Index

Symbols | A | E | F | G | M | O | P | S | T

Symbols

-acolor <color>
szmap_report command line option
-all <format>
szmap_grid command line option
-apo_box <filename>
szmap command line option
szmap_grid command line option
-apo_coords
szmap command line option
-apo_grids
szmap command line option
-apo_point_grid
szmap command line option
-aromstyle <style>
szmap_report command line option
-around <filename>
szmap command line option
-around_mol <filename>
szmap command line option
-astl <style>
szmap_report command line option
-at_coords <filename>
szmap command line option
szmap_grid command line option
-atomcolor <color>
szmap_report command line option
-atomsstl <style>
szmap_report command line option
-atomstereostyle <style>
szmap_report command line option
-bbox <xmin> <ymin> <zmin> <xmax> <ymax> <zmax>
szmap command line option
-bcolor <color>
szmap_report command line option
-bondcolor <color>
szmap_report command line option
-bondsstl <style>
szmap_report command line option
-bondstereostyle <style>
szmap_report command line option
-boundary <number>
szmap command line option
-boundary_radius <number>
szmap command line option
-boundary_spacing <number>
szmap command line option
-bounding_box <xmin> <ymin> <zmin> <xmax> <ymax> <zmax>
szmap command line option
-box_mol <filename>
szmap command line option
szmap_grid command line option
-by <number>
grid_comp command line option
-chain <letter>
szmap command line option
-clean <bool>
gameplan command line option
-cols <number>
szmap_report command line option
-coords <filename>
szmap command line option
szmap_grid command line option
-cplx_grids
szmap command line option
-cutoff <number>
grid_comp command line option
-dcutoff <number>
szmap command line option
-default <number>
grid_comp command line option
-default_value <number>
grid_comp command line option
-dielectric_model <type>
szmap command line option
-distance_cutoff <number>
szmap command line option
-eps_in <number>
szmap command line option
-eps_out <number>
szmap command line option
-fix_elements
pch command line option
-g <name>
szmap_grid command line option
-geq <number>
grid_comp command line option
-geq_mask <number>
grid_comp command line option
-grid <name>
szmap_grid command line option
-grid1 <name>
grid_comp command line option
-grid2 <name>
grid_comp command line option
-grid3 <name>
grid_comp command line option
-grid_spacing <number>
szmap command line option
-grids <type>
szmap command line option
-i <filename>
szmap_report command line option
-i <filename>
fixdupatomnames command line option
grid_comp command line option
mkhetdict command line option
pch command line option
szmap_grid command line option
-in1 <filename>
grid_comp command line option
-in2 <filename>
grid_comp command line option
-in3 <filename>
grid_comp command line option
-inner_dielectric <number>
szmap command line option
-input <filename>
szmap_report command line option
-input_file1 <filename>
grid_comp command line option
-input_file2 <filename>
grid_comp command line option
-input_file3 <filename>
grid_comp command line option
-input_mol <filename>
fixdupatomnames command line option
mkhetdict command line option
pch command line option
szmap_grid command line option
-inscode <letter>
szmap command line option
-int_method <value>
grid_comp command line option
-keep_alts
pch command line option
-keep_hydrogens
szmap_report command line option
-keep_numbers
pch command line option
-l <filename>
gameplan command line option
pch command line option
szmap command line option
-legend <bool>
szmap_report command line option
-leq <number>
grid_comp command line option
-leq_mask <number>
grid_comp command line option
-lig_box <filename>
szmap command line option
szmap_grid command line option
-lig_ch <char>
pch command line option
-lig_coords
szmap command line option
-lig_end <int>
pch command line option
-lig_grids
szmap command line option
-lig_ins <char>
pch command line option
-lig_model <int>
pch command line option
-lig_num <int>
pch command line option
-lig_point_grid
szmap command line option
-lig_res <RES>
pch command line option
-ligand <filename>
gameplan command line option
szmap command line option
-ligand_chain <char>
pch command line option
-ligand_inscode <char>
pch command line option
-ligand_model <int>
pch command line option
-ligand_res <RES>
pch command line option
-ligand_resnum <int>
pch command line option
-ligand_resnum_end <int>
pch command line option
-light_background
gameplan command line option
-light_bkg
gameplan command line option
-like_apo <filename>
szmap command line option
-like_box <filename>
szmap command line option
-like_lig <filename>
szmap command line option
-like_std <filename>
szmap command line option
-log <filename>
gameplan command line option
szmap command line option
-logfile <filename>
gameplan command line option
