Merge branch 'autosolvate_merge' of github.com:Liu-group/AutoSolvate …

…into autosolvate_merge
Liu-group · Nov 22, 2024 · f4fc325 · f4fc325
2 parents db8f295 + 2dbaf12
commit f4fc325
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Showing 75 changed files with 509 additions and 139 deletions.
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -1,4 +1,9 @@
 version: 2
-
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "mambaforge-22.9"
 conda:
   environment: devtools/conda-envs/test_env.yaml
+sphinx:
+  configuration: docs/conf.py
diff --git a/autosolvate/autosolvate.py b/autosolvate/autosolvate.py
@@ -165,6 +165,18 @@ def get_solvent(self, solvent:str, slv_xyz:str = "", solvent_frcmod:str = "", so
         return self_solvent
 
     def build(self):
+        """
+        Build the solvated system
+
+        Parameters
+        ----------
+        None
+
+        Returns
+        -------
+        None
+
+        """
         if self.charge_method == "resp":
             build_resp_terachem(self.solute, folder = self.folder)
         else:

diff --git a/autosolvate/multicomponent.py b/autosolvate/multicomponent.py
@@ -91,6 +91,46 @@ def build(self):
 
 
 class MulticomponentSolventBoxBuilder():
+    """
+    Build a solvent box for a single molecule complex as the solute and single solvent
+
+    Parameters
+    ----------
+    xyzfile : str
+        structure file of the molecular complex, can be any type within ["xyz", "pdb", "mol2"]. "prep", "lib", "off" are not supported for molecular complex.
+    slu_charge : int or dict, Optional, default: 0
+        Charge of the solute. if complex has charged fragments, provide a dictionary with the three-letter name of the residue as the key and the corresponding charge as the value. If not given, all fragment will be considered as neutral.
+    slu_spinmult : int or dict, Optional, default: 1
+        Spin multiplicity of the solute. if complex has non-singlet fragments, provide a dictionary with the three-letter name of the residue as the key and the corresponding charge as the value. If not given, all fragment will be considered as singlet.
+    charge_method : str, Optional, default: "resp"
+        name of charge fitting method (bcc, resp)
+    slu_count : int, Optional, default: 1
+        number of the solute in the system. Not recommanded to set this parameter. Be cautious about this as the solute may have more than 1 fragments.
+    solvent : str, Optional, default: "water"
+        name of the solvent. Predefined solvents include ["water", "methanol", "chloroform", "nma"].
+    solvent_frcmod : str, Optional, default: ""
+        path to the frcmod file of the solvent. Required when user have the solvent forcefield parameters prepared.
+    solvent_off : str, Optional, default: ""
+        path to the off file of the solvent. Required when user have the solvent forcefield parameters prepared.
+    solvent_box_name : str, Optional, default: "SLVBOX"
+        name of the solvent box
+    slv_generate : bool, Optional, default: False
+        whether to generate the solvent forcefield parameters with GAFF. If True, the solvent forcefield will be generated with GAFF, where 'slv_xyz' parameter will be needed. If False, the solvent will be treated as a predefined solvent in AMBER or user should provide the frcmod & prep files.
+    slv_xyz : str, Optional, default: ""
+        path to the xyz file of the solvent. Required when user want to generate the solvent forcefield parameters with GAFF.
+    slv_count : int, Optional, default: 210*8
+        number of the solvent in the system.
+    cube_size : int, Optional, default: 54
+        size of solvent cube in angstroms
+    closeness : float, Optional, default: 0.8
+        Solute-solvent closeness setting, corresponding to the tolerance parameter in packmol in Å,
+    folder : str, Optional, default: current working directory
+        the directory where the files are generated
+    outputFile : str, Optional, default: ""
+        prefix of the output .pdb, .inpcrd and .prmtop files
+    kwargs : dict
+        Other arguments that need to be included in the solute. Remained for future development.    
+    """
     def __init__(self, 
                  xyzfile:str, slu_charge=0, slu_spinmult=1, charge_method="resp", slu_count = 1,
                  solvent = "water", solvent_frcmod = "", solvent_off = "", solvent_box_name = "SLVBOX",
@@ -158,6 +198,18 @@ def get_solvent(self, solvent:str, slv_xyz:str = "", solvent_frcmod:str = "", so
         return self_solvent
 
     def build(self):
+        """
+        Build the solvated system with molecule complex as the solute and single solvent 
+
+        Parameters
+        ----------
+        None
+
+        Returns
+        -------
+        None
+        
+        """
         for m in self.solute.newmolecules:
             if self.charge_method == "resp":
                 build_resp_terachem(m, folder = self.folder)
@@ -222,7 +274,7 @@ def __init__(self, folder = WORKING_DIR, cube_size = 54, closeness = 2.0, charge
 
     def add_complex_solute(self, xyzfile:str, fragment_charge = 0, fragment_spinmult = 1, number = 1, **kwargs):
         """
-        add a molecular complex as the solute 
+        add a molecular complex as the solute. e.g. a electron transfer donor-acceptor pair
 
