From 53f430dc4775227aecdab3b14176b501866a9dd8 Mon Sep 17 00:00:00 2001
From: LIANG Bochun <zlatanbochun@outlook.com>
Date: Tue, 23 Jan 2024 11:25:57 +0800
Subject: [PATCH 01/21] Add LigpargenRunner

---
 mdgo/forcefield/__init__.py  |  5 +-
 mdgo/forcefield/ligpargen.py | 99 ++++++++++++++++++++++++++++++++++++
 2 files changed, 102 insertions(+), 2 deletions(-)
 create mode 100644 mdgo/forcefield/ligpargen.py

diff --git a/mdgo/forcefield/__init__.py b/mdgo/forcefield/__init__.py
index db3f5534..4a69e29e 100644
--- a/mdgo/forcefield/__init__.py
+++ b/mdgo/forcefield/__init__.py
@@ -8,10 +8,10 @@
 """
 
 __author__ = "Tingzheng Hou, Ryan Kingsbury"
-__version__ = "0.3.0"
+__version__ = "0.3.1"
 __maintainer__ = "Tingzheng Hou, Ryan Kingsbury"
 __email__ = "tingzheng_hou@berkeley.edu"
-__date__ = "Jul 19, 2022"
+__date__ = "Dec 19, 2023"
 
 
 from .aqueous import IonLJData, Aqueous
@@ -19,3 +19,4 @@
 from .crawler import FFcrawler
 from .maestro import MaestroRunner
 from .pubchem import PubChemRunner
+from .ligpargen import LigpargenRunner
diff --git a/mdgo/forcefield/ligpargen.py b/mdgo/forcefield/ligpargen.py
new file mode 100644
index 00000000..b1379ba9
--- /dev/null
+++ b/mdgo/forcefield/ligpargen.py
@@ -0,0 +1,99 @@
+
+"""
+This module implements a core class LigpargenRunner for generating
+LAMMPS/GROMACS data files from molecule structure using LigParGen 2.1 
+and BOSS 5.0.
+"""
+
+import subprocess
+import os
+from pymatgen.io.lammps.data import LammpsData
+from mdgo.util.dict_utils import lmp_mass_to_name
+
+class LigpargenRunner:
+
+    def __init__(
+        self,
+        structure_name: str,
+        structure_dir: str,
+        working_dir: str= "boss_files",
+        out: str = "lmp",
+        charge: int = 0,
+        opt: int = 0,
+        xyz: bool = False,        
+    ):
+        """Base constructor."""
+        self.structure = structure_dir + "/" + structure_name
+        self.name = os.path.splitext(structure_name)[0]
+        self.structure_format = os.path.splitext(structure_name)[1][1:]
+        print("Input format:", self.structure_format)
+        self.structure_dir = structure_dir
+        self.work = working_dir
+        self.out = out
+        self.charge = charge
+        self.opt = opt
+        self.xyz = xyz
+    
+
+    def data_from_structure(self, wait: float = 30):
+
+        try:
+            cmd = f"ligpargen -i {self.structure} -n {self.name} -p {self.work} -c {self.charge} -o {self.opt}"
+            subprocess.run(cmd, shell=True)
+        except subprocess.CalledProcessError as e:
+            raise ValueError(f"LigParGen failed with errorcode {e.returncode}  and stderr: {e.stderr}") from e
+        
+        if self.out == "lmp":
+            lmp_name = f"{self.name}.lmp"
+            lmp_file = f"{self.structure_dir}/{self.name}.lmp"
+            cp_lmp_data = f"cp {self.work}/{self.name}.lammps.lmp {lmp_file}"
+            subprocess.run(cp_lmp_data, shell=True)
+
+        if self.xyz:
+            lmp_file = f"{self.structure_dir}/{self.name}.lmp"
+            data_obj = LammpsData.from_file(lmp_file)
+            element_id_dict = lmp_mass_to_name(data_obj.masses)
+            coords = data_obj.atoms[["type", "x", "y", "z"]]
+            lines = []
+            lines.append(str(len(coords.index)))
+            lines.append("")
+            for _, r in coords.iterrows():
+                element_name = element_id_dict.get(int(r["type"]))
+                assert element_name is not None
+                line = element_name + " " + " ".join(str(r[loc]) for loc in ["x", "y", "z"])
+                lines.append(line)
+
+            with open(os.path.join(self.structure_dir, lmp_name + ".xyz"), "w") as xyz_file:
+                xyz_file.write("\n".join(lines))
+            print(".xyz file saved.")
+        
+    def data_from_smiles(self, wait: float = 30):
+        try:
+            cmd = f"ligpargen -s {self.name} -n {self.name} -p {self.work} -c {self.charge} -o {self.opt}"
+            subprocess.run(cmd, shell=True)
+        except subprocess.CalledProcessError as e:
+            raise ValueError(f"LigParGen failed with errorcode {e.returncode}  and stderr: {e.stderr}") from e
+        
+        if self.out == "lmp":
+            lmp_name = f"{self.name}.lmp"
+            lmp_file = f"{self.structure_dir}/{self.name}.lmp"
+            cp_lmp_data = f"cp {self.work}/{self.name}.lammps.lmp {lmp_file}"
+            subprocess.run(cp_lmp_data, shell=True)
+
+        if self.xyz:
+            lmp_file = f"{self.structure_dir}/{self.name}.lmp"
+            data_obj = LammpsData.from_file(lmp_file)
+            element_id_dict = lmp_mass_to_name(data_obj.masses)
+            coords = data_obj.atoms[["type", "x", "y", "z"]]
+            lines = []
+            lines.append(str(len(coords.index)))
+            lines.append("")
+            for _, r in coords.iterrows():
+                element_name = element_id_dict.get(int(r["type"]))
+                assert element_name is not None
+                line = element_name + " " + " ".join(str(r[loc]) for loc in ["x", "y", "z"])
+                lines.append(line)
+
+            with open(os.path.join(self.structure_dir, lmp_name + ".xyz"), "w") as xyz_file:
+                xyz_file.write("\n".join(lines))
+            print(".xyz file saved.")

From c3e7f3ed6b472560acb8c5173d75eb09b371853d Mon Sep 17 00:00:00 2001
From: Tingzheng Hou <25351437+htz1992213@users.noreply.github.com>
Date: Tue, 23 Jan 2024 15:38:35 +0800
Subject: [PATCH 02/21] move ffcrawler class to ligpargen.py

---
 mdgo/forcefield/__init__.py  |   3 +-
 mdgo/forcefield/crawler.py   | 218 +----------------------------------
 mdgo/forcefield/ligpargen.py | 191 ++++++++++++++++++++++++++++++
 tests/test_forcefield.py     |   2 +-
 4 files changed, 194 insertions(+), 220 deletions(-)

diff --git a/mdgo/forcefield/__init__.py b/mdgo/forcefield/__init__.py
index 4a69e29e..8ae75669 100644
--- a/mdgo/forcefield/__init__.py
+++ b/mdgo/forcefield/__init__.py
@@ -16,7 +16,6 @@
 
 from .aqueous import IonLJData, Aqueous
 from .charge import ChargeWriter
-from .crawler import FFcrawler
 from .maestro import MaestroRunner
 from .pubchem import PubChemRunner
-from .ligpargen import LigpargenRunner
+from .ligpargen import LigpargenRunner, FFcrawler
diff --git a/mdgo/forcefield/crawler.py b/mdgo/forcefield/crawler.py
index 6047a768..44674ba8 100644
--- a/mdgo/forcefield/crawler.py
+++ b/mdgo/forcefield/crawler.py
@@ -3,221 +3,5 @@
 # Distributed under the terms of the MIT License.
 
