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Merge pull request #1941 from bgruening/chemical_datatypes
add chemical datatypes
This commit is contained in:
John Chilton
@@ -443,6 +443,53 @@
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<datatype extension="biom1" type="galaxy.datatypes.text:Biom1" display_in_upload="True" subclass="True" mimetype="application/json" />
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<!-- Strand-specific Coordinate Count Datatype used by the Center for Eukaryotic Gene Regulation labs at Penn State -->
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<datatype extension="scidx" type="galaxy.datatypes.interval:ScIdx" display_in_upload="true" />
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<!--Cheminformatics Datatypes -->
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<datatype extension="smi" type="galaxy.datatypes.molecules:SMILES" display_in_upload="True">
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<!-- The ordering is important. The first one is considered as default converter in the build-in conversion function -> (as sdf)-->
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<converter file="smi_to_sdf_converter.xml" target_datatype="sdf"/>
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<converter file="smi_to_inchi_converter.xml" target_datatype="inchi"/>
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<converter file="smi_to_cml_converter.xml" target_datatype="cml"/>
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<converter file="smi_to_mol_converter.xml" target_datatype="mol"/>
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<converter file="smi_to_mol2_converter.xml" target_datatype="mol2"/>
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<converter file="smi_to_smi_converter.xml" target_datatype="smi"/>
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</datatype>
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<datatype extension="sdf" type="galaxy.datatypes.molecules:SDF" display_in_upload="True">
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<converter file="sdf_to_smi_converter.xml" target_datatype="smi"/>
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<converter file="sdf_to_inchi_converter.xml" target_datatype="inchi"/>
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<converter file="sdf_to_mol2_converter.xml" target_datatype="mol2"/>
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<converter file="sdf_to_cml_converter.xml" target_datatype="cml"/>
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</datatype>
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<datatype extension="inchi" type="galaxy.datatypes.molecules:InChI" display_in_upload="True">
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<converter file="inchi_to_smi_converter.xml" target_datatype="smi"/>
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<converter file="inchi_to_sdf_converter.xml" target_datatype="sdf"/>
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<converter file="inchi_to_mol_converter.xml" target_datatype="mol"/>
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<converter file="inchi_to_mol2_converter.xml" target_datatype="mol2"/>
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<converter file="inchi_to_cml_converter.xml" target_datatype="cml"/>
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</datatype>
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<datatype extension="mol" type="galaxy.datatypes.molecules:MOL" display_in_upload="True">
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<converter file="mol_to_smi_converter.xml" target_datatype="smi"/>
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<converter file="mol_to_inchi_converter.xml" target_datatype="inchi"/>
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<converter file="mol_to_mol2_converter.xml" target_datatype="mol2"/>
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<converter file="mol_to_cml_converter.xml" target_datatype="cml"/>
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</datatype>
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<datatype extension="mol2" type="galaxy.datatypes.molecules:MOL2" display_in_upload="False">
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<converter file="mol2_to_smi_converter.xml" target_datatype="smi"/>
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<converter file="mol2_to_sdf_converter.xml" target_datatype="sdf"/>
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<converter file="mol2_to_inchi_converter.xml" target_datatype="inchi"/>
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<converter file="mol2_to_mol_converter.xml" target_datatype="mol"/>
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<converter file="mol2_to_cml_converter.xml" target_datatype="cml"/>
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</datatype>
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<datatype extension="cml" type="galaxy.datatypes.molecules:CML" display_in_upload="True">
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<converter file="cml_to_smi_converter.xml" target_datatype="smi"/>
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<converter file="cml_to_inchi_converter.xml" target_datatype="inchi"/>
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<converter file="cml_to_sdf_converter.xml" target_datatype="sdf"/>
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<converter file="cml_to_mol2_converter.xml" target_datatype="mol2"/>
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</datatype>
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<datatype extension="fps" type="galaxy.datatypes.molecules:FPS" mimetype="text/html" display_in_upload="True" />
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<datatype extension="obfs" type="galaxy.datatypes.molecules:OBFS" mimetype="text/html" display_in_upload="False" />
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<datatype extension="phar" type="galaxy.datatypes.molecules:PHAR" display_in_upload="False" />
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<datatype extension="pdb" type="galaxy.datatypes.molecules:PDB" display_in_upload="True" />
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</registration>
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<sniffers>
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<!--
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@@ -484,6 +531,7 @@
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<sniffer type="galaxy.datatypes.proteomics:Msp"/>
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<sniffer type="galaxy.datatypes.proteomics:SPLib"/>
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<sniffer type="galaxy.datatypes.proteomics:ThermoRAW"/>
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<sniffer type="galaxy.datatypes.molecules:CML"/>
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<sniffer type="galaxy.datatypes.xml:GenericXml"/>
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<sniffer type="galaxy.datatypes.triples:Turtle"/>
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<sniffer type="galaxy.datatypes.triples:NTriples"/>
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@@ -493,6 +541,12 @@
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<sniffer type="galaxy.datatypes.sequence:csFasta"/>
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<sniffer type="galaxy.datatypes.qualityscore:QualityScoreSOLiD"/>
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<sniffer type="galaxy.datatypes.qualityscore:QualityScore454"/>
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<sniffer type="galaxy.datatypes.molecules:SDF"/>
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<sniffer type="galaxy.datatypes.molecules:PDB"/>
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<sniffer type="galaxy.datatypes.molecules:MOL2"/>
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<sniffer type="galaxy.datatypes.molecules:InChI"/>
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<sniffer type="galaxy.datatypes.molecules:FPS"/>
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<!-- TODO: see molecules.py <sniffer type="galaxy.datatypes.molecules:SMILES"/>-->
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<sniffer type="galaxy.datatypes.sequence:Fasta"/>
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<sniffer type="galaxy.datatypes.sequence:Fastq"/>
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<sniffer type="galaxy.datatypes.interval:Wiggle"/>
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@@ -0,0 +1,22 @@
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<tool id="CONVERTER_cml_to_inchi" name="CML to InChI" version="1.0.0">
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<description></description>
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<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
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<requirements>
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<requirement type="package" version="2.3.2">openbabel</requirement>
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</requirements>
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<command>
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<![CDATA[
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obabel -icml "${input}" -oinchi -O "${output}" -e 2>&1
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]]>
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</command>
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<inputs>
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<param name="input" type="data" format="cml" label="Molecules in CML-format"/>
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</inputs>
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<outputs>
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<data name="output" format="inchi"/>
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</outputs>
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<help>
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<![CDATA[
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]]>
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</help>
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</tool>
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@@ -0,0 +1,22 @@
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<tool id="CONVERTER_cml_to_mol2" name="CML to mol2" version="1.0.0">
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<description></description>
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<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
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<requirements>
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<requirement type="package" version="2.3.2">openbabel</requirement>
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</requirements>
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<command>
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<![CDATA[
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obabel -icml "${input}" -omol2 -O "${output}" -e 2>&1
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]]>
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</command>
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<inputs>
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<param name="input" type="data" format="cml" label="Molecules in CML-format"/>
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</inputs>
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<outputs>
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<data name="output" format="mol2"/>
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</outputs>
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<help>
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<![CDATA[
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]]>
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</help>
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</tool>
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@@ -0,0 +1,22 @@
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<tool id="CONVERTER_cml_to_sdf" name="CML to SDF" version="1.0.0">
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<description></description>
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<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
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<requirements>
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<requirement type="package" version="2.3.2">openbabel</requirement>
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</requirements>
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<command>
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<![CDATA[
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obabel -icml "${input}" -osdf "${output}" -e 2>&1
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]]>
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</command>
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<inputs>
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<param name="input" type="data" format="cml" label="Molecules in CML-format"/>
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</inputs>
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<outputs>
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<data name="output" format="sdf"/>
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</outputs>
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<help>
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<![CDATA[
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]]>
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</help>
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</tool>
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@@ -0,0 +1,48 @@
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<tool id="CONVERTER_cml_to_smiles" name="CML to SMILES" version="1.0.0">
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<description></description>
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<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
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<requirements>
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<requirement type="package" version="2.3.2">openbabel</requirement>
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</requirements>
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<command >
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<![CDATA[
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obabel
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-icml "${input}"
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#if $can:
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-ocan
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#else:
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-osmi
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#end if
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-O "${output}"
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-e
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$remove_h
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#if $iso_chi or $can or $exp_h:
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-x$iso_chi$exp_h$can
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#end if
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#if $dative_bonds:
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-b
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#end if
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#if int($ph) >= 0:
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-p $ph
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#end if
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2>&1
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]]>
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</command>
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<inputs>
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<param name="input" type="data" format="cml" label="Molecules in CML-format"/>
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<param name="iso_chi" type="boolean" label="Do not include isotopic or chiral markings (-xi)" truevalue="i" falsevalue="" checked="false" />
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<param name="can" type="boolean" label="Output in canonical form (-xc)" truevalue="c" falsevalue="" checked="false" />
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<param name="exp_h" type="boolean" label="Output explicit hydrogens as such (-xh)" truevalue="h" falsevalue="" checked="false" />
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<param name="remove_h" type="boolean" label="Delete hydrogen atoms (-d)" truevalue="-d" falsevalue="" />
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<param name="ph" type="float" value="-1" label="Add hydrogens appropriate for pH (-p)" help="-1 means deactivated"/>
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<param name="dative_bonds" type="boolean" label="Convert dative bonds (e.g. [N+]([O-])=O to N(=O)=O) (-b)" truevalue="-b" falsevalue="" />
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</inputs>
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<outputs>
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<data name="output" format="smi"/>
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</outputs>
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<help>
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<![CDATA[
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]]>
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</help>
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</tool>
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@@ -0,0 +1,22 @@
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<tool id="CONVERTER_inchi_to_cml" name="InChI to CML" version="1.0.0">
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<description></description>
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<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
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<requirements>
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<requirement type="package" version="2.3.2">openbabel</requirement>
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</requirements>
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<command>
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<![CDATA[
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obabel -iinchi "${input}" -ocml -O "${output}" -e 2>&1
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]]>
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</command>
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<inputs>
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<param name="input" type="data" format="inchi" label="Molecules in InChI format"/>
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</inputs>
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<outputs>
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<data name="output" format="cml"/>
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</outputs>
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<help>
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<![CDATA[
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]]>
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</help>
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</tool>
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@@ -0,0 +1,22 @@
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<tool id="CONVERTER_inchi_to_mol2" name="InChI to MOL2" version="1.0.0">
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<description></description>
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<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
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<requirements>
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<requirement type="package" version="2.3.2">openbabel</requirement>
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</requirements>
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<command>
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<![CDATA[
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obabel -iinchi "${input}" -omol2 -O "${output}" -e 2>&1
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]]>
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</command>
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<inputs>
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<param name="input" type="data" format="inchi" label="Molecules in InChI format"/>
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</inputs>
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<outputs>
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<data name="output" format="mol2"/>
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</outputs>
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<help>
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<![CDATA[
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]]>
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</help>
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</tool>
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@@ -0,0 +1,22 @@
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<tool id="CONVERTER_inchi_to_mol" name="InChI to MOL" version="1.0.0">
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<description></description>
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<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
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<requirements>
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<requirement type="package" version="2.3.2">openbabel</requirement>
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</requirements>
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<command>
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<![CDATA[
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obabel -iinchi "${input}" -omol -O "${output}" -e 2>&1
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]]>
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</command>
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<inputs>
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<param name="input" type="data" format="inchi" label="Molecules in InChI-format"/>
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</inputs>
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<outputs>
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<data name="output" format="mol"/>
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</outputs>
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<help>
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<![CDATA[
|