         Parameters
         ----------
@@ -233,7 +285,7 @@ def add_complex_solute(self, xyzfile:str, fragment_charge = 0, fragment_spinmult
         fragment_spinmult : dict | array_like, Optional, default: 1
             Multiplicity for each fragment. A dictionary with the three-letter name of the residue as the key and the corresponding charge as the value. If not given, all fragment will be considered as singlet.
         number : int, Optional, default: 1
-            number of the solute in the system. Be cautious about this as the solute may have more than 1 fragments.
+            number of the solute in the system. Not recommanded to set this parameter. Be cautious about this as the solute may have more than 1 fragments.
         **kwargs : dict
             Other arguments that need to be included in the solute. Remained for future development.
         """
@@ -267,10 +319,10 @@ def add_solute(self, xyzfile:str, name="", residue_name="SLU", charge=0, spinmul
             additional files needed for the solute, including "mol2", "frcmod", "lib", "prep", and "off". Will support "itp", "top" in the future.
             If the user want to skip the antechamber and leap steps, the user need to provide the "mol2" and "frcmod" files by adding the following arguments:
             
-        mol2 : str  
-            the path of the mol2 file of the solute
-        frcmod : str
-            the path of the frcmod file of the solute
+            mol2 : str  
+                the path of the mol2 file of the solute
+            frcmod : str
+                the path of the frcmod file of the solute
         """
 
         if ("mol2" in kwargs and os.path.isfile(kwargs["mol2"])) and \
@@ -314,7 +366,6 @@ def get_solvent_type(self, xyzfile = "", name = "", **kwargs):
         return solvent_type
 
     def add_solvent(self, xyzfile:str = "", name="", residue_name="SLV", charge=0, spinmult=1, number = 210*8, **kwargs):
-
         """
         add a type of solvent
 
@@ -335,6 +386,7 @@ def add_solvent(self, xyzfile:str = "", name="", residue_name="SLV", charge=0, s
         **kwargs : dict
             additional files needed for the solvent, including "mol2", "frcmod", "lib", "prep", will support "itp", "top" in the future.
             If the user want to skip the antechamber and leap steps, the user need to provide the ["mol2" or "prep"] and "frcmod" files by adding the following arguments:
+            
             mol2 : str  
                 the path of the mol2 file of the solvent
             frcmod : str
@@ -386,6 +438,18 @@ def add_solvent(self, xyzfile:str = "", name="", residue_name="SLV", charge=0, s
         self.solvents.append(self_solvent)
 
     def build(self):
+        """
+        Start to build the mixed solvent box. No parameters are needed.
+
+        Parameters
+        ----------
+        None
+
+        Returns
+        -------
+        None
+
+        """
         if not self.systemprefix:
             system_name = "-".join([m.name for m in self.solutes] + [m.name for m in self.solvents])
         else:
@@ -402,6 +466,16 @@ def build(self):
             docker.run(system)
 
 def startmulticomponent_fromdata(data:dict):
+    """
+    Start the multicomponent solvation process from a python dictionary.
+
+    Parameters
+    ----------
+    data : dict
+        dictionary containing the input parameters. Usually generated from a json file.
+    """
+
+
     data["folder"] = WORKING_DIR
     signature = inspect.signature(MixtureBuilder.__init__)
     function_params = signature.parameters
@@ -431,14 +505,22 @@ def startmulticomponent_fromdata(data:dict):
     builder.build()
 
 def startmulticomponent_fromfile(file:str):
+    """
+    Start the multicomponent solvation process from a json file.
+
+    Parameters
+    ----------
+    file : str
+        json file containing the input parameters. 
+    """
     with open(file, "r") as f:
         data = json.load(f)
     startmulticomponent_fromdata(data)
 
