0 0 0 0 0 + 29.8410 -44.0280 73.6910 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 2 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 0 0 0 0 + 6 10 1 0 0 0 0 + 6 4 2 0 0 0 0 + 7 6 1 0 0 0 0 + 8 7 1 0 0 0 0 + 9 7 2 0 0 0 0 + 9 2 1 0 0 0 0 + 10 12 1 0 0 0 0 + 11 10 1 0 0 0 0 + 12 13 2 0 0 0 0 + 14 12 1 0 0 0 0 + 15 14 1 0 0 0 0 + 16 15 1 0 0 0 0 +M END +> <MODEL> +3 + +> <REMARK> + VINA RESULT: -4.9 2.960 5.795 + Name = + 7 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_5 + 2 A between atoms: C_2 and C_12 + 3 A between atoms: C_2 and O_15 + 4 A between atoms: C_3 and O_15 + 5 A between atoms: C_4 and C_7 + 6 A between atoms: C_8 and N_13 + 7 A between atoms: C_9 and C_11 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> <TORSDO> +F 3 + +> <SCORE> +-4.9 + +> <RMSD_LB> +2.960 + +> <RMSD_UB> +5.795 + +$$$$ +pose4 + OpenBabel09021916093D + + 16 16 0 0 0 0 0 0 0 0999 V2000 + 37.9950 -46.2420 74.8040 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.6310 -45.6410 75.0530 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.6040 -45.8070 74.1360 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.3360 -45.2680 74.3380 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.2650 -45.4860 73.3050 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.1090 -44.5430 75.5180 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.1210 -44.3610 76.4750 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.9070 -43.5920 77.7580 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.3670 -44.9230 76.2110 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.8080 -43.9900 75.7470 N 0 0 0 0 0 0 0 0 0 0 0 0 + 32.6920 -43.0240 75.5920 H 0 0 0 0 0 0 0 0 0 0 0 0 + 31.7290 -44.6830 76.1560 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.7570 -45.7970 76.6620 O 0 0 0 0 0 0 0 0 0 0 0 0 + 30.3970 -44.0250 75.9240 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.3400 -43.3070 74.7170 O 0 0 0 0 0 0 0 0 0 0 0 0 + 29.7270 -44.0560 73.6700 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 9 2 0 0 0 0 + 3 4 2 0 0 0 0 + 3 2 1 0 0 0 0 + 4 6 1 0 0 0 0 + 5 4 1 0 0 0 0 + 6 10 1 0 0 0 0 + 6 7 2 0 0 0 0 + 7 8 1 0 0 0 0 + 9 7 1 0 0 0 0 + 10 12 1 0 0 0 0 + 11 10 1 0 0 0 0 + 12 13 2 0 0 0 0 + 14 12 1 0 0 0 0 + 15 14 1 0 0 0 0 + 16 15 1 0 0 0 0 +M END +> <MODEL> +4 + +> <REMARK> + VINA RESULT: -4.8 2.958 5.379 + Name = + 7 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_5 + 2 A between atoms: C_2 and C_12 + 3 A between atoms: C_2 and O_15 + 4 A between atoms: C_3 and O_15 + 5 A between atoms: C_4 and C_7 + 6 A between atoms: C_8 and N_13 + 7 A between atoms: C_9 and C_11 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> <TORSDO> +F 3 + +> <SCORE> +-4.8 + +> <RMSD_LB> +2.958 + +> <RMSD_UB> +5.379 + +$$$$ +pose5 + OpenBabel09021916093D + + 16 16 0 0 0 0 0 0 0 0999 V2000 + 38.0500 -44.6890 74.2080 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.6310 -44.7300 74.7250 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.6330 -45.3790 74.0140 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.3180 -45.4370 74.4670 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.2830 -46.1590 73.6480 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.0140 -44.8170 75.6890 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.9980 -44.1580 76.4430 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.7050 -43.4880 77.7650 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.2940 -44.1340 75.9330 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.6670 -44.8760 76.1740 N 0 0 0 0 0 0 0 0 0 0 0 0 + 32.4200 -45.6500 76.7300 H 0 0 0 0 0 0 0 0 0 0 0 0 + 31.7140 -43.9580 75.9320 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.7570 -43.1100 75.0500 O 0 0 0 0 0 0 0 0 0 0 0 0 + 30.5300 -43.9780 76.8600 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.1410 -42.6970 77.2850 O 0 0 0 0 0 0 0 0 0 0 0 0 + 30.9190 -42.2320 78.3850 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 9 2 0 0 0 0 + 3 4 2 0 0 0 0 + 3 2 1 0 0 0 0 + 