###FOR FURTHER INSTRUCTIONS PLEASE REFER TO alternateresidues.py SAMPLE FILE
sys.path.insert(0, '../')
import gmml
temp = gmml.PdbPreprocessor()
pdbfile = gmml.PdbFile("gmml/example/pdb/1RVZ_New.pdb")
#GIVE THE ADDRESS OF THE PDB FILE TO EXTRACT THE INFORMATION OR GIVE IT BY THE COMMAND LINE:
temp.ExtractCYSResidues(pdbfile)
#temp.ExtractCYSResidues(sys.argv[1])
disulfide_bonds = temp.GetDisulfideBonds()
for x in xrange(0, disulfide_bonds.size()):
disulfide_bonds[x].Print()
###UPDATING CYS RESIDUES###
disulfide_bonds[0].SetIsBonded(False)
print("Updated disulfide bond(s):")
disulfide_bonds[0].Print()
temp.UpdateCYSResidues(pdbfile, disulfide_bonds)
pdbfile.Write('cysresidues-update.pdb')
###FOR FURTHER INSTRUCTIONS PLEASE REFER TO alternateresidues.py SAMPLE FILE
import sys
sys.path.insert(0, '../')
import gmml
temp = gmml.PdbPreprocessor()
st = gmml.PdbFile()
pdbfile = st.LoadPdbFile("gmml/example/pdb/1RVZ_New.pdb")
#pdbfile = gmml.PdbFile(sys.argv[1])
temp.ExtractHISResidues(pdbfile)
histidine_mappings = temp.GetHistidineMappings()
for x in xrange(0, histidine_mappings.size()):
histidine_mappings[x].Print()
###UPDATING HISTIDINE MAPPINGS###
#MODIFYING selected_mapping ATTRIBUTE OF THE HISTIDINE MAPPINGS VECTOR (POSSIBLE OPTIONS: gmml.HIE, gmml.HIP, gmml.HID)
histidine_mappings[0].SetSelectedMapping(gmml.HIP)
print "The Updated part(s):"
histidine_mappings[0].Print()
temp.UpdateHISMapping(pdbfile, histidine_mappings)
pdbfile.Write('hisresidues-update.pdb')
elif arg == '-glycam_libs':
arguments = sys.argv[i + 1].split(',')
for argument in arguments:
glycam_libs.push_back(argument)
elif arg == '-other_libs':
arguments = sys.argv[i + 1].split(',')
for argument in arguments:
other_libs.push_back(argument)
elif arg == '-prep':
arguments = sys.argv[i + 1].split(',')
for argument in arguments:
prep.push_back(argument)
elif arg == '-pdb':
pdb = sys.argv[i + 1]
pdbfile = gmml.PdbFile(pdb)
temp.ExtractResidueInfo(pdbfile, amino_libs, glycam_libs, other_libs, prep)
###FOR GIVING THE FILES MANUALLY AND THROUGH THE COMMAND LINE USE THE FOLOWIG SECTION
#amino_libs.push_back("gmml/dat/lib/GLYCAM_amino_06h.lib")
#amino_libs.push_back("gmml/dat/lib/GLYCAM_aminoct_06h.lib")
#amino_libs.push_back("gmml/dat/lib/GLYCAM_aminont_06h.lib")
#temp.ExtractRemovedHydrogens("gmml/example/pdb/1Z7E-Mod.pdb, amino_libs, glycam_libs, other_libs, prep)
residue_info = temp.GetResidueInfoMap()
for x in residue_info:
residue_info[x].Print()
print 'Model charge is: ', temp.CalculateModelCharge(pdbfile, amino_libs,
glycam_libs, other_libs,
# python alternateresidues.py gmml/example/pdb/1Z7E-Mod.pdb
###IMPORTING THE GMML LIBRARY
import sys
sys.path.insert(0, '../')
import gmml
###BUILDING AN OBJECT OF THE PDB PREPROCESSOR AND STORING IT IN "temp" VARIABLE TO WORK WITH
temp = gmml.PdbPreprocessor()
###FIRST OPTION TO BUILD THE PDB FILE OBJECT: GIVE YOUR PDB FILE PATH IN THE FOLLOWING LINE. (IF YOU WANT TO USE THE SECOND OPTION COMMENT THE FOLLOWING LINE)
#pdbfile = gmml.PdbFile("gmml/example/1Z7E-Mod.pdb")
###SECOND OPTION TO BUILD THE PDB FILE OBJECT. (IF YOU WANT TO USE THE FIRST OPTION COMMENT THE FOLLOWING LINE)
pdbfile = gmml.PdbFile(sys.argv[1])
###EXTRACTING INFORMATION
temp.ExtractAlternateResidue(pdbfile)
###GETTING THE RESULT FOR THE ALTERNATE RESIDUES OF THE GIVEN FILE
alternate_residues_map = temp.GetAlternateResidueMap()
###IF YOU WANT TO SEE THE RESULT IN THE TERMINAL USE THE FOLLOWING FOR LOOP OTHERWISE IGNORE AND COMMENT THE LOOP
print(alternate_residues_map)
for x in alternate_residues_map:
alternate_residues_map[x].Print()
###UPDATING ALTERNATE RESIDUES###
###GETTING THE OBJECT OF FIRST RESIDUE WITH ALTERNATE LOCATIONS (KEY OF THE alternate_residues_map IS THE COMBINATION OF "residuename_chainId_sequenceNumber_insertionCode")
selected_alt_residue = alternate_residues_map[