Jekyll, GitHub's static site generator, and Bootstrap were used to create Whispernote's GitHub Project Page. This document shows how.
I wanted a stylish "brand" page for my project, and I wanted to reuse the README file I had created without a lot of copy/pasting. GitHub's Jekyll allowed me to essentially embed the file as a partial. What I got was really an enhanced README file (thanks to some jQuery and Bootstrap), which is exactly what I wanted.
| def OPLS_pot(R,SIG=10,EPS=0.05): | |
| sij=np.sqrt(SIG*3.15061) | |
| eij=np.sqrt(EPS*0.1521) | |
| return 4*eij*((sij/R)**12-(sij/R)**6) | |
| xdata = Ri | |
| ydata = pot(Ri) | |
| popt, pcov = curve_fit(OPLS_pot, xdata, ydata) | |
| print popt | |
| load ionplte1 | |
| sel lig,resname UNK | |
| sel bb, !lig | |
| select SP, bb w. 2.5 of resname UNK | |
| select CSP, br. SP | |
| color iron,lig | |
| show sticks,lig | |
| show sticks,CSP | |
| show spheres, lig | |
| set sphere_scale=0.5,lig |
| ############################################ | |
| def Sim_Anneal(ps,const): | |
| T=8.00 | |
| delta = 0.05 | |
| nmoves=10 | |
| while (T > 5e-2): | |
| accept=0 | |
| reject=0 | |
| Beta=(1.0/T) | |
| for i in range(0,nmoves): |
| def get_atom_mass_martini(atomname): | |
| database={ | |
| 'NC3': 72.0 | |
| 'PO4': 72.0 | |
| 'GL1': 72.0 | |
| 'C1A': 72.0 | |
| 'C2A': 72.0 | |
| 'C3A': 72.0 | |
| 'C4A': 72.0 | |
| 'C1B': 72.0 |
| *>>>> CHARMM Parameter file generated by ParmEd <<<< | |
| * | |
| ATOMS | |
| MASS 1 C135 12.01100 | |
| MASS 2 C136 12.01100 | |
| MASS 3 C137 12.01100 | |
| MASS 4 C145 12.01100 | |
| MASS 5 C149 12.01100 | |
| MASS 6 C157 12.01100 |
| from simtk.openmm.app import * | |
| from simtk.openmm import * | |
| from simtk.unit import * | |
| pdb = PDBFile('waterSphere.pdb') | |
| #forcefield = ForceField('amber99sb.xml', 'tip3p.xml') | |
| forcefield = ForceField('tip3p.xml') | |
| system = forcefield.createSystem(pdb.topology, nonbondedMethod=NoCutoff) | |
| forces = { system.getForce(index).__class__.__name__ : system.getForce(index) for index in range(system.getNumForces()) } |
| #!/net/nas01/leela/anaconda/bin/python | |
| ################################################# | |
| # USAGE: python Qfepzmat_bcc.py molname.z | |
| ################################################# | |
| import sys | |
| import numpy as np | |
| def new_func(linex, match): | |
| out = 0 |
| import sys | |
| import re | |
| import numpy as np | |
| import csv | |
| from rdkit import Chem | |
| names = open('fns') | |
| def raa(fname): | |
| m=Chem.MolFromMolFile('../'+fname) | |
| natoms=len(m.GetAtoms()) | |
| var=[] |
| import cirpy | |
| import sys | |
| molecule = sys.argv[1] | |
| smiles_code = cirpy.resolve(molecule, 'smiles') | |
| print smiles_code | |
| pdbfile = cirpy.resolve(smiles_code, 'pdb') | |
| oname = ''.join(molecule.split()) | |
| file_output = open(oname + '.pdb', "w+") | |
| file_output.write(pdbfile) | |
| file_output.close() |