4 6 1 0 0 0 0 + 5 4 1 0 0 0 0 + 6 10 1 0 0 0 0 + 6 7 2 0 0 0 0 + 7 8 1 0 0 0 0 + 9 7 1 0 0 0 0 + 10 11 1 0 0 0 0 + 12 10 1 0 0 0 0 + 12 14 1 0 0 0 0 + 13 12 2 0 0 0 0 + 14 15 1 0 0 0 0 + 15 16 1 0 0 0 0 +M END +> <MODEL> +5 + +> <REMARK> + VINA RESULT: -4.5 2.763 5.379 + Name = + 7 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_5 + 2 A between atoms: C_2 and C_12 + 3 A between atoms: C_2 and O_15 + 4 A between atoms: C_3 and O_15 + 5 A between atoms: C_4 and C_7 + 6 A between atoms: C_8 and N_13 + 7 A between atoms: C_9 and C_11 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> <TORSDO> +F 3 + +> <SCORE> +-4.5 + +> <RMSD_LB> +2.763 + +> <RMSD_UB> +5.379 + +$$$$ +pose6 + OpenBabel09021916093D + + 16 16 0 0 0 0 0 0 0 0999 V2000 + 33.2740 -46.1140 73.3890 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.2350 -45.2530 74.6310 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.0270 -44.8930 75.2080 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.9590 -44.1040 76.3530 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.6150 -43.7500 76.9300 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.1640 -43.6750 76.9310 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.4080 -44.0260 76.3810 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.7220 -43.5880 76.9830 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.4060 -44.8150 75.2340 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.1120 -42.8710 78.1150 N 0 0 0 0 0 0 0 0 0 0 0 0 + 33.0600 -43.3400 78.9790 H 0 0 0 0 0 0 0 0 0 0 0 0 + 33.1290 -41.5260 78.1420 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.9030 -40.7970 77.1840 O 0 0 0 0 0 0 0 0 0 0 0 0 + 33.4950 -40.8990 79.4590 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.3180 -39.7680 79.3210 O 0 0 0 0 0 0 0 0 0 0 0 0 + 35.5320 -39.8880 80.0580 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 2 0 0 0 0 + 2 9 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 0 0 0 0 + 4 6 2 0 0 0 0 + 6 10 1 0 0 0 0 + 7 6 1 0 0 0 0 + 7 8 1 0 0 0 0 + 9 7 2 0 0 0 0 + 10 12 1 0 0 0 0 + 10 11 1 0 0 0 0 + 12 14 1 0 0 0 0 + 13 12 2 0 0 0 0 + 15 14 1 0 0 0 0 + 15 16 1 0 0 0 0 +M END +> <MODEL> +6 + +> <REMARK> + VINA RESULT: -4.4 3.106 4.850 + Name = + 7 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_5 + 2 A between atoms: C_2 and C_12 + 3 A between atoms: C_2 and O_15 + 4 A between atoms: C_3 and O_15 + 5 A between atoms: C_4 and C_7 + 6 A between atoms: C_8 and N_13 + 7 A between atoms: C_9 and C_11 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> <TORSDO> +F 3 + +> <SCORE> +-4.4 + +> <RMSD_LB> +3.106 + +> <RMSD_UB> +4.850 + +$$$$ +pose7 + OpenBabel09021916093D + + 16 16 0 0 0 0 0 0 0 0999 V2000 + 37.4790 -45.2240 74.1750 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.1180 -45.0510 74.8080 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.9750 -44.3800 76.0130 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.7340 -44.2020 76.6200 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.6480 -43.4610 77.9270 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.6030 -44.7210 75.9710 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.7050 -45.3990 74.7460 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.5070 -45.9630 74.0190 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.9750 -45.5460 74.1940 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.3180 -44.5390 76.5770 N 0 0 0 0 0 0 0 0 0 0 0 0 + 31.9880 -45.2570 77.1640 H 0 0 0 0 0 0 0 0 0 0 0 0 + 31.5250 -43.4650 76.4090 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.6380 -42.6370 75.5140 O 0 0 0 0 0 0 0 0 0 0 0 0 + 30.4470 -43.2750 77.4400 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.4060 -41.9700 77.9600 O 0 0 0 0 0 0 0 0 0 0 0 0 + 31.3500 -41.7760 79.0110 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 2 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 0 0 0 0 + 6 10 1 0 0 0 0 + 6 4 2 0 0 0 0 + 7 6 1 0 0 0 0 + 8 7 1 0 0 0 0 + 9 7 2 0 0 0 0 + 9 2 1 0 0 0 0 + 10 11 1 0 0 0 0 + 12 10 