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]]>
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</help>
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</tool>
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@@ -0,0 +1,22 @@
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<tool id="CONVERTER_inchi_to_sdf" name="InChI to SDF" version="1.0.0">
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<description></description>
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<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
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<requirements>
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<requirement type="package" version="2.3.2">openbabel</requirement>
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</requirements>
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<command>
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<![CDATA[
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obabel -iinchi "${input}" -osdf -O "${output}" -e 2>&1
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]]>
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</command>
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<inputs>
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<param name="input" type="data" format="inchi" label="Molecules in InChI format"/>
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</inputs>
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<outputs>
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<data name="output" format="sdf"/>
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</outputs>
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<help>
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<![CDATA[
|
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]]>
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</help>
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</tool>
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@@ -0,0 +1,22 @@
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<tool id="CONVERTER_inchi_to_smi" name="InChI to SMILES" version="1.0.0">
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<description></description>
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<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
|
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<requirements>
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<requirement type="package" version="2.3.2">openbabel</requirement>
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</requirements>
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<command>
|
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<![CDATA[
|
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obabel -iinchi "${input}" -osmi -O "${output}" -e 2>&1
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]]>
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</command>
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<inputs>
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<param name="input" type="data" format="inchi" label="Molecules in InChI format"/>
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</inputs>
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<outputs>
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<data name="output" format="smi"/>
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</outputs>
|
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<help>
|
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<![CDATA[
|
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]]>
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</help>
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</tool>
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@@ -0,0 +1,22 @@
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<tool id="CONVERTER_mol2_to_cml" name="MOL2 to CML" version="1.0.0">
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<description></description>
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<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
|
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<requirements>
|
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<requirement type="package" version="2.3.2">openbabel</requirement>
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</requirements>
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<command>
|
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<![CDATA[
|
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obabel -imol2 "${input}" -ocml -O "${output}" -e 2>&1
|
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]]>
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</command>
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<inputs>
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<param name="input" type="data" format="mol2" label="Molecules in MOL2-format"/>
|
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</inputs>
|
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<outputs>
|
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<data name="output" format="cml"/>
|
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</outputs>
|
||||
<help>
|
||||
<![CDATA[
|
||||
]]>
|
||||
</help>
|
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</tool>
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@@ -0,0 +1,22 @@
|
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<tool id="CONVERTER_mol2_to_inchi" name="MOL2 to InChI" version="1.0.0">
|
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<description></description>
|
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<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
|
||||
<requirements>
|
||||
<requirement type="package" version="2.3.2">openbabel</requirement>
|
||||
</requirements>
|
||||
<command>
|
||||
<![CDATA[
|
||||
obabel -imol2 "${input}" -oinchi -O "${output}" -e 2>&1
|
||||
]]>
|
||||
</command>
|
||||
<inputs>
|
||||
<param name="input" type="data" format="mol2" label="Molecules in MOL2-format"/>
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data name="output" format="inchi"/>
|
||||
</outputs>
|
||||
<help>
|
||||
<![CDATA[
|
||||
]]>
|
||||
</help>
|
||||
</tool>
|
||||
@@ -0,0 +1,22 @@
|
||||
<tool id="CONVERTER_mol2_to_mol" name="MOL2 to MOL" version="1.0.0">
|
||||
<description></description>
|
||||
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
|
||||
<requirements>
|
||||
<requirement type="package" version="2.3.2">openbabel</requirement>
|
||||
</requirements>
|
||||
<command>
|
||||
<![CDATA[
|
||||
obabel -imol2 "${input}" -omol -O "${output}" -e 2>&1
|
||||
]]>
|
||||
</command>
|
||||
<inputs>
|
||||
<param name="input" type="data" format="mol2" label="Molecules in MOL2-format"/>
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data name="output" format="mol"/>
|
||||
</outputs>
|
||||
<help>
|
||||
<![CDATA[
|
||||
]]>
|
||||
</help>
|
||||
</tool>
|
||||
@@ -0,0 +1,22 @@
|
||||
<tool id="CONVERTER_mol2_to_sdf" name="MOL2 to SDF" version="1.0.0">
|
||||
<description></description>
|
||||
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
|
||||
<requirements>
|
||||
<requirement type="package" version="2.3.2">openbabel</requirement>
|
||||
</requirements>
|
||||
<command>
|
||||
<![CDATA[
|
||||
obabel -imol2 "${input}" -osdf "${output}" -e 2>&1
|
||||
]]>
|
||||
</command>
|
||||
<inputs>
|
||||
<param name="input" type="data" format="mol2" label="Molecules in MOL2-format"/>
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data name="output" format="sdf"/>
|
||||
</outputs>
|
||||
<help>
|
||||
<![CDATA[
|
||||
]]>
|
||||
</help>
|
||||
</tool>
|
||||
@@ -0,0 +1,22 @@
|
||||
<tool id="CONVERTER_mol2_to_smi" name="MOL2 to SMILES" version="1.0.0">
|
||||
<description></description>
|
||||
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
|
||||
<requirements>
|
||||
<requirement type="package" version="2.3.2">openbabel</requirement>
|
||||
</requirements>
|
||||
<command>
|
||||
<![CDATA[
|
||||
obabel -imol2 "${input}" -omol "${output}" -e 2>&1
|
||||
]]>
|
||||
</command>
|
||||
<inputs>
|
||||
<param name="input" type="data" format="mol2" label="Molecules in MOL2-format"/>
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data name="output" format="smi"/>
|
||||
</outputs>
|
||||
<help>
|
||||
<![CDATA[
|
||||
]]>
|
||||
</help>
|
||||
</tool>
|
||||
@@ -0,0 +1,21 @@
|
||||
<tool id="CONVERTER_mol_to_cml" name="MOL to CML" version="1.0.0">
|
||||
<description></description>
|
||||
<requirements>
|
||||
<requirement type="package" version="2.3.2">openbabel</requirement>
|
||||
</requirements>
|
||||
<command>
|
||||
<![CDATA[
|
||||
obabel -imol "${input}" -ocml -O "${output}" -e 2>&1
|
||||
]]>
|
||||
</command>
|
||||
<inputs>
|
||||
<param name="input" type="data" format="mol" label="Molecules in MOL-format"/>
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data name="output" format="cml"/>
|
||||
</outputs>
|
||||
<help>
|
||||
<![CDATA[
|
||||
]]>
|
||||
</help>
|
||||
</tool>
|
||||
@@ -0,0 +1,21 @@
|
||||
<tool id="CONVERTER_mol_to_mol2" name="MOL to MOL2" version="1.0.0">
|
||||
<description></description>
|
||||
<requirements>
|
||||
<requirement type="package" version="2.3.2">openbabel</requirement>
|
||||
</requirements>
|
||||
<command>
|
||||
<![CDATA[
|
||||
obabel -imol "${input}" -omol2 -O "${output}" -e 2>&1
|
||||
]]>
|
||||
</command>
|
||||
<inputs>
|
||||
<param name="input" type="data" format="mol" label="Molecules in MOL-format"/>
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data name="output" format="mol2"/>
|
||||
</outputs>
|
||||
<help>
|
||||
<![CDATA[
|
||||
]]>
|
||||
</help>
|
||||
</tool>
|
||||
@@ -0,0 +1,21 @@
|
||||
<tool id="CONVERTER_mol_to_mol2" name="MOL to MOL2" version="1.0.0">
|
||||
<description></description>
|
||||
<requirements>
|
||||
<requirement type="package" version="2.3.2">openbabel</requirement>
|
||||
</requirements>
|
||||
<command>
|
||||
<![CDATA[
|
||||
obabel -imol "${input}" -omol2 -O "${output}" -e 2>&1
|
||||
]]>
|
||||
</command>
|
||||
<inputs>
|
||||
<param name="input" type="data" format="mol" label="Molecules in MOL-format"/>
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data name="output" format="mol2"/>
|
||||
</outputs>
|
||||
<help>
|
||||
<![CDATA[
|
||||
]]>
|
||||
</help>
|
||||
</tool>
|
||||
@@ -0,0 +1,21 @@
|
||||
<tool id="CONVERTER_mol_to_smi" name="MOL to SMILES" version="1.0.0">
|
||||
<description></description>
|
||||
<requirements>
|
||||
<requirement type="package" version="2.3.2">openbabel</requirement>
|
||||
</requirements>
|
||||
<command>
|
||||
<![CDATA[
|
||||
obabel -imol "${input}" -osmi -O "${output}" -e 2>&1
|
||||
]]>
|
||||
</command>
|
||||
<inputs>
|
||||
<param name="input" type="data" format="mol" label="Molecules in MOL-format"/>
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data name="output" format="smi"/>
|
||||
</outputs>
|
||||
<help>
|
||||
<![CDATA[
|
||||
]]>
|
||||
</help>
|
||||
</tool>
|
||||
@@ -0,0 +1,22 @@
|
||||
<tool id="CONVERTER_sdf_to_cml" name="SDF to CML" version="1.0.0">
|
||||
<description></description>
|
||||
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
|
||||
<requirements>
|
||||
<requirement type="package" version="2.3.2">openbabel</requirement>
|
||||
</requirements>
|
||||
<command>
|
||||
<![CDATA[
|
||||
obabel -isdf "${input}" -ocml -O "${output}" -e 2>&1
|
||||
]]>
|
||||
</command>
|
||||
<inputs>
|
||||
<param name="input" type="data" format="sdf" label="Molecules in SDF-format"/>
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data name="output" format="cml"/>
|
||||
</outputs>
|
||||
<help>
|
||||
<![CDATA[
|
||||
]]>
|
||||
</help>
|
||||
</tool>
|
||||
@@ -0,0 +1,22 @@
|
||||
<tool id="CONVERTER_sdf_to_inchi" name="SDF to InChI" version="1.0.0">
|
||||
<description></description>
|
||||
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
|
||||
<requirements>
|
||||
<requirement type="package" version="2.3.2">openbabel</requirement>
|
||||
</requirements>
|
||||
<command>
|
||||
<![CDATA[
|
||||
obabel -isdf "${input}" -oinchi -O "${output}" -e 2>&1
|
||||
]]>
|
||||
</command>
|
||||
<inputs>
|
||||
<param name="input" type="data" format="sdf" label="Molecules in SDF-format"/>
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data name="output" format="inchi"/>
|
||||
</outputs>
|
||||
<help>
|
||||
<![CDATA[
|
||||
]]>
|
||||
</help>
|
||||
</tool>
|
||||
@@ -0,0 +1,22 @@
|
||||
<tool id="CONVERTER_sdf_to_mol2" name="SDF to mol2" version="1.0.0">
|
||||
<description></description>
|
||||
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
|
||||
<requirements>
|
||||
<requirement type="package" version="2.3.2">openbabel</requirement>
|
||||
</requirements>
|
||||
<command>
|
||||
<![CDATA[
|
||||
obabel -isdf "${input}" -omol2 -O "${output}" -e 2>&1
|
||||
]]>
|
||||
</command>
|
||||
<inputs>
|
||||
<param name="input" type="data" format="sdf" label="Molecules in SDF-format"/>
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data name="output" format="mol2"/>
|
||||
</outputs>
|
||||
<help>
|
||||
<![CDATA[
|
||||
]]>
|
||||
</help>
|
||||
</tool>
|
||||
@@ -0,0 +1,27 @@
|
||||
<tool id="CONVERTER_sdf_to_smiles" name="SDF to SMILES" version="1.0.1">
|
||||
<description></description>
|
||||
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
|
||||
<requirements>
|
||||
<requirement type="package" version="2.3.2">openbabel</requirement>
|
||||
</requirements>
|
||||
<command >
|
||||
<![CDATA[
|
||||
obabel
|
||||
-isdf "${input}"
|
||||
-ocan
|
||||
-O "${output}"
|
||||
-e
|
||||
2>&1
|
||||
]]>
|
||||
</command>
|
||||
<inputs>
|
||||
<param name="input" type="data" format="sdf" label="Molecules in SDF-format"/>
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data name="output" format="smi"/>
|
||||
</outputs>
|
||||
<help>
|
||||
<![CDATA[
|
||||
]]>
|
||||
</help>
|
||||
</tool>
|
||||
@@ -0,0 +1,22 @@
|
||||
<tool id="CONVERTER_SMILES_to_cml" name="SMILES to CML" version="1.0.0">
|
||||
<description></description>
|
||||
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
|
||||
<requirements>
|
||||
<requirement type="package" version="2.3.2">openbabel</requirement>
|
||||
</requirements>
|
||||
<command>
|
||||
<![CDATA[
|
||||
obabel -ismi "${input}" -ocml -O "${output}" -e 2>&1
|
||||
]]>
|
||||
</command>
|
||||
<inputs>
|
||||
<param name="input" type="data" format="smi" label="Molecules in SMILES format"/>
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data name="output" format="cml"/>
|
||||
</outputs>
|
||||
<help>
|
||||
<![CDATA[
|
||||
]]>
|
||||
</help>
|
||||
</tool>
|
||||
@@ -0,0 +1,22 @@
|
||||
<tool id="CONVERTER_SMILES_to_inchi" name="SMILES to InChI" version="1.0.0">
|
||||
<description></description>
|
||||
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
|
||||
<requirements>
|
||||
<requirement type="package" version="2.3.2">openbabel</requirement>
|
||||
</requirements>
|
||||
<command>
|
||||
<![CDATA[
|
||||
obabel -ismi "${input}" -oinchi -O "${output}" -e 2>&1
|
||||
]]>
|
||||
</command>
|
||||
<inputs>
|
||||
<param name="input" type="data" format="smi" label="Molecules in SMILES format"/>
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data name="output" format="inchi"/>
|
||||
</outputs>
|
||||
<help>
|
||||
<![CDATA[
|
||||
]]>
|
||||
</help>
|
||||
</tool>
|
||||
@@ -0,0 +1,22 @@
|
||||
<tool id="CONVERTER_SMILES_to_MOL2" name="SMILES to MOL2" version="1.0.0">
|
||||
<description></description>
|
||||
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
|
||||
<requirements>
|
||||
<requirement type="package" version="2.3.2">openbabel</requirement>
|
||||
</requirements>
|
||||
<command>
|
||||
<![CDATA[
|
||||
obabel -ismi "${input}" -omol2 -O "${output}" -e 2>&1
|
||||
]]>
|
||||
</command>
|
||||
<inputs>
|
||||
<param name="input" type="data" format="smi" label="Molecules in SMILES format"/>
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data name="output" format="mol2"/>
|
||||
</outputs>
|
||||
<help>
|
||||
<![CDATA[
|
||||
]]>
|
||||
</help>
|
||||
</tool>
|
||||
@@ -0,0 +1,22 @@
|
||||
<tool id="CONVERTER_SMILES_to_MOL" name="SMILES to MOL" version="1.0.0">
|
||||
<description></description>
|
||||
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
|
||||
<requirements>
|
||||
<requirement type="package" version="2.3.2">openbabel</requirement>
|
||||
</requirements>
|
||||
<command>
|
||||
<![CDATA[
|
||||
obabel -ismi "${input}" -omol -O "${output}" -e 2>&1
|
||||
]]>
|
||||
</command>
|
||||
<inputs>
|
||||
<param name="input" type="data" format="smi" label="Molecules in SMILES format"/>
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data name="output" format="mol"/>
|
||||
</outputs>
|
||||
<help>
|
||||
<![CDATA[
|
||||
]]>
|
||||
</help>
|
||||
</tool>
|
||||
@@ -0,0 +1,22 @@
|
||||
<tool id="CONVERTER_SMILES_to_sdf" name="SMILES to SDF" version="1.0.0">
|
||||
<description></description>
|
||||
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
|
||||
<requirements>
|
||||
<requirement type="package" version="2.3.2">openbabel</requirement>
|
||||
</requirements>
|
||||
<command>
|
||||
<![CDATA[
|
||||
obabel -ismi "${input}" -osdf -O "${output}" -e 2>&1
|
||||
]]>
|
||||
</command>
|
||||
<inputs>
|
||||
<param name="input" type="data" format="smi" label="Molecules in SMILES format"/>
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data name="output" format="sdf"/>
|
||||
</outputs>
|
||||
<help>
|
||||
<![CDATA[
|
||||
]]>
|
||||
</help>
|
||||
</tool>
|
||||
@@ -0,0 +1,48 @@
|
||||
<tool id="CONVERTER_smiles_to_smiles" name="SMILES to SMILES" version="1.0.0">
|
||||
<description></description>
|
||||
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
|
||||
<requirements>
|
||||
<requirement type="package" version="2.3.2">openbabel</requirement>
|
||||
</requirements>
|
||||
<command >
|
||||
<![CDATA[
|
||||
obabel
|
||||
-ismi "${input}"
|
||||
#if $can:
|
||||
-ocan
|
||||
#else:
|
||||
-osmi
|
||||
#end if
|
||||
-O "${output}"
|
||||
-e
|
||||
$remove_h
|
||||
#if $iso_chi or $can or $exp_h:
|
||||
-x$iso_chi$exp_h$can
|
||||
#end if
|
||||
#if $dative_bonds:
|
||||
-b
|
||||
#end if
|
||||
#if int($ph) >= 0:
|
||||
-p $ph
|
||||
#end if
|
||||
|
||||
2>&1
|
||||
]]>
|
||||
</command>
|
||||
<inputs>
|
||||
<param name="input" type="data" format="smi" label="Molecules in SD-format"/>
|
||||
<param name="iso_chi" type="boolean" label="Do not include isotopic or chiral markings (-xi)" truevalue="i" falsevalue="" checked="false" />
|
||||
<param name="can" type="boolean" label="Output in canonical form (-xc)" truevalue="c" falsevalue="" checked="false" />
|
||||
<param name="exp_h" type="boolean" label="Output explicit hydrogens as such (-xh)" truevalue="h" falsevalue="" checked="false" />
|
||||
<param name="remove_h" type="boolean" label="Delete hydrogen atoms (-d)" truevalue="-d" falsevalue="" />
|
||||
<param name="ph" type="float" value="-1" label="Add hydrogens appropriate for pH (-p)" help="-1 means deactivated"/>
|
||||
<param name="dative_bonds" type="boolean" label="Convert dative bonds (e.g. [N+]([O-])=O to N(=O)=O) (-b)" truevalue="-b" falsevalue="" />
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data name="output" format="smi"/>
|
||||
</outputs>
|
||||
<help>
|
||||
<![CDATA[
|
||||
]]>
|
||||
</help>
|
||||
</tool>
|
||||
@@ -0,0 +1,769 @@
|
||||
# -*- coding: utf-8 -*-
|
||||
|
||||
from galaxy.datatypes import data
|
||||
import logging
|
||||
from galaxy.datatypes.sniff import get_headers
|
||||
from galaxy.datatypes.data import get_file_peek
|
||||
from galaxy.datatypes.tabular import Tabular
|
||||
from galaxy.datatypes.binary import Binary
|
||||
from galaxy.datatypes.xml import GenericXml
|
||||
import subprocess
|
||||
import os
|
||||
|
||||
from galaxy.datatypes.metadata import MetadataElement
|
||||
from galaxy.datatypes import metadata
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
|
||||
def count_special_lines(word, filename, invert=False):
|
||||
"""
|
||||
searching for special 'words' using the grep tool
|
||||
grep is used to speed up the searching and counting
|
||||
The number of hits is returned.
|
||||
"""
|
||||
try:
|
||||
cmd = ["grep", "-c"]
|
||||
if invert:
|
||||
cmd.append('-v')
|
||||
cmd.extend([word, filename])
|
||||
out = subprocess.Popen(cmd, stdout=subprocess.PIPE)
|
||||
return int(out.communicate()[0].split()[0])
|
||||
except:
|
||||
pass
|
||||
return 0
|
||||
|
||||
|
||||
def count_lines(filename, non_empty=False):
|
||||
"""
|
||||
counting the number of lines from the 'filename' file
|
||||
"""
|
||||
try:
|
||||
if non_empty:
|
||||
out = subprocess.Popen(['grep', '-cve', '^\s*$', filename], stdout=subprocess.PIPE)
|
||||
else:
|
||||
out = subprocess.Popen(['wc', '-l', filename], stdout=subprocess.PIPE)
|
||||
return int(out.communicate()[0].split()[0])
|
||||
except:
|
||||
pass
|
||||
return 0
|
||||
|
||||
|
||||
class GenericMolFile(data.Text):
|
||||
"""
|
||||
abstract class for most of the molecule files
|
||||
"""
|
||||
MetadataElement(name="number_of_molecules", default=0, desc="Number of molecules", readonly=True, visible=True, optional=True, no_value=0)
|
||||
|
||||
def set_peek(self, dataset, is_multi_byte=False):
|
||||
if not dataset.dataset.purged:
|
||||
dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
|
||||
if (dataset.metadata.number_of_molecules == 1):
|
||||
dataset.blurb = "1 molecule"
|
||||
else:
|
||||
dataset.blurb = "%s molecules" % dataset.metadata.number_of_molecules
|
||||
dataset.peek = data.get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
|
||||
else:
|
||||
dataset.peek = 'file does not exist'
|
||||
dataset.blurb = 'file purged from disk'
|
||||
|
||||
def get_mime(self):
|
||||
return 'text/plain'
|
||||
|
||||
|
||||
class MOL(GenericMolFile):
|
||||
file_ext = "mol"
|
||||
|
||||
def set_meta(self, dataset, **kwd):
|
||||
"""
|
||||
Set the number molecules, in the case of MOL its always one.
|
||||
"""
|
||||
dataset.metadata.number_of_molecules = 1
|
||||
|
||||
|
||||
class SDF(GenericMolFile):
|
||||
file_ext = "sdf"
|
||||
|
||||
def sniff(self, filename):
|
||||
"""
|
||||
Try to guess if the file is a SDF2 file.
|
||||
|
||||
>>> from galaxy.datatypes.sniff import get_test_fname
|
||||
>>> fname = get_test_fname('drugbank_drugs.sdf')
|
||||
>>> SDF().sniff(fname)
|
||||
True
|
||||
|
||||
>>> fname = get_test_fname('drugbank_drugs.cml')
|
||||
>>> SDF().sniff(fname)
|
||||
False
|
||||
"""
|
||||
counter = count_special_lines("^M\s*END", filename) + count_special_lines("^\$\$\$\$", filename)
|
||||
if counter > 0 and counter % 2 == 0:
|
||||
return True
|
||||
else:
|
||||
return False
|
||||
|
||||
def set_meta(self, dataset, **kwd):
|
||||
"""
|
||||
Set the number of molecules in dataset.
|
||||
"""
|
||||
dataset.metadata.number_of_molecules = count_special_lines("^\$\$\$\$", dataset.file_name)
|
||||
|
||||
def split(cls, input_datasets, subdir_generator_function, split_params):
|
||||
"""
|
||||
Split the input files by molecule records.
