Removed "python" from beginning of example commands

docs/source/corr.rst

@@ -8,7 +8,7 @@ Calculating dynamic cross-correlation
 
 **Command:** :: 
 
-	python calc_correlation.py <options> --trajectory <trajectory> --topology <pdb>
+	calc_correlation.py <options> --trajectory <trajectory> --topology <pdb>
 
 **Inputs:**
 
@@ -24,7 +24,7 @@ Lazy load                  Boolean      ``--lazy-load``       Load trajectory fr
 
 Given a trajectory, ``example_small.dcd``, and topology file, ``example_small.pdb``, the following command could be used: ::
 
-	python calc_correlation.py --step 100 --prefix example_corr --trajectory example_small.dcd --topology example_small.pdb --lazy-load
+	calc_correlation.py --step 100 --prefix example_corr --trajectory example_small.dcd --topology example_small.pdb --lazy-load
 
 
 

docs/source/network.rst

@@ -19,7 +19,7 @@ Calculating BC and L
 
 **Command:** ::
 	
-	python calc_network.py <options> --topology <pdb file> <trajectory>
+	calc_network.py <options> --topology <pdb file> <trajectory>
 
 **Inputs:**
 
@@ -69,7 +69,7 @@ Calculating BC and L
 
 Given a trajectory called ``wt.dcd`` and a topology file called ``wt.pdb``, the following command could be used: ::
 
-	python calc_network.py --topology wt.pdb --threshold 7.0 --step 100 --generate-plots --calc-BC --calc-L --discard-graphs --lazy-load wt.dcd
+	calc_network.py --topology wt.pdb --threshold 7.0 --step 100 --generate-plots --calc-BC --calc-L --discard-graphs --lazy-load wt.dcd
 
 The above command will calculate the network for every 100th frame in the trajectory. Depending on the size of your trajectory, you may want to increase this ``--step``. Because ``--lazy-load`` was used, the trajectory will be iterated through and frames will be loaded one-at-a-time and then discarded once the network for that frame has been calculated. Leaving out the ``--lazy-load`` argument will result in the entire trajectory being loaded into memory. This can be faster for small trajectories, but should be avoided when analysing large trajectories. Edges in the network will be created between nodes that are within 7 Angstroms of each other. The average shortest path for each residue in each frame and the betweenness centrality of each residue in each frame will be calculated as **both flags have been set** in the above command. In addition, the ``--discard-graphs`` flag was set. As such, the networks for each frame will be discarded once BC and L have been calculated, saving disk space. By default, the networks for each frame are saved in both ``gml`` and ``graphml`` format.
 
@@ -92,7 +92,7 @@ If the ``--calc-L`` flag in the previous command is set, a number of Nx1 L matri
 
 **Command:** :: 
 
-	python calc_delta_L.py <options> --reference <frame> --alternatives <frames>
+	calc_delta_L.py <options> --reference <frame> --alternatives <frames>
 
 **Inputs:**
 
@@ -107,7 +107,7 @@ Generate plots             Boolean      ``--generate-plots``  Set to generate fi
 
 Given a set of average shortest path .dat files ``wt_*_avg_L.dat`` (generated with ``calc_network.py``), the ``wt_0_avg_L.dat`` file could be used as the reference and the rest could be used as the alternatives. If ``wt_0_avg_L.dat`` is renamed to ``ref_wt_L.dat``, the following command could be used: ::
 
-	python calc_delta_L.py --normalize --generate-plots --reference ref_wt_L.dat --alternatives wt_*_avg_L.dat
+	calc_delta_L.py --normalize --generate-plots --reference ref_wt_L.dat --alternatives wt_*_avg_L.dat
 
 The above command will generate plots as well as Nx1 matrices representing the difference in L between each alternative and the reference frame. The values will be normalized by dividing by the reference values (ΔL/L).
 