 """
-This module implements two core class FFcrawler for generating
-LAMMPS/GROMACS data files from molecule structure using
-the LigParGen web server.
-
-For using the FFcrawler class:
-
-  * Download the ChromeDriver executable that
-    matches your Chrome version via https://chromedriver.chromium.org/downloads
+This module was used to implement a core class FFcrawler, and has been moved to ligpargen module.
 """
-
-import os
-import shutil
-import time
-from typing import Optional
-
-
-from pymatgen.io.lammps.data import LammpsData
-from selenium import webdriver
-from selenium.common.exceptions import (
-    TimeoutException,
-    WebDriverException,
-)
-from selenium.webdriver.common.by import By
-from selenium.webdriver.support import expected_conditions as EC
-from selenium.webdriver.support.ui import WebDriverWait
-
-from mdgo.util.dict_utils import lmp_mass_to_name
-
-
-class FFcrawler:
-    """
-    Web scrapper that can automatically upload structure to the LigParGen
-    server and download LAMMPS/GROMACS data file.
-
-    Args:
-        write_dir: Directory for writing output.
-        chromedriver_dir: Directory to the ChromeDriver executable.
-        headless: Whether to run Chrome in headless (silent) mode.
-            Default to True.
-        xyz: Whether to write the structure in the LigParGen
-            generated data file as .xyz. Default to False. This is useful
-            because the order and the name of the atoms could be
-            different from the initial input.)
-        gromacs: Whether to save GROMACS format data files.
-            Default to False.
-
-    Examples:
-
-        >>> lpg = FFcrawler('/path/to/work/dir', '/path/to/chromedriver')
-        >>> lpg.data_from_pdb("/path/to/pdb")
-    """
-
-    def __init__(
-        self,
-        write_dir: str,
-        chromedriver_dir: Optional[str] = None,
-        headless: bool = True,
-        xyz: bool = False,
-        gromacs: bool = False,
-    ):
-        """Base constructor."""
-        self.write_dir = write_dir
-        self.xyz = xyz
-        self.gromacs = gromacs
-        self.preferences = {
-            "download.default_directory": write_dir,
-            "safebrowsing.enabled": "false",
-            "profile.managed_default_content_settings.images": 2,
-        }
-        self.options = webdriver.ChromeOptions()
-        self.server = webdriver.ChromeService(chromedriver_dir)
-        self.options.add_argument(
-            'user-agent="Mozilla/5.0 '
-            "(Macintosh; Intel Mac OS X 10_14_6) "
-            "AppleWebKit/537.36 (KHTML, like Gecko) "
-            'Chrome/88.0.4324.146 Safari/537.36"'
-        )
-        self.options.add_argument("--window-size=1920,1080")
-        self.options.add_argument("ignore-certificate-errors")
-        if headless:
-            self.options.add_argument("--headless")
-        self.options.add_experimental_option("prefs", self.preferences)
-        self.options.add_experimental_option("excludeSwitches", ["enable-automation"])
-        if chromedriver_dir is None:
-            self.web = webdriver.Chrome(options=self.options)
-        else:
-            self.web = webdriver.Chrome(service=self.server, options=self.options)
-        self.wait = WebDriverWait(self.web, 10)
-        self.web.get("http://traken.chem.yale.edu/ligpargen/")
-        time.sleep(1)
-        print("LigParGen server connected.")
-
-    def quit(self):
-        """
-        Method for quiting ChromeDriver.
-
-        """
-        self.web.quit()
-
-    def data_from_pdb(self, pdb_dir: str):
-        """
-        Use the LigParGen server to generate a LAMMPS data file from a pdb file.
-        Write out a LAMMPS data file.
-
-        Args:
-            pdb_dir: The path to the input pdb structure file.
-        """
-        self.web.get("http://traken.chem.yale.edu/ligpargen/")
-        upload_xpath = '//*[@id="exampleMOLFile"]'
-        time.sleep(1)
-        self.wait.until(EC.presence_of_element_located((By.XPATH, upload_xpath)))
-        upload = self.web.find_element(By.XPATH, upload_xpath)
-        try:
-            upload.send_keys(pdb_dir)
-            submit = self.web.find_element(By.XPATH, "/html/body/div[2]/div/div[2]/form/button[1]")
-            submit.click()
-            pdb_filename = os.path.basename(pdb_dir)
-            self.download_data(os.path.splitext(pdb_filename)[0] + ".lmp")
-        except TimeoutException:
-            print("Timeout! Web server no response for 10s, file download failed!")
-        except WebDriverException as e:
-            print(e)
-        finally:
-            self.quit()
-
-    def data_from_smiles(self, smiles_code):
-        """
-        Use the LigParGen server to generate a LAMMPS data file from a SMILES code.
-        Write out a LAMMPS data file.
-
-        Args:
-            smiles_code: The SMILES code for the LigParGen input.
-        """
-        self.web.get("http://traken.chem.yale.edu/ligpargen/")
-        time.sleep(1)
-        smile = self.web.find_element(By.XPATH, '//*[@id="smiles"]')
-        smile.send_keys(smiles_code)
-        submit = self.web.find_element(By.XPATH, "/html/body/div[2]/div/div[2]/form/button[1]")
-        submit.click()
-        try:
-            self.download_data(smiles_code + ".lmp")
-        except TimeoutException:
-            print("Timeout! Web server no response for 10s, file download failed!")
-        finally:
-            self.quit()
-
-    def download_data(self, lmp_name: str):
-        """
-        Helper function that download and write out the LAMMPS data file.
-
-        Args:
-            lmp_name: Name of the LAMMPS data file.
-        """
-        print("Structure info uploaded. Rendering force field...")
-        lmp_xpath = "/html/body/div[2]/div[2]/div[1]/div/div[14]/form/input[1]"
-        self.wait.until(EC.presence_of_element_located((By.XPATH, lmp_xpath)))
-        jmol = self.web.find_element(By.XPATH, "/html/body/div[2]/div[2]/div[2]")
-        self.web.execute_script("arguments[0].remove();", jmol)
-        self.wait.until(EC.element_to_be_clickable((By.XPATH, lmp_xpath)))
-        data_lmp = self.web.find_element(By.XPATH, lmp_xpath)
-        num_file = len([f for f in os.listdir(self.write_dir) if os.path.splitext(f)[1] == ".lmp"]) + 1
-        data_lmp.click()
-        while True:
-            files = sorted(
-                [
-                    os.path.join(self.write_dir, f)
-                    for f in os.listdir(self.write_dir)
-                    if os.path.splitext(f)[1] == ".lmp"
-                ],
-                key=os.path.getmtime,
-            )
-            # wait for file to finish download
-            if len(files) < num_file:
-                time.sleep(1)
-                print("waiting for download to be initiated")
-            else:
-                newest = files[-1]
-                if ".crdownload" in newest:
-                    time.sleep(1)
-                    print("waiting for download to complete")
-                else:
-                    break
-        print("Force field file downloaded.")
-        lmp_file = newest
-        if self.xyz:
-            data_obj = LammpsData.from_file(lmp_file)
-            element_id_dict = lmp_mass_to_name(data_obj.masses)
-            coords = data_obj.atoms[["type", "x", "y", "z"]]
-            lines = []
-            lines.append(str(len(coords.index)))
-            lines.append("")
-            for _, r in coords.iterrows():
-                element_name = element_id_dict.get(int(r["type"]))
-                assert element_name is not None
-                line = element_name + " " + " ".join(str(r[loc]) for loc in ["x", "y", "z"])
-                lines.append(line)
-
-            with open(os.path.join(self.write_dir, lmp_name + ".xyz"), "w") as xyz_file:
-                xyz_file.write("\n".join(lines))
-            print(".xyz file saved.")
-        if self.gromacs:
-            data_gro = self.web.find_element(By.XPATH, "/html/body/div[2]/div[2]/div[1]/div/div[8]/form/input[1]")
-            data_itp = self.web.find_element(By.XPATH, "/html/body/div[2]/div[2]/div[1]/div/div[9]/form/input[1]")
-            data_gro.click()
-            data_itp.click()
-            time.sleep(1)
-            gro_file = max(
-                [self.write_dir + "/" + f for f in os.listdir(self.write_dir) if os.path.splitext(f)[1] == ".gro"],
-                key=os.path.getctime,
-            )
-            itp_file = max(
-                [self.write_dir + "/" + f for f in os.listdir(self.write_dir) if os.path.splitext(f)[1] == ".itp"],
-                key=os.path.getctime,
-            )
-            shutil.move(gro_file, os.path.join(self.write_dir, lmp_name[:-4] + ".gro"))
-            shutil.move(itp_file, os.path.join(self.write_dir, lmp_name[:-4] + ".itp"))
-        shutil.move(lmp_file, os.path.join(self.write_dir, lmp_name))
-        print("Force field file saved.")
diff --git a/mdgo/forcefield/ligpargen.py b/mdgo/forcefield/ligpargen.py
index b1379ba9..ec9431e3 100644
--- a/mdgo/forcefield/ligpargen.py
+++ b/mdgo/forcefield/ligpargen.py
@@ -97,3 +97,194 @@ def data_from_smiles(self, wait: float = 30):
             with open(os.path.join(self.structure_dir, lmp_name + ".xyz"), "w") as xyz_file:
                 xyz_file.write("\n".join(lines))
             print(".xyz file saved.")
+
+
+class FFcrawler:
+    """
+    Web scrapper that can automatically upload structure to the LigParGen
+    server and download LAMMPS/GROMACS data file.
+
+    Args:
+        write_dir: Directory for writing output.
+        chromedriver_dir: Directory to the ChromeDriver executable.
+        headless: Whether to run Chrome in headless (silent) mode.
+            Default to True.
+        xyz: Whether to write the structure in the LigParGen
+            generated data file as .xyz. Default to False. This is useful
+            because the order and the name of the atoms could be
+            different from the initial input.)
+        gromacs: Whether to save GROMACS format data files.
+            Default to False.
+
+    Examples:
+
+        >>> lpg = FFcrawler('/path/to/work/dir', '/path/to/chromedriver')
+        >>> lpg.data_from_pdb("/path/to/pdb")
+    """
+
+    def __init__(
+        self,
+        write_dir: str,
+        chromedriver_dir: Optional[str] = None,
+        headless: bool = True,
+        xyz: bool = False,
+        gromacs: bool = False,
+    ):
+        """Base constructor."""
+        self.write_dir = write_dir
+        self.xyz = xyz
+        self.gromacs = gromacs
+        self.preferences = {
+            "download.default_directory": write_dir,
+            "safebrowsing.enabled": "false",
+            "profile.managed_default_content_settings.images": 2,
+        }
+        self.options = webdriver.ChromeOptions()
+        self.server = webdriver.ChromeService(chromedriver_dir)
+        self.options.add_argument(
+            'user-agent="Mozilla/5.0 '
+            "(Macintosh; Intel Mac OS X 10_14_6) "
+            "AppleWebKit/537.36 (KHTML, like Gecko) "
+            'Chrome/88.0.4324.146 Safari/537.36"'
+        )
+        self.options.add_argument("--window-size=1920,1080")
+        self.options.add_argument("ignore-certificate-errors")
+        if headless:
+            self.options.add_argument("--headless")
+        self.options.add_experimental_option("prefs", self.preferences)
+        self.options.add_experimental_option("excludeSwitches", ["enable-automation"])
+        if chromedriver_dir is None:
+            self.web = webdriver.Chrome(options=self.options)
+        else:
+            self.web = webdriver.Chrome(service=self.server, options=self.options)
+        self.wait = WebDriverWait(self.web, 10)
+        self.web.get("http://traken.chem.yale.edu/ligpargen/")
+        time.sleep(1)
+        print("LigParGen server connected.")
+
+    def quit(self):
+        """
+        Method for quiting ChromeDriver.
+
+        """
+        self.web.quit()
+
+    def data_from_pdb(self, pdb_dir: str):
+        """
+        Use the LigParGen server to generate a LAMMPS data file from a pdb file.
+        Write out a LAMMPS data file.
+
+        Args:
+            pdb_dir: The path to the input pdb structure file.
+        """
+        self.web.get("http://traken.chem.yale.edu/ligpargen/")
+        upload_xpath = '//*[@id="exampleMOLFile"]'
+        time.sleep(1)
+        self.wait.until(EC.presence_of_element_located((By.XPATH, upload_xpath)))
+        upload = self.web.find_element(By.XPATH, upload_xpath)
+        try:
+            upload.send_keys(pdb_dir)
+            submit = self.web.find_element(By.XPATH, "/html/body/div[2]/div/div[2]/form/button[1]")
+            submit.click()
+            pdb_filename = os.path.basename(pdb_dir)
+            self.download_data(os.path.splitext(pdb_filename)[0] + ".lmp")
+        except TimeoutException:
+            print("Timeout! Web server no response for 10s, file download failed!")
+        except WebDriverException as e:
+            print(e)
+        finally:
+            self.quit()
+
+    def data_from_smiles(self, smiles_code):
+        """
+        Use the LigParGen server to generate a LAMMPS data file from a SMILES code.
+        Write out a LAMMPS data file.
+
+        Args:
+            smiles_code: The SMILES code for the LigParGen input.
+        """
+        self.web.get("http://traken.chem.yale.edu/ligpargen/")
+        time.sleep(1)
+        smile = self.web.find_element(By.XPATH, '//*[@id="smiles"]')
+        smile.send_keys(smiles_code)
+        submit = self.web.find_element(By.XPATH, "/html/body/div[2]/div/div[2]/form/button[1]")
+        submit.click()
+        try:
+            self.download_data(smiles_code + ".lmp")
+        except TimeoutException:
+            print("Timeout! Web server no response for 10s, file download failed!")
+        finally:
+            self.quit()
+
+    def download_data(self, lmp_name: str):
+        """
+        Helper function that download and write out the LAMMPS data file.
+
+        Args:
+            lmp_name: Name of the LAMMPS data file.
+        """
+        print("Structure info uploaded. Rendering force field...")
+        lmp_xpath = "/html/body/div[2]/div[2]/div[1]/div/div[14]/form/input[1]"
+        self.wait.until(EC.presence_of_element_located((By.XPATH, lmp_xpath)))
+        jmol = self.web.find_element(By.XPATH, "/html/body/div[2]/div[2]/div[2]")
+        self.web.execute_script("arguments[0].remove();", jmol)
+        self.wait.until(EC.element_to_be_clickable((By.XPATH, lmp_xpath)))
+        data_lmp = self.web.find_element(By.XPATH, lmp_xpath)
+        num_file = len([f for f in os.listdir(self.write_dir) if os.path.splitext(f)[1] == ".lmp"]) + 1
+        data_lmp.click()
+        while True:
+            files = sorted(
+                [
+                    os.path.join(self.write_dir, f)
+                    for f in os.listdir(self.write_dir)
+                    if os.path.splitext(f)[1] == ".lmp"
+                ],
+                key=os.path.getmtime,
+            )
+            # wait for file to finish download
+            if len(files) < num_file:
+                time.sleep(1)
+                print("waiting for download to be initiated")
+            else:
+                newest = files[-1]
+                if ".crdownload" in newest:
+                    time.sleep(1)
+                    print("waiting for download to complete")
+                else:
+                    break
+        print("Force field file downloaded.")
+        lmp_file = newest
+        if self.xyz:
+            data_obj = LammpsData.from_file(lmp_file)
+            element_id_dict = lmp_mass_to_name(data_obj.masses)
+            coords = data_obj.atoms[["type", "x", "y", "z"]]
+            lines = []
+            lines.append(str(len(coords.index)))
+            lines.append("")
+            for _, r in coords.iterrows():
+                element_name = element_id_dict.get(int(r["type"]))
+                assert element_name is not None
+                line = element_name + " " + " ".join(str(r[loc]) for loc in ["x", "y", "z"])
+                lines.append(line)
+
+            with open(os.path.join(self.write_dir, lmp_name + ".xyz"), "w") as xyz_file:
+                xyz_file.write("\n".join(lines))
+            print(".xyz file saved.")
+        if self.gromacs:
+            data_gro = self.web.find_element(By.XPATH, "/html/body/div[2]/div[2]/div[1]/div/div[8]/form/input[1]")
+            data_itp = self.web.find_element(By.XPATH, "/html/body/div[2]/div[2]/div[1]/div/div[9]/form/input[1]")
+            data_gro.click()
+            data_itp.click()
+            time.sleep(1)
+            gro_file = max(
+                [self.write_dir + "/" + f for f in os.listdir(self.write_dir) if os.path.splitext(f)[1] == ".gro"],
+                key=os.path.getctime,
+            )
+            itp_file = max(
+                [self.write_dir + "/" + f for f in os.listdir(self.write_dir) if os.path.splitext(f)[1] == ".itp"],
+                key=os.path.getctime,
+            )
+            shutil.move(gro_file, os.path.join(self.write_dir, lmp_name[:-4] + ".gro"))
+            shutil.move(itp_file, os.path.join(self.write_dir, lmp_name[:-4] + ".itp"))
+        shutil.move(lmp_file, os.path.join(self.write_dir, lmp_name))
+        print("Force field file saved.")
diff --git a/tests/test_forcefield.py b/tests/test_forcefield.py
index 464d7d5f..71618768 100644
--- a/tests/test_forcefield.py
+++ b/tests/test_forcefield.py
@@ -7,7 +7,7 @@
 import numpy as np
 import pytest
 
-from mdgo.forcefield.crawler import *
+from mdgo.forcefield.ligpargen import *
 from mdgo.forcefield.aqueous import *
 
 test_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "test_files")

From f7de040734ad8aad46ad2bea52c7c2426c2ff89e Mon Sep 17 00:00:00 2001
From: Tingzheng Hou <25351437+htz1992213@users.noreply.github.com>
Date: Tue, 23 Jan 2024 15:39:27 +0800
Subject: [PATCH 03/21] fix lints

---
 mdgo/forcefield/ligpargen.py | 43 +++++++++++++++++++++++++++---------
 1 file changed, 33 insertions(+), 10 deletions(-)

diff --git a/mdgo/forcefield/ligpargen.py b/mdgo/forcefield/ligpargen.py
index ec9431e3..c53eeebc 100644
--- a/mdgo/forcefield/ligpargen.py
+++ b/mdgo/forcefield/ligpargen.py
@@ -1,14 +1,38 @@
+# coding: utf-8
+# Copyright (c) Tingzheng Hou.
+# Distributed under the terms of the MIT License.
 