|
||||
"""
|
||||
if split_params is None:
|
||||
return None
|
||||
|
||||
if len(input_datasets) > 1:
|
||||
raise Exception("SD-file splitting does not support multiple files")
|
||||
input_files = [ds.file_name for ds in input_datasets]
|
||||
|
||||
chunk_size = None
|
||||
if split_params['split_mode'] == 'number_of_parts':
|
||||
raise Exception('Split mode "%s" is currently not implemented for SD-files.' % split_params['split_mode'])
|
||||
elif split_params['split_mode'] == 'to_size':
|
||||
chunk_size = int(split_params['split_size'])
|
||||
else:
|
||||
raise Exception('Unsupported split mode %s' % split_params['split_mode'])
|
||||
|
||||
def _read_sdf_records(filename):
|
||||
lines = []
|
||||
with open(filename) as handle:
|
||||
for line in handle:
|
||||
lines.append(line)
|
||||
if line.startswith("$$$$"):
|
||||
yield lines
|
||||
lines = []
|
||||
|
||||
def _write_part_sdf_file(accumulated_lines):
|
||||
part_dir = subdir_generator_function()
|
||||
part_path = os.path.join(part_dir, os.path.basename(input_files[0]))
|
||||
part_file = open(part_path, 'w')
|
||||
part_file.writelines(accumulated_lines)
|
||||
part_file.close()
|
||||
|
||||
try:
|
||||
sdf_records = _read_sdf_records(input_files[0])
|
||||
sdf_lines_accumulated = []
|
||||
for counter, sdf_record in enumerate(sdf_records, start=1):
|
||||
sdf_lines_accumulated.extend(sdf_record)
|
||||
if counter % chunk_size == 0:
|
||||
_write_part_sdf_file(sdf_lines_accumulated)
|
||||
sdf_lines_accumulated = []
|
||||
if sdf_lines_accumulated:
|
||||
_write_part_sdf_file(sdf_lines_accumulated)
|
||||
except Exception, e:
|
||||
log.error('Unable to split files: %s' % str(e))
|
||||
raise
|
||||
split = classmethod(split)
|
||||
|
||||
|
||||
class MOL2(GenericMolFile):
|
||||
file_ext = "mol2"
|
||||
|
||||
def sniff(self, filename):
|
||||
"""
|
||||
Try to guess if the file is a MOL2 file.
|
||||
|
||||
>>> from galaxy.datatypes.sniff import get_test_fname
|
||||
>>> fname = get_test_fname('drugbank_drugs.mol2')
|
||||
>>> MOL2().sniff(fname)
|
||||
True
|
||||
|
||||
>>> fname = get_test_fname('drugbank_drugs.cml')
|
||||
>>> MOL2().sniff(fname)
|
||||
False
|
||||
"""
|
||||
if count_special_lines("@<TRIPOS>MOLECULE", filename) > 0:
|
||||
return True
|
||||
else:
|
||||
return False
|
||||
|
||||
def set_meta(self, dataset, **kwd):
|
||||
"""
|
||||
Set the number of lines of data in dataset.
|
||||
"""
|
||||
dataset.metadata.number_of_molecules = count_special_lines("@<TRIPOS>MOLECULE", dataset.file_name)
|
||||
|
||||
def split(cls, input_datasets, subdir_generator_function, split_params):
|
||||
"""
|
||||
Split the input files by molecule records.
|
||||
"""
|
||||
if split_params is None:
|
||||
return None
|
||||
|
||||
if len(input_datasets) > 1:
|
||||
raise Exception("MOL2-file splitting does not support multiple files")
|
||||
input_files = [ds.file_name for ds in input_datasets]
|
||||
|
||||
chunk_size = None
|
||||
if split_params['split_mode'] == 'number_of_parts':
|
||||
raise Exception('Split mode "%s" is currently not implemented for MOL2-files.' % split_params['split_mode'])
|
||||
elif split_params['split_mode'] == 'to_size':
|
||||
chunk_size = int(split_params['split_size'])
|
||||
else:
|
||||
raise Exception('Unsupported split mode %s' % split_params['split_mode'])
|
||||
|
||||
def _read_mol2_records(filename):
|
||||
lines = []
|
||||
start = True
|
||||
with open(filename) as handle:
|
||||
for line in handle:
|
||||
if line.startswith("@<TRIPOS>MOLECULE"):
|
||||
if start:
|
||||
start = False
|
||||
else:
|
||||
yield lines
|
||||
lines = []
|
||||
lines.append(line)
|
||||
|
||||
def _write_part_mol2_file(accumulated_lines):
|
||||
part_dir = subdir_generator_function()
|
||||
part_path = os.path.join(part_dir, os.path.basename(input_files[0]))
|
||||
part_file = open(part_path, 'w')
|
||||
part_file.writelines(accumulated_lines)
|
||||
part_file.close()
|
||||
|
||||
try:
|
||||
mol2_records = _read_mol2_records(input_files[0])
|
||||
mol2_lines_accumulated = []
|
||||
for counter, mol2_record in enumerate(mol2_records, start=1):
|
||||
mol2_lines_accumulated.extend(mol2_record)
|
||||
if counter % chunk_size == 0:
|
||||
_write_part_mol2_file(mol2_lines_accumulated)
|
||||
mol2_lines_accumulated = []
|
||||
if mol2_lines_accumulated:
|
||||
_write_part_mol2_file(mol2_lines_accumulated)
|
||||
except Exception, e:
|
||||
log.error('Unable to split files: %s' % str(e))
|
||||
raise
|
||||
split = classmethod(split)
|
||||
|
||||
|
||||
class FPS(GenericMolFile):
|
||||
"""
|
||||
chemfp fingerprint file: http://code.google.com/p/chem-fingerprints/wiki/FPS
|
||||
"""
|
||||
file_ext = "fps"
|
||||
|
||||
def sniff(self, filename):
|
||||
"""
|
||||
Try to guess if the file is a FPS file.
|
||||
|
||||
>>> from galaxy.datatypes.sniff import get_test_fname
|
||||
>>> fname = get_test_fname('q.fps')
|
||||
>>> FPS().sniff(fname)
|
||||
True
|
||||
|
||||
>>> fname = get_test_fname('drugbank_drugs.cml')
|
||||
>>> FPS().sniff(fname)
|
||||
False
|
||||
"""
|
||||
header = get_headers(filename, sep='\t', count=1)
|
||||
if header[0][0].strip() == '#FPS1':
|
||||
return True
|
||||
else:
|
||||
return False
|
||||
|
||||
def set_meta(self, dataset, **kwd):
|
||||
"""
|
||||
Set the number of lines of data in dataset.
|
||||
"""
|
||||
dataset.metadata.number_of_molecules = count_special_lines('^#', dataset.file_name, invert=True)
|
||||
|
||||
def split(cls, input_datasets, subdir_generator_function, split_params):
|
||||
"""
|
||||
Split the input files by fingerprint records.
|
||||
"""
|
||||
if split_params is None:
|
||||
return None
|
||||
|
||||
if len(input_datasets) > 1:
|
||||
raise Exception("FPS-file splitting does not support multiple files")
|
||||
input_files = [ds.file_name for ds in input_datasets]
|
||||
|
||||
chunk_size = None
|
||||
if split_params['split_mode'] == 'number_of_parts':
|
||||
raise Exception('Split mode "%s" is currently not implemented for MOL2-files.' % split_params['split_mode'])
|
||||
elif split_params['split_mode'] == 'to_size':
|
||||
chunk_size = int(split_params['split_size'])
|
||||
else:
|
||||
raise Exception('Unsupported split mode %s' % split_params['split_mode'])
|
||||
|
||||
def _write_part_fingerprint_file(accumulated_lines):
|
||||
part_dir = subdir_generator_function()
|
||||
part_path = os.path.join(part_dir, os.path.basename(input_files[0]))
|
||||
part_file = open(part_path, 'w')
|
||||
part_file.writelines(accumulated_lines)
|
||||
part_file.close()
|
||||
|
||||
try:
|
||||
header_lines = []
|
||||
lines_accumulated = []
|
||||
fingerprint_counter = 0
|
||||
for line in open(input_files[0]):
|
||||
if not line.strip():
|
||||
continue
|
||||
if line.startswith('#'):
|
||||
header_lines.append(line)
|
||||
else:
|
||||
fingerprint_counter += 1
|
||||
lines_accumulated.append(line)
|
||||
if fingerprint_counter != 0 and fingerprint_counter % chunk_size == 0:
|
||||
_write_part_fingerprint_file(header_lines + lines_accumulated)
|
||||
lines_accumulated = []
|
||||
if lines_accumulated:
|
||||
_write_part_fingerprint_file(header_lines + lines_accumulated)
|
||||
except Exception, e:
|
||||
log.error('Unable to split files: %s' % str(e))
|
||||
raise
|
||||
split = classmethod(split)
|
||||
|
||||
def merge(split_files, output_file):
|
||||
"""
|
||||
Merging fps files requires merging the header manually.
|
||||
We take the header from the first file.
|
||||
"""
|
||||
if len(split_files) == 1:
|
||||
# For one file only, use base class method (move/copy)
|
||||
return data.Text.merge(split_files, output_file)
|
||||
if not split_files:
|
||||
raise ValueError("No fps files given, %r, to merge into %s"
|
||||
% (split_files, output_file))
|
||||
out = open(output_file, "w")
|
||||
first = True
|
||||
for filename in split_files:
|
||||
with open(filename) as handle:
|
||||
for line in handle:
|
||||
if line.startswith('#'):
|
||||
if first:
|
||||
out.write(line)
|
||||
else:
|
||||
# line is no header and not a comment, we assume the first header is written to out and we set 'first' to False
|
||||
first = False
|
||||
out.write(line)
|
||||
out.close()
|
||||
merge = staticmethod(merge)
|
||||
|
||||
|
||||
class OBFS(Binary):
|
||||
"""OpenBabel Fastsearch format (fs)."""
|
||||
file_ext = 'fs'
|
||||
composite_type = 'basic'
|
||||
allow_datatype_change = False
|
||||
|
||||
MetadataElement(name="base_name", default='OpenBabel Fastsearch Index',
|
||||
readonly=True, visible=True, optional=True,)
|
||||
|
||||
def __init__(self, **kwd):
|
||||
"""
|
||||
A Fastsearch Index consists of a binary file with the fingerprints
|
||||
and a pointer the actual molecule file.
|
||||
"""
|
||||
Binary.__init__(self, **kwd)
|
||||
self.add_composite_file('molecule.fs', is_binary=True,
|
||||
description='OpenBabel Fastsearch Index')
|
||||
self.add_composite_file('molecule.sdf', optional=True,
|
||||
is_binary=False, description='Molecule File')
|
||||
self.add_composite_file('molecule.smi', optional=True,
|
||||
is_binary=False, description='Molecule File')
|
||||
self.add_composite_file('molecule.inchi', optional=True,
|
||||
is_binary=False, description='Molecule File')
|
||||
self.add_composite_file('molecule.mol2', optional=True,
|
||||
is_binary=False, description='Molecule File')
|
||||
self.add_composite_file('molecule.cml', optional=True,
|
||||
is_binary=False, description='Molecule File')
|
||||
|
||||
def set_peek(self, dataset, is_multi_byte=False):
|
||||
"""Set the peek and blurb text."""
|
||||
if not dataset.dataset.purged:
|
||||
dataset.peek = "OpenBabel Fastsearch Index"
|
||||
dataset.blurb = "OpenBabel Fastsearch Index"
|
||||
else:
|
||||
dataset.peek = "file does not exist"
|
||||
dataset.blurb = "file purged from disk"
|
||||
|
||||
def display_peek(self, dataset):
|
||||
"""Create HTML content, used for displaying peek."""
|
||||
try:
|
||||
return dataset.peek
|
||||
except:
|
||||
return "OpenBabel Fastsearch Index"
|
||||
|
||||
def display_data(self, trans, data, preview=False, filename=None,
|
||||
to_ext=None, size=None, offset=None, **kwd):
|
||||
"""Apparently an old display method, but still gets called.
|
||||
|
||||
This allows us to format the data shown in the central pane via the "eye" icon.
|
||||
"""
|
||||
return "This is a OpenBabel Fastsearch format. You can speed up your similarity and substructure search with it."
|
||||
|
||||
def get_mime(self):
|
||||
"""Returns the mime type of the datatype (pretend it is text for peek)"""
|
||||
return 'text/plain'
|
||||
|
||||
def merge(split_files, output_file, extra_merge_args):
|
||||
"""Merging Fastsearch indices is not supported."""
|
||||
raise NotImplementedError("Merging Fastsearch indices is not supported.")
|
||||
|
||||
def split(cls, input_datasets, subdir_generator_function, split_params):
|
||||
"""Splitting Fastsearch indices is not supported."""
|
||||
if split_params is None:
|
||||
return None
|
||||
raise NotImplementedError("Splitting Fastsearch indices is not possible.")
|
||||
|
||||
|
||||
class DRF(GenericMolFile):
|
||||
file_ext = "drf"
|
||||
|
||||
def set_meta(self, dataset, **kwd):
|
||||
"""
|
||||
Set the number of lines of data in dataset.
|
||||
"""
|
||||
dataset.metadata.number_of_molecules = count_special_lines('\"ligand id\"', dataset.file_name, invert=True)
|
||||
|
||||
|
||||
class PHAR(GenericMolFile):
|
||||
"""
|
||||
Pharmacophore database format from silicos-it.
|
||||
"""
|
||||
file_ext = "phar"
|
||||
|
||||
def set_peek(self, dataset, is_multi_byte=False):
|
||||
if not dataset.dataset.purged:
|
||||
dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
|
||||
dataset.blurb = "pharmacophore"
|
||||
else:
|
||||
dataset.peek = 'file does not exist'
|
||||
dataset.blurb = 'file purged from disk'
|
||||
|
||||
|
||||
class PDB(GenericMolFile):
|
||||
"""
|
||||
Protein Databank format.
|
||||
http://www.wwpdb.org/documentation/format33/v3.3.html
|
||||
"""
|
||||
file_ext = "pdb"
|
||||
|
||||
def sniff(self, filename):
|
||||
"""
|
||||
Try to guess if the file is a PDB file.
|
||||
|
||||
>>> from galaxy.datatypes.sniff import get_test_fname
|
||||
>>> fname = get_test_fname('5e5z.pdb')
|
||||
>>> PDB().sniff(fname)
|
||||
True
|
||||
|
||||
>>> fname = get_test_fname('drugbank_drugs.cml')
|
||||
>>> PDB().sniff(fname)
|
||||
False
|
||||
"""
|
||||
headers = get_headers(filename, sep=' ', count=300)
|
||||
h = t = c = s = k = e = False
|
||||
for line in headers:
|
||||
section_name = line[0].strip()
|
||||
if section_name == 'HEADER':
|
||||
h = True
|
||||
elif section_name == 'TITLE':
|
||||
t = True
|
||||
elif section_name == 'COMPND':
|
||||
c = True
|
||||
elif section_name == 'SOURCE':
|
||||
s = True
|
||||
elif section_name == 'KEYWDS':
|
||||
k = True
|
||||
elif section_name == 'EXPDTA':
|
||||
e = True
|
||||
|
||||
if h * t * c * s * k * e:
|
||||
return True
|
||||
else:
|
||||
return False
|
||||
|
||||
def set_peek(self, dataset, is_multi_byte=False):
|
||||
if not dataset.dataset.purged:
|
||||
atom_numbers = count_special_lines("^ATOM", dataset.file_name)
|
||||
hetatm_numbers = count_special_lines("^HETATM", dataset.file_name)
|
||||
dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
|
||||
dataset.blurb = "%s atoms and %s HET-atoms" % (atom_numbers, hetatm_numbers)
|
||||
else:
|
||||
dataset.peek = 'file does not exist'
|
||||
dataset.blurb = 'file purged from disk'
|
||||
|
||||
|
||||
class grd(data.Text):
|
||||
file_ext = "grd"
|
||||
|
||||
def set_peek(self, dataset, is_multi_byte=False):
|
||||
if not dataset.dataset.purged:
|
||||
dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
|
||||
dataset.blurb = "grids for docking"
|
||||
else:
|
||||
dataset.peek = 'file does not exist'
|
||||
dataset.blurb = 'file purged from disk'
|
||||
|
||||
|
||||
class grdtgz(Binary):
|
||||
file_ext = "grd.tgz"
|
||||
|
||||
def set_peek(self, dataset, is_multi_byte=False):
|
||||
if not dataset.dataset.purged:
|
||||
dataset.peek = 'binary data'
|
||||
dataset.blurb = "compressed grids for docking"
|
||||
else:
|
||||
dataset.peek = 'file does not exist'
|
||||
dataset.blurb = 'file purged from disk'
|
||||
|
||||
|
||||
class InChI(Tabular):
|
||||
file_ext = "inchi"
|
||||
column_names = ['InChI']
|
||||
MetadataElement(name="columns", default=2, desc="Number of columns", readonly=True, visible=False)
|
||||
MetadataElement(name="column_types", default=['str'], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False)
|
||||
MetadataElement(name="number_of_molecules", default=0, desc="Number of molecules", readonly=True, visible=True, optional=True, no_value=0)
|
||||
|
||||
def set_meta(self, dataset, **kwd):
|
||||
"""
|
||||
Set the number of lines of data in dataset.
