polyphony.cfg

This file allows the user to configure the way Polyphony runs. It holds path and url information that is best not embedded in the code itself. It is parsed using the ConfigParser module. The initial reads in variable values and stores them in a global object on running a Polyphony routine. Its initial contents are shown below. @polyphonydatadir@ is replaced by ~/Polyphony by default. This can be changed by editing the setup.py file.

[database]
user: polyphony
passwd: polyphony
host: spunky.bioc.cam.ac.uk

[directories]
tmp: /tmp/
data: @polyphonydatadir@

[files]
pdb_code_lookup : @polyphonydatadir@/pdb_code_lookup.txt

[executables]
ncont_env : /home/william/software/CCP4-Lin-generic/setup-scripts/csh/ccp4.setup
ncont : /home/william/software/CCP4-Lin-generic/ccp4-6.1.13/bin/ncont
fpocket : /usr/local/bin/fpocket
score_conservation : /home/u023206/software/conservation_code/score_conservation.py

[websites]
pdb_ftp: ftp://ftp.wwpdb.org/
pdb_rest: http://www.pdb.org/pdb/rest/

[properties]
# Use property_name with -p option of Polyphony scripts. 

# Defaults
#
# property_name     module_name                 class_name 
backbone :          Polyphony.Backbone,         Kappa_Tau_Alignment_Array
sidechain :         Polyphony.Sidechains,       SideChain_Alignment_Array
phipsi :            Polyphony.Phipsi,           Phi_Psi_Alignment_Array
bfactor :           Polyphony.Bfactors,         Bfactor_Alignment_Array
sequence :          Polyphony.Residues,         Residue_Alignment_Array
calphas :           Polyphony.Calpha_Coords,    Calpha_Coords_Array
# Requiring 3D party software or database access
#
# Uncomment lines below after installing required software
#crystal_contacts :  Polyphony.Contacts,     Contact_Alignment_Array
#ligand_contacts :   Polyphony.Credo_New,    New_Credo_Alignment_Array
#ppi :               Polyphony.Piccolo,      Piccolo_Alignment_Array
#pockets :           Polyphony.Fpocket,      Pocket_Alignment_Array