 """
-This module implements a core class LigpargenRunner for generating
-LAMMPS/GROMACS data files from molecule structure using LigParGen 2.1 
-and BOSS 5.0.
+This module implements two core class LigpargenRunner and FFcrawler for generating
+LAMMPS/GROMACS data files from molecule structure using LigParGen 2.1 + BOSS 5.0 or
+the LigParGen web server.
+
+For using the FFcrawler class:
+
+  * Download the ChromeDriver executable that
+    matches your Chrome version via https://chromedriver.chromium.org/downloads
 """
 
-import subprocess
 import os
+import subprocess
+import shutil
+import time
+from typing import Optional
+
+
 from pymatgen.io.lammps.data import LammpsData
+from selenium import webdriver
+from selenium.common.exceptions import (
+    TimeoutException,
+    WebDriverException,
+)
+from selenium.webdriver.common.by import By
+from selenium.webdriver.support import expected_conditions as EC
+from selenium.webdriver.support.ui import WebDriverWait
+
 from mdgo.util.dict_utils import lmp_mass_to_name
+from ligpargen.ligpargen import LigParGen
+
 
 class LigpargenRunner:
 
@@ -23,9 +47,8 @@ def __init__(
         xyz: bool = False,        
     ):
         """Base constructor."""
-        self.structure = structure_dir + "/" + structure_name
-        self.name = os.path.splitext(structure_name)[0]
-        self.structure_format = os.path.splitext(structure_name)[1][1:]
+        self.structure = os.path.join(structure_dir, structure_name)
+        self.name, self.structure_format = os.path.splitext(structure_name)
         print("Input format:", self.structure_format)
         self.structure_dir = structure_dir
         self.work = working_dir
@@ -54,7 +77,7 @@ def data_from_structure(self, wait: float = 30):
             data_obj = LammpsData.from_file(lmp_file)
             element_id_dict = lmp_mass_to_name(data_obj.masses)
             coords = data_obj.atoms[["type", "x", "y", "z"]]
-            lines = []
+            lines = list()
             lines.append(str(len(coords.index)))
             lines.append("")
             for _, r in coords.iterrows():
@@ -67,7 +90,7 @@ def data_from_structure(self, wait: float = 30):
                 xyz_file.write("\n".join(lines))
             print(".xyz file saved.")
         
-    def data_from_smiles(self, wait: float = 30):
+    def data_from_smiles(self):
         try:
             cmd = f"ligpargen -s {self.name} -n {self.name} -p {self.work} -c {self.charge} -o {self.opt}"
             subprocess.run(cmd, shell=True)
@@ -85,7 +108,7 @@ def data_from_smiles(self, wait: float = 30):
             data_obj = LammpsData.from_file(lmp_file)
             element_id_dict = lmp_mass_to_name(data_obj.masses)
             coords = data_obj.atoms[["type", "x", "y", "z"]]
-            lines = []
+            lines = list()
             lines.append(str(len(coords.index)))
             lines.append("")
             for _, r in coords.iterrows():

From 15a8f57434bbb862e7cf9788ce2e4b43ae319834 Mon Sep 17 00:00:00 2001
From: Tingzheng Hou <25351437+htz1992213@users.noreply.github.com>
Date: Tue, 23 Jan 2024 15:39:36 +0800
Subject: [PATCH 04/21] lint

---
 mdgo/forcefield/ligpargen.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/mdgo/forcefield/ligpargen.py b/mdgo/forcefield/ligpargen.py
index c53eeebc..eea0f5a4 100644
--- a/mdgo/forcefield/ligpargen.py
+++ b/mdgo/forcefield/ligpargen.py
@@ -56,7 +56,6 @@ def __init__(
         self.charge = charge
         self.opt = opt
         self.xyz = xyz
-    
 
     def data_from_structure(self, wait: float = 30):
 

From a5bece8994e864327ae60253bb796ad28ed41e2c Mon Sep 17 00:00:00 2001
From: Tingzheng Hou <25351437+htz1992213@users.noreply.github.com>
Date: Tue, 23 Jan 2024 15:59:20 +0800
Subject: [PATCH 05/21] lint

---
 mdgo/forcefield/ligpargen.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mdgo/forcefield/ligpargen.py b/mdgo/forcefield/ligpargen.py
index eea0f5a4..0cfbfa18 100644
--- a/mdgo/forcefield/ligpargen.py
+++ b/mdgo/forcefield/ligpargen.py
@@ -57,7 +57,7 @@ def __init__(
         self.opt = opt
         self.xyz = xyz
 
-    def data_from_structure(self, wait: float = 30):
+    def data_from_structure(self):
 
         try:
             cmd = f"ligpargen -i {self.structure} -n {self.name} -p {self.work} -c {self.charge} -o {self.opt}"

From 704dead7aa8051be977791d64cd30c3a3c42f8fa Mon Sep 17 00:00:00 2001
From: Tingzheng Hou <25351437+htz1992213@users.noreply.github.com>
Date: Tue, 23 Jan 2024 16:49:59 +0800
Subject: [PATCH 06/21] rewrite LigpargenRunner

---
 mdgo/forcefield/ligpargen.py | 76 ++++++++++++------------------------
 1 file changed, 26 insertions(+), 50 deletions(-)

diff --git a/mdgo/forcefield/ligpargen.py b/mdgo/forcefield/ligpargen.py
index 0cfbfa18..39898c72 100644
--- a/mdgo/forcefield/ligpargen.py
+++ b/mdgo/forcefield/ligpargen.py
@@ -35,20 +35,21 @@
 
 
 class LigpargenRunner:
-
     def __init__(
         self,
         structure_name: str,
         structure_dir: str,
-        working_dir: str= "boss_files",
+        working_dir: str = "boss_files",
         out: str = "lmp",
         charge: int = 0,
         opt: int = 0,
-        xyz: bool = False,        
+        xyz: bool = False,
     ):
         """Base constructor."""
         self.structure = os.path.join(structure_dir, structure_name)
         self.name, self.structure_format = os.path.splitext(structure_name)
+        if self.structure_format == "":
+            self.structure_format = "SMILES"
         print("Input format:", self.structure_format)
         self.structure_dir = structure_dir
         self.work = working_dir
@@ -57,53 +58,28 @@ def __init__(
         self.opt = opt
         self.xyz = xyz
 
-    def data_from_structure(self):
-
-        try:
-            cmd = f"ligpargen -i {self.structure} -n {self.name} -p {self.work} -c {self.charge} -o {self.opt}"
-            subprocess.run(cmd, shell=True)
-        except subprocess.CalledProcessError as e:
-            raise ValueError(f"LigParGen failed with errorcode {e.returncode}  and stderr: {e.stderr}") from e
-        
-        if self.out == "lmp":
-            lmp_name = f"{self.name}.lmp"
-            lmp_file = f"{self.structure_dir}/{self.name}.lmp"
-            cp_lmp_data = f"cp {self.work}/{self.name}.lammps.lmp {lmp_file}"
-            subprocess.run(cp_lmp_data, shell=True)
-
-        if self.xyz:
-            lmp_file = f"{self.structure_dir}/{self.name}.lmp"
-            data_obj = LammpsData.from_file(lmp_file)
-            element_id_dict = lmp_mass_to_name(data_obj.masses)
-            coords = data_obj.atoms[["type", "x", "y", "z"]]
-            lines = list()
-            lines.append(str(len(coords.index)))
-            lines.append("")
-            for _, r in coords.iterrows():
-                element_name = element_id_dict.get(int(r["type"]))
-                assert element_name is not None
-                line = element_name + " " + " ".join(str(r[loc]) for loc in ["x", "y", "z"])
-                lines.append(line)
-
-            with open(os.path.join(self.structure_dir, lmp_name + ".xyz"), "w") as xyz_file:
-                xyz_file.write("\n".join(lines))
-            print(".xyz file saved.")
-        
-    def data_from_smiles(self):
-        try:
-            cmd = f"ligpargen -s {self.name} -n {self.name} -p {self.work} -c {self.charge} -o {self.opt}"
-            subprocess.run(cmd, shell=True)
-        except subprocess.CalledProcessError as e:
-            raise ValueError(f"LigParGen failed with errorcode {e.returncode}  and stderr: {e.stderr}") from e
-        
-        if self.out == "lmp":
-            lmp_name = f"{self.name}.lmp"
-            lmp_file = f"{self.structure_dir}/{self.name}.lmp"
-            cp_lmp_data = f"cp {self.work}/{self.name}.lammps.lmp {lmp_file}"
-            subprocess.run(cp_lmp_data, shell=True)
+    def run(self):
+        if self.structure_format == "SMILES":
+            molecule_a = LigParGen(
+                smile=self.structure,
+                charge=self.charge,
+                numberOfOptimizations=self.opt,
+                molname=self.name,
+                workdir=self.work,
+            )
+        else:
+            molecule_a = LigParGen(
+                ifile=self.structure,
+                charge=self.charge,
+                numberOfOptimizations=self.opt,
+                molname=self.name,
+                workdir=self.work,
+            )
+        molecule_a.writeAllOuputs()
+        print("LigParGen finished succesfully!")
 
         if self.xyz:
-            lmp_file = f"{self.structure_dir}/{self.name}.lmp"
+            lmp_file = os.path.join(self.structure_dir, self.name + ".lmp")
             data_obj = LammpsData.from_file(lmp_file)
             element_id_dict = lmp_mass_to_name(data_obj.masses)
             coords = data_obj.atoms[["type", "x", "y", "z"]]
@@ -116,7 +92,7 @@ def data_from_smiles(self):
                 line = element_name + " " + " ".join(str(r[loc]) for loc in ["x", "y", "z"])
                 lines.append(line)
 
-            with open(os.path.join(self.structure_dir, lmp_name + ".xyz"), "w") as xyz_file:
+            with open(os.path.join(self.structure_dir, self.name + ".xyz"), "w") as xyz_file:
                 xyz_file.write("\n".join(lines))
             print(".xyz file saved.")
 
