molmaker.py 文件源码

def minimize(self):
        self.tpr = "%s.tpr" % (self.basename)
        self.mdout = "%s.out.mdp" % (self.basename)
        self.pplog = "%s.pp.log" % (self.basename)
        self.deffnm = "%s.md" % (self.basename)
        self.mdgro = "%s.gro" % (self.deffnm)
        self.mdtrr = "%s.trr" % (self.deffnm)
        self.mdlog = "%s.log" % (self.deffnm)
        self.mdedr = "%s.edr" % (self.deffnm)

        ppargs = self.grompp + ["-f",self.mdp, "-p",self.top, "-c",self.gro, "-maxwarn","3", "-po",self.mdout, "-o",self.tpr]
        mdargs = self.mdrun + ["-s",self.tpr, "-nt","1", "-deffnm",self.deffnm, "-cpt","0"]

        with open(self.pplog, "w") as pplog:
            md_env = os.environ.copy()
            md_env["GMX_SUPPRESS_DUMP"] = '1'
            md_env["GMX_MAXBACKUP"] = '-1'
            pp = subprocess.call(ppargs, stdout=pplog, stderr=pplog, env=md_env)
        if pp:
            sys.stderr.write("grompp error: check %s\n" % (self.pplog))
            sys.exit()
        md = subprocess.call(mdargs, stdout=subprocess.PIPE, stderr=subprocess.PIPE, env=md_env)
        if md:
            sys.stderr.write("mdrun error: check %s\n" % (self.mdlog))
            sys.exit()