1 0 0 0 0 + 12 14 1 0 0 0 0 + 13 12 2 0 0 0 0 + 14 15 1 0 0 0 0 + 15 16 1 0 0 0 0 +M END +> <MODEL> +7 + +> <REMARK> + VINA RESULT: -4.4 2.847 5.816 + Name = + 7 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_5 + 2 A between atoms: C_2 and C_12 + 3 A between atoms: C_2 and O_15 + 4 A between atoms: C_3 and O_15 + 5 A between atoms: C_4 and C_7 + 6 A between atoms: C_8 and N_13 + 7 A between atoms: C_9 and C_11 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> <TORSDO> +F 3 + +> <SCORE> +-4.4 + +> <RMSD_LB> +2.847 + +> <RMSD_UB> +5.816 + +$$$$ +pose8 + OpenBabel09021916093D + + 16 16 0 0 0 0 0 0 0 0999 V2000 + 29.2690 -46.5680 70.6110 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.9950 -45.8610 71.7330 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.2800 -46.2360 72.0950 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.9750 -45.6010 73.1210 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.3680 -46.0550 73.4620 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.3390 -44.5460 73.7940 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.0420 -44.1320 73.4510 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.3330 -42.9960 74.1500 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.4010 -44.8100 72.4170 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.0440 -43.8770 74.8450 N 0 0 0 0 0 0 0 0 0 0 0 0 + 32.6940 -43.1840 74.5860 H 0 0 0 0 0 0 0 0 0 0 0 0 + 31.8900 -44.1170 76.1600 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.3600 -45.1120 76.6390 O 0 0 0 0 0 0 0 0 0 0 0 0 + 32.3840 -43.0420 77.0880 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.0560 -41.7460 76.6550 O 0 0 0 0 0 0 0 0 0 0 0 0 + 32.0630 -40.8000 77.7210 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 2 0 0 0 0 + 2 9 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 0 0 0 0 + 4 6 2 0 0 0 0 + 6 10 1 0 0 0 0 + 7 6 1 0 0 0 0 + 7 8 1 0 0 0 0 + 9 7 2 0 0 0 0 + 10 12 1 0 0 0 0 + 11 10 1 0 0 0 0 + 12 13 2 0 0 0 0 + 12 14 1 0 0 0 0 + 15 14 1 0 0 0 0 + 15 16 1 0 0 0 0 +M END +> <MODEL> +8 + +> <REMARK> + VINA RESULT: -4.3 3.964 5.892 + Name = + 7 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_5 + 2 A between atoms: C_2 and C_12 + 3 A between atoms: C_2 and O_15 + 4 A between atoms: C_3 and O_15 + 5 A between atoms: C_4 and C_7 + 6 A between atoms: C_8 and N_13 + 7 A between atoms: C_9 and C_11 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> <TORSDO> +F 3 + +> <SCORE> +-4.3 + +> <RMSD_LB> +3.964 + +> <RMSD_UB> +5.892 + +$$$$ +pose9 + OpenBabel09021916093D + + 16 16 0 0 0 0 0 0 0 0999 V2000 + 36.2810 -45.5880 74.7420 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.7970 -45.3090 74.6830 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.0060 -45.8780 73.6960 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.6360 -45.6430 73.6170 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.8340 -46.2940 72.5230 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.0540 -44.8050 74.5810 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.8200 -44.2170 75.6010 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.2240 -43.3170 76.6570 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.1850 -44.4900 75.6220 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.6450 -44.5600 74.5200 N 0 0 0 0 0 0 0 0 0 0 0 0 + 30.0630 -45.1230 75.0810 H 0 0 0 0 0 0 0 0 0 0 0 0 + 30.0510 -43.6230 73.7590 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.5710 -43.0480 72.8120 O 0 0 0 0 0 0 0 0 0 0 0 0 + 28.6490 -43.2470 74.1530 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.7000 -44.2290 73.8180 O 0 0 0 0 0 0 0 0 0 0 0 0 + 27.2950 -44.1460 72.4540 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 0 0 0 + 2 9 2 0 0 0 0 + 3 2 1 0 0 0 0 + 4 3 2 0 0 0 0 + 4 6 1 0 0 0 0 + 5 4 1 0 0 0 0 + 6 7 2 0 0 0 0 + 7 9 1 0 0 0 0 + 7 8 1 0 0 0 0 + 10 6 1 0 0 0 0 + 10 11 1 0 0 0 0 + 12 14 1 0 0 0 0 + 12 10 1 0 0 0 0 + 13 12 2 0 0 0 0 + 15 14 1 0 0 0 0 + 16 15 1 0 0 0 0 +M END +> <MODEL> +9 + +> <REMARK> + VINA RESULT: -4.3 3.971 6.363 + Name = + 7 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_5 + 2 A between atoms: C_2 and C_12 + 3 A between atoms: C_2 and O_15 + 4 A between atoms: C_3 and O_15 + 5 A between atoms: C_4 and C_7 + 6 A between atoms: C_8 and N_13 + 7 A between atoms: C_9 and C_11 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> <TORSDO> +F 3 + +> <SCORE> +-4.3 + +> <RMSD_LB> +3.971 + +> <RMSD_UB> +6.363 + +$$$$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligand.tab Tue Mar 10 12:57:24 2020 -0400 @@ -0,0 +1,10 @@ +Index RMSD_LB RMSD_UB SCORE SMILES +0 0.0 0.0 -4.9 [H]N(C(=O)COC)C1C(C)=CC(C)=CC=1C +1 0.118 2.246 -4.9 [H]N(C(=O)COC)C1C(C)=CC(C)=CC=1C +2 2.96 5.795 -4.9 [H]N(C(=O)COC)C1C(C)=CC(C)=CC=1C +3 2.958 5.379 -4.8 [H]N(C(=O)COC)C1C(C)=CC(C)=CC=1C +4 2.763 5.379 -4.5 [H]N(C(=O)COC)C1C(C)=CC(C)=CC=1C +5 3.106 4.85 -4.4 [H]N(C(=O)COC)C1C(C)=CC(C)=CC=1C +6 2.847 5.816 -4.4 [H]N(C(=O)COC)C1C(C)=CC(C)=CC=1C +7 3.964 5.892 -4.3 [H]N(C(=O)COC)C1C(C)=CC(C)=CC=1C +8 3.971 6.363 -4.3 [H]N(C(=O)COC)C1C(C)=CC(C)=CC=1C
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mols.smi Tue Mar 10 12:57:24 2020 -0400 @@ -0,0 +1,3 @@ +NCCCCC(N)C(=O)O lysine +O=C(O)C(N)C alanine +N[C@@H](CC1=CC=CC=C1)C(O)=O phenylanaline
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rdkit_descriptors_result1.csv Tue Mar 10 12:57:24 2020 -0400 @@ -0,0 +1,2 @@ +BalabanJ BertzCT Chi0 Chi0n Chi0v Chi1 Chi1n Chi1v Chi2n Chi2v Chi3n Chi3v Chi4n Chi4v EState_VSA1 EState_VSA10 EState_VSA11 EState_VSA2 EState_VSA3 EState_VSA4 EState_VSA5 EState_VSA6 EState_VSA7 EState_VSA8 EState_VSA9 ExactMolWt FpDensityMorgan1 FpDensityMorgan2 FpDensityMorgan3 FractionCSP3 HallKierAlpha HeavyAtomCount HeavyAtomMolWt Ipc Kappa1 Kappa2 Kappa3 LabuteASA MaxAbsEStateIndex MaxAbsPartialCharge MaxEStateIndex MaxPartialCharge MinAbsEStateIndex MinAbsPartialCharge MinEStateIndex MinPartialCharge MolLogP MolMR MolWt NHOHCount NOCount NumAliphaticCarbocycles NumAliphaticHeterocycles NumAliphaticRings NumAromaticCarbocycles NumAromaticHeterocycles NumAromaticRings NumHAcceptors NumHDonors NumHeteroatoms NumRadicalElectrons NumRotatableBonds NumSaturatedCarbocycles NumSaturatedHeterocycles NumSaturatedRings NumValenceElectrons PEOE_VSA1 PEOE_VSA10 PEOE_VSA11 PEOE_VSA12 PEOE_VSA13 PEOE_VSA14 PEOE_VSA2 PEOE_VSA3 PEOE_VSA4 PEOE_VSA5 PEOE_VSA6 PEOE_VSA7 PEOE_VSA8 PEOE_VSA9 RingCount SMR_VSA1 SMR_VSA10 SMR_VSA2 SMR_VSA3 SMR_VSA4 SMR_VSA5 SMR_VSA6 SMR_VSA7 SMR_VSA8 SMR_VSA9 SlogP_VSA1 SlogP_VSA10 SlogP_VSA11 SlogP_VSA12 SlogP_VSA2 SlogP_VSA3 SlogP_VSA4 SlogP_VSA5 SlogP_VSA6 SlogP_VSA7 SlogP_VSA8 SlogP_VSA9 TPSA VSA_EState1 VSA_EState10 VSA_EState2 VSA_EState3 VSA_EState4 VSA_EState5 VSA_EState6 VSA_EState7 VSA_EState8 VSA_EState9 fr_Al_COO fr_Al_OH fr_Al_OH_noTert fr_ArN fr_Ar_COO fr_Ar_N fr_Ar_NH fr_Ar_OH fr_COO fr_COO2 fr_C_O fr_C_O_noCOO fr_C_S fr_HOCCN fr_Imine fr_NH0 fr_NH1 fr_NH2 fr_N_O fr_Ndealkylation1 fr_Ndealkylation2 fr_Nhpyrrole fr_SH fr_aldehyde fr_alkyl_carbamate fr_alkyl_halide fr_allylic_oxid fr_amide fr_amidine fr_aniline fr_aryl_methyl fr_azide fr_azo fr_barbitur fr_benzene fr_benzodiazepine fr_bicyclic fr_diazo fr_dihydropyridine fr_epoxide fr_ester fr_ether fr_furan fr_guanido fr_halogen fr_hdrzine fr_hdrzone fr_imidazole fr_imide fr_isocyan fr_isothiocyan fr_ketone fr_ketone_Topliss fr_lactam fr_lactone fr_methoxy fr_morpholine fr_nitrile fr_nitro fr_nitro_arom fr_nitro_arom_nonortho fr_nitroso fr_oxazole fr_oxime fr_para_hydroxylation fr_phenol fr_phenol_noOrthoHbond fr_phos_acid fr_phos_ester fr_piperdine fr_piperzine fr_priamide fr_prisulfonamd fr_pyridine fr_quatN fr_sulfide fr_sulfonamd fr_sulfone fr_term_acetylene fr_tetrazole fr_thiazole fr_thiocyan fr_thiophene fr_unbrch_alkane fr_urea qed +3037 2.370227579270102 503.6108804181844 12.413849083443592 8.821564533342674 10.333422425379583 8.0585506480638 5.008352593120903 5.764281539139358 3.7228452481073373 4.595716809051308 2.463985083856104 2.934179289431582 1.5965258413271721 1.9859262940770028 