@@ -280,7 +256,7 @@ def download_data(self, lmp_name: str):
             data_obj = LammpsData.from_file(lmp_file)
             element_id_dict = lmp_mass_to_name(data_obj.masses)
             coords = data_obj.atoms[["type", "x", "y", "z"]]
-            lines = []
+            lines = list()
             lines.append(str(len(coords.index)))
             lines.append("")
             for _, r in coords.iterrows():

From 60fd96e40283afb03a7c5540545b5e3f43bb0903 Mon Sep 17 00:00:00 2001
From: Tingzheng Hou <25351437+htz1992213@users.noreply.github.com>
Date: Tue, 23 Jan 2024 17:19:23 +0800
Subject: [PATCH 07/21] fix smile input

---
 mdgo/forcefield/ligpargen.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mdgo/forcefield/ligpargen.py b/mdgo/forcefield/ligpargen.py
index 39898c72..d1aae688 100644
--- a/mdgo/forcefield/ligpargen.py
+++ b/mdgo/forcefield/ligpargen.py
@@ -61,7 +61,7 @@ def __init__(
     def run(self):
         if self.structure_format == "SMILES":
             molecule_a = LigParGen(
-                smile=self.structure,
+                smile=self.name,
                 charge=self.charge,
                 numberOfOptimizations=self.opt,
                 molname=self.name,

From 9201787a552f93cef729bc2f9d2abc4b26dd660e Mon Sep 17 00:00:00 2001
From: Tingzheng Hou <25351437+htz1992213@users.noreply.github.com>
Date: Tue, 23 Jan 2024 17:21:28 +0800
Subject: [PATCH 08/21] drop output format designation

---
 mdgo/forcefield/ligpargen.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/mdgo/forcefield/ligpargen.py b/mdgo/forcefield/ligpargen.py
index d1aae688..8b0474f1 100644
--- a/mdgo/forcefield/ligpargen.py
+++ b/mdgo/forcefield/ligpargen.py
@@ -40,7 +40,6 @@ def __init__(
         structure_name: str,
         structure_dir: str,
         working_dir: str = "boss_files",
-        out: str = "lmp",
         charge: int = 0,
         opt: int = 0,
         xyz: bool = False,
@@ -53,7 +52,6 @@ def __init__(
         print("Input format:", self.structure_format)
         self.structure_dir = structure_dir
         self.work = working_dir
-        self.out = out
         self.charge = charge
         self.opt = opt
         self.xyz = xyz

From 88403e4c85595d49917d0659bbbae3e0ea1ea9c4 Mon Sep 17 00:00:00 2001
From: Tingzheng Hou <25351437+htz1992213@users.noreply.github.com>
Date: Tue, 23 Jan 2024 17:25:08 +0800
Subject: [PATCH 09/21] refactor ligpargen to mdgoligpargen

---
 mdgo/forcefield/__init__.py                        | 2 +-
 mdgo/forcefield/{ligpargen.py => mdgoligpargen.py} | 1 -
 tests/test_forcefield.py                           | 2 +-
 3 files changed, 2 insertions(+), 3 deletions(-)
 rename mdgo/forcefield/{ligpargen.py => mdgoligpargen.py} (99%)

diff --git a/mdgo/forcefield/__init__.py b/mdgo/forcefield/__init__.py
index 8ae75669..8b04775c 100644
--- a/mdgo/forcefield/__init__.py
+++ b/mdgo/forcefield/__init__.py
@@ -18,4 +18,4 @@
 from .charge import ChargeWriter
 from .maestro import MaestroRunner
 from .pubchem import PubChemRunner
-from .ligpargen import LigpargenRunner, FFcrawler
+from .mdgoligpargen import LigpargenRunner, FFcrawler
diff --git a/mdgo/forcefield/ligpargen.py b/mdgo/forcefield/mdgoligpargen.py
similarity index 99%
rename from mdgo/forcefield/ligpargen.py
rename to mdgo/forcefield/mdgoligpargen.py
index 8b0474f1..33b43f60 100644
--- a/mdgo/forcefield/ligpargen.py
+++ b/mdgo/forcefield/mdgoligpargen.py
@@ -14,7 +14,6 @@
 """
 
 import os
-import subprocess
 import shutil
 import time
 from typing import Optional
diff --git a/tests/test_forcefield.py b/tests/test_forcefield.py
index 71618768..709b0fea 100644
--- a/tests/test_forcefield.py
+++ b/tests/test_forcefield.py
@@ -7,7 +7,7 @@
 import numpy as np
 import pytest
 
-from mdgo.forcefield.ligpargen import *
+from mdgo.forcefield.mdgoligpargen import *
 from mdgo.forcefield.aqueous import *
 
 test_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "test_files")

From 8a081536831170335f949d6553aca4f79c4fb2e9 Mon Sep 17 00:00:00 2001
From: Tingzheng Hou <25351437+htz1992213@users.noreply.github.com>
Date: Tue, 23 Jan 2024 17:48:05 +0800
Subject: [PATCH 10/21] handle ligpargen not found

---
 tests/test_forcefield.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/tests/test_forcefield.py b/tests/test_forcefield.py
index 709b0fea..eaa563c7 100644
--- a/tests/test_forcefield.py
+++ b/tests/test_forcefield.py
@@ -8,7 +8,10 @@
 import pytest
 
 from mdgo.forcefield.mdgoligpargen import *
-from mdgo.forcefield.aqueous import *
+try:
+    from mdgo.forcefield.aqueous import *
+except ModuleNotFoundError:
+    pass
 
 test_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "test_files")
 

From 14555d9d73406875dbea0ba360621e0d261206e9 Mon Sep 17 00:00:00 2001
From: LIANG Bochun <zlatanbochun@outlook.com>
Date: Thu, 1 Feb 2024 21:51:12 +0800
Subject: [PATCH 11/21] Update mdgoligpargen.py

Add comments on parameters of the class LigpargenRunner, and add the operation of copying lmp file from 'working_dir' to 'write_dir'.
---
 mdgo/forcefield/mdgoligpargen.py | 40 +++++++++++++++++++++++++++-----
 1 file changed, 34 insertions(+), 6 deletions(-)

diff --git a/mdgo/forcefield/mdgoligpargen.py b/mdgo/forcefield/mdgoligpargen.py
index 33b43f60..34bb0b8c 100644
--- a/mdgo/forcefield/mdgoligpargen.py
+++ b/mdgo/forcefield/mdgoligpargen.py
@@ -16,6 +16,7 @@
 import os
 import shutil
 import time
+import subprocess
 from typing import Optional
 
 
@@ -34,28 +35,50 @@
 
 
 class LigpargenRunner:
+    """
+    LigpargenRunner make use of LigParGen2.1 and BOSS5.0 to generate LAMMPS
+    data file and xyz file from structure file.
+    
+    Args:
+        structure_name: Name of the input structure file including file format.
+        structure_dir: Directory of the structure file and output file.
+        working_dir: Files generated from BOSS software. Arguement of LigParGen. 
+            Default to "boss_files".
+        charge: Molecule net charge. Arguement of LigParGen. Default to 0.
+        opt: Number of optimizations. Arguement of LIgParGen. Default to 0.
+        xyz: Whether to write the structure in the LigParGen generated data file
+            as .xyz. Default to False. This is useful because the order and the 
+            name of the atoms could be different from the initial input.)
+    
+    Examples:
+
+        >>> lpg = LigpargenRunner('sturcture_name', 'path/to/structure/')
+        >>> lpg.run()
+    """
+    
     def __init__(
         self,
         structure_name: str,
-        structure_dir: str,
+        write_dir: str,
         working_dir: str = "boss_files",
         charge: int = 0,
         opt: int = 0,
         xyz: bool = False,
     ):
         """Base constructor."""
-        self.structure = os.path.join(structure_dir, structure_name)
+        
         self.name, self.structure_format = os.path.splitext(structure_name)
         if self.structure_format == "":
             self.structure_format = "SMILES"
         print("Input format:", self.structure_format)
-        self.structure_dir = structure_dir
+        self.structure_name = structure_name
+        self.write_dir = write_dir
         self.work = working_dir
         self.charge = charge
         self.opt = opt
         self.xyz = xyz
 
-    def run(self):
+    def run(self, structure_dir: str):
         if self.structure_format == "SMILES":
             molecule_a = LigParGen(
                 smile=self.name,
@@ -65,6 +88,7 @@ def run(self):
                 workdir=self.work,
             )
         else:
+            self.structure = os.path.join(structure_dir, self.structure_name)
             molecule_a = LigParGen(
                 ifile=self.structure,
                 charge=self.charge,
@@ -73,10 +97,14 @@ def run(self):
                 workdir=self.work,
             )
         molecule_a.writeAllOuputs()
+        lmp_name = f"{self.name}.lmp"
+        lmp_file = os.path.join(self.write_dir, lmp_name)
+        copy_file = os.path.join(self.work, f"{self.name}.lammps.lmp")
+        shutil.copyfile(copy_file, lmp_file)
         print("LigParGen finished succesfully!")
 
         if self.xyz:
-            lmp_file = os.path.join(self.structure_dir, self.name + ".lmp")
+            lmp_file = os.path.join(self.write_dir, self.name + ".lmp")
             data_obj = LammpsData.from_file(lmp_file)
             element_id_dict = lmp_mass_to_name(data_obj.masses)
             coords = data_obj.atoms[["type", "x", "y", "z"]]
@@ -89,7 +117,7 @@ def run(self):
                 line = element_name + " " + " ".join(str(r[loc]) for loc in ["x", "y", "z"])
                 lines.append(line)
 
-            with open(os.path.join(self.structure_dir, self.name + ".xyz"), "w") as xyz_file:
+            with open(os.path.join(self.write_dir, lmp_name + ".xyz"), "w") as xyz_file:
                 xyz_file.write("\n".join(lines))
             print(".xyz file saved.")
 

From c9dfb17285d6659a132583a0b123ec6f980ee16c Mon Sep 17 00:00:00 2001
From: LIANG Bochun <zlatanbochun@outlook.com>
Date: Thu, 1 Feb 2024 21:53:52 +0800
Subject: [PATCH 12/21] Test for LigpargenRunner

Test for LigpargenRunner using EC.
---
 tests/test_files/CCOC(=O)O.lmp     | 178 +++++++++++++++++++++++++++++
 tests/test_files/CCOC(=O)O.lmp.xyz |  14 +++
 tests/test_files/CCOC(=O)O.xyz     |  14 +++
 tests/test_files/EC.lmp            | 176 ++++++++++++++++++++++++++++
 tests/test_files/EC.lmp.xyz        |  12 ++
 tests/test_forcefield.py           |  62 +++++++++-
 6 files changed, 452 insertions(+), 4 deletions(-)
 create mode 100644 tests/test_files/CCOC(=O)O.lmp
 create mode 100644 tests/test_files/CCOC(=O)O.lmp.xyz
 create mode 100644 tests/test_files/CCOC(=O)O.xyz
 create mode 100644 tests/test_files/EC.lmp
 create mode 100644 tests/test_files/EC.lmp.xyz

