Merge pull request #23 from htz1992213/main

Fix residence time save curve path; fix ligpargen url; fix connection not private

CHANGES.rst

@@ -1,6 +1,12 @@
 Change log
 ==========
 
+v0.3.1
+------
+
+v0.3.0
+------
+
 v0.2.4
 ------
 

mdgo/__init__.py

@@ -9,4 +9,4 @@
 __email__ = "tingzheng_hou@berkeley.edu"
 __maintainer__ = "Tingzheng Hou"
 __maintainer_email__ = "tingzheng_hou@berkeley.edu"
-__version__ = "0.3.0"
+__version__ = "0.3.1"

mdgo/core/__init__.py

@@ -8,10 +8,10 @@
 """
 
 __author__ = "Tingzheng Hou"
-__version__ = "0.3.0"
+__version__ = "0.3.1"
 __maintainer__ = "Tingzheng Hou"
 __email__ = "tingzheng_hou@berkeley.edu"
-__date__ = "Jul 19, 2021"
+__date__ = "Dec 19, 2023"
 
 
 from .analysis import MdRun

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

mdgo/forcefield/crawler.py

@@ -81,6 +81,7 @@ def __init__(
             '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)
@@ -90,7 +91,7 @@ def __init__(
         else:
             self.web = webdriver.Chrome(service=self.server, options=self.options)
         self.wait = WebDriverWait(self.web, 10)
-        self.web.get("http://zarbi.chem.yale.edu/ligpargen/")
+        self.web.get("http://traken.chem.yale.edu/ligpargen/")
         time.sleep(1)
         print("LigParGen server connected.")
 
@@ -109,9 +110,11 @@ def data_from_pdb(self, pdb_dir: str):
         Args:
             pdb_dir: The path to the input pdb structure file.
         """
-        self.web.get("http://zarbi.chem.yale.edu/ligpargen/")
+        self.web.get("http://traken.chem.yale.edu/ligpargen/")
+        upload_xpath = '//*[@id="exampleMOLFile"]'
         time.sleep(1)
-        upload = self.web.find_element(By.XPATH, '//*[@id="exampleMOLFile"]')
+        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]")
@@ -133,7 +136,7 @@ def data_from_smiles(self, smiles_code):
         Args:
             smiles_code: The SMILES code for the LigParGen input.
         """
-        self.web.get("http://zarbi.chem.yale.edu/ligpargen/")
+        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)
@@ -155,9 +158,9 @@ def download_data(self, lmp_name: str):
         """
         print("Structure info uploaded. Rendering force field...")
         lmp_xpath = "/html/body/div[2]/div[2]/div[1]/div/div[14]/form/input[1]"
-        jmol_xpath = self.web.find_element(By.XPATH, "/html/body/div[2]/div[2]/div[2]")
         self.wait.until(EC.presence_of_element_located((By.XPATH, lmp_xpath)))
-        self.web.execute_script("arguments[0].remove();", jmol_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

mdgo/residence_time.py

@@ -5,6 +5,7 @@
 """
 This module calculates species correlation lifetime (residence time).
 """
+import os
 from typing import List, Dict, Union, Tuple
 
 import numpy as np
@@ -171,6 +172,7 @@ def fit_residence_time(
     acf_avg_dict: Dict[str, np.ndarray],
     cutoff_time: int,
     time_step: float,
+    save_curve: Union[str, bool] = False,
 ) -> Dict[str, np.floating]:
     """
     Use the ACF to fit the residence time (Exponential decay constant).
@@ -181,6 +183,8 @@ def fit_residence_time(
         acf_avg_dict: A dict containing the ACFs of the species.
         cutoff_time: Fitting cutoff time.
         time_step: The time step between each frame, in ps.
+        save_curve: Whether to save the curve as a csv file for post-processing.
+                Default to False.
 
     Returns:
         A dict containing residence time of each species
@@ -217,7 +221,13 @@ def fit_residence_time(
                 fitted_y,
             )
         )
-        np.savetxt(f"/Users/th/Downloads/decay{i}.csv", save_decay.T, delimiter=",")
+        if save_curve:
+            if save_curve is True:
+                np.savetxt(f"decay{i}.csv", save_decay.T, delimiter=",")
+            elif os.path.exists(str(save_curve)):
+                np.savetxt(str(save_curve) + f"decay{i}.csv", save_decay.T, delimiter=",")
+            else:
+                raise ValueError("Please specify a bool or a path in string.")
         plt.plot(
             fitted_x,
             fitted_y,

pyproject.toml

@@ -7,7 +7,7 @@ build-backend = "setuptools.build_meta"
 
 [tool.black]
 line-length = 120
-target-version = ['py38']
+target-version = ['py310']
 include = '\.pyi?$'
 exclude = '''
 

requirements.txt

@@ -4,7 +4,7 @@ numpy>=1.16.0
 pandas
 monty
 pubchempy
-pymatgen>=2022.7.8
+pymatgen
 scipy
 selenium
 setuptools

setup.py

@@ -33,7 +33,7 @@
 if __name__ == "__main__":
     setup(
         name="mdgo",
-        version="0.3.0",
+        version="0.3.1",
         description="A codebase for MD simulation setup and results analysis.",
         long_description=readme,
         long_description_content_type="text/markdown",