0.0 10.213054789681411 0.0 11.49902366656781 27.592991233802653 0.0 12.13273413692322 24.26546827384644 0.0 0.0 23.20187978046503 268.00578492 0.7647058823529411 1.1764705882352942 1.588235294117647 0.07692307692307693 -1.38 17 259.04699999999997 6943.445199590422 12.08686679380967 4.861181105580097 2.8426724700782957 109.048439398113 9.68320845930965 0.5076617533400031 9.68320845930965 0.11870889965789788 0.14701436130007584 0.11870889965789788 0.14701436130007584 -0.5076617533400031 3.9954000000000027 69.03960000000004 269.127 2 2 0 0 0 2 0 2 2 2 4 0 2 0 0 0 88 10.213054789681411 11.49902366656781 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 23.20187978046503 47.52510539416365 16.466088250408664 0.0 2 10.213054789681411 23.20187978046503 0.0 0.0 0.0 6.4208216229260096 0.0 57.5703720216463 0.0 11.49902366656781 0.0 0.0 11.49902366656781 23.20187978046503 10.213054789681411 6.4208216229260096 0.0 11.126902983393991 36.39820241076966 10.045266627482652 0.0 0.0 40.46 0.0 11.70886971249405 0.0 0.0 0.0 0.0 0.0 0.0 0.0 32.01335250972817 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.8647127178367139
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rdkit_descriptors_result1.tab Tue Mar 10 12:57:24 2020 -0400 @@ -0,0 +1,2 @@ +MoleculeID BalabanJ BertzCT Chi0 Chi0n Chi0v Chi1 Chi1n Chi1v Chi2n Chi2v Chi3n Chi3v Chi4n Chi4v EState_VSA1 EState_VSA10 EState_VSA11 EState_VSA2 EState_VSA3 EState_VSA4 EState_VSA5 EState_VSA6 EState_VSA7 EState_VSA8 EState_VSA9 ExactMolWt FpDensityMorgan1 FpDensityMorgan2 FpDensityMorgan3 FractionCSP3 HallKierAlpha HeavyAtomCount HeavyAtomMolWt Ipc Kappa1 Kappa2 Kappa3 LabuteASA MaxAbsEStateIndex MaxAbsPartialCharge MaxEStateIndex MaxPartialCharge MinAbsEStateIndex MinAbsPartialCharge MinEStateIndex MinPartialCharge MolLogP MolMR MolWt NHOHCount NOCount NumAliphaticCarbocycles NumAliphaticHeterocycles NumAliphaticRings NumAromaticCarbocycles NumAromaticHeterocycles NumAromaticRings NumHAcceptors NumHDonors NumHeteroatoms NumRadicalElectrons NumRotatableBonds NumSaturatedCarbocycles NumSaturatedHeterocycles NumSaturatedRings NumValenceElectrons PEOE_VSA1 PEOE_VSA10 PEOE_VSA11 PEOE_VSA12 PEOE_VSA13 PEOE_VSA14 PEOE_VSA2 PEOE_VSA3 PEOE_VSA4 PEOE_VSA5 PEOE_VSA6 PEOE_VSA7 PEOE_VSA8 PEOE_VSA9 RingCount SMR_VSA1 SMR_VSA10 SMR_VSA2 SMR_VSA3 SMR_VSA4 SMR_VSA5 SMR_VSA6 SMR_VSA7 SMR_VSA8 SMR_VSA9 SlogP_VSA1 SlogP_VSA10 SlogP_VSA11 SlogP_VSA12 SlogP_VSA2 SlogP_VSA3 SlogP_VSA4 SlogP_VSA5 SlogP_VSA6 SlogP_VSA7 SlogP_VSA8 SlogP_VSA9 TPSA VSA_EState1 VSA_EState10 VSA_EState2 VSA_EState3 VSA_EState4 VSA_EState5 VSA_EState6 VSA_EState7 VSA_EState8 VSA_EState9 fr_Al_COO fr_Al_OH fr_Al_OH_noTert fr_ArN fr_Ar_COO fr_Ar_N fr_Ar_NH fr_Ar_OH fr_COO fr_COO2 fr_C_O fr_C_O_noCOO fr_C_S fr_HOCCN fr_Imine fr_NH0 fr_NH1 fr_NH2 fr_N_O fr_Ndealkylation1 fr_Ndealkylation2 fr_Nhpyrrole fr_SH fr_aldehyde fr_alkyl_carbamate fr_alkyl_halide fr_allylic_oxid fr_amide fr_amidine fr_aniline fr_aryl_methyl fr_azide fr_azo fr_barbitur fr_benzene fr_benzodiazepine fr_bicyclic fr_diazo fr_dihydropyridine fr_epoxide fr_ester fr_ether fr_furan fr_guanido fr_halogen fr_hdrzine fr_hdrzone fr_imidazole fr_imide fr_isocyan fr_isothiocyan fr_ketone fr_ketone_Topliss fr_lactam fr_lactone fr_methoxy fr_morpholine fr_nitrile fr_nitro fr_nitro_arom fr_nitro_arom_nonortho fr_nitroso fr_oxazole fr_oxime fr_para_hydroxylation fr_phenol fr_phenol_noOrthoHbond fr_phos_acid fr_phos_ester fr_piperdine fr_piperzine fr_priamide fr_prisulfonamd fr_pyridine fr_quatN fr_sulfide fr_sulfonamd fr_sulfone fr_term_acetylene fr_tetrazole fr_thiazole fr_thiocyan fr_thiophene fr_unbrch_alkane fr_urea qed +3037 2.370228 503.61088 12.413849 8.821565 10.333422 8.058551 5.008353 5.764282 3.722845 4.595717 2.463985 2.934179 1.596526 1.985926 0.0 10.213055 0.0 11.499024 27.592991 0.0 12.132734 24.265468 0.0 0.0 23.20188 268.005785 0.764706 1.176471 1.588235 0.076923 -1.38 17 259.047 6943.4452 12.086867 4.861181 2.842672 109.048439 9.683208 0.507662 9.683208 0.118709 0.147014 0.118709 0.147014 -0.507662 3.9954 69.0396 269.127 2 2 0 0 0 2 0 2 2 2 4 0 2 0 0 0 88 10.213055 11.499024 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 23.20188 47.525105 16.466088 0.0 2 10.213055 23.20188 0.0 0.0 0.0 6.420822 0.0 57.570372 0.0 11.499024 0.0 0.0 11.499024 23.20188 10.213055 6.420822 0.0 11.126903 36.398202 10.045267 0.0 0.0 40.46 0.0 11.70887 0.0 0.0 0.0 0.0 0.0 0.0 0.0 32.013353 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.864713