|
||||
"""
|
||||
dataset.metadata.number_of_molecules = self.count_data_lines(dataset)
|
||||
|
||||
def set_peek(self, dataset, is_multi_byte=False):
|
||||
if not dataset.dataset.purged:
|
||||
dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
|
||||
if (dataset.metadata.number_of_molecules == 1):
|
||||
dataset.blurb = "1 molecule"
|
||||
else:
|
||||
dataset.blurb = "%s molecules" % dataset.metadata.number_of_molecules
|
||||
dataset.peek = data.get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
|
||||
else:
|
||||
dataset.peek = 'file does not exist'
|
||||
dataset.blurb = 'file purged from disk'
|
||||
|
||||
def sniff(self, filename):
|
||||
"""
|
||||
Try to guess if the file is a InChI file.
|
||||
|
||||
>>> from galaxy.datatypes.sniff import get_test_fname
|
||||
>>> fname = get_test_fname('drugbank_drugs.inchi')
|
||||
>>> InChI().sniff(fname)
|
||||
True
|
||||
|
||||
>>> fname = get_test_fname('drugbank_drugs.cml')
|
||||
>>> InChI().sniff(fname)
|
||||
False
|
||||
"""
|
||||
inchi_lines = get_headers(filename, sep=' ', count=10)
|
||||
for inchi in inchi_lines:
|
||||
if not inchi[0].startswith('InChI='):
|
||||
return False
|
||||
return True
|
||||
|
||||
|
||||
class SMILES(Tabular):
|
||||
file_ext = "smi"
|
||||
column_names = ['SMILES', 'TITLE']
|
||||
MetadataElement(name="columns", default=2, desc="Number of columns", readonly=True, visible=False)
|
||||
MetadataElement(name="column_types", default=['str', 'str'], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False)
|
||||
MetadataElement(name="number_of_molecules", default=0, desc="Number of molecules", readonly=True, visible=True, optional=True, no_value=0)
|
||||
|
||||
def set_meta(self, dataset, **kwd):
|
||||
"""
|
||||
Set the number of lines of data in dataset.
|
||||
"""
|
||||
dataset.metadata.number_of_molecules = self.count_data_lines(dataset)
|
||||
|
||||
def set_peek(self, dataset, is_multi_byte=False):
|
||||
if not dataset.dataset.purged:
|
||||
dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
|
||||
if dataset.metadata.number_of_molecules == 1:
|
||||
dataset.blurb = "1 molecule"
|
||||
else:
|
||||
dataset.blurb = "%s molecules" % dataset.metadata.number_of_molecules
|
||||
dataset.peek = data.get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
|
||||
else:
|
||||
dataset.peek = 'file does not exist'
|
||||
dataset.blurb = 'file purged from disk'
|
||||
|
||||
'''
|
||||
def sniff(self, filename):
|
||||
"""
|
||||
Its hard or impossible to sniff a SMILES File. We can
|
||||
try to import the first SMILES and check if it is a molecule, but
|
||||
currently its not possible to use external libraries in datatype definition files.
|
||||
Moreover it seems mpossible to inlcude OpenBabel as python library because OpenBabel
|
||||
is GPL licensed.
|
||||
"""
|
||||
self.molecule_number = count_lines(filename, non_empty = True)
|
||||
word_count = count_lines(filename)
|
||||
|
||||
if self.molecule_number != word_count:
|
||||
return False
|
||||
|
||||
if self.molecule_number > 0:
|
||||
# test first 3 SMILES
|
||||
smiles_lines = get_headers(filename, sep='\t', count=3)
|
||||
for smiles_line in smiles_lines:
|
||||
if len(smiles_line) > 2:
|
||||
return False
|
||||
smiles = smiles_line[0]
|
||||
try:
|
||||
# if we have atoms, we have a molecule
|
||||
if not len(pybel.readstring('smi', smiles).atoms) > 0:
|
||||
return False
|
||||
except:
|
||||
# if convert fails its not a smiles string
|
||||
return False
|
||||
return True
|
||||
else:
|
||||
return False
|
||||
'''
|
||||
|
||||
|
||||
class CML(GenericXml):
|
||||
"""
|
||||
Chemical Markup Language
|
||||
http://cml.sourceforge.net/
|
||||
"""
|
||||
file_ext = "cml"
|
||||
MetadataElement(name="number_of_molecules", default=0, desc="Number of molecules", readonly=True, visible=True, optional=True, no_value=0)
|
||||
|
||||
def set_meta(self, dataset, **kwd):
|
||||
"""
|
||||
Set the number of lines of data in dataset.
|
||||
"""
|
||||
dataset.metadata.number_of_molecules = count_special_lines('^\s*<molecule', dataset.file_name)
|
||||
|
||||
def set_peek(self, dataset, is_multi_byte=False):
|
||||
if not dataset.dataset.purged:
|
||||
dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
|
||||
if (dataset.metadata.number_of_molecules == 1):
|
||||
dataset.blurb = "1 molecule"
|
||||
else:
|
||||
dataset.blurb = "%s molecules" % dataset.metadata.number_of_molecules
|
||||
dataset.peek = data.get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
|
||||
else:
|
||||
dataset.peek = 'file does not exist'
|
||||
dataset.blurb = 'file purged from disk'
|
||||
|
||||
def sniff(self, filename):
|
||||
"""
|
||||
Try to guess if the file is a CML file.
|
||||
|
||||
>>> from galaxy.datatypes.sniff import get_test_fname
|
||||
>>> fname = get_test_fname('interval.interval')
|
||||
>>> CML().sniff(fname)
|
||||
False
|
||||
|
||||
>>> fname = get_test_fname('drugbank_drugs.cml')
|
||||
>>> CML().sniff(fname)
|
||||
True
|
||||
"""
|
||||
handle = open(filename)
|
||||
line = handle.readline()
|
||||
if line.strip() != '<?xml version="1.0"?>':
|
||||
handle.close()
|
||||
return False
|
||||
line = handle.readline()
|
||||
if line.strip().find('http://www.xml-cml.org/schema') == -1:
|
||||
handle.close()
|
||||
return False
|
||||
handle.close()
|
||||
return True
|
||||
|
||||
def split(cls, input_datasets, subdir_generator_function, split_params):
|
||||
"""
|
||||
Split the input files by molecule records.
|
||||
"""
|
||||
if split_params is None:
|
||||
return None
|
||||
|
||||
if len(input_datasets) > 1:
|
||||
raise Exception("CML-file splitting does not support multiple files")
|
||||
input_files = [ds.file_name for ds in input_datasets]
|
||||
|
||||
chunk_size = None
|
||||
if split_params['split_mode'] == 'number_of_parts':
|
||||
raise Exception('Split mode "%s" is currently not implemented for CML-files.' % split_params['split_mode'])
|
||||
elif split_params['split_mode'] == 'to_size':
|
||||
chunk_size = int(split_params['split_size'])
|
||||
else:
|
||||
raise Exception('Unsupported split mode %s' % split_params['split_mode'])
|
||||
|
||||
def _read_cml_records(filename):
|
||||
lines = []
|
||||
with open(filename) as handle:
|
||||
for line in handle:
|
||||
if line.lstrip().startswith('<?xml version="1.0"?>') or \
|
||||
line.lstrip().startswith('<cml xmlns="http://www.xml-cml.org/schema') or \
|
||||
line.lstrip().startswith('</cml>'):
|
||||
continue
|
||||
lines.append(line)
|
||||
if line.lstrip().startswith('</molecule>'):
|
||||
yield lines
|
||||
lines = []
|
||||
|
||||
header_lines = ['<?xml version="1.0"?>\n', '<cml xmlns="http://www.xml-cml.org/schema">\n']
|
||||
footer_line = ['</cml>\n']
|
||||
|
||||
def _write_part_cml_file(accumulated_lines):
|
||||
part_dir = subdir_generator_function()
|
||||
part_path = os.path.join(part_dir, os.path.basename(input_files[0]))
|
||||
part_file = open(part_path, 'w')
|
||||
part_file.writelines(header_lines)
|
||||
part_file.writelines(accumulated_lines)
|
||||
part_file.writelines(footer_line)
|
||||
part_file.close()
|
||||
|
||||
try:
|
||||
cml_records = _read_cml_records(input_files[0])
|
||||
cml_lines_accumulated = []
|
||||
for counter, cml_record in enumerate(cml_records, start=1):
|
||||
cml_lines_accumulated.extend(cml_record)
|
||||
if counter % chunk_size == 0:
|
||||
_write_part_cml_file(cml_lines_accumulated)
|
||||
cml_lines_accumulated = []
|
||||
if cml_lines_accumulated:
|
||||
_write_part_cml_file(cml_lines_accumulated)
|
||||
except Exception, e:
|
||||
log.error('Unable to split files: %s' % str(e))
|
||||
raise
|
||||
split = classmethod(split)
|
||||
|
||||
def merge(split_files, output_file):
|
||||
"""
|
||||
Merging CML files.
|
||||
"""
|
||||
if len(split_files) == 1:
|
||||
# For one file only, use base class method (move/copy)
|
||||
return data.Text.merge(split_files, output_file)
|
||||
if not split_files:
|
||||
raise ValueError("Given no CML files, %r, to merge into %s"
|
||||
% (split_files, output_file))
|
||||
with open(output_file, "w") as out:
|
||||
for filename in split_files:
|
||||
with open(filename) as handle:
|
||||
header = handle.readline()
|
||||
if not header:
|
||||
raise ValueError("CML file %s was empty" % filename)
|
||||
if not header.lstrip().startswith('<?xml version="1.0"?>'):
|
||||
out.write(header)
|
||||
raise ValueError("%s is not a valid XML file!" % filename)
|
||||
line = handle.readline()
|
||||
header += line
|
||||
if not line.lstrip().startswith('<cml xmlns="http://www.xml-cml.org/schema'):
|
||||
out.write(header)
|
||||
raise ValueError("%s is not a CML file!" % filename)
|
||||
molecule_found = False
|
||||
for line in handle.readlines():
|
||||
# We found two required header lines, the next line should start with <molecule >
|
||||
if line.lstrip().startswith('</cml>'):
|
||||
continue
|
||||
if line.lstrip().startswith('<molecule'):
|
||||
molecule_found = True
|
||||
if molecule_found:
|
||||
out.write(line)
|
||||
out.write("</cml>\n")
|
||||
merge = staticmethod(merge)
|
||||
@@ -263,8 +263,9 @@ def guess_ext( fname, sniff_order, is_multi_byte=False ):
|
||||
|
||||
>>> fname = get_test_fname('megablast_xml_parser_test1.blastxml')
|
||||
>>> from galaxy.datatypes import registry
|
||||
>>> sample_conf = os.path.join(util.galaxy_directory(), "config", "datatypes_conf.xml.sample")
|
||||
>>> datatypes_registry = registry.Registry()
|
||||
>>> datatypes_registry.load_datatypes()
|
||||
>>> datatypes_registry.load_datatypes(root_dir=util.galaxy_directory(), config=sample_conf)
|
||||
>>> sniff_order = datatypes_registry.sniff_order
|
||||
>>> guess_ext(fname, sniff_order)
|
||||
'xml'
|
||||
@@ -324,6 +325,24 @@ def guess_ext( fname, sniff_order, is_multi_byte=False ):
|
||||
>>> fname = get_test_fname('test.mz5')
|
||||
>>> guess_ext(fname, sniff_order)
|
||||
'h5'
|
||||
>>> fname = get_test_fname('drugbank_drugs.cml')
|
||||
>>> guess_ext(fname, sniff_order)
|
||||
'cml'
|
||||
>>> fname = get_test_fname('q.fps')
|
||||
>>> guess_ext(fname, sniff_order)
|
||||
'fps'
|
||||
>>> fname = get_test_fname('drugbank_drugs.inchi')
|
||||
>>> guess_ext(fname, sniff_order)
|
||||
'inchi'
|
||||
>>> fname = get_test_fname('drugbank_drugs.mol2')
|
||||
>>> guess_ext(fname, sniff_order)
|
||||
'mol2'
|
||||
>>> fname = get_test_fname('drugbank_drugs.sdf')
|
||||
>>> guess_ext(fname, sniff_order)
|
||||
'sdf'
|
||||
>>> fname = get_test_fname('5e5z.pdb')
|
||||
>>> guess_ext(fname, sniff_order)
|
||||
'pdb'
|
||||
"""
|
||||
for datatype in sniff_order:
|
||||
"""
|
||||
|
||||
@@ -0,0 +1,357 @@
|
||||
HEADER DE NOVO PROTEIN, MEMBRANE PROTEIN 09-OCT-15 5E5Z
|
||||
TITLE STRUCTURE OF THE AMYLOID FORMING PEPTIDE LVHSSN (RESIDUES
|
||||
COMPND MOL_ID: 1;
|
||||
COMPND 2 MOLECULE: LVHSSN (RESIDUES 16-21) FROM ISLET AMYLOID POLYPEPTIDE;
|
||||
COMPND 3 CHAIN: A;
|
||||
COMPND 4 ENGINEERED: YES
|
||||
SOURCE MOL_ID: 1;
|
||||
SOURCE 2 SYNTHETIC: YES;
|
||||
SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
|
||||
SOURCE 4 ORGANISM_TAXID: 9606
|
||||
KEYWDS AMYLOID-LIKE PROTOFIBRIL, DE NOVO PROTEIN, MEMBRANE PROTEIN, PROTEIN
|
||||
KEYWDS 2 FIBRIL
|
||||
EXPDTA X-RAY DIFFRACTION
|
||||
AUTHOR A.B.SORIAGA,D.EISENBERG
|
||||
REVDAT 2 20-JAN-16 5E5Z 1 JRNL
|
||||
REVDAT 1 16-DEC-15 5E5Z 0
|
||||
JRNL AUTH A.B.SORIAGA,S.SANGWAN,R.MACDONALD,M.R.SAWAYA,D.EISENBERG
|
||||
JRNL TITL CRYSTAL STRUCTURES OF IAPP AMYLOIDOGENIC SEGMENTS REVEAL A
|
||||
JRNL TITL 2 NOVEL PACKING MOTIF OF OUT-OF-REGISTER BETA SHEETS.
|
||||
JRNL REF J.PHYS.CHEM.B 2016
|
||||
JRNL REFN ISSN 1089-5647
|
||||
JRNL PMID 26629790
|
||||
JRNL DOI 10.1021/ACS.JPCB.5B09981
|
||||
REMARK 2
|
||||
REMARK 2 RESOLUTION. 1.66 ANGSTROMS.
|
||||
REMARK 3
|
||||
REMARK 3 REFINEMENT.
|
||||
REMARK 3 PROGRAM : PHENIX 1.6.4_486
|
||||
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
|
||||
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
|
||||
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
|
||||
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
|
||||
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
|
||||
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
|
||||
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
|
||||
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
|
||||
REMARK 3
|
||||
REMARK 3 REFINEMENT TARGET : LS_WUNIT_K1
|
||||
REMARK 3
|
||||
REMARK 3 DATA USED IN REFINEMENT.
|
||||
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.66
|
||||
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 9.46
|
||||
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000
|
||||
REMARK 3 COMPLETENESS FOR RANGE (%) : 89.1
|
||||
REMARK 3 NUMBER OF REFLECTIONS : 391
|
||||
REMARK 3
|
||||
REMARK 3 FIT TO DATA USED IN REFINEMENT.
|
||||
REMARK 3 R VALUE (WORKING + TEST SET) : 0.170
|
||||
REMARK 3 R VALUE (WORKING SET) : 0.167
|
||||
REMARK 3 FREE R VALUE : 0.198
|
||||
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600
|
||||
REMARK 3 FREE R VALUE TEST SET COUNT : 18
|
||||
REMARK 3
|
||||
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
|
||||
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
|
||||
REMARK 3 1 9.4587 - 1.6644 0.89 373 18 0.1673 0.1983
|
||||
REMARK 3
|
||||
REMARK 3 BULK SOLVENT MODELLING.
|
||||
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
|
||||
REMARK 3 SOLVENT RADIUS : 0.00
|
||||
REMARK 3 SHRINKAGE RADIUS : 0.00
|
||||
REMARK 3 K_SOL : 0.60
|
||||
REMARK 3 B_SOL : 251.4
|
||||
REMARK 3
|
||||
REMARK 3 ERROR ESTIMATES.
|
||||
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.310
|
||||
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.270
|
||||
REMARK 3
|
||||
REMARK 3 B VALUES.
|
||||
REMARK 3 FROM WILSON PLOT (A**2) : NULL
|
||||
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
|
||||
REMARK 3 OVERALL ANISOTROPIC B VALUE.
|
||||
REMARK 3 B11 (A**2) : 0.51090
|
||||
REMARK 3 B22 (A**2) : -3.44720
|
||||
REMARK 3 B33 (A**2) : -8.26450
|
||||
REMARK 3 B12 (A**2) : 0.00000
|
||||
REMARK 3 B13 (A**2) : 0.77970
|
||||
REMARK 3 B23 (A**2) : 0.00000
|
||||
REMARK 3
|
||||
REMARK 3 TWINNING INFORMATION.
