###FOR FURTHER INSTRUCTIONS PLEASE REFER TO alternateresidues.py SAMPLE FILE
#SAMPLE COMMAND :
# python cycle.py -amino_libs "../gmml/dat/CurrentParams/leaprc.ff12SB_2014-04-24/amino12.lib" -pdb "../../../Downloads/1.pdb" -prep "../gmml/dat/CurrentParams/leaprc_GLYCAM_06j-1_2014-03-14/GLYCAM_06j-1.prep" &> output_file_name
import sys
sys.path.insert(0, '../')
import gmml
import time
het = gmml.string_vector()
amino_libs = gmml.string_vector()
pdb_file = ''
prep_file = ''
if len(sys.argv) < 2:
print(
'Please import one pdb file using -pdb option, one prep file using -prep option and (optionally) amino library file(s) using -amino_libs option'
)
elif sys.argv[1] == '-amino_libs':
arguments = sys.argv[2].split(',')
for argument in arguments:
amino_libs.push_back(argument)
if len(sys.argv) < 4:
print(
'Please import one pdb file using -pdb option and one prep file using -prep option'
)
elif sys.argv[3] == '-pdb':
pdb_file = sys.argv[4]
if (len(sys.argv) < 6):
print('Please import one prep file using -prep option')
elif sys.argv[5] == '-prep':
prep_file = sys.argv[6]
elif sys.argv[3] == '-prep':
###FOR FURTHER INSTRUCTIONS PLEASE REFER TO alternateresidues.py SAMPLE FILE #SAMPLE COMMAND : # python aminoacidchains.py -amino_libs "gmml/dat/CurrentParams/leaprc.ff12SB_2014-04-24/amino12.lib","gmml/dat/CurrentParams/leaprc.ff12SB_2014-04-24/aminont12.lib","gmml/dat/CurrentParams/leaprc.ff12SB_2014-04-24/aminoct12.lib" -prep "gmml/dat/CurrentParams/leaprc_GLYCAM_06j-1_2014-03-14/GLYCAM_06j-1.prep" -pdb "gmml/example/pdb/1Z7E.pdb" #If you need to add other libraries for glycam there is -glycam_libs option available for the command. import sys sys.path.insert(0, '../') import gmml temp = gmml.PdbPreprocessor() amino_libs = gmml.string_vector() glycam_libs = gmml.string_vector() prep = gmml.string_vector() if sys.argv[1] == '--help': print 'Available options:' print '-amino_libs : amino acid library file(s) (e.g. gmml/dat/CurrentParams/leaprc.ff12SB_2014-04-24/amino12.lib)' print '-glycam_libs: glycam library file(s)' print '-other_libs : other kinds of library files' print '-prep : prep file(s) (e.g. gmml/dat/CurrentParams/leaprc_GLYCAM_06j-1_2014-03-14/GLYCAM_06j-1.prep)' print '-pdb : pdb file (e.g. gmml/example/pdb/1RVZ_New.pdb)' print '-cnf : configuration file as an argument. sample file format:' print 'amino_libs' print 'gmml/dat/CurrentParams/leaprc.ff12SB_2014-04-24/amino12.lib' print 'gmml/dat/CurrentParams/leaprc.ff12SB_2014-04-24/aminont12.lib' print 'glycam_libs' print 'other_libs' print 'prep' print 'gmml/dat/CurrentParams/leaprc_GLYCAM_06j-1_2014-03-14/GLYCAM_06j-1.prep' print 'pdb'
###SAMPLE COMMAND
# python residueinfo.py -amino_libs "gmml/dat/CurrentParams/leaprc.ff12SB_2014-04-24/amino12.lib","gmml/dat/CurrentParams/leaprc.ff12SB_2014-04-24/aminont12.lib","gmml/dat/CurrentParams/leaprc.ff12SB_2014-04-24/aminoct12.lib" -prep "gmml/dat/CurrentParams/leaprc_GLYCAM_06j-1_2014-03-14/GLYCAM_06j-1.prep" -pdb "gmml/example/pdb/1NXC.pdb"
#If you need to add other libraries for glycam and other residues there are -glycam_libs and -other_libs options available for the command.