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sucos_cluster.sdf Tue Mar 10 12:57:24 2020 -0400 @@ -0,0 +1,1384 @@ + + RDKit 3D + + 19 20 0 0 0 0 0 0 0 0999 V2000 + 25.8690 10.6750 17.9260 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.7660 11.4770 18.5500 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.1650 12.4880 17.8120 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.1480 13.2570 18.3640 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.7300 13.0010 19.6620 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.6190 13.8450 20.2480 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.3280 11.9670 20.4090 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.9000 11.7560 21.6900 O 0 0 0 0 0 0 0 0 0 0 0 0 + 23.1990 10.4520 22.2010 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.3800 10.3250 23.4930 C 0 0 1 0 0 0 0 0 0 0 0 0 + 22.7510 9.1510 24.2170 O 0 0 0 0 0 0 0 0 0 0 0 0 + 22.5930 11.5910 24.3570 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.2540 11.3630 25.7760 N 0 0 0 0 0 0 0 0 0 0 0 0 + 22.5710 12.5910 26.5330 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.1760 12.4110 28.0100 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.7810 12.0710 28.1350 O 0 0 0 0 0 0 0 0 0 0 0 0 + 20.5060 10.8660 27.4060 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.8170 11.0700 25.9210 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.3600 11.2090 19.8480 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 + 3 2 2 0 + 4 3 1 0 + 5 4 2 0 + 6 5 1 0 + 7 5 1 0 + 8 7 1 0 + 9 8 1 0 + 10 9 1 0 + 10 11 1 1 + 12 10 1 0 + 13 12 1 0 + 14 13 1 0 + 15 14 1 0 + 16 15 1 0 + 17 16 1 0 + 18 17 1 0 + 18 13 1 0 + 19 7 2 0 + 19 2 1 0 +M END +$$$$ + + RDKit 3D + + 11 12 0 0 0 0 0 0 0 0999 V2000 + 22.8090 9.2070 24.2800 N 0 0 0 0 0 0 0 0 0 0 0 0 + 22.4710 10.1080 23.3190 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.8900 9.6340 22.1960 N 0 0 0 0 0 0 0 0 0 0 0 0 + 21.5680 10.5170 21.2440 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.7580 11.8790 21.3690 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.3130 12.3920 22.5320 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.5210 13.7530 22.7260 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.0810 14.2110 23.9020 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.4470 13.3190 24.8860 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.2450 11.9700 24.7110 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.6750 11.4850 23.5440 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 + 3 2 2 0 + 4 3 1 0 + 5 4 2 0 + 6 5 1 0 + 7 6 2 0 + 8 7 1 0 + 9 8 2 0 + 10 9 1 0 + 11 2 1 0 + 11 10 2 0 + 11 6 1 0 +M END +$$$$ + + RDKit 3D + + 11 12 0 0 0 0 0 0 0 0999 V2000 + 22.7770 9.1670 24.9740 N 0 0 0 0 0 0 0 0 0 0 0 0 + 22.4280 10.0140 24.0880 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.6770 11.3690 24.2670 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.2930 12.2600 23.2950 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.6430 11.7880 22.1650 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.2220 12.6270 21.1460 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.5740 12.1120 20.0440 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.3400 10.7540 19.9450 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.7580 9.9010 20.9470 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.4090 10.3980 22.0610 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.7960 9.5320 23.0070 N 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 + 3 2 2 0 + 4 