 def create_parser_multicomponent():
     parser = argparse.ArgumentParser(
         description='Add solvent box to a given solute and generate related force field parameters.',
-        epilog="suggest usage: autosolvate multicomponent -f input.json \nif an input file is provided, all command line options will be ignored. \nIf using command line as the traditional way, it will only generate a single solute with single solvent. \nThis is a legacy feature, designed solely for the compatibility with the older version. It is not recommended for further use."
+        epilog="suggest usage: autosolvate multicomponent -f <JSON path> \nif an input file is provided, all command line options will be ignored. \nIf using command line as the traditional way, it will only generate a single solute with single solvent. \nThis is a legacy feature, designed solely for the compatibility with the older version. It is not recommended for further use."
     )
 
     parser.add_argument('-f', '--file',            type=str,  help='json file containing the input parameters. Will ignore all other options if provided. Required when using multiple solvents')
@@ -460,9 +542,10 @@ def startmulticomponent(args):
     r"""
     Wrap function that parses command line options for autosolvate multicomponent module,
     generate solvent box and related force field parameters.
+    suggested usage: autosolvate multicomponent -f <JSON path>
     
     Command Line Options
-    ----------
+    --------------------
         -f, --file 
             json file containing the input parameters, Required when using multiple solvents. Will ignore all other options if provided.
         -m, --main  

diff --git a/docs/_build/doctrees/advancedTutorial.doctree b/docs/_build/doctrees/advancedTutorial.doctree
diff --git a/docs/_build/doctrees/api.doctree b/docs/_build/doctrees/api.doctree
diff --git a/docs/_build/doctrees/autosummary/autosolvate.autosolvate.AmberParamsBuilder.doctree b/docs/_build/doctrees/autosummary/autosolvate.autosolvate.AmberParamsBuilder.doctree
diff --git a/docs/_build/doctrees/autosummary/autosolvate.autosolvate.solventBoxBuilder.doctree b/docs/_build/doctrees/autosummary/autosolvate.autosolvate.solventBoxBuilder.doctree
diff --git a/docs/_build/doctrees/autosummary/autosolvate.autosolvate.startboxgen.doctree b/docs/_build/doctrees/autosummary/autosolvate.autosolvate.startboxgen.doctree
diff --git a/docs/_build/doctrees/autosummary/autosolvate.clustergen.clustergen.doctree b/docs/_build/doctrees/autosummary/autosolvate.clustergen.clustergen.doctree
diff --git a/docs/_build/doctrees/autosummary/autosolvate.clustergen.startclustergen.doctree b/docs/_build/doctrees/autosummary/autosolvate.clustergen.startclustergen.doctree
diff --git a/docs/_build/doctrees/autosummary/autosolvate.generatetrajs.runMM.doctree b/docs/_build/doctrees/autosummary/autosolvate.generatetrajs.runMM.doctree
diff --git a/docs/_build/doctrees/autosummary/autosolvate.generatetrajs.runQMMM.doctree b/docs/_build/doctrees/autosummary/autosolvate.generatetrajs.runQMMM.doctree
diff --git a/docs/_build/doctrees/autosummary/autosolvate.generatetrajs.startmd.doctree b/docs/_build/doctrees/autosummary/autosolvate.generatetrajs.startmd.doctree
diff --git a/docs/_build/doctrees/autosummary/autosolvate.generatetrajs.writeMMNPTInput.doctree b/docs/_build/doctrees/autosummary/autosolvate.generatetrajs.writeMMNPTInput.doctree
diff --git a/docs/_build/doctrees/autosummary/autosolvate.generatetrajs.writeMMNVEInput.doctree b/docs/_build/doctrees/autosummary/autosolvate.generatetrajs.writeMMNVEInput.doctree
diff --git a/docs/_build/doctrees/autosummary/autosolvate.generatetrajs.writeMMheatInput.doctree b/docs/_build/doctrees/autosummary/autosolvate.generatetrajs.writeMMheatInput.doctree
diff --git a/docs/_build/doctrees/autosummary/autosolvate.generatetrajs.writeMMminInput.doctree b/docs/_build/doctrees/autosummary/autosolvate.generatetrajs.writeMMminInput.doctree
diff --git a/docs/_build/doctrees/autosummary/autosolvate.generatetrajs.writeQMMMInput.doctree b/docs/_build/doctrees/autosummary/autosolvate.generatetrajs.writeQMMMInput.doctree
diff --git a/docs/_build/doctrees/autosummary/autosolvate.generatetrajs.writeQMMMMinInput.doctree b/docs/_build/doctrees/autosummary/autosolvate.generatetrajs.writeQMMMMinInput.doctree
diff --git a/docs/_build/doctrees/autosummary/autosolvate.generatetrajs.writeQMMMTemplate.doctree b/docs/_build/doctrees/autosummary/autosolvate.generatetrajs.writeQMMMTemplate.doctree
diff --git a/docs/_build/doctrees/autosummary/autosolvate.multicomponent.MixtureBuilder.doctree b/docs/_build/doctrees/autosummary/autosolvate.multicomponent.MixtureBuilder.doctree
diff --git a/...build/doctrees/autosummary/autosolvate.multicomponent.MulticomponentParamsBuilder.doctree b/...build/doctrees/autosummary/autosolvate.multicomponent.MulticomponentParamsBuilder.doctree
diff --git a/...d/doctrees/autosummary/autosolvate.multicomponent.MulticomponentSolventBoxBuilder.doctree b/...d/doctrees/autosummary/autosolvate.multicomponent.MulticomponentSolventBoxBuilder.doctree
diff --git a/docs/_build/doctrees/autosummary/autosolvate.multicomponent.startmulticomponent.doctree b/docs/_build/doctrees/autosummary/autosolvate.multicomponent.startmulticomponent.doctree
diff --git a/...uild/doctrees/autosummary/autosolvate.multicomponent.startmulticomponent_fromfile.doctree b/...uild/doctrees/autosummary/autosolvate.multicomponent.startmulticomponent_fromfile.doctree
diff --git a/docs/_build/doctrees/citation.doctree b/docs/_build/doctrees/citation.doctree
diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/doctrees/index.doctree b/docs/_build/doctrees/index.doctree
diff --git a/docs/_build/doctrees/installation.doctree b/docs/_build/doctrees/installation.doctree
diff --git a/docs/_build/doctrees/tutorial.doctree b/docs/_build/doctrees/tutorial.doctree
diff --git a/docs/_build/doctrees/tutorialGUI.doctree b/docs/_build/doctrees/tutorialGUI.doctree
diff --git a/docs/_build/doctrees/tutorialMulticomponent.doctree b/docs/_build/doctrees/tutorialMulticomponent.doctree
diff --git a/docs/_build/doctrees/tutorial_for_metalcomplexes.doctree b/docs/_build/doctrees/tutorial_for_metalcomplexes.doctree
diff --git a/docs/_build/html/.buildinfo b/docs/_build/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 6dfb2408176e023e674008b70b83f725
+config: ae8c388f0c7dd766ea933122172e040b
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_build/html/_modules/autosolvate/autosolvate.html b/docs/_build/html/_modules/autosolvate/autosolvate.html
@@ -151,7 +151,7 @@ <h1>Source code for autosolvate.autosolvate</h1><div class="highlight"><pre>
             <span class="k">for</span> <span class="n">docker</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">bcc_pipeline</span><span class="p">:</span>
                 <span class="n">docker</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">mol</span><span class="p">)</span></div>
 
