#! /usr/bin/env ccp4-python # # Copyright (C) 2005 Ronan Keegan # # This code is distributed under the terms and conditions of the # CCP4 Program Suite Licence Agreement as a CCP4 Application. # A copy of the CCP4 licence can be obtained by writing to the # CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. # # PDBClip function # Ronan Keegan 30/06/12 import os, string, sys import shutil import subprocess import shlex if not os.environ.has_key('CCP4'): raise RuntimeError, 'CCP4 not found' if not os.environ.has_key('CBIN'): raise RuntimeError, 'CBIN not found' class PDBClip: """ A class to generate PDBClip models """ def __init__(self): self.Logile="" if os.name == "nt": self.pdbsetEXE = os.path.join(os.environ['CBIN'], 'pdbset.exe') self.pdbcurEXE = os.path.join(os.environ['CBIN'], 'pdbcur.exe') self.coord_formatEXE = os.path.join(os.environ['CBIN'], 'coord_format.exe') else: self.pdbsetEXE = os.path.join(os.environ['CBIN'], 'pdbset') self.pdbcurEXE = os.path.join(os.environ['CBIN'], 'pdbcur') self.coord_formatEXE = os.path.join(os.environ['CBIN'], 'coord_format') try: self.debug=eval(os.environ['MRBUMP_DEBUG']) except: self.debug=False def run(self, inputPDBFile, outputPDBFile, chainID, workingDIR, LITE=False): """ A function to run coord_format, pdbset and pdbcur """ ############### Coord_format ################# # Write the key file for coord_format cf_key = 'FIXBLANK\n' cf_key += 'END\n' # Write out the key file if we are running in debug mode if self.debug: cf_keyfile=os.path.join(workingDIR, 'cf_key.in') cf_key_input=open(cf_keyfile, 'w') cf_key_input.write(cf_key) cf_key_input.close() # Run coord_format to fix any chain naming errors termination=False if self.debug: sys.stdout.write("modifying with coord_format.....\n") sys.stdout.write("\n") # Set the logfile self.Logfile=os.path.join(workingDIR, 'pdbclip.log') # Set the command line command_line=self.coord_formatEXE + ' xyzin ' + inputPDBFile \ + ' xyzout ' + os.path.join(workingDIR, 'cf_output.pdb') # Write it out if running in debug mode if self.debug: sys.stdout.write("Coord_format command line:\n") sys.stdout.write(command_line + "\n") sys.stdout.write("\n") # Launch coord_format if os.name == "nt": process_args = shlex.split(command_line, posix=False) p = subprocess.Popen(process_args, shell="True", stdin = subprocess.PIPE, stdout = subprocess.PIPE) else: process_args = shlex.split(command_line) p = subprocess.Popen(process_args, stdin = subprocess.PIPE, stdout = subprocess.PIPE) (child_stdout, child_stdin) = (p.stdout, p.stdin) child_stdin.write(cf_key) child_stdin.close() # Watch the output for successful termination out=child_stdout.readline() log=open(self.Logfile, "w") log.write("\n############### Coord Format ###############\n\n") log.write(out) while out: if 'Normal termination' in out: termination=True out = child_stdout.readline() log.write(out) child_stdout.close() log.close() if not termination: sys.stdout.write("PDBClip log: coord_format failed for:\n %s\n" % inputPDBFile) if self.debug: sys.stdout.write("PDBClip log: log file can be found at: \n %s" % self.Logfile) ############### PDBset ################# # Write the key file for pdbset if chainID.upper() == "ALL": ps_key = '' else: ps_key = 'SELECT CHAIN ' + chainID + '\n' ps_key += 'EXCLUDE HOH\n' ps_key += 'EXCLUDE HYDROGRENS\n' ps_key += 'SELECT OCCUPANCY\n' ps_key += 'END\n' # Write out the key file if we are running in debug mode if self.debug: ps_keyfile=os.path.join(workingDIR, 'ps_key.in') ps_key_input=open(ps_keyfile, 'w') ps_key_input.write(ps_key) ps_key_input.close() # Run pdbset to remove the waters termination=False if self.debug: sys.stdout.write("modifying with pdbset.....