3 1 0 + 5 4 2 0 + 6 5 1 0 + 7 6 2 0 + 8 7 1 0 + 9 8 2 0 + 10 9 1 0 + 10 5 1 0 + 11 10 2 0 + 11 2 1 0 +M END +$$$$ + + RDKit 3D + + 15 16 0 0 0 0 0 0 0 0999 V2000 + 22.4510 9.0090 24.4670 N 0 0 0 0 0 0 0 0 0 0 0 0 + 22.5180 10.3550 24.1060 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.9990 11.2350 24.9790 N 0 0 0 0 0 0 0 0 0 0 0 0 + 23.1030 12.5320 24.7160 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.7060 13.0330 23.4860 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.1940 12.1570 22.5380 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.0810 10.8000 22.8500 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.5800 9.9040 21.8960 N 0 0 0 0 0 0 0 0 0 0 0 0 + 21.5550 10.3020 20.4800 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.9570 10.4800 19.9210 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.0930 10.2030 20.6880 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.3650 10.3660 20.1600 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.5090 10.8070 18.8530 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.3830 11.0830 18.0860 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.1090 10.9240 18.6170 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 + 3 2 2 0 + 4 3 1 0 + 5 4 2 0 + 6 5 1 0 + 7 2 1 0 + 7 6 2 0 + 8 7 1 0 + 9 8 1 0 + 10 9 1 0 + 11 10 2 0 + 12 11 1 0 + 13 12 2 0 + 14 13 1 0 + 15 10 1 0 + 15 14 2 0 +M END +$$$$ + + RDKit 3D + + 14 15 0 0 0 0 0 0 0 0999 V2000 + 25.2210 12.3240 18.0720 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.2950 10.9960 18.4640 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.3010 10.4520 19.2480 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.2220 11.2280 19.6570 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.1370 10.6280 20.5110 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.4080 10.7370 21.9940 C 0 0 1 0 0 0 0 0 0 0 0 0 + 21.4270 9.8630 22.7750 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.7420 9.8660 24.2600 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.1460 9.4340 24.4920 N 0 0 0 0 0 0 0 0 0 0 0 0 + 24.1030 10.3610 23.8220 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.8510 10.3500 22.3260 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.1570 12.5620 19.2690 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.1500 13.1090 18.4810 C 0 0 0 0 0 0 0 0 0 0 0 0 + 26.1900 12.8500 17.2940 F 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 2 0 + 3 2 1 0 + 4 3 2 0 + 5 4 1 0 + 6 5 1 6 + 7 6 1 0 + 8 7 1 0 + 9 8 1 0 + 10 9 1 0 + 11 10 1 0 + 11 6 1 0 + 12 4 1 0 + 13 12 2 0 + 13 1 1 0 + 14 1 1 0 +M END +$$$$ + + RDKit 3D + + 18 20 0 0 0 0 0 0 0 0999 V2000 + 22.7740 9.2060 24.7160 N 0 0 0 0 0 0 0 0 0 0 0 0 + 22.6730 10.1680 23.8290 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.6480 11.5040 24.2160 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.5410 12.4950 23.2640 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.4360 12.1560 21.9280 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.4390 10.8180 21.5470 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.3390 10.4160 20.0980 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.4770 9.5130 19.6670 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.8250 10.1870 19.6920 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.0890 11.2540 18.8350 C 0 0 0 0 0 0 0 0 0 0 0 0 + 26.3260 11.8750 18.8250 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.3220 11.4120 19.6750 C 0 0 0 0 0 0 0 0 0 0 0 0 + 28.6590 11.7950 19.9160 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.1750 10.9440 20.8960 C 0 0 0 0 0 0 0 0 0 0 0 0 + 28.2120 10.0690 21.2490 N 0 0 0 0 0 0 0 0 0 0 0 0 + 27.0680 10.3360 20.5270 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.8240 9.7170 20.5400 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.5470 9.8480 22.5050 N 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 + 3 2 2 0 + 4 3 1 0 + 5 4 2 0 + 6 5 1 0 + 7 6 1 0 + 8 7 1 0 + 9 8 1 0 + 10 9 2 0 + 11 10 1 0 + 12 11 2 0 + 13 12 1 0 + 14 