diff --git a/tests/test_files/CCOC(=O)O.lmp b/tests/test_files/CCOC(=O)O.lmp
new file mode 100644
index 00000000..6c023380
--- /dev/null
+++ b/tests/test_files/CCOC(=O)O.lmp
@@ -0,0 +1,178 @@
+LAMMPS data file generated with LigParGen (israel.cabezadevaca@yale.edu)
+
+      12 atoms
+      11 bonds
+      17 angles
+      16 dihedrals
+       1 impropers
+
+      12 atom types
+      11 bond types
+      17 angle types
+      16 dihedral types
+       1 improper types
+
+   -2.525000    47.475000 xlo xhi
+   -1.664000    48.336000 ylo yhi
+   -1.488000    48.512000 zlo zhi
+
+Masses
+
+       1     12.011
+       2     15.999
+       3     15.999
+       4     15.999
+       5     12.011
+       6     12.011
+       7      1.008
+       8      1.008
+       9      1.008
+      10      1.008
+      11      1.008
+      12      1.008
+
+Pair Coeffs
+
+       1      0.070  3.5500000
+       2      0.140  2.9000000
+       3      0.210  2.9600000
+       4      0.170  3.1200000
+       5      0.066  3.5000000
+       6      0.066  3.5000000
+       7      0.030  2.5000000
+       8      0.030  2.5000000
+       9      0.030  2.5000000
+      10      0.030  2.5000000
+      11      0.030  2.5000000
+      12      0.000  0.0000000
+
+Bond Coeffs
+
+       1   214.0000     1.3270
+       2   570.0000     1.2290
+       3   450.0000     1.3640
+       4   320.0000     1.4100
+       5   268.0000     1.5290
+       6   340.0000     1.0900
+       7   340.0000     1.0900
+       8   340.0000     1.0900
+       9   340.0000     1.0900
+      10   340.0000     1.0900
+      11   553.0000     0.9450
+
+Angle Coeffs
+
+       1     83.000    123.400
+       2     70.130    117.450
+       3     83.000    116.900
+       4     50.000    109.500
+       5     37.500    110.700
+       6     37.500    110.700
+       7     37.500    110.700
+       8     35.000    109.500
+       9     35.000    109.500
+      10     35.000    113.000
+      11     80.000    121.000
+      12     37.500    110.700
+      13     37.500    110.700
+      14     33.000    107.800
+      15     33.000    107.800
+      16     33.000    107.800
+      17     33.000    107.800
+
+Dihedral Coeffs
+
+       1      0.000      5.124      0.000      0.000
+       2     -1.220     -0.126      0.422      0.000
+       3      0.000      0.000      0.468      0.000
+       4      0.000      0.000      0.468      0.000
+       5      0.000      0.000      0.468      0.000
+       6      0.000      0.000      0.198      0.000
+       7      0.000      0.000      0.198      0.000
+       8      0.000      5.500      0.000      0.000
+       9      0.000      5.500      0.000      0.000
+      10      4.669      5.124      0.000      0.000
+      11      0.000      0.000      0.300      0.000
+      12      0.000      0.000      0.300      0.000
+      13      0.000      0.000      0.300      0.000
+      14      0.000      0.000      0.300      0.000
+      15      0.000      0.000      0.300      0.000
+      16      0.000      0.000      0.300      0.000
+
+Improper Coeffs
+
+       1     10.500      -1       2
+
+Atoms
+
+     1      1      1   0.589708  1.45900 -0.07400  0.01300
+     2      1      2  -0.316075  0.46100 -1.02200  0.18800
+     3      1      3  -0.521319  1.26800  0.98800 -0.62500
+     4      1      4  -0.548751  2.74000 -0.25400  0.54300
+     5      1      5   0.030243 -0.81200 -0.76900 -0.37800
+     6      1      6  -0.299103 -1.42400  0.48800  0.16700
+     7      1      7   0.109289 -2.52500  0.43200  0.01900
+     8      1      8   0.109289 -1.01900  1.37200 -0.33100
+     9      1      9   0.109289 -1.27100  0.57200  1.28100
+    10      1     10   0.123815 -0.71600 -0.64200 -1.48800
+    11      1     11   0.123815 -1.43200 -1.66400 -0.16600
+    12      1     12   0.489800  3.27000  0.57400  0.77800
+
+Bonds
+
+     1      1      2      1
+     2      2      3      1
+     3      3      4      1
+     4      4      5      2
+     5      5      6      5
+     6      6      7      6
+     7      7      8      6
+     8      8      9      6
+     9      9     10      5
+    10     10     11      5
+    11     11     12      4
+
+Angles
+
+     1      1      3      1      2
+     2      2      4      1      2
+     3      3      5      2      1
+     4      4      6      5      2
+     5      5      7      6      5
+     6      6      8      6      5
+     7      7      9      6      5
+     8      8     10      5      2
+     9      9     11      5      2
+    10     10     12      4      1
+    11     11      4      1      3
+    12     12     10      5      6
+    13     13     11      5      6
+    14     14      8      6      7
+    15     15      9      6      7
+    16     16      9      6      8
+    17     17     11      5     10
+
+Dihedrals
+
+     1      1      5      2      1      3
+     2      2      6      5      2      1
+     3      3      7      6      5      2
+     4      4      8      6      5      2
+     5      5      9      6      5      2
+     6      6     10      5      2      1
+     7      7     11      5      2      1
+     8      8     12      4      1      2
+     9      9     12      4      1      3
+    10     10      5      2      1      4
+    11     11     10      5      6      7
+    12     12     11      5      6      7
+    13     13     10      5      6      8
+    14     14     11      5      6      8
+    15     15     10      5      6      9
+    16     16     11      5      6      9
+
+Impropers
+
+     1      1      2      1      3      4
+
+
diff --git a/tests/test_files/CCOC(=O)O.lmp.xyz b/tests/test_files/CCOC(=O)O.lmp.xyz
new file mode 100644
index 00000000..a0272bf5
--- /dev/null
+++ b/tests/test_files/CCOC(=O)O.lmp.xyz
@@ -0,0 +1,14 @@
+12
+
+C 1.459 -0.074 0.013
+O 0.461 -1.022 0.188
+O 1.268 0.988 -0.625
+O 2.74 -0.254 0.543
+C -0.812 -0.769 -0.378
+C -1.424 0.488 0.167
+H -2.525 0.432 0.019
+H -1.019 1.372 -0.331
+H -1.271 0.572 1.281
+H -0.716 -0.642 -1.488
+H -1.432 -1.664 -0.166
+H 3.27 0.574 0.778
\ No newline at end of file
diff --git a/tests/test_files/CCOC(=O)O.xyz b/tests/test_files/CCOC(=O)O.xyz
new file mode 100644
index 00000000..a0272bf5
--- /dev/null
+++ b/tests/test_files/CCOC(=O)O.xyz
@@ -0,0 +1,14 @@
+12
+
+C 1.459 -0.074 0.013
+O 0.461 -1.022 0.188
+O 1.268 0.988 -0.625
+O 2.74 -0.254 0.543
+C -0.812 -0.769 -0.378
+C -1.424 0.488 0.167
+H -2.525 0.432 0.019
+H -1.019 1.372 -0.331
+H -1.271 0.572 1.281
+H -0.716 -0.642 -1.488
+H -1.432 -1.664 -0.166
+H 3.27 0.574 0.778
\ No newline at end of file
diff --git a/tests/test_files/EC.lmp b/tests/test_files/EC.lmp
new file mode 100644
index 00000000..9d92f47c
--- /dev/null
+++ b/tests/test_files/EC.lmp
@@ -0,0 +1,176 @@
+LAMMPS data file generated with LigParGen (israel.cabezadevaca@yale.edu)
+
+      10 atoms
+      10 bonds
+      17 angles
+      19 dihedrals
+       1 impropers
+
+      10 atom types
+      10 bond types
+      17 angle types
+      19 dihedral types
+       1 improper types
+
+   -2.065000    47.935000 xlo xhi
+   -1.301000    48.699000 ylo yhi
+   -1.234000    48.766000 zlo zhi
+
+Masses
+
+       1     15.999
+       2     15.999
+       3     15.999
+       4     12.011
+       5     12.011
+       6     12.011
+       7      1.008
+       8      1.008
+       9      1.008
+      10      1.008
+
+Pair Coeffs
+
+       1      0.140  2.9000000
+       2      0.140  2.9000000
+       3      0.210  2.9600000
+       4      0.066  3.5000000
+       5      0.066  3.5000000
+       6      0.070  3.5500000
+       7      0.030  2.5000000
+       8      0.030  2.5000000
+       9      0.030  2.5000000
+      10      0.030  2.5000000
+
+Bond Coeffs
+
+       1   214.0000     1.3270
+       2   214.0000     1.3270
+       3   570.0000     1.2290
+       4   320.0000     1.4100
+       5   268.0000     1.5290
+       6   340.0000     1.0900
+       7   340.0000     1.0900
+       8   340.0000     1.0900
+       9   340.0000     1.0900
+      10   320.0000     1.4100
+
+Angle Coeffs
+
+       1     70.130    117.450
+       2     83.000    123.400
+       3     83.000    116.900
+       4     50.000    109.500
+       5     35.000    109.500
+       6     35.000    109.500
+       7     37.500    110.700
+       8     37.500    110.700
+       9     83.000    123.400
+      10     37.500    110.700
+      11     37.500    110.700
+      12     83.000    116.900
+      13     33.000    107.800
+      14     35.000    109.500
+      15     33.000    107.800
+      16     35.000    109.500
+      17     50.000    109.500
+
+Dihedral Coeffs
+
+       1      4.669      5.124      0.000      0.000
+       2     -1.220     -0.126      0.422      0.000
+       3      0.000      0.000      0.198      0.000
+       4      0.000      0.000      0.198      0.000
+       5      0.000      0.000      0.468      0.000
+       6      0.000      0.000      0.468      0.000
+       7      4.669      5.124      0.000      0.000
+       8      0.000      5.124      0.000      0.000
+       9      0.000      5.124      0.000      0.000
+      10      0.000      0.000      0.468      0.000
+      11      0.000      0.000      0.300      0.000
+      12      0.000      0.000      0.300      0.000
+      13      0.000      0.000      0.468      0.000
+      14      0.000      0.000      0.300      0.000
+      15      0.000      0.000      0.300      0.000
+      16      0.000      0.000      0.198      0.000
+      17      0.000      0.000      0.198      0.000
+      18     -0.550      0.000      0.000      0.000
+      19     -1.220     -0.126      0.422      0.000
+
+Improper Coeffs
+
+       1     10.500      -1       2
+
+Atoms
+
+     1      1      1  -0.324734 -0.01800  1.11900 -0.11200
+     2      1      2  -0.324709 -0.01800 -1.12000  0.11200
+     3      1      3  -0.368343  1.98200  0.00000  0.00000
+     4      1      4  -0.041460 -1.35300  0.72800  0.17200
+     5      1      5  -0.042098 -1.35300 -0.72700 -0.17200
+     6      1      6   0.559059  0.76000  0.00000  0.00000
+     7      1      7   0.135599 -2.06500  1.30200 -0.42600
+     8      1      8   0.135599 -1.54800  0.90700  1.23500
+     9      1      9   0.135544 -2.06500 -1.30100  0.42700
+    10      1     10   0.135543 -1.55000 -0.90600 -1.23400
+
+Bonds
+
+     1      1      1      6
+     2      2      2      6
+     3      3      3      6
+     4      4      4      1
+     5      5      5      4
+     6      6      7      4
+     7      7      8      4
+     8      8      9      5
+     9      9     10      5
+    10     10      5      2
+
+Angles
+
+     1      1      2      6      1
+     2      2      3      6      1
+     3      3      4      1      6
+     4      4      5      4      1
+     5      5      7      4      1
+     6      6      8      4      1
+     7      7      9      5      4
+     8      8     10      5      4
+     9      9      3      6      2
+    10     10      7      4      5
+    11     11      8      4      5
+    12     12      6      2      5
+    13     13      8      4      7
+    14     14      2      5      9
+    15     15     10      5      9
+    16     16      2      5     10
+    17     17      4      5      2
+
+Dihedrals
+
+     1      1      4      1      6      2
+     2      2      5      4      1      6
+     3      3      7      4      1      6
+     4      4      8      4      1      6
+     5      5      9      5      4      1
+     6      6     10      5      4      1
+     7      7      5      2      6      1
+     8      8      4      1      6      3
+     9      9      5      2      6      3
+    10     10      2      5      4      7
+    11     11      9      5      4      7
+    12     12     10      5      4      7
+    13     13      2      5      4      8
+    14     14      9      5      4      8
+    15     15     10      5      4      8
+    16     16      6      2      5      9
+    17     17      6      2      5     10
+    18     18      1      4      5      2
+    19     19      6      2      5      4
+
+Impropers
+
+     1      1      1      6      2      3
+
+
diff --git a/tests/test_files/EC.lmp.xyz b/tests/test_files/EC.lmp.xyz
new file mode 100644
index 00000000..158dea4a
--- /dev/null
+++ b/tests/test_files/EC.lmp.xyz
@@ -0,0 +1,12 @@
+10
+
+O -0.018 1.119 -0.112
+O -0.018 -1.12 0.112
+O 1.982 0.0 0.0
+C -1.353 0.728 0.172
+C -1.353 -0.727 -0.172
+C 0.76 0.0 0.0
+H -2.065 1.302 -0.426
+H -1.548 0.907 1.235
+H -2.065 -1.301 0.427
+H -1.55 -0.906 -1.234
\ No newline at end of file
diff --git a/tests/test_forcefield.py b/tests/test_forcefield.py
index eaa563c7..ab0367cd 100644
--- a/tests/test_forcefield.py
+++ b/tests/test_forcefield.py
@@ -8,14 +8,68 @@
 import pytest
 
 from mdgo.forcefield.mdgoligpargen import *
-try:
-    from mdgo.forcefield.aqueous import *
-except ModuleNotFoundError:
-    pass
+#from mdgo.forcefield.crawler import *
+from mdgo.forcefield.aqueous import *
 
 test_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "test_files")
 
