diff --git a/README.md b/README.md
index 774ca1750db316566854426b533bc725ed9f37db..b42b7715187e038f8aaa2005c820ed7ff437c319 100644
--- a/README.md
+++ b/README.md
@@ -16,13 +16,6 @@ For instance, a pre-equilibrated atomistic membrane may be used to create starti
PyCGTOOL makes it easy to test multiple variations in mapping and bond topology by making simple changes to the config files.
-This version has several advantages over the original C++ implementation CGTOOL:
-* PyCGTOOL is able to run anywhere the necessary library dependencies are available (all available from pip)
-* Does not require that residues are present in contiguous sorted blocks
-* May map multiple residues with a single pass
-* Support for polymers such as DNA or proteins making use of GROMACS' pdb2gmx
-* Much more automated testing ensures that regressions will be identified quickly
-
If you find this useful, please cite as:
```
Graham, J. (2017). PyCGTOOL, https://doi.org/10.5281/zenodo.598143
@@ -44,7 +37,11 @@ For more information see [MDTraj/#1572](https://github.com/mdtraj/mdtraj/issues/
## Usage
-Input to PyCGTOOL is GROMACS GRO and XTC files, along with two custom files: MAP and BND. These files provide the atomistic-to-CG mapping and bonded topology respectively. Example files are present in the [test/data](https://github.com/jag1g13/pycgtool/tree/master/test/data) directory. The format of these files is described in the [full documentation](https://pycgtool.readthedocs.io/en/master/index.html).
+Input to PyCGTOOL is an atomistic simulation trajectory in the form of a topology (e.g. PDB, GRO, etc.) and a trajectory file (e.g. XTC, DCD, etc.), along with two custom files: MAP and BND.
+These files provide the atomistic-to-CG mapping and bonded topology respectively.
+
+Example files are present in the [test/data](https://github.com/jag1g13/pycgtool/tree/master/test/data) directory.
+The format of these files is described in the [full documentation](https://pycgtool.readthedocs.io/en/master/index.html).
For more information, see [the tutorial](https://pycgtool.readthedocs.io/en/master/tutorial.html).
It is important to perform validation of any new parameter set; a brief example is present at the end of the tutorial.
@@ -58,19 +55,19 @@ pycgtool -h
To generate a CG model from an atomistic simulation:
```
-pycgtool -g <GRO file> -x <XTC file> -m <MAP file> -b <BND file>
+pycgtool <topology file> <trajectory file> -m <MAP file> -b <BND file>
```
### Map Only
To use PyCGTOOL to convert a set of atomistic simulation coordinates to CG coordinates:
```
-pycgtool -g <GRO file> -m <MAP file>
+pycgtool <topology file> -m <trajectory file>
```
Or to convert a complete simulation trajectory:
```
-pycgtool -g <GRO file> -x <XTC file> -m <MAP file>
+pycgtool <topology file> <trajectory file> -m <MAP file>
```
## Maintainers
diff --git a/docs/source/index.rst b/docs/source/index.rst
index d44fdd928629085a26ff44b38f749de25989b3a2..fc11bdb3678367ec4663391c7b08c47c3ee113b0 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -40,14 +40,14 @@ Basic Usage
-----------
PyCGTOOL requires four input files to generate a coarse-grained model:
--g GROMACS gro coordinate file
--x GROMACS xtc trajectory file
--m PyCGTOOL mapping definition file
--b PyCGTOOL bond definition file
+- AA simulation topology file (e.g. PDB, GRO, etc.)
+- AA simulation trajectory file (e.g. XTC, DCD, etc.)
+- PyCGTOOL mapping definition file
+- PyCGTOOL bond definition file
The program is called by::
- pycgtool.py -g <GRO file> -x <XTC file> -m <MAP file> -b <BND file>
+ pycgtool <topology file> <trajectory file> -m <MAP file> -b <BND file>
Example mapping and bond definition files are present in the ``test/data`` directory. Their format is explained below.
@@ -127,9 +127,6 @@ If no angles are defined for a molecule, PyCGTOOL will construct all angles from
C5 O5 C1 C2
O5 C1 C2 C3
-
-
-
Advanced Usage
--------------
@@ -146,7 +143,7 @@ For full detail see: :doc:`mapping-only`.
This mode may be invoked by::
- pycgtool.py -g <GRO file> -m <MAP file>
+ pycgtool <topology file> -m <MAP file>
Measure Only
@@ -156,7 +153,7 @@ Measure-only mode may be used to aid in the testing of a coarse-grained model by
These bond measurements may be compared directly to those collected from the pseudo-coarse-grained trajectory used to generate the model.
