MBN-tools 0.1__tar.gz

MBN_tools-0.1/MBN_tools/MBN_tools.py

@@ -0,0 +1,119 @@
+'''
+MBN Tools
+
+A series of functions for use with the MBN Explorer software (https://mbnresearch.com/get-mbn-explorer-software).
+
+Functions include running MBN Explorer simulations, data analysis and file manipulation.
+'''
+
+def run_MBN(task_file, MBN_path, show_output=False):
+    '''This function will run an MBN Explorer simulation using a specified Task file. Function returns the
+stanard output and standard error. The show_output optional argument will print the simulation output to
+the screen.'''
+    import subprocess
+    result = subprocess.run(MBN_path + ' -t ' + task_file, capture_output=True, text=True, creationflags=0x08000000)
+
+    if show_output:
+        print('Output:')
+        if len(result.stdout) > 0:
+            print(result.stdout)
+        else:
+            print(result.stderr)
+
+    return result.stdout, result.stderr
+
+
+def read_task_file(task_file):
+    '''This function splits a given Task file into a a dictionary of task file options and their respective
+parameters. Useful if you want to get a specific set of task file options for use in calculations for example.'''
+    file_options = {}
+    with open(task_file) as f:
+        data = f.read().split('\n')
+
+    for i in data:
+        if '=' in i:
+            i=i.split('=')
+            try:
+                file_options[i[0].strip()] = eval(i[1].strip())
+            except (NameError, SyntaxError):
+                file_options[i[0].strip()] = i[1].strip()
+
+    return file_options
+
+
+def read_trajectory(dcd_file, frame=None):
+''' This function uses the mdtraj module to return the coordinates of a particular DCD file.
+A frame number can be specified. Note that this function is only compatible on unix systems
+due to the mdtraj module.'''
+    loaded = False
+    try:
+        import mdtraj.formats as md
+        loaded = True
+    except:
+        assert loaded, 'Cannot import the mdtraj module; please run in unix'
+
+    with md.DCDTrajectoryFile(dcd_file) as f:
+        xyz, cell_lengths, cell_angles = f.read()
+        coords = (xyz)
+
+    if frame:
+        return coords[frame]
+    else:
+        return coords
+        
+        
+def xyz_to_pdb(xyz_file, pdb_file):
+    '''This function is meant to update coordinates of a particular system from an XYZ file
+to a corresponding PDB file for the same system. It receives an XYZ file (xyz_file)
+containing the new coordinates and a PDB file (pdb_file) containing old coordinates to
+be updated, and returns a PDB file with the name of the one supplied prefixed by 'new_'.
+It assumes one is using only the record types 'ATOM' or 'HETATM' on the PDB file, but can
+be adjusted for other usages provided the string updated_atom is correctly modified.'''
+    with open(xyz_file) as xyz:
+        lines = xyz.readlines()
+        xyz_list = [line.strip().split() for line in lines[2:]]
+
+    with open(pdb_file) as pdb:
+        lines = pdb.readlines()
+        head = []
+        atoms = []
+        foot = []
+        atoms_done = False
+        for line in lines:
+            if line.startswith('ATOM'):
+                atoms.append(line.strip().split())
+            elif line.startswith('END'):
+                atoms_done = True
+                foot.append(line)
+            elif atoms_done:
+                foot.append(line)
+            else:
+                head.append(line)
+
+    with open('new_' + pdb_file, 'w') as new_pdb:
+        for line in head:
+            new_pdb.write(line)
+        for idx, atom in enumerate(atoms):
+            updated_atom = "{ATOM}{atom_num} {atom_name}{alt_loc_ind}{res_name} {chain_id}{res_seq_num}{res_code}   {x_coord}{y_coord}{z_coord}{occ}{temp}      {seg_id}{element}{charge}\n".format( #The values on the lines below can be edited to comply with other PDB types
+                ATOM=atom[0].ljust(6),
+                atom_num=atom[1].rjust(5),
+                atom_name=atom[2].ljust(4),
+                alt_loc_ind=' ',
+                res_name=atom[3].rjust(3),
+                chain_id=' ',
+                res_seq_num=atom[4].rjust(4),
+                res_code=' ',
+                x_coord=str('%3.3f' % (float(xyz_list[idx][1]))).rjust(8),
+                y_coord=str('%3.3f' % (float(xyz_list[idx][2]))).rjust(8),
+                z_coord=str('%3.3f' % (float(xyz_list[idx][3]))).rjust(8),
+                occ=str('%1.2f' % (float(atom[8]))).rjust(6),
+                temp=str('%1.2f' % (float(atom[9]))).rjust(6),
+                seg_id=atom[10].ljust(4),
+                element=atom[11].rjust(2),
+                charge='  '
+            )
+
+            new_pdb.write(updated_atom)
+        for line in foot:
+            new_pdb.write(line)
+

MBN_tools-0.1/PKG-INFO

@@ -0,0 +1,16 @@
+Metadata-Version: 1.1
+Name: MBN_tools
+Version: 0.1
+Summary: Useful tools for MBN Explorer simulations and analysis
+Home-page: https://github.com/mattdickers/MBN_tools
+Author: Matthew Dickers
+Author-email: mattdickers@gmail.com
+License: MIT
+Download-URL: https://github.com/mattdickers/MBN_tools/archive/refs/tags/v_0.1.tar.gz
+Description: UNKNOWN
+Keywords: MBN Explorer,MBN Studio,Molecular Dynamics,MD,Data Analysis
+Platform: UNKNOWN
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3

MBN_tools-0.1/setup.cfg

@@ -0,0 +1,2 @@
+[metadata]
+description-file = README.md

MBN_tools-0.1/setup.py

@@ -0,0 +1,23 @@
+from distutils.core import setup
+setup(
+  name = 'MBN_tools',
+  packages = ['MBN_tools'],
+  version = '0.1',
+  license='MIT',
+  description = 'Useful tools for MBN Explorer simulations and analysis',
+  author = 'Matthew Dickers',
+  author_email = 'mattdickers@gmail.com',
+  url = 'https://github.com/mattdickers/MBN_tools',
+  download_url = 'https://github.com/mattdickers/MBN_tools/archive/refs/tags/v_0.1.tar.gz',
+  keywords = ['MBN Explorer', 'MBN Studio', 'Molecular Dynamics', 'MD', 'Data Analysis'],
+  install_requires=[
+          'numpy',
+          'mdtraj',
+      ],
+  classifiers=[
+    'Development Status :: 3 - Alpha',      # Chose either "3 - Alpha", "4 - Beta" or "5 - Production/Stable" as the current state of your package
+    'Intended Audience :: Science/Research',
+    'License :: OSI Approved :: MIT License',
+    'Programming Language :: Python :: 3',
+  ],
+)