#!/usr/bin/env python # Python script # # # Copyright (C) 2014 --- 2019 Fei Long, Murshudov # # This code is distributed under the terms and conditions of the # CCP4 Program Suite Licence Agreement as a CCP4 Library. # #==================================================================== ## The date of last modification: 11/07/2014 import os,os.path,sys import glob,shutil import re,string from optparse import OptionParser import time import math import select if os.name != 'nt': import fcntl import signal def listComp(a_list, b_list): if a_list[1] > b_list[1]: return 1 elif a_list[1] < b_list[1]: return -1 if len(a_list[0]) < len(b_list[0]): return 1 elif len(a_list[0]) > len(b_list[0]): return -1 if a_list[0] > b_list[0]: return 1 elif a_list[0] == b_list[0]: return 0 elif a_list[0] < b_list[0]: return -1 ################################################# class CExeCode : """ A generic abstract base class that is to be inheritted by other classes that warp a executable code. Basically this class defines two main methods that characterize the procedures a job by an executable code, i.e. forming a command line object and then run the code according to the command line object""" def __init__( self ): # set pathes self.exitCode = 0 # test self._setCmdLineAndFile() def _setCmdLineAndFile(self ): # will be overrided by individual derived classes self._cmdline = 'ls ' self.batch_name = None self._log_name = None def subExecute(self, mode = 0, err_str ="" ): if self._log_name : if os.name == 'nt': self.logModeWin(mode, err_str) else: self.logModeLin(mode, err_str) else : self.interactiveMode() def logModeLin(self, mode = 0, err_str=""): """ execute self._cmdline and output to a log file (self._log_name) in a nonblocking way""" logfile = open(self._log_name, 'w') logfile.write("\n============ PROCESS INFORMATION =============\n") # spawn a sub-process for a job and connect to its input/output(and error) # streams using pipes try : import subprocess subProcess = subprocess.Popen(self._cmdline, shell=True, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE, close_fds=True) subProcess.stdin.close() outfile_sub = subProcess.stdout outfd_sub = outfile_sub.fileno() except ImportError: print "module 'subprocess' has not be found, you use a version of PYTHON below 2.4" print "Import module 'popen2' instead, the calculations will not be affected" import popen2 subProcess = popen2.Popen4(self._cmdline) subProcess.tochild.close() outfile_sub = subProcess.fromchild outfd_sub = outfile_sub.fileno() self._pid = subProcess.pid pid_c = self._pid + 1 p_name = os.path.basename(self._cmdline.strip().split()[0]) t__log_name = os.path.basename(self._log_name) log_size = 0 log_max = 100000000 outfile_eof = 0 if not mode: self._nonBlockingFile(outfd_sub) while not outfile_eof : ready_to_read, ready_to_write, in_error = \ select.select([outfd_sub],[],[],60.0) if outfd_sub in ready_to_read: out_quantum = outfile_sub.read() out_quantum_bt = len(out_quantum) log_size = log_size + out_quantum_bt if log_size > log_max: logfile.write("\nTHE SIZE OF LOG FILE, %s, EXCEEDED THE LIMIT AND PROCESS STOPPED\n"%t__log_name) logfile.write("The process running %s is killed\n"%p_name) logfile.close() os.kill(self._pid, signal.SIGKILL) os.kill(pid_c, signal.SIGKILL) print "The process running %s is killed " %p_name time.sleep(1.0) # be safe stop all process sys.exit(1) else : if out_quantum == '': outfile_eof = 1 logfile.write(out_quantum) logfile.flush() else : self._nonBlockingFile(outfd_sub) while not outfile_eof : ready_to_read, ready_to_write, in_error = \ select.select([outfd_sub],[],[],10) if outfd_sub in ready_to_read: out_quantum = outfile_sub.read() if out_quantum == '': outfile_eof = 1 logfile.write(out_quantum) logfile.flush() # allProcInfo.append(out_quantum) self.exitCode = subProcess.wait() # if mode: # for item in allProcInfo: # logfile.write(item) logfile.write("=========END OF PROCESS INFORMATION\n ==========\n") logfile.close() outfile_sub.close() if self.exitCode: print "#-----------------------------------------------------------#" print "The process stoped because of a runtime error in code '%s'!"%p_name if err_str: print "%s"%err_str else: print "See the associated log file '%s'."%t__log_name print "#-----------------------------------------------------------#" if not err_str: # if normal runtime errors, stop the program(using log. no err_str) sys.exit(1) return True def logModeWin(self, mode = 0, err_str=""): """ execute self._cmdline and output to a log file (self._log_name) under Windows system""" pass def _nonBlockingFile(self,fd): f_flag = fcntl.fcntl(fd, fcntl.F_GETFL,0) fcntl.fcntl(fd, fcntl.F_SETFL, f_flag | os.O_NONBLOCK) def interactiveMode(self): """ execute self._cmdline just like what is done in a shell """ os.system(self._cmdline) # end class Acedrg(CExeCode ): def __init__( self, t_argvs): if len(sys.argv)==1: print "Look for help: %s -h "%(os.path.basename(sys.argv[0])) self.errMessage = [] self.errLevel = 0 self.scrDir = "" self.outRoot = "" self.baseRoot = "" self.geneInFileName = "" self.geneInFileType = "" self.inStdCifName = "" self.inStdCifDir = "" self.inMmCifName = "" self.inSmiName = "" self.inMdlName = "" self.inPdbName = "" self.inSDFName = "" self.inMol2Name = "" self.outRstCifName = "" self.outRstPdb = "" self.outAtmTypeName = "" self.monomRoot = "" self.acedrgTables = "" self.libmol = "" self.libmolLogName = "" self.libcheck = "" self.libcheckLogName = "" self.refmac = "" self.refmacLogName = "" self.workMode = 0 self.molGen = False self.repCrds = False self.testMode = False self.versionInfo = {} self.allBondsAndAngles = {} self.allBondsAndAngles["atomClasses"] = {} self.allBondsAndAngles["bonds"] = {} self.allBondsAndAngles["angles"] = {} self.acedrg = os.path.abspath(sys.argv[0]) self.acedrgDir = os.path.dirname(os.path.dirname(self.acedrg)) #print self.acedrgDir inputOptionsP = self.InputParser(t_argvs) #if inputOptionsP.geneInFileName: # self.checInputFormat() self.setWorkMode(inputOptionsP) self.checkDependency() self.checkVersionInfo() self.execute() def InputParser(self, t_argvs): usage = "Serveral Examples: \n\ (1) Input a mmCif file to get a ligand/Dictionary/restraint files (mmCif fomat) \n\ acedrg -c your_mmCif_file -r your_monomer_name(optional) -o output_name_root(optional) \n\n\ (2) Input a SMILES string in a command line (the SMILES string is a pair of quotation marks) or \n \ a file containing a SMILES string to get a ligand/Dictionary/restraint files (mmCif fomat) \n\ acedrg -i your_SMILES_file -r your_monomer_name(optional) -o output_name_root(optional) \n\n\ (3) Input a MOL file to get a ligand/Dictionary/restraint files (mmCif fomat) \n\ acedrg -m your_mol_file -r your_monomer_name(optional) -o output_name_root(optional) \n\n\ (4) Input a small molecule CIF file to get two files describing your molecules, atom types, \n\ bond lengths and angles (text format)\n\ acedrg -e -b your_CIF_file -r your_monomer_name(optional) -o output_name_root(optional) \n\n\ 5) Input a directory containing a number of molecule CIF files to get files describing your\n\ molecules, atom types, bond lengths and angles, and their statistics \n\ acedrg -e -d your_dir_of_CIF_files -o output_name_root(optional) \n\n" self.inputParser = OptionParser(usage=usage) # Options # input file format self.inputParser.add_option("-b", "--stdcif", dest="inStdCifName", metavar="FILE", action="store", type="string", help="Input small molecule CIF File containing coordinates and crystal information") self.inputParser.add_option("-c", "--mmcif", dest="inMmCifName", metavar="FILE", action="store", type="string", help="Input MMCIF File containing coordinates and bonds") self.inputParser.add_option("-d", "--cifdir", dest="inStdCifDir", metavar="FILE", action="store", type="string", help="An input directory to store a group of small molecule CIF Files containing coordinates and crystal information") self.inputParser.add_option("-e", "--molgen", dest="molGen", action="store_true", default=False, help="The option when the user want to generate molecules and values of the associated bonds and angles in a cif file") self.inputParser.add_option("-f", "--infile", dest="geneInFileName", action="store", type="string", help="user's input file, regardless what format it is") self.inputParser.add_option("-g", "--mol2", dest="inMol2Name", metavar="FILE", action="store", type="string", help="Input SYBL_MOL2 File containing coordinates and bonds") self.inputParser.add_option("-i", "--smi", dest="inSmiName", metavar="FILE", action="store", type="string", help="Input File containing a SMILE string") self.inputParser.add_option("-m", "--mol", dest="inMdlName", metavar="FILE", action="store", type="string", help="Input File of MOL format containing coordinates and bonds") self.inputParser.add_option("-n", "--typeOut", dest="typeOut", action="store_true", default=False, help="The option when the user want to output two kinds of atom types (CCP4 and Acedrg) only") self.inputParser.add_option("-o", "--out", dest="outRoot", action="store", type="string", help="A name root that users want their output files called(without extension)") self.inputParser.add_option("-p", "--pdb", dest="inPdbName", metavar="FILE", action="store", type="string", help="Input File of PDB format containing atomic coordinates ") self.inputParser.add_option("-r", "--res", dest="monomRoot", action="store", type="string", help="The name of the chemical components users want to put into output files(e.g. PDB or MMCIF)") self.inputParser.add_option("-s", "--sdf", dest="inSdfName", metavar="FILE", action="store", type="string", help="Input File of SDF format containing coordinates and bonds") self.inputParser.add_option("-t", "--tab", dest="acedrgTables", metavar="FILE", action="store", type="string", help="Input path that stores all bond and angle tables (if no input, default CCP4 location will be used)") self.inputParser.add_option("-v", "--ver", dest="versionInfo", action="store_true", default=False, help="The option for checking version information of acedrg") self.inputParser.add_option("-y", "--repcrd", action="store_true", dest="repCrd", default=False, help="Use this keyword if you want to replace the atomic coordinates in the input mmCif with those in the input PDB") self.inputParser.add_option("-z", "--noGeoOpt", dest="noGeoOpt", action="store_true", default=False, help="The option for not doing geometry optimization on coordinates") self.inputParser.add_option("-T", "--Test", dest="testMode", action="store_true", default=False, help="The option for internal tests") (inputOptionsP, inputOptionsU) = self.inputParser.parse_args(t_argvs) if inputOptionsU: print "Line arguments for those keywords are missing " for a_opt in inputOptionsU: print "Keyword %s ?"