def __init__(self,pdb='mol.pdb',top='topol.top'):
os.system('mkdir res') #qm jobs will go in here ;-)
#--lamda stuff
self.R1=1.0
self.R2=6.0
#--end
self.pdb = gmx_pdb(pdb)
self.top = gmx_topology()
self.top.read_top(top)
self.assign_bonds() #each atom gets a list of other atoms it is bound to
#print self.pdb.atoms[1002].bonds
self.qm_connect = self.assign_qmgroups() # list of [ [groupmembers],[partners] ] with [partners]=[[groupmember],[outsideatom]] so [ [1,2,3], [[2,5],[3,7]]
#print self.pdb.atoms[1002].qm_group
#print self.qm_connect[self.pdb.atoms[1002].qm_group]
self.center = [self.pdb.atoms[1008-1].x,self.pdb.atoms[1008-1].y,self.pdb.atoms[1008-1].z]
self.azone,self.zone_id_list,self.azone_center_id = self.find_azone(self.center,radius=self.R2,center_atom_number=1008)
self.zones = self.create_adaptive_zones()
self.mm=[]
self.mm_ids=[]
self.qm=[]
self.qm_ids=[]
self.input_overhead=[]
self.read_gin()
self.create_zones_top()
self.fort7=self.read_fort7()
def __init__(self,pdb='mol.pdb',top='topol.top'):
self.pdb = gmx_pdb(pdb)
self.top = gmx_topology()
self.top.read_top('topol.top')
self.zoneatoms = []
self.read_zoneatoms('qm_atomlist.dat')
self.assign_bonds()
self.qm_connect = self.assign_qmgroups() # list of [ [groupmembers],[partners] ] with [partners]=[[groupmember],[outsideatom]] so [ [1,2,3], [[2,5],[3,7]]
self.azone,self.zone_id_list,self.azone_center_id=self.find_azone()
self.create_zones_top_working()