inprogress-0.1.2

README.md

@@ -11,19 +11,50 @@ We then compare results of the simulation to Hi-C maps or microscopy, and to oth
 Polychrom is not designed to make a simulation based on a Hi-C map alone, without a hypothesis in mind. 
 For distinction between mechanistic and data-driven models see https://pubmed.ncbi.nlm.nih.gov/26364723/ 
 
+## Requirements
+
+The following are required before installing polychrom:
+
+* Python 3.7+
+* `numpy`
+* `cython`
+* OpenMM
+
+Polychrom requires OpenMM, which we currently recommend installing via conda: 
+```sh
+conda install -c omnia openmm
+```
+See http://docs.openmm.org/latest/userguide/application.html#installing-openmm. 
+In our experience, adding ``-c conda-forge`` listed in the link above is optional. 
+CUDA is the fastest GPU-assisted backend to OpenMM. To use this feature with polychrom, see OpenMM CUDA installation instructions. 
+
+Other polychrom dependencies are simple, and are listed in requirements.txt. 
+All but joblib are installable from either conda/pip, and joblib installs well with pip. 
+
+
+## Installation
+
+After installing cython and OpenMM, we recommend cloning the polychrom repository, going to its folder, and installing via:
+```sh
+pip install -e ./
+```
+
+## Getting Started 
 Polychrom documentation is hosted on readthedocs. 
 https://polychrom.readthedocs.io/en/latest/
 
-One of the main uses of polychrom now is to simulate loop extrusion. An example loop extrusion simulation is presented here.
-https://github.com/mirnylab/polychrom/tree/master/examples/loopExtrusion . It is a good starting point for loop extrusion simulations. 
-
-Simplest example simulation that does nothing, which is a good starting point for novel simulations or polymer physics projects.  
+A good starting point for novel simulations or polymer physics projects is a simulation of a single un-modified polymer chain:  
 https://github.com/mirnylab/polychrom/blob/master/examples/example/example.py
 
+One of the current main uses of polychrom is to simulate loop extrusion. An example loop extrusion simulation is presented here:
+https://github.com/mirnylab/polychrom/tree/master/examples/loopExtrusion, and provides a good starting point for loop extrusion simulations. 
+
+
 ### Transitioning from openmm-polymer ("openmmlib")
-Compared to openmm-polymer, it has a new storage format described here: https://github.com/mirnylab/polychrom/blob/master/examples/storage_formats/hdf5_reporter.ipynb
-For backwards compatibility with analysis routines, we have legacy reporter that saves into openmmlib format 
+A main difference between polychrom and openmm-polymer is its new storage format, described here:
+https://github.com/mirnylab/polychrom/blob/master/examples/storage_formats/hdf5_reporter.ipynb
+
+For backwards compatibility with analysis routines, a legacy reporter can save to openmmlib format 
 https://github.com/mirnylab/polychrom/blob/master/examples/storage_formats/legacy_reporter.ipynb
 
-polychrom.polymerutils.load function  is backwards compatible with both new and old style 
-format. https://github.com/mirnylab/polychrom/blob/master/polychrom/polymerutils.py#L22
+polychrom.polymerutils.load function is backwards compatible with both new and old formats: https://github.com/mirnylab/polychrom/blob/master/polychrom/polymerutils.py#L22

examples/example/example.py

@@ -11,16 +11,15 @@
 from polychrom import simulation, starting_conformations, forces, forcekits
 import simtk.openmm as openmm
 import os
-from polychrom.hdf5_format import HDF5Reporter
+from polychrom.storage import HDF5Reporter
 
 N=10000
 
 reporter = HDF5Reporter(folder="trajectory", max_data_length=5, overwrite=True)
 sim = simulation.Simulation(
-    platform="CUDA", 
+    platform="reference", 
     integrator="variableLangevin",
     error_tol=0.003,
-    GPU="0",
     collision_rate=0.03,
     N=N,
     save_decimals=2,

polychrom/cli/README.txt

@@ -1,5 +1,5 @@
 This folder contains files that could be placed in your PATH folder. 
-They provide quick visualization using RasMol, and quick rMSD between two conformations. Both files use 
-the same path format that is aimed at quick command line experience (see docstrings inside the files). 
+They provide quick rMSD between two conformations with a path format 
+that is aimed at quick command line experience (see docstrings inside the files). 
 
 It is not by default added to PATH, but probably should be.