|
||||
REMARK 3 FRACTION: NULL
|
||||
REMARK 3 OPERATOR: NULL
|
||||
REMARK 3
|
||||
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
|
||||
REMARK 3 RMSD COUNT
|
||||
REMARK 3 BOND : 0.004 46
|
||||
REMARK 3 ANGLE : 0.975 62
|
||||
REMARK 3 CHIRALITY : 0.056 8
|
||||
REMARK 3 PLANARITY : 0.004 8
|
||||
REMARK 3 DIHEDRAL : 10.740 15
|
||||
REMARK 3
|
||||
REMARK 3 TLS DETAILS
|
||||
REMARK 3 NUMBER OF TLS GROUPS : 1
|
||||
REMARK 3 TLS GROUP : 1
|
||||
REMARK 3 SELECTION: ALL
|
||||
REMARK 3 ORIGIN FOR THE GROUP (A): 4.5323 0.1096 3.9760
|
||||
REMARK 3 T TENSOR
|
||||
REMARK 3 T11: -0.1260 T22: -0.0788
|
||||
REMARK 3 T33: -0.0487 T12: 0.0821
|
||||
REMARK 3 T13: -0.0518 T23: 0.0723
|
||||
REMARK 3 L TENSOR
|
||||
REMARK 3 L11: 0.1003 L22: 0.0184
|
||||
REMARK 3 L33: 0.0647 L12: -0.0319
|
||||
REMARK 3 L13: 0.0506 L23: -0.0233
|
||||
REMARK 3 S TENSOR
|
||||
REMARK 3 S11: 0.0084 S12: -0.0300 S13: -0.0565
|
||||
REMARK 3 S21: 0.0231 S22: 0.0090 S23: 0.0127
|
||||
REMARK 3 S31: -0.0046 S32: -0.0049 S33: -0.0009
|
||||
REMARK 3
|
||||
REMARK 3 NCS DETAILS
|
||||
REMARK 3 NUMBER OF NCS GROUPS : NULL
|
||||
REMARK 3
|
||||
REMARK 3 OTHER REFINEMENT REMARKS: NULL
|
||||
REMARK 4
|
||||
REMARK 4 5E5Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
|
||||
REMARK 100
|
||||
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-OCT-15.
|
||||
REMARK 100 THE DEPOSITION ID IS D_1000214421.
|
||||
REMARK 200
|
||||
REMARK 200 EXPERIMENTAL DETAILS
|
||||
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
|
||||
REMARK 200 DATE OF DATA COLLECTION : 10-MAR-10
|
||||
REMARK 200 TEMPERATURE (KELVIN) : 291
|
||||
REMARK 200 PH : NULL
|
||||
REMARK 200 NUMBER OF CRYSTALS USED : NULL
|
||||
REMARK 200
|
||||
REMARK 200 SYNCHROTRON (Y/N) : Y
|
||||
REMARK 200 RADIATION SOURCE : APS
|
||||
REMARK 200 BEAMLINE : 24-ID-E
|
||||
REMARK 200 X-RAY GENERATOR MODEL : NULL
|
||||
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
|
||||
REMARK 200 WAVELENGTH OR RANGE (A) : 0.979
|
||||
REMARK 200 MONOCHROMATOR : NULL
|
||||
REMARK 200 OPTICS : NULL
|
||||
REMARK 200
|
||||
REMARK 200 DETECTOR TYPE : CCD
|
||||
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315
|
||||
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
|
||||
REMARK 200 DATA SCALING SOFTWARE : NULL
|
||||
REMARK 200
|
||||
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 1136
|
||||
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600
|
||||
REMARK 200 RESOLUTION RANGE LOW (A) : 100.000
|
||||
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
|
||||
REMARK 200
|
||||
REMARK 200 OVERALL.
|
||||
REMARK 200 COMPLETENESS FOR RANGE (%) : 92.9
|
||||
REMARK 200 DATA REDUNDANCY : 2.900
|
||||
REMARK 200 R MERGE (I) : 0.07600
|
||||
REMARK 200 R SYM (I) : NULL
|
||||
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.8600
|
||||
REMARK 200
|
||||
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
|
||||
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
|
||||
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
|
||||
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
|
||||
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
|
||||
REMARK 200 R MERGE FOR SHELL (I) : NULL
|
||||
REMARK 200 R SYM FOR SHELL (I) : NULL
|
||||
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
|
||||
REMARK 200
|
||||
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
|
||||
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
|
||||
REMARK 200 SOFTWARE USED: PHASER
|
||||
REMARK 200 STARTING MODEL: NULL
|
||||
REMARK 200
|
||||
REMARK 200 REMARK: NULL
|
||||
REMARK 280
|
||||
REMARK 280 CRYSTAL
|
||||
REMARK 280 SOLVENT CONTENT, VS (%): 6.59
|
||||
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.32
|
||||
REMARK 280
|
||||
REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MG/ML IN WATER AND MIXED WITH 0.09
|
||||
REMARK 280 M HEPES PH 7.5, 1.26M TRI-SODIUM CITRATE, AND 10% GLYCEROL,
|
||||
REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K
|
||||
REMARK 290
|
||||
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
|
||||
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
|
||||
REMARK 290
|
||||
REMARK 290 SYMOP SYMMETRY
|
||||
REMARK 290 NNNMMM OPERATOR
|
||||
REMARK 290 1555 X,Y,Z
|
||||
REMARK 290 2555 -X,Y+1/2,-Z
|
||||
REMARK 290
|
||||
REMARK 290 WHERE NNN -> OPERATOR NUMBER
|
||||
REMARK 290 MMM -> TRANSLATION VECTOR
|
||||
REMARK 290
|
||||
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
|
||||
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
|
||||
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
|
||||
REMARK 290 RELATED MOLECULES.
|
||||
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
|
||||
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
|
||||
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
|
||||
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
|
||||
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 4.80450
|
||||
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
|
||||
REMARK 290
|
||||
REMARK 290 REMARK: NULL
|
||||
REMARK 300
|
||||
REMARK 300 BIOMOLECULE: 1
|
||||
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
|
||||
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
|
||||
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
|
||||
REMARK 300 BURIED SURFACE AREA.
|
||||
REMARK 350
|
||||
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
|
||||
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
|
||||
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
|
||||
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
|
||||
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
|
||||
REMARK 350
|
||||
REMARK 350 BIOMOLECULE: 1
|
||||
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DECAMERIC
|
||||
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
|
||||
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
|
||||
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
|
||||
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
|
||||
REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000
|
||||
REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 -9.60900
|
||||
REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000
|
||||
REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 0.00000
|
||||
REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 9.60900
|
||||
REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000
|
||||
REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 9.64300
|
||||
REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 0.00000
|
||||
REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000
|
||||
REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 9.64300
|
||||
REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 -9.60900
|
||||
REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000
|
||||
REMARK 350 BIOMT1 6 1.000000 0.000000 0.000000 9.64300
|
||||
REMARK 350 BIOMT2 6 0.000000 1.000000 0.000000 9.60900
|
||||
REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 0.00000
|
||||
REMARK 350 BIOMT1 7 -1.000000 0.000000 0.000000 9.64300
|
||||
REMARK 350 BIOMT2 7 0.000000 1.000000 0.000000 -4.80450
|
||||
REMARK 350 BIOMT3 7 0.000000 0.000000 -1.000000 0.00000
|
||||
REMARK 350 BIOMT1 8 -1.000000 0.000000 0.000000 9.64300
|
||||
REMARK 350 BIOMT2 8 0.000000 1.000000 0.000000 4.80450
|
||||
REMARK 350 BIOMT3 8 0.000000 0.000000 -1.000000 0.00000
|
||||
REMARK 350 BIOMT1 9 -1.000000 0.000000 0.000000 19.28600
|
||||
REMARK 350 BIOMT2 9 0.000000 1.000000 0.000000 -4.80450
|
||||
REMARK 350 BIOMT3 9 0.000000 0.000000 -1.000000 0.00000
|
||||
REMARK 350 BIOMT1 10 -1.000000 0.000000 0.000000 19.28600
|
||||
REMARK 350 BIOMT2 10 0.000000 1.000000 0.000000 4.80450
|
||||
REMARK 350 BIOMT3 10 0.000000 0.000000 -1.000000 0.00000
|
||||
REMARK 900
|
||||
REMARK 900 RELATED ENTRIES
|
||||
REMARK 900 RELATED ID: 5E5V RELATED DB: PDB
|
||||
REMARK 900 RELATED ID: 5E5X RELATED DB: PDB
|
||||
REMARK 900 RELATED ID: 5E61 RELATED DB: PDB
|
||||
DBREF 5E5Z A 1 6 PDB 5E5Z 5E5Z 1 6
|
||||
SEQRES 1 A 6 LEU VAL HIS SER SER ASN
|
||||
FORMUL 2 HOH *(H2 O)
|
||||
CRYST1 9.643 9.609 19.029 90.00 101.22 90.00 P 1 21 1 2
|
||||
ORIGX1 1.000000 0.000000 0.000000 0.00000
|
||||
ORIGX2 0.000000 1.000000 0.000000 0.00000
|
||||
ORIGX3 0.000000 0.000000 1.000000 0.00000
|
||||
SCALE1 0.103702 0.000000 0.020579 0.00000
|
||||
SCALE2 0.000000 0.104069 0.000000 0.00000
|
||||
SCALE3 0.000000 0.000000 0.053576 0.00000
|
||||
ATOM 1 N LEU A 1 6.078 -0.306 -5.753 1.00 0.00 N
|
||||
ANISOU 1 N LEU A 1 0 0 0 0 0 0 N
|
||||
ATOM 2 CA LEU A 1 5.166 -0.026 -4.647 1.00 2.42 C
|
||||
ANISOU 2 CA LEU A 1 307 307 307 0 0 0 C
|
||||
ATOM 3 C LEU A 1 5.682 -0.642 -3.356 1.00 3.48 C
|
||||
ANISOU 3 C LEU A 1 435 443 445 1 1 9 C
|
||||
ATOM 4 O LEU A 1 6.056 -1.814 -3.322 1.00 3.52 O
|
||||
ANISOU 4 O LEU A 1 436 449 454 2 2 16 O
|
||||
ATOM 5 CB LEU A 1 3.755 -0.555 -4.967 1.00 1.86 C
|
||||
ANISOU 5 CB LEU A 1 232 237 238 1 1 5 C
|
||||
ATOM 6 CG LEU A 1 2.596 -0.354 -3.975 1.00 6.87 C
|
||||
ANISOU 6 CG LEU A 1 861 873 877 2 2 14 C
|
||||
ATOM 7 CD1 LEU A 1 2.753 -1.182 -2.704 1.00 11.83 C
|
||||
ANISOU 7 CD1 LEU A 1 1481 1504 1512 4 4 27 C
|
||||
ATOM 8 CD2 LEU A 1 2.404 1.122 -3.638 1.00 4.27 C
|
||||
ANISOU 8 CD2 LEU A 1 537 543 544 1 2 7 C
|
||||
ATOM 9 N VAL A 2 5.715 0.161 -2.297 1.00 0.61 N
|
||||
ANISOU 9 N VAL A 2 71 80 82 2 2 11 N
|
||||
ATOM 10 CA VAL A 2 5.968 -0.352 -0.960 1.00 0.12 C
|
||||
ANISOU 10 CA VAL A 2 1 20 24 4 4 22 C
|
||||
ATOM 11 C VAL A 2 4.976 0.281 0.000 1.00 3.40 C
|
||||
ANISOU 11 C VAL A 2 413 437 440 5 5 27 C
|
||||
ATOM 12 O VAL A 2 4.746 1.489 -0.046 1.00 3.22 O
|
||||
ANISOU 12 O VAL A 2 395 414 414 4 5 20 O
|
||||
ATOM 13 CB VAL A 2 7.400 -0.027 -0.475 1.00 3.56 C
|
||||
ANISOU 13 CB VAL A 2 440 456 458 3 3 18 C
|
||||
ATOM 14 CG1 VAL A 2 7.566 -0.421 0.993 1.00 7.93 C
|
||||
ANISOU 14 CG1 VAL A 2 986 1012 1016 5 5 30 C
|
||||
ATOM 15 CG2 VAL A 2 8.429 -0.722 -1.342 1.00 6.71 C
|
||||
ANISOU 15 CG2 VAL A 2 841 853 856 2 2 14 C
|
||||
ATOM 16 N HIS A 3 4.367 -0.537 0.850 1.00 0.22 N
|
||||
ANISOU 16 N HIS A 3 1 38 44 7 8 41 N
|
||||
ATOM 17 CA HIS A 3 3.603 -0.011 1.971 1.00 1.73 C
|
||||
ANISOU 17 CA HIS A 3 189 233 237 10 10 48 C
|
||||
ATOM 18 C HIS A 3 4.003 -0.675 3.280 1.00 1.84 C
|
||||
ANISOU 18 C HIS A 3 194 250 255 12 12 61 C
|
||||
ATOM 19 O HIS A 3 4.208 -1.889 3.338 1.00 0.73 O
|
||||
ANISOU 19 O HIS A 3 47 109 120 11 12 69 O
|
||||
ATOM 20 CB HIS A 3 2.095 -0.177 1.781 1.00 2.62 C
|
||||
ANISOU 20 CB HIS A 3 296 346 351 11 11 54 C
|
||||
ATOM 21 CG HIS A 3 1.324 0.074 3.040 1.00 2.97 C
|
||||
ANISOU 21 CG HIS A 3 335 396 399 14 14 66 C
|
||||
ATOM 22 ND1 HIS A 3 0.950 -0.937 3.900 1.00 4.29 N
|
||||
ANISOU 22 ND1 HIS A 3 491 566 573 16 17 82 N
|
||||
ATOM 23 CD2 HIS A 3 0.921 1.230 3.620 1.00 4.90 C
|
||||
ANISOU 23 CD2 HIS A 3 581 642 639 16 16 64 C
|
||||
ATOM 24 CE1 HIS A 3 0.321 -0.417 4.940 1.00 5.53 C
|
||||
ANISOU 24 CE1 HIS A 3 644 727 729 20 20 89 C
|
||||
ATOM 25 NE2 HIS A 3 0.290 0.896 4.794 1.00 6.02 N
|
||||
ANISOU 25 NE2 HIS A 3 714 790 785 20 19 78 N
|
||||
ATOM 26 N SER A 4 4.099 0.141 4.326 1.00 0.34 N
|
||||
ANISOU 26 N SER A 4 3 63 63 14 14 62 N
|
||||
ATOM 27 CA SER A 4 4.357 -0.330 5.683 1.00 1.49 C
|
||||
ANISOU 27 CA SER A 4 141 213 213 16 16 75 C
|
||||
ATOM 28 C SER A 4 3.814 0.686 6.681 1.00 2.14 C
|
||||
ANISOU 28 C SER A 4 222 299 292 20 19 78 C
|
||||
ATOM 29 O SER A 4 4.008 1.889 6.507 1.00 3.47 O
|
||||
ANISOU 29 O SER A 4 397 465 454 19 18 68 O
|
||||
ATOM 30 CB SER A 4 5.858 -0.513 5.905 1.00 5.61 C
|
||||
ANISOU 30 CB SER A 4 665 734 734 15 15 72 C
|
||||
ATOM 31 OG SER A 4 6.132 -0.771 7.272 1.00 9.89 O
|
||||
ANISOU 31 OG SER A 4 1200 1280 1278 18 18 83 O
|
||||
ATOM 32 N SER A 5 3.138 0.213 7.725 1.00 2.34 N
|
||||
ANISOU 32 N SER A 5 239 330 322 24 23 93 N
|
||||
ATOM 33 CA SER A 5 2.651 1.119 8.765 1.00 0.66 C
|
||||
ANISOU 33 CA SER A 5 24 123 106 28 26 97 C
|
||||
ATOM 34 C SER A 5 3.677 1.311 9.885 1.00 2.66 C
|
||||
ANISOU 34 C SER A 5 275 378 356 30 27 100 C
|
||||
ATOM 35 O SER A 5 3.411 2.024 10.851 1.00 2.02 O
|
||||
ANISOU 35 O SER A 5 193 303 273 35 30 104 O
|
||||
ATOM 36 CB SER A 5 1.318 0.639 9.350 1.00 2.68 C
|
||||
ANISOU 36 CB SER A 5 269 383 365 32 29 113 C
|
||||
ATOM 37 OG SER A 5 1.478 -0.544 10.117 1.00 2.49 O
|
||||
ANISOU 37 OG SER A 5 236 363 349 33 31 128 O
