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#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific.
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove this copyright notice.
#F* -------------------------------------------------------------------
#G* Please see the accompanying LICENSE file for further information.
#H* -------------------------------------------------------------------
#I* Additional authors of this source file include:
#-*
#-*
#-*
#Z* -------------------------------------------------------------------
from chempy import Storage,Atom
from chempy.models import Indexed
class PDB(Storage):
#---------------------------------------------------------------------------------
def fromList(self,list): # currently no handling of conect records
model = Indexed()
# read atoms
cnt = 0
at = None
for rec in list:
if (rec[0:4]=='ATOM') or (rec[0:6]=='HETATM'):
at = Atom()
if rec[0]=='A': at.hetatm=0 # default is 1
at.index = cnt
at.name = rec[12:16].strip()
at.alt = rec[16:17].strip()
at.resn = rec[17:20].strip()
at.chain = rec[21:22].strip()
at.resi = rec[22:27].strip() # note: insertion is part of resi
at.resi_number = int(rec[22:26])
at.coord = [float(rec[30:38]),
float(rec[38:46]),
float(rec[46:54])]
try:
at.q = float(rec[54:60])
except ValueError:
at.q = 1.0
try:
at.b = float(rec[60:66])
except ValueError:
at.b = 0.0
at.segi = rec[72:76].strip()
at.symbol = rec[76:78].strip()
if not len(at.symbol):
at.symbol = at.name[0:1]
if at.symbol in '012345678':
at.symbol = at.name[1:2]
cnt = cnt + 1
model.add_atom(at)
elif (rec[0:3]=='TER'):
if at:
at.ter=1
return(model)
#---------------------------------------------------------------------------------
def toList(self,model):
list = []
cnt = 1
for at in model.atom:
if at.hetatm:
het = 'HETATM'
else:
het = 'ATOM '
latn = len(at.name)
if latn and (latn<4):
if at.name[0] in '0123456789':
name=at.name
else:
name=' '+at.name
else:
name=at.name
lrsi = len(at.resi)
if lrsi and (lrsi<5):
if at.resi[lrsi-1] in '0123456789':
resi=at.resi+' '
else:
resi=at.resi
list.append(
"%6s%5i %-4s%1s%3s %1s%5s %8.3f%8.3f%8.3f%6.2f%6.2f %-4s%2s\n" %
(het,cnt,name,at.alt,at.resn,at.chain,resi,
at.coord[0],at.coord[1],at.coord[2],at.q,at.b,at.segi,at.symbol))
if hasattr(at,'ter'):
if at.ter:
cnt = cnt + 1
list.append(
"%6s%5i %3s %1s%4s\n" %
('TER ',cnt,at.resn,at.chain,at.resi))
cnt = cnt + 1
list.append("END\n")
return(list)
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