 
+class LigpargenRunnerTest(unittest.TestCase):
+    def test_run(self) -> None:
+        with open(os.path.join(test_dir, "EC.lmp")) as f:
+            pdf = f.readlines()
+        with open(os.path.join(test_dir, "EC.lmp.xyz")) as f:
+            xyz = f.readlines()
+        with open(os.path.join(test_dir, "CCOC(=O)O.lmp")) as f:
+            smiles = f.readlines()
+        with open(os.path.join(test_dir, "CCOC(=O)O.lmp.xyz")) as f:
+            xyz_smiles = f.readlines()
+
+        saved_stdout = sys.stdout
+        download_dir = tempfile.mkdtemp()
+        try:
+            out = StringIO()
+            sys.stdout = out
+            
+            lpg = LigpargenRunner("EC.pdb", download_dir, xyz=True)
+            lpg.run(test_dir)
+            self.assertIn(
+                "Input format: .pdb\n"
+                "LigParGen finished succesfully!\n"
+                ".xyz file saved.",
+                out.getvalue(),
+                )
+            self.assertTrue(os.path.exists(os.path.join(download_dir, "EC.lmp")))
+            self.assertTrue(os.path.exists(os.path.join(download_dir, "EC.lmp.xyz")))
+            with open(os.path.join(download_dir, "EC.lmp")) as f:
+                pdf_actual = f.readlines()
+                self.assertListEqual(pdf, pdf_actual)
+            with open(os.path.join(download_dir, "EC.lmp.xyz")) as f:
+                xyz_actual = f.readlines()
+                self.assertListEqual(xyz, xyz_actual)
+            
+            lpg = LigpargenRunner("CCOC(=O)O", download_dir, xyz=True)
+            lpg.run(test_dir)
+            self.assertIn(
+                "Input format: SMILES\n"
+                "LigParGen finished succesfully!\n"
+                ".xyz file saved.",
+                out.getvalue(),
+                )
+            self.assertTrue(os.path.exists(os.path.join(download_dir, "CCOC(=O)O.lmp")))
+            self.assertTrue(os.path.exists(os.path.join(download_dir, "CCOC(=O)O.lmp.xyz")))
+            with open(os.path.join(download_dir, "CCOC(=O)O.lmp")) as f:
+                smiles_actual = f.readlines()
+                self.assertListEqual(smiles, smiles_actual)
+            with open(os.path.join(download_dir, "CCOC(=O)O.lmp.xyz")) as f:
+                xyz_actual = f.readlines()
+                self.assertListEqual(xyz_smiles, xyz_actual)
+
+        finally:
+            sys.stdout = saved_stdout
+            shutil.rmtree(download_dir)
+
+
 class FFcrawlerTest(unittest.TestCase):
     def test_chrome(self) -> None:
         with open(os.path.join(test_dir, "EMC.lmp")) as f:

From 97bbbce5be206d24a11c1d5bf806d32c115433eb Mon Sep 17 00:00:00 2001
From: Tingzheng Hou <25351437+htz1992213@users.noreply.github.com>
Date: Fri, 2 Feb 2024 12:08:36 +0800
Subject: [PATCH 13/21] revert wrong changes

---
 mdgo/forcefield/mdgoligpargen.py | 1 -
 tests/test_forcefield.py         | 6 ++++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/mdgo/forcefield/mdgoligpargen.py b/mdgo/forcefield/mdgoligpargen.py
index 34bb0b8c..13c9b3fa 100644
--- a/mdgo/forcefield/mdgoligpargen.py
+++ b/mdgo/forcefield/mdgoligpargen.py
@@ -16,7 +16,6 @@
 import os
 import shutil
 import time
-import subprocess
 from typing import Optional
 
 
diff --git a/tests/test_forcefield.py b/tests/test_forcefield.py
index ab0367cd..b7bf3c6f 100644
--- a/tests/test_forcefield.py
+++ b/tests/test_forcefield.py
@@ -8,8 +8,10 @@
 import pytest
 
 from mdgo.forcefield.mdgoligpargen import *
-#from mdgo.forcefield.crawler import *
-from mdgo.forcefield.aqueous import *
+try:
+    from mdgo.forcefield.aqueous import *
+except ModuleNotFoundError:
+    pass
 
 test_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "test_files")
 

From 19436e6dd48e07ed52a0e1cce08d1214735a8a3e Mon Sep 17 00:00:00 2001
From: LIANG Bochun <zlatanbochun@outlook.com>
Date: Fri, 2 Feb 2024 18:56:01 +0800
Subject: [PATCH 14/21] Change Args for LigpargenRunner and the run function.

Change Args for LigpargenRunner and the function 'run'. Add docstrings for the fuction 'run'.
---
 mdgo/forcefield/mdgoligpargen.py | 23 +++++++++++++++--------
 tests/test_forcefield.py         |  6 +++---
 2 files changed, 18 insertions(+), 11 deletions(-)

diff --git a/mdgo/forcefield/mdgoligpargen.py b/mdgo/forcefield/mdgoligpargen.py
index 13c9b3fa..1b156c4f 100644
--- a/mdgo/forcefield/mdgoligpargen.py
+++ b/mdgo/forcefield/mdgoligpargen.py
@@ -39,8 +39,8 @@ class LigpargenRunner:
     data file and xyz file from structure file.
     
     Args:
-        structure_name: Name of the input structure file including file format.
-        structure_dir: Directory of the structure file and output file.
+        structure_file: The input structure file including path to file.
+        write_dir: Directory to write the output file.
         working_dir: Files generated from BOSS software. Arguement of LigParGen. 
             Default to "boss_files".
         charge: Molecule net charge. Arguement of LigParGen. Default to 0.
@@ -51,13 +51,13 @@ class LigpargenRunner:
     
     Examples:
 
-        >>> lpg = LigpargenRunner('sturcture_name', 'path/to/structure/')
+        >>> lpg = LigpargenRunner('sturcture_file', 'path/to/write/output')
         >>> lpg.run()
     """
     
     def __init__(
         self,
-        structure_name: str,
+        structure_file: str,
         write_dir: str,
         working_dir: str = "boss_files",
         charge: int = 0,
@@ -65,19 +65,27 @@ def __init__(
         xyz: bool = False,
     ):
         """Base constructor."""
-        
+        structure_dir, structure_name = os.path.split(structure_file)
         self.name, self.structure_format = os.path.splitext(structure_name)
         if self.structure_format == "":
             self.structure_format = "SMILES"
         print("Input format:", self.structure_format)
-        self.structure_name = structure_name
+        self.structure = structure_file
         self.write_dir = write_dir
         self.work = working_dir
         self.charge = charge
         self.opt = opt
         self.xyz = xyz
 
-    def run(self, structure_dir: str):
+    def run(self):
+        """
+        Run LigParGen2.1 to generate a LAMMPS data file from a structrure file
+        (pdb/mol/mol2...) supported by BOSS5.0.
+        Write out a LAMMPS data file.
+        
+        Args:
+            None
+        """
         if self.structure_format == "SMILES":
             molecule_a = LigParGen(
                 smile=self.name,
@@ -87,7 +95,6 @@ def run(self, structure_dir: str):
                 workdir=self.work,
             )
         else:
-            self.structure = os.path.join(structure_dir, self.structure_name)
             molecule_a = LigParGen(
                 ifile=self.structure,
                 charge=self.charge,
diff --git a/tests/test_forcefield.py b/tests/test_forcefield.py
index b7bf3c6f..51ea9059 100644
--- a/tests/test_forcefield.py
+++ b/tests/test_forcefield.py
@@ -33,8 +33,8 @@ def test_run(self) -> None:
             out = StringIO()
             sys.stdout = out
             
-            lpg = LigpargenRunner("EC.pdb", download_dir, xyz=True)
-            lpg.run(test_dir)
+            lpg = LigpargenRunner(os.path.join(test_dir, "EC.pdb"), download_dir, xyz=True)
+            lpg.run()
             self.assertIn(
                 "Input format: .pdb\n"
                 "LigParGen finished succesfully!\n"
@@ -51,7 +51,7 @@ def test_run(self) -> None:
                 self.assertListEqual(xyz, xyz_actual)
             
             lpg = LigpargenRunner("CCOC(=O)O", download_dir, xyz=True)
-            lpg.run(test_dir)
+            lpg.run()
             self.assertIn(
                 "Input format: SMILES\n"
                 "LigParGen finished succesfully!\n"

From fb1f1e125a3baef8087a95083366ae2db65aede7 Mon Sep 17 00:00:00 2001
From: LIANG Bochun <zlatanbochun@outlook.com>
Date: Fri, 2 Feb 2024 22:26:18 +0800
Subject: [PATCH 15/21] Some coding/typo errors

---
 mdgo/forcefield/mdgoligpargen.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/mdgo/forcefield/mdgoligpargen.py b/mdgo/forcefield/mdgoligpargen.py
index 1b156c4f..faaa4bc4 100644
--- a/mdgo/forcefield/mdgoligpargen.py
+++ b/mdgo/forcefield/mdgoligpargen.py
@@ -29,8 +29,9 @@
 from selenium.webdriver.support import expected_conditions as EC
 from selenium.webdriver.support.ui import WebDriverWait
 
-from mdgo.util.dict_utils import lmp_mass_to_name
 from ligpargen.ligpargen import LigParGen
+from mdgo.util.dict_utils import lmp_mass_to_name
+
 
 
 class LigpargenRunner:
@@ -47,7 +48,7 @@ class LigpargenRunner:
         opt: Number of optimizations. Arguement of LIgParGen. Default to 0.
         xyz: Whether to write the structure in the LigParGen generated data file
             as .xyz. Default to False. This is useful because the order and the 
-            name of the atoms could be different from the initial input.)
+            name of the atoms could be different from the initial input.
     
     Examples:
 
@@ -84,7 +85,7 @@ def run(self):
         Write out a LAMMPS data file.
         
         Args:
-            None
+            None.
         """
         if self.structure_format == "SMILES":
             molecule_a = LigParGen(
@@ -141,7 +142,7 @@ class FFcrawler:
         xyz: Whether to write the structure in the LigParGen
             generated data file as .xyz. Default to False. This is useful
             because the order and the name of the atoms could be
-            different from the initial input.)
+            different from the initial input.
         gromacs: Whether to save GROMACS format data files.
             Default to False.
 

From 652e1c55a5932ee46f5026c28473f042ffc49d69 Mon Sep 17 00:00:00 2001
From: Tingzheng Hou <25351437+htz1992213@users.noreply.github.com>
Date: Sun, 4 Feb 2024 10:03:38 +0800
Subject: [PATCH 16/21] black

---
 mdgo/forcefield/mdgoligpargen.py | 18 ++++++++++--------
 tests/test_forcefield.py         | 28 +++++++++-------------------
 2 files changed, 19 insertions(+), 27 deletions(-)

diff --git a/mdgo/forcefield/mdgoligpargen.py b/mdgo/forcefield/mdgoligpargen.py
index faaa4bc4..4360f2ca 100644
--- a/mdgo/forcefield/mdgoligpargen.py
+++ b/mdgo/forcefield/mdgoligpargen.py
@@ -29,33 +29,35 @@
 from selenium.webdriver.support import expected_conditions as EC
 from selenium.webdriver.support.ui import WebDriverWait
 
-from ligpargen.ligpargen import LigParGen
+try:
+    from ligpargen.ligpargen import LigParGen
+except ModuleNotFoundError:
+    pass
 from mdgo.util.dict_utils import lmp_mass_to_name
 
 
-
 class LigpargenRunner:
     """
     LigpargenRunner make use of LigParGen2.1 and BOSS5.0 to generate LAMMPS
     data file and xyz file from structure file.
-    
+
     Args:
         structure_file: The input structure file including path to file.
         write_dir: Directory to write the output file.
-        working_dir: Files generated from BOSS software. Arguement of LigParGen. 
+        working_dir: Files generated from BOSS software. Arguement of LigParGen.
             Default to "boss_files".
         charge: Molecule net charge. Arguement of LigParGen. Default to 0.
         opt: Number of optimizations. Arguement of LIgParGen. Default to 0.
         xyz: Whether to write the structure in the LigParGen generated data file
-            as .xyz. Default to False. This is useful because the order and the 
+            as .xyz. Default to False. This is useful because the order and the
             name of the atoms could be different from the initial input.
-    
+
     Examples:
 
         >>> lpg = LigpargenRunner('sturcture_file', 'path/to/write/output')
         >>> lpg.run()
     """
-    
+
     def __init__(
         self,
         structure_file: str,
@@ -83,7 +85,7 @@ def run(self):
         Run LigParGen2.1 to generate a LAMMPS data file from a structrure file
         (pdb/mol/mol2...) supported by BOSS5.0.
         Write out a LAMMPS data file.
-        
+
         Args:
             None.
         """
diff --git a/tests/test_forcefield.py b/tests/test_forcefield.py
index 51ea9059..10c85ca8 100644
--- a/tests/test_forcefield.py
+++ b/tests/test_forcefield.py
@@ -8,10 +8,7 @@
 import pytest
 
 from mdgo.forcefield.mdgoligpargen import *
-try:
-    from mdgo.forcefield.aqueous import *
-except ModuleNotFoundError:
-    pass
+from mdgo.forcefield.aqueous import *
 
 test_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "test_files")
 
