Add modules

auto_namd/job.py

@@ -0,0 +1,113 @@
+import os
+import sys
+import glob
+
+from auto_namd.functions import *
+from auto_namd.simulation import Simulation
+
+
+class Job:
+    """
+    A class that represents a job/system residing in a unique directory path
+
+    Attributes:
+    self.path = absolute job directory path
+    self.name = name of the job, derived from parent directory
+    self.prefix = self.path + self.name
+    self.pdb = latest .pdb file
+    self.psf = latest .psf file
+    self.coor = latest .coor file
+    self.stage = current simulation stage
+    self.step = current simulation steps
+    """
+
+    def __init__(self, path):
+        self.path = path
+        self.name = self.get_job_name()
+        self.prefix = os.path.join(self.path, self.name)
+        self.pdb, self.psf = self.get_pdb_and_psf()
+        self.stage, self.step, self.coor = self.get_stage()
+
+
+    def get_job_name(self):
+        '''Get job name from path'''
+        name = os.path.basename(self.path)
+        return name
+
+
+    def get_pdb_and_psf(self):
+        pdb = glob.glob(f'{self.prefix}*_solv_ion.pdb')
+        psf = glob.glob(f'{self.prefix}*_solv_ion.psf')
+        if len(pdb) == 1 and len(psf) == 1:
+            return pdb[0], psf[0]
+        pdb = glob.glob(f'{self.prefix}.pdb')
+        psf = glob.glob(f'{self.prefix}.psf')
+        if len(pdb) == 1 and len(psf) == 1:
+            return pdb[0], psf[0]
+        else:
+            print('No PDB or PSF files found, exiting...')
+            sys.exit(1)
+
+
+    def get_stage(self):
+        coors_path = self.prefix + '*.coor'
+        coors = glob.glob(coors_path)
+        coors.sort(key=natural_key)
+        if len(coors) >= 1:
+            coor = coors[-1]
+            stage = coor.split('_')[-2].split('.')[0]
+            step = int(coor.split('_')[-1].split('.')[0])
+        else:
+            coor = ''
+            stage = ''
+            step = 0
+        return stage, int(step), coor
+
+
+    # allow the Simulation class to instantiate via the simulate() method
+    def simulate(self, ffs_path, steps, namdbin, params):
+        Simulation(self, ffs_path, steps, namdbin, params)
+
+
+    def info(self):
+        print(f'Job Path: {self.path}\n'
+              f'Name: {self.name}\n'
+              f'Working PDB: {self.pdb}\n'
+              f'Working PSF: {self.psf}\n'
+              f'Previous Step: {self.stage}\n'
+              f'Previous Step Number: {str(self.step)}\n'
+              )
+
+
+"""Job control"""
+def get_next_job(jobs_path):
+    jobs_path = san_path(jobs_path)
+    job_dirs_l = get_jobs_from_path(jobs_path)
+    jobs = create_job_instances(job_dirs_l)
+    next_job = get_youngest_job(jobs)
+    return next_job
+
+
+def get_jobs_from_path(jobs_path):
+    # Only return job paths with a pdb file
+    jobs_path = os.path.join(jobs_path, '**/*.pdb')
+    job_dirs = glob.glob(jobs_path, recursive=True)
+    job_dirs_l = []
+    for job_dir in job_dirs:
+        job_dirs_l.append(os.path.dirname(job_dir))
+    if len(job_dirs_l) < 1:
+        print('No valid jobs found in jobs path!')
+        sys.exit(1)
+    return job_dirs_l
+
+
+def create_job_instances(job_paths):
+    job_instances = []
+    for job_path in job_paths:
+        job_instances.append(Job(job_path))
+    return job_instances
+
+
+def get_youngest_job(jobs):
+    jobs.sort(key=lambda x: (x.stage, x.step))
+    return jobs[0]