%a_opt sys.exit() return inputOptionsP def checkDependency(self): if os.environ.has_key("CCP4"): tRefmac = os.path.join(os.environ['CBIN'], "refmac5") if not glob.glob(tRefmac): print "refmac5 could not be found" sys.exit() else: self.refmac = tRefmac tLibcheck = os.path.join(os.environ['CBIN'], "libcheck") if not glob.glob(tLibcheck): print "libcheck could not be found" sys.exit() else: self.libcheck = tLibcheck tLibmol = os.path.join(os.environ['CCP4'], "libexec", "libmol") if glob.glob(tLibmol): self.libmol = tLibmol tAcedrgTables = os.path.join(os.environ['CCP4'], "share/acedrg/tables") if glob.glob(tAcedrgTables): self.acedrgTables = tAcedrgTables else : print "You need to install CCP4 suite" print "or activate ccp4.setup" sys.exit() if not self.libmol : if os.environ.has_key("LIBMOL_ROOT"): tLibmol = os.path.join(os.environ['LIBMOL_ROOT'], "libexec/libmol") if glob.glob(tLibmol): self.libmol = tLibmol else: print "libmol could not be found at %s"%tLibmol sys.exit() if not self.libmol: if glob.glob(self.acedrgDir): tLibmol = os.path.join(self.acedrgDir, "libexec/libmol") if glob.glob(tLibmol): self.libmol = tLibmol else: print "libmol could not be found at %s"%tLibmol sys.exit() else: print "Can not find where the acedrg is installed" sys.exit() if not self.libmol: print "can not find libmol at libexec/" sys.exit() if not self.acedrgTables: if os.environ.has_key("LIBMOL_ROOT"): tAcedrgTables = os.path.join(os.environ['LIBMOL_ROOT'], "share/acedrg/tables") if os.path.isdir(tAcedrgTables): self.acedrgTables = tAcedrgTables else: print "Tables required could not be found at %s"%tAcedrgTables sys.exit() if not self.acedrgTables: tAcedrgTables = os.path.join(self.acedrgDir, "share/acedrg/tables") # print tAcedrgTables if os.path.isdir(tAcedrgTables): self.acedrgTables = tAcedrgTables else: print "Bond and angle tables required could not be found " sys.exit() def checkVersionInfo(self): self.versionInfo["man"] = os.path.join(self.acedrgTables, "manifest.txt") if not os.path.isfile(self.versionInfo["man"]): print "Version infomation is not available." else: # print self.versionInfo["man"] try: vInfo = open(self.versionInfo["man"], "r") except IOError: print self.versionInfo["man"], " Could not be opened for reading" print "Version infomation is not available." else: for aL in vInfo.readlines(): if aL.find(":") !=-1: strs = aL.strip().split(":") if len(strs)==2: self.versionInfo[strs[0]] = strs[1] def checInputFormat(self): try: tF =open(self.geneInFileName, "r") except IOError: print "%s can not be open for reading "%tFName sys.exit() else: tLines = tF.readlines() tF.close() for aL in tLines: strs = aL.strip().split() if aL.find("_chem_comp_atom") != -1: self.inFileType = "MMCIF" break elif aL.find("_atom_site_") != -1: self.geneInName = "CIF" break elif len(strs)==8: if strs[7].find("V2000") != -1 or strs[7].find("V3000") != -1 : self.geneInName = "MOL" break def setMonoRoot(self): if self.inMdlName != "": try: tF =open(self.inMdlName, "r") except IOError: print "%s can not be open for reading "%self.inMdlName sys.exit() else: tL = tF.readline().strip() print tL tF.close() if len(tL) ==3: self.monomRoot= tL elif len(tL) >3: self.monomRoot= tL[:4] elif self.inMmCifName != "": try: tF =open(self.inMmCifName, "r") except IOError: print "%s can not be open for reading "%self.inMmCifName sys.exit() else: tLs = tF.readlines() tF.close() for aL in tLs: if aL.find("data_comp_") != -1: strs = aL.strip().split("_") if len(strs) ==3: if len(strs[2]) ==3: self.monomRoot = strs[2] break if len(self.monomRoot) < 3: self.monomRoot = "UNL" def setWorkMode(self, t_inputOptionsP = None): # Sequnence for check the locations of acedrg tables # (1) Check if the user provides the location # (2) If not, check CCP4 suite default location. # (3) If not, check if the environment variable LIBMOL_ROOT is defined in the user's machine. # (4) If none of them, program exits. if not t_inputOptionsP.acedrgTables: if os.environ.has_key("CCP4"): tAcedrgTables = os.path.join(os.environ['CCP4'], "share/acedrg/tables") if glob.glob(tAcedrgTables): self.acedrgTables = tAcedrgTables else: print "You need to install CCP4 suite" sys.exit() else: if os.path.isdir(t_inputOptionsP.acedrgTables): self.acedrgTables = t_inputOptionsP.acedrgTables if not self.acedrgTables or not glob.glob(self.acedrgTables): if os.environ.has_key("LIBMOL_ROOT"): tAcedrgTables = os.path.join(os.environ['LIBMOL_ROOT'], "share/acedrg/tables") print tAcedrgTables if os.path.isdir(tAcedrgTables): self.acedrgTables = tAcedrgTables if not self.acedrgTables : tAcedrgTables = os.path.join(self.acedrgDir, "share/acedrg/tables") print tAcedrgTables if os.path.isdir(tAcedrgTables): self.acedrgTables = tAcedrgTables else: print "Bond and angle tables required could not be found " sys.exit() if not t_inputOptionsP.molGen and not t_inputOptionsP.repCrd and not t_inputOptionsP.typeOut: if not t_inputOptionsP.noGeoOpt: if t_inputOptionsP.inMmCifName: self.inMmCifName = t_inputOptionsP.inMmCifName self.workMode = 11 elif t_inputOptionsP.inSmiName: self.inSmiName = t_inputOptionsP.inSmiName self.workMode = 12 elif t_inputOptionsP.inMdlName: self.inMdlName = t_inputOptionsP.inMdlName self.workMode = 13 elif t_inputOptionsP.inSdfName: self.inSdfName = t_inputOptionsP.inSdfName self.workMode = 14 elif t_inputOptionsP.inMol2Name: self.inMol2Name = t_inputOptionsP.inMol2Name self.workMode = 15 else: if t_inputOptionsP.inMmCifName: self.inMmCifName = t_inputOptionsP.inMmCifName self.workMode = 111 elif t_inputOptionsP.inSmiName: self.inSmiName = t_inputOptionsP.inSmiName self.workMode = 121 elif t_inputOptionsP.inMdlName: self.inMdlName = t_inputOptionsP.inMdlName self.workMode = 131 elif t_inputOptionsP.inSdfName: self.inSdfName = t_inputOptionsP.inSdfName self.workMode = 141 elif t_inputOptionsP.inMol2Name: self.inMol2Name = t_inputOptionsP.inMol2Name self.workMode = 151 elif t_inputOptionsP.molGen: if t_inputOptionsP.inStdCifName: self.inStdCifName = t_inputOptionsP.inStdCifName