@@ -127,7 +127,7 @@ If the ``--calc-BC`` flag was set when running the ``calc_network.py`` script, a
 
 **Command:** :: 
 
-	python calc_delta_BC.py <options> --reference <frame> --alternatives <frames>
+	calc_delta_BC.py <options> --reference <frame> --alternatives <frames>
 
 **Inputs:**
 
@@ -141,7 +141,7 @@ Generate plots             Boolean      ``--generate-plots``  Set to generate fi
 
 Given a set of BC .dat files ``wt_*_bc.dat`` (generated with ``calc_network.py``), the ``wt_0_bc.dat`` file could be used as the reference and the rest could be used as the alternatives. If the ``wt_0_bc.dat`` is renamed to ``ref_wt_bc.dat``, the following command could be used: ::
 
-	python calc_delta_BC.py --generate-plots --reference ref_wt_bc.dat --alternatives wt_*_bc.dat
+	calc_delta_BC.py --generate-plots --reference ref_wt_bc.dat --alternatives wt_*_bc.dat
 
 The above command will generate plots as well as Nx1 matrices representing the difference in BC between each alternative and the reference frame.
 
@@ -162,7 +162,7 @@ The ``avg_network.py`` script can be used to calculate and plot the average BC a
 
 **Command:** ::
 	
-	python avg_network.py <options> --data-type <BC/delta-BC/L/delta-L> --data <matrices>
+	avg_network.py <options> --data-type <BC/delta-BC/L/delta-L> --data <matrices>
 
 **Inputs:**
 
@@ -188,7 +188,7 @@ X-axis start value 2       Integer      ``--initial-x-2``     The start index of
 
 Given a set of .dat files generated by one of the previous commands (e.g. ``wt_*_bc_delta_BC.dat``), the following command could be used: ::
 	
-	python avg_network.py --data wt_*_bc_delta_BC.dat --data-type delta-BC --prefix wt --generate-plots --x-label "Residues" --y-label "Avg delta BC" --title "Wild Type"
+	avg_network.py --data wt_*_bc_delta_BC.dat --data-type delta-BC --prefix wt --generate-plots --x-label "Residues" --y-label "Avg delta BC" --title "Wild Type"
 
 The above command will generate two new .dat files and a PNG plot. The first .dat file, ``wt_delta_bc_avg.dat``, contains an Nx1 matrix with the average ΔBC values for each residue over the course of the simulation. The second .dat file, ``wt_delta_bc_std_dev.dat``, contains the standard deviation of ΔBC for each residue over the course of the simulation. The graph plots residues on the X axis and ΔBC on the Y axis. The average values are shown as a line and the standard deviation, representing the fluctuation of ΔBC over the course of the trajectory, are shown as error bars over each residue. *Note that in the above example, we have calculated the average and standard deviation of ΔBC, but avg_network.py can be used with any set of Nx1 matrix (BC/ΔBC/L/ΔL).*
 
@@ -209,7 +209,7 @@ Two scripts have been added for comparing BC/ΔBC/L/ΔL graphs. Essentially, all
 
 **Command:** ::
 
-	python compare_networks.py <options> --reference <reference .dat> --alternative <alternative .dat>
+	compare_networks.py <options> --reference <reference .dat> --alternative <alternative .dat>
 
 **Inputs:**
 
@@ -235,8 +235,8 @@ For example, if we had two trajectories, ``wt.dcd`` and ``mutant.dcd``, and we a
 
 We could compare the above files with the following two commands: ::
 	
-	python compare_networks.py --prefix "wt_mutant_avg" --reference-label Wild-type --alternative-label Mutant --y-label "Delta BC" --reference wt_delta_bc_avg.dat --alternative mutant_delta_bc_avg.dat
-	python compare_networks.py --prefix "wt_mutant_std_dev" --reference-label Wild-type --alternative-label Mutant --y-label "Delta BC" --reference wt_delta_bc_std_dev.dat --alternative mutant_delta_bc_std_dev.dat
+	compare_networks.py --prefix "wt_mutant_avg" --reference-label Wild-type --alternative-label Mutant --y-label "Delta BC" --reference wt_delta_bc_avg.dat --alternative mutant_delta_bc_avg.dat
+	compare_networks.py --prefix "wt_mutant_std_dev" --reference-label Wild-type --alternative-label Mutant --y-label "Delta BC" --reference wt_delta_bc_std_dev.dat --alternative mutant_delta_bc_std_dev.dat
 
 The output of these commands will provide two figures containing the average ΔBC of the mutant and wild type trajectories plotted against each other for comparison purposes.
 