\n") # Set the command line #command_line = self.pdbsetEXE + ' xyzin ' + os.path.join(workingDIR, 'cf_output.pdb') \ # + ' xyzout ' + os.path.join(workingDIR, 'ps_output.pdb') command_line = self.pdbsetEXE + ' xyzin ' + os.path.join(workingDIR, 'cf_output.pdb') \ + ' xyzout ' + outputPDBFile # Write it out if running in debug mode if self.debug: sys.stdout.write("Pdbset command line:\n") sys.stdout.write(command_line + "\n") sys.stdout.write("\n") # Launch pdbset if os.name == "nt": process_args = shlex.split(command_line, posix=False) p = subprocess.Popen(process_args, shell="True", stdin = subprocess.PIPE, stdout = subprocess.PIPE) else: process_args = shlex.split(command_line) p = subprocess.Popen(process_args, stdin = subprocess.PIPE, stdout = subprocess.PIPE) (child_stdout, child_stdin) = (p.stdout, p.stdin) child_stdin.write(ps_key) child_stdin.close() # Watch the output for successful termination out=child_stdout.readline() log=open(self.Logfile, "a") log.write("\n############### PDBset ###############\n\n") log.write(out) while out: if 'Normal completion PDBSET' in out: termination=True out = child_stdout.readline() log.write(out) child_stdout.close() log.close() if not termination: sys.stdout.write("PDBClip log: pdbset failed for:\n %s\n" % inputPDBFile) if self.debug: sys.stdout.write("PDBClip log: log file can be found at:\n %s\n " % self.Logfile) ############### PDBcur ################# # Write the key file for pdbcur # if chainID.upper() == "ALL": # pc_key = '' # else: # pc_key = 'lvchain /1/' + chainID + '\n' # pc_key += 'mostprob\n' # pc_key += 'end\n' # # # Write out the key file if we are running in debug mode # if self.debug: # pc_keyfile=os.path.join(workingDIR, 'pc_key.in') # pc_key_input=open(pc_keyfile, 'w') # pc_key_input.write(pc_key) # pc_key_input.close() # # # Run pdbcur to strip chains and do some other editing # termination=False # if self.debug: # print "modifying with pdbcur....." # # # Set the command line # command_line = self.pdbcurEXE + ' xyzin ' + os.path.join(workingDIR, 'ps_output.pdb') \ # + ' xyzout ' + outputPDBFile # # # Write it out if running in debug mode # if self.debug: # sys.stdout.write("Pdbcur command line:\n") # sys.stdout.write(command_line + "\n") # sys.stdout.write("\n") # # # Launch pdbset # if os.name == "nt": # process_args = shlex.split(command_line, posix=False) # p = subprocess.Popen(process_args, shell="True", stdin = subprocess.PIPE, # stdout = subprocess.PIPE) # else: # process_args = shlex.split(command_line) # p = subprocess.Popen(process_args, stdin = subprocess.PIPE, # stdout = subprocess.PIPE) # # (child_stdout, child_stdin) = (p.stdout, p.stdin) # # child_stdin.write(pc_key) # child_stdin.close() # # # Watch the output for successful termination # out=child_stdout.readline() # log=open(self.Logfile, "a") # log.write("\n############### PDBcur ###############\n\n") # log.write(out) # # while out: # if 'Normal termination' in out: # termination=True # out = child_stdout.readline() # log.write(out) # # child_stdout.close() # log.close() # # if not termination: # sys.stdout.write("PDBClip log: pdbcur failed for:\n %s\n" % inputPDBFile) # if self.debug: # sys.stdout.write("PDBClip log: log file can be found at:\n %s\n" % self.Logfile) #################################################### # If running in LITE mode remove excess files if LITE: if os.path.isfile(os.path.join(workingDIR, 'cf_output.pdb')): os.remove(os.path.join(workingDIR, 'cf_output.pdb')) if self.debug: sys.stdout.write("\n") if __name__ == "__main__": workingDIR=os.path.join(os.environ["CCP4_SCR"], "pdbclip_insulin_test") if os.path.isdir(workingDIR): shutil.rmtree(workingDIR) os.mkdir(workingDIR) inputPDBFile=os.path.join(os.environ["CEXAM"], "data", "insulin.pdb") outputPDBFile=os.path.join(workingDIR, "test.pdb") chainID="A" p=PDBClip() p.run(inputPDBFile, outputPDBFile, chainID, workingDIR, LITE=False)