-<div class="viewcode-block" id="solventBoxBuilder"><a class="viewcode-back" href="../../autosummary/autosolvate.autosolvate.solventBoxBuilder.html#autosolvate.autosolvate.solventBoxBuilder">[docs]</a><span class="k">class</span> <span class="nc">solventBoxBuilder</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+<div class="viewcode-block" id="solventBoxBuilder"><a class="viewcode-back" href="../../autosummary/autosolvate.solventBoxBuilder.html#autosolvate.autosolvate.solventBoxBuilder">[docs]</a><span class="k">class</span> <span class="nc">solventBoxBuilder</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
 <span class="w">    </span><span class="sa">r</span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Solvated molecule in specified solvent.</span>
 <span class="sd">    </span>
@@ -176,7 +176,7 @@ <h1>Source code for autosolvate.autosolvate</h1><div class="highlight"><pre>
 <span class="sd">    None</span>
 <span class="sd">        To run solvation, call build function.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-<div class="viewcode-block" id="solventBoxBuilder.__init__"><a class="viewcode-back" href="../../autosummary/autosolvate.autosolvate.solventBoxBuilder.html#autosolvate.autosolvate.solventBoxBuilder.__init__">[docs]</a>    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> 
+<div class="viewcode-block" id="solventBoxBuilder.__init__"><a class="viewcode-back" href="../../autosummary/autosolvate.solventBoxBuilder.html#autosolvate.autosolvate.solventBoxBuilder.__init__">[docs]</a>    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> 
                  <span class="n">xyzfile</span><span class="p">:</span><span class="nb">str</span><span class="p">,</span> <span class="n">slu_netcharge</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">slu_spinmult</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">charge_method</span><span class="o">=</span><span class="s2">&quot;resp&quot;</span><span class="p">,</span> <span class="n">slu_count</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
                  <span class="n">solvent</span> <span class="o">=</span> <span class="s2">&quot;water&quot;</span><span class="p">,</span> <span class="n">solvent_frcmod</span> <span class="o">=</span> <span class="s2">&quot;&quot;</span><span class="p">,</span> <span class="n">solvent_off</span> <span class="o">=</span> <span class="s2">&quot;&quot;</span><span class="p">,</span> <span class="n">solvent_box_name</span> <span class="o">=</span> <span class="s2">&quot;SLVBOX&quot;</span><span class="p">,</span>
                  <span class="n">slv_generate</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">slv_xyz</span> <span class="o">=</span> <span class="s2">&quot;&quot;</span><span class="p">,</span> <span class="n">slv_count</span> <span class="o">=</span> <span class="mi">210</span><span class="o">*</span><span class="mi">8</span><span class="p">,</span>
@@ -244,7 +244,19 @@ <h1>Source code for autosolvate.autosolvate</h1><div class="highlight"><pre>
             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;Solvent not found&quot;</span><span class="p">)</span>
         <span class="k">return</span> <span class="n">self_solvent</span>
 