@@ -32,15 +29,13 @@ def test_run(self) -> None:
         try:
             out = StringIO()
             sys.stdout = out
-            
+
             lpg = LigpargenRunner(os.path.join(test_dir, "EC.pdb"), download_dir, xyz=True)
             lpg.run()
             self.assertIn(
-                "Input format: .pdb\n"
-                "LigParGen finished succesfully!\n"
-                ".xyz file saved.",
+                "Input format: .pdb\n" "LigParGen finished succesfully!\n" ".xyz file saved.",
                 out.getvalue(),
-                )
+            )
             self.assertTrue(os.path.exists(os.path.join(download_dir, "EC.lmp")))
             self.assertTrue(os.path.exists(os.path.join(download_dir, "EC.lmp.xyz")))
             with open(os.path.join(download_dir, "EC.lmp")) as f:
@@ -49,15 +44,13 @@ def test_run(self) -> None:
             with open(os.path.join(download_dir, "EC.lmp.xyz")) as f:
                 xyz_actual = f.readlines()
                 self.assertListEqual(xyz, xyz_actual)
-            
+
             lpg = LigpargenRunner("CCOC(=O)O", download_dir, xyz=True)
             lpg.run()
             self.assertIn(
-                "Input format: SMILES\n"
-                "LigParGen finished succesfully!\n"
-                ".xyz file saved.",
+                "Input format: SMILES\n" "LigParGen finished succesfully!\n" ".xyz file saved.",
                 out.getvalue(),
-                )
+            )
             self.assertTrue(os.path.exists(os.path.join(download_dir, "CCOC(=O)O.lmp")))
             self.assertTrue(os.path.exists(os.path.join(download_dir, "CCOC(=O)O.lmp.xyz")))
             with open(os.path.join(download_dir, "CCOC(=O)O.lmp")) as f:
@@ -94,14 +87,11 @@ def test_chrome(self) -> None:
             lpg = FFcrawler(download_dir, xyz=True, gromacs=True)
             lpg.data_from_pdb(os.path.join(test_dir, "EMC.pdb"))
             self.assertIn(
-                "LigParGen server connected.\n"
-                "Structure info uploaded. Rendering force field...\n",
+                "LigParGen server connected.\n" "Structure info uploaded. Rendering force field...\n",
                 out.getvalue(),
             )
             self.assertIn(
-                "Force field file downloaded.\n"
-                ".xyz file saved.\n"
-                "Force field file saved.\n",
+                "Force field file downloaded.\n" ".xyz file saved.\n" "Force field file saved.\n",
                 out.getvalue(),
             )
             self.assertTrue(os.path.exists(os.path.join(download_dir, "EMC.lmp")))

From fa53ce8c8228245e888641aa2299b46cf5bb5499 Mon Sep 17 00:00:00 2001
From: Tingzheng Hou <25351437+htz1992213@users.noreply.github.com>
Date: Sun, 4 Feb 2024 10:22:10 +0800
Subject: [PATCH 17/21] improve file copy step

---
 mdgo/forcefield/mdgoligpargen.py | 22 +++++++---------------
 1 file changed, 7 insertions(+), 15 deletions(-)

diff --git a/mdgo/forcefield/mdgoligpargen.py b/mdgo/forcefield/mdgoligpargen.py
index 4360f2ca..b909b6a3 100644
--- a/mdgo/forcefield/mdgoligpargen.py
+++ b/mdgo/forcefield/mdgoligpargen.py
@@ -43,9 +43,7 @@ class LigpargenRunner:
 
     Args:
         structure_file: The input structure file including path to file.
-        write_dir: Directory to write the output file.
-        working_dir: Files generated from BOSS software. Arguement of LigParGen.
-            Default to "boss_files".
+        work_dir: Directory to write the output file.
         charge: Molecule net charge. Arguement of LigParGen. Default to 0.
         opt: Number of optimizations. Arguement of LIgParGen. Default to 0.
         xyz: Whether to write the structure in the LigParGen generated data file
@@ -61,8 +59,7 @@ class LigpargenRunner:
     def __init__(
         self,
         structure_file: str,
-        write_dir: str,
-        working_dir: str = "boss_files",
+        work_dir: str,
         charge: int = 0,
         opt: int = 0,
         xyz: bool = False,
@@ -74,8 +71,7 @@ def __init__(
             self.structure_format = "SMILES"
         print("Input format:", self.structure_format)
         self.structure = structure_file
-        self.write_dir = write_dir
-        self.work = working_dir
+        self.work_dir = work_dir
         self.charge = charge
         self.opt = opt
         self.xyz = xyz
@@ -95,7 +91,7 @@ def run(self):
                 charge=self.charge,
                 numberOfOptimizations=self.opt,
                 molname=self.name,
-                workdir=self.work,
+                workdir=self.work_dir,
             )
         else:
             molecule_a = LigParGen(
@@ -103,17 +99,13 @@ def run(self):
                 charge=self.charge,
                 numberOfOptimizations=self.opt,
                 molname=self.name,
-                workdir=self.work,
+                workdir=self.work_dir,
             )
         molecule_a.writeAllOuputs()
-        lmp_name = f"{self.name}.lmp"
-        lmp_file = os.path.join(self.write_dir, lmp_name)
-        copy_file = os.path.join(self.work, f"{self.name}.lammps.lmp")
-        shutil.copyfile(copy_file, lmp_file)
         print("LigParGen finished succesfully!")
 
         if self.xyz:
-            lmp_file = os.path.join(self.write_dir, self.name + ".lmp")
+            lmp_file = os.path.join(self.work_dir, self.name + ".lmp")
             data_obj = LammpsData.from_file(lmp_file)
             element_id_dict = lmp_mass_to_name(data_obj.masses)
             coords = data_obj.atoms[["type", "x", "y", "z"]]
@@ -126,7 +118,7 @@ def run(self):
                 line = element_name + " " + " ".join(str(r[loc]) for loc in ["x", "y", "z"])
                 lines.append(line)
 
-            with open(os.path.join(self.write_dir, lmp_name + ".xyz"), "w") as xyz_file:
+            with open(os.path.join(self.work_dir, self.name + ".xyz"), "w") as xyz_file:
                 xyz_file.write("\n".join(lines))
             print(".xyz file saved.")
 

From 6e92ccef051e6c7b5ef6ea8c89941afcf8434691 Mon Sep 17 00:00:00 2001
From: Tingzheng Hou <25351437+htz1992213@users.noreply.github.com>
Date: Sun, 4 Feb 2024 10:46:44 +0800
Subject: [PATCH 18/21] update list literals

---
 mdgo/forcefield/mdgoligpargen.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/mdgo/forcefield/mdgoligpargen.py b/mdgo/forcefield/mdgoligpargen.py
index b909b6a3..be4bc5c2 100644
--- a/mdgo/forcefield/mdgoligpargen.py
+++ b/mdgo/forcefield/mdgoligpargen.py
@@ -109,7 +109,7 @@ def run(self):
             data_obj = LammpsData.from_file(lmp_file)
             element_id_dict = lmp_mass_to_name(data_obj.masses)
             coords = data_obj.atoms[["type", "x", "y", "z"]]
-            lines = list()
+            lines = []
             lines.append(str(len(coords.index)))
             lines.append("")
             for _, r in coords.iterrows():
@@ -282,7 +282,7 @@ def download_data(self, lmp_name: str):
             data_obj = LammpsData.from_file(lmp_file)
             element_id_dict = lmp_mass_to_name(data_obj.masses)
             coords = data_obj.atoms[["type", "x", "y", "z"]]
-            lines = list()
+            lines = []
             lines.append(str(len(coords.index)))
             lines.append("")
             for _, r in coords.iterrows():

From 24026775a0dd94a408754707ad05466e31c77e63 Mon Sep 17 00:00:00 2001
From: Tingzheng Hou <25351437+htz1992213@users.noreply.github.com>
Date: Mon, 5 Feb 2024 12:51:52 +0800
Subject: [PATCH 19/21] move ffcrawler to mdgoligpargen; linting

---
 mdgo/forcefield/crawler.py       | 200 -------------------------------
 mdgo/forcefield/mdgoligpargen.py |  25 ++--
 2 files changed, 9 insertions(+), 216 deletions(-)

diff --git a/mdgo/forcefield/crawler.py b/mdgo/forcefield/crawler.py
index d17aa7f1..27c5c38c 100644
--- a/mdgo/forcefield/crawler.py
+++ b/mdgo/forcefield/crawler.py
@@ -5,204 +5,4 @@
 This module was used to implement a core class FFcrawler, and has been moved to ligpargen module.
 """
 