self.workMode = 21 elif t_inputOptionsP.inStdCifDir: self.inStdCifDir = t_inputOptionsP.inStdCifDir self.workMode = 22 elif t_inputOptionsP.typeOut: if t_inputOptionsP.inMmCifName: self.inMmCifName = t_inputOptionsP.inMmCifName self.workMode = 31 elif t_inputOptionsP.inSmiName: self.inSmiName = t_inputOptionsP.inSmiName self.workMode = 32 elif t_inputOptionsP.inMdlName: self.inMdlName = t_inputOptionsP.inMdlName self.workMode = 33 elif t_inputOptionsP.inSdfName: self.inSdfName = t_inputOptionsP.inSdfName self.workMode = 34 if t_inputOptionsP.inStdCifName: self.inStdCifName = t_inputOptionsP.inStdCifName self.workMode = 35 elif t_inputOptionsP.repCrd : if t_inputOptionsP.inPdbName and t_inputOptionsP.inMmCifName: self.inMmCifName = t_inputOptionsP.inMmCifName self.inPdbName = t_inputOptionsP.inPdbName self.workMode = 41 if t_inputOptionsP.testMode : self.testMode = True if t_inputOptionsP.monomRoot: self.monomRoot = t_inputOptionsP.monomRoot else: print self.inMdlName print "Here" self.setMonoRoot() # self.monomRoot = "UNL" if t_inputOptionsP.outRoot: self.outRoot = t_inputOptionsP.outRoot self.baseRoot = os.path.basename(t_inputOptionsP.outRoot) tDir = os.path.dirname(t_inputOptionsP.outRoot) if tDir: tStrGrp = os.path.abspath(tDir).strip().split("/") tCurDir = "/" for tSub in tStrGrp: tCurDir = os.path.join(tCurDir, tSub) if not os.path.isdir(tCurDir): os.mkdir(tCurDir) else: self.outRoot = "AcedrgOut" self.baseRoot = "AcedrgOut" self.scrDir = self.outRoot + "_TMP" if not os.path.isdir(self.scrDir): os.mkdir(self.scrDir) if self.inSmiName !="": if not os.path.isfile(self.inSmiName): tName = os.path.join(self.scrDir, "inputSmiles.smi") try : tF =open(tName, "w") except IOError: print "Could not put the input smiles in a file " sys.exit(1) else: tF.write(self.inSmiName+ "\n") tF.close() self.inSmiName = tName print tName def printJobs(self): print "=====================================================================" if self.versionInfo.has_key("ACEDRG_VERSION"): print "| ACEDRG version: %s|"%self.versionInfo["ACEDRG_VERSION"].ljust(49) else: print "=====================================================================" print "| ACEDRG version is not available |" if self.versionInfo.has_key("DATABASE_VERSION"): print "| ACEDRG database version: %s|"%self.versionInfo["DATABASE_VERSION"].ljust(40) else: print "| ACEDRG Database version is not available |" print "=====================================================================" if self.workMode == 11 or self.workMode==12 or self.workMode ==13 or self.workMode==14 or self.workMode==15 \ or self.workMode == 111 or self.workMode==121 or self.workMode ==131 or self.workMode==141 or self.workMode==151 : print "=====================================================================" print "| Your job is generating the dictionary (cif) and coord(pdb) files |" print "| for your ligand and/or monomer |" print "=====================================================================" if self.workMode==11 or self.workMode==111: print "Input file: %s"%os.path.basename(self.inMmCifName) if self.workMode==12 or self.workMode==121: print "Input file: %s"%os.path.basename(self.inSmiName) if self.workMode==13 or self.workMode==131: print "Input file: %s"%os.path.basename(self.inMdlName) if self.workMode==14 or self.workMode==141: print "Input file: %s"%os.path.basename(self.inSdfName) if self.workMode==15 or self.workMode==151: print "Input file: %s"%os.path.basename(self.inMol2Name) print "Output dictionary file: %s"%self.outRoot + ".cif" if self.workMode == 11 or self.workMode==12 or self.workMode ==13 or self.workMode==14 or self.workMode==15: print "Output coordinate file: %s"%self.outRoot + ".pdb" if self.workMode == 21 or self.workMode==22: print "=====================================================================" print "| Your job is to generate molecules (sets of connected atoms), to |" print "| get unique bonds and angles within the molecules and cluster them |" print "| by specificted desigend atom types. |" print "=====================================================================" if self.workMode == 21: print "Input file: %s"%os.path.basename(self.inStdCifName) print "Output molecules: %s"%self.outRoot + "_all_mols.txt" print "Output bonds and angles : %s"%self.outRoot + "_unique_bond_and_angles.txt" elif self.workMode==22: print "Input directory where cif files are: %s"%self.inStdCifDir print "Output bond and angle file : %s "%(self.outRoot + "_all_bonds_and_angles.table") def runLibmol(self, tIn=None): self._cmdline = self.libmol self._log_name = os.path.join(self.scrDir, self.baseRoot + "_cod.log") if self.workMode == 11 or self.workMode==12 or self.workMode ==13 or self.workMode==14 \ or self.workMode == 111 or self.workMode == 121 or self.workMode == 131 \ or self.workMode==141 or self.workMode==151: print "===================================================================" print "| Generate the dictionary file using the internal database |" print "===================================================================" self.outRstCifName = os.path.join(self.scrDir, self.baseRoot + "_cod.rst") self.outRstPdbName = os.path.join(self.scrDir, self.baseRoot + "_cod.pdb") if self.workMode == 11 or self.workMode == 12 or self.workMode == 111 or self.workMode == 121: if tIn: self.inMmCifName = tIn self._cmdline +=" -c %s -D %s "%(self.inMmCifName, self.acedrgTables) self._cmdline += " -r %s -o %s "%(self.monomRoot, self.outRstCifName) #print self._cmdline #os.system(self._cmdline) self.subExecute() if self.workMode == 13 or self.workMode == 14 or