|
||||
ATOM 38 N ASN A 6 4.838 0.672 9.758 1.00 2.94 N
|
||||
ANISOU 38 N ASN A 6 311 412 394 28 25 98 N
|
||||
ATOM 39 CA ASN A 6 5.912 0.838 10.741 1.00 4.68 C
|
||||
ANISOU 39 CA ASN A 6 530 634 613 29 26 100 C
|
||||
ATOM 40 C ASN A 6 6.574 2.203 10.638 1.00 10.84 C
|
||||
ANISOU 40 C ASN A 6 1320 1413 1387 28 24 87 C
|
||||
ATOM 41 O ASN A 6 7.335 2.594 11.519 1.00 13.68 O
|
||||
ANISOU 41 O ASN A 6 1680 1775 1745 30 26 88 O
|
||||
ATOM 42 CB ASN A 6 6.986 -0.243 10.589 1.00 5.08 C
|
||||
ANISOU 42 CB ASN A 6 579 682 668 27 25 102 C
|
||||
ATOM 43 CG ASN A 6 6.592 -1.558 11.236 1.00 8.08 C
|
||||
ANISOU 43 CG ASN A 6 948 1067 1057 28 27 120 C
|
||||
ATOM 44 OD1 ASN A 6 5.576 -1.644 11.923 1.00 8.72 O
|
||||
ANISOU 44 OD1 ASN A 6 1022 1152 1139 32 30 131 O
|
||||
ATOM 45 ND2 ASN A 6 7.409 -2.588 11.030 1.00 9.89 N
|
||||
ANISOU 45 ND2 ASN A 6 1174 1293 1290 25 25 122 N
|
||||
ATOM 46 OXT ASN A 6 6.383 2.933 9.667 1.00 14.02 O
|
||||
ANISOU 46 OXT ASN A 6 1730 1811 1787 25 22 75 O
|
||||
TER 47 ASN A 6
|
||||
HETATM 48 O HOH A 101 8.203 1.052 -4.564 1.00 12.67 O
|
||||
ANISOU 48 O HOH A 101 1605 1605 1605 0 0 0 O
|
||||
MASTER 227 0 0 0 0 0 0 6 47 1 0 1
|
||||
END
|
||||
@@ -0,0 +1,385 @@
|
||||
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||||
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||||
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||||
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|
||||
<bond atomRefs2="a39 a40" order="1"/>
|
||||
<bond atomRefs2="a40 a41" order="1"/>
|
||||
<bond atomRefs2="a41 a42" order="1"/>
|
||||
<bond atomRefs2="a41 a43" order="2"/>
|
||||
<bond atomRefs2="a44 a49" order="1"/>
|
||||
<bond atomRefs2="a45 a47" order="1"/>
|
||||
<bond atomRefs2="a45 a52" order="1"/>
|
||||
<bond atomRefs2="a45 a46" order="2"/>
|
||||
<bond atomRefs2="a46 a53" order="1"/>
|
||||
<bond atomRefs2="a48 a47" order="1"/>
|
||||
<bond atomRefs2="a48 a61" order="1"/>
|
||||
<bond atomRefs2="a48 a49" order="1"/>
|
||||
<bond atomRefs2="a49 a62" order="2"/>
|
||||
<bond atomRefs2="a50 a51" order="1"/>
|
||||
<bond atomRefs2="a50 a52" order="2"/>
|
||||
<bond atomRefs2="a51 a53" order="2"/>
|
||||
<bond atomRefs2="a54 a55" order="1"/>
|
||||
<bond atomRefs2="a54 a60" order="1"/>
|
||||
<bond atomRefs2="a55 a56" order="1"/>
|
||||
<bond atomRefs2="a55 a70" order="2"/>
|
||||
<bond atomRefs2="a56 a57" order="1"/>
|
||||
<bond atomRefs2="a58 a59" order="2"/>
|
||||
<bond atomRefs2="a58 a60" order="1"/>
|
||||
<bond atomRefs2="a58 a61" order="1"/>
|
||||
<bond atomRefs2="a60 a63" order="1"/>
|
||||
<bond atomRefs2="a63 a65" order="1"/>
|
||||
<bond atomRefs2="a64 a66" order="2"/>
|
||||
<bond atomRefs2="a64 a65" order="1"/>
|
||||
<bond atomRefs2="a65 a68" order="2"/>
|
||||
<bond atomRefs2="a66 a67" order="1"/>
|
||||
<bond atomRefs2="a67 a69" order="2"/>
|
||||
<bond atomRefs2="a67 a71" order="1"/>
|
||||
<bond atomRefs2="a68 a69" order="1"/>
|
||||
<bond atomRefs2="a72 a73" order="2"/>
|
||||
<bond atomRefs2="a72 a74" order="1"/>
|
||||
</bondArray>
|
||||
</molecule>
|
||||
</cml>
|
||||
@@ -0,0 +1,2 @@
|
||||
InChI=1S/C59H84N18O14/c1-31(2)22-40(49(82)68-39(12-8-20-64-57(60)61)56(89)77-21-9-13-46(77)55(88)75-76-58(62)90)69-54(87)45(29-91-59(3,4)5)74-50(83)41(23-32-14-16-35(79)17-15-32)70-53(86)44(28-78)73-51(84)42(24-33-26-65-37-11-7-6-10-36(33)37)71-52(85)43(25-34-27-63-30-66-34)72-48(81)38-18-19-47(80)67-38/h6-7,10-11,14-17,26-27,30-31,38-46,65,78-79H,8-9,12-13,18-25,28-29H2,1-5H3,(H,63,66)(H,67,80)(H,68,82)(H,69,87)(H,70,86)(H,71,85)(H,72,81)(H,73,84)(H,74,83)(H,75,88)(H4,60,61,64)(H3,62,76,90)/t38-,39-,40-,41-,42-,43-,44-,45+,46-/m0/s1
|
||||
InChI=1S/C46H64N14O12S2/c47-35(62)15-14-29-40(67)58-32(22-36(48)63)43(70)59-33(45(72)60-18-5-9-34(60)44(71)56-28(8-4-17-52-46(50)51)39(66)53-23-37(49)64)24-74-73-19-16-38(65)54-30(21-26-10-12-27(61)13-11-26)41(68)57-31(42(69)55-29)20-25-6-2-1-3-7-25/h1-3,6-7,10-13,28-34,61H,4-5,8-9,14-24H2,(H2,47,62)(H2,48,63)(H2,49,64)(H,53,66)(H,54,65)(H,55,69)(H,56,71)(H,57,68)(H,58,67)(H,59,70)(H4,50,51,52)/t28-,29-,30-,31-,32-,33-,34-/m0/s1
|
||||
@@ -0,0 +1,354 @@
|
||||
@<TRIPOS>MOLECULE
|
||||
Goserelin
|
||||
91 96 0 0 0
|
||||
SMALL
|
||||
GASTEIGER
|
||||
|
||||
@<TRIPOS>ATOM
|
||||
1 O 12.8548 -2.6382 0.0000 O.2 4 UNK4 -0.2730
|
||||
2 O 13.9726 -2.5226 0.0000 O.2 4 UNK4 -0.2699
|
||||
3 O 10.1766 -3.9327 0.0000 O.2 4 UNK4 -0.2715
|
||||
4 O 11.2019 -0.7961 0.0000 O.3 4 UNK4 -0.3562
|
||||
5 O 8.7800 -1.3064 0.0000 O.2 4 UNK4 -0.2714
|
||||
6 O 16.8589 -3.2421 0.0000 O.2 4 UNK4 -0.2457
|
||||
7 O 10.3562 1.2163 0.0000 O.2 4 UNK4 -0.2715
|
||||
8 O 3.2702 4.8341 0.0000 O.2 1 UNK1 -0.2715
|
||||
9 O 2.3500 8.2734 0.0000 O.2 1 UNK1 -0.2733
|
||||
10 O 3.8213 4.2201 0.0000 O.2 2 HIS2 -0.2715
|
||||
11 O 5.2178 1.5938 0.0000 O.2 3 TRP3 -0.2715
|
||||
12 O 7.8960 2.8883 0.0000 O.2 4 UNK4 -0.2714
|
||||
13 O 7.1271 0.5358 0.0000 O.3 4 UNK4 -0.2179
|
||||
14 O 12.4834 3.1249 0.0000 O.3 4 UNK4 -0.2866
|
||||
15 N 13.1495 -4.0364 0.0000 N.am 4 UNK4 -0.2715
|
||||
16 N 11.2402 -2.9784 0.0000 N.am 4 UNK4 -0.1964
|
||||
17 N 15.2089 -3.2393 0.0000 N.am 4 UNK4 -0.0850
|
||||
18 N 10.1383 -1.7503 0.0000 N.am 4 UNK4 -0.1963
|
||||
19 N 15.6226 -2.5255 0.0000 N.am 4 UNK4 -0.0678
|
||||
20 N 12.3806 -6.3890 0.0000 N.pl3 4 UNK4 -0.0865
|
||||
21 N 9.2926 0.2619 0.0000 N.am 4 UNK4 -0.1937
|
||||
22 N 3.1485 7.0391 0.0000 N.am 1 UNK1 -0.1978
|
||||
23 N 4.3338 5.7884 0.0000 N.am 2 HIS2 -0.1959
|
||||
24 N 16.8613 -1.8132 0.0000 N.am 4 UNK4 -0.0665
|
||||
25 N 8.1907 1.4900 0.0000 N.am 4 UNK4 -0.1959
|
||||
26 N 5.1795 3.7761 0.0000 N.am 3 TRP3 -0.1960
|
||||
27 N 6.2814 2.5480 0.0000 N.am 4 UNK4 -0.1936
|
||||
28 N 11.3170 -7.3433 0.0000 N.pl3 4 UNK4 0.1354
|
||||
29 N 12.6753 -7.7873 0.0000 N.pl3 4 UNK4 0.1354
|
||||
30 NE1 3.8596 0.7098 0.0000 N.ar 3 TRP3 -0.2442
|
||||
31 ND1 6.7335 6.3823 0.0000 N.ar 2 HIS2 -0.2267
|
||||
32 NE2 5.9507 7.4636 0.0000 N.ar 2 HIS2 -0.2212
|
||||
33 C 13.9701 -3.9516 0.0000 C.3 4 UNK4 0.1552
|
||||
34 C 14.3043 -4.7058 0.0000 C.3 4 UNK4 0.0311
|
||||
35 C 13.6903 -5.2569 0.0000 C.3 4 UNK4 0.0237
|
||||
36 C 12.9766 -4.8431 0.0000 C.3 4 UNK4 0.0939
|
||||
37 C 12.5984 -3.4224 0.0000 C.2 4 UNK4 0.2458
|
||||
38 C 11.7912 -3.5925 0.0000 C.3 4 UNK4 0.1714
|
||||
39 C 14.3838 -3.2378 0.0000 C.2 4 UNK4 0.2788
|
||||
40 C 11.5349 -4.3767 0.0000 C.3 4 UNK4 0.0347
|
||||
41 C 12.0859 -4.9907 0.0000 C.3 4 UNK4 0.0492
|
||||
42 C 9.8819 -2.5345 0.0000 C.3 4 UNK4 0.1728
|
||||
43 C 10.4330 -3.1486 0.0000 C.2 4 UNK4 0.2616
|
||||
44 C 9.0747 -2.7046 0.0000 C.3 4 UNK4 0.0311
|
||||
45 C 8.8184 -3.4889 0.0000 C.3 4 UNK4 0.0022
|
||||
46 C 11.8295 -5.7750 0.0000 C.3 4 UNK4 0.2205
|
||||
47 C 8.0112 -3.6590 0.0000 C.3 4 UNK4 0.0001
|
||||
48 C 9.3694 -4.1029 0.0000 C.3 4 UNK4 0.0001
|
||||
49 C 9.5873 -1.1363 0.0000 C.2 4 UNK4 0.2642
|
||||
50 C 9.8436 -0.3521 0.0000 C.3 4 UNK4 0.2021
|
||||
51 C 10.6509 -0.1820 0.0000 C.3 4 UNK4 0.1729
|
||||
52 C 16.4476 -2.5269 0.0000 C.2 4 UNK4 0.3786
|
||||
53 C 2.9756 6.2324 0.0000 C.3 1 UNK1 0.1732
|
||||
54 C 12.0091 -0.6259 0.0000 C.3 4 UNK4 0.0931
|
||||
55 C 8.9979 1.6602 0.0000 C.3 4 UNK4 0.1771
|
||||
56 C 9.5489 1.0461 0.0000 C.2 4 UNK4 0.2620
|
||||
57 C 12.1242 -7.1732 0.0000 C.cat 4 UNK4 0.5346
|
||||
58 C 2.1549 6.1475 0.0000 C.3 1 UNK1 0.0407
|
||||
59 CA 4.8848 5.1744 0.0000 C.3 2 HIS2 0.1787
|
||||
60 CA 4.9232 2.9920 0.0000 C.3 3 TRP3 0.1771
|
||||
61 C 1.8207 6.9019 0.0000 C.3 1 UNK1 0.0891
|
||||
62 C 9.2542 2.4444 0.0000 C.3 4 UNK4 0.0574
|
||||
63 CB 4.1159 2.8219 0.0000 C.3 3 TRP3 0.0590
|
||||
64 C 3.5266 5.6183 0.0000 C.2 1 UNK1 0.2616
|
||||
65 C 2.4348 7.4528 0.0000 C.2 1 UNK1 0.2418
|
||||
66 CB 5.6921 5.3445 0.0000 C.3 2 HIS2 0.0785
|
||||
67 C 6.8324 1.9340 0.0000 C.3 4 UNK4 0.2055
|
||||
68 C 4.6285 4.3902 0.0000 C.2 2 HIS2 0.2620
|
||||
69 C 12.1793 -1.4332 0.0000 C.3 4 UNK4 0.0296
|
||||
70 C 12.8164 -0.4557 0.0000 C.3 4 UNK4 0.0296
|
||||
71 C 11.8389 0.1814 0.0000 C.3 4 UNK4 0.0296
|
||||
72 CG 3.8596 2.0376 0.0000 C.ar 3 TRP3 0.0006
|
||||
73 C 5.4742 2.3779 0.0000 C.2 3 TRP3 0.2620
|
||||
74 C 7.6397 2.1041 0.0000 C.2 4 UNK4 0.2643
|
||||
75 C 10.0615 2.6145 0.0000 C.ar 4 UNK4 -0.0198
|
||||
76 CD2 3.0790 1.7862 0.0000 C.ar 3 TRP3 0.0152
|
||||
77 CG 5.9484 6.1287 0.0000 C.ar 2 HIS2 0.0821
|
||||
78 CD1 4.3411 1.3737 0.0000 C.ar 3 TRP3 0.0946
|
||||
79 CE2 3.0790 0.9612 0.0000 C.ar 3 TRP3 0.0810
|
||||
80 C 6.5761 1.1498 0.0000 C.3 4 UNK4 0.2130
|
||||
81 CE3 2.3645 2.1987 0.0000 C.ar 3 TRP3 0.0012
|
||||
82 C 10.3178 3.3987 0.0000 C.ar 4 UNK4 -0.0009
|
||||
83 C 10.6125 2.0005 0.0000 C.ar 4 UNK4 -0.0009
|
||||
84 CZ2 2.3645 0.5487 0.0000 C.ar 3 TRP3 0.0191
|
||||
85 CD2 5.4646 6.7970 0.0000 C.ar 2 HIS2 0.1154
|
||||
86 CZ3 1.6500 1.7862 0.0000 C.ar 3 TRP3 0.0001
|
||||
87 CH2 1.6500 0.9612 0.0000 C.ar 3 TRP3 0.0015
|
||||
88 C 11.1251 3.5688 0.0000 C.ar 4 UNK4 0.0417
|
||||
89 C 11.4198 2.1706 0.0000 C.ar 4 UNK4 0.0417
|
||||
90 CE1 6.7349 7.2073 0.0000 C.ar 2 HIS2 0.1986
|
||||
91 C 11.6761 2.9548 0.0000 C.ar 4 UNK4 0.1957
|
||||
@<TRIPOS>BOND
|
||||
1 1 37 2
|
||||
2 2 39 2
|
||||
3 3 43 2
|
||||
4 4 51 1
|
||||
5 4 54 1
|
||||
6 5 49 2
|
||||
7 6 52 2
|
||||
8 7 56 2
|
||||
9 8 64 2
|
||||
10 9 65 2
|
||||
11 10 68 2
|
||||
12 11 73 2
|
||||
13 12 74 2
|
||||
14 13 80 1
|
||||
15 14 91 1
|
||||
16 15 33 1
|
||||
17 15 36 1
|
||||
18 15 37 am
|
||||
19 38 16 1
|
||||
20 16 43 am
|
||||
21 17 19 1
|
||||
22 17 39 am
|
||||
23 42 18 1
|
||||
24 18 49 am
|
||||
25 19 52 am
|
||||
26 20 46 1
|
||||
27 20 57 2
|
||||
28 50 21 1
|
||||
29 21 56 am
|
||||
30 22 53 1
|
||||
31 22 65 am
|
||||
32 59 23 1
|
||||
33 23 64 am
|
||||
34 24 52 am
|
||||
35 55 25 1
|
||||
36 25 74 am
|
||||
37 60 26 1
|
||||
38 26 68 am
|
||||
39 67 27 1
|
||||
40 27 73 am
|
||||
41 28 57 1
|
||||
42 29 57 1
|
||||
43 30 78 ar
|
||||
44 30 79 ar
|
||||
45 31 77 ar
|
||||
46 31 90 ar
|
||||
47 32 85 ar
|
||||
48 32 90 ar
|
||||
49 33 34 1
|
||||
50 33 39 1
|
||||
51 34 35 1
|
||||
52 35 36 1
|
||||
53 37 38 1
|
||||
54 38 40 1
|
||||
55 40 41 1
|
||||
56 41 46 1
|
||||
57 42 43 1
|
||||
58 42 44 1
|
||||
59 44 45 1
|
||||
60 45 47 1
|
||||
61 45 48 1
|
||||
62 49 50 1
|
||||
63 50 51 1
|
||||
64 53 58 1
|
||||
65 53 64 1
|
||||
66 54 69 1
|
||||
67 54 70 1
|
||||
68 54 71 1
|
||||
69 55 56 1
|
||||
70 55 62 1
|
||||
71 58 61 1
|
||||
72 59 66 1
|
||||
73 59 68 1
|
||||
74 60 63 1
|
||||
75 60 73 1
|
||||
76 61 65 1
|
||||
77 62 75 1
|
||||
78 63 72 1
|
||||
79 66 77 1
|
||||
80 67 74 1
|
||||
81 67 80 1
|
||||
82 72 76 ar
|
||||
83 72 78 ar
|
||||
84 75 82 ar
|
||||
85 75 83 ar
|
||||
86 76 79 ar
|
||||
87 76 81 ar
|
||||
88 77 85 ar
|
||||
89 79 84 ar
|
||||
90 81 86 ar
|
||||
91 82 88 ar
|
||||
92 83 89 ar
|
||||
93 84 87 ar
|
||||
94 86 87 ar
|
||||
95 88 91 ar
|
||||
96 89 91 ar
|
||||
@<TRIPOS>MOLECULE
|
||||
Desmopressin
|
||||
74 77 0 0 0
|
||||
SMALL
|
||||
GASTEIGER
|
||||
|
||||
@<TRIPOS>ATOM
|
||||
1 N 0.0000 -7.8646 0.0000 N.am 1 LIG1 -0.0862
|
||||
2 C 0.6741 -7.4601 0.0000 C.2 1 LIG1 0.2828
|
||||
3 C 1.3932 -7.8646 0.0000 C.3 1 LIG1 0.2031
|
||||
4 N 2.1122 -7.4601 0.0000 N.am 1 LIG1 -0.1939
|
||||
5 C 2.8313 -7.8646 0.0000 C.2 1 LIG1 0.2617
|
||||
6 C 3.5503 -7.4601 0.0000 C.3 1 LIG1 0.1729
|
||||
7 N 4.2693 -7.8646 0.0000 N.am 1 LIG1 -0.1964
|
||||
8 C 4.9435 -7.4601 0.0000 C.2 1 LIG1 0.2598
|
||||
9 O 5.6625 -7.8646 0.0000 O.2 1 LIG1 -0.2715
|
||||
10 O 0.6741 -6.6512 0.0000 O.2 1 LIG1 -0.2697
|
||||
11 O 2.8313 -8.7184 0.0000 O.2 1 LIG1 -0.2715
|
||||
12 C 3.5503 -6.6512 0.0000 C.3 1 LIG1 0.0348
|
||||
13 C 2.8313 -6.2467 0.0000 C.3 1 LIG1 0.0492
|
||||
14 C 2.8313 -5.4378 0.0000 C.3 1 LIG1 0.2205
|
||||
15 N 2.1122 -5.0333 0.0000 N.pl3 1 LIG1 -0.0865
|
||||
16 C 4.9435 -6.6512 0.0000 C.3 1 LIG1 0.1536
|
||||
17 C 4.3143 -6.1568 0.0000 C.3 1 LIG1 0.0310
|
||||
18 N 5.6176 -6.1568 0.0000 N.am 1 LIG1 -0.2715
|
||||
19 C 4.5390 -5.3929 0.0000 C.3 1 LIG1 0.0237
|
||||
20 C 5.3479 -5.3929 0.0000 C.3 1 LIG1 0.0939
|
||||
21 C 6.3366 -6.5613 0.0000 C.2 1 LIG1 0.2467
|
||||
22 C 7.0557 -6.1568 0.0000 C.3 1 LIG1 0.1828
|
||||
23 N 7.7747 -6.5613 0.0000 N.am 1 LIG1 -0.1954
|
||||
24 C 8.4488 -6.1568 0.0000 C.2 1 LIG1 0.2621
|
||||
25 C 9.1678 -6.5613 0.0000 C.3 1 LIG1 0.1819
|
||||
26 N 9.8869 -6.1568 0.0000 N.am 1 LIG1 -0.1958
|
||||
27 O 6.3366 -7.4152 0.0000 O.2 1 LIG1 -0.2730
|
||||
28 C 7.0557 -5.3479 0.0000 C.3 1 LIG1 0.0996