szmap command line option
-mask_cutoff <number>
szmap command line option
szmap_grid command line option
-mask_vdw
grid_comp command line option
-masked_point_cutoff <number>
grid_comp command line option
-merge <number>
gameplan command line option
-method <value>
grid_comp command line option
-model <type>
szmap command line option
-mol <filename>
szmap_grid command line option
-mpi_hostfile <filename>
szmap command line option
-mpi_np <number>
szmap command line option
-new_value <number>
grid_comp command line option
-no_fixup
pch command line option
-no_table
szmap_grid command line option
-nonsym
pch command line option
-nonsymmetrized_charges
pch command line option
-num_orientations <number>
szmap command line option
-o <filename>
szmap_report command line option
-o <filename.txt>
mkhetdict command line option
-o <filename>
fixdupatomnames command line option
gameplan command line option
grid_comp command line option
szmap command line option
szmap_grid command line option
-op <value>
grid_comp command line option
-operation <value>
grid_comp command line option
-outer_dielectric <number>
szmap command line option
-output <filename>
gameplan command line option
szmap_report command line option
-output_all_format <format>
szmap_grid command line option
-output_grid <filename>
grid_comp command line option
szmap_grid command line option
-output_lig <filename>
pch command line option
-output_mol <filename>
fixdupatomnames command line option
szmap command line option
szmap_grid command line option
-output_prot <filename>
pch command line option
-output_txt <filename.txt>
mkhetdict command line option
-output_waters <filename>
pch command line option
-p <filename>
gameplan command line option
pch command line option
szmap command line option
-pagesize <size>
szmap_report command line option
-param <filename>
gameplan command line option
szmap command line option
-point_grid
szmap command line option
-prefix <prefix>
gameplan command line option
szmap command line option
-prefix <text>
szmap_grid command line option
-progress <style>
gameplan command line option
szmap command line option
-properties <type>
szmap command line option
-protein <filename>
gameplan command line option
szmap command line option
-res <number>
szmap command line option
-residue_chain <letter>
szmap command line option
-residue_insert <letter>
szmap command line option
-residue_number <number>
szmap command line option
-resolution <level>
szmap_report command line option
-restrict_calc <level>
szmap command line option
-results_set <type>
szmap command line option
-rot <number>
szmap command line option
-rows <number>
szmap_report command line option
-salt <number>
szmap command line option
-salt_conc <number>
szmap command line option
-scale <number>
grid_comp command line option
-separate
szmap_report command line option
-size <size>
szmap_report command line option
-slice
szmap_grid command line option
-sp3_aromatic <bool>
gameplan command line option
-sp3aromatic <bool>
gameplan command line option
-space <number>
szmap command line option
-split_lig
szmap command line option
-stabilization
szmap command line option
-stabilization <bool>
gameplan command line option
-standard_grids
szmap command line option
-stbl
szmap command line option
-stbl <bool>
gameplan command line option
-std_box <filename>
szmap command line option
szmap_grid command line option
-std_coords
szmap command line option
-std_grids
szmap command line option
-surf
szmap command line option
-surface <bool>
szmap_report command line option
-surface_points
szmap command line option
-szmap_mpi_hostfile <filename>
gameplan command line option
-szmap_mpi_np <number>
gameplan command line option
-t <prop>
szmap_report command line option
-table <filename>
szmap command line option
-tag_set <set>
szmap_report command line option
-tagname <prop>
szmap_report command line option
-title <text>
szmap_report command line option
-to <number>
grid_comp command line option
-use_apo_from <filename>
szmap command line option
-v
fixdupatomnames command line option
gameplan command line option
grid_comp command line option
mkhetdict command line option
pch command line option
szmap command line option
szmap_grid command line option
szmap_report command line option
-value_cutoff <number>
szmap command line option
-vcutoff <number>
szmap command line option
-vdw_scale <number>
szmap command line option
-verbose
fixdupatomnames command line option
gameplan command line option
grid_comp command line option
mkhetdict command line option
pch command line option
szmap command line option
szmap_grid command line option
szmap_report command line option
-warn_if_missing_hydrogens
gameplan command line option
szmap command line option
-water_charge <type>
szmap command line option
-waters <filename>
pch command line option
-zap_spacing <number>
szmap command line option