13 2 0 + 15 14 1 0 + 16 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9.6220 22.6190 N 0 0 0 0 0 0 0 0 0 0 0 0 + 19.3450 9.6270 21.1760 O 0 0 0 0 0 0 0 0 0 0 0 0 + 22.4790 11.8080 24.2920 S 0 0 0 0 0 0 0 0 0 0 0 0 + 19.5140 11.7630 22.5130 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.7100 9.2150 24.7670 N 0 0 0 0 0 0 0 0 0 0 0 0 + 20.5550 9.7530 20.5440 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.8590 10.7120 20.6250 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.1020 10.1890 21.0270 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.2620 10.3730 20.2980 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.8630 11.5080 19.3970 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.5800 10.5280 21.4490 C 0 0 2 0 0 0 0 0 0 0 0 0 + 20.9500 11.9060 21.9290 C 0 0 2 0 0 0 0 0 0 0 0 0 + 21.9600 12.7150 22.7910 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.3230 10.0930 23.7780 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.0040 11.6730 18.6170 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.2010 11.1170 19.0930 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.7570 12.0240 18.8700 F 0 0 0 0 0 0 0 0 0 0 0 0 + 26.3200 11.2980 18.4090 F 0 0 0 0 0 0 0 0 0 0 0 0 + 3 1 1 0 + 5 1 1 0 + 7 3 1 0 + 9 8 2 0 + 10 9 1 0 + 11 8 1 0 + 12 7 1 0 + 12 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26.4280 11.2380 18.0020 F 0 0 0 0 0 0 0 0 0 0 0 0 + 4 1 1 6 + 4 2 1 0 + 6 4 1 0 + 7 6 1 0 + 7 3 1 0 + 8 5 1 0 + 8 2 2 0 + 8 3 1 0 + 9 4 1 0 + 10 9 2 0 + 11 10 1 0 + 12 11 2 0 + 13 12 1 0 + 14 9 1 0 + 14 13 2 0 + 15 14 1 0 + 16 12 1 0 +M END +$$$$ + + RDKit 3D + + 11 12 0 0 0 0 0 0 0 0999 V2000 + 23.8920 10.9750 19.7100 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.1430 9.6540 19.8400 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.7820 11.7530 20.9950 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.6770 9.8870 20.1680 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.1750 12.7870 22.6090 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.3660 10.1400 23.6660 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.3180 11.9530 21.3510 C 0 0 2 0 0 0 0 0 0 0 0 0 + 21.5250 10.6490 21.4640 C 0 0 2 0 0 0 0 0 0 0 0 0 + 22.7380 9.3100 24.6900 N 0 0 0 0 0 0 0 0 0 0 0 0 + 21.9210 9.6990 22.5310 N 0 0 0 0 0 0 0 0 0 0 0 0 + 22.5620 11.8400 24.1130 S 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 + 3 1 1 0 + 4 2 1 0 + 7 3 1 1 + 7 5 1 0 + 8 4 1 6 + 8 7 1 0 + 9 6 1 0 + 10 8 1 0 + 10 6 2 0 + 11 6 1 0 + 11 5 1 0 +M END +$$$$ + + RDKit 3D + + 18 20 0 0 0 0 0 0 0 0999 V2000 + 28.6970 10.5240 20.4750 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.9220 11.6800 20.9560 N 0 0 0 0 0 0 0 0 0 0 0 0 + 28.7880 12.6650 21.6350 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.0810 12.2010 19.9710 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.4190 13.2930 19.2740 N 0 0 0 0 0 0 0 0 0 0 0 0 + 26.6450 13.8320 18.3200 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.4810 13.2870 17.9980 N 0 0 0 0 0 0 0 0 0 0 0 0 + 25.0290 12.1840 18.6310 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.7860 11.6150 18.3040 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.3430 10.5040 18.9720 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.1080 9.9180 19.9810 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.3250 10.4360 20.3200 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.8200 11.5870 19.6640 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.1160 14.9710 17.6690 N 0 0 0 0 0 0 0 0 0 0 0 0 + 27.3480 16.1150 18.5710 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.6660 17.2890 17.6050 C 0 0 0 0 0 0 0 0 0 0 0 0 + 26.8670 16.9430 16.3140 C 0 0 0 0 0 0 0 0 0 0 0 0 + 26.3130 15.5200 16.5590 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 + 3 2 1 0 + 4 2 1 0 + 5 4 2 0 + 6 5 1 0 + 7 6 2 0 + 8 7 1 0 + 9 8 2 0 + 10 9 1 0 + 11 10 2 0 + 12 11 1 0 + 13 12 2 0 + 13 8 1 0 + 13 4 1 0 + 14 6 1 0 + 15 14 1 0 + 16 15 1 0 + 17 16 1 0 + 18 14 1 0 + 18 17 1 0 +M END +$$$$