Python scripts to convert from and to .ndb file format
Usage: gro2ndb.py -f file.gro -n name_NDB_file
Other options:
-res {int} : Resolution for each bead -chroID {string} : String up to 2 characters with the chain identifier : Default = C -chro {int} : Chromosome number in the *.gro file to be converted -loops {file} : Text file that contains loop annotations -sigma {float} : Value for the Variance of DNA Distribution
Usage: pdb2ndb.py -f file.pdb -n name_NDB_file
Other options:
-res {int} : Resolution for each bead -chroID {string} : String up to 2 characters with the chain identifier : Default = C -loops {file} : Text file that contains loop annotations -sigma {float} : Value for the Variance of DNA Distribution
Usage: csv2ndb.py -f file.csv -n name_NDB_file
This corverter was originally wrote to convert data from Bintu et. al. (2018) Science.
Other options:
-res {int} : Resolution for each bead -chroID {string} : String up to 2 characters with the chain identifier : Default = C -loops {file} : Text file that contains loop annotations -sigma {float} : Value for the Variance of DNA Distribution
Usage: spw2ndb.py -f file.spw -n name_NDB_file
Other options:
-res {int} : Resolution for each bead -chroID {string} : String up to 2 characters with the chain identifier : Default = C -loops {file} : Text file that contains loop annotations -sigma {float} : Value for the Variance of DNA Distribution
Usage: cndb2ndb.py -f file.cndb -n name_NDB_file
Usage: ndb2pdb.py -f file.ndb -n name_PDB_file
Usage: ndb2spw.py -f file.ndb -n name_SPW_file
Other options:
-t {string} : Value of field "name" at spw header -g {string} : Assembly of genome -c {string} : Number of chromosome
ndb2cndb.py -f file.ndb -n name_CNDB_file