update docs and docstrings to sfCIF capabilities

rs-station · Oct 12, 2023 · fbfbabf · fbfbabf
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diff --git a/docs/quickstart.md b/docs/quickstart.md
@@ -39,10 +39,10 @@ At this point, you should be good to go! Please [file an issue on github](https:
 ## Input files
 
 To run `matchmaps`, you will need:
- - one `.pdb` file containing a refined structural model corresponding to your "off" data.
- - two `.mtz` files corresponding to your "on" and "off" data respectively.
+ - one `.pdb` (or `.cif`) file containing a refined structural model corresponding to your "off" data.
+ - two `.mtz` (or `.cif`) files corresponding to your "on" and "off" data respectively.
 
-You will also need to know the names of the columns in these `mtz`s containing your observed structure factor amplitudes and uncertainties. Depending on what software you used to produce these files, this may be something like `FP`/`SIGFP`, `Fobs`/`SIGFobs`, or similar. If you don't know these off-hand, you can figure it out using [`reciprocalspaceship`](https://rs-station.github.io/reciprocalspaceship/)'s `rs.mtzdump` utility, which is installed along with `matchmaps`. You can do this right in the command-line as:
+You will also need to know the names of the columns in these `mtz`/`cif`s containing your observed structure factor amplitudes and uncertainties. Depending on what software you used to produce these files, this may be something like `FP`/`SIGFP`, `Fobs`/`SIGFobs`, or similar. If you don't know these off-hand and your input is an `.mtz` file, you can figure it out using [`reciprocalspaceship`](https://rs-station.github.io/reciprocalspaceship/)'s `rs.mtzdump` utility, which is installed along with `matchmaps`. You can do this right in the command-line as:
 ```bash
 rs.mtzdump mymtz.mtz
 ```

diff --git a/src/matchmaps/_compute_mr_diff.py b/src/matchmaps/_compute_mr_diff.py
@@ -252,7 +252,7 @@ def parse_arguments():
         metavar=("mtzfileoff", "Foff", "SigFoff"),
         required=True,
         help=(
-            "MTZ containing off/apo/ground/dark state data. "
+            "MTZ or sfCIF containing off/apo/ground/dark state data. "
             "Specified as [filename F SigF]"
         ),
     )
@@ -264,7 +264,7 @@ def parse_arguments():
         metavar=("mtzfileon", "Fon", "SigFon"),
         required=True,
         help=(
-            "MTZ containing on/bound/excited/bright state data. "
+            "MTZ or SFCIF containing on/bound/excited/bright state data. "
             "Specified as [filename F SigF]"
             "This file may be in a different spacegroup / crystal packing than mtzoff"
         ),
@@ -275,7 +275,7 @@ def parse_arguments():
         "-p",
         required=True,
         help=(
-            "Reference pdb/cif corresponding to the off/apo/ground/dark state. "
+            "Reference PDB or mmCIF corresponding to the off/apo/ground/dark state. "
             "Used as a molecular replacement solution for mtzon and for rigid-body refinement of both input MTZs to generate phases."
             "Should match mtzoff well enough that molecular replacement is not necessary."
         ),
@@ -295,7 +295,7 @@ def parse_arguments():
         "-i",
         required=False,
         default="./",
-        help="Path to input mtzs and pdb. Optional, defaults to './' (current directory)",
+        help="Path to input files. Optional, defaults to './' (current directory)",
     )
 
     parser.add_argument(

diff --git a/src/matchmaps/_compute_ncs_diff.py b/src/matchmaps/_compute_ncs_diff.py
@@ -139,7 +139,7 @@ def parse_arguments():
         # metavar=("mtzfile", "F", "SigF"),
         required=True,
         help=(
-            "MTZ file containing structure factor amplitudes. "
+            "MTZ or sfCIF file containing structure factor amplitudes. "
             "Specified as [filename F SigF] or [filename F]. "
             "SigF is not necessary if phases are also provided"
         ),
@@ -150,7 +150,7 @@ def parse_arguments():
         required=False,
         default=None,
         help=(
-            "Optional. Column in MTZ file containing phases. "
+            "Optional. Column in MTZ/sfCIF file containing phases. "
             "If phases are not provided, phases will be computed via rigid-body refinement of "
             "the provided model and structure factor amplitudes."
         ),
@@ -161,8 +161,8 @@ def parse_arguments():
         "-p",
         required=True,
         help=(
-            "Reference pdb/cif. "
-            "If phases are not provided, used for rigid-body refinement of input MTZ to generate phases."
+            "Reference PDB or mmCIF. "
+            "If phases are not provided, used for rigid-body refinement of input MTZ/sfCIF to generate phases."
         ),
     )
 
@@ -200,7 +200,7 @@ def parse_arguments():
         "-i",
         required=False,
         default="./",
-        help="Path to input mtz and pdb. Optional, defaults to './' (current directory)",
+        help="Path to input files. Optional, defaults to './' (current directory)",
     )
 
     parser.add_argument(

diff --git a/src/matchmaps/_compute_realspace_diff.py b/src/matchmaps/_compute_realspace_diff.py
@@ -259,7 +259,7 @@ def parse_arguments():
         metavar=("mtzfileoff", "Foff", "SigFoff"),
         required=True,
         help=(
-            "MTZ containing off/apo/ground/dark state data. "
+            "MTZ or sfCIF containing off/apo/ground/dark state data. "
             "Specified as [filename F SigF]"
         ),
     )
@@ -271,7 +271,7 @@ def parse_arguments():
         metavar=("mtzfileon", "Fon", "SigFon"),
         required=True,
         help=(
-            "MTZ containing on/bound/excited/bright state data. "
+            "MTZ or sfCIF containing on/bound/excited/bright state data. "
             "Specified as [filename F SigF]"
         ),
     )
@@ -281,7 +281,7 @@ def parse_arguments():
         "-p",
         required=True,
         help=(
-            "Reference pdb/cif corresponding to the off/apo/ground/dark state. "
+            "Reference PDB or mmCIF corresponding to the off/apo/ground/dark state. "
             "Used for rigid-body refinement of both input MTZs to generate phases."
         ),
     )
@@ -300,7 +300,7 @@ def parse_arguments():
         "-i",
         required=False,
         default="./",
-        help="Path to input mtzs and pdb. Optional, defaults to './' (current directory)",
+        help="Path to input files. Optional, defaults to './' (current directory)",
     )
 
     parser.add_argument(