### Sample usage from testbin directory: python query4.py &> [YOUR-OUTPUT-FILE] ### This query searches Glycan structures based on the given chemical code. ExtractOntologyInfoByStringChemicalCode(chemical_code, output_type) import sys sys.path.insert(0, '../') import gmml temp = gmml.Assembly() ### chemical_code is the linear version of the Glycode. more information on Glycode: http://glycam.org/docs/gmml/2016/03/31/glycode-internal-monosaccharide-representation/ ### Change the first input argument in the function calls as you desire. ExtractOntologyInfoByStringChemicalCode(chemical_code, output_type) if len(sys.argv) == 2: temp.ExtractOntologyInfoByStringChemicalCode("_4^2^3P^a^+1", sys.argv[1]) else: temp.ExtractOntologyInfoByStringChemicalCode("_4^2^3P^a^+1")
###FOR FURTHER INSTRUCTIONS PLEASE REFER TO alternateresidues.py SAMPLE FILE #SAMPLE COMMAND : # python sequencesanitycheck.py -seq "LManpa1-2[LGalpa1-3LGlcpa1-4]DGalpa1-4DGlcpa1-6DAllpa1-OH" -prep "../gmml/dat/CurrentParams/leaprc_GLYCAM_06j-1_2014-03-14/GLYCAM_06j-1.prep" -parm "../gmml/dat/CurrentParams/leaprc_GLYCAM_06j-1_2014-03-14/GLYCAM_06j.dat" import sys sys.path.insert(0, '../') import gmml import time if len(sys.argv) < 2: print 'Please enter a sequence using -seq option' elif len(sys.argv) < 8: assembly = gmml.Assembly() prep_residues = gmml.condensedsequence_amber_prep_residue_tree() if assembly.CheckCondensedSequenceSanity(sys.argv[2], prep_residues): print sys.argv[2], ' is valid' assembly.BuildAssemblyFromCondensedSequence(sys.argv[2], sys.argv[4], sys.argv[6], True) pdb_file = assembly.BuildPdbFileStructureFromAssembly() pdb_file.Write('pdb_file.pdb') print 'Charge: ' + str(assembly.GetTotalCharge()) condensed_sequence = gmml.CondensedSequence(sys.argv[2]) rotamers_glycosidic_angles_info = condensed_sequence.GetCondensedSequenceRotamersAndGlycosidicAnglesInfo( condensed_sequence.GetCondensedSequenceResidueTree()) # Remove tg rotamer of OMEGA angle for 'DGalpA1-6DGlcpA' linkage if exists in selected rotamers for the specific linkage new_rotamers_glycosidic_angles_info = gmml.rotamer_angle_info_vector() for rotamers_name, rotamers_info in rotamers_glycosidic_angles_info: if rotamers_name == 'DGalpA1-6DGlcpA': new_selected_rotamers = gmml.string_vector_string_pair_vector() for sr_name, sr_val in rotamers_info.selected_rotamers_: if sr_name == 'omega':
if sys.argv[3] == '-amino_libs': arguments = sys.argv[4].split(',') for argument in arguments: amino_libs.push_back(argument) elif sys.argv[3] == '-amino_libs': arguments = sys.argv[4].split(',') for argument in arguments: amino_libs.push_back(argument) if len(sys.argv) < 6: print('Please import a pdb file using -pdb option') elif sys.argv[5] == '-pdb': pdb_file = sys.argv[6] else: print( 'Please import one pdb file using -pdb option and (optionally) amino library file(s) using -amino_libs option' ) if pdb_file != '': het.push_back(pdb_file) temp = gmml.Assembly(het, gmml.PDB) empty = gmml.string_vector() start = time.time() temp.BuildStructureByDistance(10) end = time.time() print('Time of building structure by distance:', end - start, '(sec)') oligos = temp.ExtractSugars(amino_libs) res_map = temp.ExtractResidueGlycamNamingMap(oligos) temp.UpdateResidueName2GlycamName(res_map, prep_file) pdb = temp.BuildPdbFileStructureFromAssembly() pdb.Write('glycam_pdb.pdb')
import sys sys.path.insert(0, '../') import gmml import time assembly = gmml.Assembly() assembly.BuildAssemblyFromPdbFile(sys.argv[1]) assembly.BuildStructureByDistance(1) assembly.Solvation(8, 3, sys.argv[2]) pdb_file = assembly.BuildPdbFileStructureFromAssembly() pdb_file.Write('solvated.pdb') solvent = gmml.Assembly() solute = gmml.Assembly() assembly.SplitSolvent(solvent, solute) llc_solvent = gmml.Coordinate() urc_solvent = gmml.Coordinate() solvent.GetBoundary(llc_solvent, urc_solvent) llc_solute = gmml.Coordinate() urc_solute = gmml.Coordinate() solute.GetBoundary(llc_solute, urc_solute) solvent_box_size = urc_solvent solvent_box_size - llc_solvent print 'Solvent box size: ' + str(solvent_box_size.GetX()) + ' x ' + str( solvent_box_size.GetY()) + ' x ' + str(solvent_box_size.GetZ()) urc_buffer = urc_solvent urc_buffer - urc_solute llc_buffer = llc_solute llc_buffer - llc_solvent print 'Buffer size => +X: ' + str(urc_buffer.GetX()) + ' +Y: ' + str( urc_buffer.GetY()) + ' +Z: ' + str(urc_buffer.GetZ()) + ' -X: ' + str( llc_buffer.GetX()) + ' -Y: ' + str(llc_buffer.GetY()) + ' -Z: ' + str(