###IMPORTING THE GMML LIBRARY
import sys
sys.path.insert(0, '../')
import gmml
temp = gmml.PdbPreprocessor()
amino_libs = gmml.string_vector()
glycam_libs = gmml.string_vector()
other_libs = gmml.string_vector()
prep = gmml.string_vector()
if sys.argv[1] == '--help':
print 'Available options:'
print '-amino_libs : amino acid library file(s) (e.g. gmml/dat/CurrentParams/leaprc.ff12SB_2014-04-24/amino12.lib)'
print '-glycam_libs: glycam library file(s)'
print '-other_libs : other kinds of library files'
print '-prep : prep file(s) (e.g. gmml/dat/CurrentParams/leaprc_GLYCAM_06j-1_2014-03-14/GLYCAM_06j-1.prep)'
print '-pdb : pdb file (e.g. gmml/example/pdb/1RVZ_New.pdb)'
print '-cnf : configuration file as an argument. sample file format:'
print 'amino_libs'
print 'gmml/dat/CurrentParams/leaprc.ff12SB_2014-04-24/amino12.lib'
print 'gmml/dat/CurrentParams/leaprc.ff12SB_2014-04-24/aminont12.lib'
print 'glycam_libs'
print 'other_libs'
print 'prep'
###FOR FURTHER INSTRUCTIONS PLEASE REFER TO alternateresidues.py SAMPLE FILE
#SAMPLE COMMAND :
# python gapsinaminoacidchains.py -amino_libs "gmml/dat/CurrentParams/leaprc.ff12SB_2014-04-24/amino12.lib","gmml/dat/CurrentParams/leaprc.ff12SB_2014-04-24/aminont12.lib","gmml/dat/CurrentParams/leaprc.ff12SB_2014-04-24/aminoct12.lib" -pdb "gmml/example/pdb/1Z7E.pdb"
import sys
sys.path.insert(0, '../')
import gmml
temp = gmml.PdbPreprocessor()
amino_libs = gmml.string_vector()
if sys.argv[1] == '--help':
print("""
Available options:
-amino_libs : amino acid library file(s) (e.g. gmml/dat/CurrentParams/leaprc.ff12SB_2014-04-24/amino12.lib)
-glycam_libs: glycam library file(s)
-other_libs : other kinds of library files
-prep : prep file(s) (e.g. gmml/dat/CurrentParams/leaprc_GLYCAM_06j-1_2014-03-14/GLYCAM_06j-1.prep)
-pdb : pdb file (e.g. gmml/example/pdb/1RVZ_New.pdb)
-cnf : configuration file as an argument.
Sample file format:
amino_libs
gmml/dat/CurrentParams/leaprc.ff12SB_2014-04-24/amino12.lib
gmml/dat/CurrentParams/leaprc.ff12SB_2014-04-24/aminont12.lib
glycam_libs
other_libs
prep
gmml/dat/CurrentParams/leaprc_GLYCAM_06j-1_2014-03-14/GLYCAM_06j-1.prep
pdb
gmml/example/pdb/1RVZ_New.pdb
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':
new_omega_selected_rotamers = gmml.string_vector()
for val in sr_val:
if val != 'tg':
new_omega_selected_rotamers.push_back(val)
new_selected_rotamers.push_back(
[sr_name, new_omega_selected_rotamers])
else:
new_selected_rotamers.push_back([sr_name, sr_val])
rotamers_info.selected_rotamers_ = new_selected_rotamers
new_rotamers_glycosidic_angles_info.push_back(
[rotamers_name, rotamers_info])
rotamers_glycosidic_angles_info = new_rotamers_glycosidic_angles_info
# Add tg rotamer of OMEGA for 'DGalpA1-6DGlcpA' linkage if tg is one of the possible rotamers for the specifi linkage
new_rotamers_glycosidic_angles_info = gmml.rotamer_angle_info_vector()
for rotamers_name, rotamers_info in rotamers_glycosidic_angles_info:
import sys
sys.path.insert(0, '../')
import gmml
import time
empty_vector = gmml.string_vector()
preps = gmml.string_vector()
preps.push_back(sys.argv[2])
assembly = gmml.Assembly()
assembly.BuildAssemblyFromPdbFile(sys.argv[1], empty_vector, empty_vector,
empty_vector, preps, sys.argv[3])
assembly.BuildStructureByDistance(1)
output = assembly.BuildPrepFileStructureFromAssembly(sys.argv[3])
output.Write(sys.argv[4])
###FOR FURTHER INSTRUCTIONS PLEASE REFER TO alternateresidues.py SAMPLE FILE
#SAMPLE COMMAND :
# python cycle.py -amino_libs "../gmml/dat/CurrentParams/leaprc.ff12SB_2014-04-24/amino12.lib" -pdb "../../../Downloads/1.pdb" &> output_file_name
import sys
sys.path.insert(0, '../')
import gmml
import time
het = gmml.string_vector()
amino_libs = gmml.string_vector()
pdb_file = ''
if len(sys.argv) < 2:
print('Please import one pdb file using -pdb option and (optionally) amino library file(s) using -amino_libs option')
elif sys.argv[1] == '-amino_libs':
arguments = sys.argv[2].split(',')
for argument in arguments:
amino_libs.push_back(argument)
if len(sys.argv) < 4:
print('Please import one pdb file using -pdb option')
elif sys.argv[3] == '-pdb':
pdb_file = sys.argv[4]
elif sys.argv[1] == '-pdb':
pdb_file = sys.argv[2]
if len(sys.argv) > 3:
if sys.argv[3] == '-amino_libs':
arguments = sys.argv[4].split(',')
for argument in arguments:
amino_libs.push_back(argument)
else:
print('Please import one pdb file using -pdb option and (optionally) amino library file(s) using -amino_libs option')
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':
new_omega_selected_rotamers = gmml.string_vector()
for val in sr_val:
if val != 'tg':
new_omega_selected_rotamers.push_back(val)
new_selected_rotamers.push_back([sr_name, new_omega_selected_rotamers])
else:
new_selected_rotamers.push_back([sr_name, sr_val])
rotamers_info.selected_rotamers_ = new_selected_rotamers
new_rotamers_glycosidic_angles_info.push_back([rotamers_name, rotamers_info])
rotamers_glycosidic_angles_info = new_rotamers_glycosidic_angles_info
# Add tg rotamer of OMEGA for 'DGalpA1-6DGlcpA' linkage if tg is one of the possible rotamers for the specifi 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':
is_possible = False
import sys
sys.path.insert(0, '../')
import gmml
temp = gmml.Assembly()
### ring_type can be "P" or "F"
### orientations can be "Up" or "Down" which shows the position of the exocyclic atoms with respect to the ring
### anomeric_orientation: orientation of the exocyclic oxygen/nitrogen attached to the anomeric carbon of the ring
### anomeric_side_carbon_orientation: orientation of the exocyclic carbon attached to the anomeric carbon of the ring
### index_two_orientation: orientation of the exocyclic oxygen/nitrogen attached to the second carbon of the ring
### index_three_orientation: orientation of the exocyclic oxygen/nitrogen attached to the third carbon of the ring
### index_four_orientation: orientation of the exocyclic oxygen/nitrogen attached to the fourth carbon of the ring (specific to pyranoses)
### last_c_orientation: orientation of the exocyclic oxygen/nitrogen attached to the last carbon of the ring
### In the following lines the 3D structure of the first sugar is being defiend based on the orientation of the exocyclic atoms with respect to the ring
structure1 = gmml.string_vector()
### Change the following line based on the ring type (P or F)
structure1.push_back("P")
### Change the following line based on the orientation of the exocyclic oxygen/nitrogen attached to the anomeric carbon of the ring. leave "" if don't want to specify.
structure1.push_back("Up")
### Change the following line based on the orientation of the exocyclic carbon attached to the anomeric carbon of the ring. leave "" if don't want to specify.
structure1.push_back("")
### Change the following line based on the orientation of the exocyclic oxygen/nitrogen attached to the second carbon of the ring. leave "" if don't want to specify.
structure1.push_back("Down")
### Change the following line based on the orientation of the exocyclic oxygen/nitrogen attached to the third carbon of the ring. leave "" if don't want to specify.
structure1.push_back("Up")
### Change the following line based on the orientation of the exocyclic oxygen/nitrogen attached to the fourth carbon of the ring (specific to pyranoses). leave "" if don't want to specify.
structure1.push_back("Down")
### Change the following line based on the orientation of the exocyclic oxygen/nitrogen attached to the third carbon of the ring. leave "" if don't want to specify.
structure1.push_back("Up")
import sys sys.path.insert(0, '../') import gmml import time empty_vector = gmml.string_vector() preps = gmml.string_vector() preps.push_back(sys.argv[2]) assembly = gmml.Assembly() assembly.BuildAssemblyFromPdbFile(sys.argv[1], empty_vector, empty_vector, empty_vector, preps, sys.argv[3]) assembly.BuildStructureByDistance(1) output = assembly.BuildPrepFileStructureFromAssembly(sys.argv[3]) output.Write(sys.argv[4])