self.workMode == 131 or self.workMode == 141: if tIn: self.inMmCifName = tIn self._cmdline += " -s %s -D %s "%(self.inMmCifName, self.acedrgTables) self._cmdline += " -r %s -o %s "%(self.monomRoot, self.outRstCifName) #print self._cmdline #os.system(self._cmdline) self.subExecute() if self.workMode == 15 or self.workMode == 151 : if tIn: self.inMmCifName = tIn self._cmdline += " -g %s -D %s "%(self.inMmCifName, self.acedrgTables) self._cmdline += " -r %s -o %s "%(self.monomRoot, self.outRstCifName) #print self._cmdline #os.system(self._cmdline) self.subExecute() if self.workMode == 21 : if tIn: self.inStdCifName = tIn self.outRstCifName = self.outRoot + ".cif" self.outMolsName = self.monomRoot + "_all_mols.txt" self.outBondsAndAnglesName = self.monomRoot + "_unique_bond_and_angles.txt" self._cmdline += " -b %s "%self.inStdCifName self._cmdline += " -m yes -r %s -o %s "%(self.monomRoot, self.outRstCifName) #print self.cmdline self.subExecute() if self.workMode == 22 : if os.path.isdir(self.inStdCifDir): bTable = self.outRoot + "_all_atoms_bonds_angles.table" self.workMode == 21 tAllBondInMols = [] tExcludedCif = [] for aCif in glob.glob(self.inStdCifDir+"/*.cif"): tMonomRoot = os.path.basename(aCif).split(".")[0] print "Generate molecules, bonds and angles from ", aCif self._cmdline = self.libmol self.outMolsName = os.path.join(self.scrDir,tMonomRoot + "_all_mols.txt") self.outBondsAndAnglesName = os.path.join(self.scrDir, tMonomRoot + "_unique_bond_and_angles.txt") self._log_name = os.path.join(self.scrDir,tMonomRoot + "_cod.log") self._cmdline += " -b %s "%aCif self._cmdline += " -m yes -r %s -o %s.cif "%(tMonomRoot, self.scrDir+"/"+tMonomRoot) #print self._cmdline self.subExecute() if os.path.isfile(self.outBondsAndAnglesName): tAllBondInMols.append(self.outBondsAndAnglesName) else: print "No bonds and angles are generated from ", aCif tExcludedCif.append(aCif) if len(tAllBondInMols) !=0: self.getBondsAndAngles(bTable, tAllBondInMols) if len(tExcludedCif) !=0: print "The following cif files have been excluded from calculations because their large R factors" for aExCif in tExcludedCif: print aExCif if self.workMode == 31 or self.workMode == 32 or self.workMode == 33 or self.workMode == 34 or self.workMode == 35 : print "===================================================================" print "| Generate atom types of Acedrg style and CCP4 style |" print "===================================================================" if self.workMode == 31 or self.workMode == 32: if tIn: self.inMmCifName = tIn self.outAtmTypeName = self.outRoot + "_atomTypes.txt" self._cmdline +=" -A yes -D %s -c %s -o %s "%(self.acedrgTables, self.inMmCifName, self.outAtmTypeName) print self._cmdline self.subExecute() if self.workMode == 41 : self._cmdline += " -p %s -c %s "%(self.inPdbName, self.inMmCifName) self._cmdline += " -y y -o %s "%(self.outRstCifName) #print self._cmdline self.subExecute() def getBondsAndAngles(self, tFName, tMolTabs): for aMonTab in tMolTabs: try: f1 = open(aMonTab, "r") except IOError: print "%s has not been found for reading"%aMonTab else: f1_lines = f1.readlines() f1.close() aSetStrs = os.path.basename(aMonTab).strip().split("_") aFileIdx = aSetStrs[0] lBo = False lAn = False for aL in f1_lines: strGrp = aL.strip().split() if lBo and len(strGrp)==6: # get sorted bonds aElem = self.getElemFromAtomClass(strGrp[0]) bElem = self.getElemFromAtomClass(strGrp[1]) aSet = [strGrp[0], aElem, strGrp[2]] bSet = [strGrp[1], bElem, strGrp[3]] tSets = [aSet, bSet] tSets.sort(listComp) if not self.allBondsAndAngles["bonds"].has_key(tSets[0][1]): # class 1 self.allBondsAndAngles["bonds"][tSets[0][1]] = {} if not self.allBondsAndAngles["bonds"][tSets[0][1]].has_key(tSets[1][1]): # class 2 self.allBondsAndAngles["bonds"][tSets[0][1]][tSets[1][1]] = {} if not self.allBondsAndAngles["bonds"][tSets[0][1]][tSets[1][1]].has_key(tSets[0][0]): # id 1 self.allBondsAndAngles["bonds"][tSets[0][1]][tSets[1][1]][tSets[0][0]] ={} if not self.allBondsAndAngles["bonds"][tSets[0][1]][tSets[1][1]][tSets[0][0]].has_key(tSets[1][0]): # id 2 self.allBondsAndAngles["bonds"][tSets[0][1]][tSets[1][1]][tSets[0][0]][tSets[1][0]] = {} if not self.allBondsAndAngles["bonds"][tSets[0][1]][tSets[1][1]][tSets[0][0]][tSets[1][0]].has_key(strGrp[5]): self.allBondsAndAngles["bonds"][tSets[0][1]][tSets[1][1]][tSets[0][0]][tSets[1][0]][strGrp[5]] = {} self.allBondsAndAngles["bonds"][tSets[0][1]][tSets[1][1]][tSets[0][0]][tSets[1][0]][strGrp[5]]["observations"] = [] self.allBondsAndAngles["bonds"][tSets[0][1]][tSets[1][1]][tSets[0][0]][tSets[1][0]][strGrp[5]]["stats"] = {} aTup = [tSets[0][2], tSets[1][2], float(strGrp[4]), aFileIdx] # atom1_id, atom2_id, bond length and the file index self.allBondsAndAngles["bonds"][tSets[0][1]][tSets[1][1]][tSets[0][0]][tSets[1][0]][strGrp[5]]["observations"].append(aTup) # Get sorted atom types if not self.allBondsAndAngles["atomClasses"].has_key(tSets[0][1]): # atom 1 element type self.allBondsAndAngles["atomClasses"][tSets[0][1]] = {} if not self.allBondsAndAngles["atomClasses"][tSets[0][1]].has_key(tSets[0][0]): # atom 1 class type self.allBondsAndAngles["atomClasses"][tSets[0][1]][tSets[0][0]] = 1 else: self.allBondsAndAngles["atomClasses"][tSets[0][1]][tSets[0][0]] +=1 if not self.allBondsAndAngles["atomClasses"].has_key(tSets[1][1]): # atom 2 element type self.allBondsAndAngles["atomClasses"][tSets[1][1]] = {} if not self.allBondsAndAngles["atomClasses"][tSets[1][1]].has_key(tSets[1][0]): # atom 2 class type self.allBondsAndAngles["atomClasses"][tSets[1][1]][tSets[1][0]] = 1 else: self.allBondsAndAngles["atomClasses"][tSets[1][1]][tSets[1][0]] +=1 elif lAn and len(strGrp)==7: # get sorted bond-angles cenElem = self.getElemFromAtomClass(strGrp[0]) aElem = self.getElemFromAtomClass(strGrp[1]) bElem = self.getElemFromAtomClass(strGrp[2]) aSet = [strGrp[0], cenElem, strGrp[3]] bSet = [strGrp[1], aElem, strGrp[4]] cSet = [strGrp[2], bElem, strGrp[5]] tSets = [bSet, cSet] tSets.sort(listComp) if not self.allBondsAndAngles["angles"].has_key(aSet[1]): # center atom element self.allBondsAndAngles["angles"][aSet[1]] = {} if not self.allBondsAndAngles["angles"][aSet[1]].has_key(tSets[0][1]): # atom1 element self.allBondsAndAngles["angles"][aSet[1]][tSets[0][1]] = {} if not self.allBondsAndAngles["angles"][aSet[1]][tSets[0][1]].has_key(tSets[1][1]) : # atom2 elment self.allBondsAndAngles["angles"][aSet[1]][tSets[0][1]][tSets[1][1]] = {} if not self.allBondsAndAngles["angles"][aSet[1]][tSets[0][1]][tSets[1][1]].has_key(aSet[0]): # center atom class self.allBondsAndAngles["angles"][aSet[1]][tSets[0][1]][tSets[1][1]][aSet[0]] = {} if not self.allBondsAndAngles["angles"][aSet[1]][tSets[0][1]][tSets[1][1]][aSet[0]].has_key(tSets[0][0]): # atom1 class self.allBondsAndAngles["angles"][aSet[1]][tSets[0][1]][tSets[1][1]][aSet[0]][tSets[0][0]] = {} if not self.allBondsAndAngles["angles"][aSet[1]][tSets[0][1]][tSets[1][1]][aSet[0]][tSets[0][0]].has_key(tSets[1][0]): # atom1 class self.allBondsAndAngles["angles"][aSet[1]][tSets[0][1]][tSets[1][1]][aSet[0]][tSets[0][0]][tSets[1][0]] = {} self.allBondsAndAngles["angles"][aSet[1]][tSets[0][1]][tSets[1][1]][aSet[0]][tSets[0][0]][tSets[1][0]]["observations"] = [] self.allBondsAndAngles["angles"][aSet[1]][tSets[0][1]][tSets[1][1]][aSet[0]][tSets[0][0]][tSets[1][0]]["stats"] = {} aTup = [aSet[2], tSets[0][2], tSets[1][2], float(strGrp[6]), aFileIdx] # cen_atom_id, atom1_id, atom2_id, bond length and the file index self.allBondsAndAngles["angles"][aSet[1]][tSets[0][1]][tSets[1][1]][aSet[0]][tSets[0][0]][tSets[1][0]]["observations"].append(aTup) elif aL.find("Bond_length") != -1: lBo = True elif aL.find("Angle_") !=-1: lAn = True lBo = False # output atom types, bonds and angles try: f2 = open(tFName, "w") except IOError: print "%s has not been found for writing"%tFName else: if len(self.allBondsAndAngles["atomClasses"]): f2.write("All unique atom types: \n") for aElem in sorted(self.allBondsAndAngles["atomClasses"].iterkeys()): for aCl in sorted(self.allBondsAndAngles["atomClasses"][aElem].iterkeys()): f2.write("%s %s \n"%(aElem,aCl)) if len(self.allBondsAndAngles["bonds"]): f2.write("All bond lengths: \n") for aElem in sorted(self.allBondsAndAngles["bonds"].iterkeys()): for bElem in sorted(self.allBondsAndAngles["bonds"][aElem].iterkeys()): for aCl in sorted(self.allBondsAndAngles["bonds"][aElem][bElem].iterkeys()): for bCl in sorted(self.allBondsAndAngles["bonds"][aElem][bElem][aCl].iterkeys()): for rP in sorted(self.allBondsAndAngles["bonds"][aElem][bElem][aCl][bCl].iterkeys()): self.getStatsForOneBondClass(self.allBondsAndAngles["bonds"][aElem][bElem][aCl][bCl][rP]["observations"], \ self.allBondsAndAngles["bonds"][aElem][bElem][aCl][bCl][rP]["stats"]) for aSet in self.allBondsAndAngles["bonds"][aElem][bElem][aCl][bCl][rP]["observations"]: if self.testMode: f2.write("%s %s %s %s %s %s %s %7.5f %s\n" \ %(aElem, bElem, aCl, bCl, aSet[0], aSet[1], rP, aSet[2], aSet[3])) else: f2.write("%s %s %s %s %s %s %s %7.5f\n" \ %(aElem, bElem, aCl, bCl, aSet[0], aSet[1], rP, aSet[2])) f2.write("\nAll bond lengths stats: \n") if self.testMode: bCaseIdx =0 casesDir = os.path.join(self.scrDir, "CasesNSTATS") if not glob.glob(casesDir): os.mkdir(casesDir) for aElem in sorted(self.allBondsAndAngles["bonds"].iterkeys()): for bElem in sorted(self.allBondsAndAngles["bonds"][aElem].iterkeys()): for aCl in sorted(self.allBondsAndAngles["bonds"][aElem][bElem].iterkeys()): for bCl in sorted(self.allBondsAndAngles["bonds"][aElem][bElem][aCl].iterkeys()): for rP in sorted(self.allBondsAndAngles["bonds"][aElem][bElem][aCl][bCl].iterkeys()): ave = self.allBondsAndAngles["bonds"][aElem][bElem][aCl][bCl][rP]["stats"]["mean"] sig = self.allBondsAndAngles["bonds"][aElem][bElem][aCl][bCl][rP]["stats"]["sig"] num = self.allBondsAndAngles["bonds"][aElem][bElem][aCl][bCl][rP]["stats"]["nObs"] f2.write("%s %s %7.5f %7.5f %d\n" %(aCl, bCl, ave, sig, num)) if self.testMode and num > 20 and aElem !="H" and bElem != "H" : bCaseIdx +=1 tCasesNameR = aElem + "_" + bElem + str(bCaseIdx) + ".txt" tCasesName = os.path.join(casesDir, tCasesNameR) tCases = open(tCasesName, "w") for aSet in self.allBondsAndAngles["bonds"][aElem][bElem][aCl][bCl][rP]["observations"]: tCases.write("%s %s %s %s %s %7.5f %s\n" \ %(aCl, bCl, aSet[0], aSet[1], rP, aSet[2], aSet[3])) tCases.close() if len(self.allBondsAndAngles["angles"]): f2.write("\n\nAll bond angles: \n") for cenElem in sorted(self.allBondsAndAngles["angles"].iterkeys()): for aElem in sorted(self.allBondsAndAngles["angles"][cenElem].iterkeys()): for bElem in sorted(self.allBondsAndAngles["angles"][cenElem][aElem].iterkeys()): for cenC in sorted(self.allBondsAndAngles["angles"][cenElem][aElem][bElem].iterkeys()): for aC in sorted(self.allBondsAndAngles["angles"][cenElem][aElem][bElem][cenC].iterkeys()): for bC in sorted(self.allBondsAndAngles["angles"][cenElem][aElem][bElem][cenC][aC].iterkeys()): self.getStatsForOneAngleClass(self.allBondsAndAngles["angles"][cenElem][aElem][bElem][cenC][aC][bC]["observations"], \ self.allBondsAndAngles["angles"][cenElem][aElem][bElem][cenC][aC][bC]["stats"]) for aSet in self.allBondsAndAngles["angles"][cenElem][aElem][bElem][cenC][aC][bC]["observations"]: if self.testMode: f2.write("%s %s %s %s %s %s %s %s %s %7.5f %s\n" \ %(cenElem, aElem, bElem, cenC, aC, bC, aSet[0], aSet[1], aSet[2], aSet[3], aSet[4])) else: f2.write("%s %s %s %s %s %s %s %s %s %7.5f\n" \ %(cenElem, aElem, bElem, cenC, aC, bC, aSet[0], aSet[1], aSet[2], aSet[3])) f2.write("\nAll bond angle stats : \n") for cenElem in sorted(self.allBondsAndAngles["angles"].iterkeys()): for aElem in sorted(self.allBondsAndAngles["angles"][cenElem].iterkeys()): for bElem in sorted(self.allBondsAndAngles["angles"][cenElem][aElem].iterkeys()): for cenC in sorted(self.allBondsAndAngles["angles"][cenElem][aElem][bElem].iterkeys()): for aC in sorted(self.allBondsAndAngles["angles"][cenElem][aElem][bElem][cenC].iterkeys()): for bC in sorted(self.allBondsAndAngles["angles"][cenElem][aElem][bElem][cenC][aC].iterkeys()): ave = self.allBondsAndAngles["angles"][cenElem][aElem][bElem][cenC][aC][bC]["stats"]["mean"] sig = self.allBondsAndAngles["angles"][cenElem][aElem][bElem][cenC][aC][bC]["stats"]["sig"] nObs = self.allBondsAndAngles["angles"][cenElem][aElem][bElem][cenC][aC][bC]["stats"]["nObs"] f2.write("%s %s %s %7.5f %7.5f %d\n" \ %(cenC, aC, bC, ave, sig, nObs)) f2.close() def getElemFromAtomClass(self, tAtm): tElem = "" if len(tAtm) != 0: tStrs = tAtm.strip().split("(") if len(tStrs) != 0: if tStrs[0].find("[")==-1: tElem = tStrs[0] else : tElem = tStrs[0].split("[")[0] return tElem def getStatsForOneBondClass(self, tBondObjList, tBondStatsDict): numObjs = len(tBondObjList) if numObjs: tBondStatsDict["nObs"] = numObjs tBondStatsDict["max"] = 0.0 tBondStatsDict["min"] = 100.0 sum = 0.0 for aTup in tBondObjList: if len(aTup)==4: sum = sum + aTup[2] if aTup[2] > tBondStatsDict["max"]: tBondStatsDict["max"] = aTup[2] if aTup[2] < tBondStatsDict["min"]: tBondStatsDict["min"] = aTup[2] else: print "Bug. error in ", aTup sys.exit(1) tBondStatsDict["mean"] = sum/numObjs sum_diff_sq = 0.0 for aTup in tBondObjList: sum_diff_sq +=((aTup[2]- tBondStatsDict["mean"])*(aTup[2]- tBondStatsDict["mean"])) if numObjs > 1: tBondStatsDict["sig"] = math.sqrt(sum_diff_sq/(numObjs-1)) else: tBondStatsDict["sig"] = 0.0 def getStatsForOneAngleClass(self, tAngleObjList, tAngleStatsDict): numObjs = len(tAngleObjList) if numObjs: tAngleStatsDict["nObs"] = numObjs tAngleStatsDict["max"] = 0.0 tAngleStatsDict["min"] = 360.0 sum = 0.0 for aTup in tAngleObjList: if len(aTup)==5: if (aTup[3] > 180.0): aTup[3] = 360.0-aTup[3] elif (aTup[3] < 0.0): aTup[3] = math.fabs(aTup[3]) sum = sum + aTup[3] if aTup[3] > tAngleStatsDict["max"]: tAngleStatsDict["max"] = aTup[3] if aTup[3] < tAngleStatsDict["min"]: tAngleStatsDict["min"] = aTup[3] else: print "Bug. error in ", aTup sys.exit(1) tAngleStatsDict["mean"] = sum/numObjs sum_diff_sq = 0.0 for aTup in tAngleObjList: sum_diff_sq +=((aTup[3]- tAngleStatsDict["mean"])*(aTup[3]- tAngleStatsDict["mean"])) if numObjs > 1: tAngleStatsDict["sig"] = math.sqrt(sum_diff_sq/(numObjs-1)) else: tAngleStatsDict["sig"] = 0.0 def setLibcheckBat(self, tSmiName, tOutRoot): self._cmdline = self.libcheck libcheckBatName = os.path.join(self.scrDir, self.baseRoot + "_libcheck.bat") try: libcheckBat = open(libcheckBatName,"w") except IOError: print libcheckBatName, " could not be opened for write " sys.exit() else: libcheckBat.write(" N \n") libcheckBat.write("FILE_SMILE %s\n"%tSmiName) libcheckBat.write("FILE_O %s \n\n"%tOutRoot) libcheckBat.close() self._cmdline +=" < %s "%(libcheckBatName) #print self.cmdline def runLibcheck(self, tSmiName=None): if tSmiName: self.inSmiName = tSmiName self._log_name = os.path.join(self.scrDir, self.baseRoot + "_libcheck.log") self.libcheckOutRoot = os.path.join(self.scrDir, self.baseRoot + "_libcheck") self.libcheckLibName = self.libcheckOutRoot +".lib" self.setLibcheckBat(self.inSmiName, self.libcheckOutRoot) self.subExecute() def setRefmacCom(self, tPdbIn, tLibIn, tPdbOut, tStage=2): self._cmdline = self.refmac if tStage==1: self._cmdline += " xyzin %s libin %s xyzout %s < 1000 and os.path.getsize(self.outRstCifName) > 500: print "===================================================================" print "| Geometrical Optimization |" print "===================================================================" stageNow = 1 self.runRefmac(self.outRstPdbName, self.outRstCifName, stageNow) if os.path.isfile(self.refmacXYZOUTName): tPdb1 = self.refmacXYZOUTName stageNow = 2 self.runRefmac(tPdb1, self.outRstCifName, stageNow) if os.path.isfile(self.refmacXYZOUTName): tPdb1 = self.refmacXYZOUTName stageNow = 3 self.runRefmac(tPdb1, self.outRstCifName, stageNow) if os.path.isfile(self.refmacXYZOUTName): tPdb1 = self.refmacXYZOUTName stageNow = 4 self.runRefmac(tPdb1, self.outRstCifName, stageNow) if os.path.isfile(self.refmacXYZOUTName): finPdb = self.outRoot + ".pdb" finRst = self.outRoot + ".cif" #os.system("cp %s %s "%(self.refmacXYZOUTName, finPdb)) shutil.copy(self.refmacXYZOUTName, finPdb) #os.system("cp %s %s "%(self.outRstCifName, finRst)) if os.path.isfile(finPdb): self.inPdbName = finPdb self.inMmCifName = self.outRstCifName self.outRstCifName = finRst self.transCoordsPdbToCif(self.inPdbName, self.inMmCifName, self.outRstCifName) print "===================================================================" else: print "Failed to produce %s after final geometrical optimization"%finPdb else: print "Failed to produce the final coordinates at stage 4 optimization" else: print "Failed to produce the coordinates at stage 3 optimization" else: print "Failed to produce the coordinates at stage 2 optimization" else: print "Failed to produce the coordinates at stage 1 optimization" else: print "No dictionary file produced ! " else: print "No dictionary file produced ! " def transCoordsPdbToCif(self, tPdbInName, tCifInName, tCifOutName): cifCont = {} cifCont['head'] = [] cifCont['atoms'] = [] cifCont['others'] = [] pdbAtoms = {} try: tPdbIn = open(tPdbInName, "r") except IOError: print "%s can not be opened for reading"%tPdbInName sys.exit() else: try: tCifIn = open(tCifInName, "r") except IOError: print "%s can not be opened for reading"%tCifInName sys.exit() else: allPdbLines = tPdbIn.readlines() tPdbIn.close() for aLine in allPdbLines: aLine = aLine.strip() if aLine.find("ATOM") !