This mode may be invoked by::
- pycgtool.py -g <GRO file> -x <XTC file> -b <BND file>
+ pycgtool <topology file> <trajectory file> -b <BND file>
Advanced Options
diff --git a/docs/source/mapping-only.rst b/docs/source/mapping-only.rst
index 976ae608a94de7d73580e7b61e2496fc2bf34a77..aee79af28aa01372ef159852bd2c90385982b443 100644
--- a/docs/source/mapping-only.rst
+++ b/docs/source/mapping-only.rst
@@ -11,12 +11,10 @@ The main uses of the functionality are:
In order to perform the AA to CG mapping, a PyCGTOOL mapping file is required.
For guidance on the creation of this file see the full :doc:`tutorial`.
-To perform a mapping from a single snapshot `.gro` file use the command::
+To perform a mapping from a single snapshot file (e.g. PDB, GRO, etc.) use the command::
- pycgtool.py -g <GRO file> -m <MAP file>
+ pycgtool <topology file> -m <MAP file>
-To perform a mapping of a complete `.xtc` trajectory use the command::
+To perform a mapping of a complete trajectory (e.g. XTC, DCD, etc.) use the command::
- pycgtool.py -g <GRO file> -x <XTC file> -m <MAP file>
-
-But note that mapping an entire trajectory requires that the optional dependency `MDTraj` is installed.
+ pycgtool <topology file> <trajectory file> -m <MAP file>
diff --git a/docs/source/tutorial.rst b/docs/source/tutorial.rst
index c4a167e0a8fbc18dcaadc3cf0d1cc64a4b696309..b29962c6061600ebceb0d776cad00939f4e3f57f 100644
--- a/docs/source/tutorial.rst
+++ b/docs/source/tutorial.rst
@@ -72,7 +72,7 @@ Model Generation
The process of model generation after having created the mapping and bond definition files is automated by PyCGTOOL.
In the simplest case, a parameter set may be generated simply by passing the four input files to PyCGTOOL::
- pycgtool.py -g ref.gro -x ref.xtc -m atenolol.map -b atenolol.bnd
+ pycgtool ref.gro ref.xtc -m atenolol.map -b atenolol.bnd
This will create two output files ``out.gro``, the mapped CG coordinates, and ``out.itp``, the calculated CG model parameters.
@@ -111,7 +111,7 @@ Additionally, other methods of validation should be applied relevant to the clas
To compare the distribution of bonded terms, we must first rerun PyCGTOOL to generate samples of the bonded measurements.
For the atomistic reference simulation, this can be done by running::
- pycgtool.py -g ref.gro -x ref.xtc -m atenolol.map -b atenolol.bnd --dump_measurements
+ pycgtool ref.gro ref.xtc -m atenolol.map -b atenolol.bnd --dump_measurements
PyCGTOOL will now output a sample of each measured bond length and angle (but since the reference trajectory is short, the target sample size is not met and all values are collected), in the files ``36KB_length.dat`` and ``36KB_angle.dat``.
@@ -119,7 +119,7 @@ PyCGTOOL will now output a sample of each measured bond length and angle (but si
Since we will be collecting samples of the same measurements from the CG simulation, these files should be renamed to, for instance, `ref_length.dat` and `ref_angle.dat`.
Collect the same samples for the CG simulation using::
- pycgtool.py -g md.gro -x md.xtc -b atenolol.bnd
+ pycgtool md.gro md.xtc -b atenolol.bnd
Since we provide a bond file, but not a mapping file, PyCGTOOL will know that this is intended to simply collect bond measurements and will automatically set the `dump_measurements` option to `True`.
Again, the files created will be called ``36KB_length.dat`` and ``36KB_angle.dat``.
diff --git a/docs/tutorial_files/Makefile b/docs/tutorial_files/Makefile
index 35bd7f9b1bff280a3cc536db19ecc05e6a8bb807..543529a1dfcd86bdb8af141ffc01e10b79069ef4 100644
--- a/docs/tutorial_files/Makefile
+++ b/docs/tutorial_files/Makefile
@@ -1,7 +1,7 @@
all: pycgtool cgprepare em npt md samples rgyr
pycgtool:
- ../../pycgtool.py -g ref.gro -x ref.xtc -m atenolol.map -b atenolol.bnd
+ pycgtool ref.gro ref.xtc -m atenolol.map -b atenolol.bnd
cgprepare:
gmx solvate -cp out.gro -cs ../../data/water.gro -o solv.gro -radius 0.21
@@ -21,10 +21,10 @@ md:
gmx mdrun -deffnm md -v
samples:
- ../../pycgtool.py -g ref.gro -x ref.xtc -m atenolol.map -b atenolol.bnd --advanced
+ pycgtool ref.gro ref.xtc -m atenolol.map -b atenolol.bnd --advanced
mv {36KB,ref}_length.dat
mv {36KB,ref}_angle.dat
- ../../pycgtool.py -g md.gro -x md.xtc -b atenolol.bnd
+ pycgtool md.gro md.xtc -b atenolol.bnd
comparesamples:
./average_columns.py ref_length.dat 36KB_length.dat