@@ -255,7 +255,7 @@ Where the above script allows the comparison of two matrices, the second compari
 
 **Command:** ::
 
-	python delta_networks.py <options> --reference <reference avg .dat> --reference-std <reference std dev .dat> --alternatives <alternative avg .dats> --alternatives-std <alternative std dev .dats>
+	delta_networks.py <options> --reference <reference avg .dat> --reference-std <reference std dev .dat> --alternatives <alternative avg .dats> --alternatives-std <alternative std dev .dats>
 
 **Input:**
 
@@ -281,7 +281,7 @@ X-axis start value 2              Integer      ``--initial-x-2``        The star
 
 Given a set of analyzed trajectories, they can be compared to a wild type trajectory using the following command: ::
 	
-    python delta_networks.py --reference wt_delta_BC_avg.dat --reference-std wt_delta_BC_std_dev.dat --alternatives mutant_*_delta_BC_avg.dat --alternatives-std mutant_*_delta_BC_std_dev.dat --absolute --prefix my_protein_delta --title "My Protein" --x-label "Residues" --y-label "Proteins"
+    delta_networks.py --reference wt_delta_BC_avg.dat --reference-std wt_delta_BC_std_dev.dat --alternatives mutant_*_delta_BC_avg.dat --alternatives-std mutant_*_delta_BC_std_dev.dat --absolute --prefix my_protein_delta --title "My Protein" --x-label "Residues" --y-label "Proteins"
 
 The above command will produce a PNG with 2 heatmaps for comparing the average and standard deviation Nx1 BC matrices of the wild-type protein with those of the mutated proteins.
 
@@ -300,7 +300,7 @@ A weighted residue contact map allows the user to determine how often, throughou
 
 **Command:** ::
 
-	python contact_map.py <options> --trajectory <trajectory> --topology <pdb file>
+	contact_map.py <options> --trajectory <trajectory> --topology <pdb file>
 
 **Input:**
 
@@ -316,8 +316,8 @@ Prefix                            Text         ``--prefix``             Prefix u
 
 Given two trajectories, ``wt.dcd`` and ``mutant.dcd``, where a mutation, ``THR405ALA``, occurs, the following could be used to build contact maps around position 405 in both trajectories: ::
 	
-	python contact_map.py --residue THR405 --prefix wt --topology wt.pdb wt.dcd
-	python contact_map.py --residue ALA405 --prefix mutant --topology mutant.pdb mutant.dcd
+	contact_map.py --residue THR405 --prefix wt --topology wt.pdb wt.dcd
+	contact_map.py --residue ALA405 --prefix mutant --topology mutant.pdb mutant.dcd
 
 For each of the commands above, a contact map in PDF format will be produced, as well as a CSV file containing the calculated values. The contact maps can be compared visually to give an idea of the changes cause by the mutation.
 

docs/source/prs.rst

@@ -8,7 +8,7 @@ Performing PRS
 
 **Command:** :: 
 
-	python prs.py <options> --final <final.xyz> --trajectory <trajectory> --topology <pdb>
+	prs.py <options> --final <final.xyz> --trajectory <trajectory> --topology <pdb>
 
 **Inputs:**
 
@@ -27,7 +27,7 @@ Prefix                       Text         ``--prefix``          Prefix used to n
 
 Given a trajectory, ``example_small.dcd``, with initial and target co-odinate files, ``initial.xyz`` and ``final.xyz``, respectively, and topology file, ``example_small.pdb``, the following command could be used: ::
 
-	python prs.py --initial initial.xyz --final final.xyz --perturbations 100 --step 100 --prefix result --topology example_small.pdb example_small.dcd 
+	prs.py --initial initial.xyz --final final.xyz --perturbations 100 --step 100 --prefix result --topology example_small.pdb example_small.dcd 
 
 
 **Outputs:**