fabian-paul

fabian-paul

fabian-paul

# Python version of the following original work:
# Title:	Sorting Real Schur Forms
# Author:	Jan Brandts
# E-Mail:	brandts-AT-science.uva.nl
# http://m2matlabdb.ma.tum.de/download.jsp?MC_ID=3&MP_ID=119
# http://dx.doi.org/10.1002/nla.274
# Institution:	University of Amsterdam
# Description:	In Matlab 6, there exists a command to generate a real Schur form, wheras another transforms a real
# Schur form into a complex one. There do not exist commands to prescribe the order in which the eigenvalues appear on
# the diagonal of the upper (quasi-) triangular factor T.

fabian-paul

#!/usr/bin/env python
import numpy as np
import mdtraj


def tl(filename, chunk=100):
    with mdtraj.open(filename, mode='r') as fh:
        try:
            return (len(fh) - 1) // chunk + 1
        except:

fabian-paul

import numpy as np
import scipy
import scipy.optimize
import warnings

__all__ = ['VAMP42']
__author__ = 'Fabian Paul <fapa@uchicago.edu>'

def sigma(x):
    return scipy.special.expit(x)

fabian-paul

fabian-paul

import pyparsing as pp
from pyparsing import pyparsing_common as ppc

__all__ = ['load_colvars', 'handle_colvars']

pp.ParserElement.setDefaultWhitespaceChars(' \t')

vector = pp.Group(pp.Literal('(').suppress() + 
                  pp.delimitedList(ppc.number, delim=',') + 
                  pp.Literal(')').suppress())

fabian-paul

import numpy as np
import mdtraj
import os
import os.path
import argparse

def prepare_maps(mut_pdb='mutant.pdb', wt_pdb=None):
    if wt_pdb is None:
        wt_pdb = os.path.expanduser('~/system/crystal.pdb')

fabian-paul

import numpy as np
import rdkit.Chem

def reorder_atoms(mol_pdb_fname, template_pdb_fname, output_pdb_fname):
    from rdkit.Chem import rdmolfiles

    mol_to_transform = rdkit.Chem.rdmolfiles.MolFromPDBFile(mol_pdb_fname, removeHs=False)
    transform_order = list(rdmolfiles.CanonicalRankAtoms(mol_to_transform))

    mol_template = rdkit.Chem.rdmolfiles.MolFromPDBFile(template_pdb_fname, removeHs=False)

fabian-paul