dssr_block.py: A simple "x3dna-dssr --block-file" wrapper

Author: speleo3

dssr_block.py

@@ -0,0 +1,106 @@
+'''
+http://pymolwiki.org/index.php/dssr_block
+
+(c) Thomas Holder, Schrodinger LLC
+
+License: BSD-2
+'''
+
+from pymol import cmd, CmdException
+
+def dssr_block(selection='all', state=-1,
+        block_file='face',
+        block_depth=0.5,
+        name='',
+        exe='x3dna-dssr',
+        quiet=1):
+    '''
+DESCRIPTION
+
+    Create a nucleic acid base "block" cartoon with DSSR.
+
+    Requires the "x3dna-dssr" program, available from http://x3dna.org/
+
+USAGE
+
+    dssr_block [ selection [, state [, block_file [, block_depth
+        [, name [, exe ]]]]]]
+
+ARGUMENTS
+
+    selection = str: atom selection {default: all}
+
+    state = int: object state (0 for all states) {default: -1, current state}
+
+    block_file = face|edge|wc|equal|minor|gray: Corresponds to the --block-file
+    option (see DSSR manual). Values can be combined, e.g. "wc-minor".
+    {default: face}
+
+    block_depth = float: thickness of rectangular blocks {default: 0.5}
+
+    name = str: name of new CGO object {default: dssr_block##}
+
+    exe = str: path to "x3dna-dssr" executable {default: x3dna-dssr}
+
+EXAMPLE
+
+    fetch 1ehz, async=0
+    as cartoon
+    dssr_block
+    set cartoon_ladder_radius, 0.1
+    set cartoon_ladder_color, gray
+    set cartoon_nucleic_acid_mode, 1
+
+    # multi-state
+    fetch 2n2d, async=0
+    dssr_block 2n2d, 0
+    set all_states
+    '''
+    import subprocess
+    import tempfile, os
+
+    state, quiet = int(state), int(quiet)
+
+    tmpfilepdb = tempfile.mktemp('.pdb')
+    tmpfiler3d = tempfile.mktemp('.r3d')
+
+    args = [exe,
+        '--block-file=' + block_file,
+        '--block-depth=' + str(block_depth),
+        '-i=' + tmpfilepdb,
+        '-o=' + tmpfiler3d,
+    ]
+
+    if not name:
+        name = cmd.get_unused_name('dssr_block')
+
+    states = [state] if state != 0 else \
+            range(1, cmd.count_states(selection) + 1)
+
+    try:
+        for state in states:
+            cmd.save(tmpfilepdb, selection, state)
+            subprocess.check_call(args)
+            cmd.load(tmpfiler3d, name, max(1, state), zoom=0)
+    except subprocess.CalledProcessError:
+        raise CmdException('"' + exe + '" failed')
+    except OSError:
+        raise CmdException('Cannot execute exe="' + exe + '"')
+    finally:
+        try:
+            os.remove(tmpfilepdb)
+            os.remove(tmpfiler3d)
+        except OSError:
+            pass
+
+cmd.extend('dssr_block', dssr_block)
+
+# tab-completion of arguments
+cmd.auto_arg[0].update({
+    'dssr_block'    : cmd.auto_arg[0]['zoom'],
+})
+cmd.auto_arg[2].update({
+    'dssr_block'    : [cmd.Shortcut(['face', 'edge', 'wc', 'equal', 'minor', 'gray']), 'block_file', ''],
+})
+
+# vi: expandtab:smarttab