=-1 or aLine.find("HETATM") !=-1 : tName = aLine[12:16].strip() tX = aLine[30:38].strip() tY = aLine[38:46].strip() tZ = aLine[46:54].strip() pdbAtoms[tName] = [] pdbAtoms[tName].append(tX) pdbAtoms[tName].append(tY) pdbAtoms[tName].append(tZ) allCifLines = tCifIn.readlines() tCifIn.close() lStart = True lAtom = False lOther = False for aLine in allCifLines: if aLine.find("_chem_comp_atom.z") != -1: cifCont['head'].append(aLine) lStart = False lAtom = True elif lAtom and aLine.find("loop") != -1: lAtom = False lOther = True cifCont['others'].append(aLine) elif lStart: cifCont['head'].append(aLine) elif lAtom: strGrp = aLine.split() tName = "" tID = strGrp[1].strip() if tID.find("\"") !=-1: for aC in tID: if aC !="\"": tName +=aC else: tName = tID if pdbAtoms.has_key(tName): bLine = "%s%s%s%s%s%s%s%s\n"%(strGrp[0].ljust(8), tID.ljust(8), strGrp[2].ljust(8), \ strGrp[3].ljust(8), strGrp[4].ljust(8), \ pdbAtoms[tName][0].ljust(12), pdbAtoms[tName][1].ljust(12), \ pdbAtoms[tName][2].ljust(12)) cifCont['atoms'].append(bLine) else: print "Bug. can not find atom %s in Pdb file %s "%(tName, tPdbInName) sys.exit() elif lOther: cifCont['others'].append(aLine) try: tOutCif = open(tCifOutName, "w") except IOError: print "%s can not be opened for reading"%tCifOutName sys.exit() else: for aL in cifCont['head']: tOutCif.write(aL) for aL in cifCont['atoms']: tOutCif.write(aL) for aL in cifCont['others']: tOutCif.write(aL) tOutCif.close() def execute(self): self.printJobs() if self.workMode == 11 or self.workMode == 111: # Stage 1: dictionary generation using a mmcif file if os.path.isfile(self.inMmCifName): self.runLibmol(self.inMmCifName) else: print "%s does not exist"%self.inMmCifName sys.exit() if self.workMode == 11 : # Stage 2: optimization self.runGeoOpt() if self.workMode == 12 or self.workMode == 121: # Stage 1: Transfer the SMILE input into a mmcif file if os.path.isfile(self.inSmiName): self.runLibcheck(self.inSmiName) else: print "%s does not exist"%self.inSmiName sys.exit() # Stage 2: dictionary generation using a mmcif file if os.path.isfile(self.libcheckLibName): self.runLibmol(self.libcheckLibName) else: print "%s does not exist"%self.inMmCifName sys.exit() if self.workMode == 12: # Stage 3: optimization self.runGeoOpt() if self.workMode == 13 or self.workMode == 131 : # Stage 1: dictionary generation using a mdl file if os.path.isfile(self.inMdlName): self.runLibmol(self.inMdlName) else: print "can not find %s to read "%self.inMdlName sys.exit() if self.workMode == 13 : # Stage 2: optimization self.runGeoOpt() if self.workMode == 14 or self.workMode == 141 : # Stage 1: dictionary generation using a sdf file if os.path.isfile(self.inSdfName): self.runLibmol(self.inSdfName) else: print "%s does not exist"%self.inSdfName sys.exit() if self.workMode == 14: # Stage 2: optimization self.runGeoOpt() if self.workMode == 15 or self.workMode == 151 : # Stage 1: dictionary generation using a mol2 file if os.path.isfile(self.inMol2Name): self.runLibmol(self.inMol2Name) else: print "%s does not exist"%self.inMol2Name sys.exit() if self.workMode == 15: # Stage 2: optimization self.runGeoOpt() if self.workMode == 21: # Stage 1: generate molecules and the associated bond and bond-angle values # using a small molecule cif file if os.path.isfile(self.inStdCifName): self.runLibmol(self.inStdCifName) else: print "Can not find the input file ", self.inStdCifName if self.workMode == 22: # 1. Generate molecules using the small molecule cif files at the input directory. # 2. Generate atom classes for atoms in the molecules. # 3. Obtain unique bond lengths and angles and cluster them according to their # component atoms in tables. if os.path.isdir(self.inStdCifDir): self.runLibmol() else: print "Can not find the input directory ", self.inStdCifDir if self.workMode == 31: print "work mode ", self.workMode if os.path.isfile(self.inMmCifName): self.runLibmol() if self.workMode == 32: print "work mode ", self.workMode if os.path.isfile(self.inSmiName): self.runLibcheck(self.inSmiName) else: print "%s does not exist"%self.inSmiName sys.exit() if os.path.isfile(self.libcheckLibName): self.runLibmol(self.libcheckLibName) else: print "%s does not exist"%self.inMmCifName sys.exit() if self.workMode == 33: print "work mode ", self.workMode if os.path.isfile(self.inMdlName): self.runLibmol() if self.workMode == 34: print "work mode ", self.workMode if os.path.isfile(self.inSdfName): self.runLibmol() if self.workMode == 35: print "work mode ", self.workMode if os.path.isfile(self.inStdCifName): self.runLibmol() if self.workMode ==111 or self.workMode ==121 or self.workMode ==131 or self.workMode ==141: if os.path.isfile(self.outRstCifName): tCif = self.outRoot + ".cif" #os.system("cp %s %s"%(self.outRstCifName, tCif)) shutil.copy(self.outRstCifName, tCif) else: print "acedrg failed to generate a dictionary file" # Other supplement functions def main(): acedrgObj = Acedrg(sys.argv[1:]) if __name__ == "__main__": main()