-from __future__ import annotations
 
-import os
-import shutil
-import time
-
-from pymatgen.io.lammps.data import LammpsData
-from selenium import webdriver
-from selenium.common.exceptions import TimeoutException, WebDriverException
-from selenium.webdriver.common.by import By
-from selenium.webdriver.support import expected_conditions as EC
-from selenium.webdriver.support.ui import WebDriverWait
-
-from mdgo.util.dict_utils import lmp_mass_to_name
-
-
-class FFcrawler:
-    """
-    Web scrapper that can automatically upload structure to the LigParGen
-    server and download LAMMPS/GROMACS data file.
-
-    Args:
-        write_dir: Directory for writing output.
-        chromedriver_dir: Directory to the ChromeDriver executable.
-        headless: Whether to run Chrome in headless (silent) mode.
-            Default to True.
-        xyz: Whether to write the structure in the LigParGen
-            generated data file as .xyz. Default to False. This is useful
-            because the order and the name of the atoms could be
-            different from the initial input.)
-        gromacs: Whether to save GROMACS format data files.
-            Default to False.
-
-    Examples:
-        >>> lpg = FFcrawler('/path/to/work/dir', '/path/to/chromedriver')
-        >>> lpg.data_from_pdb("/path/to/pdb")
-    """
-
-    def __init__(
-        self,
-        write_dir: str,
-        chromedriver_dir: str | None = None,
-        headless: bool = True,
-        xyz: bool = False,
-        gromacs: bool = False,
-    ):
-        """Base constructor."""
-        self.write_dir = write_dir
-        self.xyz = xyz
-        self.gromacs = gromacs
-        self.preferences = {
-            "download.default_directory": write_dir,
-            "safebrowsing.enabled": "false",
-            "profile.managed_default_content_settings.images": 2,
-        }
-        self.options = webdriver.ChromeOptions()
-        self.server = webdriver.ChromeService(chromedriver_dir)
-        self.options.add_argument(
-            'user-agent="Mozilla/5.0 '
-            "(Macintosh; Intel Mac OS X 10_14_6) "
-            "AppleWebKit/537.36 (KHTML, like Gecko) "
-            'Chrome/88.0.4324.146 Safari/537.36"'
-        )
-        self.options.add_argument("--window-size=1920,1080")
-        self.options.add_argument("ignore-certificate-errors")
-        if headless:
-            self.options.add_argument("--headless")
-        self.options.add_experimental_option("prefs", self.preferences)
-        self.options.add_experimental_option("excludeSwitches", ["enable-automation"])
-        if chromedriver_dir is None:
-            self.web = webdriver.Chrome(options=self.options)
-        else:
-            self.web = webdriver.Chrome(service=self.server, options=self.options)
-        self.wait = WebDriverWait(self.web, 10)
-        self.web.get("http://traken.chem.yale.edu/ligpargen/")
-        time.sleep(1)
-        print("LigParGen server connected.")
-
-    def quit(self):
-        """Method for quiting ChromeDriver."""
-        self.web.quit()
-
-    def data_from_pdb(self, pdb_dir: str):
-        """
-        Use the LigParGen server to generate a LAMMPS data file from a pdb file.
-        Write out a LAMMPS data file.
-
-        Args:
-            pdb_dir: The path to the input pdb structure file.
-        """
-        self.web.get("http://traken.chem.yale.edu/ligpargen/")
-        upload_xpath = '//*[@id="exampleMOLFile"]'
-        time.sleep(1)
-        self.wait.until(EC.presence_of_element_located((By.XPATH, upload_xpath)))
-        upload = self.web.find_element(By.XPATH, upload_xpath)
-        try:
-            upload.send_keys(pdb_dir)
-            submit = self.web.find_element(By.XPATH, "/html/body/div[2]/div/div[2]/form/button[1]")
-            submit.click()
-            pdb_filename = os.path.basename(pdb_dir)
-            self.download_data(os.path.splitext(pdb_filename)[0] + ".lmp")
-        except TimeoutException:
-            print("Timeout! Web server no response for 10s, file download failed!")
-        except WebDriverException as e:
-            print(e)
-        finally:
-            self.quit()
-
-    def data_from_smiles(self, smiles_code):
-        """
-        Use the LigParGen server to generate a LAMMPS data file from a SMILES code.
-        Write out a LAMMPS data file.
-
-        Args:
-            smiles_code: The SMILES code for the LigParGen input.
-        """
-        self.web.get("http://traken.chem.yale.edu/ligpargen/")
-        time.sleep(1)
-        smile = self.web.find_element(By.XPATH, '//*[@id="smiles"]')
-        smile.send_keys(smiles_code)
-        submit = self.web.find_element(By.XPATH, "/html/body/div[2]/div/div[2]/form/button[1]")
-        submit.click()
-        try:
-            self.download_data(smiles_code + ".lmp")
-        except TimeoutException:
-            print("Timeout! Web server no response for 10s, file download failed!")
-        finally:
-            self.quit()
-
-    def download_data(self, lmp_name: str):
-        """
-        Helper function that download and write out the LAMMPS data file.
-
-        Args:
-            lmp_name: Name of the LAMMPS data file.
-        """
-        print("Structure info uploaded. Rendering force field...")
-        lmp_xpath = "/html/body/div[2]/div[2]/div[1]/div/div[14]/form/input[1]"
-        self.wait.until(EC.presence_of_element_located((By.XPATH, lmp_xpath)))
-        jmol = self.web.find_element(By.XPATH, "/html/body/div[2]/div[2]/div[2]")
-        self.web.execute_script("arguments[0].remove();", jmol)
-        self.wait.until(EC.element_to_be_clickable((By.XPATH, lmp_xpath)))
-        data_lmp = self.web.find_element(By.XPATH, lmp_xpath)
-        num_file = len([f for f in os.listdir(self.write_dir) if os.path.splitext(f)[1] == ".lmp"]) + 1
-        data_lmp.click()
-        while True:
-            files = sorted(
-                [
-                    os.path.join(self.write_dir, f)
-                    for f in os.listdir(self.write_dir)
-                    if os.path.splitext(f)[1] == ".lmp"
-                ],
-                key=os.path.getmtime,
-            )
-            # wait for file to finish download
-            if len(files) < num_file:
-                time.sleep(1)
-                print("waiting for download to be initiated")
-            else:
-                newest = files[-1]
-                if ".crdownload" in newest:
-                    time.sleep(1)
-                    print("waiting for download to complete")
-                else:
-                    break
-        print("Force field file downloaded.")
-        lmp_file = newest
-        if self.xyz:
-            data_obj = LammpsData.from_file(lmp_file)
-            element_id_dict = lmp_mass_to_name(data_obj.masses)
-            coords = data_obj.atoms[["type", "x", "y", "z"]]
-            lines = []
-            lines.append(str(len(coords.index)))
-            lines.append("")
-            for _, r in coords.iterrows():
-                element_name = element_id_dict.get(int(r["type"]))
-                assert element_name is not None
-                line = element_name + " " + " ".join(str(r[loc]) for loc in ["x", "y", "z"])
-                lines.append(line)
-
-            with open(os.path.join(self.write_dir, lmp_name + ".xyz"), "w") as xyz_file:
-                xyz_file.write("\n".join(lines))
-            print(".xyz file saved.")
-        if self.gromacs:
-            data_gro = self.web.find_element(By.XPATH, "/html/body/div[2]/div[2]/div[1]/div/div[8]/form/input[1]")
-            data_itp = self.web.find_element(By.XPATH, "/html/body/div[2]/div[2]/div[1]/div/div[9]/form/input[1]")
-            data_gro.click()
-            data_itp.click()
-            time.sleep(1)
-            gro_file = max(
-                [self.write_dir + "/" + f for f in os.listdir(self.write_dir) if os.path.splitext(f)[1] == ".gro"],
-                key=os.path.getctime,
-            )
-            itp_file = max(
-                [self.write_dir + "/" + f for f in os.listdir(self.write_dir) if os.path.splitext(f)[1] == ".itp"],
-                key=os.path.getctime,
-            )
-            shutil.move(gro_file, os.path.join(self.write_dir, lmp_name[:-4] + ".gro"))
-            shutil.move(itp_file, os.path.join(self.write_dir, lmp_name[:-4] + ".itp"))
-        shutil.move(lmp_file, os.path.join(self.write_dir, lmp_name))
-        print("Force field file saved.")
diff --git a/mdgo/forcefield/mdgoligpargen.py b/mdgo/forcefield/mdgoligpargen.py
index be4bc5c2..1622a698 100644
--- a/mdgo/forcefield/mdgoligpargen.py
+++ b/mdgo/forcefield/mdgoligpargen.py
@@ -1,4 +1,3 @@
-# coding: utf-8
 # Copyright (c) Tingzheng Hou.
 # Distributed under the terms of the MIT License.
 
@@ -13,27 +12,25 @@
     matches your Chrome version via https://chromedriver.chromium.org/downloads
 """
 
+from __future__ import annotations
+
 import os
 import shutil
 import time
-from typing import Optional
-
 
 from pymatgen.io.lammps.data import LammpsData
 from selenium import webdriver
-from selenium.common.exceptions import (
-    TimeoutException,
-    WebDriverException,
-)
+from selenium.common.exceptions import TimeoutException, WebDriverException
 from selenium.webdriver.common.by import By
 from selenium.webdriver.support import expected_conditions as EC
 from selenium.webdriver.support.ui import WebDriverWait
 
+from mdgo.util.dict_utils import lmp_mass_to_name
+
 try:
     from ligpargen.ligpargen import LigParGen
 except ModuleNotFoundError:
     pass
-from mdgo.util.dict_utils import lmp_mass_to_name
 
 
 class LigpargenRunner:
@@ -50,8 +47,8 @@ class LigpargenRunner:
             as .xyz. Default to False. This is useful because the order and the
             name of the atoms could be different from the initial input.
 
-    Examples:
 
+    Examples:
         >>> lpg = LigpargenRunner('sturcture_file', 'path/to/write/output')
         >>> lpg.run()
     """
@@ -136,12 +133,11 @@ class FFcrawler:
         xyz: Whether to write the structure in the LigParGen
             generated data file as .xyz. Default to False. This is useful
             because the order and the name of the atoms could be
-            different from the initial input.
+            different from the initial input.)
         gromacs: Whether to save GROMACS format data files.
             Default to False.
 
     Examples:
-
         >>> lpg = FFcrawler('/path/to/work/dir', '/path/to/chromedriver')
         >>> lpg.data_from_pdb("/path/to/pdb")
     """
@@ -149,7 +145,7 @@ class FFcrawler:
     def __init__(
         self,
         write_dir: str,
-        chromedriver_dir: Optional[str] = None,
+        chromedriver_dir: str | None = None,
         headless: bool = True,
         xyz: bool = False,
         gromacs: bool = False,
@@ -187,10 +183,7 @@ def __init__(
         print("LigParGen server connected.")
 
     def quit(self):
-        """
-        Method for quiting ChromeDriver.
-
-        """
+        """Method for quiting ChromeDriver."""
         self.web.quit()
 
     def data_from_pdb(self, pdb_dir: str):

From 74587f9adf20f843e57082f2255a6012fc4eaedf Mon Sep 17 00:00:00 2001
From: Tingzheng Hou <25351437+htz1992213@users.noreply.github.com>
Date: Mon, 5 Feb 2024 12:57:44 +0800
Subject: [PATCH 20/21] lint fixes

---
 mdgo/forcefield/__init__.py |  2 +-
 mdgo/forcefield/crawler.py  |  4 +---
 tests/test_forcefield.py    | 29 ++++++++++++-----------------
 3 files changed, 14 insertions(+), 21 deletions(-)

diff --git a/mdgo/forcefield/__init__.py b/mdgo/forcefield/__init__.py
index b9dd20d3..b6ee340f 100644
--- a/mdgo/forcefield/__init__.py
+++ b/mdgo/forcefield/__init__.py
@@ -18,5 +18,5 @@
 from .aqueous import Aqueous, IonLJData
 from .charge import ChargeWriter
 from .maestro import MaestroRunner
+from .mdgoligpargen import FFcrawler, LigpargenRunner
 from .pubchem import PubChemRunner
-from .mdgoligpargen import LigpargenRunner, FFcrawler
diff --git a/mdgo/forcefield/crawler.py b/mdgo/forcefield/crawler.py
index 27c5c38c..6e94f8cd 100644
--- a/mdgo/forcefield/crawler.py
+++ b/mdgo/forcefield/crawler.py
@@ -1,8 +1,6 @@
 # Copyright (c) Tingzheng Hou.
 # Distributed under the terms of the MIT License.
 
-"""
-This module was used to implement a core class FFcrawler, and has been moved to ligpargen module.
-"""
+"""This module was used to implement a core class FFcrawler, and has been moved to ligpargen module."""
 
 
diff --git a/tests/test_forcefield.py b/tests/test_forcefield.py
index e3fda47f..ce9c9411 100644
--- a/tests/test_forcefield.py
+++ b/tests/test_forcefield.py
@@ -9,10 +9,11 @@
 
 import numpy as np
 import pytest
+from numpy.testing import assert_equal
 from pymatgen.io.lammps.data import LammpsData
 
 from mdgo.forcefield.aqueous import Aqueous, Ion
-from mdgo.forcefield.crawler import FFcrawler
+from mdgo.forcefield.mdgoligpargen import FFcrawler, LigpargenRunner
 
 test_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "test_files")
 
@@ -36,33 +37,27 @@ def test_run(self) -> None:
 
             lpg = LigpargenRunner(os.path.join(test_dir, "EC.pdb"), download_dir, xyz=True)
             lpg.run()
-            self.assertIn(
-                "Input format: .pdb\n" "LigParGen finished succesfully!\n" ".xyz file saved.",
-                out.getvalue(),
-            )
-            self.assertTrue(os.path.exists(os.path.join(download_dir, "EC.lmp")))
-            self.assertTrue(os.path.exists(os.path.join(download_dir, "EC.lmp.xyz")))
+            assert "Input format: .pdb\nLigParGen finished succesfully!\n.xyz file saved." in out.getvalue()
+            assert os.path.exists(os.path.join(download_dir, "EC.lmp"))
+            assert os.path.exists(os.path.join(download_dir, "EC.lmp.xyz"))
             with open(os.path.join(download_dir, "EC.lmp")) as f:
                 pdf_actual = f.readlines()
-                self.assertListEqual(pdf, pdf_actual)
+                assert_equal(pdf, pdf_actual)
             with open(os.path.join(download_dir, "EC.lmp.xyz")) as f:
                 xyz_actual = f.readlines()
-                self.assertListEqual(xyz, xyz_actual)
+                assert_equal(xyz, xyz_actual)
 
             lpg = LigpargenRunner("CCOC(=O)O", download_dir, xyz=True)
             lpg.run()
-            self.assertIn(
-                "Input format: SMILES\n" "LigParGen finished succesfully!\n" ".xyz file saved.",
-                out.getvalue(),
-            )
-            self.assertTrue(os.path.exists(os.path.join(download_dir, "CCOC(=O)O.lmp")))
-            self.assertTrue(os.path.exists(os.path.join(download_dir, "CCOC(=O)O.lmp.xyz")))
+            assert "Input format: SMILES\nLigParGen finished succesfully!\n.xyz file saved." in out.getvalue()
+            assert os.path.exists(os.path.join(download_dir, "CCOC(=O)O.lmp"))
+            assert os.path.exists(os.path.join(download_dir, "CCOC(=O)O.lmp.xyz"))
             with open(os.path.join(download_dir, "CCOC(=O)O.lmp")) as f:
                 smiles_actual = f.readlines()
-                self.assertListEqual(smiles, smiles_actual)
+                assert_equal(smiles, smiles_actual)
             with open(os.path.join(download_dir, "CCOC(=O)O.lmp.xyz")) as f:
                 xyz_actual = f.readlines()
-                self.assertListEqual(xyz_smiles, xyz_actual)
+                assert_equal(xyz_smiles, xyz_actual)
 
         finally:
             sys.stdout = saved_stdout

From 3f0e83f362f13874f96b80a696f416b7d27af79b Mon Sep 17 00:00:00 2001
From: Tingzheng Hou <25351437+htz1992213@users.noreply.github.com>
Date: Mon, 5 Feb 2024 12:59:49 +0800
Subject: [PATCH 21/21] ruff format fix

---
 mdgo/forcefield/crawler.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/mdgo/forcefield/crawler.py b/mdgo/forcefield/crawler.py
index 6e94f8cd..d746fa34 100644
--- a/mdgo/forcefield/crawler.py
+++ b/mdgo/forcefield/crawler.py
@@ -2,5 +2,3 @@
 # Distributed under the terms of the MIT License.
 
 """This module was used to implement a core class FFcrawler, and has been moved to ligpargen module."""
-
-