|
||||
29 S 6.3366 -4.9435 0.0000 S.3 1 LIG1 -0.0798
|
||||
30 S 6.3366 -4.1345 0.0000 S.3 1 LIG1 -0.0816
|
||||
31 O 8.4488 -5.3479 0.0000 O.2 1 LIG1 -0.2715
|
||||
32 C 9.1678 -7.4152 0.0000 C.3 1 LIG1 0.1195
|
||||
33 C 9.8869 -7.8197 0.0000 C.2 1 LIG1 0.2630
|
||||
34 O 9.8869 -8.6286 0.0000 O.2 1 LIG1 -0.2716
|
||||
35 N 10.6060 -7.4152 0.0000 N.am 1 LIG1 -0.0877
|
||||
36 C 9.8869 -5.3479 0.0000 C.2 1 LIG1 0.2616
|
||||
37 C 10.6060 -4.9435 0.0000 C.3 1 LIG1 0.1733
|
||||
38 O 9.1678 -4.9435 0.0000 O.2 1 LIG1 -0.2715
|
||||
39 C 11.3250 -5.3479 0.0000 C.3 1 LIG1 0.0408
|
||||
40 C 12.0441 -4.9435 0.0000 C.3 1 LIG1 0.0908
|
||||
41 C 12.7631 -5.3479 0.0000 C.2 1 LIG1 0.2608
|
||||
42 N 13.4822 -4.9435 0.0000 N.am 1 LIG1 -0.0878
|
||||
43 O 12.7631 -6.2018 0.0000 O.2 1 LIG1 -0.2717
|
||||
44 N 10.6060 -4.1345 0.0000 N.am 1 LIG1 -0.1963
|
||||
45 C 11.3250 -2.8762 0.0000 C.ar 1 LIG1 -0.0200
|
||||
46 C 11.3250 -3.7300 0.0000 C.ar 1 LIG1 -0.0042
|
||||
47 C 10.6060 -2.4717 0.0000 C.3 1 LIG1 0.0574
|
||||
48 C 9.8869 -2.8762 0.0000 C.3 1 LIG1 0.1771
|
||||
49 C 9.8869 -3.7300 0.0000 C.2 1 LIG1 0.2619
|
||||
50 C 12.7631 -2.8762 0.0000 C.ar 1 LIG1 -0.0003
|
||||
51 C 12.7631 -3.7300 0.0000 C.ar 1 LIG1 -0.0000
|
||||
52 C 12.0441 -2.4717 0.0000 C.ar 1 LIG1 -0.0042
|
||||
53 C 12.0441 -4.1345 0.0000 C.ar 1 LIG1 -0.0003
|
||||
54 N 7.0557 -2.8762 0.0000 N.am 1 LIG1 -0.1974
|
||||
55 C 6.3366 -2.4717 0.0000 C.2 1 LIG1 0.2427
|
||||
56 C 5.6176 -2.8762 0.0000 C.3 1 LIG1 0.0993
|
||||
57 C 5.6176 -3.7300 0.0000 C.3 1 LIG1 0.0783
|
||||
58 C 8.4488 -2.8762 0.0000 C.2 1 LIG1 0.2620
|
||||
59 O 8.4488 -3.7300 0.0000 O.2 1 LIG1 -0.2715
|
||||
60 C 7.7747 -2.4717 0.0000 C.3 1 LIG1 0.1770
|
||||
61 N 9.1678 -2.4717 0.0000 N.am 1 LIG1 -0.1960
|
||||
62 O 9.1678 -4.1345 0.0000 O.2 1 LIG1 -0.2715
|
||||
63 C 7.7747 -1.6628 0.0000 C.3 1 LIG1 0.0574
|
||||
64 C 9.1678 -1.6628 0.0000 C.ar 1 LIG1 -0.0009
|
||||
65 C 8.4488 -1.2583 0.0000 C.ar 1 LIG1 -0.0198
|
||||
66 C 9.8869 -1.2583 0.0000 C.ar 1 LIG1 0.0417
|
||||
67 C 9.8869 -0.4045 0.0000 C.ar 1 LIG1 0.1957
|
||||
68 C 8.4488 -0.4045 0.0000 C.ar 1 LIG1 -0.0009
|
||||
69 C 9.1678 0.0000 0.0000 C.ar 1 LIG1 0.0417
|
||||
70 O 6.3366 -1.6628 0.0000 O.2 1 LIG1 -0.2733
|
||||
71 O 10.6060 0.0000 0.0000 O.3 1 LIG1 -0.2866
|
||||
72 C 1.3932 -5.4378 0.0000 C.cat 1 LIG1 0.5346
|
||||
73 N 1.3932 -6.2467 0.0000 N.pl3 1 LIG1 0.1354
|
||||
74 N 0.6741 -5.0333 0.0000 N.pl3 1 LIG1 0.1354
|
||||
@<TRIPOS>BOND
|
||||
1 1 2 am
|
||||
2 2 3 1
|
||||
3 2 10 2
|
||||
4 3 4 1
|
||||
5 4 5 am
|
||||
6 5 6 1
|
||||
7 5 11 2
|
||||
8 6 7 1
|
||||
9 6 12 1
|
||||
10 7 8 am
|
||||
11 8 9 2
|
||||
12 16 8 1
|
||||
13 12 13 1
|
||||
14 13 14 1
|
||||
15 14 15 1
|
||||
16 15 72 1
|
||||
17 16 17 1
|
||||
18 16 18 1
|
||||
19 17 19 1
|
||||
20 18 20 1
|
||||
21 18 21 am
|
||||
22 19 20 1
|
||||
23 22 21 1
|
||||
24 21 27 2
|
||||
25 22 23 1
|
||||
26 22 28 1
|
||||
27 23 24 am
|
||||
28 24 25 1
|
||||
29 24 31 2
|
||||
30 25 26 1
|
||||
31 25 32 1
|
||||
32 26 36 am
|
||||
33 28 29 1
|
||||
34 29 30 1
|
||||
35 30 57 1
|
||||
36 32 33 1
|
||||
37 33 34 2
|
||||
38 33 35 am
|
||||
39 36 37 1
|
||||
40 36 38 2
|
||||
41 37 39 1
|
||||
42 37 44 1
|
||||
43 39 40 1
|
||||
44 40 41 1
|
||||
45 41 42 am
|
||||
46 41 43 2
|
||||
47 44 49 am
|
||||
48 45 47 1
|
||||
49 45 52 ar
|
||||
50 45 46 ar
|
||||
51 46 53 ar
|
||||
52 48 47 1
|
||||
53 48 61 1
|
||||
54 48 49 1
|
||||
55 49 62 2
|
||||
56 50 51 ar
|
||||
57 50 52 ar
|
||||
58 51 53 ar
|
||||
59 54 55 am
|
||||
60 54 60 1
|
||||
61 55 56 1
|
||||
62 55 70 2
|
||||
63 56 57 1
|
||||
64 58 59 2
|
||||
65 58 60 1
|
||||
66 58 61 am
|
||||
67 60 63 1
|
||||
68 63 65 1
|
||||
69 64 66 ar
|
||||
70 64 65 ar
|
||||
71 65 68 ar
|
||||
72 66 67 ar
|
||||
73 67 69 ar
|
||||
74 67 71 1
|
||||
75 68 69 ar
|
||||
76 72 73 2
|
||||
77 72 74 1
|
||||
@@ -0,0 +1,491 @@
|
||||
Goserelin
|
||||
Mrv0541 04221219462D
|
||||
|
||||
91 96 0 0 1 0 999 V2000
|
||||
12.8548 -2.6382 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
13.9726 -2.5226 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
10.1766 -3.9327 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
11.2019 -0.7961 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
8.7800 -1.3064 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
16.8589 -3.2421 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
10.3562 1.2163 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
3.2702 4.8341 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
2.3500 8.2734 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
3.8213 4.2201 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
5.2178 1.5938 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
7.8960 2.8883 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
7.1271 0.5358 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
12.4834 3.1249 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
13.1495 -4.0364 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
11.2402 -2.9784 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
15.2089 -3.2393 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
10.1383 -1.7503 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
15.6226 -2.5255 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
12.3806 -6.3890 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
9.2926 0.2619 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
3.1485 7.0391 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
4.3338 5.7884 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
16.8613 -1.8132 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
8.1907 1.4900 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
5.1795 3.7761 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
6.2814 2.5480 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
11.3170 -7.3433 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
12.6753 -7.7873 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
3.8596 0.7098 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
6.7335 6.3823 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
5.9507 7.4636 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
13.9701 -3.9516 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
|
||||
14.3043 -4.7058 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
13.6903 -5.2569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
12.9766 -4.8431 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
12.5984 -3.4224 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
11.7912 -3.5925 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
|
||||
14.3838 -3.2378 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
11.5349 -4.3767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
12.0859 -4.9907 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
9.8819 -2.5345 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
|
||||
10.4330 -3.1486 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
9.0747 -2.7046 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
8.8184 -3.4889 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
11.8295 -5.7750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
8.0112 -3.6590 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
9.3694 -4.1029 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
9.5873 -1.1363 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
9.8436 -0.3521 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
|
||||
10.6509 -0.1820 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
16.4476 -2.5269 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
2.9756 6.2324 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
|
||||
12.0091 -0.6259 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
8.9979 1.6602 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
|
||||
9.5489 1.0461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
12.1242 -7.1732 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
2.1549 6.1475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
4.8848 5.1744 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
|
||||
4.9232 2.9920 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
|
||||
1.8207 6.9019 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
9.2542 2.4444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
4.1159 2.8219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
3.5266 5.6183 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
2.4348 7.4528 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
5.6921 5.3445 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
6.8324 1.9340 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
|
||||
4.6285 4.3902 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
12.1793 -1.4332 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
12.8164 -0.4557 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
11.8389 0.1814 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
3.8596 2.0376 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
5.4742 2.3779 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
7.6397 2.1041 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
10.0615 2.6145 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
3.0790 1.7862 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
5.9484 6.1287 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
4.3411 1.3737 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
3.0790 0.9612 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
6.5761 1.1498 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
2.3645 2.1987 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
10.3178 3.3987 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
10.6125 2.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
2.3645 0.5487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
5.4646 6.7970 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.6500 1.7862 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.6500 0.9612 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
11.1251 3.5688 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
11.4198 2.1706 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
6.7349 7.2073 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
11.6761 2.9548 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1 37 2 0 0 0 0
|
||||
2 39 2 0 0 0 0
|
||||
3 43 2 0 0 0 0
|
||||
4 51 1 0 0 0 0
|
||||
4 54 1 0 0 0 0
|
||||
5 49 2 0 0 0 0
|
||||
6 52 2 0 0 0 0
|
||||
7 56 2 0 0 0 0
|
||||
8 64 2 0 0 0 0
|
||||
9 65 2 0 0 0 0
|
||||
10 68 2 0 0 0 0
|
||||
11 73 2 0 0 0 0
|
||||
12 74 2 0 0 0 0
|
||||
13 80 1 0 0 0 0
|
||||
14 91 1 0 0 0 0
|
||||
15 33 1 0 0 0 0
|
||||
15 36 1 0 0 0 0
|
||||
15 37 1 0 0 0 0
|
||||
38 16 1 6 0 0 0
|
||||
16 43 1 0 0 0 0
|
||||
17 19 1 0 0 0 0
|
||||
17 39 1 0 0 0 0
|
||||
42 18 1 6 0 0 0
|
||||
18 49 1 0 0 0 0
|
||||
19 52 1 0 0 0 0
|
||||
20 46 1 0 0 0 0
|
||||
20 57 2 0 0 0 0
|
||||
50 21 1 6 0 0 0
|
||||
21 56 1 0 0 0 0
|
||||
22 53 1 0 0 0 0
|
||||
22 65 1 0 0 0 0
|
||||
59 23 1 1 0 0 0
|
||||
23 64 1 0 0 0 0
|
||||
24 52 1 0 0 0 0
|
||||
55 25 1 1 0 0 0
|
||||
25 74 1 0 0 0 0
|
||||
60 26 1 6 0 0 0
|
||||
26 68 1 0 0 0 0
|
||||
67 27 1 6 0 0 0
|
||||
27 73 1 0 0 0 0
|
||||
28 57 1 0 0 0 0
|
||||
29 57 1 0 0 0 0
|
||||
30 78 1 0 0 0 0
|
||||
30 79 1 0 0 0 0
|
||||
31 77 1 0 0 0 0
|
||||
31 90 1 0 0 0 0
|
||||
32 85 1 0 0 0 0
|
||||
32 90 2 0 0 0 0
|
||||
33 34 1 0 0 0 0
|
||||
33 39 1 6 0 0 0
|
||||
34 35 1 0 0 0 0
|
||||
35 36 1 0 0 0 0
|
||||
37 38 1 0 0 0 0
|
||||
38 40 1 0 0 0 0
|
||||
40 41 1 0 0 0 0
|
||||
41 46 1 0 0 0 0
|
||||
42 43 1 0 0 0 0
|
||||
42 44 1 0 0 0 0
|
||||
44 45 1 0 0 0 0
|
||||
45 47 1 0 0 0 0
|
||||
45 48 1 0 0 0 0
|
||||
49 50 1 0 0 0 0
|
||||
50 51 1 0 0 0 0
|
||||
53 58 1 0 0 0 0
|
||||
53 64 1 6 0 0 0
|
||||
54 69 1 0 0 0 0
|
||||
54 70 1 0 0 0 0
|
||||
54 71 1 0 0 0 0
|
||||
55 56 1 0 0 0 0
|
||||
55 62 1 0 0 0 0
|
||||
58 61 1 0 0 0 0
|
||||
59 66 1 0 0 0 0
|
||||
59 68 1 0 0 0 0
|
||||
60 63 1 0 0 0 0
|
||||
60 73 1 0 0 0 0
|
||||
61 65 1 0 0 0 0
|
||||
62 75 1 0 0 0 0
|
||||
63 72 1 0 0 0 0
|
||||
66 77 1 0 0 0 0
|
||||
67 74 1 0 0 0 0
|
||||
67 80 1 0 0 0 0
|
||||
72 76 1 0 0 0 0
|
||||
72 78 2 0 0 0 0
|
||||
75 82 2 0 0 0 0
|
||||
75 83 1 0 0 0 0
|
||||
76 79 1 0 0 0 0
|
||||
76 81 2 0 0 0 0
|
||||
77 85 2 0 0 0 0
|
||||
79 84 2 0 0 0 0
|
||||
81 86 1 0 0 0 0
|
||||
82 88 1 0 0 0 0
|
||||
83 89 2 0 0 0 0
|
||||