A

Appendix 1
Appendix 2
APPNAME_OE_ARCH

E

environment variable
APPNAME_OE_ARCH
OE_ARCH, [1], [2], [3]
OE_LICENSE
PATH, [1], [2], [3], [4]

F

fixdupatomnames command line option
-i <filename>
-input_mol <filename>
-o <filename>
-output_mol <filename>
-v
-verbose

G

gameplan command line option
-clean <bool>
-l <filename>
-ligand <filename>
-light_background
-light_bkg
-log <filename>
-logfile <filename>
-merge <number>
-o <filename>
-output <filename>
-p <filename>
-param <filename>
-prefix <prefix>
-progress <style>
-protein <filename>
-sp3_aromatic <bool>
-sp3aromatic <bool>
-stabilization <bool>
-stbl <bool>
-szmap_mpi_hostfile <filename>
-szmap_mpi_np <number>
-v
-verbose
-warn_if_missing_hydrogens
grid_comp command line option
-by <number>
-cutoff <number>
-default <number>
-default_value <number>
-geq <number>
-geq_mask <number>
-grid1 <name>
-grid2 <name>
-grid3 <name>
-i <filename>
-in1 <filename>
-in2 <filename>
-in3 <filename>
-input_file1 <filename>
-input_file2 <filename>
-input_file3 <filename>
-int_method <value>
-leq <number>
-leq_mask <number>
-mask_vdw
-masked_point_cutoff <number>
-method <value>
-new_value <number>
-o <filename>
-op <value>
-operation <value>
-output_grid <filename>
-scale <number>
-to <number>
-v
-verbose

M

mkhetdict command line option
-i <filename>
-input_mol <filename>
-o <filename.txt>
-output_txt <filename.txt>
-v
-verbose

O

OE_ARCH, [1], [2], [3]
OE_LICENSE

P

PATH, [1], [2], [3], [4]
pch command line option
-fix_elements
-i <filename>
-input_mol <filename>
-keep_alts
-keep_numbers
-l <filename>
-lig_ch <char>
-lig_end <int>
-lig_ins <char>
-lig_model <int>
-lig_num <int>
-lig_res <RES>
-ligand_chain <char>
-ligand_inscode <char>
-ligand_model <int>
-ligand_res <RES>
-ligand_resnum <int>
-ligand_resnum_end <int>
-no_fixup
-nonsym
-nonsymmetrized_charges
-output_lig <filename>
-output_prot <filename>
-output_waters <filename>
-p <filename>
-v
-verbose
-waters <filename>
Philosophy and Design
Preparation
Pronunciation

S

szmap command line option
-apo_box <filename>
-apo_coords
-apo_grids
-apo_point_grid
-around <filename>
-around_mol <filename>
-at_coords <filename>
-bbox <xmin> <ymin> <zmin> <xmax> <ymax> <zmax>
-boundary <number>
-boundary_radius <number>
-boundary_spacing <number>
-bounding_box <xmin> <ymin> <zmin> <xmax> <ymax> <zmax>
-box_mol <filename>
-chain <letter>
-coords <filename>
-cplx_grids
-dcutoff <number>
-dielectric_model <type>
-distance_cutoff <number>
-eps_in <number>
-eps_out <number>
-grid_spacing <number>
-grids <type>
-inner_dielectric <number>
-inscode <letter>
-l <filename>
-lig_box <filename>
-lig_coords
-lig_grids
-lig_point_grid
-ligand <filename>
-like_apo <filename>
-like_box <filename>
-like_lig <filename>
-like_std <filename>
-log <filename>
-logfile <filename>
-mask_cutoff <number>
-model <type>
-mpi_hostfile <filename>
-mpi_np <number>
-num_orientations <number>
-o <filename>
-outer_dielectric <number>
-output_mol <filename>
-p <filename>
-param <filename>
-point_grid
-prefix <prefix>
-progress <style>
-properties <type>
-protein <filename>
-res <number>
-residue_chain <letter>
-residue_insert <letter>
-residue_number <number>
-restrict_calc <level>
-results_set <type>
-rot <number>
-salt <number>
-salt_conc <number>
-space <number>
-split_lig
-stabilization
-standard_grids
-stbl
-std_box <filename>
-std_coords
-std_grids
-surf
-surface_points
-table <filename>
-use_apo_from <filename>
-v
-value_cutoff <number>
-vcutoff <number>
-vdw_scale <number>
-verbose
-warn_if_missing_hydrogens
-water_charge <type>
-zap_spacing <number>
szmap_grid command line option
-all <format>
-apo_box <filename>
-at_coords <filename>
-box_mol <filename>
-coords <filename>
-g <name>
-grid <name>
-i <filename>
-input_mol <filename>
-lig_box <filename>
-mask_cutoff <number>
-mol <filename>
-no_table
-o <filename>
-output_all_format <format>
-output_grid <filename>
-output_mol <filename>
-prefix <text>
-slice
-std_box <filename>
-v
-verbose
szmap_report command line option
-acolor <color>
-aromstyle <style>
-astl <style>
-atomcolor <color>
-atomsstl <style>
-atomstereostyle <style>
-bcolor <color>
-bondcolor <color>
-bondsstl <style>
-bondstereostyle <style>
-cols <number>
-i <filename>
-input <filename>
-keep_hydrogens
-legend <bool>
-o <filename>
-output <filename>
-pagesize <size>
-resolution <level>
-rows <number>
-separate
-size <size>
-surface <bool>
-t <prop>
-tag_set <set>
-tagname <prop>
-title <text>
-v
-verbose

T

Technical Details