-    <span class="k">def</span> <span class="nf">build</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<div class="viewcode-block" id="solventBoxBuilder.build"><a class="viewcode-back" href="../../autosummary/autosolvate.solventBoxBuilder.build.html#autosolvate.autosolvate.solventBoxBuilder.build">[docs]</a>    <span class="k">def</span> <span class="nf">build</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Build the solvated system</span>
+
+<span class="sd">        Parameters</span>
+<span class="sd">        ----------</span>
+<span class="sd">        None</span>
+
+<span class="sd">        Returns</span>
+<span class="sd">        -------</span>
+<span class="sd">        None</span>
+
+<span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">charge_method</span> <span class="o">==</span> <span class="s2">&quot;resp&quot;</span><span class="p">:</span>
             <span class="n">build_resp_terachem</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">solute</span><span class="p">,</span> <span class="n">folder</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">folder</span><span class="p">)</span>
         <span class="k">else</span><span class="p">:</span>
@@ -258,9 +270,9 @@ <h1>Source code for autosolvate.autosolvate</h1><div class="highlight"><pre>
             <span class="bp">self</span><span class="o">.</span><span class="n">prebuilt_solvation</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">system</span><span class="p">)</span>
         <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">solvent</span><span class="p">,</span> <span class="n">Molecule</span><span class="p">):</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">custom_solvation</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">system</span><span class="p">)</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">custom_solvation</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">system</span><span class="p">)</span></div>
+            <span class="bp">self</span><span class="o">.</span><span class="n">custom_solvation</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">system</span><span class="p">)</span></div></div>
 
-<div class="viewcode-block" id="startboxgen"><a class="viewcode-back" href="../../autosummary/autosolvate.autosolvate.startboxgen.html#autosolvate.autosolvate.startboxgen">[docs]</a><span class="k">def</span> <span class="nf">startboxgen</span><span class="p">(</span><span class="n">argumentList</span><span class="p">):</span>
+<div class="viewcode-block" id="startboxgen"><a class="viewcode-back" href="../../autosummary/autosolvate.startboxgen.html#autosolvate.autosolvate.startboxgen">[docs]</a><span class="k">def</span> <span class="nf">startboxgen</span><span class="p">(</span><span class="n">argumentList</span><span class="p">):</span>
 <span class="w">    </span><span class="sa">r</span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Wrap function that parses command line options for autosolvate boxgen,</span>
 <span class="sd">    adds solvent box to a given solute,</span>
@@ -411,7 +423,7 @@ <h1>Source code for autosolvate.autosolvate</h1><div class="highlight"><pre>
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2022, Liu Group. Project structure based on the Computational Molecular Science Python Cookiecutter version 1.3.</p>
+    <p>&#169; Copyright 2024, Liu Group. Project structure based on the Computational Molecular Science Python Cookiecutter version 1.3.</p>
   </div>
 
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