84 87 1 0 0 0 0
|
||||
86 87 2 0 0 0 0
|
||||
88 91 2 0 0 0 0
|
||||
89 91 1 0 0 0 0
|
||||
M END
|
||||
> <DRUGBANK_ID>
|
||||
DB00014
|
||||
|
||||
> <DRUG_GROUPS>
|
||||
approved
|
||||
|
||||
> <GENERIC_NAME>
|
||||
Goserelin
|
||||
|
||||
> <SALTS>
|
||||
Goserelin acetate
|
||||
|
||||
> <BRANDS>
|
||||
Zoladex
|
||||
|
||||
> <CHEMICAL_FORMULA>
|
||||
C59H84N18O14
|
||||
|
||||
> <MOLECULAR_WEIGHT>
|
||||
1269.4105
|
||||
|
||||
> <EXACT_MASS>
|
||||
1268.641439486
|
||||
|
||||
> <IUPAC_NAME>
|
||||
(2S)-1-[(2S)-2-[(2S)-2-[(2R)-3-(tert-butoxy)-2-[(2S)-2-[(2S)-3-hydroxy-2-[(2S)-2-[(2S)-3-(1H-imidazol-5-yl)-2-{[(2S)-5-oxopyrrolidin-2-yl]formamido}propanamido]-3-(1H-indol-3-yl)propanamido]propanamido]-3-(4-hydroxyphenyl)propanamido]propanamido]-4-methylpentanamido]-5-[(diaminomethylidene)amino]pentanoyl]-N-(carbamoylamino)pyrrolidine-2-carboxamide
|
||||
|
||||
> <INCHI_IDENTIFIER>
|
||||
InChI=1S/C59H84N18O14/c1-31(2)22-40(49(82)68-39(12-8-20-64-57(60)61)56(89)77-21-9-13-46(77)55(88)75-76-58(62)90)69-54(87)45(29-91-59(3,4)5)74-50(83)41(23-32-14-16-35(79)17-15-32)70-53(86)44(28-78)73-51(84)42(24-33-26-65-37-11-7-6-10-36(33)37)71-52(85)43(25-34-27-63-30-66-34)72-48(81)38-18-19-47(80)67-38/h6-7,10-11,14-17,26-27,30-31,38-46,65,78-79H,8-9,12-13,18-25,28-29H2,1-5H3,(H,63,66)(H,67,80)(H,68,82)(H,69,87)(H,70,86)(H,71,85)(H,72,81)(H,73,84)(H,74,83)(H,75,88)(H4,60,61,64)(H3,62,76,90)/t38-,39-,40-,41-,42-,43-,44-,45+,46-/m0/s1
|
||||
|
||||
> <INCHI_KEY>
|
||||
InChIKey=BLCLNMBMMGCOAS-URPVMXJPSA-N
|
||||
|
||||
> <SMILES>
|
||||
CC(C)C[C@H](NC(=O)[C@@H](COC(C)(C)C)NC(=O)[C@H](CC1=CC=C(O)C=C1)NC(=O)[C@H](CO)NC(=O)[C@H](CC1=CNC2=CC=CC=C12)NC(=O)[C@H](CC1=CN=CN1)NC(=O)[C@@H]1CCC(=O)N1)C(=O)N[C@@H](CCCN=C(N)N)C(=O)N1CCC[C@H]1C(=O)NNC(N)=O
|
||||
|
||||
> <JCHEM_ACCEPTOR_COUNT>
|
||||
18
|
||||
|
||||
> <JCHEM_DONOR_COUNT>
|
||||
17
|
||||
|
||||
> <JCHEM_ACIDIC_PKA>
|
||||
9.82
|
||||
|
||||
> <ALOGPS_LOGP>
|
||||
0.3
|
||||
|
||||
> <JCHEM_LOGP>
|
||||
-5.2
|
||||
|
||||
> <ALOGPS_LOGS>
|
||||
-4.7
|
||||
|
||||
> <JCHEM_POLARIZABILITY>
|
||||
131.22
|
||||
|
||||
> <JCHEM_POLAR_SURFACE_AREA>
|
||||
495.89
|
||||
|
||||
> <JCHEM_REFRACTIVITY>
|
||||
325.84
|
||||
|
||||
> <JCHEM_ROTATABLE_BOND_COUNT>
|
||||
33
|
||||
|
||||
> <ALOGPS_SOLUBILITY>
|
||||
2.83e-02 g/l
|
||||
|
||||
$$$$
|
||||
Desmopressin
|
||||
Mrv0541 04221221522D
|
||||
|
||||
74 77 0 0 1 0 999 V2000
|
||||
0.0000 -7.8646 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.6741 -7.4601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.3932 -7.8646 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
2.1122 -7.4601 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
2.8313 -7.8646 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
3.5503 -7.4601 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
|
||||
4.2693 -7.8646 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
4.9435 -7.4601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
5.6625 -7.8646 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.6741 -6.6512 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
2.8313 -8.7184 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
3.5503 -6.6512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
2.8313 -6.2467 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
2.8313 -5.4378 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
2.1122 -5.0333 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
4.9435 -6.6512 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
|
||||
4.3143 -6.1568 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
5.6176 -6.1568 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
4.5390 -5.3929 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
5.3479 -5.3929 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
6.3366 -6.5613 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
7.0557 -6.1568 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
|
||||
7.7747 -6.5613 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
8.4488 -6.1568 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
9.1678 -6.5613 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
|
||||
9.8869 -6.1568 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
6.3366 -7.4152 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
7.0557 -5.3479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
6.3366 -4.9435 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
6.3366 -4.1345 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
8.4488 -5.3479 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
9.1678 -7.4152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
9.8869 -7.8197 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
9.8869 -8.6286 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
10.6060 -7.4152 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
9.8869 -5.3479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
10.6060 -4.9435 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
|
||||
9.1678 -4.9435 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
11.3250 -5.3479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
12.0441 -4.9435 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
12.7631 -5.3479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
13.4822 -4.9435 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
12.7631 -6.2018 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
10.6060 -4.1345 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
11.3250 -2.8762 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
11.3250 -3.7300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
10.6060 -2.4717 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
9.8869 -2.8762 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
|
||||
9.8869 -3.7300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
12.7631 -2.8762 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
12.7631 -3.7300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
12.0441 -2.4717 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
12.0441 -4.1345 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
7.0557 -2.8762 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
6.3366 -2.4717 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
5.6176 -2.8762 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
5.6176 -3.7300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
8.4488 -2.8762 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
8.4488 -3.7300 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
7.7747 -2.4717 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
|
||||
9.1678 -2.4717 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
9.1678 -4.1345 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
7.7747 -1.6628 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
9.1678 -1.6628 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
8.4488 -1.2583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
9.8869 -1.2583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
9.8869 -0.4045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
8.4488 -0.4045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
9.1678 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
6.3366 -1.6628 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
10.6060 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.3932 -5.4378 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.3932 -6.2467 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.6741 -5.0333 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1 2 1 0 0 0 0
|
||||
2 3 1 0 0 0 0
|
||||
2 10 2 0 0 0 0
|
||||
3 4 1 0 0 0 0
|
||||
4 5 1 0 0 0 0
|
||||
5 6 1 0 0 0 0
|
||||
5 11 2 0 0 0 0
|
||||
6 7 1 0 0 0 0
|
||||
6 12 1 6 0 0 0
|
||||
7 8 1 0 0 0 0
|
||||
8 9 2 0 0 0 0
|
||||
16 8 1 6 0 0 0
|
||||
12 13 1 0 0 0 0
|
||||
13 14 1 0 0 0 0
|
||||
14 15 1 0 0 0 0
|
||||
15 72 1 0 0 0 0
|
||||
16 17 1 0 0 0 0
|
||||
16 18 1 0 0 0 0
|
||||
17 19 1 0 0 0 0
|
||||
18 20 1 0 0 0 0
|
||||
18 21 1 0 0 0 0
|
||||
19 20 1 0 0 0 0
|
||||
22 21 1 6 0 0 0
|
||||
21 27 2 0 0 0 0
|
||||
22 23 1 0 0 0 0
|
||||
22 28 1 0 0 0 0
|
||||
23 24 1 0 0 0 0
|
||||
24 25 1 0 0 0 0
|
||||
24 31 2 0 0 0 0
|
||||
25 26 1 0 0 0 0
|
||||
25 32 1 1 0 0 0
|
||||
26 36 1 0 0 0 0
|
||||
28 29 1 0 0 0 0
|
||||
29 30 1 0 0 0 0
|
||||
30 57 1 0 0 0 0
|
||||
32 33 1 0 0 0 0
|
||||
33 34 2 0 0 0 0
|
||||
33 35 1 0 0 0 0
|
||||
36 37 1 0 0 0 0
|
||||
36 38 2 0 0 0 0
|
||||
37 39 1 1 0 0 0
|
||||
37 44 1 0 0 0 0
|
||||
39 40 1 0 0 0 0
|
||||
40 41 1 0 0 0 0
|
||||
41 42 1 0 0 0 0
|
||||
41 43 2 0 0 0 0
|
||||
44 49 1 0 0 0 0
|
||||
45 47 1 0 0 0 0
|
||||
45 52 1 0 0 0 0
|
||||
45 46 2 0 0 0 0
|
||||
46 53 1 0 0 0 0
|
||||
48 47 1 1 0 0 0
|
||||
48 61 1 0 0 0 0
|
||||
48 49 1 0 0 0 0
|
||||
49 62 2 0 0 0 0
|
||||
50 51 1 0 0 0 0
|
||||
50 52 2 0 0 0 0
|
||||
51 53 2 0 0 0 0
|
||||
54 55 1 0 0 0 0
|
||||
54 60 1 0 0 0 0
|
||||
55 56 1 0 0 0 0
|
||||
55 70 2 0 0 0 0
|
||||
56 57 1 0 0 0 0
|
||||
58 59 2 0 0 0 0
|
||||
58 60 1 0 0 0 0
|
||||
58 61 1 0 0 0 0
|
||||
60 63 1 1 0 0 0
|
||||
63 65 1 0 0 0 0
|
||||
64 66 2 0 0 0 0
|
||||
64 65 1 0 0 0 0
|
||||
65 68 2 0 0 0 0
|
||||
66 67 1 0 0 0 0
|
||||
67 69 2 0 0 0 0
|
||||
67 71 1 0 0 0 0
|
||||
68 69 1 0 0 0 0
|
||||
72 73 2 3 0 0 0
|
||||
72 74 1 0 0 0 0
|
||||
M END
|
||||
> <DRUGBANK_ID>
|
||||
DB00035
|
||||
|
||||
> <DRUG_GROUPS>
|
||||
approved
|
||||
|
||||
> <GENERIC_NAME>
|
||||
Desmopressin
|
||||
|
||||
> <SYNONYMS>
|
||||
1-Desamino-8-D-arginine vasopressin; Desmopresina [INN-Spanish]; Desmopressine [INN-French]; Desmopressinum [INN-Latin]
|
||||
|
||||
> <SALTS>
|
||||
Desmopressin acetate
|
||||
|
||||
> <BRANDS>
|
||||
Adiuretin; Concentraid; DDAVP; Minirin; Stimate
|
||||
|
||||
> <CHEMICAL_FORMULA>
|
||||
C46H64N14O12S2
|
||||
|
||||
> <MOLECULAR_WEIGHT>
|
||||
1069.217
|
||||
|
||||
> <EXACT_MASS>
|
||||
1068.426954962
|
||||
|
||||
> <IUPAC_NAME>
|
||||
(2S)-2-{[(2S)-1-{[(4R,7S,10S,13S,16S)-13-benzyl-10-(2-carbamoylethyl)-7-(carbamoylmethyl)-16-[(4-hydroxyphenyl)methyl]-6,9,12,15,18-pentaoxo-1,2-dithia-5,8,11,14,17-pentaazacycloicosan-4-yl]carbonyl}pyrrolidin-2-yl]formamido}-5-carbamimidamido-N-(carbamoylmethyl)pentanamide
|
||||
|
||||
> <INCHI_IDENTIFIER>
|
||||
InChI=1S/C46H64N14O12S2/c47-35(62)15-14-29-40(67)58-32(22-36(48)63)43(70)59-33(45(72)60-18-5-9-34(60)44(71)56-28(8-4-17-52-46(50)51)39(66)53-23-37(49)64)24-74-73-19-16-38(65)54-30(21-26-10-12-27(61)13-11-26)41(68)57-31(42(69)55-29)20-25-6-2-1-3-7-25/h1-3,6-7,10-13,28-34,61H,4-5,8-9,14-24H2,(H2,47,62)(H2,48,63)(H2,49,64)(H,53,66)(H,54,65)(H,55,69)(H,56,71)(H,57,68)(H,58,67)(H,59,70)(H4,50,51,52)/t28-,29-,30-,31-,32-,33-,34-/m0/s1
|
||||
|
||||
> <INCHI_KEY>
|
||||
InChIKey=NFLWUMRGJYTJIN-NXBWRCJVSA-N
|
||||
|
||||
> <SMILES>
|
||||
NC(=O)CC[C@@H]1NC(=O)[C@H](CC2=CC=CC=C2)NC(=O)[C@H](CC2=CC=C(O)C=C2)NC(=O)CCSSC[C@H](NC(=O)[C@H](CC(N)=O)NC1=O)C(=O)N1CCC[C@H]1C(=O)N[C@@H](CCCNC(N)=N)C(=O)NCC(N)=O
|
||||
|
||||
> <JCHEM_ACCEPTOR_COUNT>
|
||||
15
|
||||
|
||||
> <JCHEM_DONOR_COUNT>
|
||||
14
|
||||
|
||||
> <JCHEM_ACIDIC_PKA>
|
||||
11.34
|
||||
|
||||
> <ALOGPS_LOGP>
|
||||
-1
|
||||
|
||||
> <JCHEM_LOGP>
|
||||
-6.1
|
||||
|
||||
> <ALOGPS_LOGS>
|
||||
-4
|
||||
|
||||
> <JCHEM_POLARIZABILITY>
|
||||
106.19
|
||||
|
||||
> <JCHEM_POLAR_SURFACE_AREA>
|
||||
435.41
|
||||
|
||||
> <JCHEM_REFRACTIVITY>
|
||||
279.78
|
||||
|
||||
> <JCHEM_ROTATABLE_BOND_COUNT>
|
||||
19
|
||||
|
||||
> <ALOGPS_SOLUBILITY>
|
||||
1.10e-01 g/l
|
||||
|
||||
$$$$
|
||||
@@ -0,0 +1,2 @@
|
||||
O=C(N1[C@@H](CCC1)C(=O)NNC(=O)N)[C@@H](NC(=O)[C@@H](NC(=O)[C@H](NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@H]1NC(=O)CC1)Cc1[nH]cnc1)Cc1c2c([nH]c1)cccc2)CO)Cc1ccc(O)cc1)COC(C)(C)C)CC(C)C)CCCN=C(N)N Goserelin
|
||||
NC(=O)CNC(=O)[C@@H](NC(=O)[C@@H]1CCCN1C(=O)[C@H]1NC(=O)[C@@H](NC(=O)[C@H](CCC(=O)N)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@@H](NC(=O)CCSSC1)Cc1ccc(cc1)O)CC(=O)N)CCCNC(=N)N Desmopressin
|
||||
@@ -0,0 +1,7 @@
|
||||
#FPS1
|
||||
#num_bits=881
|
||||
#type=CACTVS-E_SCREEN/1.0 extended=2
|
||||
#software=CACTVS/unknown
|
||||
#source=CID_28434379.sdf
|
||||
#date=2012-02-03T13:08:39
|
||||
07ce04000000000000000000000000000080060000000c060000000000001a800f0000780008100000101487e9608c0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000000100200000040080000010000002000000000000 28434379
|
||||
Reference in New Issue
Block a user