added PDB trajectory writing capabilities

cctk/__init__.py

@@ -9,4 +9,5 @@
 from .mol2_file import MOL2File
 from .mae_file import MAEFile
 from .orca_file import OrcaFile
+from .pdb_file import PDBFile
 

cctk/pdb_file.py

@@ -0,0 +1,62 @@
+import sys
+import re
+import numpy as np
+
+from abc import abstractmethod
+
+from cctk import File, Molecule, ConformationalEnsemble
+from cctk.helper_functions import get_symbol
+
+class PDBFile(File):
+    """
+    Generic class for all ``.pdb`` files.
+    """
+
+    def __init__(self, molecule, title=None):
+        pass
+
+    @classmethod
+    def read_file(cls, filename):
+        pass
+
+    @classmethod
+    def write_molecule_to_file(cls, filename, molecule, num=1, append=False):
+        """
+        Write a ``.pdb`` file, using object attributes.
+
+        Args:
+            filename (str): path to the new file
+            molecule (Molecule): ``Molecule`` object
+            num (int): model number
+            append (Bool): whether to write to file normally or append
+        """
+        text = f"MODEL {num}\n"
+
+        for idx, Z in enumerate(molecule.atomic_numbers, start=1):
+            line = molecule.get_vector(idx)
+            symb = get_symbol(Z)
+            text += f"HETATM {idx:>4}  {symb:<2}    *     0     {line[0]:7.3f} {line[1]:7.3f} {line[2]:7.3f}  1.00  0.00           {symb:<2}\n"
+
+        text += f"ENDMDL\n"
+
+        if append:
+            super().append_to_file(filename, text)
+        else:
+            super().write_file(filename, text)
+
+
+    @classmethod
+    def write_ensemble_to_trajectory(cls, filename, ensemble):
+        """
+        Writes a ``ConformationalEnsemble`` to a trajectory file.
+
+        Args:
+            filename (str): where to write the file
+            ensemble (Ensemble): ``Ensemble`` object to write
+        """
+        for idx, molecule in enumerate(ensemble.molecules):
+            if idx == 0:
+                cls.write_molecule_to_file(filename, molecule, num=idx+1, append=False)
+            else:
+                cls.write_molecule_to_file(filename, molecule, num=idx+1, append=True)
+

docs/intro.rst

@@ -74,6 +74,50 @@ Now, run ``conda activate cctk`` to enter the ``cctk`` Python environment (and `
 
 (More complete guides to ``conda`` usage can be found elsewhere.)
 
+**Upgrading**
+
+To get the latest version of *cctk*, navigate to the correct ``conda`` environment and run::
+
+    $ pip install --upgrade cctk
+
+Your First *cctk* Script
+------------------------
+
+Once you have *cctk* properly installed, you can write a simple "hello world" program. 
+
+Create a sample ``.xyz`` file (for instance, ``water.xyz``)::
+
+    3
+    hello world
+    O 0.0 0.0 0.0
+    H 1.0 0.0 0.0
+    H 0.0 1.0 0.0
+
+Now create a file called ``hello_world.py``::
+
+    import cctk
+
+    file = cctk.XYZFile.read_file("water.xyz")
+
+    print(f"{file.title} is title")
+    print(f"{file.molecule.atomic_numbers} is atomic numbers")
+    
+    angle = file.molecule.get_angle(2,1,3)
+    print(f"The angle between atoms 2, 1, and 3 is {angle} degrees")
+
+    if angle < 105:
+        print("This is a strained water molecule!")
+
+Running this script produces the following output::
+
+    $ ls
+    hello_world.py  water.xyz
+    $ python hello_world.py
+    hello world is title
+    [8 1 1] is atomic numbers
+    The angle between atoms 2, 1, and 3 is 90.0 degrees
+    This is a strained water molecule!  
+
 Using *cctk*
 ____________
 

scripts/monitor.py

@@ -63,5 +63,5 @@
             distances[i]
         ))
 
-except ValueError as e:
-    print(f"job has not finished any iterations: {e}")
+except:
+    print(f"job has not finished any iterations")

setup.py

@@ -10,13 +10,13 @@
     packages=["cctk", "cctk.data", "cctk.groups"],
 #    include_package_data=True,
     package_data={"cctk.data": ["*"], "cctk.groups": ["*"],},
-    version="v0.1.2",
+    version="v0.1.3",
     license="Apache 2.O",
     description="computational chemistry toolkit",
     author="Corin Wagen and Eugene Kwan",
     author_email="corin.wagen@gmail.com",
     url="https://github.com/ekwan/cctk",
-    download_url="https://github.com/ekwan/cctk/archive/v0.1.2.tar.gz",
+    download_url="https://github.com/ekwan/cctk/archive/v0.1.3.tar.gz",
     install_requires=["numpy", "networkx", "importlib_resources"],
     long_description=long_description,
     long_description_content_type='text/markdown',