# mutate a single amino acid - to derivatized version.
# read in coordinates of the original protein and build in the positions of
# the new atoms.
#
#
xplor.requireVersion("2.12")

xplor.parseArguments() # check for typos on the command-line

seq="""
MET ALA ALA VAL GLN LEU SER GLU LEU ARG
ASP ARG GLN ALA ILE PHE GLU THR LEU VAL
ALA LYS GLY ARG GLU LEU LEU ALA CYS ASP
ARG VAL ILE VAL TYR ALA PHE ASP ASP ASN
TYR VAL GLY THR VAL VAL ALA GLU SER VAL
ALA GLU GLY TRP PRO GLN ALA ARG ASP GLN
VAL ILE GLU ASP PRO CYS PHE ARG GLU HIS
TRP VAL GLU ALA TYR ARG GLN GLY ARG ILE
GLN ALA THR THR ASP ILE PHE LYS ALA GLY
LEU THR GLU CYC HIS LEU ASN GLN LEU ARG
PRO LEU LYS VAL ARG ALA ASN LEU VAL VAL
PRO MET VAL ILE ASP ASP GLN LEU PHE GLY
LEU LEU ILE ALA HIS GLN ALA SER GLU PRO
ARG GLN TRP GLN GLU ILE GLU ILE ASP GLN
PHE SER GLU LEU ALA SER THR GLY SER LEU
VAL LEU GLU ARG LEU HIS PHE LEU GLU GLN
THR ILE ALA SER LEU
"""

simWorld.setRandomSeed(5521)

import protocol
protocol.initTopology(('protein','cyc_impr_bridge_flex.top'))
protocol.initParams(('protein','cyc_impr_bridge_flex.par'))

import psfGen
psfGen.seqToPSF(seq,seqType='prot',startResid=1)

from pdbTool import PDBTool
PDBTool('xray.pdb').read()

protocol.addUnknownAtoms(dyn_stepsize=0.01)

#xplor.command("write psf output=pixj_pcb.psf end")
PDBTool("xray_h_build.pdb").write()